first commit

.gitignore

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+.DS_Store
+*.pyc
+__pycache__
+.git

.idea/.gitignore

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+# Default ignored files
+/shelf/
+/workspace.xml

.idea/Data.iml

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+<?xml version="1.0" encoding="UTF-8"?>
+<module type="PYTHON_MODULE" version="4">
+  <component name="NewModuleRootManager">
+    <content url="file://$MODULE_DIR$" />
+    <orderEntry type="inheritedJdk" />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+  <component name="PyDocumentationSettings">
+    <option name="format" value="PLAIN" />
+    <option name="myDocStringFormat" value="Plain" />
+  </component>
+  <component name="TestRunnerService">
+    <option name="PROJECT_TEST_RUNNER" value="py.test" />
+  </component>
+</module>

.idea/inspectionProfiles/Project_Default.xml

@@ -0,0 +1,26 @@
+<component name="InspectionProjectProfileManager">
+  <profile version="1.0">
+    <option name="myName" value="Project Default" />
+    <inspection_tool class="PyPackageRequirementsInspection" enabled="true" level="WARNING" enabled_by_default="true">
+      <option name="ignoredPackages">
+        <value>
+          <list size="6">
+            <item index="0" class="java.lang.String" itemvalue="requests" />
+            <item index="1" class="java.lang.String" itemvalue="Flask" />
+            <item index="2" class="java.lang.String" itemvalue="tqdm" />
+            <item index="3" class="java.lang.String" itemvalue="tensorboardX" />
+            <item index="4" class="java.lang.String" itemvalue="torch" />
+            <item index="5" class="java.lang.String" itemvalue="numpy" />
+          </list>
+        </value>
+      </option>
+    </inspection_tool>
+    <inspection_tool class="PyPep8NamingInspection" enabled="true" level="WEAK WARNING" enabled_by_default="true">
+      <option name="ignoredErrors">
+        <list>
+          <option value="N801" />
+        </list>
+      </option>
+    </inspection_tool>
+  </profile>
+</component>

.idea/inspectionProfiles/profiles_settings.xml

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+<component name="InspectionProjectProfileManager">
+  <settings>
+    <option name="USE_PROJECT_PROFILE" value="false" />
+    <version value="1.0" />
+  </settings>
+</component>

.idea/misc.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.9 (base) (2)" project-jdk-type="Python SDK" />
+</project>

.idea/modules.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/.idea/Data.iml" filepath="$PROJECT_DIR$/.idea/Data.iml" />
+    </modules>
+  </component>
+</project>

.idea/vcs.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="VcsDirectoryMappings">
+    <mapping directory="$PROJECT_DIR$" vcs="Git" />
+    <mapping directory="$PROJECT_DIR$/Azure/AzureStorage" vcs="Git" />
+    <mapping directory="$PROJECT_DIR$/Azure/azure-multiapi-storage-python" vcs="Git" />
+    <mapping directory="$PROJECT_DIR$/Azure/python-text-classification" vcs="Git" />
+    <mapping directory="$PROJECT_DIR$/BI/BusinessIntelligence-Kaggle" vcs="Git" />
+    <mapping directory="$PROJECT_DIR$/Hash/Encryption_And_Hashing" vcs="Git" />
+    <mapping directory="$PROJECT_DIR$/ML/Machine_Learning_and_Having_It_Deep_and_Structured" vcs="Git" />
+    <mapping directory="$PROJECT_DIR$/NATS/NatsExample" vcs="Git" />
+    <mapping directory="$PROJECT_DIR$/NATS/asyncio-nats-examples" vcs="Git" />
+    <mapping directory="$PROJECT_DIR$/Pseudonym/Data-Masking" vcs="Git" />
+    <mapping directory="$PROJECT_DIR$/S3/NatsExample" vcs="Git" />
+    <mapping directory="$PROJECT_DIR$/S3/odoo-s3-storage" vcs="Git" />
+    <mapping directory="$PROJECT_DIR$/S3/s3-concat" vcs="Git" />
+    <mapping directory="$PROJECT_DIR$/archive/auto-archiver" vcs="Git" />
+    <mapping directory="$PROJECT_DIR$/kafka/Calories-Alert-Kafka" vcs="Git" />
+    <mapping directory="$PROJECT_DIR$/kafka/MessageCorps" vcs="Git" />
+    <mapping directory="$PROJECT_DIR$/kafka/ai-project-fraud-detection" vcs="Git" />
+    <mapping directory="$PROJECT_DIR$/kafka/kafka-fraud-detector" vcs="Git" />
+    <mapping directory="$PROJECT_DIR$/kafka/kafkaesk" vcs="Git" />
+    <mapping directory="$PROJECT_DIR$/kafka/scrapy-kafka" vcs="Git" />
+    <mapping directory="$PROJECT_DIR$/kafka/tail2kafka" vcs="Git" />
+    <mapping directory="$PROJECT_DIR$/visualize/Visualization-of-popular-algorithms-in-Python" vcs="Git" />
+  </component>
+</project>

Azure/.vscode/settings.json

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+{
+    "python.formatting.provider": "black"
+}

Azure/AddUp/Azure-blob-storage.py

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+from azure.storage.blob import BlobClient, BlobServiceClient
+import os
+import requests
+
+def list_files() -> list:
+    file_list = []
+    
+    for root, dirs, files in os.walk("data"):
+        for name in files:
+            file_list.append({"file_name": name, "local_path": os.path.join(root,name)})
+
+    return file_list
+
+def get_filename_from_url(url: str) -> str:
+    file_name=url.split('/')[-1]
+    return file_name
+
+def get_random_images() -> list:
+    # helper function uses loremflickr.com to get a random list of images 
+    images = []
+
+    for i in range(10):
+        resp = requests.get(url=f"https://loremflickr.com/json/320/240?random={i}")
+        resp_json = resp.json()
+        images.append(resp_json["file"])
+
+    return images
+
+def create_blob_from_url(storage_connection_string,container_name):
+    try:
+        # urls to fetch into blob storage
+        url_list = get_random_images()
+
+        # Instantiate a new BlobServiceClient and a new ContainerClient
+        blob_service_client = BlobServiceClient.from_connection_string(storage_connection_string)
+        container_client = blob_service_client.get_container_client(container_name)
+
+        for u in url_list:
+            # Download file from url then upload blob file
+            r = requests.get(u, stream = True)
+            if r.status_code == 200:
+                r.raw.decode_content = True
+                blob_client = container_client.get_blob_client(get_filename_from_url(u))
+                blob_client.upload_blob(r.raw,overwrite=True)
+        return True
+        
+    except Exception as e:
+        print(e.message, e.args)
+        return False 
+
+def create_blob_from_path(storage_connection_string,container_name):
+    try:
+        # Instantiate a new BlobServiceClient and a new ContainerClient
+        blob_service_client = BlobServiceClient.from_connection_string(storage_connection_string)
+        container_client = blob_service_client.get_container_client(container_name)
+
+        for f in list_files():
+            with open(f["local_path"], "rb") as data:
+                blob_client = container_client.get_blob_client(f["file_name"])
+                blob_client.upload_blob(data,overwrite=True)
+        return True
+
+    except Exception as e:
+        print(e.message, e.args)
+        return False
+
+if __name__ == '__main__':
+
+    # get storage account settings
+    storage_connection_string = os.environ.get("STORAGE_CONNECTION_STRING")
+    container_name = os.environ.get("STORAGE_CONTAINER")
+
+    # # if you want to copy from a public url
+    result = create_blob_from_url(storage_connection_string,container_name)
+    
+    # OR if you want to upload form your local drive
+    #create_blob_from_path(storage_connection_string,container_name)
+
+    if(result):
+        print("Done!")
+    else:
+        print("An error occured!")

Azure/AddUp/blob-upload-1.py

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+import os
+from flask import Flask, request, redirect, url_for
+from werkzeug import secure_filename
+from azure.storage.blob import BlockBlobService
+import string, random, requests
+
+app = Flask(__name__, instance_relative_config=True)
+
+app.config.from_pyfile('config.py')
+account = app.config['ACCOUNT']   # Azure account name
+key = app.config['STORAGE_KEY']      # Azure Storage account access key  
+container = app.config['CONTAINER'] # Container name
+
+blob_service = BlockBlobService(account_name=account, account_key=key)
+
+@app.route('/', methods=['GET', 'POST'])
+def upload_file():
+    if request.method == 'POST':
+        file = request.files['file']
+        filename = secure_filename(file.filename)
+        fileextension = filename.rsplit('.',1)[1]
+        Randomfilename = id_generator()
+        filename = Randomfilename + '.' + fileextension
+        try:
+            blob_service.create_blob_from_stream(container, filename, file)
+        except Exception:
+            print ('Exception=' + Exception)
+            pass
+        ref =  'http://'+ account + '.blob.core.windows.net/' + container + '/' + filename
+        return '''
+	    <!doctype html>
+	    <title>File Link</title>
+	    <h1>Uploaded File Link</h1>
+	    <p>''' + ref + '''</p>
+	    <img src="'''+ ref +'''">
+	    '''
+    return '''
+    <!doctype html>
+    <title>Upload new File</title>
+    <h1>Upload new File</h1>
+    <form action="" method=post enctype=multipart/form-data>
+      <p><input type=file name=file>
+         <input type=submit value=Upload>
+    </form>
+    '''
+
+def id_generator(size=32, chars=string.ascii_uppercase + string.digits):
+    return ''.join(random.choice(chars) for _ in range(size))
+
+if __name__ == '__main__':
+    app.run(debug=True)

Azure/AddUp/blob-upload-2.py

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+import mimetypes
+import datetime
+
+from azure.common import AzureMissingResourceHttpError
+from azure.storage.blob import BlobService
+
+from django.core.files.storage import Storage
+from django.conf import settings
+
+try:
+    from django.utils.deconstruct import deconstructible
+except ImportError:
+    # Support for django 1.7 and below
+    def deconstructible(func):
+        return func
+
+
+@deconstructible
+class AzureStorage(Storage):
+    """
+    Custom file storage system for Azure
+    """
+
+    container = settings.AZURE_STORAGE.get('CONTAINER')
+    account_name = settings.AZURE_STORAGE.get('ACCOUNT_NAME')
+    account_key = settings.AZURE_STORAGE.get('ACCOUNT_KEY')
+    cdn_host = settings.AZURE_STORAGE.get('CDN_HOST')
+    use_ssl = settings.AZURE_STORAGE.get('USE_SSL')
+
+    def __init__(self, account_name=None, account_key=None, container=None,
+         use_ssl=None, cdn_host=None):
+
+        if account_name is not None:
+            self.account_name = account_name
+
+        if account_key is not None:
+            self.account_key = account_key
+
+        if container is not None:
+            self.container = container
+
+        if use_ssl is not None:
+            self.use_ssl = use_ssl
+
+        if cdn_host is not None:
+            self.cdn_host = cdn_host
+
+    def __getstate__(self):
+        return dict(
+            account_name=self.account_name,
+            account_key=self.account_key,
+            container=self.container,
+            cdn_host=self.cdn_host,
+            use_ssl=self.use_ssl
+        )
+
+    def _get_service(self):
+        if not hasattr(self, '_blob_service'):
+            self._blob_service = BlobService(
+                account_name=self.account_name,
+                account_key=self.account_key,
+                protocol='https' if self.use_ssl else 'http'
+            )
+
+        return self._blob_service
+
+    def _get_properties(self, name):
+        return self._get_service().get_blob_properties(
+            container_name=self.container,
+            blob_name=name
+        )
+
+    def _open(self, name, mode='rb'):
+        """
+        Return the AzureStorageFile.
+        """
+
+        from django.core.files.base import ContentFile
+
+        contents = self._get_service().get_blob_to_bytes(
+            container_name=self.container,
+            blob_name=name
+        )
+
+        return ContentFile(contents)
+
+    def _save(self, name, content):
+        """
+        Use the Azure Storage service to write ``content`` to a remote file
+        (called ``name``).
+        """
+        
+
+        content.open()
+
+        content_type = None
+
+        if hasattr(content.file, 'content_type'):
+            content_type = content.file.content_type
+        else:
+            content_type = mimetypes.guess_type(name)[0]
+
+        cache_control = self.get_cache_control(
+            self.container,
+            name,
+            content_type
+        )
+
+        self._get_service().put_block_blob_from_file(
+            container_name=self.container,
+            blob_name=name,
+            stream=content,
+            x_ms_blob_content_type=content_type,
+            cache_control=cache_control,
+            x_ms_blob_cache_control=cache_control
+        )
+
+        content.close()
+
+        return name
+
+    def listdir(self, path):
+        """
+        Lists the contents of the specified path, returning a 2-tuple of lists;
+        the first item being directories, the second item being files.
+        """
+
+        files = []
+
+        if path and not path.endswith('/'):
+            path = '%s/' % path
+
+        path_len = len(path)
+
+        if not path:
+            path = None
+
+        blob_list = self._get_service().list_blobs(self.container, prefix=path)
+
+        for name in blob_list:
+            files.append(name[path_len:])
+
+        return ([], files)
+
+    def exists(self, name):
+        """
+        Returns True if a file referenced by the given name already exists in
+        the storage system, or False if the name is available for a new file.
+        """
+        try:
+            self._get_properties(name)
+
+            return True
+        except AzureMissingResourceHttpError:
+            return False
+
+    def delete(self, name):
+        """
+        Deletes the file referenced by name.
+        """
+
+        try:
+            self._get_service().delete_blob(self.container, name)
+        except AzureMissingResourceHttpError:
+            pass
+
+    def get_cache_control(self, container, name, content_type):
+        """
+        Get the Cache-Control value for a blob, used when saving the blob on
+        Azure.  Returns `None` by default to remain compatible with the
+        default setting for the SDK.
+        """
+
+        return None
+
+    def size(self, name):
+        """
+        Returns the total size, in bytes, of the file referenced by name.
+        """
+
+        try:
+            properties = self._get_properties(name)
+
+            return int(properties['content-length'])
+        except AzureMissingResourceHttpError:
+            pass
+
+    def url(self, name):
+        """
+        Returns the URL where the contents of the file referenced by name can
+        be accessed.
+        """
+
+        blob_url_args = {
+            'container_name': self.container,
+            'blob_name': name,
+        }
+
+        if self.cdn_host:
+            # The account name should be built into the cdn hostname
+            blob_url_args['account_name'] = ''
+            blob_url_args['host_base'] = self.cdn_host
+
+        return self._get_service().make_blob_url(
+            **blob_url_args
+        )
+
+    def modified_time(self, name):
+        """
+        Returns a datetime object containing the last modified time.
+        """
+
+        try:
+            properties = self._get_properties(name)
+
+            return datetime.datetime.strptime(
+                properties['last-modified'],
+                '%a, %d %b %Y %H:%M:%S %Z'
+            )
+        except AzureMissingResourceHttpError:
+            pass

Azure/AddUp/blob-upload.py

@@ -0,0 +1,107 @@
+# ----------------------------------------------------------------------------------
+# MIT License
+#
+# Copyright(c) Microsoft Corporation. All rights reserved.
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+# ----------------------------------------------------------------------------------
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+
+
+import os
+import uuid
+import sys
+from azure.storage.blob import BlockBlobService, PublicAccess
+
+# ---------------------------------------------------------------------------------------------------------
+# Method that creates a test file in the 'Sample' folder.
+# This sample application creates a test file, uploads the test file to the Blob storage,
+# lists the blobs in the container, and downloads the file with a new name.
+# ---------------------------------------------------------------------------------------------------------
+# Documentation References:
+# Associated Article - https://docs.microsoft.com/en-us/azure/storage/blobs/storage-quickstart-blobs-python
+# What is a Storage Account - http://azure.microsoft.com/en-us/documentation/articles/storage-whatis-account/
+# Getting Started with Blobs-https://docs.microsoft.com/en-us/azure/storage/blobs/storage-python-how-to-use-blob-storage
+# Blob Service Concepts - http://msdn.microsoft.com/en-us/library/dd179376.aspx
+# Blob Service REST API - http://msdn.microsoft.com/en-us/library/dd135733.aspx
+# ----------------------------------------------------------------------------------------------------------
+
+
+def run_sample():
+    try:
+        # Create the BlockBlobService that is used to call the Blob service for the storage account
+        blob_service_client = BlockBlobService(
+            account_name='accountname', account_key='accountkey')
+
+        # Create a container called 'quickstartblobs'.
+        container_name = 'quickstartblobs'
+        blob_service_client.create_container(container_name)
+
+        # Set the permission so the blobs are public.
+        blob_service_client.set_container_acl(
+            container_name, public_access=PublicAccess.Container)
+
+        # Create Sample folder if it not exists, and create a file in folder Sample to test the upload and download.
+        local_path = os.path.expanduser("~/Sample")
+        if not os.path.exists(local_path):
+            os.makedirs(os.path.expanduser("~/Sample"))
+        local_file_name = "QuickStart_" + str(uuid.uuid4()) + ".txt"
+        full_path_to_file = os.path.join(local_path, local_file_name)
+
+        # Write text to the file.
+        file = open(full_path_to_file,  'w')
+        file.write("Hello, World!")
+        file.close()
+
+        print("Temp file = " + full_path_to_file)
+        print("\nUploading to Blob storage as blob" + local_file_name)
+
+        # Upload the created file, use local_file_name for the blob name
+        blob_service_client.create_blob_from_path(
+            container_name, local_file_name, full_path_to_file)
+
+        # List the blobs in the container
+        print("\nList blobs in the container")
+        generator = blob_service_client.list_blobs(container_name)
+        for blob in generator:
+            print("\t Blob name: " + blob.name)
+
+        # Download the blob(s).
+        # Add '_DOWNLOADED' as prefix to '.txt' so you can see both files in Documents.
+        full_path_to_file2 = os.path.join(local_path, str.replace(
+            local_file_name ,'.txt', '_DOWNLOADED.txt'))
+        print("\nDownloading blob to " + full_path_to_file2)
+        blob_service_client.get_blob_to_path(
+            container_name, local_file_name, full_path_to_file2)
+
+        sys.stdout.write("Sample finished running. When you hit <any key>, the sample will be deleted and the sample "
+                         "application will exit.")
+        sys.stdout.flush()
+        input()
+
+        # Clean up resources. This includes the container and the temp files
+        blob_service_client.delete_container(container_name)
+        os.remove(full_path_to_file)
+        os.remove(full_path_to_file2)
+    except Exception as e:
+        print(e)
+
+
+# Main method.
+if __name__ == '__main__':
+    run_sample()

Azure/AddUp/circuitbreaker.py

@@ -0,0 +1,231 @@
+# ----------------------------------------------------------------------------------
+# MIT License
+#
+# Copyright(c) Microsoft Corporation. All rights reserved.
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+# ----------------------------------------------------------------------------------
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+# ----------------------------------------------------------------------------------
+
+import os
+import uuid
+import time
+import sys
+from azure.storage.blob import BlockBlobService
+from azure.storage.common.models import LocationMode
+from azure.storage.common.retry import LinearRetry
+
+
+# ----------------------------------------------------------------------------------
+# Azure Storage Circuit Breaker Demo
+# INSTRUCTIONS
+# Please see the README.md file for an overview explaining this application and how to run it.
+# ----------------------------------------------------------------------------------
+# Documentation References:
+# Associated Article - https://docs.microsoft.com/en-us/azure/storage/blobs/storage-create-geo-redundant-storage-python
+# Designing HA Apps with RA-GRS storage -https://docs.microsoft.com/azure/storage/storage-designing-ha-apps-with-ra-grs/
+# Getting Started with Blobs-https://docs.microsoft.com/en-us/azure/storage/blobs/storage-python-how-to-use-blob-storage
+# Azure Storage Replication - https://docs.microsoft.com/azure/storage/storage-redundancy
+# ----------------------------------------------------------------------------------
+
+account_name = os.environ.get('accountname')
+account_key = os.environ.get('accountkey')
+
+# Track how many times retry events occur.
+retry_count = 0  # Number of retries that have occurred
+retry_threshold = 5  # Threshold number of retries before switching to secondary
+secondary_read_count = 0  # Number of reads from secondary that have occurred
+secondary_threshold = 20  # Threshold number of reads from secondary before switching back to primary
+
+# This is the CloudBlobClient object used to access the blob service
+blob_client = None
+
+# This is the container used to store and access the blob to be used for testing
+container_name = None
+
+'''
+Main method. Sets up the objects needed, the performs a loop to perform blob
+ operation repeatedly, responding to the Retry and Response Received events.
+'''
+
+
+def run_circuit_breaker():
+    # Name of image to use for testing.
+    image_to_upload = "HelloWorld.png"
+
+    global blob_client
+    global container_name
+    try:
+
+        # Create a reference to the blob client and container using the storage account name and key
+        blob_client = BlockBlobService(account_name, account_key)
+
+        # Make the container unique by using a UUID in the name.
+        container_name = "democontainer" + str(uuid.uuid4())
+        blob_client.create_container(container_name)
+
+    except Exception as ex:
+        print("Please make sure you have put the correct storage account name and key.")
+        print(ex)
+
+    # Define a reference to the actual blob and upload the block_blob to the newly created container
+    full_path_to_file = os.path.join(os.path.dirname(__file__), image_to_upload)
+    blob_client.create_blob_from_path(container_name, image_to_upload, full_path_to_file)
+
+    # Set the location mode to secondary, so you can check just the secondary data center.
+    blob_client.location_mode = LocationMode.SECONDARY
+    blob_client.retry = LinearRetry(backoff=0).retry
+
+    # Before proceeding, wait until the blob has been replicated to the secondary data center.
+    # Loop and check for the presence of the blob once in a second until it hits 60 seconds
+    # or until it finds it
+    counter = 0
+    while counter < 60:
+        counter += 1
+        sys.stdout.write("\nAttempt {0} to see if the blob has replicated to the secondary storage yet.".format(counter))
+        sys.stdout.flush()
+        if blob_client.exists(container_name, image_to_upload):
+            break
+
+        # Wait a second, then loop around and try again
+        # When it's finished replicating to the secondary, continue.
+        time.sleep(1)
+
+    # Set the starting LocationMode to Primary, then Secondary.
+    # Here we use the linear retry by default, but allow it to retry to secondary if
+    # the initial request to primary fails.
+    # Note that the default is Primary. You must have RA-GRS enabled to use this
+    blob_client.location_mode = LocationMode.PRIMARY
+    blob_client.retry = LinearRetry(max_attempts=retry_threshold, backoff=1).retry
+
+    ''' 
+        ************INSTRUCTIONS**************k
+        To perform the test, first replace the 'accountname' and 'accountkey' with your storage account name and key.
+        Every time it calls get_blob_to_path it will hit the response_callback function.
+
+        Next, run this app. While this loop is running, pause the program by pressing any key, and
+        put the intercept code in Fiddler (that will intercept and return a 503).
+
+        For instructions on modifying Fiddler, look at the Fiddler_script.text file in this project.
+        There are also full instructions in the ReadMe_Instructions.txt file included in this project.
+
+        After adding the custom script to Fiddler, calls to primary storage will fail with a retryable
+        error which will trigger the Retrying event (above).
+        Then it will switch over and read the secondary. It will do that 20 times, then try to
+        switch back to the primary.
+        After seeing that happen, pause this again and remove the intercepting Fiddler code
+        Then you'll see it return to the primary and finish.
+        '''
+
+    print("\n\nThe application will pause at 200 unit interval")
+
+    for i in range(0, 1000):
+        if blob_client.location_mode == LocationMode.SECONDARY:
+            sys.stdout.write("S{0} ".format(str(i)))
+        else:
+            sys.stdout.write("P{0} ".format(str(i)))
+        sys.stdout.flush()
+
+        try:
+
+            # These function is called immediately after retry evaluation is performed.
+            # It is used to trigger the change from primary to secondary and back
+            blob_client.retry_callback = retry_callback
+
+            # Download the file
+            blob_client.get_blob_to_path(container_name, image_to_upload,
+                                                str.replace(full_path_to_file, ".png", "Copy.png"))
+
+            # Set the application to pause at 200 unit intervals to implement simulated failures
+            if i == 200 or i == 400 or i == 600 or i == 800:
+                sys.stdout.write("\nPress the Enter key to resume")
+                sys.stdout.flush()
+                if sys.version_info[0] < 3:
+                    raw_input()
+                else:
+                    input()
+        except Exception as ex:
+            print(ex)
+        finally:
+            # Force an exists call to succeed by resetting the status
+            blob_client.response_callback = response_callback
+
+    # Clean up resources
+    blob_client.delete_container(container_name)
+
+
+'''
+RequestCompleted Event handler
+If it's not pointing at the secondary, let it go through. It was either successful,
+or it failed with a non-retryable event.
+If it's pointing at the secondary, increment the read count.
+If the number of reads has hit the threshold of how many reads you want to do against the secondary,
+before you switch back to primary, switch back and reset the secondary_read_count.
+'''
+
+
+def response_callback(response):
+    global secondary_read_count
+    if blob_client.location_mode == LocationMode.SECONDARY:
+
+        # You're reading the secondary. Let it read the secondary [secondaryThreshold] times,
+        # then switch back to the primary and see if it is available now.
+        secondary_read_count += 1
+        if secondary_read_count >= secondary_threshold:
+            blob_client.location_mode = LocationMode.PRIMARY
+            secondary_read_count = 0
+
+
+'''
+Retry Event handler
+If it has retried more times than allowed, and it's not already pointed to the secondary,
+flip it to the secondary and reset the retry count.
+If it has retried more times than allowed, and it's already pointed to the secondary throw an exception.
+'''
+
+
+def retry_callback(retry_context):
+    global retry_count
+    retry_count = retry_context.count
+    sys.stdout.write("\nRetrying event because of failure reading the primary. RetryCount= {0}".format(retry_count))
+    sys.stdout.flush()
+
+    # Check if we have more than n-retries in which case switch to secondary
+    if retry_count >= retry_threshold:
+
+        # Check to see if we can fail over to secondary.
+        if blob_client.location_mode != LocationMode.SECONDARY:
+            blob_client.location_mode = LocationMode.SECONDARY
+            retry_count = 0
+        else:
+            raise Exception("Both primary and secondary are unreachable. "
+                            "Check your application's network connection.")
+
+
+if __name__ == '__main__':
+    print("Azure storage Circuit Breaker Sample \n")
+    try:
+        run_circuit_breaker()
+    except Exception as e:
+        print("Error thrown = {0}".format(e))
+    sys.stdout.write("\nPress any key to exit.")
+    sys.stdout.flush()
+    if sys.version_info[0]<3:
+        raw_input()
+    else:
+        input()

Azure/AddUp/datafactory.py

@@ -0,0 +1,138 @@
+from azure.common.credentials import ServicePrincipalCredentials
+from azure.mgmt.resource import ResourceManagementClient
+from azure.mgmt.datafactory import DataFactoryManagementClient
+from azure.mgmt.datafactory.models import *
+from datetime import datetime, timedelta
+import time
+
+def print_item(group):
+    """Print an Azure object instance."""
+    print("\tName: {}".format(group.name))
+    print("\tId: {}".format(group.id))
+    if hasattr(group, 'location'):
+        print("\tLocation: {}".format(group.location))
+    if hasattr(group, 'tags'):
+        print("\tTags: {}".format(group.tags))
+    if hasattr(group, 'properties'):
+        print_properties(group.properties)
+    print("\n")        
+
+def print_properties(props):
+    """Print a ResourceGroup properties instance."""
+    if props and hasattr(props, 'provisioning_state') and props.provisioning_state:
+        print("\tProperties:")
+        print("\t\tProvisioning State: {}".format(props.provisioning_state))
+    print("\n")
+
+def print_activity_run_details(activity_run):
+    """Print activity run details."""
+    print("\n\tActivity run details\n")
+    print("\tActivity run status: {}".format(activity_run.status))    
+    if activity_run.status == 'Succeeded':
+        print("\tNumber of bytes read: {}".format(activity_run.output['dataRead']))       
+        print("\tNumber of bytes written: {}".format(activity_run.output['dataWritten']))           
+        print("\tCopy duration: {}".format(activity_run.output['copyDuration']))           
+    else:
+        print("\tErrors: {}".format(activity_run.error['message']))
+
+def main():
+
+    # Azure subscription ID
+    subscription_id = '<Azure subscription ID>'
+
+    # This program creates this resource group. If it's an existing resource group, comment out the code that creates the resource group
+    rg_name = '<Azure resource group name>'
+
+    # The data factory name. It must be globally unique.
+    df_name = '<Data factory name>'        
+
+    # Specify your Active Directory client ID, client secret, and tenant ID
+    credentials = ServicePrincipalCredentials(client_id='<AAD application ID>', secret='<AAD app authentication key>', tenant='<AAD tenant ID>')
+    resource_client = ResourceManagementClient(credentials, subscription_id)
+    adf_client = DataFactoryManagementClient(credentials, subscription_id)
+
+    rg_params = {'location':'eastus'}
+    df_params = {'location':'eastus'}
+
+    # create the resource group
+    # comment out if the resource group already exits
+    resource_client.resource_groups.create_or_update(rg_name, rg_params)
+
+    # Create a data factory
+    df_resource = Factory(location='eastus')
+    df = adf_client.factories.create_or_update(rg_name, df_name, df_resource)
+    print_item(df)
+    while df.provisioning_state != 'Succeeded':
+        df = adf_client.factories.get(rg_name, df_name)
+        time.sleep(1)
+
+    # Create an Azure Storage linked service
+    ls_name = 'storageLinkedService'
+
+    # Specify the name and key of your Azure Storage account
+    storage_string = SecureString('DefaultEndpointsProtocol=https;AccountName=<Azure storage account>;AccountKey=<Azure storage authentication key>')
+
+    ls_azure_storage = AzureStorageLinkedService(connection_string=storage_string)
+    ls = adf_client.linked_services.create_or_update(rg_name, df_name, ls_name, ls_azure_storage)
+    print_item(ls)
+
+    # Create an Azure blob dataset (input)
+    ds_name = 'ds_in'
+    ds_ls = LinkedServiceReference(ls_name)
+    blob_path= 'adftutorial/inputpy'
+    blob_filename = 'input.txt'
+    ds_azure_blob= AzureBlobDataset(ds_ls, folder_path=blob_path, file_name = blob_filename)
+    ds = adf_client.datasets.create_or_update(rg_name, df_name, ds_name, ds_azure_blob)
+    print_item(ds)
+
+    # Create an Azure blob dataset (output)
+    dsOut_name = 'ds_out'
+    output_blobpath = 'adftutorial/outputpy'
+    dsOut_azure_blob = AzureBlobDataset(ds_ls, folder_path=output_blobpath)
+    dsOut = adf_client.datasets.create_or_update(rg_name, df_name, dsOut_name, dsOut_azure_blob)
+    print_item(dsOut)
+
+    # Create a copy activity
+    act_name =  'copyBlobtoBlob'
+    blob_source = BlobSource()
+    blob_sink = BlobSink()
+    dsin_ref = DatasetReference(ds_name)
+    dsOut_ref = DatasetReference(dsOut_name)
+    copy_activity = CopyActivity(act_name,inputs=[dsin_ref], outputs=[dsOut_ref], source=blob_source, sink=blob_sink)
+
+    # Create a pipeline with the copy activity
+    p_name =  'copyPipeline'
+    params_for_pipeline = {}
+    p_obj = PipelineResource(activities=[copy_activity], parameters=params_for_pipeline)
+    p = adf_client.pipelines.create_or_update(rg_name, df_name, p_name, p_obj)
+    print_item(p)
+
+    # Create a pipeline run
+    run_response = adf_client.pipelines.create_run(rg_name, df_name, p_name,
+        {
+        }
+    )
+
+    # Monitor the pipeilne run
+    time.sleep(30)
+    pipeline_run = adf_client.pipeline_runs.get(rg_name, df_name, run_response.run_id)
+    print("\n\tPipeline run status: {}".format(pipeline_run.status))
+    activity_runs_paged = list(adf_client.activity_runs.list_by_pipeline_run(rg_name, df_name, pipeline_run.run_id, datetime.now() - timedelta(1),  datetime.now() + timedelta(1)))
+    print_activity_run_details(activity_runs_paged[0])
+
+    # Create a trigger
+    tr_name = 'mytrigger'
+    scheduler_recurrence = ScheduleTriggerRecurrence(frequency='Minute', interval='15',start_time=datetime.now(), end_time=datetime.now() + timedelta(1), time_zone='UTC') 
+    pipeline_parameters = {'inputPath':'adftutorial/inputpy', 'outputPath':'adftutorial/outputpy'}
+    pipelines_to_run = []
+    pipeline_reference = PipelineReference('copyPipeline')
+    pipelines_to_run.append(TriggerPipelineReference(pipeline_reference, pipeline_parameters))
+    tr_properties = ScheduleTrigger(description='My scheduler trigger', pipelines = pipelines_to_run, recurrence=scheduler_recurrence)    
+    adf_client.triggers.create_or_update(rg_name, df_name, tr_name, tr_properties)
+
+    # start the trigger
+    adf_client.triggers.start(rg_name, df_name, tr_name)
+    
+
+# Start the main method
+main()

Azure/AddUp/file_advanced_samples.py

@@ -0,0 +1,202 @@
+#-------------------------------------------------------------------------
+# Microsoft Developer & Platform Evangelism
+#
+# Copyright (c) Microsoft Corporation. All rights reserved.
+#
+# THIS CODE AND INFORMATION ARE PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND, 
+# EITHER EXPRESSED OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE IMPLIED WARRANTIES 
+# OF MERCHANTABILITY AND/OR FITNESS FOR A PARTICULAR PURPOSE.
+#----------------------------------------------------------------------------------
+# The example companies, organizations, products, domain names,
+# e-mail addresses, logos, people, places, and events depicted
+# herein are fictitious. No association with any real company,
+# organization, product, domain name, email address, logo, person,
+# places, or events is intended or should be inferred.
+#--------------------------------------------------------------------------
+
+import os
+from random_data import RandomData
+
+from azure.storage.fileshare import ShareServiceClient
+from azure.storage.fileshare import CorsRule, RetentionPolicy, Metrics
+
+#
+# Azure File Service Sample - Demonstrate how to perform common tasks using the Microsoft Azure File Service.  
+#  
+# Documentation References:  
+#  - What is a Storage Account - http://azure.microsoft.com/en-us/documentation/articles/storage-whatis-account/  
+#  - Getting Started with Files - https://azure.microsoft.com/en-us/documentation/articles/storage-python-how-to-use-file-storage/  
+#  - File Service Concepts - http://msdn.microsoft.com/en-us/library/dn166972.aspx  
+#  - File Service REST API - http://msdn.microsoft.com/en-us/library/dn167006.aspx  
+#  - Storage Emulator - http://azure.microsoft.com/en-us/documentation/articles/storage-use-emulator/
+#  
+class FileAdvancedSamples():
+
+    def __init__(self):
+        self.random_data = RandomData()
+    
+    # Runs all samples for Azure Storage File service.
+    def run_all_samples(self, connection_string):
+        print('Azure Storage File Advanced samples - Starting.')
+        
+        try:
+            # Create an instance of ShareServiceClient
+            service = ShareServiceClient.from_connection_string(conn_str=connection_string)
+
+            # List shares
+            print('\n\n* List shares *\n')
+            self.list_shares(service)
+
+            # Set Cors
+            print('\n\n* Set cors rules *\n')
+            self.set_cors_rules(service)
+
+            # Set Service Properties
+            print('\n\n* Set service properties *\n')
+            self.set_service_properties(service)
+
+            # Share, directory and file properties and metadata
+            print('\n\n* Metadata and properties *\n')
+            self.metadata_and_properties(service)
+
+        except Exception as e:
+            print('Error occurred in the sample.', e) 
+
+        finally:
+            print('\nAzure Storage File Advanced samples - Completed.\n')
+    
+    # List file shares
+    def list_shares(self, service):
+        share_prefix = 'sharesample' + self.random_data.get_random_name(6)
+
+        try:        
+            print('1. Create multiple shares with prefix: ', share_prefix)
+            for i in range(5):
+                service.create_share(share_name=share_prefix + str(i))
+            
+            print('2. List shares')
+            shares = service.list_shares()
+            for share in shares:
+                print('  Share name:' + share.name)
+
+        except Exception as e:
+            print(e) 
+
+        finally:
+            print('3. Delete shares with prefix:' + share_prefix) 
+            for i in range(5):
+                service.delete_share(share_prefix + str(i))
+    
+
+    # Set CORS
+    def set_cors_rules(self, service):
+        print('1. Get Cors Rules')
+        original_cors_rules = service.get_service_properties()['cors']
+
+        print('2. Overwrite Cors Rules')
+        cors_rule = CorsRule(
+            allowed_origins=['*'], 
+            allowed_methods=['POST', 'GET'],
+            allowed_headers=['*'],
+            exposed_headers=['*'],
+            max_age_in_seconds=3600)
+
+        try:
+            service.set_service_properties(cors=[cors_rule])
+        except Exception as e:
+            print(e)
+        finally:
+            #reverting cors rules back to the original ones
+            print('3. Revert Cors Rules back the original ones')
+            service.set_service_properties(cors=original_cors_rules)
+        
+        print("CORS sample completed")
+    
+
+    # Manage properties of the File service, including logging and metrics settings, and the default service version.
+    def set_service_properties(self, service):
+
+        print('1. Get File service properties')
+        props = service.get_service_properties()
+
+        retention = RetentionPolicy(enabled=True, days=5)
+        hour_metrics = Metrics(enabled=True, include_apis=True, retention_policy=retention)
+        minute_metrics = Metrics(enabled=False)
+
+        try:
+            print('2. Ovewrite File service properties')
+            service.set_service_properties(hour_metrics=hour_metrics, minute_metrics=minute_metrics)
+
+        finally:
+            print('3. Revert File service properties back to the original ones')
+            service.set_service_properties(hour_metrics=props['hour_metrics'], minute_metrics=props['minute_metrics'])
+
+        print('4. Set File service properties completed')
+    
+
+    # Manage metadata and properties of the share
+    def metadata_and_properties(self, service):
+        share_name = 'sharename' + self.random_data.get_random_name(6)
+
+        try:
+            # All directories and share must be created in a parent share.
+            # Max capacity: 5TB per share
+            print('1. Create sample share with name ' + share_name)
+            quota = 1 # in GB
+            metadata = { "foo": "bar", "baz": "foo" }
+            share_client = service.create_share(share_name=share_name)
+            print('Sample share "'+ share_name +'" created.')
+
+            print('2. Get share properties.')
+            properties = share_client.get_share_properties()
+
+            print('3. Get share metadata.')
+            get_metadata = properties['metadata']
+            for k, v in get_metadata.items():
+                print("\t" + k + ": " + v)
+
+            dir_name = 'dirname' + self.random_data.get_random_name(6)
+
+            print('4. Create sample directory with name ' + dir_name)
+            metadata = { "abc": "def", "jkl": "mno" }
+            directory_client = share_client.create_directory(dir_name, metadata=metadata)
+            print('Sample directory "'+ dir_name +'" created.')
+
+            print('5. Get directory properties.')
+            properties = directory_client.get_directory_properties()
+            
+            print('6. Get directory metadata.')
+            get_metadata = properties['metadata']
+            for k, v in get_metadata.items():
+                print("\t" + k + ": " + v)
+
+            file_name = 'sample.txt'
+            # Uploading text to share_name/dir_name/sample.txt in Azure Files account.
+            # Max capacity: 1TB per file
+            print('7. Upload sample file from text to directory.')
+            metadata = { "prop1": "val1", "prop2": "val2" }
+            file_client = directory_client.get_file_client(file_name)
+            file_client.upload_file('Hello World! - from text sample', metadata=metadata)
+            print('Sample file "' + file_name + '" created and uploaded to: ' + share_name + '/' + dir_name)        
+
+            print('8. Get file properties.')
+            properties = file_client.get_file_properties()
+
+            print('9. Get file metadata.')
+            get_metadata = properties['metadata']
+            for k, v in get_metadata.items():
+                print("\t" + k + ": " + v)
+
+            # This is for demo purposes, all files will be deleted when share is deleted
+            print('10. Delete file.')
+            file_client.delete_file()
+
+            # This is for demo purposes, all directories will be deleted when share is deleted
+            print('11. Delete directory.')
+            directory_client.delete_directory()
+
+        finally:
+            print('12. Delete share.')
+            share_client.delete_share(share_name)
+
+        print("Metadata and properties sample completed")

Azure/AddUp/file_basic_samples.py

@@ -0,0 +1,190 @@
+#-------------------------------------------------------------------------
+# Microsoft Developer & Platform Evangelism
+#
+# Copyright (c) Microsoft Corporation. All rights reserved.
+#
+# THIS CODE AND INFORMATION ARE PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND, 
+# EITHER EXPRESSED OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE IMPLIED WARRANTIES 
+# OF MERCHANTABILITY AND/OR FITNESS FOR A PARTICULAR PURPOSE.
+#----------------------------------------------------------------------------------
+# The example companies, organizations, products, domain names,
+# e-mail addresses, logos, people, places, and events depicted
+# herein are fictitious. No association with any real company,
+# organization, product, domain name, email address, logo, person,
+# places, or events is intended or should be inferred.
+#--------------------------------------------------------------------------
+
+from random_data import RandomData
+import tempfile
+import os
+
+from azure.storage.fileshare import ShareServiceClient
+
+
+class FileBasicSamples():
+
+    def __init__(self):
+        self.random_data = RandomData()
+
+    # Runs all samples for Azure Storage File service.
+    def run_all_samples(self, connection_string):
+        print('Azure Storage File Basis samples - Starting.')
+        
+        #declare variables
+        filename = 'filesample' + self.random_data.get_random_name(6)
+        sharename = 'sharesample' + self.random_data.get_random_name(6)
+        
+        try:
+            # Create an instance of ShareServiceClient
+            service = ShareServiceClient.from_connection_string(conn_str=connection_string)
+
+            print('\n\n* Basic file operations *\n')
+            self.basic_file_operations(sharename, filename, service)
+
+        except Exception as e:
+            print('error:' + e) 
+
+        finally:
+            # Delete all Azure Files created in this sample
+            self.file_delete_samples(sharename, filename, service)
+
+        print('\nAzure Storage File Basic samples - Completed.\n')
+    
+    def basic_file_operations(self, sharename, filename, service):
+        # Creating an SMB file share in your Azure Files account.
+        print('\nAttempting to create a sample file from text for upload demonstration.')   
+        # All directories and share must be created in a parent share.
+        # Max capacity: 5TB per share
+
+        print('Creating sample share.')
+        share_client = service.create_share(share_name=sharename)
+        print('Sample share "'+ sharename +'" created.')
+
+
+        # Creating an optional file directory in your Azure Files account.
+        print('Creating a sample directory.')    
+        # Get the directory client
+        directory_client = share_client.create_directory("mydirectory")
+        print('Sample directory "mydirectory" created.')
+
+
+        # Uploading text to sharename/mydirectory/my_text_file in Azure Files account.
+        # Max capacity: 1TB per file
+        print('Uploading a sample file from text.')   
+        # create_file_client
+        file_client = directory_client.get_file_client(filename)
+        # Upload a file
+        file_client.upload_file('Hello World! - from text sample')
+        print('Sample file "' + filename + '" created and uploaded to: ' + sharename + '/mydirectory')
+  
+
+        # Demonstrate how to copy a file
+        print('\nCopying file ' + filename)
+        # Create another file client which will copy the file from url
+        destination_file_client = share_client.get_file_client('file1copy')
+
+        # Copy the sample source file from the url to the destination file
+        copy_resp = destination_file_client.start_copy_from_url(source_url=file_client.url)
+        if copy_resp['copy_status'] ==  'pending':
+            # Demonstrate how to abort a copy operation (just for demo, probably will never get here)
+            print('Abort copy operation')
+            destination_file.abort_copy()
+        else:
+            print('Copy was a ' + copy_resp['copy_status'])
+        
+
+        # Demonstrate how to create a share and upload a file from a local temporary file path
+        print('\nAttempting to upload a sample file from path for upload demonstration.')  
+        # Creating a temporary file to upload to Azure Files
+        print('Creating a temporary file from text.') 
+        with tempfile.NamedTemporaryFile(delete=False) as my_temp_file:
+            my_temp_file.file.write(b"Hello world!")
+        print('Sample temporary file created.') 
+
+        # Uploading my_temp_file to sharename folder in Azure Files
+        # Max capacity: 1TB per file
+        print('Uploading a sample file from local path.')
+        # Create file_client
+        file_client = share_client.get_file_client(filename)
+
+        # Upload a file
+        with open(my_temp_file.name, "rb") as source_file:
+            file_client.upload_file(source_file)
+
+        print('Sample file "' + filename + '" uploaded from path to share: ' + sharename)
+
+        # Close the temp file
+        my_temp_file.close()
+
+        # Get the list of valid ranges and write to the specified range
+        print('\nGet list of valid ranges of the file.') 
+        file_ranges = file_client.get_ranges()
+
+        data = b'abcdefghijkl'
+        print('Put a range of data to the file.')
+        
+        file_client.upload_range(data=data, offset=file_ranges[0]['start'], length=len(data))
+
+
+        # Demonstrate how to download a file from Azure Files
+        # The following example download the file that was previously uploaded to Azure Files
+        print('\nAttempting to download a sample file from Azure files for demonstration.')
+
+        destination_file = tempfile.tempdir + '\mypathfile.txt'
+
+        with open(destination_file, "wb") as file_handle:
+            data = file_client.download_file()
+            data.readinto(file_handle)
+
+        print('Sample file downloaded to: ' + destination_file)
+
+
+        # Demonstrate how to list files and directories contains under Azure File share
+        print('\nAttempting to list files and directories directory under share "' + sharename + '":')
+
+        # Create a generator to list directories and files under share
+        # This is not a recursive listing operation
+        generator = share_client.list_directories_and_files()
+
+        # Prints the directories and files under the share
+        for file_or_dir in generator:
+            print(file_or_dir['name'])
+        
+        # remove temp file
+        os.remove(my_temp_file.name)
+
+        print('Files and directories under share "' + sharename + '" listed.')
+        print('\nCompleted successfully - Azure basic Files operations.')
+
+
+    # Demonstrate how to delete azure files created for this demonstration
+    # Warning: Deleting a share or directory will also delete all files and directories that are contained in it.
+    def file_delete_samples(self, sharename, filename, service):
+        print('\nDeleting all samples created for this demonstration.')
+
+        try:
+            # Deleting file: 'sharename/mydirectory/filename'
+            # This is for demo purposes only, it's unnecessary, as we're deleting the share later
+            print('Deleting a sample file.')
+
+            share_client = service.get_share_client(sharename)
+            directory_client = share_client.get_directory_client('mydirectory')
+            
+            directory_client.delete_file(file_name=filename)
+            print('Sample file "' + filename + '" deleted from: ' + sharename + '/mydirectory' )
+
+            # Deleting directory: 'sharename/mydirectory'
+            print('Deleting sample directory and all files and directories under it.')
+            share_client.delete_directory('mydirectory')
+            print('Sample directory "/mydirectory" deleted from: ' + sharename)
+
+            # Deleting share: 'sharename'
+            print('Deleting sample share ' + sharename + ' and all files and directories under it.')
+            share_client.delete_share(sharename)
+            print('Sample share "' + sharename + '" deleted.')
+
+            print('\nCompleted successfully - Azure Files samples deleted.')
+
+        except Exception as e:
+            print('********ErrorDelete***********')
+            print(e)

Azure/AddUp/python-quick-start.py

@@ -0,0 +1,415 @@
+# python quickstart client Code Sample
+#
+# Copyright (c) Microsoft Corporation
+#
+# All rights reserved.
+#
+# MIT License
+#
+# Permission is hereby granted, free of charge, to any person obtaining a
+# copy of this software and associated documentation files (the "Software"),
+# to deal in the Software without restriction, including without limitation
+# the rights to use, copy, modify, merge, publish, distribute, sublicense,
+# and/or sell copies of the Software, and to permit persons to whom the
+# Software is furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED *AS IS*, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+# DEALINGS IN THE SOFTWARE.
+
+"""
+Create a pool of nodes to output text files from azure blob storage.
+"""
+
+import datetime
+import io
+import os
+import sys
+import time
+
+from azure.storage.blob import (
+    BlobServiceClient,
+    BlobSasPermissions,
+    generate_blob_sas
+)
+from azure.batch import BatchServiceClient
+from azure.batch.batch_auth import SharedKeyCredentials
+import azure.batch.models as batchmodels
+from azure.core.exceptions import ResourceExistsError
+
+import config
+
+DEFAULT_ENCODING = "utf-8"
+
+
+# Update the Batch and Storage account credential strings in config.py with values
+# unique to your accounts. These are used when constructing connection strings
+# for the Batch and Storage client objects.
+
+def query_yes_no(question: str, default: str = "yes") -> str:
+    """
+    Prompts the user for yes/no input, displaying the specified question text.
+
+    :param str question: The text of the prompt for input.
+    :param str default: The default if the user hits <ENTER>. Acceptable values
+    are 'yes', 'no', and None.
+    :return: 'yes' or 'no'
+    """
+    valid = {'y': 'yes', 'n': 'no'}
+    if default is None:
+        prompt = ' [y/n] '
+    elif default == 'yes':
+        prompt = ' [Y/n] '
+    elif default == 'no':
+        prompt = ' [y/N] '
+    else:
+        raise ValueError(f"Invalid default answer: '{default}'")
+
+    choice = default
+
+    while 1:
+        user_input = input(question + prompt).lower()
+        if not user_input:
+            break
+        try:
+            choice = valid[user_input[0]]
+            break
+        except (KeyError, IndexError):
+            print("Please respond with 'yes' or 'no' (or 'y' or 'n').\n")
+
+    return choice
+
+
+def print_batch_exception(batch_exception: batchmodels.BatchErrorException):
+    """
+    Prints the contents of the specified Batch exception.
+
+    :param batch_exception:
+    """
+    print('-------------------------------------------')
+    print('Exception encountered:')
+    if batch_exception.error and \
+            batch_exception.error.message and \
+            batch_exception.error.message.value:
+        print(batch_exception.error.message.value)
+        if batch_exception.error.values:
+            print()
+            for mesg in batch_exception.error.values:
+                print(f'{mesg.key}:\t{mesg.value}')
+    print('-------------------------------------------')
+
+
+def upload_file_to_container(blob_storage_service_client: BlobServiceClient,
+                             container_name: str, file_path: str) -> batchmodels.ResourceFile:
+    """
+    Uploads a local file to an Azure Blob storage container.
+
+    :param blob_storage_service_client: A blob service client.
+    :param str container_name: The name of the Azure Blob storage container.
+    :param str file_path: The local path to the file.
+    :return: A ResourceFile initialized with a SAS URL appropriate for Batch
+    tasks.
+    """
+    blob_name = os.path.basename(file_path)
+    blob_client = blob_storage_service_client.get_blob_client(container_name, blob_name)
+
+    print(f'Uploading file {file_path} to container [{container_name}]...')
+
+    with open(file_path, "rb") as data:
+        blob_client.upload_blob(data, overwrite=True)
+
+    sas_token = generate_blob_sas(
+        config.STORAGE_ACCOUNT_NAME,
+        container_name,
+        blob_name,
+        account_key=config.STORAGE_ACCOUNT_KEY,
+        permission=BlobSasPermissions(read=True),
+        expiry=datetime.datetime.utcnow() + datetime.timedelta(hours=2)
+    )
+
+    sas_url = generate_sas_url(
+        config.STORAGE_ACCOUNT_NAME,
+        config.STORAGE_ACCOUNT_DOMAIN,
+        container_name,
+        blob_name,
+        sas_token
+    )
+
+    return batchmodels.ResourceFile(
+        http_url=sas_url,
+        file_path=blob_name
+    )
+
+
+def generate_sas_url(
+    account_name: str,
+    account_domain: str,
+    container_name: str,
+    blob_name: str,
+    sas_token: str
+) -> str:
+    """
+    Generates and returns a sas url for accessing blob storage
+    """
+    return f"https://{account_name}.{account_domain}/{container_name}/{blob_name}?{sas_token}"
+
+
+def create_pool(batch_service_client: BatchServiceClient, pool_id: str):
+    """
+    Creates a pool of compute nodes with the specified OS settings.
+
+    :param batch_service_client: A Batch service client.
+    :param str pool_id: An ID for the new pool.
+    :param str publisher: Marketplace image publisher
+    :param str offer: Marketplace image offer
+    :param str sku: Marketplace image sku
+    """
+    print(f'Creating pool [{pool_id}]...')
+
+    # Create a new pool of Linux compute nodes using an Azure Virtual Machines
+    # Marketplace image. For more information about creating pools of Linux
+    # nodes, see:
+    # https://azure.microsoft.com/documentation/articles/batch-linux-nodes/
+    new_pool = batchmodels.PoolAddParameter(
+        id=pool_id,
+        virtual_machine_configuration=batchmodels.VirtualMachineConfiguration(
+            image_reference=batchmodels.ImageReference(
+                publisher="canonical",
+                offer="0001-com-ubuntu-server-focal",
+                sku="20_04-lts",
+                version="latest"
+            ),
+            node_agent_sku_id="batch.node.ubuntu 20.04"),
+        vm_size=config.POOL_VM_SIZE,
+        target_dedicated_nodes=config.POOL_NODE_COUNT
+    )
+    batch_service_client.pool.add(new_pool)
+
+
+def create_job(batch_service_client: BatchServiceClient, job_id: str, pool_id: str):
+    """
+    Creates a job with the specified ID, associated with the specified pool.
+
+    :param batch_service_client: A Batch service client.
+    :param str job_id: The ID for the job.
+    :param str pool_id: The ID for the pool.
+    """
+    print(f'Creating job [{job_id}]...')
+
+    job = batchmodels.JobAddParameter(
+        id=job_id,
+        pool_info=batchmodels.PoolInformation(pool_id=pool_id))
+
+    batch_service_client.job.add(job)
+
+
+def add_tasks(batch_service_client: BatchServiceClient, job_id: str, resource_input_files: list):
+    """
+    Adds a task for each input file in the collection to the specified job.
+
+    :param batch_service_client: A Batch service client.
+    :param str job_id: The ID of the job to which to add the tasks.
+    :param list resource_input_files: A collection of input files. One task will be
+     created for each input file.
+    """
+
+    print(f'Adding {resource_input_files} tasks to job [{job_id}]...')
+
+    tasks = []
+
+    for idx, input_file in enumerate(resource_input_files):
+
+        command = f"/bin/bash -c \"cat {input_file.file_path}\""
+        tasks.append(batchmodels.TaskAddParameter(
+            id=f'Task{idx}',
+            command_line=command,
+            resource_files=[input_file]
+        )
+        )
+
+    batch_service_client.task.add_collection(job_id, tasks)
+
+
+def wait_for_tasks_to_complete(batch_service_client: BatchServiceClient, job_id: str,
+                               timeout: datetime.timedelta):
+    """
+    Returns when all tasks in the specified job reach the Completed state.
+
+    :param batch_service_client: A Batch service client.
+    :param job_id: The id of the job whose tasks should be to monitored.
+    :param timeout: The duration to wait for task completion. If all
+    tasks in the specified job do not reach Completed state within this time
+    period, an exception will be raised.
+    """
+    timeout_expiration = datetime.datetime.now() + timeout
+
+    print(f"Monitoring all tasks for 'Completed' state, timeout in {timeout}...", end='')
+
+    while datetime.datetime.now() < timeout_expiration:
+        print('.', end='')
+        sys.stdout.flush()
+        tasks = batch_service_client.task.list(job_id)
+
+        incomplete_tasks = [task for task in tasks if
+                            task.state != batchmodels.TaskState.completed]
+        if not incomplete_tasks:
+            print()
+            return True
+
+        time.sleep(1)
+
+    print()
+    raise RuntimeError("ERROR: Tasks did not reach 'Completed' state within "
+                       "timeout period of " + str(timeout))
+
+
+def print_task_output(batch_service_client: BatchServiceClient, job_id: str,
+                      text_encoding: str=None):
+    """
+    Prints the stdout.txt file for each task in the job.
+
+    :param batch_client: The batch client to use.
+    :param str job_id: The id of the job with task output files to print.
+    """
+
+    print('Printing task output...')
+
+    tasks = batch_service_client.task.list(job_id)
+
+    for task in tasks:
+
+        node_id = batch_service_client.task.get(
+            job_id, task.id).node_info.node_id
+        print(f"Task: {task.id}")
+        print(f"Node: {node_id}")
+
+        stream = batch_service_client.file.get_from_task(
+            job_id, task.id, config.STANDARD_OUT_FILE_NAME)
+
+        file_text = _read_stream_as_string(
+            stream,
+            text_encoding)
+
+        if text_encoding is None:
+            text_encoding = DEFAULT_ENCODING
+
+        sys.stdout = io.TextIOWrapper(sys.stdout.detach(), encoding = text_encoding)
+        sys.stderr = io.TextIOWrapper(sys.stderr.detach(), encoding = text_encoding)
+
+        print("Standard output:")
+        print(file_text)
+
+
+def _read_stream_as_string(stream, encoding) -> str:
+    """
+    Read stream as string
+
+    :param stream: input stream generator
+    :param str encoding: The encoding of the file. The default is utf-8.
+    :return: The file content.
+    """
+    output = io.BytesIO()
+    try:
+        for data in stream:
+            output.write(data)
+        if encoding is None:
+            encoding = DEFAULT_ENCODING
+        return output.getvalue().decode(encoding)
+    finally:
+        output.close()
+
+
+if __name__ == '__main__':
+
+    start_time = datetime.datetime.now().replace(microsecond=0)
+    print(f'Sample start: {start_time}')
+    print()
+
+    # Create the blob client, for use in obtaining references to
+    # blob storage containers and uploading files to containers.
+    blob_service_client = BlobServiceClient(
+        account_url=f"https://{config.STORAGE_ACCOUNT_NAME}.{config.STORAGE_ACCOUNT_DOMAIN}/",
+        credential=config.STORAGE_ACCOUNT_KEY
+    )
+
+    # Use the blob client to create the containers in Azure Storage if they
+    # don't yet exist.
+    input_container_name = 'input'      # pylint: disable=invalid-name
+    try:
+        blob_service_client.create_container(input_container_name)
+    except ResourceExistsError:
+        pass
+
+    # The collection of data files that are to be processed by the tasks.
+    input_file_paths = [os.path.join(sys.path[0], 'taskdata0.txt'),
+                        os.path.join(sys.path[0], 'taskdata1.txt'),
+                        os.path.join(sys.path[0], 'taskdata2.txt')]
+
+    # Upload the data files.
+    input_files = [
+        upload_file_to_container(blob_service_client, input_container_name, file_path)
+        for file_path in input_file_paths]
+
+    # Create a Batch service client. We'll now be interacting with the Batch
+    # service in addition to Storage
+    credentials = SharedKeyCredentials(config.BATCH_ACCOUNT_NAME,
+        config.BATCH_ACCOUNT_KEY)
+
+    batch_client = BatchServiceClient(
+        credentials,
+        batch_url=config.BATCH_ACCOUNT_URL)
+
+    try:
+        # Create the pool that will contain the compute nodes that will execute the
+        # tasks.
+        create_pool(batch_client, config.POOL_ID)
+
+        # Create the job that will run the tasks.
+        create_job(batch_client, config.JOB_ID, config.POOL_ID)
+
+        # Add the tasks to the job.
+        add_tasks(batch_client, config.JOB_ID, input_files)
+
+        # Pause execution until tasks reach Completed state.
+        wait_for_tasks_to_complete(batch_client,
+                                   config.JOB_ID,
+                                   datetime.timedelta(minutes=30))
+
+        print("  Success! All tasks reached the 'Completed' state within the "
+              "specified timeout period.")
+
+        # Print the stdout.txt and stderr.txt files for each task to the console
+        print_task_output(batch_client, config.JOB_ID)
+
+        # Print out some timing info
+        end_time = datetime.datetime.now().replace(microsecond=0)
+        print()
+        print(f'Sample end: {end_time}')
+        elapsed_time = end_time - start_time
+        print(f'Elapsed time: {elapsed_time}')
+        print()
+        input('Press ENTER to exit...')
+
+    except batchmodels.BatchErrorException as err:
+        print_batch_exception(err)
+        raise
+
+    finally:
+      # Clean up storage resources
+        print(f'Deleting container [{input_container_name}]...')
+        blob_service_client.delete_container(input_container_name)
+
+        # Clean up Batch resources (if the user so chooses).
+        if query_yes_no('Delete job?') == 'yes':
+            batch_client.job.delete(config.JOB_ID)
+
+        if query_yes_no('Delete pool?') == 'yes':
+            batch_client.pool.delete(config.POOL_ID)
+ 

Azure/AddUp/table_advanced_samples.py

@@ -0,0 +1,218 @@
+#-------------------------------------------------------------------------
+# Microsoft Developer & Platform Evangelism
+#
+# Copyright (c) Microsoft Corporation. All rights reserved.
+#
+# THIS CODE AND INFORMATION ARE PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND, 
+# EITHER EXPRESSED OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE IMPLIED WARRANTIES 
+# OF MERCHANTABILITY AND/OR FITNESS FOR A PARTICULAR PURPOSE.
+#----------------------------------------------------------------------------------
+# The example companies, organizations, products, domain names,
+# e-mail addresses, logos, people, places, and events depicted
+# herein are fictitious. No association with any real company,
+# organization, product, domain name, email address, logo, person,
+# places, or events is intended or should be inferred.
+#--------------------------------------------------------------------------
+import config
+import datetime
+import time
+from random_data import RandomData
+from tablestorageaccount import TableStorageAccount
+from azure.storage import CloudStorageAccount, AccessPolicy
+from azure.storage.table import TableService, Entity, TablePermissions
+from azure.storage.models import CorsRule, Logging, Metrics, RetentionPolicy, ResourceTypes, AccountPermissions
+
+#
+# Azure Table Service Sample - Demonstrate how to perform common tasks using the Microsoft Azure Table Service
+# including creating a table, CRUD operations and different querying techniques.
+#
+# Documentation References:
+#  - What is a Storage Account - http://azure.microsoft.com/en-us/documentation/articles/storage-whatis-account/
+#  - Getting Started with Tables - https://azure.microsoft.com/en-us/documentation/articles/storage-python-how-to-use-table-storage/
+#  - Table Service Concepts - http://msdn.microsoft.com/en-us/library/dd179463.aspx
+#  - Table Service REST API - http://msdn.microsoft.com/en-us/library/dd179423.aspx
+#  - Table Service Python API - http://azure.github.io/azure-storage-python/ref/azure.storage.table.html
+#  - Storage Emulator - http://azure.microsoft.com/en-us/documentation/articles/storage-use-emulator/
+#
+class TableAdvancedSamples():
+
+    def __init__(self):
+        self.random_data = RandomData()
+
+    # Runs all samples for Azure Storage Table service.
+    def run_all_samples(self, account):
+        table_service = account.create_table_service()
+        print('Azure Storage Advanced Table samples - Starting.')
+        
+        print('\n\n* List tables *\n')
+        self.list_tables(table_service)
+        
+        if not account.is_azure_cosmosdb_table():
+           print('\n\n* Set service properties *\n')
+           self.set_service_properties(table_service)
+        
+           print('\n\n* Set Cors rules *\n')
+           self.set_cors_rules(table_service)
+        
+           print('\n\n* ACL operations *\n')
+           self.table_acl_operations(table_service)
+        
+        if (config.IS_EMULATED):
+            print('\n\n* Shared Access Signature is not supported in emulator *\n')
+        else:
+            print('\n\n* SAS operations *\n')
+            self.table_operations_with_sas(account)
+
+        print('\nAzure Storage Advanced Table samples - Completed.\n')
+
+    # Manage tables including creating, listing and deleting
+    def list_tables(self, table_service):
+        table_prefix = 'table' + self.random_data.get_random_name(6)
+
+        try:        
+            # Create tables
+            for i in range(5):
+                table_name = table_prefix + str(i)
+                print('1. Create a table with name - ' + table_name)
+                table_service.create_table(table_name)
+            
+            # List all the tables 
+            print('2. List tables')
+            tables = table_service.list_tables()
+            for table in tables:
+                print('\Table Name: ' + table.name)
+
+        finally:
+            # Delete the tables
+            print("3. Delete Tables")
+            for i in range(5):
+                table_name = table_prefix + str(i)
+                if(table_service.exists(table_name)):
+                    table_service.delete_table(table_name)
+            
+        print("List tables sample completed")
+    
+    # Manage properties of the Table service, including logging and metrics settings, and the default service version.
+    def set_service_properties(self, table_service):
+        print('1. Get Table service properties')
+        props = table_service.get_table_service_properties()
+
+        retention = RetentionPolicy(enabled=True, days=5)
+        logging = Logging(delete=True, read=False, write=True, retention_policy=retention)
+        hour_metrics = Metrics(enabled=True, include_apis=True, retention_policy=retention)
+        minute_metrics = Metrics(enabled=False)
+
+        try:
+            print('2. Ovewrite Table service properties')
+            table_service.set_table_service_properties(logging=logging, hour_metrics=hour_metrics, minute_metrics=minute_metrics)
+
+        finally:
+            print('3. Revert Table service properties back to the original ones')
+            table_service.set_table_service_properties(logging=props.logging, hour_metrics=props.hour_metrics, minute_metrics=props.minute_metrics)
+
+        print('4. Set Table service properties completed')
+    
+    # Manage CORS rules on the table service
+    def set_cors_rules(self, table_service):
+        cors_rule = CorsRule(
+            allowed_origins=['*'], 
+            allowed_methods=['POST', 'GET'],
+            allowed_headers=['*'],
+            exposed_headers=['*'],
+            max_age_in_seconds=3600)
+        
+        print('1. Get Cors Rules')
+        original_cors_rules = table_service.get_table_service_properties().cors
+
+        try:        
+            print('2. Overwrite Cors Rules')
+            table_service.set_table_service_properties(cors=[cors_rule])
+
+        finally:
+            #reverting cors rules back to the original ones
+            print('3. Revert Cors Rules back the original ones')
+            table_service.set_table_service_properties(cors=original_cors_rules)
+        
+        print("CORS sample completed")
+
+    # Manage table access policy
+    def table_acl_operations(self, table_service):
+        table_name = 'acltable' + self.random_data.get_random_name(6)
+
+        try:        
+            print('1. Create a table with name - ' + table_name)
+            table_service.create_table(table_name)
+                
+            print('2. Set access policy for table')
+            access_policy = AccessPolicy(permission=TablePermissions.QUERY,
+                                        expiry=datetime.datetime.utcnow() + datetime.timedelta(hours=1))
+            identifiers = {'id': access_policy}
+            table_service.set_table_acl(table_name, identifiers)
+
+            print('3. Wait 30 seconds for acl to propagate')
+            time.sleep(30)
+
+            print('4. Get access policy from table')
+            acl = table_service.get_table_acl(table_name)
+
+            print('5. Clear access policy in table')
+            table_service.set_table_acl(table_name)
+
+        finally:
+            print('5. Delete table')
+            if(table_service.exists(table_name)):
+                table_service.delete_table(table_name)
+            
+        print("Table ACL operations sample completed")
+    
+    # Manage shared access signature on a table
+    def table_operations_with_sas(self, account):
+        table_name = 'sastable' + self.random_data.get_random_name(6)
+        
+        try:
+            # Create a Table Service object
+            table_service = account.create_table_service()
+            
+            print('1. Create table with name - ' + table_name)
+            table_service.create_table(table_name)
+            
+            # Create a Shared Access Signature for the table
+            print('2. Get sas for table')
+            
+            table_sas = table_service.generate_table_shared_access_signature(
+                table_name, 
+                TablePermissions.QUERY + TablePermissions.ADD + TablePermissions.UPDATE + TablePermissions.DELETE, 
+                datetime.datetime.utcnow() + datetime.timedelta(hours=1))
+
+            shared_account = TableStorageAccount(account_name=account.account_name, sas_token=table_sas, endpoint_suffix=account.endpoint_suffix)
+            shared_table_service = shared_account.create_table_service()
+
+            # Create a sample entity to insert into the table
+            customer = {'PartitionKey': 'Harp', 'RowKey': '1', 'email' : 'harp@contoso.com', 'phone' : '555-555-5555'}
+
+            # Insert the entity into the table
+            print('3. Insert new entity into table with sas - ' + table_name)
+            shared_table_service.insert_entity(table_name, customer)
+            
+            # Demonstrate how to query the entity
+            print('4. Read the inserted entity with sas.')
+            entity = shared_table_service.get_entity(table_name, 'Harp', '1')
+            
+            print(entity['email'])
+            print(entity['phone'])
+
+            # Demonstrate how to update the entity by changing the phone number
+            print('5. Update an existing entity by changing the phone number with sas')
+            customer = {'PartitionKey': 'Harp', 'RowKey': '1', 'email' : 'harp@contoso.com', 'phone' : '425-123-1234'}
+            shared_table_service.update_entity(table_name, customer)
+
+            # Demonstrate how to delete an entity
+            print('6. Delete the entity with sas')
+            shared_table_service.delete_entity(table_name, 'Harp', '1')
+
+        finally:
+            print('7. Delete table')
+            if(table_service.exists(table_name)):
+                table_service.delete_table(table_name)
+            
+        print("Table operations with sas completed")

Azure/AddUp/table_basic_samples.py

@@ -0,0 +1,96 @@
+#-------------------------------------------------------------------------
+# Microsoft Developer & Platform Evangelism
+#
+# Copyright (c) Microsoft Corporation. All rights reserved.
+#
+# THIS CODE AND INFORMATION ARE PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND, 
+# EITHER EXPRESSED OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE IMPLIED WARRANTIES 
+# OF MERCHANTABILITY AND/OR FITNESS FOR A PARTICULAR PURPOSE.
+#----------------------------------------------------------------------------------
+# The example companies, organizations, products, domain names,
+# e-mail addresses, logos, people, places, and events depicted
+# herein are fictitious. No association with any real company,
+# organization, product, domain name, email address, logo, person,
+# places, or events is intended or should be inferred.
+#--------------------------------------------------------------------------
+import config
+from random_data import RandomData
+from azure.storage import CloudStorageAccount
+from azure.storage.table import TableService, Entity
+
+#
+# Azure Table Service Sample - Demonstrate how to perform common tasks using the Microsoft Azure Table Service
+# including creating a table, CRUD operations and different querying techniques.
+#
+# Documentation References:
+#  - What is a Storage Account - http://azure.microsoft.com/en-us/documentation/articles/storage-whatis-account/
+#  - Getting Started with Tables - https://azure.microsoft.com/en-us/documentation/articles/storage-python-how-to-use-table-storage/
+#  - Table Service Concepts - http://msdn.microsoft.com/en-us/library/dd179463.aspx
+#  - Table Service REST API - http://msdn.microsoft.com/en-us/library/dd179423.aspx
+#  - Table Service Python API - http://azure.github.io/azure-storage-ruby/
+#  - Storage Emulator - http://azure.microsoft.com/en-us/documentation/articles/storage-use-emulator/
+#
+class TableBasicSamples():
+
+    def __init__(self):
+        self.random_data = RandomData()
+
+    # Runs all samples for Azure Storage Table service.
+    def run_all_samples(self, account):
+        print('Azure Storage Basic Table samples - Starting.')
+        table_name = 'tablebasics' + self.random_data.get_random_name(6)
+        table_service = None
+        try:
+            table_service = account.create_table_service()
+
+            # Create a new table
+            print('Create a table with name - ' + table_name)
+
+            try:
+                table_service.create_table(table_name)
+            except Exception as err:
+                print('Error creating table, ' + table_name + 'check if it already exists')
+ 
+            # Create a sample entity to insert into the table
+            customer = {'PartitionKey': 'Harp', 'RowKey': '1', 'email' : 'harp@contoso.com', 'phone' : '555-555-5555'}
+
+            # Insert the entity into the table
+            print('Inserting a new entity into table - ' + table_name)
+            table_service.insert_entity(table_name, customer)
+            print('Successfully inserted the new entity')
+
+            # Demonstrate how to query the entity
+            print('Read the inserted entity.')
+            entity = table_service.get_entity(table_name, 'Harp', '1')
+            print(entity['email'])
+            print(entity['phone'])
+
+            # Demonstrate how to update the entity by changing the phone number
+            print('Update an existing entity by changing the phone number')
+            customer = {'PartitionKey': 'Harp', 'RowKey': '1', 'email' : 'harp@contoso.com', 'phone' : '425-123-1234'}
+            table_service.update_entity(table_name, customer)
+
+            # Demonstrate how to query the updated entity, filter the results with a filter query and select only the value in the phone column
+            print('Read the updated entity with a filter query')
+            entities = table_service.query_entities(table_name, filter="PartitionKey eq 'Harp'", select='phone')
+            for entity in entities:
+                print(entity['phone'])
+
+            # Demonstrate how to delete an entity
+            print('Delete the entity')
+            table_service.delete_entity(table_name, 'Harp', '1')
+            print('Successfully deleted the entity')
+
+        except Exception as e:
+            if (config.IS_EMULATED):
+                print('Error occurred in the sample. If you are using the emulator, please make sure the emulator is running.', e)
+            else: 
+                print('Error occurred in the sample. Please make sure the account name and key are correct.', e)
+        finally:
+            # Demonstrate deleting the table, if you don't want to have the table deleted comment the below block of code
+            print('Deleting the table.')
+            if(table_service.exists(table_name)):
+                table_service.delete_table(table_name)
+            print('Successfully deleted the table')
+
+        print('\nAzure Storage Basic Table samples - Completed.\n')

Azure/AzureStorage/.circleci/config.yml

@@ -0,0 +1,50 @@
+# Use the latest 2.1 version of CircleCI pipeline process engine.
+# See: https://circleci.com/docs/2.0/configuration-reference
+version: 2.1
+
+# Create the orb for the code coverage upload
+orbs:
+  codecov: codecov/codecov@3.2.2
+
+# Define a job to be invoked later in a workflow.
+# See: https://circleci.com/docs/2.0/configuration-reference/#jobs
+jobs:
+  azure-storage:
+    # Specify the execution environment. You can specify an image from Dockerhub or use one of our Convenience Images from CircleCI's Developer Hub.
+    # See: https://circleci.com/docs/2.0/configuration-reference/#docker-machine-macos-windows-executor
+    docker:
+      - image: ubuntu:20.04
+    # Add steps to the job
+    # See: https://circleci.com/docs/2.0/configuration-reference/#steps
+    steps:
+      - checkout
+      - run:
+          name: Setup Environment and Run Tests
+          command: |
+            apt update
+            apt install -y wget coreutils curl gnupg
+            wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O $HOME/miniconda.sh;
+            bash $HOME/miniconda.sh -b -p $HOME/miniconda
+            export PATH="$HOME/miniconda/bin:$PATH"
+            conda config --set always_yes yes --set changeps1 no
+            conda update -y conda
+            conda config --add channels conda-forge
+            conda create -n azure_storage python=3.8.5
+            source activate azure_storage
+            conda install -c olcbioinformatics azure_storage
+            mkdir /invalid
+            chmod -R 000 /invalid
+            python -m pytest tests/ --cov=azure_storage --cov-config=.coveragec --cov-report=xml:test_reports/azure_storage.xml
+      - store_artifacts:
+          path: test_reports/
+          destination: circleci-docs
+      - codecov/upload:
+          file: /root/project/test_reports/azure_storage.xml
+          xtra_args: -R /root/project/
+workflows:
+    build_and_test:
+        jobs:
+          - azure-storage:
+              filters:
+                branches:
+                  ignore: gh-pages

Azure/AzureStorage/.coveragec

@@ -0,0 +1,6 @@
+# Regexes for lines to exclude from consideration
+[report]
+exclude_lines =
+        
+    # Don't complain if non-runnable code isn't run:
+    if __name__ == .__main__.:

Azure/AzureStorage/.gitignore

@@ -0,0 +1,27 @@
+# Compiled Python Files #
+#########################
+*.pyc
+
+# Edited text files #
+#####################
+*~
+
+# Log files #
+#############
+*.log
+
+# Package files #
+#################
+build/
+dist/
+*.egg-info/
+
+# pycache files #
+#################
+__pycache__/
+
+# coverage files #
+##################
+coverage_reports/
+.coverage
+codecov

Azure/AzureStorage/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2022 Government of Canada
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

Azure/AzureStorage/README.md

@@ -0,0 +1,64 @@
+## AzureStorage
+
+[![CircleCI](https://circleci.com/gh/OLC-LOC-Bioinformatics/AzureStorage/tree/main.svg?style=shield)](https://circleci.com/gh/OLC-LOC-Bioinformatics/AzureStorage/tree/main)
+[![codecov](https://codecov.io/gh/OLC-LOC-Bioinformatics/AzureStorage/branch/main/graph/badge.svg?token=B65SOEV6QE)](https://codecov.io/gh/OLC-LOC-Bioinformatics/AzureStorage)
+[![Anaconda-Server Badge](https://img.shields.io/badge/install%20with-conda-brightgreen)](https://anaconda.org/olcbioinformatics/azure_storage)
+![GitHub release (latest by date)](https://img.shields.io/github/v/release/OLC-LOC-Bioinformatics/AzureStorage?label=version)
+[![GitHub issues](https://img.shields.io/github/issues/OLC-LOC-Bioinformatics/AzureStorage)](https://github.com/OLC-LOC-Bioinformatics/AzureStorage/issues)
+[![Documentation Status](https://readthedocs.org/projects/pip/badge/?version=stable)](https://OLC-LOC-Bioinformatics.github.io/AzureStorage/?badge=stable)
+[![license](https://img.shields.io/badge/license-MIT-brightgreen)](https://github.com/OLC-LOC-Bioinformatics/AzureStorage/blob/main/LICENSE)
+
+This suite of tools (written in Python) allows you to manipulate containers/files/folders in your Azure storage account.
+
+Full documentation available at the [AzureStorage GitHub pages site](https://OLC-LOC-Bioinformatics.github.io/AzureStorage/)
+
+## Quickstart
+
+Conda is required to install AzureStorage. See the [documentation](http://bioconda.github.io/) or [AzureStorage installation](https://olc-loc-bioinformatics.github.io/AzureStorage/install/) for instructions of getting conda installed on your system
+
+`conda install -c olc-bioinformatics azure-storage=0.0.2`
+
+### Credentials
+
+You must enter your Azure storage connection string and account name into the system keyring before running any of the other scripts
+
+`AzureCredentials store`
+
+### Tests
+
+If you encounter issues with the AzureStorage package, tests are available to ensure that the installation was successful and your credentials are valid.
+
+You will need to clone this repository and run the tests with pytest:
+
+
+`git clone https://github.com/OLC-LOC-Bioinformatics/AzureStorage.git`
+
+`cd AzureStorage`
+
+`python -m pytest tests/ --cov=azure_storage --cov-config=.coveragec`
+
+Ensure that all tests complete successfully before proceeding
+
+## Scripts
+
+1. [`AzureCredentials`](https://olc-loc-bioinformatics.github.io/AzureStorage/credentials/): enter, modify, or delete your Azure connection string and account name in your system keyring
+2. [`AzureUpload`](https://olc-loc-bioinformatics.github.io/AzureStorage/upload/): upload a file or folder to a container in your Azure storage account
+3. [`AzureSAS`](https://olc-loc-bioinformatics.github.io/AzureStorage/sas_url/): create SAS (shared access signature) URLs for a file, a folder, or an entire container in your Azure storage account
+4. [`AzureMove`](https://olc-loc-bioinformatics.github.io/AzureStorage/move/): move a file, folder, or an entire container within your Azure storage account
+5. [`AzureDownload`](https://olc-loc-bioinformatics.github.io/AzureStorage/download/): download a file, folder, or an entire container from your Azure storage account
+6. [`AzureTier`](https://olc-loc-bioinformatics.github.io/AzureStorage/set_tier/): set the storage tier of a file, folder, or an entire container from your Azure storage account
+7. [`AzureDelete`](https://olc-loc-bioinformatics.github.io/AzureStorage/delete/): delete a file, folder, or an entire container from your Azure storage account
+8. [`AzureAutomate`](https://olc-loc-bioinformatics.github.io/AzureStorage/automate/): run upload, sas, move, download, set_tier, and/or delete in batch
+9. [`AzureList`](https://olc-loc-bioinformatics.github.io/AzureStorage/list/): List and optionally filter containers and/or files in your Azure storage account
+
+## License
+
+MIT License
+
+Copyright (c) 2022 Government of Canada
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Azure/AzureStorage/azure_storage/azure_automate.py

@@ -0,0 +1,1024 @@
+#!/usr/bin/env python
+from azure_storage.methods import arg_dict_cleanup, create_batch_dict, create_parent_parser, parse_batch_file, \
+    setup_arguments
+from azure_storage.azure_upload import AzureUpload
+from azure_storage.azure_sas import AzureContainerSAS, AzureSAS
+from azure_storage.azure_move import AzureContainerMove, AzureMove
+from azure_storage.azure_download import AzureContainerDownload, AzureDownload
+from azure_storage.azure_tier import AzureContainerTier, AzureTier
+from azure_storage.azure_delete import AzureContainerDelete, AzureDelete
+from argparse import ArgumentParser, RawTextHelpFormatter
+import coloredlogs
+import logging
+import sys
+import os
+
+
+def file_upload(args, batch_dict=None):
+    """
+    Read in the batch file, clean up the arguments to work with code base, run the AzureUpload class for each file
+    :param args: type ArgumentParser arguments
+    :param batch_dict: type Pandas dataframe.transpose().to_dict()
+    """
+    # If batch_dict has not been supplied by the batch function, extract the batch information from the file
+    if not batch_dict:
+        batch_dict = create_batch_dict(batch_file=args.batch_file,
+                                       headers=['container', 'file', 'reset_path', 'storage_tier'])
+    # The format of the dictionary is: {primary key: {header: value, ...}, primary key: {header:value, ...}, ....}
+    # e.g. {1 : {container_name: $CONTAINER_NAME, file: $FILE_NAME...}, 2: {container_name: ...}, ...}
+    for key, arg_dict in batch_dict.items():
+        # Clean up the arguments, as some are optional, or not interpreted correctly
+        arg_dict = arg_dict_cleanup(arg_dict=arg_dict)
+        # Run the file upload
+        try:
+            # Create the upload_file object
+            upload_file = AzureUpload(
+                object_name=arg_dict['file'],
+                account_name=args.account_name,
+                container_name=arg_dict['container'],
+                passphrase=args.passphrase,
+                path=arg_dict['reset_path'],
+                storage_tier=arg_dict['storage_tier'],
+                category='file'
+            )
+            # Run the file upload
+            upload_file.main()
+        # Don't crash on SystemExits
+        except SystemExit:
+            pass
+
+
+def folder_upload(args, batch_dict=None):
+    """
+    Read in the batch file, clean up the arguments to work with code base, run the AzureUpload class for each folder
+    :param args: type ArgumentParser arguments
+    :param batch_dict: type Pandas dataframe.transpose().to_dict()
+    """
+    # If batch_dict has not been supplied by the batch function, extract the batch information from the file
+    if not batch_dict:
+        batch_dict = create_batch_dict(batch_file=args.batch_file,
+                                       headers=['container', 'folder', 'reset_path', 'storage_tier'])
+    # The format of the dictionary is: {primary key: {header: value, ...}, primary key: {header:value, ...}, ....}
+    # e.g. {1 : {container_name: $CONTAINER_NAME, file: $FOLDER_NAME...}, 2: {container_name: ...}, ...}
+    for key, arg_dict in batch_dict.items():
+        # Clean up the arguments, as some are optional, or not interpreted correctly
+        arg_dict = arg_dict_cleanup(arg_dict=arg_dict)
+        try:
+            # Create the upload_folder object
+            upload_folder = AzureUpload(
+                object_name=arg_dict['folder'],
+                account_name=args.account_name,
+                container_name=arg_dict['container'],
+                passphrase=args.passphrase,
+                path=arg_dict['reset_path'],
+                storage_tier=arg_dict['storage_tier'],
+                category='folder'
+            )
+            # Run the folder upload
+            upload_folder.main()
+        # Don't crash on SystemExits
+        except SystemExit:
+            pass
+
+
+def container_sas(args, batch_dict=None):
+    """
+    Read in the batch file, clean up the arguments to work with code base, run the AzureSAS class for each container
+    :param args: type ArgumentParser arguments
+    :param batch_dict: type Pandas dataframe.transpose().to_dict()
+    """
+    # If batch_dict has not been supplied by the batch function, extract the batch information from the file
+    if not batch_dict:
+        batch_dict = create_batch_dict(batch_file=args.batch_file,
+                                       headers=['container', 'expiry', 'output_file'])
+    # The format of the dictionary is: {primary key: {header: value, ...}, primary key: {header:value, ...}, ....}
+    # e.g. {1 : {container_name: $CONTAINER_NAME, expiry: $EXPIRY...}, 2: {container_name: ...}, ...}
+    for key, arg_dict in batch_dict.items():
+        # Clean up the arguments, as some are optional, or not interpreted correctly
+        arg_dict = arg_dict_cleanup(arg_dict=arg_dict)
+        try:
+            # Create the sas_container object
+            sas_container = AzureContainerSAS(
+                container_name=arg_dict['container'],
+                output_file=arg_dict['output_file'],
+                account_name=args.account_name,
+                passphrase=args.passphrase,
+                expiry=arg_dict['expiry'],
+                verbosity=args.verbosity
+            )
+            # Run the container SAS URL creation
+            sas_container.main()
+        # Don't crash on SystemExits
+        except SystemExit:
+            pass
+
+
+def file_sas(args, batch_dict=None):
+    """
+    Read in the batch file, clean up the arguments to work with code base, run the AzureSAS class for each file
+    :param args: type ArgumentParser arguments
+    :param batch_dict: type Pandas dataframe.transpose().to_dict()
+    """
+    # If batch_dict has not been supplied by the batch function, extract the batch information from the file
+    if not batch_dict:
+        batch_dict = create_batch_dict(batch_file=args.batch_file,
+                                       headers=['container', 'file', 'expiry', 'output_file'])
+    # The format of the dictionary is: {primary key: {header: value, ...}, primary key: {header:value, ...}, ....}
+    # e.g. {1 : {container_name: $CONTAINER_NAME, file: $FILE...}, 2: {container_name: ...}, ...}
+    for key, arg_dict in batch_dict.items():
+        # Clean up the arguments, as some are optional, or not interpreted correctly
+        arg_dict = arg_dict_cleanup(arg_dict=arg_dict)
+        try:
+            # Create the sas_file object
+            sas_file = AzureSAS(
+                object_name=arg_dict['file'],
+                container_name=arg_dict['container'],
+                output_file=arg_dict['output_file'],
+                account_name=args.account_name,
+                passphrase=args.passphrase,
+                expiry=arg_dict['expiry'],
+                verbosity=args.verbosity,
+                category='file',
+            )
+            # Run the container SAS URL creation
+            sas_file.main()
+        # Don't crash on SystemExits
+        except SystemExit:
+            pass
+
+
+def folder_sas(args, batch_dict=None):
+    """
+    Read in the batch file, clean up the arguments to work with code base, run the AzureSAS class for each file
+    :param args: type ArgumentParser arguments
+    :param batch_dict: type Pandas dataframe.transpose().to_dict()
+        """
+    # If batch_dict has not been supplied by the batch function, extract the batch information from the file
+    if not batch_dict:
+        batch_dict = create_batch_dict(batch_file=args.batch_file,
+                                       headers=['container', 'folder', 'expiry', 'output_file'])
+    # The format of the dictionary is: {primary key: {header: value, ...}, primary key: {header:value, ...}, ....}
+    # e.g. {1 : {container_name: $CONTAINER_NAME, folder: $FOLDER...}, 2: {container_name: ...}, ...}
+    for key, arg_dict in batch_dict.items():
+        # Clean up the arguments, as some are optional, or not interpreted correctly
+        arg_dict = arg_dict_cleanup(arg_dict=arg_dict)
+        try:
+            # Create the sas_file object
+            sas_folder = AzureSAS(
+                object_name=arg_dict['folder'],
+                container_name=arg_dict['container'],
+                output_file=arg_dict['output_file'],
+                account_name=args.account_name,
+                passphrase=args.passphrase,
+                expiry=arg_dict['expiry'],
+                verbosity=args.verbosity,
+                category='folder',
+            )
+            # Run the container SAS URL creation
+            sas_folder.main()
+        # Don't crash on SystemExits
+        except SystemExit:
+            pass
+
+
+def container_move(args, batch_dict=None):
+    """
+    Read in the batch file, clean up the arguments to work with code base, run the AzureContainerMove class
+    for each container
+    :param args: type ArgumentParser arguments
+    :param batch_dict: type Pandas dataframe.transpose().to_dict()
+    """
+    # If batch_dict has not been supplied by the batch function, extract the batch information from the file
+    if not batch_dict:
+        batch_dict = create_batch_dict(batch_file=args.batch_file,
+                                       headers=['container', 'target', 'reset_path', 'storage_tier'])
+    # The format of the dictionary is: {primary key: {header: value, ...}, primary key: {header:value, ...}, ....}
+    # e.g. {1 : {container_name: $CONTAINER_NAME, target: $TARGET...}, 2: {container_name: ...}, ...}
+    for key, arg_dict in batch_dict.items():
+        # Clean up the arguments, as some are optional, or not interpreted correctly
+        arg_dict = arg_dict_cleanup(arg_dict=arg_dict)
+        try:
+            # Create the move_container object
+            move_container = AzureContainerMove(
+                container_name=arg_dict['container'],
+                account_name=args.account_name,
+                passphrase=args.passphrase,
+                target_container=arg_dict['target'],
+                path=arg_dict['reset_path'],
+                storage_tier=arg_dict['storage_tier']
+            )
+            # Run the container move
+            move_container.main()
+        # Don't crash on SystemExits
+        except SystemExit:
+            pass
+
+
+def file_move(args, batch_dict=None):
+    """
+    Read in the batch file, clean up the arguments to work with code base, run the AzureMove class for each file
+    :param args: type ArgumentParser arguments
+    :param batch_dict: type Pandas dataframe.transpose().to_dict()
+    """
+    # If batch_dict has not been supplied by the batch function, extract the batch information from the file
+    if not batch_dict:
+        batch_dict = create_batch_dict(batch_file=args.batch_file,
+                                       headers=['container', 'target', 'file', 'reset_path', 'storage_tier'])
+    # The format of the dictionary is: {primary key: {header: value, ...}, primary key: {header:value, ...}, ....}
+    # e.g. {1 : {container_name: $CONTAINER_NAME, target: $TARGET...}, 2: {container_name: ...}, ...}
+    for key, arg_dict in batch_dict.items():
+        # Clean up the arguments, as some are optional, or not interpreted correctly
+        arg_dict = arg_dict_cleanup(arg_dict=arg_dict)
+        try:
+            # Create the move_file object
+            move_file = AzureMove(
+                object_name=arg_dict['file'],
+                container_name=arg_dict['container'],
+                account_name=args.account_name,
+                passphrase=args.passphrase,
+                target_container=arg_dict['target'],
+                path=arg_dict['reset_path'],
+                storage_tier=arg_dict['storage_tier'],
+                category='file'
+            )
+            # Run the file move
+            move_file.main()
+        # Don't crash on SystemExits
+        except SystemExit:
+            pass
+
+
+def folder_move(args, batch_dict=None):
+    """
+    Read in the batch file, clean up the arguments to work with code base, run the AzureMove class for each folder
+    :param args: type ArgumentParser arguments
+    :param batch_dict: type Pandas dataframe.transpose().to_dict()
+        """
+    # If batch_dict has not been supplied by the batch function, extract the batch information from the file
+    if not batch_dict:
+        batch_dict = create_batch_dict(batch_file=args.batch_file,
+                                       headers=['container', 'target', 'folder', 'reset_path', 'storage_tier'])
+    # The format of the dictionary is: {primary key: {header: value, ...}, primary key: {header:value, ...}, ....}
+    # e.g. {1 : {container_name: $CONTAINER_NAME, target: $TARGET...}, 2: {container_name: ...}, ...}
+    for key, arg_dict in batch_dict.items():
+        # Clean up the arguments, as some are optional, or not interpreted correctly
+        arg_dict = arg_dict_cleanup(arg_dict=arg_dict)
+        try:
+            # Create the move_folder object
+            move_folder = AzureMove(
+                object_name=arg_dict['folder'],
+                container_name=arg_dict['container'],
+                account_name=args.account_name,
+                passphrase=args.passphrase,
+                target_container=arg_dict['target'],
+                path=arg_dict['reset_path'],
+                storage_tier=arg_dict['storage_tier'],
+                category='folder'
+            )
+            # Run the folder move
+            move_folder.main()
+        # Don't crash on SystemExits
+        except SystemExit:
+            pass
+
+
+def container_download(args, batch_dict=None):
+    """
+    Read in the batch file, clean up the arguments, run the AzureContainerDownload class for each container
+    :param args: type ArgumentParser arguments
+    :param batch_dict: type Pandas dataframe.transpose().to_dict()
+    """
+    # If batch_dict has not been supplied by the batch function, extract the batch information from the file
+    if not batch_dict:
+        batch_dict = create_batch_dict(batch_file=args.batch_file,
+                                       headers=['container', 'output_path'])
+    # The format of the dictionary is: {primary key: {header: value, ...}, primary key: {header:value, ...}, ....}
+    # e.g. {1 : {container_name: $CONTAINER_NAME, output_path: $OUTPUT_PATH...}, 2: {container_name: ...}, ...}
+    for key, arg_dict in batch_dict.items():
+        # Clean up the arguments, as some are optional, or not interpreted correctly
+        arg_dict = arg_dict_cleanup(arg_dict=arg_dict)
+        try:
+            # Create the download_container object
+            download_container = AzureContainerDownload(
+                container_name=arg_dict['container'],
+                account_name=args.account_name,
+                passphrase=args.passphrase,
+                output_path=arg_dict['output_path']
+            )
+            # Run the container download
+            download_container.main()
+        # Don't crash on SystemExits
+        except SystemExit:
+            pass
+
+
+def file_download(args, batch_dict=None):
+    """
+    Read in the batch file, clean up the arguments, run the AzureDownload class for each file
+    :param args: type ArgumentParser arguments
+    :param batch_dict: type Pandas dataframe.transpose().to_dict()
+    """
+    # If batch_dict has not been supplied by the batch function, extract the batch information from the file
+    if not batch_dict:
+        batch_dict = create_batch_dict(batch_file=args.batch_file,
+                                       headers=['container', 'file', 'output_path'])
+    # The format of the dictionary is: {primary key: {header: value, ...}, primary key: {header:value, ...}, ....}
+    # e.g. {1 : {container_name: $CONTAINER_NAME, file: $FILE...}, 2: {container_name: ...}, ...}
+    for key, arg_dict in batch_dict.items():
+        # Clean up the arguments, as some are optional, or not interpreted correctly
+        arg_dict = arg_dict_cleanup(arg_dict=arg_dict)
+        try:
+            # Create the download_file object
+            download_file = AzureDownload(
+                container_name=arg_dict['container'],
+                object_name=arg_dict['file'],
+                account_name=args.account_name,
+                passphrase=args.passphrase,
+                output_path=arg_dict['output_path'],
+                category='file'
+            )
+            # Run the file download
+            download_file.main()
+        # Don't crash on SystemExits
+        except SystemExit:
+            pass
+
+
+def folder_download(args, batch_dict=None):
+    """
+    Read in the batch file, clean up the arguments, run the AzureDownload class for each folder
+    :param args: type ArgumentParser arguments
+    :param batch_dict: type Pandas dataframe.transpose().to_dict()
+    """
+    # If batch_dict has not been supplied by the batch function, extract the batch information from the file
+    if not batch_dict:
+        batch_dict = create_batch_dict(batch_file=args.batch_file,
+                                       headers=['container', 'folder', 'output_path'])
+    # The format of the dictionary is: {primary key: {header: value, ...}, primary key: {header:value, ...}, ....}
+    # e.g. {1 : {container_name: $CONTAINER_NAME, folder: $FOLDER...}, 2: {container_name: ...}, ...}
+    for key, arg_dict in batch_dict.items():
+        # Clean up the arguments, as some are optional, or not interpreted correctly
+        arg_dict = arg_dict_cleanup(arg_dict=arg_dict)
+        try:
+            # Create the download_folder object
+            download_folder = AzureDownload(
+                container_name=arg_dict['container'],
+                object_name=arg_dict['folder'],
+                account_name=args.account_name,
+                passphrase=args.passphrase,
+                output_path=arg_dict['output_path'],
+                category='folder'
+            )
+            # Run the folder download
+            download_folder.main()
+        # Don't crash on SystemExits
+        except SystemExit:
+            pass
+
+
+def container_tier(args, batch_dict=None):
+    """
+    Read in the batch file, clean up the arguments, run the AzureContainerTier class for each container
+    :param args: type ArgumentParser arguments
+    :param batch_dict: type Pandas dataframe.transpose().to_dict()
+    """
+    # If batch_dict has not been supplied by the batch function, extract the batch information from the file
+    if not batch_dict:
+        batch_dict = create_batch_dict(batch_file=args.batch_file,
+                                       headers=['container', 'storage_tier'])
+    # The format of the dictionary is: {primary key: {header: value, ...}, primary key: {header:value, ...}, ....}
+    # e.g. {1 : {container_name: $CONTAINER_NAME, storage_tier: $STORAGE_TIER ...}, 2: {container_name: ...}, ...}
+    for key, arg_dict in batch_dict.items():
+        # Clean up the arguments, as some are optional, or not interpreted correctly
+        arg_dict = arg_dict_cleanup(arg_dict=arg_dict)
+        try:
+            # Create the tier_container object
+            tier_container = AzureContainerTier(
+                container_name=arg_dict['container'],
+                account_name=args.account_name,
+                passphrase=args.passphrase,
+                storage_tier=arg_dict['storage_tier']
+            )
+            # Run the container tier
+            tier_container.main()
+        # Don't crash on SystemExits
+        except SystemExit:
+            pass
+
+
+def file_tier(args, batch_dict=None):
+    """
+    Read in the batch file, clean up the arguments, run the AzureTier class for each file
+    :param args: type ArgumentParser arguments
+    :param batch_dict: type Pandas dataframe.transpose().to_dict()
+    """
+    # If batch_dict has not been supplied by the batch function, extract the batch information from the file
+    if not batch_dict:
+        batch_dict = create_batch_dict(batch_file=args.batch_file,
+                                       headers=['container', 'file', 'storage_tier'])
+    # The format of the dictionary is: {primary key: {header: value, ...}, primary key: {header:value, ...}, ....}
+    # e.g. {1 : {container_name: $CONTAINER_NAME, file: $FILE ...}, 2: {container_name: ...}, ...}
+    for key, arg_dict in batch_dict.items():
+        # Clean up the arguments, as some are optional, or not interpreted correctly
+        arg_dict = arg_dict_cleanup(arg_dict=arg_dict)
+        try:
+            # Create the tier_file object
+            tier_file = AzureTier(
+                container_name=arg_dict['container'],
+                object_name=arg_dict['file'],
+                account_name=args.account_name,
+                passphrase=args.passphrase,
+                storage_tier=arg_dict['storage_tier'],
+                category='file'
+            )
+            # Run the file tier
+            tier_file.main()
+        # Don't crash on SystemExits
+        except SystemExit:
+            pass
+
+
+def folder_tier(args, batch_dict=None):
+    """
+    Read in the batch file, clean up the arguments, run the AzureTier class for each folder
+    :param args: type ArgumentParser arguments
+    :param batch_dict: type Pandas dataframe.transpose().to_dict()
+    """
+    # If batch_dict has not been supplied by the batch function, extract the batch information from the file
+    if not batch_dict:
+        batch_dict = create_batch_dict(batch_file=args.batch_file,
+                                       headers=['container', 'folder', 'storage_tier'])
+    # The format of the dictionary is: {primary key: {header: value, ...}, primary key: {header:value, ...}, ....}
+    # e.g. {1 : {container_name: $CONTAINER_NAME, folder: $FOLDER ...}, 2: {container_name: ...}, ...}
+    for key, arg_dict in batch_dict.items():
+        # Clean up the arguments, as some are optional, or not interpreted correctly
+        arg_dict = arg_dict_cleanup(arg_dict=arg_dict)
+        try:
+            # Create the tier_folder object
+            tier_folder = AzureTier(
+                container_name=arg_dict['container'],
+                object_name=arg_dict['folder'],
+                account_name=args.account_name,
+                passphrase=args.passphrase,
+                storage_tier=arg_dict['storage_tier'],
+                category='folder'
+            )
+            # Run the folder tier
+            tier_folder.main()
+        # Don't crash on SystemExits
+        except SystemExit:
+            pass
+
+
+def container_delete(args, batch_dict=None):
+    """
+    Read in the batch file, clean up the arguments, run the AzureContainerDelete class for each container
+    :param args: type ArgumentParser arguments
+    :param batch_dict: type Pandas dataframe.transpose().to_dict()
+    """
+    # If batch_dict has not been supplied by the batch function, extract the batch information from the file
+    if not batch_dict:
+        batch_dict = create_batch_dict(batch_file=args.batch_file,
+                                       headers=['container'])
+    # The format of the dictionary is: {primary key: {header: value, ...}, primary key: {header:value, ...}, ....}
+    # e.g. {1 : {container_name: $CONTAINER_NAME}, 2: {container_name: $CONTAINER_NAME}, ...}
+    for key, arg_dict in batch_dict.items():
+        # Clean up the arguments, as some are optional, or not interpreted correctly
+        arg_dict = arg_dict_cleanup(arg_dict=arg_dict)
+        try:
+            # Create the delete_container object
+            delete_container = AzureContainerDelete(
+                container_name=arg_dict['container'],
+                account_name=args.account_name,
+                passphrase=args.passphrase,
+            )
+            # Run the container delete
+            delete_container.main()
+        # Don't crash on SystemExits
+        except SystemExit:
+            pass
+
+
+def file_delete(args, batch_dict=None):
+    """
+    Read in the batch file, clean up the arguments, run the AzureDelete class for each file
+    :param args: type ArgumentParser arguments
+    :param batch_dict: type Pandas dataframe.transpose().to_dict()
+    """
+    # If batch_dict has not been supplied by the batch function, extract the batch information from the file
+    if not batch_dict:
+        batch_dict = create_batch_dict(batch_file=args.batch_file,
+                                       headers=['container', 'file', 'retention_time'])
+    # The format of the dictionary is: {primary key: {header: value, ...}, primary key: {header:value, ...}, ....}
+    # e.g. {1 : {container_name: $CONTAINER_NAME, file: $FILE ...}, 2: {container_name: ...}, ...}
+    for key, arg_dict in batch_dict.items():
+        # Clean up the arguments, as some are optional, or not interpreted correctly
+        arg_dict = arg_dict_cleanup(arg_dict=arg_dict)
+        try:
+            # Create the delete_file object
+            delete_file = AzureDelete(
+                container_name=arg_dict['container'],
+                object_name=arg_dict['file'],
+                account_name=args.account_name,
+                passphrase=args.passphrase,
+                retention_time=arg_dict['retention_time'],
+                category='file'
+            )
+            # Run the file delete
+            delete_file.main()
+        # Don't crash on SystemExits
+        except SystemExit:
+            pass
+
+
+def folder_delete(args, batch_dict=None):
+    """
+    Read in the batch file, clean up the arguments, run the AzureDelete class for each folder
+    :param args: type ArgumentParser arguments
+    :param batch_dict: type Pandas dataframe.transpose().to_dict()
+    """
+    # If batch_dict has not been supplied by the batch function, extract the batch information from the file
+    if not batch_dict:
+        batch_dict = create_batch_dict(batch_file=args.batch_file,
+                                       headers=['container', 'folder', 'retention_time'])
+    # The format of the dictionary is: {primary key: {header: value, ...}, primary key: {header:value, ...}, ....}
+    # e.g. {1 : {container_name: $CONTAINER_NAME, folder: $FOLDER ...}, 2: {container_name: ...}, ...}
+    for key, arg_dict in batch_dict.items():
+        # Clean up the arguments, as some are optional, or not interpreted correctly
+        arg_dict = arg_dict_cleanup(arg_dict=arg_dict)
+        try:
+            # Create the delete_folder object
+            delete_folder = AzureDelete(
+                container_name=arg_dict['container'],
+                object_name=arg_dict['folder'],
+                account_name=args.account_name,
+                passphrase=args.passphrase,
+                retention_time=arg_dict['retention_time'],
+                category='folder'
+            )
+            # Run the folder delete
+            delete_folder.main()
+        # Don't crash on SystemExits
+        except SystemExit:
+            pass
+
+
+def batch(args):
+    """
+    Read in the batch file, and run the appropriate function for each requested command and subcommand combination
+    :param args: type ArgumentParser arguments
+    """
+    # Ensure that the batch file exists
+    try:
+        assert os.path.isfile(args.batch_file)
+    except AssertionError:
+        logging.error(f'Could not locate the supplied batch file {args.batch_file}. Please ensure the you entered '
+                      f'the name and path correctly')
+        raise SystemExit
+    # Create a dictionary of all the functions with the corresponding command and subcommands as keys
+    function_dict = {
+        'upload': {
+            'file': file_upload,
+            'folder': folder_upload
+        },
+        'sas': {
+            'container': container_sas,
+            'file': file_sas,
+            'folder': folder_sas
+        },
+        'move': {
+            'container': container_move,
+            'file': file_move,
+            'folder': folder_move
+        },
+        'download': {
+            'container': container_download,
+            'file': file_download,
+            'folder': folder_download
+        },
+        'tier': {
+            'container': container_tier,
+            'file': file_tier,
+            'folder': folder_tier
+        },
+        'delete': {
+            'container': container_delete,
+            'file': file_delete,
+            'folder': folder_delete
+        }
+    }
+    # Read in the batch file
+    with open(args.batch_file, 'r') as batch_doc:
+        for line in batch_doc:
+            # Ignore commented lines
+            if not line.startswith('#'):
+                # Convert the line to a dictionary with appropriate header: value pairs. Extract the command, and
+                # subcommand
+                command, subcommand, batch_dict = parse_batch_file(line=line)
+                # Run the appropriate function for the supplied command, subcommand combination
+                function_dict[command][subcommand](args, batch_dict=batch_dict)
+
+
+def cli():
+    parser = ArgumentParser(
+        description='Automate the submission of multiple AzureStorage commands'
+    )
+    # Create the parental parser, and the subparser
+    subparsers, parent_parser = create_parent_parser(
+        parser=parser,
+        container=False
+    )
+    # Upload parser
+    upload = subparsers.add_parser(
+        parents=[],
+        name='upload',
+        description='Upload files/folders to Azure storage',
+        formatter_class=RawTextHelpFormatter,
+        help='Upload files/folders to Azure storage'
+    )
+    # Upload subparser
+    upload_subparsers = upload.add_subparsers(
+        title='Upload functionality',
+        dest='upload'
+    )
+    # File upload subparser
+    upload_file_subparser = upload_subparsers.add_parser(
+        parents=[parent_parser],
+        name='file',
+        description='Upload files to Azure storage',
+        formatter_class=RawTextHelpFormatter,
+        help='Upload files to Azure storage'
+    )
+    upload_file_subparser.add_argument(
+        '-b', '--batch_file',
+        required=True,
+        type=str,
+        help='Tab-separated file with the following fields:\n '
+             'container name, file name, destination path (optional), storage tier (optional)'
+    )
+    upload_file_subparser.set_defaults(func=file_upload)
+    # Folder upload subparser
+    upload_folder_subparser = upload_subparsers.add_parser(
+        parents=[parent_parser],
+        name='folder',
+        description='Upload folders to Azure storage',
+        formatter_class=RawTextHelpFormatter,
+        help='Upload folders to Azure storage'
+    )
+    upload_folder_subparser.add_argument(
+        '-b', '--batch_file',
+        required=True,
+        type=str,
+        help='Tab-separated file with the following fields (one entry per line):\n '
+             'container name, folder name, destination path (optional), storage tier (optional)'
+    )
+
+    upload_folder_subparser.set_defaults(func=folder_upload)
+    # SAS URLs subparser
+    sas_urls = subparsers.add_parser(
+        parents=[],
+        name='sas',
+        description='Create SAS URLs for containers/files/folders in Azure storage',
+        formatter_class=RawTextHelpFormatter,
+        help='Create SAS URLs for containers/files/folders in Azure storage')
+    sas_url_subparsers = sas_urls.add_subparsers(
+        title='SAS URL creation functionality',
+        dest='sas'
+    )
+    # Container SAS URL subparser
+    sas_url_container_subparser = sas_url_subparsers.add_parser(
+        parents=[parent_parser],
+        name='container',
+        description='Create SAS URLs for containers in Azure storage',
+        formatter_class=RawTextHelpFormatter,
+        help='Create SAS URLs for containers in Azure storage'
+    )
+    sas_url_container_subparser.add_argument(
+        '-b', '--batch_file',
+        required=True,
+        type=str,
+        help='Tab-separated file with the following fields: \n'
+             'container name, expiry (optional), output file (optional)'
+    )
+    sas_url_container_subparser.set_defaults(func=container_sas)
+    # File SAS URL subparser
+    sas_url_file_subparser = sas_url_subparsers.add_parser(
+        parents=[parent_parser],
+        name='file',
+        description='Create SAS URLs for files in Azure storage',
+        formatter_class=RawTextHelpFormatter,
+        help='Create SAS URLs for files in Azure storage'
+    )
+    sas_url_file_subparser.add_argument(
+        '-b', '--batch_file',
+        required=True,
+        type=str,
+        help='Tab-separated file with the following fields:\n '
+             'container name, file name and path, expiry (optional), output file (optional)'
+    )
+    sas_url_file_subparser.set_defaults(func=file_sas)
+    # Folder SAS URL subparser
+    sas_url_folder_subparser = sas_url_subparsers.add_parser(
+        parents=[parent_parser],
+        name='folder',
+        description='Create SAS URLs for folders in Azure storage',
+        formatter_class=RawTextHelpFormatter,
+        help='Create SAS URLs for folders in Azure storage'
+    )
+    sas_url_folder_subparser.add_argument(
+        '-b', '--batch_file',
+        required=True,
+        type=str,
+        help='Tab-separated file with the following fields:\n '
+             'container name, folder name and path, expiry (optional), output file (optional)'
+    )
+    sas_url_folder_subparser.set_defaults(func=folder_sas)
+    # Move subparser
+    move = subparsers.add_parser(
+        parents=[],
+        name='move',
+        description='Move containers/files/folders in Azure storage',
+        formatter_class=RawTextHelpFormatter,
+        help='Move containers/files/folders in Azure storage'
+    )
+    move_subparsers = move.add_subparsers(
+        title='Move functionality',
+        dest='move'
+    )
+    # Container move subparser
+    move_container_subparser = move_subparsers.add_parser(
+        parents=[parent_parser],
+        name='container',
+        description='Move containers in Azure storage',
+        formatter_class=RawTextHelpFormatter,
+        help='Move containers in Azure storage'
+    )
+    move_container_subparser.add_argument(
+        '-b', '--batch_file',
+        required=True,
+        type=str,
+        help='Tab-separated file with the following fields:\n '
+             'container name, target container, destination path (optional), storage tier (optional)'
+    )
+    move_container_subparser.set_defaults(func=container_move)
+    # File move subparser
+    move_file_subparser = move_subparsers.add_parser(
+        parents=[parent_parser],
+        name='file',
+        description='Move files in Azure storage',
+        formatter_class=RawTextHelpFormatter,
+        help='Move files in Azure storage'
+    )
+    move_file_subparser.add_argument(
+        '-b', '--batch_file',
+        required=True,
+        type=str,
+        help='Tab-separated file with the following fields:\n '
+             'container name, target container, file name, destination path (optional), storage tier (optional)'
+    )
+    move_file_subparser.set_defaults(func=file_move)
+    # Folder move subparser
+    move_folder_subparser = move_subparsers.add_parser(
+        parents=[parent_parser],
+        name='folder',
+        description='Move folders in Azure storage',
+        formatter_class=RawTextHelpFormatter,
+        help='Move folders in Azure storage'
+    )
+    move_folder_subparser.add_argument(
+        '-b', '--batch_file',
+        required=True,
+        type=str,
+        help='Tab-separated file with the following fields:\n '
+             'container name, target container, folder name, destination path (optional), storage tier (optional)'
+    )
+    move_folder_subparser.set_defaults(func=folder_move)
+    # Download subparser
+    download = subparsers.add_parser(
+        parents=[],
+        name='download',
+        description='Download containers/files/folders in Azure storage',
+        formatter_class=RawTextHelpFormatter,
+        help='Download containers/files/folders in Azure storage'
+    )
+    download_subparsers = download.add_subparsers(
+        title='Download functionality',
+        dest='download'
+    )
+    # Container download subparser
+    download_container_subparser = download_subparsers.add_parser(
+        parents=[parent_parser],
+        name='container',
+        description='Download containers from Azure storage',
+        formatter_class=RawTextHelpFormatter,
+        help='Download containers from Azure storage'
+    )
+    download_container_subparser.add_argument(
+        '-b', '--batch_file',
+        required=True,
+        type=str,
+        help='Tab-separated file with the following fields:\n '
+             'container name, output path (optional)'
+    )
+    download_container_subparser.set_defaults(func=container_download)
+    # File download subparser
+    download_file_subparser = download_subparsers.add_parser(
+        parents=[parent_parser],
+        name='file',
+        description='Download files from Azure storage',
+        formatter_class=RawTextHelpFormatter,
+        help='Download files from Azure storage'
+    )
+    download_file_subparser.add_argument(
+        '-b', '--batch_file',
+        required=True,
+        type=str,
+        help='Tab-separated file with the following fields:\n '
+             'container name, file name, output path (optional)'
+    )
+    download_file_subparser.set_defaults(func=file_download)
+    # Folder download subparser
+    download_folder_subparser = download_subparsers.add_parser(
+        parents=[parent_parser],
+        name='folder',
+        description='Download folders from Azure storage',
+        formatter_class=RawTextHelpFormatter,
+        help='Download folders from Azure storage'
+    )
+    download_folder_subparser.add_argument(
+        '-b', '--batch_file',
+        required=True,
+        type=str,
+        help='Tab-separated file with the following fields:\n '
+             'container name, folder name, output path (optional)'
+    )
+    download_folder_subparser.set_defaults(func=folder_download)
+    # Storage tier subparser
+    tier = subparsers.add_parser(
+        parents=[],
+        name='tier',
+        description='Set the storage tier of containers/files/folders in Azure storage',
+        formatter_class=RawTextHelpFormatter,
+        help='Set the storage tier of containers/files/folders in Azure storage'
+    )
+    tier_subparsers = tier.add_subparsers(
+        title='Storage tier setting functionality',
+        dest='tier'
+    )
+    # Container storage tier subparser
+    tier_container_subparser = tier_subparsers.add_parser(
+        parents=[parent_parser],
+        name='container',
+        description='Set the storage tier of containers in Azure storage',
+        formatter_class=RawTextHelpFormatter,
+        help='Set the storage tier of containers in Azure storage'
+    )
+    tier_container_subparser.add_argument(
+        '-b', '--batch_file',
+        required=True,
+        type=str,
+        help='Tab-separated file with the following fields:\n '
+             'container name, storage tier'
+    )
+    tier_container_subparser.set_defaults(func=container_tier)
+    # File storage tier subparser
+    tier_file_subparser = tier_subparsers.add_parser(
+        parents=[parent_parser],
+        name='file',
+        description='Set the storage tier of files in Azure storage',
+        formatter_class=RawTextHelpFormatter,
+        help='Set the storage tier of files in Azure storage'
+    )
+    tier_file_subparser.add_argument(
+        '-b', '--batch_file',
+        required=True,
+        type=str,
+        help='Tab-separated file with the following fields:\n '
+             'container name, file name, storage tier'
+    )
+    tier_file_subparser.set_defaults(func=file_tier)
+    # Folder storage tier subparser
+    tier_folder_subparser = tier_subparsers.add_parser(
+        parents=[parent_parser],
+        name='folder',
+        description='Set the storage tier of folders in Azure storage',
+        formatter_class=RawTextHelpFormatter,
+        help='Set the storage tier of folders in Azure storage'
+    )
+    tier_folder_subparser.add_argument(
+        '-b', '--batch_file',
+        required=True,
+        type=str,
+        help='Tab-separated file with the following fields:\n '
+             'container name, folder name, storage tier'
+    )
+    tier_folder_subparser.set_defaults(func=folder_tier)
+    # Delete subparser
+    delete = subparsers.add_parser(
+        parents=[],
+        name='delete',
+        description='Delete containers/files/folders in Azure storage',
+        formatter_class=RawTextHelpFormatter,
+        help='Delete containers/files/folders in Azure storage'
+    )
+    delete_subparsers = delete.add_subparsers(
+        title='Delete functionality',
+        dest='delete'
+    )
+    # Container delete subparser
+    delete_container_subparser = delete_subparsers.add_parser(
+        parents=[parent_parser],
+        name='container',
+        description='Delete containers in Azure storage',
+        formatter_class=RawTextHelpFormatter,
+        help='Delete containers in Azure storage'
+    )
+    delete_container_subparser.add_argument(
+        '-b', '--batch_file',
+        required=True,
+        type=str,
+        help='File with the following field:\n '
+             'container name'
+    )
+    delete_container_subparser.set_defaults(func=container_delete)
+    # File delete subparser
+    delete_file_subparser = delete_subparsers.add_parser(
+        parents=[parent_parser],
+        name='file',
+        description='Delete files in Azure storage',
+        formatter_class=RawTextHelpFormatter,
+        help='Delete files in Azure storage'
+    )
+    delete_file_subparser.add_argument(
+        '-b', '--batch_file',
+        required=True,
+        type=str,
+        help='Tab-separated file with the following fields:\n '
+             'container name, file name, retention time (optional)'
+    )
+    delete_file_subparser.set_defaults(func=file_delete)
+    # Folder delete subparser
+    delete_folder_subparser = delete_subparsers.add_parser(
+        parents=[parent_parser],
+        name='folder',
+        description='Delete folders in Azure storage',
+        formatter_class=RawTextHelpFormatter,
+        help='Delete folders in Azure storage'
+    )
+    delete_folder_subparser.add_argument(
+        '-b', '--batch_file',
+        required=True,
+        type=str,
+        help='Tab-separated file with the following fields:\n '
+             'container name, folder name, retention time (optional)'
+    )
+    delete_folder_subparser.set_defaults(func=folder_delete)
+    # Batch subparser
+    batch_subparser = subparsers.add_parser(
+        parents=[parent_parser],
+        name='batch',
+        description='Perform multiple different operations in batch',
+        formatter_class=RawTextHelpFormatter,
+        help='Perform multiple different operations in batch'
+    )
+    batch_subparser.add_argument(
+        '-b', '--batch_file',
+        required=True,
+        type=str,
+        help='Tab-separated file in the following format:\n'
+             'command, sub-command, arguments\n\n'
+             'Below is the complete list of functionalities:\n'
+             'upload, file, container name, file name, destination path (optional), storage tier (optional)\n'
+             'upload, folder, container name, folder name, destination path (optional), storage tier (optional)\n'
+             'sas, container, container name, expiry (optional), output file (optional)\n'
+             'sas, file, container name, file name and path, expiry (optional), output file (optional)\n'
+             'sas, folder, container name, folder name and path, expiry (optional), output file (optional)\n'
+             'move, container, container name, target container, destination path (optional), storage tier (optional)\n'
+             'move, file, container name, target container, file name, destination path (optional), '
+             'storage tier (optional)\n'
+             'move, folder, container name, target container, folder name, destination path (optional), '
+             'storage tier (optional)\n'
+             'download, container, container name, output path (optional)\n'
+             'download, file, container name, file name, output path (optional)\n'
+             'download, folder, container name, folder name, output path (optional)\n'
+             'tier, container, container name, storage tier\n'
+             'tier, file, container name, file name, storage tier\n'
+             'tier, folder, container name, folder name, storage tier\n'
+             'delete, container, container name\n'
+             'delete, file, container name, file name, retention time (optional)\n'
+             'delete, folder, container name, folder name, retention time (optional)'
+    )
+    batch_subparser.set_defaults(func=batch)
+    # Set up the arguments, and run the appropriate subparser
+    arguments = setup_arguments(parser=parser)
+    # Return to the requested logging level, as it has been increased to WARNING to suppress the log being filled with
+    # information from azure.core.pipeline.policies.http_logging_policy
+    coloredlogs.install(level=arguments.verbosity.upper())
+    logging.info('Operations complete')
+    # Prevent the arguments being printed to the console (they are returned in order for the tests to work)
+    sys.stderr = open(os.devnull, 'w')
+    return arguments
+
+
+if __name__ == '__main__':
+    cli()

Azure/AzureStorage/azure_storage/azure_credentials.py

@@ -0,0 +1,66 @@
+#!/usr/bin/env python
+from azure_storage.methods import create_parent_parser, delete_keyring_credentials, \
+    set_account_name, set_connection_string, setup_arguments
+from argparse import ArgumentParser, RawTextHelpFormatter
+import logging
+import sys
+import os
+
+
+def store_credentials(args):
+    """
+    Run the credentials setting methods
+    :param args: type ArgumentParser arguments
+    """
+    logging.info('Setting Azure storage credentials from system keyring')
+    # Set the account name in the keyring
+    set_account_name(passphrase=args.passphrase,
+                     account_name=args.account_name)
+    # Set the connection string in the keyring
+    set_connection_string(passphrase=args.passphrase,
+                          account_name=args.account_name)
+
+
+def delete_credentials(args):
+    """
+    Run the credentials deleting methods
+    :param args: type ArgumentParser arguments
+    """
+    logging.info('Deleting Azure storage credentials from system keyring')
+    # Delete the account name in the keyring
+    delete_keyring_credentials(passphrase=args.passphrase,
+                               account_name=args.passphrase)
+    # Delete the connection string in the keyring
+    delete_keyring_credentials(passphrase=args.passphrase,
+                               account_name=args.account_name)
+
+
+def cli():
+    parser = ArgumentParser(description='Set, modify, or delete Azure storage credentials in the system keyring')
+    # Create the parental parser, and the subparser
+    subparsers, parent_parser = create_parent_parser(parser=parser,
+                                                     container=False)
+    # Credentials storing/modifying subparser
+    store_subparser = subparsers.add_parser(parents=[parent_parser],
+                                            name='store',
+                                            description='Store or update Azure storage credentials in the system '
+                                                        'keyring',
+                                            formatter_class=RawTextHelpFormatter,
+                                            help='Store or update Azure storage credentials in the system keyring')
+    store_subparser.set_defaults(func=store_credentials)
+    # Credentials deleting subparser
+    delete_subparser = subparsers.add_parser(parents=[parent_parser],
+                                             name='delete',
+                                             description='Delete Azure storage credentials in the system keyring',
+                                             formatter_class=RawTextHelpFormatter,
+                                             help='Delete Azure storage credentials in the system keyring')
+    delete_subparser.set_defaults(func=delete_credentials)
+    # Set up the arguments, and run the appropriate subparser
+    arguments = setup_arguments(parser=parser)
+    # Prevent the arguments being printed to the console (they are returned in order for the tests to work)
+    sys.stderr = open(os.devnull, 'w')
+    return arguments
+
+
+if __name__ == '__main__':
+    cli()

Azure/AzureStorage/azure_storage/azure_delete.py

@@ -0,0 +1,183 @@
+#!/usr/bin/env python
+from azure_storage.methods import client_prep, create_parent_parser, delete_container, delete_file, \
+    delete_folder, setup_arguments, set_blob_retention_policy
+from argparse import ArgumentParser, RawTextHelpFormatter
+import coloredlogs
+import logging
+import sys
+import os
+
+
+class AzureContainerDelete(object):
+
+    def main(self):
+        self.container_name, self.connect_str, self.blob_service_client, container_client = \
+            client_prep(container_name=self.container_name,
+                        passphrase=self.passphrase,
+                        account_name=self.account_name)
+        # Hide the INFO-level messages sent to the logger from Azure by increasing the logging level to WARNING
+        logging.getLogger().setLevel(logging.WARNING)
+        delete_container(blob_service_client=self.blob_service_client,
+                         container_name=self.container_name,
+                         account_name=self.account_name)
+
+    def __init__(self, container_name, account_name, passphrase):
+        # Set the container name variable
+        self.container_name = container_name
+        # Initialise necessary class variables
+        self.passphrase = passphrase
+        self.account_name = account_name
+        self.connect_str = str()
+        self.blob_service_client = None
+
+
+class AzureDelete(object):
+
+    def main(self):
+        self.container_name, self.connect_str, self.blob_service_client, self.container_client = \
+            client_prep(container_name=self.container_name,
+                        passphrase=self.passphrase,
+                        account_name=self.account_name)
+        # Hide the INFO-level messages sent to the logger from Azure by increasing the logging level to WARNING
+        logging.getLogger().setLevel(logging.WARNING)
+        # Set the file retention policy
+        self.blob_service_client = set_blob_retention_policy(blob_service_client=self.blob_service_client,
+                                                             days=self.retention_time)
+        # Run the proper method depending on whether a file or a folder is requested
+        if self.category == 'file':
+            delete_file(container_client=self.container_client,
+                        object_name=self.object_name,
+                        blob_service_client=self.blob_service_client,
+                        container_name=self.container_name)
+        elif self.category == 'folder':
+            delete_folder(container_client=self.container_client,
+                          object_name=self.object_name,
+                          blob_service_client=self.blob_service_client,
+                          container_name=self.container_name,
+                          account_name=self.account_name)
+        else:
+            logging.error(f'Something is wrong. There is no {self.category} option available')
+            raise SystemExit
+
+    def __init__(self, object_name, container_name, account_name, passphrase, retention_time, category):
+        self.object_name = object_name
+        # Set the container name variable
+        self.container_name = container_name
+        # Initialise necessary class variables
+        self.passphrase = passphrase
+        self.account_name = account_name
+        self.retention_time = retention_time
+        # Ensure that the retention time provided is valid
+        try:
+            assert 0 < self.retention_time < 366
+        except AssertionError:
+            logging.error(f'The provided retention time ({self.retention_time}) is invalid. '
+                          f'It must be between 1 and 365 days')
+            raise SystemExit
+        self.category = category
+        self.connect_str = str()
+        self.blob_service_client = None
+        self.container_client = None
+
+
+def container_delete(args):
+    """
+    Run the AzureContainerDelete method
+    :param args: type ArgumentParser arguments
+    """
+    logging.info(f'Deleting container {args.container_name} from Azure storage account {args.account_name}')
+    del_container = AzureContainerDelete(container_name=args.container_name,
+                                         account_name=args.account_name,
+                                         passphrase=args.passphrase)
+    del_container.main()
+
+
+def file_delete(args):
+    """
+    Run the AzureDelete method for a file
+    :param args: type ArgumentParser arguments
+    """
+    logging.info(f'Deleting file {args.file} from container {args.container_name} in Azure storage account '
+                 f'{args.account_name}')
+    del_file = AzureDelete(object_name=args.file,
+                           container_name=args.container_name,
+                           account_name=args.account_name,
+                           passphrase=args.passphrase,
+                           retention_time=args.retention_time,
+                           category='file')
+    del_file.main()
+
+
+def folder_delete(args):
+    """
+    Run the AzureDelete method for a folder
+    :param args: type ArgumentParser arguments
+    """
+    logging.info(f'Deleting folder {args.folder} from container {args.container_name} in Azure storage account '
+                 f'{args.account_name}')
+    del_folder = AzureDelete(object_name=args.folder,
+                             container_name=args.container_name,
+                             account_name=args.account_name,
+                             passphrase=args.passphrase,
+                             retention_time=args.retention_time,
+                             category='folder')
+    del_folder.main()
+
+
+def cli():
+    parser = ArgumentParser(description='Move and/or delete containers, files, or folders in Azure storage')
+    # Create the parental parser, and the subparser
+    subparsers, parent_parser = create_parent_parser(parser=parser)
+    # Container delete subparser
+    container_delete_subparser = subparsers.add_parser(parents=[parent_parser],
+                                                       name='container',
+                                                       description='Delete a container in Azure storage',
+                                                       formatter_class=RawTextHelpFormatter,
+                                                       help='Delete a container in Azure storage')
+    container_delete_subparser.set_defaults(func=container_delete)
+    # File delete subparser
+    file_delete_subparser = subparsers.add_parser(parents=[parent_parser],
+                                                  name='file',
+                                                  description='Delete a file in Azure storage',
+                                                  formatter_class=RawTextHelpFormatter,
+                                                  help='Delete a file in Azure storage')
+    file_delete_subparser.add_argument('-f', '--file',
+                                       type=str,
+                                       required=True,
+                                       help='Name of blob file to delete in Azure storage. '
+                                            'e.g. 2022-SEQ-0001_S1_L001_R1_001.fastq.gz')
+    file_delete_subparser.add_argument('-r', '--retention_time',
+                                       type=int,
+                                       default=8,
+                                       help='Retention time for deleted files. Default is 8 days. Must be between '
+                                            '1 and 365')
+    file_delete_subparser.set_defaults(func=file_delete)
+    # Folder delete subparser
+    folder_delete_subparser = subparsers.add_parser(parents=[parent_parser],
+                                                    name='folder',
+                                                    description='Delete a folder in Azure storage',
+                                                    formatter_class=RawTextHelpFormatter,
+                                                    help='Delete a folder in Azure storage')
+    folder_delete_subparser.add_argument('-f', '--folder',
+                                         type=str,
+                                         required=True,
+                                         help='Name of folder to delete in Azure storage. '
+                                              'e.g. InterOp')
+    folder_delete_subparser.add_argument('-r', '--retention_time',
+                                         type=int,
+                                         default=8,
+                                         help='Retention time for deleted files. Default is 8 days')
+    folder_delete_subparser.set_defaults(func=folder_delete)
+    # Set up the arguments, and run the appropriate subparser
+    arguments = setup_arguments(parser=parser)
+    # Return to the requested logging level, as it has been increased to WARNING to suppress the log being filled with
+    # information from azure.core.pipeline.policies.http_logging_policy
+    coloredlogs.install(level=arguments.verbosity.upper())
+    logging.info('Deletion complete')
+    # Prevent the arguments being printed to the console (they are returned in order for the tests to work)
+    sys.stderr = open(os.devnull, 'w')
+    return arguments
+
+
+if __name__ == '__main__':
+    cli()

Azure/AzureStorage/azure_storage/azure_download.py

@@ -0,0 +1,319 @@
+#!/usr/bin/env python
+from azure_storage.methods import client_prep, create_blob_client, create_parent_parser, setup_arguments
+from argparse import ArgumentParser, RawTextHelpFormatter
+import coloredlogs
+import logging
+import azure
+import sys
+import os
+
+
+class AzureContainerDownload(object):
+
+    def main(self):
+        self.container_name, self.connect_str, self.blob_service_client, self.container_client = \
+            client_prep(container_name=self.container_name,
+                        passphrase=self.passphrase,
+                        account_name=self.account_name,
+                        create=False)
+        self.download_container(container_client=self.container_client,
+                                blob_service_client=self.blob_service_client,
+                                container_name=self.container_name,
+                                output_path=self.output_path)
+
+    @staticmethod
+    def download_container(container_client, blob_service_client, container_name, output_path):
+        """
+        Download the container from Azure storage
+        :param container_client: type azure.storage.blob.BlobServiceClient.ContainerClient
+        :param blob_service_client: type: azure.storage.blob.BlobServiceClient
+        :param container_name: type str: Name of the container of interest
+        :param output_path: type str: Name and path of the folder into which the container is to be downloaded
+        """
+        # Create a generator containing all the blobs in the container
+        generator = container_client.list_blobs()
+        try:
+            # Hide the INFO-level messages sent to the logger from Azure by increasing the logging level to WARNING
+            logging.getLogger().setLevel(logging.WARNING)
+            for blob_file in generator:
+                # Create the blob client
+                blob_client = create_blob_client(blob_service_client=blob_service_client,
+                                                 container_name=container_name,
+                                                 blob_file=blob_file)
+                # Extract the folder structure of the blob e.g. 220202-m05722/InterOp
+                folder_structure = os.path.split(os.path.dirname(blob_file.name))
+                # Determine the path to output the file. Join the supplied path, the name of the container and
+                # the joined (splatted) folder structure. Logic: https://stackoverflow.com/a/14826889
+                download_path = os.path.join(output_path, container_name, os.path.join(*folder_structure))
+                # Create the path if required
+                os.makedirs(download_path, exist_ok=True)
+                # Set the name of file by removing any path information
+                file_name = os.path.basename(blob_file.name)
+                # Finally, set the name and the path of the output file
+                download_file = os.path.join(download_path, file_name)
+                # Open the target output file as binary
+                with open(download_file, 'wb') as downloaded_file:
+                    # Write the data from the blob client to the local file
+                    downloaded_file.write(blob_client.download_blob().readall())
+        except azure.core.exceptions.ResourceNotFoundError:
+            logging.error(f' The specified container, {container_name}, does not exist.')
+            raise SystemExit
+
+    def __init__(self, container_name, output_path, account_name, passphrase):
+        # Set the container name variable
+        self.container_name = container_name
+        # Output path
+        if output_path.startswith('~'):
+            self.output_path = os.path.abspath(os.path.expanduser(os.path.join(output_path)))
+        else:
+            self.output_path = os.path.abspath(os.path.join(output_path))
+        # Create the output path
+        try:
+            os.makedirs(self.output_path, exist_ok=True)
+        except PermissionError:
+            logging.error(f'Could not use the supplied output path: {self.output_path}')
+            raise SystemExit
+        # Initialise necessary class variables
+        self.passphrase = passphrase
+        self.account_name = account_name
+        self.connect_str = str()
+        self.blob_service_client = None
+        self.container_client = None
+
+
+class AzureDownload(object):
+
+    def main(self):
+        self.container_name, self.connect_str, self.blob_service_client, self.container_client = \
+            client_prep(container_name=self.container_name,
+                        passphrase=self.passphrase,
+                        account_name=self.account_name,
+                        create=False)
+        # Run the proper method depending on whether a file or a folder is requested
+        if self.category == 'file':
+            self.download_file(container_client=self.container_client,
+                               blob_service_client=self.blob_service_client,
+                               container_name=self.container_name,
+                               object_name=self.object_name,
+                               output_path=self.output_path)
+        elif self.category == 'folder':
+            self.download_folder(container_client=self.container_client,
+                                 blob_service_client=self.blob_service_client,
+                                 container_name=self.container_name,
+                                 object_name=self.object_name,
+                                 output_path=self.output_path)
+        else:
+            logging.error(f'Something is wrong. There is no {self.category} option available')
+            raise SystemExit
+
+    @staticmethod
+    def download_file(container_client, blob_service_client, container_name, object_name, output_path):
+        """
+        Download the specified file from Azure storage
+        :param container_client: type azure.storage.blob.BlobServiceClient.ContainerClient
+        :param blob_service_client: type: azure.storage.blob.BlobServiceClient
+        :param container_name: type str: Name of the container of interest
+        :param object_name: type str: Name and path of file to download from Azure storage
+        :param output_path: type str: Name and path of the folder into which the file is to be downloaded
+        """
+        # Create a generator containing all the blobs in the container
+        generator = container_client.list_blobs()
+        # Create a boolean to determine if the file has been located
+        present = False
+        # Hide the INFO-level messages sent to the logger from Azure by increasing the logging level to WARNING
+        logging.getLogger().setLevel(logging.WARNING)
+        try:
+            for blob_file in generator:
+                # Filter for the blob name
+                if blob_file.name == object_name:
+                    # Update the file presence variable
+                    present = True
+                    # Create the blob client
+                    blob_client = create_blob_client(blob_service_client=blob_service_client,
+                                                     container_name=container_name,
+                                                     blob_file=blob_file)
+                    # Set the name of file by removing any path information
+                    file_name = os.path.basename(blob_file.name)
+                    # Finally, set the name and the path of the output file
+                    download_file = os.path.join(output_path, file_name)
+                    # Open the target output file as binary
+                    with open(download_file, 'wb') as downloaded_file:
+                        # Write the data from the blob client to the local file
+                        downloaded_file.write(blob_client.download_blob().readall())
+            # Send an error to the user that the file could not be found
+            if not present:
+                logging.error(f'Could not locate the desired file {object_name} in {container_name}')
+                raise SystemExit
+        except azure.core.exceptions.ResourceNotFoundError:
+            logging.error(f' The specified container, {container_name}, does not exist.')
+            raise SystemExit
+
+    @staticmethod
+    def download_folder(container_client, blob_service_client, container_name, object_name, output_path):
+        """
+        Download the specified folder from Azure storage
+        :param container_client: type azure.storage.blob.BlobServiceClient.ContainerClient
+        :param blob_service_client: type: azure.storage.blob.BlobServiceClient
+        :param container_name: type str: Name of the container of interest
+        :param object_name: type str: Name and path of folder to download from Azure storage
+        :param output_path: type str: Name and path of the folder into which the folder is to be downloaded
+        """
+        # Create a generator containing all the blobs in the container
+        generator = container_client.list_blobs()
+        # Boolean to track whether the folder was located
+        present = False
+        # Hide the INFO-level messages sent to the logger from Azure by increasing the logging level to WARNING
+        logging.getLogger().setLevel(logging.WARNING)
+        try:
+            for blob_file in generator:
+                # Create the path of the file by adding the container name to the path of the file
+                blob_path = os.path.join(container_name, os.path.split(blob_file.name)[0])
+                # Ensure that the supplied folder path is present in the blob path
+                if os.path.normpath(object_name) in os.path.normpath(blob_path):
+                    # Update the folder presence boolean
+                    present = True
+                    # Create the blob client
+                    blob_client = create_blob_client(blob_service_client=blob_service_client,
+                                                     container_name=container_name,
+                                                     blob_file=blob_file)
+                    # Determine the path to output the file. Join the supplied path and the path of the blob
+                    download_path = os.path.join(output_path, os.path.join(os.path.dirname(blob_file.name)))
+                    # Create the path if required
+                    os.makedirs(download_path, exist_ok=True)
+                    # Set the name of file by removing any path information
+                    file_name = os.path.basename(blob_file.name)
+                    # Finally, set the name and the path of the output file
+                    download_file = os.path.join(download_path, file_name)
+                    # Open the target output file as binary
+                    with open(download_file, 'wb') as downloaded_file:
+                        # Write the data from the blob client to the local file
+                        downloaded_file.write(blob_client.download_blob().readall())
+            # Send an error to the user that the folder could not be found
+            if not present:
+                logging.error(f'Could not locate the desired folder {object_name} in container {container_name}')
+                raise SystemExit
+        except azure.core.exceptions.ResourceNotFoundError:
+            logging.error(f' The specified container, {container_name}, does not exist.')
+            raise SystemExit
+
+    def __init__(self, object_name, container_name, output_path, account_name, passphrase, category):
+        # Set the name of the file/folder to download
+        self.object_name = object_name
+        # Set the container name variable
+        self.container_name = container_name
+        # Output path
+        if output_path.startswith('~'):
+            self.output_path = os.path.abspath(os.path.expanduser(os.path.join(output_path)))
+        else:
+            self.output_path = os.path.abspath(os.path.join(output_path))
+        # Create the output path
+        try:
+            os.makedirs(self.output_path, exist_ok=True)
+        except PermissionError:
+            logging.error(f'Could not use the supplied output path: {self.output_path}')
+            raise SystemExit
+        # Initialise necessary class variables
+        self.passphrase = passphrase
+        self.account_name = account_name
+        self.category = category
+        self.connect_str = str()
+        self.blob_service_client = None
+        self.container_client = None
+
+
+def container_download(args):
+    """
+    Run the AzureContainerDownload method
+    :param args: type ArgumentParser arguments
+    """
+    logging.info(f'Downloading Azure container {args.container_name}')
+    # Create the container download object
+    container_downloader = AzureContainerDownload(container_name=args.container_name,
+                                                  output_path=args.output_path,
+                                                  account_name=args.account_name,
+                                                  passphrase=args.passphrase)
+    container_downloader.main()
+
+
+def file_download(args):
+    """
+    Run the AzureDownload class for a file
+    :param args: type ArgumentParser arguments
+    """
+    logging.info(f'Downloading {args.file} from Azure storage')
+    # Create the file download object
+    file_downloader = AzureDownload(object_name=args.file,
+                                    container_name=args.container_name,
+                                    output_path=args.output_path,
+                                    account_name=args.account_name,
+                                    passphrase=args.passphrase,
+                                    category='file')
+    file_downloader.main()
+
+
+def folder_download(args):
+    """
+    Run the AzureDownload class for a folder
+    :param args: type ArgumentParser arguments
+    """
+    logging.info(f'Downloading contents of folder {args.folder} from Azure storage')
+    folder_downloader = AzureDownload(object_name=args.folder,
+                                      container_name=args.container_name,
+                                      output_path=args.output_path,
+                                      account_name=args.account_name,
+                                      passphrase=args.passphrase,
+                                      category='folder')
+    folder_downloader.main()
+
+
+def cli():
+    parser = ArgumentParser(description='Download containers/files/folders from Azure storage')
+    # Create the parental parser, and the subparser
+    subparsers, parent_parser = create_parent_parser(parser=parser)
+    parent_parser.add_argument('-o', '--output_path',
+                               default=os.getcwd(),
+                               help='Name and path of directory in which the outputs are to be saved. Default is '
+                                    'your $CWD')
+    # Container downloading parser
+    container_subparser = subparsers.add_parser(parents=[parent_parser],
+                                                name='container',
+                                                description='Download a container from Azure storage',
+                                                formatter_class=RawTextHelpFormatter,
+                                                help='Download a container from Azure storage')
+    container_subparser.set_defaults(func=container_download)
+    # Blob (file) downloading subparser
+    file_subparser = subparsers.add_parser(parents=[parent_parser],
+                                           name='file',
+                                           description='Download a file from Azure storage',
+                                           formatter_class=RawTextHelpFormatter,
+                                           help='Download a file from Azure storage')
+    file_subparser.add_argument('-f', '--file',
+                                type=str,
+                                required=True,
+                                help='Name of file to download from Azure storage.'
+                                     'e.g. 2022-SEQ-0001_S1_L001_R1_001.fastq.gz')
+    file_subparser.set_defaults(func=file_download)
+    # Folder downloading subparser
+    folder_subparser = subparsers.add_parser(parents=[parent_parser],
+                                             name='folder',
+                                             description='Download a folder from Azure storage',
+                                             formatter_class=RawTextHelpFormatter,
+                                             help='Download a folder from Azure storage')
+    folder_subparser.add_argument('-f', '--folder',
+                                  type=str,
+                                  required=True,
+                                  help='Name of the folder to download from Azure storage e.g. InterOp')
+    folder_subparser.set_defaults(func=folder_download)
+    # Set up the arguments, and run the appropriate subparser
+    arguments = setup_arguments(parser=parser)
+    # Return to the requested logging level, as it has been increased to WARNING to suppress the log being filled with
+    # information from azure.core.pipeline.policies.http_logging_policy
+    coloredlogs.install(level=arguments.verbosity.upper())
+    logging.info('Download complete')
+    # Prevent the arguments being printed to the console (they are returned in order for the tests to work)
+    sys.stderr = open(os.devnull, 'w')
+    return arguments
+
+
+if __name__ == '__main__':
+    cli()

Azure/AzureStorage/azure_storage/azure_list.py

@@ -0,0 +1,379 @@
+#!/usr/bin/env python
+from azure_storage.methods import create_blob_service_client, client_prep, create_parent_parser, \
+    extract_connection_string, setup_arguments
+from argparse import ArgumentParser, RawTextHelpFormatter
+from termcolor import colored
+import coloredlogs
+import logging
+import pathlib
+import sys
+import os
+import re
+
+
+class AzureContainerList(object):
+
+    def main(self):
+        # Hide the INFO-level messages sent to the logger from Azure by increasing the logging level to WARNING
+        logging.getLogger().setLevel(logging.WARNING)
+        # Extract the connection string from the system keyring
+        self.connect_str = extract_connection_string(passphrase=self.passphrase,
+                                                     account_name=self.account_name)
+        # Create the blob service client using the connection string
+        self.blob_service_client = create_blob_service_client(connect_str=self.connect_str)
+        containers = self.list_containers(blob_service_client=self.blob_service_client,
+                                          expression=self.expression,
+                                          print_container=self.print_container,
+                                          output_file=self.output_file)
+        return containers
+
+    @staticmethod
+    def list_containers(blob_service_client, expression, print_container, output_file):
+        """
+        List all containers in a storage account. If an expression is provided, find all containers that
+        match the expression
+        :param blob_service_client: type: azure.storage.blob.BlobServiceClient
+        :param expression: type str: Expression to match. Can be a regular expression or 'normal' expression
+        :param print_container: type bool: Boolean on whether to print container matches to the terminal
+        :param output_file: type str: Name and path of file in which container names are to be written. Optional
+        :return: container_matches: List of containers that match the expression
+        """
+        # Create a generator of all the containers in the storage account
+        containers = blob_service_client.list_containers()
+        # Prepare a list to store the containers that match the expression
+        container_matches = list()
+        # Allow a quiet exit on keyboard interrupts
+        try:
+            for container in containers:
+                # Boolean to determine whether the expression matched the container name
+                match = False
+                # If the expression contains non-alphanumeric characters either at the start or anywhere, treat
+                # it as a regular expression
+                if re.match(r'.*\W', expression.replace('-', '_')):
+                    # Use re.sub to convert * to .* to be consistent with regex rules
+                    # It seemed unintuitive to force the user to use .* rather than just * for simple queries.
+                    # If .* was provided, don't add the '.' by using a negative lookbehind assertion
+                    regex_expression = re.sub(r'(?<!\.)\*', '.*', expression)
+                    # Use re.fullmatch to determine if the expression matches the container name
+                    if re.fullmatch(rf'{regex_expression}$', container.name):
+                        # Update the match boolean and append the container to the list of matches
+                        match = True
+                        container_matches.append(container)
+                # The expression doesn't appear to be a regular expression
+                else:
+                    # Ensure a perfect match for non regex queries
+                    if expression == container.name:
+                        # Update the match boolean and append the container to the list of matches
+                        match = True
+                        container_matches.append(container)
+                # Print the name of the container on a match
+                if print_container and match:
+                    # Use termcolor to print the name in bold green
+                    print(colored(container.name, 'green', attrs=['bold']))
+                # If requested, write the name of the container to the output file on a match
+                if output_file and match:
+                    with open(output_file, 'a+') as output:
+                        output.write(f'{container.name}\n')
+        except KeyboardInterrupt:
+            raise SystemExit
+        return container_matches
+
+    def __init__(self, expression, account_name, output_file, passphrase, print_container=True):
+        self.expression = expression if expression else '*'
+        self.account_name = account_name
+        self.passphrase = passphrase
+        # Ensure that the output file can be used
+        if output_file:
+            # Output file
+            if output_file.startswith('~'):
+                self.output_file = os.path.abspath(os.path.expanduser(os.path.join(output_file)))
+            else:
+                self.output_file = os.path.abspath(os.path.join(output_file))
+                # Ensure that the output file can be used
+                if not os.path.isfile(self.output_file):
+                    try:
+                        # Create the parental directory for the output file as required
+                        os.makedirs(os.path.dirname(self.output_file), exist_ok=True)
+                    except PermissionError:
+                        logging.error(f'Insufficient permissions to create output file {self.output_file}')
+                        raise SystemExit
+                    try:
+                        open(self.output_file, 'w').close()
+                    except IsADirectoryError:
+                        logging.error(
+                            f'A directory or an empty file name was provided for the output file {self.output_file}')
+                        raise SystemExit
+                    except PermissionError:
+                        logging.error(f'Insufficient permissions to create output file {self.output_file}')
+                        raise SystemExit
+        else:
+            self.output_file = str()
+        self.connect_str = str()
+        self.blob_service_client = None
+        # Boolean on whether the container name should be printed to terminal
+        self.print_container = print_container
+
+
+class AzureList(object):
+    def main(self):
+        # Hide the INFO-level messages sent to the logger from Azure by increasing the logging level to WARNING
+        logging.getLogger().setLevel(logging.WARNING)
+        # If the container name was provided, and does not look like a regular expression, run the client_prep method
+        # to validate the container name, extract the connection string, and create the blob service client and
+        # container client
+        if self.container_name and not re.match(r'.*\W', self.container_name.replace('-', '_')):
+            self.container_name, self.connect_str, self.blob_service_client, container_client = \
+                client_prep(container_name=self.container_name,
+                            passphrase=self.passphrase,
+                            account_name=self.account_name)
+            # List all the files that match the expression
+            self.list_files(container_client=container_client,
+                            expression=self.expression,
+                            output_file=self.output_file,
+                            container_name=self.container_name)
+        # If the container name wasn't provided, or looks like a regular expression, use the AzureContainerList class
+        # to find containers that match the provided expression
+        else:
+            list_containers = AzureContainerList(
+                expression=self.container_name,
+                account_name=self.account_name,
+                output_file=str(),
+                passphrase=self.passphrase,
+                print_container=False
+            )
+            containers = list_containers.main()
+            # Extract the connection string from the system keyring
+            self.connect_str = extract_connection_string(passphrase=self.passphrase,
+                                                         account_name=self.account_name)
+            # Create the blob service client using the connection string
+            self.blob_service_client = create_blob_service_client(connect_str=self.connect_str)
+            # List all the files in each of the containers that match the provided expression
+            for container in containers:
+                # Create a container client for the container
+                container_client = self.blob_service_client.get_container_client(container.name)
+                # Run the list_files method to list and optionally filter the files
+                self.list_files(container_client=container_client,
+                                expression=self.expression,
+                                output_file=self.output_file,
+                                container_name=container.name)
+
+    @staticmethod
+    def list_files(container_client, expression, output_file, container_name):
+        """
+        List and optionally filter (with a user-provided expression) all files in a container
+        :param container_client: type azure.storage.blob.BlobServiceClient.ContainerClient
+        :param expression: type str: Expression to match. Can be a regular expression or 'normal' expression
+        :param output_file: type str: Name and path of file in which container names are to be written. Optional
+        :param container_name: type str: Name of the container of interest
+        """
+        # Create a generator containing all the blobs in the container
+        generator = container_client.list_blobs()
+        # Allow a quiet exit on keyboard interrupts
+        try:
+            # Iterate through all the files in the container
+            for blob_file in generator:
+                # Store the file name and path in a variable
+                filename = blob_file.name
+                # Initialise a variable to track whether this file is a match to the expression
+                match = False
+                # Use pathlib to create a path object from the file name
+                path_obj = pathlib.Path(os.path.normpath(filename))
+                # Split the file name into its separate components
+                components = path_obj.parts
+                # Check whether the expression contains non-alphanumeric characters. If it does, treat it as a
+                # regular expression. Ignore dashes as a non-alphanumeric character.
+                if re.match(r'.*\W', expression.replace('-', '_')):
+                    # If the expression is targeted to nested files/folders, split the expression into its
+                    # path components e.g. reports/outputs/output.tsv contains three components
+                    expression_obj = pathlib.Path(os.path.normpath(expression))
+                    expression_components = list(expression_obj.parts)
+                    # The number of matches required is the number of path components
+                    # e.g. reports/outputs/output.tsv requires three matches
+                    matches_required = len(expression_components)
+                    # Initialise a dictionary to track matches to each of the components
+                    component_matches = dict()
+                    # Search through all the path components of the file name
+                    for i, component in enumerate(components):
+                        # Check for nested files/folders
+                        if len(expression_components) > 1:
+                            while len(expression_components) < len(components):
+                                expression_components.insert(-1, '*')
+                            # Reset the number of matches required to the new length of the expression components
+                            matches_required = len(expression_components)
+                            # Use re.sub to convert * to .* to be consistent with regex rules
+                            regex_expression = re.sub(r'(?<!\.)\*', '.*', expression_components[i])
+                            # If the components match, increment the number of matches
+                            if re.fullmatch(rf'{regex_expression}$', component):
+                                # Set the match to the current component to true
+                                component_matches[component] = True
+                        else:
+                            # Use re.sub to convert * to .* to be consistent with regex rules
+                            regex_expression = re.sub(r'(?<!\.)\*', '.*', expression)
+                            # If the component matches, set the match boolean to True
+                            if re.fullmatch(rf'{regex_expression}$', component):
+                                match = True
+                    # Check to see if the number of matches observed in a multi-component expression is the number
+                    # matches required for a match before setting the match boolean to True
+                    if len(component_matches) == matches_required:
+                        match = True
+                # The expression does not look like a regular expression
+                else:
+                    for component in components:
+                        # An exact match is required to be considered a match
+                        if expression == component:
+                            match = True
+                # Only proceed if the file matches the expression
+                if match:
+                    # If the output file has been provided, write the file name to it
+                    if output_file:
+                        with open(output_file, 'a+') as output:
+                            output.write(f'{container_name}\t{filename}\n')
+                    # Initialise a variable to store the path information of the file
+                    file_path = None
+                    # Use termcolor to print the container name in bold green
+                    container = colored(container_name, 'green', attrs=['bold'])
+                    # Determine if the file is nested in one or more folders
+                    if len(path_obj.parts) > 1:
+                        # Use termcolor to print the path in bold blue
+                        file_path = colored(f'{os.sep.join(components[:-1])}{os.sep}', 'blue', attrs=['bold'])
+                    # Remove any path information from the file name
+                    filename = os.path.basename(filename)
+                    # Use termcolor to print any archive files as bold red
+                    if filename.endswith('.gz') or filename.endswith('.bz2') or filename.endswith('.zip'):
+                        filename = colored(filename, 'red', attrs=['bold'])
+                    # If the file was nested, print the extracted path information
+                    if file_path:
+                        print(f'{container}\t{file_path}{filename}')
+                    # Otherwise, only print the file name
+                    else:
+                        print(f'{container}\t{filename}')
+        except KeyboardInterrupt:
+            raise SystemExit
+
+    def __init__(self, container_name, expression, output_file, account_name, passphrase):
+        # If the container name wasn't provided, set it to *
+        self.container_name = container_name if container_name else '*'
+        self.expression = expression if expression else '*'
+        self.account_name = account_name
+        if output_file:
+            # Output file
+            if output_file.startswith('~'):
+                self.output_file = os.path.abspath(os.path.expanduser(os.path.join(output_file)))
+            else:
+                self.output_file = os.path.abspath(os.path.join(output_file))
+                # Ensure that the output file can be used
+                if not os.path.isfile(self.output_file):
+                    try:
+                        # Create the parental directory for the output file as required
+                        os.makedirs(os.path.dirname(self.output_file), exist_ok=True)
+                    except PermissionError:
+                        logging.error(f'Insufficient permissions to create output file {self.output_file}')
+                        raise SystemExit
+                    try:
+                        open(self.output_file, 'w').close()
+                    except IsADirectoryError:
+                        logging.error(
+                            f'A directory or an empty file name was provided for the output file {self.output_file}')
+                        raise SystemExit
+                    except PermissionError:
+                        logging.error(f'Insufficient permissions to create output file {self.output_file}')
+                        raise SystemExit
+        else:
+            self.output_file = str()
+        self.passphrase = passphrase
+        self.connect_str = str()
+        self.blob_service_client = None
+
+
+def container_search(args):
+    """
+    Run the AzureContainerList class
+    :param args: type ArgumentParser arguments
+    """
+    # Welcome message that is adjusted depending on whether an expression has been provided
+    phrase = f'Listing containers in Azure storage account {args.account_name}.'
+    if args.expression:
+        phrase += f'\nFiltering containers with the expression: {args.expression}'
+    logging.info(phrase)
+    list_containers = AzureContainerList(
+        expression=args.expression,
+        account_name=args.account_name,
+        output_file=args.output_file,
+        passphrase=args.passphrase
+    )
+    list_containers.main()
+
+
+def azure_search(args):
+    """
+    Run the AzureList class with the provided command line arguments
+    :param args: type ArgumentParser arguments
+    """
+    # Welcome message that is adjusted depending on whether a container and/or an expression have been provided
+    phrase = f'Searching for files in Azure storage account {args.account_name}.'
+    if args.container_name:
+        phrase += f'\nFiltering containers with the expression: {args.container_name}'
+    phrase += f'\nFiltering files with the expression: {args.expression}'
+    logging.info(phrase)
+    list_files = AzureList(
+        container_name=args.container_name,
+        expression=args.expression,
+        account_name=args.account_name,
+        output_file=args.output_file,
+        passphrase=args.passphrase
+    )
+    list_files.main()
+
+
+def cli():
+    parser = ArgumentParser(description='Explore your Azure storage account')
+    subparsers, parent_parser = create_parent_parser(parser=parser,
+                                                     container=False)
+    parent_parser.add_argument('expression',
+                               nargs='?',  # This allows the argument to be optional so things behave like actual ls.
+                               default=None,
+                               type=str,
+                               help='Expression to search. This command supports regular expressions. '
+                                    'e.g. 1912* will return all containers starting with 1912, including 191216-dar '
+                                    'Note that since the regular expression is being entered on the command line, '
+                                    'you may need to escape certain characters e.g. ! should be \\!')
+    parent_parser.add_argument('-o', '--output_file',
+                               default=str(),
+                               help='Optionally provide the name and path of file in which the outputs '
+                                    'are to be saved.')
+    container_subparser = subparsers.add_parser(parents=[parent_parser],
+                                                name='container',
+                                                description='Filter and list containers in your Azure storage account',
+                                                formatter_class=RawTextHelpFormatter,
+                                                help='Filter and list containers in your Azure storage account')
+    container_subparser.set_defaults(func=container_search)
+    ls_subparser = subparsers.add_parser(parents=[parent_parser],
+                                         name='search',
+                                         description='Filter files in a container (or containers) in Azure storage',
+                                         formatter_class=RawTextHelpFormatter,
+                                         help='Filter files in a container (or containers) in Azure storage')
+    ls_subparser.add_argument('-c', '--container_name',
+                              nargs='?',
+                              type=str,
+                              default=str(),
+                              help='Name of the Azure storage container. This command supports regular expressions '
+                                   'e.g. 1912* will return all containers starting with 1912.'
+                                   'Note that since the regular expression is being entered on the command line, '
+                                   'you may need to escape certain characters e.g. ! should be \\! '
+                                   'You can make your queries as complex as you wish: '
+                                   '1912\\d{2}-\\D{3}\(\?\!*output\) will only return '
+                                   'containers that start with 1912, and have two additional digits. If '
+                                   'the word output is present, any matches are ignored. There also '
+                                   'have to be exactly three letters following a dash and the first six numbers '
+                                   'e.g. 191216-dar and 191227-dar will be returned but not 191216-dar-outputs '
+                                   '191202-test, 191216dar, 1912162-dar, 191203-m05722, 191114-gta, '
+                                   'or 200105-dar (and many others)')
+    ls_subparser.set_defaults(func=azure_search)
+    # Set up the arguments, and run the appropriate subparser
+    arguments = setup_arguments(parser=parser)
+    # Return to the requested logging level, as it has been increased to WARNING to suppress the log being filled with
+    # information from azure.core.pipeline.policies.http_logging_policy
+    coloredlogs.install(level=arguments.verbosity.upper())
+    # Prevent the arguments being printed to the console (they are returned in order for the tests to work)
+    sys.stderr = open(os.devnull, 'w')
+    return arguments

Azure/AzureStorage/azure_storage/azure_move.py

@@ -0,0 +1,322 @@
+#!/usr/bin/env python
+from azure_storage.methods import copy_blob, create_parent_parser, delete_container, delete_file, delete_folder,  \
+     extract_common_path, move_prep, setup_arguments
+from argparse import ArgumentParser, RawTextHelpFormatter
+import coloredlogs
+import logging
+import sys
+import os
+
+
+class AzureContainerMove(object):
+
+    def main(self):
+        # Validate the container names, and prepare all the necessary clients
+        self.container_name, self.target_container, self.blob_service_client, self.source_container_client, \
+            self.target_container_client = move_prep(
+                passphrase=self.passphrase,
+                account_name=self.account_name,
+                container_name=self.container_name,
+                target_container=self.target_container)
+        # Rename (move) the container
+        self.move_container(source_container_client=self.source_container_client,
+                            blob_service_client=self.blob_service_client,
+                            container_name=self.container_name,
+                            target_container=self.target_container,
+                            path=self.path,
+                            storage_tier=self.storage_tier)
+        # Delete the original container once the copy is complete
+        delete_container(blob_service_client=self.blob_service_client,
+                         container_name=self.container_name,
+                         account_name=self.account_name)
+
+    @staticmethod
+    def move_container(source_container_client, blob_service_client, container_name, target_container, path,
+                       storage_tier):
+        """
+        Rename (move) the specified container in Azure storage
+        :param source_container_client: type azure.storage.blob.BlobServiceClient.ContainerClient for source container
+        :param blob_service_client: type: azure.storage.blob.BlobServiceClient
+        :param container_name: type str: Name of the container in which the folder is located
+        :param target_container: type str: Name of the container into which the folder is to be moved
+        :param path: type str: Path of folders in which the files are to be placed
+        :param storage_tier: type str: Storage tier to use for the container
+        """
+        # Create a generator containing all the blobs in the container
+        generator = source_container_client.list_blobs()
+        for blob_file in generator:
+            # Copy the file to the new container
+            copy_blob(blob_file=blob_file,
+                      blob_service_client=blob_service_client,
+                      container_name=container_name,
+                      target_container=target_container,
+                      path=path,
+                      storage_tier=storage_tier,
+                      category='container')
+
+    def __init__(self, container_name, account_name, passphrase, target_container, path, storage_tier):
+        # Set the container name variable
+        self.container_name = container_name
+        # Initialise necessary class variables
+        self.passphrase = passphrase
+        self.account_name = account_name
+        self.target_container = target_container
+        self.path = path
+        self.storage_tier = storage_tier
+        self.connect_str = str()
+        self.blob_service_client = None
+        self.source_container_client = None
+        self.target_container_client = None
+
+
+class AzureMove(object):
+
+    def main(self):
+        # Validate the container names, and prepare all the necessary clients
+        self.container_name, self.target_container, self.blob_service_client, self.source_container_client, \
+            self.target_container_client = move_prep(
+                passphrase=self.passphrase,
+                account_name=self.account_name,
+                container_name=self.container_name,
+                target_container=self.target_container)
+        # Run the proper method depending on whether a file or a folder is requested
+        if self.category == 'file':
+            self.move_file(source_container_client=self.source_container_client,
+                           object_name=self.object_name,
+                           blob_service_client=self.blob_service_client,
+                           container_name=self.container_name,
+                           target_container=self.target_container,
+                           path=self.path,
+                           storage_tier=self.storage_tier)
+            delete_file(container_client=self.source_container_client,
+                        object_name=self.object_name,
+                        blob_service_client=self.blob_service_client,
+                        container_name=self.container_name)
+        elif self.category == 'folder':
+            self.move_folder(source_container_client=self.source_container_client,
+                             object_name=self.object_name,
+                             blob_service_client=self.blob_service_client,
+                             container_name=self.container_name,
+                             target_container=self.target_container,
+                             path=self.path,
+                             category=self.category,
+                             storage_tier=self.storage_tier)
+            delete_folder(container_client=self.source_container_client,
+                          object_name=self.object_name,
+                          blob_service_client=self.blob_service_client,
+                          container_name=self.container_name,
+                          account_name=self.account_name)
+        else:
+            logging.error(f'Something is wrong. There is no {self.category} option available')
+            raise SystemExit
+
+    @staticmethod
+    def move_file(source_container_client, object_name, blob_service_client, container_name, target_container,
+                  path, storage_tier):
+        """
+        Move the specified file to the desired container in Azure storage
+        :param source_container_client: type azure.storage.blob.BlobServiceClient.ContainerClient for source container
+        :param object_name: type str: Name and path of folder to move in Azure storage
+        :param blob_service_client: type: azure.storage.blob.BlobServiceClient
+        :param container_name: type str: Name of the container in which the folder is located
+        :param target_container: type str: Name of the container into which the folder is to be moved
+        :param path: type str: Path of folders in which the files are to be placed
+        :param storage_tier: type str: Storage tier to use for the file
+        """
+        # Create a generator containing all the blobs in the container
+        generator = source_container_client.list_blobs()
+        # Create a boolean to determine if the blob has been located
+        present = False
+        for blob_file in generator:
+            # Filter for the blob name
+            if blob_file.name == object_name:
+                # Update the blob presence variable
+                present = True
+                # Copy the file to the new container
+                copy_blob(blob_file=blob_file,
+                          blob_service_client=blob_service_client,
+                          container_name=container_name,
+                          target_container=target_container,
+                          path=path,
+                          storage_tier=storage_tier)
+        # Send a warning to the user that the blob could not be found
+        if not present:
+            logging.error(f'Could not locate the desired file {object_name}')
+            raise SystemExit
+
+    @staticmethod
+    def move_folder(source_container_client, object_name, blob_service_client, container_name, target_container, path,
+                    storage_tier, category):
+        """
+        Move the specified folder (and its contents) to the desired container in Azure storage
+        :param source_container_client: type azure.storage.blob.BlobServiceClient.ContainerClient for source container
+        :param object_name: type str: Name and path of folder to move in Azure storage
+        :param blob_service_client: type: azure.storage.blob.BlobServiceClient
+        :param container_name: type str: Name of the container in which the folder is located
+        :param target_container: type str: Name of the container into which the folder is to be moved
+        :param path: type str: Path of folders in which the files are to be placed
+        :param storage_tier: type str: Storage tier to use for the moved folder
+        :param category: type str: Category of object to be copied. Limited to file or folder
+        """
+        # Create a generator containing all the blobs in the container
+        generator = source_container_client.list_blobs()
+        # Create a boolean to determine if the blob has been located
+        present = False
+        for blob_file in generator:
+            # Extract the common path between the current file and the requested folder
+            common_path = extract_common_path(object_name=object_name,
+                                              blob_file=blob_file)
+            # Only copy the file if there is a common path between the object path and the blob path (they match)
+            if common_path is not None:
+                # Update the blob presence variable
+                present = True
+                # Copy the file to the new container
+                copy_blob(blob_file=blob_file,
+                          blob_service_client=blob_service_client,
+                          container_name=container_name,
+                          target_container=target_container,
+                          path=path,
+                          object_name=object_name,
+                          category=category,
+                          common_path=common_path,
+                          storage_tier=storage_tier)
+        # Send a warning to the user that the blob could not be found
+        if not present:
+            logging.error(f'Could not locate the desired folder {object_name}')
+            raise SystemExit
+
+    def __init__(self, object_name, container_name, account_name, passphrase, target_container, path,
+                 storage_tier, category):
+        self.object_name = object_name
+        # Set the container name variable
+        self.container_name = container_name
+        # Initialise necessary class variables
+        self.passphrase = passphrase
+        self.account_name = account_name
+        self.target_container = target_container
+        self.path = path
+        self.storage_tier = storage_tier
+        self.category = category
+        self.connect_str = str()
+        self.blob_service_client = None
+        self.source_container_client = None
+        self.target_container_client = None
+
+
+def container_move(args):
+    """
+    Run the AzureContainerMove method
+    :param args: type ArgumentParser arguments
+    """
+    logging.info(f'Renaming container {args.container_name} to {args.target_container} in Azure storage '
+                 f'account {args.account_name}')
+    move_container = AzureContainerMove(container_name=args.container_name,
+                                        account_name=args.account_name,
+                                        passphrase=args.passphrase,
+                                        target_container=args.target_container,
+                                        path=args.reset_path,
+                                        storage_tier=args.storage_tier)
+    move_container.main()
+
+
+def file_move(args):
+    """
+    Run the AzureMove method for a file
+    :param args: type ArgumentParser arguments
+    """
+    logging.info(f'Moving file {args.file} from {args.container_name} to {args.target_container} in Azure storage '
+                 f'account {args.account_name}')
+    move_file = AzureMove(object_name=args.file,
+                          container_name=args.container_name,
+                          account_name=args.account_name,
+                          passphrase=args.passphrase,
+                          target_container=args.target_container,
+                          path=args.reset_path,
+                          storage_tier=args.storage_tier,
+                          category='file')
+    move_file.main()
+
+
+def folder_move(args):
+    """
+    Run the AzureMove method for a folder
+    :param args: type ArgumentParser arguments
+    """
+    logging.info(f'Moving folder {args.folder} from {args.container_name} to {args.target_container} in Azure storage '
+                 f'account {args.account_name}')
+    move_folder = AzureMove(object_name=args.folder,
+                            container_name=args.container_name,
+                            account_name=args.account_name,
+                            passphrase=args.passphrase,
+                            target_container=args.target_container,
+                            path=args.reset_path,
+                            storage_tier=args.storage_tier,
+                            category='folder')
+    move_folder.main()
+
+
+def cli():
+    parser = ArgumentParser(description='Move containers, files, or folders in Azure storage')
+    # Create the parental parser, and the subparser
+    subparsers, parent_parser = create_parent_parser(parser=parser)
+    parent_parser.add_argument('-t', '--target_container',
+                               required=True,
+                               help='The target container to which the container/file/folder is to be moved '
+                                    '(this can be the same as the container_name if you want to move a file/folder'
+                                    ' within a container')
+    parent_parser.add_argument('-r', '--reset_path',
+                               type=str,
+                               help='Set the path of the container/file/folder within a folder in the target container '
+                                    'e.g. sequence_data/220202-m05722. If you want to place it directly in the '
+                                    'container without any nesting, use or \'\'')
+    parent_parser.add_argument('-s', '--storage_tier',
+                               type=str,
+                               default='Hot',
+                               choices=['Hot', 'Cool', 'Archive'],
+                               metavar='STORAGE_TIER',
+                               help='Set the storage tier for the container/file/folder to be moved. '
+                                    'Options are "Hot", "Cool", and "Archive". Default is Hot')
+    # Container move subparser
+    container_move_subparser = subparsers.add_parser(parents=[parent_parser],
+                                                     name='container',
+                                                     description='Move a container in Azure storage',
+                                                     formatter_class=RawTextHelpFormatter,
+                                                     help='Move a container in Azure storage')
+    container_move_subparser.set_defaults(func=container_move)
+    # File move subparser
+    file_move_subparser = subparsers.add_parser(parents=[parent_parser],
+                                                name='file',
+                                                description='Move a file within Azure storage',
+                                                formatter_class=RawTextHelpFormatter,
+                                                help='Move a file within Azure storage')
+    file_move_subparser.add_argument('-f', '--file',
+                                     type=str,
+                                     required=True,
+                                     help='Name of blob file to move in Azure storage. '
+                                          'e.g. 2022-SEQ-0001_S1_L001_R1_001.fastq.gz')
+    file_move_subparser.set_defaults(func=file_move)
+    # Folder move subparser
+    folder_move_subparser = subparsers.add_parser(parents=[parent_parser],
+                                                  name='folder',
+                                                  description='Move a folder within Azure storage',
+                                                  formatter_class=RawTextHelpFormatter,
+                                                  help='Move a folder within Azure storage')
+    folder_move_subparser.add_argument('-f', '--folder',
+                                       type=str,
+                                       required=True,
+                                       help='Name of folder to move in Azure storage. '
+                                            'e.g. InterOp')
+    folder_move_subparser.set_defaults(func=folder_move)
+    # Set up the arguments, and run the appropriate subparser
+    arguments = setup_arguments(parser=parser)
+    # Return to the requested logging level, as it has been increased to WARNING to suppress the log being filled with
+    # information from azure.core.pipeline.policies.http_logging_policy
+    coloredlogs.install(level=arguments.verbosity.upper())
+    logging.info('Move complete')
+    # Prevent the arguments being printed to the console (they are returned in order for the tests to work)
+    sys.stderr = open(os.devnull, 'w')
+    return arguments
+
+
+if __name__ == '__main__':
+    cli()

Azure/AzureStorage/azure_storage/azure_sas.py

@@ -0,0 +1,389 @@
+#!/usr/bin/env python
+from azure_storage.methods import create_blob_sas, create_parent_parser, sas_prep, setup_arguments, write_sas
+from argparse import ArgumentParser, RawTextHelpFormatter
+import coloredlogs
+import logging
+import azure
+import sys
+import os
+
+
+class AzureContainerSAS(object):
+
+    def main(self):
+        # Validate container name, retrieve connection string, extract account key, create blob service client and
+        # container clients
+        self.container_name, \
+            self.connect_str, \
+            self.account_key, \
+            self.blob_service_client, \
+            self.container_client = sas_prep(container_name=self.container_name,
+                                             passphrase=self.passphrase,
+                                             account_name=self.account_name,
+                                             create=False)
+        # Create the SAS URLs for the files in the container
+        self.sas_urls = self.container_sas(container_client=self.container_client,
+                                           account_name=self.account_name,
+                                           container_name=self.container_name,
+                                           account_key=self.account_key,
+                                           expiry=self.expiry,
+                                           sas_urls=self.sas_urls)
+        # Return to the requested logging level, as it has been increased to WARNING to suppress the log being
+        # filled with information from azure.core.pipeline.policies.http_logging_policy
+        coloredlogs.install(level=self.verbosity.upper())
+        write_sas(output_file=self.output_file,
+                  sas_urls=self.sas_urls)
+        # Write the SAS URLs to the output file
+        write_sas(output_file=self.output_file,
+                  sas_urls=self.sas_urls)
+
+    @staticmethod
+    def container_sas(container_client, account_name, container_name, account_key, expiry, sas_urls):
+        """
+        Create SAS URLs for all files in the container
+        :param container_client: type azure.storage.blob.BlobServiceClient.ContainerClient
+        :param account_name: type str: Name of the Azure storage account
+        :param container_name: type str: Name of the container of interest
+        :param account_key: type str: Account key of Azure storage account
+        :param expiry: type int: Number of days that the SAS URL will be valid
+        :param sas_urls: type dict: Dictionary of file name: SAS URL (empty)
+        :return: populated sas_urls
+        """
+        # Create a generator containing all the blobs in the container
+        generator = container_client.list_blobs()
+        try:
+            # Hide the INFO-level messages sent to the logger from Azure by increasing the logging level to WARNING
+            logging.getLogger().setLevel(logging.WARNING)
+            for blob_file in generator:
+                # Create the SAS URLs
+                sas_urls = create_blob_sas(blob_file=blob_file,
+                                           account_name=account_name,
+                                           container_name=container_name,
+                                           account_key=account_key,
+                                           expiry=expiry,
+                                           sas_urls=sas_urls)
+        except azure.core.exceptions.ResourceNotFoundError:
+            logging.error(f' The specified container, {container_name}, does not exist.')
+            raise SystemExit
+        return sas_urls
+
+    def __init__(self, container_name, output_file, account_name, passphrase, expiry, verbosity):
+        # Set the container name variable
+        self.container_name = container_name
+        # Output file
+        if output_file.startswith('~'):
+            self.output_file = os.path.abspath(os.path.expanduser(os.path.join(output_file)))
+        else:
+            self.output_file = os.path.abspath(os.path.join(output_file))
+        # Ensure that the output file can be used
+        if not os.path.isfile(self.output_file):
+            try:
+                # Create the parental directory for the output file as required
+                os.makedirs(os.path.dirname(self.output_file), exist_ok=True)
+            except PermissionError:
+                logging.error(f'Insufficient permissions to create output file {self.output_file}')
+                raise SystemExit
+            try:
+                open(self.output_file, 'w').close()
+            except IsADirectoryError:
+                logging.error(f'A directory or an empty file name was provided for the output file {self.output_file}')
+                raise SystemExit
+            except PermissionError:
+                logging.error(f'Insufficient permissions to create output file {self.output_file}')
+                raise SystemExit
+        else:
+            open(self.output_file, 'w').close()
+        # Ensure that the expiry provided is valid
+        try:
+            assert 0 < expiry < 366
+        except AssertionError:
+            logging.error(f'The provided expiry ({expiry}) is invalid. It must be between 1 and 365')
+            raise SystemExit
+        self.expiry = expiry
+        self.verbosity = verbosity
+        # Initialise necessary class variables
+        self.passphrase = passphrase
+        self.account_name = account_name
+        self.account_key = str()
+        self.connect_str = str()
+        self.blob_service_client = None
+        self.container_client = None
+        self.sas_urls = dict()
+
+
+class AzureSAS(object):
+
+    def main(self):
+        # Validate container name, retrieve connection string, extract account key, create blob service client and
+        # container clients
+        self.container_name, \
+            self.connect_str, \
+            self.account_key, \
+            self.blob_service_client, \
+            self.container_client = sas_prep(container_name=self.container_name,
+                                             passphrase=self.passphrase,
+                                             account_name=self.account_name,
+                                             create=False)
+        # Run the proper method depending on whether a file or a folder is requested
+        if self.category == 'file':
+            self.sas_urls = self.file_sas(container_client=self.container_client,
+                                          account_name=self.account_name,
+                                          container_name=self.container_name,
+                                          object_name=self.object_name,
+                                          account_key=self.account_key,
+                                          expiry=self.expiry,
+                                          sas_urls=self.sas_urls)
+        elif self.category == 'folder':
+            self.sas_urls = self.folder_sas(container_client=self.container_client,
+                                            account_name=self.account_name,
+                                            container_name=self.container_name,
+                                            object_name=self.object_name,
+                                            account_key=self.account_key,
+                                            expiry=self.expiry,
+                                            sas_urls=self.sas_urls)
+        else:
+            logging.error(f'Something is wrong. There is no {self.category} option available')
+            raise SystemExit
+        # Return to the requested logging level, as it has been increased to WARNING to suppress the log being
+        # filled with information from azure.core.pipeline.policies.http_logging_policy
+        coloredlogs.install(level=self.verbosity.upper())
+        write_sas(output_file=self.output_file,
+                  sas_urls=self.sas_urls)
+
+    @staticmethod
+    def file_sas(container_client, account_name, container_name, object_name, account_key, expiry, sas_urls):
+        """
+        Create a SAS URL for the specified file in Azure storage
+        :param container_client: type azure.storage.blob.BlobServiceClient.ContainerClient
+        :param account_name: type str: Name of the Azure storage account
+        :param container_name: type str: Name of the container of interest
+        :param object_name: type str: Name and path of file for which a SAS URL is to be created
+        :param account_key: type str: Account key of Azure storage account
+        :param expiry: type int: Number of days that the SAS URL will be valid
+        :param sas_urls: type dict: Dictionary of file name: SAS URL (empty)
+        :return: populated sas_urls
+        """
+        # Create a generator containing all the blobs in the container
+        generator = container_client.list_blobs()
+        # Create a boolean to determine if the blob has been located
+        present = False
+        # Hide the INFO-level messages sent to the logger from Azure by increasing the logging level to WARNING
+        logging.getLogger().setLevel(logging.WARNING)
+        for blob_file in generator:
+            # Filter for the blob name
+            if blob_file.name == object_name:
+                # Update the blob presence variable
+                present = True
+                sas_urls = create_blob_sas(blob_file=blob_file,
+                                           account_name=account_name,
+                                           container_name=container_name,
+                                           account_key=account_key,
+                                           expiry=expiry,
+                                           sas_urls=sas_urls)
+        # Send a warning to the user that the blob could not be found
+        if not present:
+            logging.error(f'Could not locate the desired file {object_name} in container {container_name}')
+            raise SystemExit
+        return sas_urls
+
+    @staticmethod
+    def folder_sas(container_client, account_name, container_name, object_name, account_key, expiry, sas_urls):
+        """
+        Create SAS URLs for all the files in the specified folder in Azure storage
+        :param container_client: type azure.storage.blob.BlobServiceClient.ContainerClient
+        :param account_name: type str: Name of the Azure storage account
+        :param container_name: type str: Name of the container of interest
+        :param object_name: type str: Name and path of folder containing files for which SAS URLs are to be created
+        :param account_key: type str: Account key of Azure storage account
+        :param expiry: type int: Number of days that the SAS URL will be valid
+        :param sas_urls: type dict: Dictionary of file name: SAS URL (empty)
+        :return: populated sas_urls
+        """
+        # Create a generator containing all the blobs in the container
+        generator = container_client.list_blobs()
+        # Boolean to track whether the folder was located
+        present = False
+        # Hide the INFO-level messages sent to the logger from Azure by increasing the logging level to WARNING
+        logging.getLogger().setLevel(logging.WARNING)
+        for blob_file in generator:
+            # Create the path of the file by adding the container name to the path of the file
+            blob_path = os.path.join(container_name, os.path.split(blob_file.name)[0])
+            # Ensure that the supplied folder path is present in the blob path
+            if os.path.normpath(object_name) in os.path.normpath(blob_path):
+                # Update the folder presence boolean
+                present = True
+                sas_urls = create_blob_sas(blob_file=blob_file,
+                                           account_name=account_name,
+                                           container_name=container_name,
+                                           account_key=account_key,
+                                           expiry=expiry,
+                                           sas_urls=sas_urls)
+        # Send a warning to the user that the blob could not be found
+        if not present:
+            logging.error(f'Could not locate the desired folder {object_name} in container {container_name}')
+            raise SystemExit
+        return sas_urls
+
+    def __init__(self, object_name, container_name, output_file, account_name, passphrase, expiry, verbosity, category):
+        # Set the name of the file/folder of interest
+        self.object_name = object_name
+        # Set the container name variable
+        self.container_name = container_name
+        # Output file
+        if output_file.startswith('~'):
+            self.output_file = os.path.abspath(os.path.expanduser(os.path.join(output_file)))
+        else:
+            self.output_file = os.path.abspath(os.path.join(output_file))
+        # Ensure that the output file can be used
+        if not os.path.isfile(self.output_file):
+            try:
+                # Create the parental directory for the output file as required
+                os.makedirs(os.path.dirname(self.output_file), exist_ok=True)
+            except PermissionError:
+                logging.error(f'Insufficient permissions to create output file {self.output_file}')
+                raise SystemExit
+            try:
+                open(self.output_file, 'w').close()
+            except IsADirectoryError:
+                logging.error(f'A directory or an empty file name was provided for the output file {self.output_file}')
+                raise SystemExit
+            except PermissionError:
+                logging.error(f'Insufficient permissions to create output file {self.output_file}')
+                raise SystemExit
+        else:
+            open(self.output_file, 'w').close()
+        # Ensure that the expiry provided is valid
+        try:
+            assert 0 < expiry < 366
+        except AssertionError:
+            logging.error(f'The provided expiry ({expiry}) is invalid. It must be between 1 and 365')
+            raise SystemExit
+        self.expiry = expiry
+        self.verbosity = verbosity
+        self.category = category
+        # Initialise necessary class variables
+        self.passphrase = passphrase
+        self.account_name = account_name
+        self.account_key = str()
+        self.connect_str = str()
+        self.blob_service_client = None
+        self.container_client = None
+        self.sas_urls = dict()
+
+
+def container_sas(args):
+    """
+   Run the AzureContainerSAS method
+   :param args: type ArgumentParser arguments
+   """
+    logging.info(f'Creating SAS URLs for all files in Azure container {args.container_name}')
+    # Create the container SAS object
+    sas = AzureContainerSAS(container_name=args.container_name,
+                            output_file=args.output_file,
+                            account_name=args.account_name,
+                            passphrase=args.passphrase,
+                            expiry=args.expiry,
+                            verbosity=args.verbosity)
+    sas.main()
+
+
+def file_sas(args):
+    """
+    Run the AzureSAS class for a file
+    :param args: type ArgumentParser arguments
+    """
+    logging.info(f'Creating SAS URL for {args.file} in container {args.container_name} Azure storage account '
+                 f'{args.account_name}')
+    # Create the file SAS object
+    sas_file = AzureSAS(object_name=args.file,
+                        container_name=args.container_name,
+                        output_file=args.output_file,
+                        account_name=args.account_name,
+                        passphrase=args.passphrase,
+                        expiry=args.expiry,
+                        verbosity=args.verbosity,
+                        category='file')
+    sas_file.main()
+
+
+def folder_sas(args):
+    """
+    Run the AzureSAS class for a folder
+    :param args: type ArgumentParser arguments
+    """
+    logging.info(f'Creating SAS URLs for all files in folder {args.folder} in container {args.container_name} in '
+                 f'Azure storage account '
+                 f'{args.account_name}')
+    # Create the folder SAS object
+    sas_folder = AzureSAS(object_name=args.folder,
+                          container_name=args.container_name,
+                          output_file=args.output_file,
+                          account_name=args.account_name,
+                          passphrase=args.passphrase,
+                          expiry=args.expiry,
+                          verbosity=args.verbosity,
+                          category='folder')
+    sas_folder.main()
+
+
+def cli():
+    parser = ArgumentParser(description='Create shared access signatures (SAS) URLs for containers/files/folders in '
+                                        'Azure storage. Note that each file in a container/folder has to be downloaded '
+                                        'separately, so if there are 1000 files in the container, 1000 SAS URLs will '
+                                        'be provided')
+    # Create the parental parser, and the subparser
+    subparsers, parent_parser = create_parent_parser(parser=parser)
+    parent_parser.add_argument('-e', '--expiry',
+                               default=10,
+                               type=int,
+                               help='The number of days that the SAS URL will be valid. The minimum is 1, and the '
+                                    'maximum is 365. The default is 10.')
+    parent_parser.add_argument('-o', '--output_file',
+                               default=os.path.join(os.getcwd(), 'sas.txt'),
+                               help='Name and path of file in which the SAS URLs are to be saved. '
+                                    'Default is $CWD/sas.txt')
+    # Container SAS subparser
+    container_subparser = subparsers.add_parser(parents=[parent_parser],
+                                                name='container',
+                                                description='Create SAS URLs for all files in a container in Azure '
+                                                            'storage',
+                                                formatter_class=RawTextHelpFormatter,
+                                                help='Create SAS URLs for all files in a container in Azure storage')
+    container_subparser.set_defaults(func=container_sas)
+    # File SAS subparser
+    file_subparser = subparsers.add_parser(parents=[parent_parser],
+                                           name='file',
+                                           description='Create a SAS URL for a file in Azure storage',
+                                           formatter_class=RawTextHelpFormatter,
+                                           help='Create a SAS URL for a file in Azure storage')
+    file_subparser.add_argument('-f', '--file',
+                                type=str,
+                                required=True,
+                                help='Path of file in Azure storage from which a SAS URL is to be created. '
+                                     'e.g. 2022-SEQ-0001_S1_L001_R1_001.fastq.gz')
+    file_subparser.set_defaults(func=file_sas)
+    # Folder SAS subparser
+    folder_subparser = subparsers.add_parser(parents=[parent_parser],
+                                             name='folder',
+                                             description='Create SAS URLs for all files in a folder in Azure storage',
+                                             formatter_class=RawTextHelpFormatter,
+                                             help='Create SAS URLs for all files in a folder in Azure storage')
+    folder_subparser.add_argument('-f', '--folder',
+                                  type=str,
+                                  required=True,
+                                  help='Name of the folder for which SAS URLs are to be created for all files. '
+                                       'e.g. InterOp')
+    folder_subparser.set_defaults(func=folder_sas)
+    # Set up the arguments, and run the appropriate subparser
+    arguments = setup_arguments(parser=parser)
+    # Return to the requested logging level, as it has been increased to WARNING to suppress the log being filled with
+    # information from azure.core.pipeline.policies.http_logging_policy
+    coloredlogs.install(level=arguments.verbosity.upper())
+    logging.info('SAS creation complete')
+    # Prevent the arguments being printed to the console (they are returned in order for the tests to work)
+    sys.stderr = open(os.devnull, 'w')
+    return arguments
+
+
+if __name__ == '__main__':
+    cli()

Azure/AzureStorage/azure_storage/azure_tier.py

@@ -0,0 +1,277 @@
+#!/usr/bin/env python
+from azure_storage.methods import client_prep, create_blob_client, create_parent_parser, setup_arguments
+from argparse import ArgumentParser, RawTextHelpFormatter
+import coloredlogs
+import logging
+import azure
+import sys
+import os
+
+
+class AzureContainerTier(object):
+
+    def main(self):
+        self.container_name, self.connect_str, self.blob_service_client, self.container_client = \
+            client_prep(container_name=self.container_name,
+                        passphrase=self.passphrase,
+                        account_name=self.account_name,
+                        create=False)
+        self.container_tier(container_client=self.container_client,
+                            blob_service_client=self.blob_service_client,
+                            container_name=self.container_name,
+                            storage_tier=self.storage_tier)
+
+    @staticmethod
+    def container_tier(container_client, blob_service_client, container_name, storage_tier):
+        """
+        Set the storage tier for the specified container in Azure storage
+        :param container_client: type azure.storage.blob.BlobServiceClient.ContainerClient
+        :param blob_service_client: type: azure.storage.blob.BlobServiceClient
+        :param container_name: type str: Name of the container of interest
+        :param storage_tier: type str: Storage tier to use for the container
+        """
+        # Create a generator containing all the blobs in the container
+        generator = container_client.list_blobs()
+        try:
+            # Hide the INFO-level messages sent to the logger from Azure by increasing the logging level to WARNING
+            logging.getLogger().setLevel(logging.WARNING)
+            for blob_file in generator:
+                # Create the blob client
+                blob_client = create_blob_client(blob_service_client=blob_service_client,
+                                                 container_name=container_name,
+                                                 blob_file=blob_file)
+                # Set the storage tier
+                blob_client.set_standard_blob_tier(standard_blob_tier=storage_tier)
+        except azure.core.exceptions.ResourceNotFoundError:
+            logging.error(f' The specified container, {container_name}, does not exist.')
+            raise SystemExit
+
+    def __init__(self, container_name, account_name, passphrase, storage_tier):
+        # Set the container name variable
+        self.container_name = container_name
+        # Initialise necessary class variables
+        self.passphrase = passphrase
+        self.account_name = account_name
+        self.storage_tier = storage_tier
+        self.connect_str = str()
+        self.blob_service_client = None
+        self.container_client = None
+
+
+class AzureTier(object):
+
+    def main(self):
+        self.container_name, self.connect_str, self.blob_service_client, self.container_client = \
+            client_prep(container_name=self.container_name,
+                        passphrase=self.passphrase,
+                        account_name=self.account_name,
+                        create=False)
+        # Run the proper method depending on whether a file or a folder is requested
+        if self.category == 'file':
+            self.file_tier(container_client=self.container_client,
+                           object_name=self.object_name,
+                           blob_service_client=self.blob_service_client,
+                           container_name=self.container_name,
+                           storage_tier=self.storage_tier)
+        elif self.category == 'folder':
+            self.folder_tier(container_client=self.container_client,
+                             object_name=self.object_name,
+                             blob_service_client=self.blob_service_client,
+                             container_name=self.container_name,
+                             storage_tier=self.storage_tier)
+        else:
+            logging.error(f'Something is wrong. There is no {self.category} option available')
+            raise SystemExit
+
+    @staticmethod
+    def file_tier(container_client, object_name, blob_service_client, container_name, storage_tier):
+        """
+        Set the storage tier for the specified file in Azure storage
+        :param container_client: type azure.storage.blob.BlobServiceClient.ContainerClient
+        :param object_name: type str: Name and path of file for which a SAS URL is to be created
+        :param blob_service_client: type: azure.storage.blob.BlobServiceClient
+        :param container_name: type str: Name of the container of interest
+        :param storage_tier: type str: Storage tier to use for the file
+        """
+        # Create a generator containing all the blobs in the container
+        generator = container_client.list_blobs()
+        # Create a boolean to determine if the blob has been located
+        present = False
+        # Hide the INFO-level messages sent to the logger from Azure by increasing the logging level to WARNING
+        logging.getLogger().setLevel(logging.WARNING)
+        try:
+            for blob_file in generator:
+                # Filter for the blob name
+                if blob_file.name == object_name:
+                    # Update the blob presence variable
+                    present = True
+                    # Create the blob client
+                    blob_client = create_blob_client(blob_service_client=blob_service_client,
+                                                     container_name=container_name,
+                                                     blob_file=blob_file)
+                    # Set the storage tier
+                    blob_client.set_standard_blob_tier(standard_blob_tier=storage_tier)
+            # Send an error to the user that the blob could not be found
+            if not present:
+                logging.error(f'Could not locate the desired file {object_name} in {container_name}')
+                raise SystemExit
+        except azure.core.exceptions.ResourceNotFoundError:
+            logging.error(f' The specified container, {container_name}, does not exist.')
+            raise SystemExit
+
+    @staticmethod
+    def folder_tier(container_client, object_name, blob_service_client, container_name, storage_tier):
+        """
+        Set the storage tier for the specified folder in Azure storage
+        :param container_client: type azure.storage.blob.BlobServiceClient.ContainerClient
+        :param object_name: type str: Name and path of file for which a SAS URL is to be created
+        :param blob_service_client: type: azure.storage.blob.BlobServiceClient
+        :param container_name: type str: Name of the container of interest
+        :param storage_tier: type str: Storage tier to use for the folder
+        """
+        # Create a generator containing all the blobs in the container
+        generator = container_client.list_blobs()
+        # Create a boolean to determine if the blob has been located
+        present = False
+        # Hide the INFO-level messages sent to the logger from Azure by increasing the logging level to WARNING
+        logging.getLogger().setLevel(logging.WARNING)
+        try:
+            for blob_file in generator:
+                # Create the path of the file by extracting the path of the file
+                blob_path = os.path.join(os.path.split(blob_file.name)[0])
+                # Ensure that the supplied folder path is present in the blob path
+                if os.path.normpath(object_name) in os.path.normpath(blob_path):
+                    # Update the folder presence boolean
+                    present = True
+                    # Create the blob client
+                    blob_client = create_blob_client(blob_service_client=blob_service_client,
+                                                     container_name=container_name,
+                                                     blob_file=blob_file)
+                    # Set the storage tier
+                    blob_client.set_standard_blob_tier(standard_blob_tier=storage_tier)
+            # Send an error to the user that the folder could not be found
+            if not present:
+                logging.error(f'Could not locate the desired folder {object_name} in container {container_name}')
+                raise SystemExit
+        except azure.core.exceptions.ResourceNotFoundError:
+            logging.error(f' The specified container, {container_name}, does not exist.')
+            raise SystemExit
+
+    def __init__(self, object_name, container_name, account_name, passphrase, storage_tier, category):
+        # Set the name of the file/folder to have its storage tier set
+        self.object_name = object_name
+        # Set the container name variable
+        self.container_name = container_name
+        # Initialise necessary class variables
+        self.passphrase = passphrase
+        self.account_name = account_name
+        self.storage_tier = storage_tier
+        self.category = category
+        self.connect_str = str()
+        self.blob_service_client = None
+        self.container_client = None
+
+
+def container_tier(args):
+    """
+    Run the AzureContainerTier method
+    :param args: type ArgumentParser arguments
+        """
+    logging.info(f'Setting the storage tier for Azure container {args.container_name} to {args.storage_tier}')
+    # Create the container tier object
+    container_tier_set = AzureContainerTier(container_name=args.container_name,
+                                            account_name=args.account_name,
+                                            passphrase=args.passphrase,
+                                            storage_tier=args.storage_tier)
+    container_tier_set.main()
+
+
+def file_tier(args):
+    """
+    Run the AzureTier method for a file
+    :param args: type ArgumentParser arguments
+    """
+    logging.info(f'Setting the storage tier for file {args.file} in Azure container {args.container_name} to '
+                 f'{args.storage_tier}')
+    # Create the file tier object
+    file_tier_set = AzureTier(container_name=args.container_name,
+                              object_name=args.file,
+                              account_name=args.account_name,
+                              passphrase=args.passphrase,
+                              storage_tier=args.storage_tier,
+                              category='file')
+    file_tier_set.main()
+
+
+def folder_tier(args):
+    """
+    Run the AzureTier method for a file
+    :param args: type ArgumentParser arguments
+    """
+    logging.info(f'Setting the storage tier for folder {args.folder} in Azure container {args.container_name} to '
+                 f'{args.storage_tier}')
+    # Create the folder tier object
+    folder_tier_set = AzureTier(container_name=args.container_name,
+                                object_name=args.folder,
+                                account_name=args.account_name,
+                                passphrase=args.passphrase,
+                                storage_tier=args.storage_tier,
+                                category='folder')
+    folder_tier_set.main()
+
+
+def cli():
+    parser = ArgumentParser(description='Set the storage tier of containers/files/folders in Azure storage')
+    # Create the parental parser, and the subparser
+    subparsers, parent_parser = create_parent_parser(parser=parser)
+    parent_parser.add_argument('-s', '--storage_tier',
+                               type=str,
+                               required=True,
+                               choices=['Hot', 'Cool', 'Archive'],
+                               metavar='STORAGE_TIER',
+                               help='Set the storage tier for a container/file/folder. Options are "Hot", '
+                                    '"Cool", and "Archive"')
+    # Container tier setting parser
+    container_subparser = subparsers.add_parser(parents=[parent_parser],
+                                                name='container',
+                                                description='Change the storage tier of a container in Azure storage',
+                                                formatter_class=RawTextHelpFormatter,
+                                                help='Change the storage tier of a container in Azure storage')
+    container_subparser.set_defaults(func=container_tier)
+    # File tier setting parser
+    file_subparser = subparsers.add_parser(parents=[parent_parser],
+                                           name='file',
+                                           description='Change the storage tier of a file in Azure storage',
+                                           formatter_class=RawTextHelpFormatter,
+                                           help='Change the storage tier of a file in Azure storage')
+    file_subparser.add_argument('-f', '--file',
+                                type=str,
+                                required=True,
+                                help='Name of file in Azure storage that will have its storage tier set'
+                                     'e.g. 220202-m05722/2022-SEQ-0001_S1_L001_R1_001.fastq.gz')
+    file_subparser.set_defaults(func=file_tier)
+    # Folder downloading subparser
+    folder_subparser = subparsers.add_parser(parents=[parent_parser],
+                                             name='folder',
+                                             description='Change the storage tier of a folder in Azure storage',
+                                             formatter_class=RawTextHelpFormatter,
+                                             help='Change the storage tier of a folder in Azure storage')
+    folder_subparser.add_argument('-f', '--folder',
+                                  type=str,
+                                  required=True,
+                                  help='Name of the folder in Azure storage that will have its storage tier set '
+                                       'e.g. InterOp')
+    folder_subparser.set_defaults(func=folder_tier)
+    # Set up the arguments, and run the appropriate subparser
+    arguments = setup_arguments(parser=parser)
+    # Return to the requested logging level, as it has been increased to WARNING to suppress the log being filled with
+    # information from azure.core.pipeline.policies.http_logging_policy
+    coloredlogs.install(level=arguments.verbosity.upper())
+    logging.info('Storage tier set')
+    # Prevent the arguments being printed to the console (they are returned in order for the tests to work)
+    sys.stderr = open(os.devnull, 'w')
+    return arguments
+
+
+if __name__ == '__main__':
+    cli()

Azure/AzureStorage/azure_storage/azure_upload.py

@@ -0,0 +1,257 @@
+#!/usr/bin/env python
+from azure_storage.methods import client_prep, create_blob_client, create_parent_parser, setup_arguments
+from argparse import ArgumentParser, RawTextHelpFormatter
+import coloredlogs
+import logging
+import azure
+import sys
+import os
+
+
+class AzureUpload(object):
+
+    def main(self):
+        self.container_name, self.connect_str, self.blob_service_client, self.container_client = \
+            client_prep(container_name=self.container_name,
+                        passphrase=self.passphrase,
+                        account_name=self.account_name)
+        # Hide the INFO-level messages sent to the logger from Azure by increasing the logging level to WARNING
+        logging.getLogger().setLevel(logging.WARNING)
+        # Run the proper method depending on whether a file or a folder is requested
+        if self.category == 'file':
+            # If the container doesn't exist, run the container creation method, and re-run the upload
+            self.upload_file(object_name=self.object_name,
+                             blob_service_client=self.blob_service_client,
+                             container_name=self.container_name,
+                             account_name=self.account_name,
+                             path=self.path,
+                             storage_tier=self.storage_tier)
+        elif self.category == 'folder':
+            self.upload_folder(object_name=self.object_name,
+                               blob_service_client=self.blob_service_client,
+                               container_name=self.container_name,
+                               account_name=self.account_name,
+                               path=self.path,
+                               storage_tier=self.storage_tier)
+
+    @staticmethod
+    def upload_file(object_name, blob_service_client, container_name, account_name, path, storage_tier):
+        """
+        Upload a single file to Azure storage
+        :param object_name: type str: Name and path of file/folder to download from Azure storage
+        :param blob_service_client: type: azure.storage.blob.BlobServiceClient
+        :param container_name: type str: Name of the container of interest
+        :param account_name: type str: Name of the Azure storage account
+        :param path: type str: Path of folders in which the files are to be placed
+        :param storage_tier: type str: Storage tier to use for the file
+        """
+        # Extract the name of the file from the provided name, as it may include the path
+        file_name = os.path.basename(object_name)
+        if path is not None:
+            file_name = os.path.join(path, file_name)
+        # Create a blob client for this file in the container in which it will be stored
+        blob_client = create_blob_client(blob_service_client=blob_service_client,
+                                         container_name=container_name,
+                                         blob_file=file_name)
+        # Attempt to upload the file to the specified container.
+        try:
+            # Read in the file data as binary
+            with open(object_name, "rb") as data:
+                # Upload the file data to the blob
+                blob_client.upload_blob(data)
+                # Set the storage tier
+                blob_client.set_standard_blob_tier(standard_blob_tier=storage_tier)
+        # If a file with that name already exists in that container, warn the user
+        except azure.core.exceptions.ResourceExistsError:
+            logging.warning(f'The file {file_name} already exists in container {container_name} in '
+                            f'storage account {account_name}')
+            raise SystemExit
+        # Despite the attempt to correct the container name, it may still be invalid
+        except azure.core.exceptions.HttpResponseError as e:
+            if 'ContainerNotFound' in str(e):
+                logging.warning(f'Could not create container {container_name}')
+                raise SystemExit
+        except FileNotFoundError:
+            logging.error(f'Could not find the specified file {object_name} to upload. Please ensure that the '
+                          f'supplied name and path are correct.')
+            raise SystemExit
+
+    @staticmethod
+    def upload_folder(object_name, blob_service_client, container_name, account_name, path, storage_tier):
+        """
+        Upload all the files (and sub-folders as applicable) in the specified folder to Azure storage
+        :param object_name: type str: Name and path of file/folder to download from Azure storage
+        :param blob_service_client: type: azure.storage.blob.BlobServiceClient
+        :param container_name: type str: Name of the container of interest
+        :param account_name: type str: Name of the Azure storage account
+        :param path: type str: Path of folders in which the files are to be placed
+        :param storage_tier: type str: Storage tier to use for the folder
+        """
+        # Use os.walk to find all the files and folders in the supplied directory
+        for root, dirs, files in os.walk(object_name):
+            # Determine the relative path for the current sub-folder to the supplied root folder by creating a list
+            # from the splitting of the root path using the OS-appropriate separator (os.sep) and slicing the list to
+            # remove the first entry (the root) e.g. outputs/files/reports, where 'outputs/files' is the supplied
+            # directory, would return 'files/reports'
+            rel_path = os.path.join(os.sep.join(root.split(os.sep)[1:]))
+            # Using the same logic as above, extract the root directory e.g. outputs/files/reports, where
+            # 'outputs/files' is the supplied  directory, would return 'outputs'
+            # root_path = root.split(os.sep)[0]
+            # Ensure that the root path starts with the appropriate separator when an absolute path is provided
+            # if object_name.startswith(os.sep):
+            #     root_path = os.sep + root_path
+            for file_name in files:
+                # If the path is supplied, the folders of interest must be extract in order to keep the original
+                # folder structure
+                if path is not None:
+                    # Set the target folder as the relative path between the root and the supplied folder name
+                    #  e.g. /home/users/files/folder/nested_folder and /home/users/files/folder would return
+                    # nested_folder, while identical root and folder would return a dot (.)
+                    target_folder = os.path.relpath(root, start=object_name.rstrip(os.sep))
+                    # If the target_folder is a dot, treat it as empty
+                    target_folder = target_folder if target_folder != '.' else ''
+                    # Create the target file in the container by joining the desired path, the target folder and the
+                    # name of the file
+                    target_file = os.path.join(path, target_folder, file_name)
+                # Add the file name to the calculated relative path to set the name of the blob in Azure storage e.g.
+                # files/reports/summary.tsv
+                else:
+                    target_file = os.path.join(rel_path, file_name)
+                # Create a blob client for this file using the supplied container name
+                blob_client = create_blob_client(blob_service_client=blob_service_client,
+                                                 container_name=container_name,
+                                                 blob_file=target_file)
+                # Set the local name and path of the file, so it can be opened
+                local_file = os.path.join(root, file_name)
+                # Attempt to upload the file to the specified container
+                try:
+                    # Re-add the root path to find the file on the local system
+                    with open(os.path.join(local_file), "rb") as data:
+                        # Upload the file to Azure storage
+                        blob_client.upload_blob(data)
+                        # Set the storage tier
+                        blob_client.set_standard_blob_tier(standard_blob_tier=storage_tier)
+                # Print a warning if a file with that name already exists in the specified container
+                except azure.core.exceptions.ResourceExistsError:
+                    logging.warning(f'The file {local_file} already exists in container {container_name} '
+                                    f'in storage account {account_name} as {target_file}')
+
+    def __init__(self, object_name, container_name, account_name, passphrase, path, storage_tier, category):
+        # Set the name of the file/folder to upload
+        self.object_name = object_name
+        if category == 'file':
+            try:
+                assert os.path.isfile(self.object_name)
+            except AssertionError:
+                logging.error(f'Cannot locate the specified file to upload: {self.object_name}')
+                raise SystemExit
+        elif category == 'folder':
+            try:
+                assert os.path.isdir(self.object_name)
+            except AssertionError:
+                logging.error(f'Cannot located the specified folder to upload: {self.object_name}')
+                raise SystemExit
+        else:
+            logging.error(f'Something is wrong. There is no {category} option available')
+            raise SystemExit
+        # Initialise necessary class variables
+        self.passphrase = passphrase
+        self.account_name = account_name
+        self.container_name = container_name
+        self.path = path
+        self.storage_tier = storage_tier
+        self.category = category
+        self.connect_str = str()
+        self.blob_service_client = None
+        self.container_client = None
+        self.retry = False
+
+
+def file_upload(args):
+    """
+    Run the AzureUpload class for a file
+    :param args: type ArgumentParser arguments
+    """
+    logging.info(f'Uploading {args.file} to container {args.container_name} in Azure storage account '
+                 f'{args.account_name}')
+    # Create the file_upload object
+    file_uploader = AzureUpload(object_name=args.file,
+                                account_name=args.account_name,
+                                container_name=args.container_name,
+                                passphrase=args.passphrase,
+                                path=args.reset_path,
+                                storage_tier=args.storage_tier,
+                                category='file')
+    file_uploader.main()
+
+
+def folder_upload(args):
+    """
+    Run the AzureUpload class for a folder
+    :param args: type ArgumentParser arguments
+    """
+    logging.info(f'Uploading folder (and its contents) {args.folder} to container {args.container_name} in Azure '
+                 f'storage account {args.account_name}')
+    folder_uploader = AzureUpload(object_name=args.folder,
+                                  account_name=args.account_name,
+                                  container_name=args.container_name,
+                                  passphrase=args.passphrase,
+                                  path=args.reset_path,
+                                  storage_tier=args.storage_tier,
+                                  category='folder')
+    folder_uploader.main()
+
+
+def cli():
+    parser = ArgumentParser(description='Upload files or folders to Azure storage')
+    # Create the parental parser, and the subparser
+    subparsers, parent_parser = create_parent_parser(parser=parser)
+    parent_parser.add_argument('-r', '--reset_path',
+                               type=str,
+                               help='Set the path of the file/folder within a folder in the target container '
+                                    'e.g. sequence_data/220202-m05722. If you want to place it directly in the '
+                                    'container without any nesting, use or \'\'')
+    parent_parser.add_argument('-s', '--storage_tier',
+                               type=str,
+                               default='Hot',
+                               choices=['Hot', 'Cool', 'Archive'],
+                               metavar='STORAGE_TIER',
+                               help='Set the storage tier for the file/folder to be uploaded. Options are "Hot", '
+                                    '"Cool", and "Archive". Default is Hot')
+    # File upload subparser
+    file_subparser = subparsers.add_parser(parents=[parent_parser],
+                                           name='file',
+                                           description='Upload a file to Azure storage',
+                                           formatter_class=RawTextHelpFormatter,
+                                           help='Upload a file to Azure storage')
+    file_subparser.add_argument('-f', '--file',
+                                type=str,
+                                required=True,
+                                help='Name and path of the file to upload to Azure storage.'
+                                     'e.g. /mnt/sequences/220202_M05722/2022-SEQ-0001_S1_L001_R1_001.fastq.gz')
+    file_subparser.set_defaults(func=file_upload)
+    # Folder upload subparser
+    folder_subparser = subparsers.add_parser(parents=[parent_parser],
+                                             name='folder',
+                                             description='Upload a folder to Azure storage',
+                                             formatter_class=RawTextHelpFormatter,
+                                             help='Upload a folder to Azure storage')
+    folder_subparser.add_argument('-f', '--folder',
+                                  type=str,
+                                  required=True,
+                                  help='Name and path of the folder to upload to Azure storage.'
+                                       'e.g. /mnt/sequences/220202_M05722/')
+    folder_subparser.set_defaults(func=folder_upload)
+    # Set up the arguments, and run the appropriate subparser
+    arguments = setup_arguments(parser=parser)
+    # Return to the requested logging level, as it has been increased to WARNING to suppress the log being filled with
+    # information from azure.core.pipeline.policies.http_logging_policy
+    coloredlogs.install(level=arguments.verbosity.upper())
+    logging.info('Upload complete')
+    # Prevent the arguments being printed to the console (they are returned in order for the tests to work)
+    sys.stderr = open(os.devnull, 'w')
+    return arguments
+
+
+if __name__ == '__main__':
+    cli()

Azure/AzureStorage/azure_storage/methods.py

@@ -0,0 +1,831 @@
+#!/usr/bin/env python
+from azure.storage.blob import BlobSasPermissions, BlobServiceClient, generate_blob_sas, RetentionPolicy
+from argparse import ArgumentParser
+from io import StringIO
+import pandas as pd
+import numpy as np
+import coloredlogs
+import datetime
+import logging
+import getpass
+import keyring
+import pathlib
+import pandas
+import azure
+import time
+import os
+import re
+
+
+def create_parent_parser(parser, container=True):
+    """
+    Create a parent parser with arguments common to multiple scripts
+    :param parser: type ArgumentParser object
+    :param container: type bool: Boolean on whether the container argument should be added to the parser
+    :return: subparsers: type ArgumentParser.add_subparsers
+    :return: parent_parser: type ArgumentParser: Populated ArgumentParser object
+    """
+    subparsers = parser.add_subparsers(title='Available functionality')
+    # Create a parental parser that can be inherited by subparsers
+    parent_parser = ArgumentParser(add_help=False)
+    if container:
+        parent_parser.add_argument('-c', '--container_name',
+                                   required=True,
+                                   type=str,
+                                   default=str(),
+                                   help='Name of the Azure storage container. Note that container names must be '
+                                        'lowercase, between 3 and 63 characters, start with a letter or number, and '
+                                        'can contain only letters, numbers, and the dash (-) character. Consecutive '
+                                        'dashes are not permitted.')
+    parent_parser.add_argument('-a', '--account_name',
+                               required=True,
+                               type=str,
+                               help='Name of the Azure storage account')
+    parent_parser.add_argument('-p', '--passphrase',
+                               default='AzureStorage',
+                               type=str,
+                               help='The passphrase to use when encrypting the azure storage-specific connection '
+                                    'string to the system keyring. Default is "AzureStorage".')
+    parent_parser.add_argument('-v', '--verbosity',
+                               choices=['debug', 'info', 'warning', 'error', 'critical'],
+                               metavar='VERBOSITY',
+                               default='info',
+                               help='Set the logging level. Options are debug, info, warning, error, and critical. '
+                                    'Default is info.')
+    return subparsers, parent_parser
+
+
+def setup_logging(arguments):
+    """
+    Set the custom colour scheme and message format to used by coloredlogs
+    :param arguments: type parsed ArgumentParser object
+    """
+    # Set up logging
+    coloredlogs.DEFAULT_LEVEL_STYLES = {'debug': {'bold': True, 'color': 'green'},
+                                        'info': {'bold': True, 'color': 'blue'},
+                                        'warning': {'bold': True, 'color': 'yellow'},
+                                        'error': {'bold': True, 'color': 'red'},
+                                        'critical': {'bold': True, 'background': 'red'}
+                                        }
+    coloredlogs.DEFAULT_LOG_FORMAT = '%(asctime)s %(levelname)s %(message)s'
+    coloredlogs.install(level=arguments.verbosity.upper())
+
+
+def setup_arguments(parser):
+    """
+    Finalise setting up the ArgumentParser arguments into an object, and running subparser functions, or displaying the
+    help message
+    :param parser: type: ArgumentParser object
+    :return: parsed ArgumentParser object
+    """
+    # Get the arguments into an object
+    arguments = parser.parse_args()
+    # Run the appropriate function for each sub-parser.
+    if hasattr(arguments, 'func'):
+        # Set up logging
+        setup_logging(arguments=arguments)
+        arguments.func(arguments)
+    # If the 'func' attribute doesn't exist, display the basic help for the appropriate subparser (if any)
+    else:
+        try:
+            # Determine which subparser was called by extracting it from the arguments. Note that this requires the
+            # use of the desc keyword when creating subparsers
+            command = list(vars(arguments).keys())[0]
+            # If the extracted command exists, use the command-specific subparser help
+            if command:
+                parser.parse_args([command, '-h'])
+            # Otherwise, use the basic help
+            else:
+                parser.parse_args(['-h'])
+        # If the were no subparsers specified (the list of keys in the arguments is empty), use the basic help
+        except IndexError:
+            parser.parse_args(['-h'])
+    return arguments
+
+
+def set_account_name(passphrase, account_name=None):
+    """
+    Store the account name in the system keyring
+    :param passphrase: type str: Simple passphrase to use to store the connection string in the system keyring
+    :param account_name: type str: Name of the Azure storage account
+    """
+    # Only prompt the user for the account name if it was not provided
+    if account_name is None:
+        # Prompt the user for the account name
+        account_name = input('Please enter your account name\n').encode('utf-8').decode()
+    # Set the account name into the keyring. Treat it as a password, and use the passphrase as both the service ID,
+    # and the username
+    keyring.set_password(passphrase, passphrase, account_name)
+    return account_name
+
+
+def set_connection_string(passphrase, account_name):
+    """
+    Prompt the user for the connection string, and store it the system keyring
+    Uses logic from https://stackoverflow.com/a/31882203
+    :param passphrase: type str: Simple passphrase to use to store the connection string in the system keyring
+    :param account_name: type str: Name of the Azure storage account
+    :return: connect_str: String of the connection string
+    """
+    # Prompt the user for the connection string. Use decode to convert from bytes. Use getpass, so the plain text
+    # password isn't printed to the screen
+    connect_str = getpass.getpass(prompt='Please enter the connection string for your Azure storage account:\n')\
+        .encode('utf-8').decode()
+    # Ensure that the account name provided and the account name specified in the connection string match
+    confirm_account_match(account_name=account_name,
+                          connect_str=connect_str)
+    # Set the password in the keyring. Use the passphrase as the service ID, the account name as the username,
+    # and the connection string as the password
+    keyring.set_password(passphrase, account_name, connect_str)
+    logging.info('Successfully entered credentials into keyring')
+    return connect_str
+
+
+def confirm_account_match(account_name, connect_str):
+    """
+    Ensure that the account name provided matches the account name stored in the connection string
+    :param connect_str: type str: Connection string for the Azure storage account
+    :param account_name: type str: Name of the Azure storage account
+    """
+    # Attempt to extract the account name from the connection string
+    try:
+        connect_str_account_name = connect_str.split(';')[1].split('AccountName=')[-1]
+        # Ensure that the account name provided matches the account name found in the connection string
+        if account_name != connect_str_account_name:
+            logging.error(f'The supplied account name {account_name} does not match the account name stored in the '
+                          f'connection string ({connect_str_account_name}). Please ensure that you are providing the '
+                          f'appropriate connection string for your account.')
+            raise SystemExit
+    # If splitting on 'AccountName=' fails, the connection string is either malformed or invalid
+    except IndexError:
+        logging.error('Could not parse the account key from the connection string in the keyring. Please ensure that '
+                      'it has been entered, and the it conforms to the proper format: '
+                      'DefaultEndpointsProtocol=https;AccountName=[REDACTED];AccountKey=[REDACTED];'
+                      'EndpointSuffix=core.windows.net')
+        raise SystemExit
+    return True
+
+
+def extract_connection_string(passphrase, account_name):
+    """
+    Extract the connection string from the keyring using the account name and passphrase
+    :param passphrase: type str: Simple passphrase to use to store the connection string in the system keyring
+    :param account_name: type str: Name of the Azure storage account
+    :return: connect_str: String of the connection string
+    """
+    # Use the passphrase and the account name to extract the connection string from the keyring
+    connect_str = keyring.get_password(passphrase,
+                                       account_name)
+    # If the connection string can't be found in the keyring using the supplied passphrase, prompt the user for
+    # the passphrase, and store it
+    if not connect_str:
+        logging.warning(f'Connection string linked to the provided passphrase {passphrase} and account name '
+                        f'{account_name} was not found in the system keyring. You will now be prompted to enter it.')
+        connect_str = set_connection_string(passphrase=passphrase,
+                                            account_name=account_name)
+    # Confirm that the account name provided matches the one found in the connection string
+    confirm_account_match(account_name=account_name,
+                          connect_str=connect_str)
+    return connect_str
+
+
+def extract_account_name(passphrase):
+    """
+    Extract the account name from the system keyring
+    :param passphrase: type str: Simple passphrase to use to store the connection string in the system keyring
+    :return: account_name: Name of the Azure storage account
+    """
+    # Use the passphrase to extract the account name
+    account_name = keyring.get_password(passphrase,
+                                        passphrase)
+    # If the account name hasn't been entered into the keyring, prompt the user to enter it
+    if not account_name:
+        logging.warning(f'Account name linked to the provided passphrase {passphrase} was not found in the system '
+                        f'keyring. You will now be prompted to enter it.')
+        account_name = set_account_name(passphrase=passphrase)
+    return account_name
+
+
+def extract_account_key(connect_str):
+    """
+    Extract the account key from the connection string. This is necessary for the method that creates the blob SAS,
+    as it doesn't accept connection strings
+    :param connect_str: type str: Connection string for the Azure storage account
+    :return account_key: String of the account key extracted from the connection string
+    """
+    # Split the connection string on ';', use the entry corresponding to the account key, and strip off the
+    # 'AccountKey='
+    # DefaultEndpointsProtocol=https;AccountName=[REDACTED];AccountKey=[REDACTED];EndpointSuffix=core.windows.net
+    try:
+        account_key = connect_str.split(';')[2].split('AccountKey=')[-1]
+    except IndexError:
+        logging.error('Could not parse the account key from the connection string in the keyring. Please ensure that '
+                      'it has been entered, and the it conforms to the proper format: '
+                      'DefaultEndpointsProtocol=https;AccountName=[REDACTED];AccountKey=[REDACTED];'
+                      'EndpointSuffix=core.windows.net')
+        raise SystemExit
+    return account_key
+
+
+def delete_keyring_credentials(passphrase, account_name=None):
+    """
+    Delete the password associated with the passphrase and account name from the system keyring
+    :param passphrase: type str: Simple passphrase to use to store the connection string in the system keyring
+    :param account_name: type str: Name of the Azure storage account
+    :return: account_name: Name of the Azure storage account
+    """
+    if not account_name:
+        # Prompt the user for the account name
+        account_name = input('Please enter your account name\n').encode('utf-8').decode()
+    try:
+        # Delete the password from the system keyring
+        keyring.delete_password(passphrase, account_name)
+    except keyring.errors.PasswordDeleteError:
+        logging.error(f'Connection string associated with passphrase {passphrase} and account name {account_name} '
+                      f'not found in system keyring. Please ensure that you supplied the correct arguments.')
+        raise SystemExit
+    return account_name
+
+
+def validate_container_name(container_name, object_type='container'):
+    """
+    Use a regex to check if the supplied name follows the guidelines for Azure nomenclature. If it doesn't, attempt to
+    rename the container/object
+    :param container_name: type str: Name of the container/object of interest
+    :param object_type: type str: Name of the object being validated. Default is container, but target container, and
+    target path are other options
+    :return: container_name: String of sanitised container name
+    """
+    if not re.match('^[a-z0-9](?!.*--)[a-z0-9-]{1,61}[a-z0-9]$', container_name):
+        logging.warning(f'{object_type.capitalize()} name, {container_name} is invalid. {object_type.capitalize()} '
+                        f'names must be between 3 and 63 characters, start with a letter or number, and can contain '
+                        f'only letters, numbers, and the dash (-) character. Every dash (-) character must be '
+                        f'immediately preceded and followed by a letter or number; consecutive dashes are not '
+                        f'permitted in {object_type} names. All letters in a {object_type} name must be lowercase.')
+        logging.info(f'Attempting to fix the {object_type} name')
+        # Swap out dashes for underscores, as they will be removed in the following regex
+        container_name = container_name.replace('-', '_')
+        # Use re to remove all non-word characters (including dashes)
+        container_name = re.sub(r'[^\w]', '', container_name)
+        # Replace multiple underscores with a single one. Uses logic from: https://stackoverflow.com/a/46701355
+        # Also ensure that the container name is in lowercase
+        container_name = re.sub(r'[^\w\s]|(_)(?=\1)', '', container_name).lower()
+        # Swap out underscores for dashes
+        container_name = container_name.replace('_', '-')
+        # Ensure that the container name doesn't start or end with a dash
+        container_name = re.sub(r'^-+', '', container_name)
+        container_name = re.sub(r'-+$', '', container_name)
+    # Ensure that the container name isn't length zero, or the while loop below will be infinite
+    if len(container_name) == 0:
+        logging.error(f'Attempting to fix the {object_type} name left zero valid characters! '
+                      'Please enter a new name.')
+        raise SystemExit
+    # If the container name is too long, slice it to be 63 characters
+    if len(container_name) >= 63:
+        logging.warning(f'{object_type.capitalize()} name {container_name} was too long. Using {container_name[:62]} '
+                        f'instead')
+        container_name = container_name[:62]
+    # If the container name is too short, keep adding the container name to itself to bump up the length
+    while len(container_name) < 3:
+        logging.warning(f'{object_type.capitalize()} name {container_name} was too short (only {len(container_name)} '
+                        f'characters). Using {container_name + container_name} instead')
+        container_name = container_name + container_name
+    # Use the validated container name
+    logging.info(f'Using {container_name} as the {object_type} name')
+    return container_name
+
+
+def create_blob_service_client(connect_str):
+    """
+    Create a blob service client using the connection string
+    :param connect_str: type str: Connection string for Azure storage
+    :return: blob_service_client: type azure.storage.blob.BlobServiceClient
+    """
+    try:
+        blob_service_client = BlobServiceClient.from_connection_string(connect_str)
+        return blob_service_client
+    except ValueError:
+        logging.error('Your connection string was rejected. Please ensure that you entered it properly, and that it '
+                      'is valid')
+        raise SystemExit
+
+
+def create_container(blob_service_client, container_name):
+    """
+    Create a new container and container-specific client from the blob service client
+    :param blob_service_client: type: type azure.storage.blob.BlobServiceClient
+    :param container_name: type str: Name of the container of interest
+    :return: container_client: type azure.storage.blob.BlobServiceClient.ContainerClient
+    """
+    # Hide the INFO-level messages sent to the logger from Azure by increasing the logging level to WARNING
+    logging.getLogger().setLevel(logging.WARNING)
+    try:
+        container_client = blob_service_client.create_container(container_name)
+    except azure.core.exceptions.ResourceExistsError as e:
+        if 'The specified container already exists.' in str(e):
+            container_client = create_container_client(blob_service_client=blob_service_client,
+                                                       container_name=container_name)
+        elif 'The specified container is being deleted. Try operation later.' in str(e):
+            logging.error(f'Could not create the requested container {container_name}. As it has recently been '
+                          f'deleted, please try again in a few moments')
+            raise SystemExit
+        else:
+            logging.error(f'Could not create container {container_name}')
+            raise SystemExit
+    return container_client
+
+
+def create_container_client(blob_service_client, container_name, create=True):
+    """
+    Create a container-specific client from the blob service client
+    :param blob_service_client: type: azure.storage.blob.BlobServiceClient
+    :param container_name: type str: Name of the container of interest
+    :param create: type bool: Boolean whether to create a container if it doesn't exist
+    :return: container_client: type azure.storage.blob.BlobServiceClient.ContainerClient
+    """
+    # Create the container client from the blob service client with the get container client method
+    # and the container name
+    container_client = blob_service_client.get_container_client(container_name)
+    # Create the container if it does not exist
+    if not container_client.exists() and create:
+        container_client = create_container(blob_service_client=blob_service_client,
+                                            container_name=container_name)
+    return container_client
+
+
+def create_blob_client(blob_service_client, container_name, blob_file):
+    """
+    Create a blob-specific client
+    :param blob_service_client: type: azure.storage.blob.BlobServiceClient
+    :param container_name: type str: Name of the container of interest
+    :param blob_file: type iterable from azure.storage.blob.BlobServiceClient.ContainerClient.list_blobs
+    :return: blob_client: type azure.storage.blob.BlobServiceClient.BlobClient
+    """
+    # Create a blob client for the current blob
+    blob_client = blob_service_client.get_blob_client(container=container_name,
+                                                      blob=blob_file)
+    return blob_client
+
+
+def create_blob_sas(blob_file, account_name, container_name, account_key, expiry, sas_urls):
+    """
+    Create SAS URL for blob
+    :param blob_file: type container_client.list_blobs() object
+    :param account_name: type str: Name of Azure storage account
+    :param container_name: type str: Name of container in Azure storage in which the file is located
+    :param account_key: type str: Account key of Azure storage account
+    :param expiry: type int: Number of days that the SAS URL will be valid
+    :param sas_urls: type dict: Dictionary of file name: SAS URL (empty)
+    :return: populated sas_urls
+    """
+    # Set the name of file by removing any path information
+    file_name = os.path.basename(blob_file.name)
+    # Create the blob SAS. Use a start time 15 minutes in the past, and the requested expiry
+    sas_token = generate_blob_sas(
+        account_name=account_name,
+        container_name=container_name,
+        blob_name=blob_file.name,
+        account_key=account_key,
+        permission=BlobSasPermissions(read=True),
+        start=datetime.datetime.utcnow() - datetime.timedelta(minutes=15),
+        expiry=datetime.datetime.utcnow() + datetime.timedelta(days=expiry))
+    # Create the SAS URL, and add it to the dictionary with the file_name as the key
+    sas_urls[file_name] = create_sas_url(account_name=account_name,
+                                         container_name=container_name,
+                                         blob_name=blob_file.name,
+                                         sas_token=sas_token)
+    return sas_urls
+
+
+def client_prep(container_name, passphrase, account_name, create=True):
+    """
+    Validate the container name, and prepare the necessary clients
+    :param container_name: type str: Name of the container of interest
+    :param passphrase: type str: Simple passphrase to use to store the connection string in the system keyring
+    :param account_name: type str: Name of the Azure storage account
+    :param create: type bool: Boolean whether to create a container if it doesn't exist
+    :return: container_name: Validated container name
+    :return: connect_str: String of the connection string
+    :return: blob_service_client: azure.storage.blob.BlobServiceClient
+    :return: container_client: azure.storage.blob.BlobServiceClient.ContainerClient
+    """
+    # Validate the container name
+    container_name = validate_container_name(container_name=container_name)
+    # Extract the connection string from the system keyring
+    connect_str = extract_connection_string(passphrase=passphrase,
+                                            account_name=account_name)
+    # Create the blob service client using the connection string
+    blob_service_client = create_blob_service_client(connect_str=connect_str)
+    # Create the container client for the desired container with the blob service client
+    container_client = create_container_client(blob_service_client=blob_service_client,
+                                               container_name=container_name,
+                                               create=create)
+    return container_name, connect_str, blob_service_client, container_client
+
+
+def sas_prep(container_name, passphrase, account_name, create=True):
+    """
+    Validate container names, extract connection strings, and account keys, and create necessary clients for
+    SAS URL creation
+    :param container_name: type str: Name of the container of interest
+    :param passphrase: type str: Simple passphrase to use to store the connection string in the system keyring
+    :param account_name: type str: Name of the Azure storage account
+    :param create: type bool: Boolean whether to create a container if it doesn't exist
+    :return: container_name: Validated container name
+    :return: connect_str: Connection string for Azure storage
+    :return: account_key: Account key for Azure storage
+    :return: blob_service_client: azure.storage.blob.BlobServiceClient
+    :return: container_client: azure.storage.blob.BlobServiceClient.ContainerClient
+    """
+    # Validate the container name
+    container_name = validate_container_name(container_name=container_name)
+    # Retrieve the connection string from the system keyring
+    connect_str = extract_connection_string(passphrase=passphrase,
+                                            account_name=account_name)
+    # Extract the account key from the connection string
+    account_key = extract_account_key(connect_str=connect_str)
+    # Create the blob service client
+    blob_service_client = create_blob_service_client(connect_str=connect_str)
+    # Create the container client from the blob service client
+    container_client = create_container_client(blob_service_client=blob_service_client,
+                                               container_name=container_name,
+                                               create=create)
+    return container_name, connect_str, account_key, blob_service_client, container_client
+
+
+def create_sas_url(account_name, container_name, blob_name, sas_token):
+    """
+    Create the SAS URL from the required components
+    :param account_name: type str: Name of Azure storage account
+    :param container_name: type str: Name of the container of interest
+    :param blob_name: type str: Name and path of the file of interest
+    :param sas_token: type azure.storage.blob.generate_blob_sas
+    :return: sas_url: String of the SAS URL
+    """
+    # Generate the SAS URL using the account name, the domain, the container name, the blob name, and the
+    # SAS token in the following format:
+    # 'https://' + account_name + '.blob.core.windows.net/' + container_name + '/' + blob_name + '?' + blob
+    sas_url = f'https://{account_name}.blob.core.windows.net/{container_name}/{blob_name}?{sas_token}'
+    return sas_url
+
+
+def write_sas(output_file, sas_urls):
+    """
+    Write the SAS URLs to the output file
+    :param output_file: type str: Name and path of the file in which the SAS URLs are to be written
+    :param sas_urls: type dict: Dictionary of file name: SAS URL
+    """
+    # Create the output file
+    with open(output_file, 'w') as output:
+        for file_name, sas_url in sas_urls.items():
+            # Write the SAS URL to the output file
+            output.write(f'{sas_url}\n')
+            # Print the file name and SAS URL to the terminal
+            logging.info(f'{file_name}\t{sas_url}')
+
+
+def set_blob_retention_policy(blob_service_client, days=8):
+    """
+    Set the retention policy for a blob
+    :param blob_service_client: type: azure.storage.blob.BlobServiceClient
+    :param days: type int: Number of days to retain deleted blobs. Default is 8
+    :return: blob_service_client: Client with the retention policy implemented
+    """
+    # Create a retention policy to retain deleted blobs
+    delete_retention_policy = RetentionPolicy(enabled=True, days=days)
+    # Set the retention policy on the service
+    blob_service_client.set_service_properties(delete_retention_policy=delete_retention_policy)
+    return blob_service_client
+
+
+def move_prep(passphrase, account_name, container_name, target_container):
+    """
+    Prepare all the necessary clients for moving container/files/folders in Azure storage
+    :param passphrase: type str: Simple passphrase to use to store the connection string in the system keyring
+    :param account_name: type str: Name of Azure storage account
+    :param container_name: type str: Name of the container of interest
+    :param target_container: type str: Name of the new container into which the container/file/folder is to be copied
+    :return: blob_service_client: type azure.storage.blob.BlobServiceClient
+    :return: source_container_client: type azure.storage.blob.BlobServiceClient.ContainerClient for source container
+    :return: target_container_client: type azure.storage.blob.BlobServiceClient.ContainerClient for target container
+    """
+    # Validate the container names
+    container_name = validate_container_name(container_name=container_name)
+    target_container = validate_container_name(container_name=target_container,
+                                               object_type='target container')
+    # Extract the connection string from the system keyring
+    connect_str = extract_connection_string(passphrase=passphrase,
+                                            account_name=account_name)
+    blob_service_client = create_blob_service_client(connect_str=connect_str)
+    source_container_client = create_container_client(blob_service_client=blob_service_client,
+                                                      container_name=container_name)
+    # Hide the INFO-level messages sent to the logger from Azure by increasing the logging level to WARNING
+    logging.getLogger().setLevel(logging.WARNING)
+    target_container_client = create_container(blob_service_client=blob_service_client,
+                                               container_name=target_container)
+    return container_name, target_container, blob_service_client, source_container_client, target_container_client
+
+
+def copy_blob(blob_file, blob_service_client, container_name, target_container, path, storage_tier,
+              object_name=None, category=None, common_path=None):
+    """
+    Copy a blob from one container to another
+    :param blob_file: type iterable from azure.storage.blob.BlobServiceClient.ContainerClient.list_blobs
+    :param container_name: type str: Name of the container in which the file is located
+    :param blob_service_client: type: azure.storage.blob.BlobServiceClient
+    :param target_container: type str: Name of the new container into which the file is to be copied
+    :param path: type str: Path of folders in which the files are to be placed
+    :param storage_tier: type str: Storage tier to use for the copied file/folder
+    :param object_name: type str: Name and path of file/folder to download from Azure storage
+    :param category: type str: Category of object to be copied. Limited to file or folder
+    :param common_path: type str: Calculated common path between the specified file/folder and the blob_file.name
+    """
+    # Create the blob client
+    blob_client = create_blob_client(blob_service_client=blob_service_client,
+                                     container_name=container_name,
+                                     blob_file=blob_file)
+    # Extract the folder structure of the blob e.g. 220202-m05722/InterOp
+    folder_structure = list(os.path.split(os.path.dirname(blob_file.name)))
+    # Add the nested folder to the path as requested
+    target_path = os.path.join(path, os.path.join(*folder_structure))
+    # Set the name of file by removing any path information
+    file_name = os.path.basename(blob_file.name)
+    # Finally, set the name and the path of the output file
+    if category is None:
+        target_file = os.path.join(path, file_name)
+    # If a folder is being moved, join the path, the common path between the blob file and the supplied folder name
+    # with the file name
+    else:
+        if object_name is not None:
+            target_file = os.path.join(path, common_path, os.path.basename(blob_file.name))
+        # If a container is being moved, join the target path and the name of the directory of the blob_file to the
+        # file name
+        else:
+            # Create a pathlib.Path object from the blob file
+            file_path = pathlib.Path(blob_file.name)
+            # Determine the parental path of the file. If the file is in the root, it will be a dot. This won't work
+            # with the joining logic, so change it to ''
+            nested_path = file_path.parent if file_path.parent == '.' else ''
+            # Join the target path, nested path, and file name
+            target_file = os.path.join(target_path, nested_path, file_name)
+    # Create a blob client for the target blob
+    target_blob_client = blob_service_client.get_blob_client(target_container, target_file)
+    # Copy the source file to the target file - allow up to 1000 seconds total
+    target_blob_client.start_copy_from_url(blob_client.url)
+    # Set the storage tier
+    target_blob_client.set_standard_blob_tier(standard_blob_tier=storage_tier)
+    # Ensure that the copy is complete before proceeding
+    for i in range(100):
+        # Extract the properties of the target blob client
+        target_blob_properties = target_blob_client.get_blob_properties()
+        # Break when the status is set to 'success'. The copy is successful
+        if target_blob_properties.copy.status == 'success':
+            # Copy finished
+            break
+        # Sleep for 10 seconds
+        time.sleep(10)
+
+
+def delete_container(blob_service_client, container_name, account_name):
+    """
+    Delete a container in Azure storage
+    :param blob_service_client: type: azure.storage.blob.BlobServiceClient
+    :param container_name: type str: Name of the container of interest
+    :param account_name: type str: Name of the Azure storage account
+    """
+    # Delete container if it exists
+    try:
+        blob_service_client.delete_container(container_name)
+    except azure.core.exceptions.ResourceNotFoundError:
+        logging.error(f'Could not locate {container_name} in {account_name}. Perhaps it has already been deleted?')
+        raise SystemExit
+
+
+def extract_common_path(object_name, blob_file):
+    """
+    Extract the common path (if any) between a file in Azure storage, and a user-supplied folder name
+    :param object_name: type str: Name and path of file/folder to download from Azure storage
+    :param blob_file: type iterable from azure.storage.blob.BlobServiceClient.ContainerClient.list_blobs
+    :return: common_path: The calculated common path between the folder and the file in blob storage (can be None)
+    """
+    # Create the pathlib.Path objects for both the folder and the blob file
+    object_path = pathlib.Path(os.path.normpath(object_name))
+    blob_path = pathlib.Path(blob_file.name).parent
+    # If there is a common path between the folder and the blob file path, then there is a match
+    try:
+        common_path = blob_path.relative_to(object_path)
+        # Change the dot returned by an exact match to the directory with ''
+        common_path = common_path if str(common_path) != '.' else ''
+    except ValueError:
+        common_path = None
+    return common_path
+
+
+def delete_file(container_client, object_name, blob_service_client, container_name):
+    """
+    Delete a file from Azure storage
+    :param container_client: type azure.storage.blob.BlobServiceClient.ContainerClient
+    :param object_name: type str: Name and path of file/folder to download from Azure storage
+    :param blob_service_client: type: azure.storage.blob.BlobServiceClient
+    :param container_name: type str: Name of the container of interest
+    """
+    # Create a generator containing all the blobs in the container
+    generator = container_client.list_blobs()
+    # Create a boolean to determine if the blob has been located
+    present = False
+    for blob_file in generator:
+        # Filter for the blob name
+        if os.path.join(blob_file.name) == object_name:
+            # Update the blob presence variable
+            present = True
+            # Create the blob client
+            blob_client = create_blob_client(blob_service_client=blob_service_client,
+                                             container_name=container_name,
+                                             blob_file=blob_file)
+            # Soft delete the blob
+            blob_client.delete_blob()
+    # Send a warning to the user that the blob could not be found
+    if not present:
+        logging.error(f'Could not locate the desired file {object_name}')
+        raise SystemExit
+
+
+def delete_folder(container_client, object_name, blob_service_client, container_name, account_name):
+    """
+    Delete a folder from Azure storage
+    :param container_client: type azure.storage.blob.BlobServiceClient.ContainerClient
+    :param object_name: type str: Name and path of file/folder to download from Azure storage
+    :param blob_service_client: type: azure.storage.blob.BlobServiceClient
+    :param container_name: type str: Name of the container of interest
+    :param account_name: type str: Name of the Azure storage account
+    """
+    # Create a generator containing all the blobs in the container
+    generator = container_client.list_blobs()
+    # Create a boolean to determine if the blob has been located
+    present = False
+    for blob_file in generator:
+        common_path = extract_common_path(object_name=object_name,
+                                          blob_file=blob_file)
+        # Only copy the file if there is a common path between the object path and the blob path (they match)
+        if common_path is not None:
+            # Update the folder presence boolean
+            present = True
+            # Create the blob client
+            blob_client = create_blob_client(blob_service_client=blob_service_client,
+                                             container_name=container_name,
+                                             blob_file=blob_file)
+            # Soft delete the blob
+            blob_client.delete_blob()
+    # Log an error that the folder could not be found
+    if not present:
+        logging.error(
+            f'There was an error deleting folder {object_name} in container {container_name}, '
+            f'in Azure storage account {account_name}. Please ensure that all arguments have been '
+            f'entered correctly')
+        raise SystemExit
+
+
+def arg_dict_cleanup(arg_dict):
+    """
+    Clean up the argument dictionary to be consistent with the format required for the AzureStorage classes
+    :param arg_dict: type dict: Dictionary of argument name: value e.g. storage tier: nan
+    :return: arg_dict: Cleaned argument dictionary
+    """
+    try:
+        # Double single quotes are not automatically changed into an empty string
+        arg_dict['reset_path'] = arg_dict['reset_path'] if arg_dict['reset_path'] != "''" else str()
+    except KeyError:
+        pass
+    # For optional argument, the nan value supplied for empty values will not work with downstream code; find and
+    # change them to the appropriate empty/default value
+    try:
+        arg_dict['reset_path'] = arg_dict['reset_path'] if str(arg_dict['reset_path']) != str(np.nan) else None
+    except KeyError:
+        pass
+    try:
+        arg_dict['storage_tier'] = arg_dict['storage_tier'] if str(arg_dict['storage_tier']) != str(np.nan) else 'Hot'
+    except KeyError:
+        pass
+    try:
+        arg_dict['output_file'] = arg_dict['output_file'] if str(arg_dict['output_file']) != str(np.nan) \
+            else os.path.join(os.getcwd(), 'sas_urls.txt')
+    except KeyError:
+        pass
+    try:
+        arg_dict['output_path'] = arg_dict['output_path'] if str(arg_dict['output_path']) != str(np.nan) \
+            else os.getcwd()
+    except KeyError:
+        pass
+    try:
+        arg_dict['expiry'] = arg_dict['expiry'] if str(arg_dict['expiry']) != str(np.nan) else 10
+    except KeyError:
+        pass
+    try:
+        arg_dict['retention_time'] = arg_dict['retention_time'] if str(arg_dict['retention_time']) != str(np.nan) else 8
+    except KeyError:
+        pass
+    # Reading in numerical container names e.g. 220202 returns an integer, so typecast it to string
+    arg_dict['container'] = str(arg_dict['container'])
+    try:
+        arg_dict['target'] = str(arg_dict['target'])
+    except KeyError:
+        pass
+    return arg_dict
+
+
+def create_batch_dict(batch_file, headers):
+    """
+    Read in the supplied file of arguments with pandas. Create a dictionary of the arguments from a transposed dataframe
+    :param batch_file: type str: Name and path of file containing requested operations
+    :param headers: type list: Names of all the headers present in the file
+    :return: Pandas dataframe.transpose().to_dict() of header: value extracted from the desired operation
+    """
+    # Ensure that the batch file exists
+    try:
+        assert os.path.isfile(batch_file)
+    except AssertionError:
+        logging.error(f'Could not locate the supplied batch file {batch_file}. Please ensure the you entered '
+                      f'the name and path correctly')
+        raise SystemExit
+    # Read in the batch file using pandas.read_csv. Use tabs as the separator, and provide the header names.
+    # Transpose the data, and convert the dataframe to a dictionary
+    batch_dict = pd.read_csv(
+        batch_file,
+        sep='\t',
+        names=headers
+    ).transpose().to_dict()
+    return batch_dict
+
+
+def parse_batch_file(line):
+    """
+    Extract the requested command and subcommand from a line from an AzureAutomate batch file. Create a dictionary with
+    the appropriate header:value for that command and subcommand combination
+    :param line: type str: Individual line of text from batch file detailing requested operations. Format is:
+    command;subcommand;operation-specific arguments
+    :return: command: type str: Desired command to run e.g. upload, sas, move, download, tier, delete
+    :return: subcommand: Subcommand for operation e.g. container, file, folder
+    :return: batch_dict: Pandas dataframe.transpose().to_dict() of header: value extracted from the desired operation
+    """
+    # Create a dictionary of the appropriate headers for each command and subcommand combination
+    header_dict = {
+        'upload': {
+            'file': ['command', 'subcommand', 'container', 'file', 'reset_path', 'storage_tier'],
+            'folder': ['command', 'subcommand', 'container', 'folder', 'reset_path', 'storage_tier']
+        },
+        'sas': {
+            'container': ['command', 'subcommand', 'container', 'expiry', 'output_file'],
+            'file': ['command', 'subcommand', 'container', 'file', 'expiry', 'output_file'],
+            'folder': ['command', 'subcommand', 'container', 'folder', 'expiry', 'output_file']
+        },
+        'move': {
+            'container': ['command', 'subcommand', 'container', 'target', 'reset_path', 'storage_tier'],
+            'file': ['command', 'subcommand', 'container', 'target', 'file', 'reset_path', 'storage_tier'],
+            'folder': ['command', 'subcommand', 'container', 'target', 'folder', 'reset_path', 'storage_tier']
+        },
+        'download': {
+            'container': ['command', 'subcommand', 'container', 'output_path'],
+            'file': ['command', 'subcommand', 'container', 'file', 'output_path'],
+            'folder': ['command', 'subcommand', 'container', 'folder', 'output_path']
+        },
+        'tier': {
+            'container': ['command', 'subcommand', 'container', 'storage_tier'],
+            'file': ['command', 'subcommand', 'container', 'file', 'storage_tier'],
+            'folder': ['command', 'subcommand', 'container', 'folder', 'storage_tier']
+        },
+        'delete': {
+            'container': ['command', 'subcommand', 'container'],
+            'file': ['command', 'subcommand', 'container', 'file', 'retention_time'],
+            'folder': ['command', 'subcommand', 'container', 'folder', 'retention_time']
+        }
+    }
+    # Extract the command and subcommand from the line. They will be the first two entries
+    try:
+        command = line.split('\t')[0]
+        subcommand = line.split('\t')[1]
+    except IndexError:
+        logging.error(f'Could not extract the desired command and subcommand from your file. Please review the '
+                      f'following line {line}')
+        raise SystemExit
+    # Use the extracted command and subcommand to determine the appropriate headers
+    try:
+        headers = header_dict[command][subcommand]
+    except KeyError:
+        logging.error(f'Could not find the requested command {command} and subcommand {subcommand} in the list of '
+                      f'commands. Please ensure that you created your batch file correctly')
+        raise SystemExit
+    # Use StringIO to convert the string into a format that can be read by pandas.read_csv
+    input_string = StringIO(line.rstrip())
+    # Read in the line using pandas.read_csv. Use tabs as the separator, and provide the header names.
+    # Transpose the data, and convert the dataframe to a dictionary
+    try:
+        batch_dict = pd.read_csv(
+            input_string,
+            sep='\t',
+            names=headers
+        ).transpose().to_dict()
+    except pandas.errors.ParserError as e:
+        logging.error(f'Pandas error parsing data: {e}')
+        raise SystemExit
+    # Return the command, subcommand, and parsed dictionary
+    return command, subcommand, batch_dict

Azure/AzureStorage/docs/automate.md

@@ -0,0 +1,901 @@
+## AzureAutomate
+
+Perform multiple upload, SAS URL creation, move, download, storage tier setting, or delete actions. Alternatively, perform multiple actions in a single call
+
+Choose either the [`upload`](#azureautomate-upload), [`sas`](#azureautomate-sas), [`move`](#azureautomate-move), [`download`](#azureautomate-download), [`tier`](#azureautomate-tier), [`delete`](#azureautomate-delete), or [`batch`](#azureautomate-batch) functionality
+
+#### General usage
+
+```
+usage: AzureAutomate [-h] {upload,sas,move,download,tier,delete,batch} ...
+
+Automate the submission of multiple AzureStorage commands
+
+optional arguments:
+  -h, --help            show this help message and exit
+
+Available functionality:
+  {upload,sas,move,download,tier,delete,batch}
+    upload              Upload files/folders to Azure storage
+    sas                 Create SAS URLs for containers/files/folders in Azure storage
+    move                Move containers/files/folders in Azure storage
+    download            Download containers/files/folders in Azure storage
+    tier                Set the storage tier of containers/files/folders in Azure storage
+    delete              Delete containers/files/folders in Azure storage
+    batch               Perform multiple different operations in batch
+```
+### AzureAutomate upload
+
+Choose either the [`file`](#azureautomate-upload-file) or [`folder`](#azureautomate-upload-folder) functionality
+
+#### General usage
+
+```
+usage: AzureAutomate upload [-h] {file,folder} ...
+
+Upload files/folders to Azure storage
+
+optional arguments:
+  -h, --help     show this help message and exit
+
+Upload functionality:
+  {file,folder}
+    file         Upload files to Azure storage
+    folder       Upload folders to Azure storage
+```
+
+### AzureAutomate upload file
+
+Automate the upload of multiple files to your Azure storage account
+
+#### Required arguments:
+- container name
+- account name
+- name and path of batch file
+
+#### Optional arguments:
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+
+#### Batch file format
+
+Tab-separated file with the following fields:
+
+`container name, file name, destination path (optional), storage tier (optional)`
+
+For additional details on running file uploads, please see the [`AzureUpload file`](upload.md#azureupload-file) section
+
+#### Usage
+
+```
+usage: AzureAutomate upload file [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Upload files to Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file with the following fields:
+                         container name, file name, destination path (optional), storage tier (optional)
+```
+
+### AzureAutomate upload folder
+
+Automate the upload of multiple folders to your Azure storage account
+
+#### Required arguments:
+- container name
+- account name
+- name and path of batch file
+
+#### Optional arguments:
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+
+#### Batch file format
+
+Tab-separated file with the following fields:
+
+`container name, folder name, destination path (optional), storage tier (optional)`
+
+For additional details on running folder uploads, please see the [`AzureUpload folder`](upload.md#azureupload-folder) section
+
+#### Usage
+
+```
+usage: AzureAutomate upload folder [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Upload folders to Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file with the following fields (one entry per line):
+                         container name, folder name, destination path (optional), storage tier (optional)
+```
+
+### AzureAutomate sas
+
+Choose either the [`container`](#azureautomate-sas-container), [`file`](#azureautomate-sas-file), or [`folder`](#azureautomate-sas-folder) functionality
+
+#### General usage
+
+```
+usage: AzureAutomate sas [-h] {container,file,folder} ...
+
+Create SAS URLs for containers/files/folders in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+
+SAS URL creation functionality:
+  {container,file,folder}
+    container           Create SAS URLs for containers in Azure storage
+    file                Create SAS URLs for files in Azure storage
+    folder              Create SAS URLs for folders in Azure storage
+```
+
+#### AzureAutomate sas container
+
+Automate the creation of SAS URLs for multiple containers in your Azure storage account
+
+#### Required arguments:
+- container name
+- account name
+- name and path of batch file
+
+#### Optional arguments:
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+
+#### Batch file format
+
+Tab-separated file with the following fields:
+
+`container name, expiry (optional), output file (optional)`
+
+For additional details on creating SAS URLs for containers, please see the [`AzureSAS container`](sas_url.md#azuresas-container) section
+
+#### Usage
+
+```
+usage: AzureAutomate sas container [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Create SAS URLs for containers in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file with the following fields:
+                        container name, expiry (optional), output file (optional)
+```
+
+#### AzureAutomate sas file
+
+Automate the creation of SAS URLs for multiple files in your Azure storage account
+
+#### Required arguments:
+- container name
+- account name
+- name and path of batch file
+
+#### Optional arguments:
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+
+#### Batch file format
+
+Tab-separated file with the following fields:
+
+`container name, file name and path, expiry (optional), output file (optional)`
+
+For additional details on creating SAS URLs for files, please see the [`AzureSAS file`](sas_url.md#azuresas-file) section
+
+#### Usage
+
+```
+usage: AzureAutomate sas file [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Create SAS URLs for files in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file with the following fields:
+                         container name, file name and path, expiry (optional), output file (optional)
+```
+
+#### AzureAutomate sas folder
+
+Automate the creation of SAS URLs for multiple folders in your Azure storage account
+
+#### Required arguments:
+- container name
+- account name
+- name and path of batch file
+
+#### Optional arguments:
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+
+#### Batch file format
+
+Tab-separated file with the following fields:
+
+`container name, folder name and path, expiry (optional), output file (optional)`
+
+For additional details on creating SAS URLs for folders, please see the [`AzureSAS folder`](sas_url.md#azuresas-folder) section
+
+#### Usage
+
+```
+usage: AzureAutomate sas folder [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Create SAS URLs for folders in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file with the following fields:
+                         container name, folder name and path, expiry (optional), output file (optional)
+```
+
+### AzureAutomate move
+
+Choose either the [`container`](#azureautomate-move-container), [`file`](#azureautomate-move-file), or [`folder`](#azureautomate-move-folder) functionality
+
+#### General usage
+
+```
+usage: AzureAutomate move [-h] {container,file,folder} ...
+
+Move containers/files/folders in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+
+Move functionality:
+  {container,file,folder}
+    container           Move containers in Azure storage
+    file                Move files in Azure storage
+    folder              Move folders in Azure storage
+```
+
+#### AzureAutomate move container
+
+Automate the moving of multiple containers in your Azure storage account
+
+#### Required arguments:
+- container name
+- account name
+- name and path of batch file
+
+#### Optional arguments:
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+
+#### Batch file format
+
+Tab-separated file with the following fields:
+
+`container name, target container, destination path (optional), storage tier (optional)`
+
+For additional details on moving containers, please see the [`AzureMove container`](move.md#azuremove-container) section
+
+#### Usage
+
+```
+usage: AzureAutomate move container [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Move containers in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file with the following fields:
+                         container name, target container, destination path (optional), storage tier (optional)
+```
+
+#### AzureAutomate move file
+
+Automate the moving of multiple files in your Azure storage account
+
+#### Required arguments:
+- container name
+- account name
+- name and path of batch file
+
+#### Optional arguments:
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+
+#### Batch file format
+
+Tab-separated file with the following fields:
+
+`container name, target container, file name, destination path (optional), storage tier (optional)`
+
+For additional details on moving files, please see the [`AzureMove file`](move.md#azuremove-file) section
+
+#### Usage
+
+```
+usage: AzureAutomate move file [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Move files in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file with the following fields:
+                         container name, target container, file name, destination path (optional), storage tier (optional)
+```
+
+#### AzureAutomate move folder
+
+Automate the moving of multiple folders in your Azure storage account
+
+#### Required arguments:
+- container name
+- account name
+- name and path of batch file
+
+#### Optional arguments:
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+
+#### Batch file format
+
+Tab-separated file with the following fields:
+
+`container name, target container, folder name, destination path (optional), storage tier (optional)`
+
+For additional details on moving folders, please see the [`AzureMove folder`](move.md#azuremove-folder) section
+
+#### Usage
+
+```
+usage: AzureAutomate move folder [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Move folders in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file with the following fields:
+                         container name, target container, folder name, destination path (optional), storage tier (optional)
+
+```
+
+### AzureAutomate download
+
+Choose either the [`container`](#azureautomate-download-container), [`file`](#azureautomate-download-file), or [`folder`](#azureautomate-download-folder) functionality
+
+#### General usage
+
+```
+usage: AzureAutomate download [-h] {container,file,folder} ...
+
+Download containers/files/folders in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+
+Download functionality:
+  {container,file,folder}
+    container           Download containers from Azure storage
+    file                Download files from Azure storage
+    folder              Download folders from Azure storage
+```
+
+### AzureAutomate download container
+
+Automate the downloading of multiple containers from your Azure storage account
+
+#### Required arguments:
+- container name
+- account name
+- name and path of batch file
+
+#### Optional arguments:
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+
+#### Batch file format
+
+Tab-separated file with the following fields:
+
+`container name, output path (optional)`
+
+For additional details on downloading containers, please see the [`AzureDownload container`](download.md#azuredownload-container) section
+
+#### Usage
+
+```
+usage: AzureAutomate download container [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Download containers from Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file with the following fields:
+                         container name, output path (optional)
+```
+
+### AzureAutomate download file
+
+Automate the downloading of multiple files from your Azure storage account
+
+#### Required arguments:
+- container name
+- account name
+- name and path of batch file
+
+#### Optional arguments:
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+
+#### Batch file format
+
+Tab-separated file with the following fields:
+
+`container name, file name, output path (optional)`
+
+For additional details on downloading files, please see the [`AzureDownload file`](download.md#azuredownload-file) section
+
+#### Usage
+
+```
+usage: AzureAutomate download file [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Download files from Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file with the following fields:
+                         container name, file name, output path (optional)
+```
+
+### AzureAutomate download folder
+
+Automate the downloading of multiple folders from your Azure storage account
+
+#### Required arguments:
+- container name
+- account name
+- name and path of batch file
+
+#### Optional arguments:
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+
+#### Batch file format
+
+Tab-separated file with the following fields:
+
+`container name, folder name, output path (optional)`
+
+For additional details on downloading folders, please see the [`AzureDownload folder`](download.md#azuredownload-folder) section
+
+#### Usage
+
+```
+usage: AzureAutomate download folder [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Download folders from Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file with the following fields:
+                         container name, folder name, output path (optional)
+```
+
+### AzureAutomate tier
+
+Choose either the [`container`](#azureautomate-tier-container), [`file`](#azureautomate-tier-file), or [`folder`](#azureautomate-tier-folder) functionality
+
+#### General usage
+
+```
+usage: AzureAutomate tier [-h] {container,file,folder} ...
+
+Set the storage tier of containers/files/folders in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+
+Storage tier setting functionality:
+  {container,file,folder}
+    container           Set the storage tier of containers in Azure storage
+    file                Set the storage tier of files in Azure storage
+    folder              Set the storage tier of folders in Azure storage
+```
+
+### AzureAutomate tier container
+
+Automate setting the storage tier for multiple containers in your Azure storage account
+
+#### Required arguments:
+- container name
+- account name
+- name and path of batch file
+
+#### Optional arguments:
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+
+#### Batch file format
+
+Tab-separated file with the following fields:
+
+`container name, storage tier`
+
+For additional details on setting the storage tier of containers, please see the [`AzureTier container`](set_tier.md#azuretier-container) section
+
+#### Usage
+
+```
+usage: AzureAutomate tier container [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Set the storage tier of containers in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file with the following fields:
+                         container name, storage tier
+
+```
+
+### AzureAutomate tier file
+
+Automate setting the storage tier for multiple files in your Azure storage account
+
+#### Required arguments:
+- container name
+- account name
+- name and path of batch file
+
+#### Optional arguments:
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+
+#### Batch file format
+
+Tab-separated file with the following fields:
+
+`container name, file name, storage tier`
+
+For additional details on setting the storage tier of files, please see the [`AzureTier file`](set_tier.md#azuretier-file) section
+
+#### Usage
+
+```
+usage: AzureAutomate tier file [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Set the storage tier of files in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file with the following fields:
+                         container name, file name, storage tier
+```
+
+### AzureAutomate tier folder
+
+Automate setting the storage tier for multiple folders in your Azure storage account
+
+#### Required arguments:
+- container name
+- account name
+- name and path of batch file
+
+#### Optional arguments:
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+
+#### Batch file format
+
+Tab-separated file with the following fields:
+
+`container name, folder name, storage tier`
+
+For additional details on setting the storage tier of folders, please see the [`AzureTier folder`](set_tier.md#azuretier-folder) section
+
+#### Usage
+
+```
+usage: AzureAutomate tier folder [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Set the storage tier of folders in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file with the following fields:
+                         container name, folder name, storage tier
+```
+
+### AzureAutomate delete
+
+Choose either the [`container`](#azureautomate-delete-container), [`file`](#azureautomate-delete-file), or [`folder`](#azureautomate-delete-folder) functionality
+
+#### General usage
+
+```
+usage: AzureAutomate delete [-h] {container,file,folder} ...
+
+Delete containers/files/folders in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+
+Delete functionality:
+  {container,file,folder}
+    container           Delete containers in Azure storage
+    file                Delete files in Azure storage
+    folder              Delete folders in Azure storage
+```
+
+### AzureAutomate delete container
+
+Automate deleting multiple containers in your Azure storage account
+
+#### Required arguments:
+- container name
+- account name
+- name and path of batch file
+
+#### Optional arguments:
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+
+#### Batch file format
+
+File with the following field:
+
+`container name`
+
+For additional details on deleting containers, please see the [`AzureDelete container`](delete.md#azuredelete-container) section
+
+#### Usage
+
+```
+usage: AzureAutomate delete container [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Delete containers in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        File with the following field:
+                         container name
+```
+
+### AzureAutomate delete file
+
+Automate deleting multiple files in your Azure storage account
+
+#### Required arguments:
+- container name
+- account name
+- name and path of batch file
+
+#### Optional arguments:
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+
+#### Batch file format
+
+Tab-separated file with the following fields:
+
+`container name, file name, retention time (optional)`
+
+For additional details on deleting files, please see the [`AzureDelete file`](delete.md#azuredelete-file) section
+
+#### Usage
+
+```
+usage: AzureAutomate delete file [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Delete files in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file with the following fields:
+                         container name, file name, retention time (optional)
+
+```
+
+### AzureAutomate delete folder
+
+Automate deleting multiple folders in your Azure storage account
+
+#### Required arguments:
+- container name
+- account name
+- name and path of batch file
+
+#### Optional arguments:
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+
+#### Batch file format
+
+Tab-separated file with the following fields:
+
+`container name, folder name, retention time (optional)`
+
+For additional details on deleting folders, please see the [`AzureDelete folder`](delete.md#azuredelete-folder) section
+
+#### Usage
+
+```
+usage: AzureAutomate delete folder [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Delete folders in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file with the following fields:
+                         container name, folder name, retention time (optional)
+```
+
+### AzureAutomate batch
+
+Automate multiple operations
+
+### Batch file format
+
+Tab-separated file in the following format:
+
+`command, sub-command, command:subcommand-specific arguments`
+
+Please review the [`AzureAutomate`](#azureautomate) documentation for all the possible operations
+
+### Usage
+
+```
+usage: AzureAutomate batch [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Perform multiple different operations in batch
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file in the following format:
+                        command, sub-command, arguments
+
+                        Below is the complete list of functionalities:
+                        upload, file, container name, file name, destination path (optional), storage tier (optional)
+                        upload, folder, container name, folder name, destination path (optional), storage tier (optional)
+                        sas, container, container name, expiry (optional), output file (optional)
+                        sas, file, container name, file name and path, expiry (optional), output file (optional)
+                        sas, folder, container name, folder name and path, expiry (optional), output file (optional)
+                        move, container, container name, target container, destination path (optional), storage tier (optional)
+                        move, file, container name, target container, file name, destination path (optional), storage tier (optional)
+                        move, folder, container name, target container, folder name, destination path (optional), storage tier (optional)
+                        download, container, container name, output path (optional)
+                        download, file, container name, file name, output path (optional)
+                        download, folder, container name, folder name, output path (optional)
+                        tier, container, container name, storage tier
+                        tier, file, container name, file name, storage tier
+                        tier, folder, container name, folder name, storage tier
+                        delete, container, container name
+                        delete, file, container name, file name, retention time (optional)
+                        delete, folder, container name, folder name, retention time (optional)
+```

Azure/AzureStorage/docs/credentials.md

@@ -0,0 +1,111 @@
+## AzureCredentials
+
+AzureCredentials allows you to store, modify, or delete your Azure account name and connection string in the system keyring
+
+Choose either the [`store`](#azure-credentials-store) or [`delete`](#azure-credentials-delete) functionality
+
+[Find your connection string](https://docs.microsoft.com/en-us/azure/storage/common/storage-configure-connection-string#:~:text=You%20can%20find%20your%20storage,primary%20and%20secondary%20access%20keys.)
+
+[Find your account key](https://www.zenko.io/blog/how-to-find-keys-and-account-info-for-aws-azure-and-google/#:~:text=Azure%20Account%20Name%C2%A0%3D%20the%20name%20of%20your%20Azure%20storage%20account%20located%20on%20the%20top%20of%20the%20Azure%20Portal%20(screenshot%20below%20%E2%80%93%20%E2%80%9Cscalitydemo%E2%80%9D%20is%20Azure%20Account%20Name).)
+
+
+#### General Usage
+
+```
+usage: AzureCredentials [-h] {store,delete} ...
+
+Set, modify, or delete Azure storage credentials in the system keyring
+
+optional arguments:
+  -h, --help      show this help message and exit
+
+Available functionality:
+  {store,delete}
+    store         Store or update Azure storage credentials in the system keyring
+    delete        Delete Azure storage credentials in the system keyring
+
+```
+
+### Azure credentials store
+
+Store or modify your account name and connection string in the system keyring
+
+#### Required arguments:
+- account name
+
+#### Optional arguments:
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+
+#### Example commands:
+
+To store the account name `account_name` and your connection string in the system keyring
+
+`AzureCredentials store -a account_name`
+
+NOTE: You will be prompted to enter your connection string by the script. Note that, as a security precaution, you will not see the text you entered.
+
+To store the account name `account_name` and your connection string in the system keyring using the passphrase `passphrase`
+
+`AzureCredentials store -a account_name -p passphrase`
+
+NOTE: You will be prompted to enter your connection string by the script. Note that, as a security precaution, you will not see the text you entered. 
+
+#### Usage
+```
+usage: AzureCredentials store [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY]
+
+Store or update Azure storage credentials in the system keyring
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+```
+
+### Azure credentials delete
+
+Delete your account name and connection string from the system keyring
+
+#### Required arguments:
+- account name
+
+#### Optional arguments:
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+
+#### Example command:
+
+To delete the account name `account_name` and your connection string from the system keyring
+
+`AzureCredentials delete -a account_name`
+
+NOTE: You will be prompted to enter your connection string by the script. Note that, as a security precaution, you will not see the text you entered.
+
+To delete the account name `account_name` and your connection string from the system keyring stored using the passphrase `passphrase`
+
+`AzureCredentials delete -a account_name -p passphrase`
+
+NOTE: You will be prompted to enter your connection string by the script. Note that, as a security precaution, you will not see the text you entered.
+
+
+#### Usage
+
+```
+usage: AzureCredentials delete [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY]
+
+Delete Azure storage credentials in the system keyring
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+```

Azure/AzureStorage/docs/delete.md

@@ -0,0 +1,158 @@
+## AzureDelete
+
+Delete containers, files, or folders from your Azure storage account
+
+Choose either the [`container`](#azuredelete-container), [`file`](#azuredelete-file), or  [`folder`](#azuredelete-folder) functionality
+
+#### General usage
+
+```
+usage: AzureDelete [-h] {container,file,folder} ...
+
+Move and/or delete containers, files, or folders in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+
+Available functionality:
+  {container,file,folder}
+    container           Delete a container in Azure storage
+    file                Delete a file in Azure storage
+    folder              Delete a folder in Azure storage
+```
+
+### AzureDelete container
+
+Delete a container from your Azure storage account
+
+#### Required arguments:
+- container name
+- account name
+
+#### Optional arguments:
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+
+#### Example command:
+
+These commands will use `container-name` as the name of the container and `account_name` as the name of the storage account
+
+To delete a container from your Azure storage account
+
+`AzureDelete container -a account_name -c container-name`
+
+#### Usage
+
+```
+usage: AzureDelete container [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY]
+
+Delete a container in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -c CONTAINER_NAME, --container_name CONTAINER_NAME
+                        Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted.
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+```
+
+### AzureDelete file
+
+Delete a file from your Azure storage account
+
+#### Required arguments:
+- container name
+- account name
+- file name
+
+#### Optional arguments:
+- retention time: time to retain deleted files. Default is 8 days
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+
+#### Example commands:
+
+These commands will use `container-name` as the name of the container and `account_name` as the name of the storage account
+
+To delete the file `file_name.gz` from your Azure storage account
+
+`AzureDelete file -a account_name -c container-name -f file_name.gz`
+
+To delete the file `file_name.gz` nested in folder outputs from your Azure storage account, and retain it for 10 days
+
+`AzureDelete file -a account_name -c container-name -f outputs/file_name.gz -r 10`
+
+#### Usage
+
+```
+usage: AzureDelete file [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -f FILE [-r RETENTION_TIME]
+
+Delete a file in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -c CONTAINER_NAME, --container_name CONTAINER_NAME
+                        Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted.
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -f FILE, --file FILE  Name of blob file to delete in Azure storage. e.g. 2022-SEQ-0001_S1_L001_R1_001.fastq.gz
+  -r RETENTION_TIME, --retention_time RETENTION_TIME
+                        Retention time for deleted files. Default is 8 days. Must be between 1 and 365
+```
+
+### AzureDelete folder
+
+Delete a folder from your Azure storage account
+
+#### Required arguments:
+- container name
+- account name
+- folder name
+
+#### Optional arguments:
+- retention time: time to retain deleted files in the folder. Default is 8 days
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+
+#### Example commands:
+
+These commands will use `container-name` as the name of the container and `account_name` as the name of the storage account
+
+To delete the folder `folder_name` from your Azure storage account
+
+`AzureDelete folder -a account_name -c container-name -f folder_name`
+
+To delete the folder `folder_name` nested in folder outputs from your Azure storage account, and retain it for 10 days
+
+`AzureDelete folder -a account_name -c container-name -f outputs/folder_name -r 10`
+
+#### Usage
+
+```
+usage: AzureDelete folder [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -f FOLDER [-r RETENTION_TIME]
+
+Delete a folder in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -c CONTAINER_NAME, --container_name CONTAINER_NAME
+                        Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted.
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -f FOLDER, --folder FOLDER
+                        Name of folder to delete in Azure storage. e.g. InterOp
+  -r RETENTION_TIME, --retention_time RETENTION_TIME
+                        Retention time for deleted files. Default is 8 days
+```

Azure/AzureStorage/docs/download.md

@@ -0,0 +1,187 @@
+## AzureDownload
+
+Download containers, files, or folders from your Azure storage account
+
+Choose either the [`container`](#azuredownload-container), [`file`](#azuredownload-file), or  [`folder`](#azuredownload-folder) functionality
+
+#### General usage
+
+```
+usage: AzureDownload [-h] {container,file,folder} ...
+
+Download containers/files/folders from Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+
+Available functionality:
+  {container,file,folder}
+    container           Download a container from Azure storage
+    file                Download a file from Azure storage
+    folder              Download a folder from Azure storage
+```
+
+
+### AzureDownload container
+
+Download a container from your Azure storage account
+
+#### Required arguments:
+- container name
+- account name
+
+#### Optional arguments:
+- output path: local path where container is to be saved. Default is your current working directory
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+
+#### Example commands:
+
+These commands will use `container-name` as the name of the container and `account_name` as the name of the storage account
+
+To perform a basic container download (download to your current working directory)
+
+`AzureDownload container -a account name -c container-name`
+
+To download a container to the folder `outputs` in your current working directory
+
+`AzureDownload container -a account name -c container-name -o outputs`
+
+To download a container to the folder `/home/users/outputs` 
+
+`AzureDownload container -a account name -c container-name -o /home/users/outputs`
+
+#### Usage
+
+```
+usage: AzureDownload container [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] [-o OUTPUT_PATH]
+
+Download a container from Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -c CONTAINER_NAME, --container_name CONTAINER_NAME
+                        Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted.
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -o OUTPUT_PATH, --output_path OUTPUT_PATH
+                        Name and path of directory in which the outputs are to be saved. Default is your $CWD
+```
+
+### AzureDownload file
+
+Download a file from your Azure storage account
+
+#### Required arguments:
+- container name
+- account name
+- file name
+
+#### Optional arguments:
+- output path: local path where container is to be saved. Default is your current working directory
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+
+#### Example commands:
+
+These commands will use `container-name` as the name of the container and `account_name` as the name of the storage account
+
+To download the file `file_name.gz` to your current working directory
+
+`AzureDownload file -a account name -c container-name -f file_name.gz`
+
+To download the file `file_name.gz` nested in the `outputs` folder to your current working directory
+
+`AzureDownload file -a account name -c container-name -f outputs/file_name.gz`
+
+To download the file `file_name.gz` nested in the `outputs` folder to the folder `files` in your current working directory
+
+`AzureDownload file -a account name -c container-name -f outputs/file_name.gz -o files`
+
+To download the file `file_name.gz` to the folder `/home/users/outputs` 
+
+`AzureDownload file -a account name -c container-name -f file_name.gz -o /home/users/outputs`
+
+
+#### Usage
+
+```
+usage: AzureDownload file [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] [-o OUTPUT_PATH] -f FILE
+
+Download a file from Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -c CONTAINER_NAME, --container_name CONTAINER_NAME
+                        Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted.
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -o OUTPUT_PATH, --output_path OUTPUT_PATH
+                        Name and path of directory in which the outputs are to be saved. Default is your $CWD
+  -f FILE, --file FILE  Name of file to download from Azure storage.e.g. 2022-SEQ-0001_S1_L001_R1_001.fastq.gz
+```
+
+### AzureDownload folder
+
+Download a folder from your Azure storage account
+
+#### Required arguments:
+- container name
+- account name
+- folder name
+
+#### Optional arguments:
+- output path: local path where container is to be saved. Default is your current working directory
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+
+#### Example commands:
+
+These commands will use `container-name` as the name of the container and `account_name` as the name of the storage account
+
+To download the folder `folder_name` to your current working directory
+
+`AzureDownload folder -a account name -c container-name -f folder_name`
+
+To download the folder `folder_name` nested in the `outputs` folder to your current working directory
+
+`AzureDownload folder -a account name -c container-name -f outputs/folder_name`
+
+To download the folder `folder_name` nested in the `outputs` folder to the folder `folders` in your current working directory
+
+`AzureDownload folder -a account name -c container-name -f outputs/folder_name -o folders`
+
+To download the folder `folder_name` to the folder `/home/users/outputs` 
+
+`AzureDownload folder -a account name -c container-name -f folder_name -o /home/users/outputs`
+
+#### Usage 
+
+```
+usage: AzureDownload folder [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] [-o OUTPUT_PATH] -f FOLDER
+
+Download a folder from Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -c CONTAINER_NAME, --container_name CONTAINER_NAME
+                        Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted.
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -o OUTPUT_PATH, --output_path OUTPUT_PATH
+                        Name and path of directory in which the outputs are to be saved. Default is your $CWD
+  -f FOLDER, --folder FOLDER
+                        Name of the folder to download from Azure storage e.g. InterOp
+```

Azure/AzureStorage/docs/index.md

@@ -0,0 +1,20 @@
+## OLC Bioinformatics AzureStorage tools
+
+This suite of tools (written in Python) allows you to manipulate containers/files/folders in your Azure storage account.
+
+There are nine scripts in this package:
+
+1. [`AzureCredentials`](credentials.md): enter, modify, or delete your Azure connection string and account name into your system keyring, avoiding storing plain text passwords, environmental variables, and entering the connection string every time you run one of the scripts in the package
+2. [`AzureUpload`](upload.md): upload a file or folder to a container in your Azure storage account
+3. [`AzureSAS`](sas_url.md): create SAS (shared access signature) URLs for a file, a folder, or an entire container in your Azure storage account.
+4. [`AzureMove`](move.md): move a file, folder, or an entire container within your Azure storage account
+5. [`AzureDownload`](download.md): download a file, folder, or an entire container from your Azure storage account
+6. [`AzureTier`](set_tier.md): set the storage tier of a file, folder, or an entire container from your Azure storage account
+7. [`AzureDelete`](delete.md): delete a file, folder, or an entire container from your Azure storage account
+8. [`AzureAutomate`](automate.md): run upload, sas, move, download, set_tier, and/or delete in batch
+9. [`AzureList`](list.md): List and optionally filter containers and/or files in your Azure storage account
+
+
+### Feedback
+
+If you encounter any issues installing or running AzureStorage, have feature requests, or need assistance, please [open an issue on GitHub](https://github.com/OLC-LOC-Bioinformatics/AzureStorage/issues/new/choose), or email me at `adam.koziol@inspection.gc.ca`  

Azure/AzureStorage/docs/install.md

@@ -0,0 +1,49 @@
+## Installation
+
+AzureStorage is available as a conda package, so conda must be installed on your system.
+
+### Conda
+
+Skip this step if you have already installed conda
+
+```
+wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+bash miniconda.sh -b -p $HOME/miniconda
+conda update -q conda
+```
+
+### AzureStorage
+
+You can now install the AzureStorage package:
+
+`conda install -c olc-bioinformatics azure-storage=0.0.2`
+
+### Credentials 
+
+You must enter your Azure storage connection string and account name into the system keyring before running any of the other scripts
+
+[Find your connection string](https://docs.microsoft.com/en-us/azure/storage/common/storage-configure-connection-string#:~:text=You%20can%20find%20your%20storage,primary%20and%20secondary%20access%20keys.)
+
+[Find your account key](https://www.zenko.io/blog/how-to-find-keys-and-account-info-for-aws-azure-and-google/#:~:text=Azure%20Account%20Name%C2%A0%3D%20the%20name%20of%20your%20Azure%20storage%20account%20located%20on%20the%20top%20of%20the%20Azure%20Portal%20(screenshot%20below%20%E2%80%93%20%E2%80%9Cscalitydemo%E2%80%9D%20is%20Azure%20Account%20Name).)
+
+Once you know your account key and connection string, run:
+
+`AzureCredentials store`
+
+Your credentials will be securely stored in the system keyring
+
+### Tests
+
+If you encounter issues with the AzureStorage package, tests are available to ensure that the installation was successful and your credentials are valid.
+
+You will need to clone this repository and run the tests with pytest
+
+
+`git clone https://github.com/OLC-LOC-Bioinformatics/AzureStorage.git`
+
+`cd AzureStorage`
+
+`python -m pytest tests/ --cov=azure_storage --cov-config=.coveragec`
+
+
+

Azure/AzureStorage/docs/list.md

@@ -0,0 +1,165 @@
+## AzureList
+
+List and optionally filter containers and/or files in your Azure storage account
+
+Choose either the [`container`](#azurelist-container), or the [`search`](#azurelist-search) functionality
+
+This script allows you to filter using regular expressions, so make sure you [know what you're doing](https://docs.python.org/3/howto/regex.html), [check out a tutorial](https://docs.python.org/3/howto/regex.html), [look at a cheatsheet](https://www.dataquest.io/blog/regex-cheatsheet/), and/or [test your expressions](https://pythex.org/)
+
+**Important:** since the regular expressions are being entered on the command line, you will need to escape certain characters e.g. ! should be \!
+
+#### General Usage
+
+```
+usage: AzureList [-h] {container,search} ...
+
+Explore your Azure storage account
+
+optional arguments:
+  -h, --help          show this help message and exit
+
+Available functionality:
+  {container,search}
+    container         Filter and list containers in your Azure storage account
+    search            Search files in a container (or containers) in Azure storage
+```
+
+### AzureList container
+
+List and optionally filter containers in your Azure storage account
+
+#### AzureList container required arguments
+- account name
+
+#### AzureList container optional arguments
+- expression: expression to use to filter the containers. Regular expressions are supported. Note that since the regular expression is being entered on the command line, you may need to escape certain characters e.g. ! should be \\!
+- output_file: name and path of file in which the outputs are to be saved.
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+
+#### AzureList container example commands
+
+These commands will use `account_name` as the name of the storage account
+
+To list all containers in your Azure storage account
+
+`AzureList container -a account_name`
+
+To confirm the container `191216-dar` is present in your account
+
+`AzureList container -a account_name 191216-dar`
+
+To filter the list of containers to those starting with `19`
+
+`AzureList container -a account_name 19*`
+
+To filter the list of container to those starting with `19` and four additional digits followed by a dash
+
+`AzureList container -a account_name 19d{4}-*`
+
+To filter the list of containers to those starting with six digits, a dash, and three digits
+
+`AzureList container -a account_name \\d{6}-\\D{3}`
+
+To filter the list of containers to those ending with `outputs`
+
+`AzureList container -a account_name *outputs\$`
+
+To filter the list of containers to those that start with `19` and four additional digits, followed by a dash, three letters, and does not contain the word `outputs`
+
+`AzureList container -a account_name 1912\\d{2}-\\D{3}\(\?\!*output\)`
+
+#### AzureList container usage
+
+```
+usage: AzureList container [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] [-o OUTPUT_FILE]
+                           [expression]
+
+Filter and list containers in your Azure storage account
+
+positional arguments:
+  expression            Expression to search. This command supports regular expressions. e.g. 1912* will return all containers starting with 1912, including 191216-dar Note that since the regular expression is being entered on the command line, you may need to escape certain characters e.g. ! should be \!
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -o OUTPUT_FILE, --output_file OUTPUT_FILE
+                        Optionally provide the name and path of file in which the outputs are to be saved.
+```
+
+### AzureList search
+
+Filter files in a container (or containers) in Azure storage
+
+#### AzureList search required arguments
+- account name
+
+#### AzureList search optional arguments
+- container_name: name of the Azure storage container. Regular expressions are supported. Note that since the regular expression is being entered on the command line, you may need to escape certain characters e.g. ! should be \\!
+- expression: expression to use to filter the containers. Regular expressions are supported. Note that since the regular expression is being entered on the command line, you may need to escape certain characters e.g. ! should be \\!
+- output_file: name and path of file in which the outputs are to be saved.
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+
+#### AzureList search example commands
+
+These commands will use `account_name` as the name of the storage account. Note that all the regex examples used in [`AzureList container`](#azurelist-container-example-commands) can be used here
+
+To list all files in all containers in your storage account
+
+`AzureList search -a account_name`
+
+To list all files in all containers ending with `.gz`
+
+`AzureList search -a account_name \*.gz`
+
+To list all files in the container `container-name`
+
+`AzureList search -a account_name -c container_name`
+
+To list all files in the container `container-name` starting with `reports`
+
+`AzureList search -a account_name -c container_name reports*`
+
+To list all files in the container `container-name` ending with `.gz`
+
+`AzureList search -a account_name -c container-name \*.gz`
+
+To list all files in the container `container-name` that contain `.gz` 
+
+`AzureList search -a account_name -c container-name \*.gz*`
+
+To list all files in the container `container-name` that contain `.gz` (but not at the end)
+
+`AzureList search -a account_name -c container-name \*.gz.+`
+
+#### AzureList search usage
+
+```
+usage: AzureList search [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] [-o OUTPUT_FILE]
+                        [-c [CONTAINER_NAME]]
+                        [expression]
+
+Filter files in a container (or containers) in Azure storage
+
+positional arguments:
+  expression            Expression to search. This command supports regular expressions. e.g. 1912* will return all containers starting with 1912, including 191216-dar Note that since the regular expression is being entered on the command line, you may need to escape certain characters e.g. ! should be \!
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -o OUTPUT_FILE, --output_file OUTPUT_FILE
+                        Optionally provide the name and path of file in which the outputs are to be saved.
+  -c [CONTAINER_NAME], --container_name [CONTAINER_NAME]
+                        Name of the Azure storage container. This command supports regular expressions e.g. 1912* will return all containers starting with 1912.Note that since the regular expression is being entered on the command line, you may need to escape certain characters e.g. ! should be \! You can make your queries as complex as you wish: 1912\d{2}-\D{3}\(\?\!*output\) will only return containers that start with 1912, and have two additional digits. If the word output is present, any matches are ignored. There also have to be exactly three letters following a dash and the first six numbers e.g. 191216-dar and 191227-dar will be returned but not 191216-dar-outputs 191202-test, 191216dar, 1912162-dar, 191203-m05722, 191114-gta, or 200105-dar (and many others)
+```

Azure/AzureStorage/docs/move.md

@@ -0,0 +1,232 @@
+## AzureMove
+
+Move containers, files, or folders within your Azure storage account.
+
+Choose either the [`container`](#azuremove-container), [`file`](#azuremove-file), or  [`folder`](#azuremove-folder) functionality
+
+#### General usage
+
+```
+usage: AzureMove [-h] {container,file,folder} ...
+
+Move containers, files, or folders in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+
+Available functionality:
+  {container,file,folder}
+    container           Move a container in Azure storage
+    file                Move a file within Azure storage 
+    folder              Move a folder within Azure storage
+
+```
+
+### AzureMove container
+
+Move a container within your Azure storage account
+
+#### Required arguments:
+- container name
+- account name
+
+#### Optional arguments:
+- target container: name of the container into which the container is to be moved
+- path to store the container: nest the container within the target container
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+- storage tier: set the storage tier of the file in Azure storage. Options are Hot, Cool, Archive. Default is Hot
+
+#### Example commands:
+
+These commands will use `container-name` as the name of the container, `target-container` as the name of the target container, and `account_name` as the name of the storage account
+
+To perform a basic move (this also renames a container):
+
+`AzureMove container -a account_name -c container-name -t target-container`
+
+To move a container, and set the storage tier to `Cool`
+
+`AzureMove container -a account_name -c container-name -t target-container -s Cool`
+
+To move a container and nest it into folder `outputs`:
+
+`AzureMove container -a account_name -c container-name -t target-container -r outputs`
+
+
+#### Usage
+
+```
+usage: AzureMove container [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -t TARGET_CONTAINER [-r RESET_PATH]
+                           [-s STORAGE_TIER]
+
+Move a container in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -c CONTAINER_NAME, --container_name CONTAINER_NAME
+                        Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted.
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -t TARGET_CONTAINER, --target_container TARGET_CONTAINER
+                        The target container to which the container/file/folder is to be moved (this can be the same as the container_name if you want to move a file/folder within a container
+  -r RESET_PATH, --reset_path RESET_PATH
+                        Set the path of the container/file/folder within a folder in the target container e.g. sequence_data/220202-m05722. If you want to place it directly in the container without any nesting, use or ''
+  -s STORAGE_TIER, --storage_tier STORAGE_TIER
+                        Set the storage tier for the container/file/folder to be moved. Options are "Hot", "Cool", and "Archive". Default is Hot
+```
+
+### AzureMove file
+
+Move a file within your Azure storage account
+
+#### Required arguments:
+- container name
+- account name
+- file name
+
+#### Optional arguments:
+- target container: name of the container into which the container is to be moved
+- path to store the container: nest the container within the target container
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+- storage tier: set the storage tier of the file in Azure storage. Options are Hot, Cool, Archive. Default is Hot
+
+#### Example commands:
+
+These commands will use `container-name` as the name of the container, `target-container` as the name of the target container, and `account_name` as the name of the storage account
+
+To move the file `file_name.gz`
+
+`AzureMove file -a account_name -c container-name -t target-container -f file_name.gz`
+
+To move the file `file_name.gz`, and set the storage tier to `Cool`
+
+`AzureMove file -a account_name -c container-name -t target-container -f file_name.gz -s Cool`
+
+To move the file `file_name.gz` nested in folder `outputs`
+
+`AzureMove file -a account_name -c container-name -t target-container -f outputs/file_name.gz`
+
+To move the file `file_name.gz` nested in folder `outputs` to the root of the source container
+
+`AzureMove file -a account_name -c container-name -t container-name -f outputs/file_name.gz -r ""`
+
+To move the file `file_name.gz` nested in folder `outputs` to folder `results` in the source container
+
+`AzureMove file -a account_name -c container-name -t container-name -f outputs/file_name.gz -r results`
+
+To move the file `file_name.gz` nested in folder `outputs` to the root of the target container
+
+`AzureMove file -a account_name -c container-name -t target-container -f outputs/file_name.gz -r ""`
+
+To move the file `file_name.gz` nested in folder `outputs` to folder `results` in the target container
+
+`AzureMove file -a account_name -c container-name -t target-container -f outputs/file_name.gz -r results`
+
+#### Usage
+
+```
+usage: AzureMove file [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -t TARGET_CONTAINER [-r RESET_PATH]
+                      [-s STORAGE_TIER] -f FILE
+
+Move a file within Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -c CONTAINER_NAME, --container_name CONTAINER_NAME
+                        Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted.
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -t TARGET_CONTAINER, --target_container TARGET_CONTAINER
+                        The target container to which the container/file/folder is to be moved (this can be the same as the container_name if you want to move a file/folder within a container
+  -r RESET_PATH, --reset_path RESET_PATH
+                        Set the path of the container/file/folder within a folder in the target container e.g. sequence_data/220202-m05722. If you want to place it directly in the container without any nesting, use or ''
+  -s STORAGE_TIER, --storage_tier STORAGE_TIER
+                        Set the storage tier for the container/file/folder to be moved. Options are "Hot", "Cool", and "Archive". Default is Hot
+  -f FILE, --file FILE  Name of blob file to move in Azure storage. e.g. 2022-SEQ-0001_S1_L001_R1_001.fastq.gz
+```
+
+### AzureMove folder
+
+Move a folder within your Azure storage account
+
+#### Required arguments:
+- container name
+- account name
+- folder name
+
+#### Optional arguments:
+- target container: name of the container into which the container is to be moved
+- path to store the container: nest the container within the target container
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+- storage tier: set the storage tier of the file in Azure storage. Options are Hot, Cool, Archive. Default is Hot
+
+#### Example commands:
+
+These commands will use `container-name` as the name of the container, `target-container` as the name of the target container, and `account_name` as the name of the storage account
+
+To move the folder `folder_name`
+
+`AzureMove folder -a account_name -c container-name -t target-container -f folder_name`
+
+To move the folder `folder_name`, and set the storage tier to `Cool`
+
+`AzureMove folder -a account_name -c container-name -t target-container -f folder_name -s Cool`
+
+To move the folder `folder_name` nested in folder `outputs`
+
+`AzureMove folder -a account_name -c container-name -t target-container -f outputs/folder_name`
+
+To move the folder `folder_name` nested in folder `outputs` to the root of the source container
+
+`AzureMove folder -a account_name -c container-name -t container-name -f outputs/folder_name -r ""`
+
+To move the folder `folder_name` nested in folder `outputs` to folder `results` in the source container
+
+`AzureMove folder -a account_name -c container-name -t container-name -f outputs/folder_name -r results`
+
+To move the folder `folder_name` nested in folder `outputs` to the root of the target container
+
+`AzureMove folder -a account_name -c container-name -t target-container -f outputs/folder_name -r ""`
+
+To move the folder `folder_name` nested in folder `outputs` to folder `results` in the target container
+
+`AzureMove folder -a account_name -c container-name -t target-container -f outputs/folder_name -r results`
+
+#### Usage
+
+```
+usage: AzureMove folder [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -t TARGET_CONTAINER [-r RESET_PATH]
+                        [-s STORAGE_TIER] -f FOLDER
+
+Move a folder within Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -c CONTAINER_NAME, --container_name CONTAINER_NAME
+                        Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted.
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -t TARGET_CONTAINER, --target_container TARGET_CONTAINER
+                        The target container to which the container/file/folder is to be moved (this can be the same as the container_name if you want to move a file/folder within a container
+  -r RESET_PATH, --reset_path RESET_PATH
+                        Set the path of the container/file/folder within a folder in the target container e.g. sequence_data/220202-m05722. If you want to place it directly in the container without any nesting, use or ''
+  -s STORAGE_TIER, --storage_tier STORAGE_TIER
+                        Set the storage tier for the container/file/folder to be moved. Options are "Hot", "Cool", and "Archive". Default is Hot
+  -f FOLDER, --folder FOLDER
+                        Name of folder to move in Azure storage. e.g. InterOp
+```

Azure/AzureStorage/docs/sas_url.md

@@ -0,0 +1,210 @@
+## AzureSAS
+
+Create shared access signatures (SAS) URLs for containers, files, folders in your Azure storage account.
+
+Note that each file in a container/folder has to be downloaded separately, so if there are 1000 files in the container, 1000 SAS URLs will be provided
+
+Choose either the [`container`](#azuresas-container), [`file`](#azuresas-file), or  [`folder`](#azuresas-folder) functionality
+
+#### General usage
+
+```
+usage: AzureSAS [-h] {container,file,folder} ...
+
+Create shared access signatures (SAS) for containers/files/folders from Azure storage.
+Note that each file in the container/folder has to be downloaded separately, so if
+there are 1000 files in the container, 1000 SAS will be provided
+
+optional arguments:
+  -h, --help            show this help message and exit
+
+Available functionality:
+  {container,file,folder}
+    container           Create SAS for all files in a container in Azure storage
+    file                Create a SAS for a file in Azure storage
+    folder              Create SAS for all files in a folder in Azure storage
+```
+
+### AzureSAS container
+
+Create SAS URLs for all files in a container in your Azure storage account
+
+#### Required arguments:
+- container name
+- account name
+
+#### Optional arguments:
+- output file: file in which the SAS URLs are to be written. Default is `sas.txt` in your current working directory
+- expiry: the number of days the SAS URL with be valid. Minimum is 1, maximum is 365. Default is 10
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+
+#### Example commands:
+
+These commands will use `container-name` as the name of the container, and `account_name` as the name of the storage account
+
+To create SAS URLs with default settings:
+
+`AzureSAS container -a account_name -c container-name`
+
+To create SAS URLs with an expiry of 15 days:
+
+`AzureSAS container -a account_name -c container-name -e 15`
+
+To create SAS URLs, and save them to the file `sas_urls.txt` in your current working directory:
+
+`AzureSAS container -a account_name -c container-name -o sas_urls.txt`
+
+To create SAS URLs, and save them to the file `sas_urls.txt` nested in folder `outputs` in your current working directory:
+
+`AzureSAS container -a account_name -c container-name -o outputs/sas_urls.txt`
+
+#### Usage
+```
+usage: AzureSAS container [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] [-e EXPIRY] [-o OUTPUT_FILE]
+
+Create SAS URLs for all files in a container in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -c CONTAINER_NAME, --container_name CONTAINER_NAME
+                        Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted.
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -e EXPIRY, --expiry EXPIRY
+                        The number of days that the SAS URL will be valid. The minimum is 1, and the maximum is 365. The default is 10.
+  -o OUTPUT_FILE, --output_file OUTPUT_FILE
+                        Name and path of file in which the SAS URLs are to be saved. Default is $CWD/sas.txt
+```
+
+### AzureSAS file
+
+Create a SAS URL for a file in a container in your Azure storage account
+
+#### Required arguments:
+- container name
+- account name
+- file name
+
+#### Optional arguments:
+- output file: file in which the SAS URLs are to be written. Default is `sas.txt` in your current working directory
+- expiry: the number of days the SAS URL with be valid. Minimum is 1, maximum is 365. Default is 10
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+
+#### Example commands:
+
+These commands will use `container-name` as the name of the container, and `account_name` as the name of the storage account
+
+To create a SAS URL for file `file_name.gz` with default settings:
+
+`AzureSAS file -a account_name -c container-name -f file_name.gz`
+
+To create a SAS URL for file `file_name.gz` nested in folder `outputs` with default settings:
+
+`AzureSAS file -a account_name -c container-name -f outputs/file_name.gz`
+
+To create a SAS URL for file `file_name.gz` with an expiry of 15 days:
+
+`AzureSAS file -a account_name -c container-name f file_name.gz -e 15`
+
+To create a SAS URL for file `file_name.gz`, and save it to the file `sas_urls.txt` in your current working directory:
+
+`AzureSAS file -a account_name -c container-name -f file_name.gz -o sas_urls.txt`
+
+To create a SAS URL for file `file_name.gz`, and save it to the file `sas_urls.txt` nested in folder `outputs` in your current working directory:
+
+`AzureSAS file -a account_name -c container-name -f file_name.gz -o outputs/sas_urls.txt`
+
+#### Usage
+
+```
+usage: AzureSAS file [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] [-e EXPIRY] [-o OUTPUT_FILE] -f FILE
+
+Create a SAS URL for a file in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -c CONTAINER_NAME, --container_name CONTAINER_NAME
+                        Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted.
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -e EXPIRY, --expiry EXPIRY
+                        The number of days that the SAS URL will be valid. The minimum is 1, and the maximum is 365. The default is 10.
+  -o OUTPUT_FILE, --output_file OUTPUT_FILE
+                        Name and path of file in which the SAS URLs are to be saved. Default is $CWD/sas.txt
+  -f FILE, --file FILE  Path of file in Azure storage from which a SAS URL is to be created. e.g. 2022-SEQ-0001_S1_L001_R1_001.fastq.gz
+```
+
+### AzureSAS folder
+
+Create SAS URLs for all files in a folder in your Azure storage account
+
+#### Required arguments:
+- container name
+- account name
+- folder name
+
+#### Optional arguments:
+- output file: file in which the SAS URLs are to be written. Default is `sas.txt` in your current working directory
+- expiry: the number of days the SAS URL with be valid. Minimum is 1, maximum is 365. Default is 10
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+
+#### Example commands:
+
+These commands will use `container-name` as the name of the container, and `account_name` as the name of the storage account
+
+To create SAS URLs for all files in folder `folder_name` with default settings:
+
+`AzureSAS folder -a account_name -c container-name -f folder_name`
+
+To create SAS URLs for all files in folder `folder_name` nested in folder `outputs` with default settings:
+
+`AzureSAS folder -a account_name -c container-name -f outputs/folder_name`
+
+To create SAS URLs for all files in folder `folder_name` with an expiry of 15 days:
+
+`AzureSAS folder -a account_name -c container-name f folder_name -e 15`
+
+To create SAS URLs for all files in folder `folder_name`, and save them to the file `sas_urls.txt` in your current working directory:
+
+`AzureSAS folder -a account_name -c container-name -f folder_name -o sas_urls.txt`
+
+To create SAS URLs for all files in folder `folder_name`, and save them to the file `sas_urls.txt` nested in folder `outputs` in your current working directory:
+
+`AzureSAS folder -a account_name -c container-name -f folder_name -o outputs/sas_urls.txt`
+
+
+#### Usage
+
+```
+usage: AzureSAS folder [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] [-e EXPIRY] [-o OUTPUT_FILE] -f FOLDER
+
+Create SAS URLs for all files in a folder in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -c CONTAINER_NAME, --container_name CONTAINER_NAME
+                        Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted.
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -e EXPIRY, --expiry EXPIRY
+                        The number of days that the SAS URL will be valid. The minimum is 1, and the maximum is 365. The default is 10.
+  -o OUTPUT_FILE, --output_file OUTPUT_FILE
+                        Name and path of file in which the SAS URLs are to be saved. Default is $CWD/sas.txt
+  -f FOLDER, --folder FOLDER
+                        Name of the folder for which SAS URLs are to be created for all files. e.g. InterOp
+```

Azure/AzureStorage/docs/set_tier.md

@@ -0,0 +1,156 @@
+## AzureTier
+
+Set the storage tier (`Hot`, `Cool`, or `Archive`) for containers, files, or folders in your Azure storage account
+
+Choose either the [`container`](#azuretier-container), [`file`](#azuretier-file), or  [`folder`](#azuretier-folder) functionality
+
+#### General usage
+
+```
+usage: AzureTier [-h] {container,file,folder} ...
+
+Set the storage tier of containers/files/folders in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+
+Available functionality:
+  {container,file,folder}
+    container           Change the storage tier of a container in Azure storage
+    file                Change the storage tier of a file in Azure storage
+    folder              Change the storage tier of a folder in Azure storage
+```
+
+### AzureTier container
+
+Set the storage tier of a container in your Azure storage account
+
+#### Required arguments:
+- container name
+- account name
+- storage tier
+
+#### Optional arguments:
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+
+#### Example command:
+
+These commands will use `container-name` as the name of the container and `account_name` as the name of the storage account
+
+To change the storage tier of a container to `Cool`
+
+`AzureTier -a account_name -c container-name -s Cool`
+
+#### Usage
+
+```
+usage: AzureTier container [-h] -c CONTAINER_NAME -a ACCOUNT_NAME
+                           [-p PASSPHRASE] [-v VERBOSITY] -s STORAGE_TIER
+
+Change the storage tier of a container in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -c CONTAINER_NAME, --container_name CONTAINER_NAME
+                        Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted.
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -s STORAGE_TIER, --storage_tier STORAGE_TIER
+                        Set the storage tier for a container/file/folder. Options are "Hot", "Cool", and "Archive"
+```
+
+### AzureTier file
+
+Set the storage tier of a file in your Azure storage account
+
+#### Required arguments:
+- container name
+- account name
+- file name
+- storage tier
+
+#### Optional arguments:
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+
+#### Example command:
+
+These commands will use `container-name` as the name of the container and `account_name` as the name of the storage account
+
+To change the storage tier of the file `file_name.gz` to `Archive`
+
+`AzureTier -a account_name -c container-name -f file_name.gz -s Archive`
+
+#### Usage
+
+```
+usage: AzureTier file [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE]
+                      [-v VERBOSITY] -s STORAGE_TIER -f FILE
+
+Change the storage tier of a file in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -c CONTAINER_NAME, --container_name CONTAINER_NAME
+                        Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted.
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -s STORAGE_TIER, --storage_tier STORAGE_TIER
+                        Set the storage tier for a container/file/folder. Options are "Hot", "Cool", and "Archive"
+  -f FILE, --file FILE  Name of file in Azure storage that will have its storage tier sete.g. 220202-m05722/2022-SEQ-0001_S1_L001_R1_001.fastq.gz
+```
+
+### AzureTier folder
+
+Set the storage tier of a folder in your Azure storage account
+
+#### Required arguments:
+- container name
+- account name
+- folder name
+- storage tier
+
+#### Optional arguments:
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+
+#### Example command:
+
+These commands will use `container-name` as the name of the container and `account_name` as the name of the storage account
+
+To change the storage tier of the folder `results/folder_name` to `Hot`
+
+`AzureTier -a account_name -c container-name -f results/folder_name -s Hot`
+
+#### Usage
+
+```
+usage: AzureTier folder [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE]
+                        [-v VERBOSITY] -s STORAGE_TIER -f FOLDER
+
+Change the storage tier of a folder in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -c CONTAINER_NAME, --container_name CONTAINER_NAME
+                        Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted.
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -s STORAGE_TIER, --storage_tier STORAGE_TIER
+                        Set the storage tier for a container/file/folder. Options are "Hot", "Cool", and "Archive"
+  -f FOLDER, --folder FOLDER
+                        Name of the folder in Azure storage that will have its storage tier set e.g. InterOp
+```

Azure/AzureStorage/docs/upload.md

@@ -0,0 +1,177 @@
+## AzureUpload
+
+AzureUpload allows you to upload a file or a folder to your Azure storage account.
+
+Choose either the [`file`](#azureupload-file) or [`folder`](#azureupload-folder) functionality
+
+#### General Usage
+```
+usage: AzureUpload [-h] {file,folder} ...
+
+Upload files or folders to Azure storage
+
+optional arguments:
+  -h, --help     show this help message and exit
+
+Available functionality:
+  {file,folder}
+    file         Upload a file to Azure storage
+    folder       Upload a folder to Azure storage
+```
+
+### AzureUpload file
+
+Upload a single file to your Azure storage account. 
+
+#### Required arguments:
+- container name
+- account name
+- name and path of file to upload
+
+#### Optional arguments:
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+- path to store the file: change the folder structure of the file in Azure storage compared to your local system
+- storage tier: set the storage tier of the file in Azure storage. Options are Hot, Cool, Archive. Default is Hot
+
+#### Example commands:
+
+These commands will use `container-name` as the name of the container, and `account_name` as the name of the storage account
+
+To upload the file `file_name.gz` in your current working directory:
+
+`AzureUpload file -a account_name -c container-name -f file_name.gz`
+
+To upload the file `file_name.gz` in your current working directory and set the storage tier to `Cool`:
+
+`AzureUpload file -a account_name -c container-name -f file_name.gz -s Cool`
+
+To upload the file `file_name.gz` nested in the folder `outputs` in your current working directory:
+
+`AzureUpload file -a account_name -c container-name -f outputs/file_name.gz`
+
+To upload the file `file_name.gz` nested in the folder `outputs` in your current working directory to the root of the container:
+
+`AzureUpload file -a account_name -c container-name -f outputs/file_name.gz -r ""`
+
+To upload the file `file_name.gz` nested in the folder `outputs` in your current working directory to the folder `results/parsing` in the container:
+
+`AzureUpload file -a account_name -c container-name -f outputs/file_name.gz -r results/parsing`
+
+To upload the file `/home/users/account/files/file_name.gz` to path `data`:
+
+`AzureUpload file -a account_name -c container-name -f /home/users/account/files/file_name.gz -r data`
+
+To upload that same file to the root of the container:
+
+`AzureUpload file -a account_name -c container-name -f /home/users/account/files/file_name.gz -r ""`
+
+To retain the path of the file:
+
+`AzureUpload file -a account_name -c container-name -f /home/users/account/files/file_name.gz`
+
+#### Usage
+
+```
+usage: AzureUpload file [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE]
+                        [-v {debug,info,warning,error,critical}] [-r RESET_PATH]
+                        [-s {Hot,Cool,Archive}] -f FILE
+
+Upload a file to Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -c CONTAINER_NAME, --container_name CONTAINER_NAME
+                         Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted.
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v {debug,info,warning,error,critical}, --verbosity {debug,info,warning,error,critical}
+                        Set the logging level. Default is info.
+  -r RESET_PATH, --reset_path RESET_PATH
+                        Set the path of the file/folder within a folder in the target container e.g. sequence_data/220202-m05722. If you want to place it directly in the container without any nesting, use "" or ''
+  -s {Hot,Cool,Archive}, --storage_tier {Hot,Cool,Archive}
+                        Set the storage tier for the file/folder to be uploaded. Options are "Hot", "Cool", and "Archive". Default is Hot
+  -f FILE, --file FILE  Name and path of the file to upload to Azure storage.e.g. /mnt/sequences/220202_M05722/2022-SEQ-0001_S1_L001_R1_001.fastq.gz
+```
+
+### AzureUpload folder
+
+Upload a single folder (and its contents) to your Azure storage account. Note that having a trailing slash ('/') at the end of your folder name will not affect the script
+
+#### Required arguments:
+- container name
+- account name
+- name and path of folder to upload
+
+#### Optional arguments:
+- passphrase used to store your connection string in the system keyring (default is AzureStorage)
+- verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info
+- path to store the file: change the folder structure of the file in Azure storage compared to your local system
+- storage tier: set the storage tier of the file in Azure storage. Options are Hot, Cool, Archive. Default is Hot
+
+#### Example commands:
+
+These commands will use `container-name` as the name of the container, and `account_name` as the name of the storage account
+
+To upload the folder `folder_name` in your current working directory:
+
+`AzureUpload folder -a account_name -c container-name -f folder_name`
+
+To upload the folder `folder_name` in your current working directory and set the storage tier to `Cool`:
+
+`AzureUpload folder -a account_name -c container-name -f folder_name -s Cool`
+
+To upload the folder `folder_name` nested in the folder `outputs` in your current working directory:
+
+`AzureUpload folder -a account_name -c container-name -f outputs/folder_name`
+
+To upload the folder `folder_name` nested in the folder `outputs` in your current working directory to the root of the container:
+
+`AzureUpload folder -a account_name -c container-name -f outputs/file_name.gz -r ""`
+
+To upload the folder `folder_name` nested in the folder `outputs` in your current working directory to the folder `results/parsing` in the container:
+
+`AzureUpload folder -a account_name -c container-name -f outputs/folder_namw -r results/parsing`
+
+To upload the folder `/home/users/account/files/` to path `data`:
+
+`AzureUpload folder -a account_name -c container-name -f /home/users/account/files/ -r data`
+
+To upload that same folder to the root of the container:
+
+`AzureUpload folder -a account_name -c container-name -f /home/users/account/files -r ""`
+
+To retain the path of the folder:
+
+`AzureUpload folder -a account_name -c container-name -f /home/users/account/files/`
+
+
+#### Usage
+
+```
+usage: AzureUpload folder [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE]
+                          [-v {debug,info,warning,error,critical}] [-r RESET_PATH]
+                          [-s {Hot,Cool,Archive}] -f FOLDER
+
+Upload a folder to Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -c CONTAINER_NAME, --container_name CONTAINER_NAME
+                         Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted.
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is "AzureStorage".
+  -v {debug,info,warning,error,critical}, --verbosity {debug,info,warning,error,critical}
+                        Set the logging level. Default is info.
+  -r RESET_PATH, --reset_path RESET_PATH
+                        Set the path of the file/folder within a folder in the target container e.g. sequence_data/220202-m05722. If you want to place it directly in the container without any nesting, use "" or ''
+  -s {Hot,Cool,Archive}, --storage_tier {Hot,Cool,Archive}
+                        Set the storage tier for the file/folder to be uploaded. Options are "Hot", "Cool", and "Archive". Default is Hot
+  -f FOLDER, --folder FOLDER
+                        Name and path of the folder to upload to Azure storage.e.g. /mnt/sequences/220202_M05722/
+
+```

Azure/AzureStorage/mkdocs.yml

@@ -0,0 +1,19 @@
+site_name: OLC Bioinformatics Azure Storage
+site_url:  https://OLC-LOC-Bioinformatics.github.io/AzureStorage/
+site_description: Tools for manipulating files in Azure storage, including upload, download, SAS URL creation, move, delete
+repo_url:  https://github.com/OLC-LOC-Bioinformatics/AzureStorage/
+edit_uri: edit/main/docs/
+theme: readthedocs
+
+nav:
+  - Home: 'index.md'
+  - Installation: 'install.md'
+  - Credentials: 'credentials.md'
+  - Upload: 'upload.md'
+  - SAS URL: 'sas_url.md'
+  - Move: 'move.md'
+  - Download: 'download.md'
+  - Set Tier: 'set_tier.md'
+  - Delete: 'delete.md'
+  - Automate: 'automate.md'
+  - List: 'list.md'

Azure/AzureStorage/outputs.txt

@@ -0,0 +1,3 @@
+0000	testo/vir-typer-22-142152.zip
+0000000	testo/vir-typer-22-142152.zip
+0000000	vir-typer-22-142152.zip

Azure/AzureStorage/pytest.ini

@@ -0,0 +1,3 @@
+[pytest]
+filterwarnings =
+    ignore::DeprecationWarning

Azure/AzureStorage/setup.py

@@ -0,0 +1,24 @@
+#!/usr/bin/env python
+from setuptools import setup, find_packages
+setup(
+    name="AzureStorage",
+    version="0.0.2",
+    entry_points={
+        'console_scripts': [
+            'AzureCredentials = azure_storage.azure_credentials:cli',
+            'AzureAutomate = azure_storage.azure_automate:cli',
+            'AzureDownload = azure_storage.azure_download:cli',
+            'AzureDelete = azure_storage.azure_delete:cli',
+            'AzureUpload = azure_storage.azure_upload:cli',
+            'AzureList = azure_storage.azure_list:cli',
+            'AzureMove = azure_storage.azure_move:cli',
+            'AzureTier = azure_storage.azure_tier:cli',
+            'AzureSAS = azure_storage.azure_sas:cli'
+        ],
+    },
+    packages=find_packages(),
+    include_package_data=True,
+    author="Adam Koziol",
+    author_email="adam.koziol@inspection.gc.ca",
+    url="https://github.com/OLC-LOC-Bioinformatics/AzureStorage",
+)

Azure/AzureStorage/site/404.html

@@ -0,0 +1,164 @@
+<!DOCTYPE html>
+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
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+  <script>hljs.initHighlightingOnLoad();</script> 
+  
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+        <div role="search">
+  <form id ="rtd-search-form" class="wy-form" action="/AzureStorage//search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" title="Type search term here" />
+  </form>
+</div>
+      </div>
+
+      <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="/AzureStorage/.">Home</a>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="/AzureStorage/install/">Installation</a>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="/AzureStorage/credentials/">Credentials</a>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="/AzureStorage/upload/">Upload</a>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="/AzureStorage/sas_url/">SAS URL</a>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="/AzureStorage/move/">Move</a>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="/AzureStorage/download/">Download</a>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="/AzureStorage/set_tier/">Set Tier</a>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="/AzureStorage/delete/">Delete</a>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="/AzureStorage/automate/">Automate</a>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="/AzureStorage/list/">List</a>
+                    </li>
+                </ul>
+      </div>
+    </div>
+    </nav>
+
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+        };
+    </script>
+
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Azure/AzureStorage/site/automate/index.html

@@ -0,0 +1,1185 @@
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+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="../credentials/">Credentials</a>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="../upload/">Upload</a>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="../sas_url/">SAS URL</a>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="../move/">Move</a>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="../download/">Download</a>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="../set_tier/">Set Tier</a>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="../delete/">Delete</a>
+                    </li>
+                </ul>
+                <ul class="current">
+                    <li class="toctree-l1 current"><a class="reference internal current" href="./">Automate</a>
+    <ul class="current">
+    <li class="toctree-l2"><a class="reference internal" href="#general-usage">General usage</a>
+    </li>
+    <li class="toctree-l2"><a class="reference internal" href="#azureautomate-upload">AzureAutomate upload</a>
+        <ul>
+    <li class="toctree-l3"><a class="reference internal" href="#general-usage_1">General usage</a>
+    </li>
+        </ul>
+    </li>
+    <li class="toctree-l2"><a class="reference internal" href="#azureautomate-upload-file">AzureAutomate upload file</a>
+        <ul>
+    <li class="toctree-l3"><a class="reference internal" href="#required-arguments">Required arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#optional-arguments">Optional arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#batch-file-format">Batch file format</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#usage">Usage</a>
+    </li>
+        </ul>
+    </li>
+    <li class="toctree-l2"><a class="reference internal" href="#azureautomate-upload-folder">AzureAutomate upload folder</a>
+        <ul>
+    <li class="toctree-l3"><a class="reference internal" href="#required-arguments_1">Required arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#optional-arguments_1">Optional arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#batch-file-format_1">Batch file format</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#usage_1">Usage</a>
+    </li>
+        </ul>
+    </li>
+    <li class="toctree-l2"><a class="reference internal" href="#azureautomate-sas">AzureAutomate sas</a>
+        <ul>
+    <li class="toctree-l3"><a class="reference internal" href="#general-usage_2">General usage</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#azureautomate-sas-container">AzureAutomate sas container</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#required-arguments_2">Required arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#optional-arguments_2">Optional arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#batch-file-format_2">Batch file format</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#usage_2">Usage</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#azureautomate-sas-file">AzureAutomate sas file</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#required-arguments_3">Required arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#optional-arguments_3">Optional arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#batch-file-format_3">Batch file format</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#usage_3">Usage</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#azureautomate-sas-folder">AzureAutomate sas folder</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#required-arguments_4">Required arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#optional-arguments_4">Optional arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#batch-file-format_4">Batch file format</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#usage_4">Usage</a>
+    </li>
+        </ul>
+    </li>
+    <li class="toctree-l2"><a class="reference internal" href="#azureautomate-move">AzureAutomate move</a>
+        <ul>
+    <li class="toctree-l3"><a class="reference internal" href="#general-usage_3">General usage</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#azureautomate-move-container">AzureAutomate move container</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#required-arguments_5">Required arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#optional-arguments_5">Optional arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#batch-file-format_5">Batch file format</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#usage_5">Usage</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#azureautomate-move-file">AzureAutomate move file</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#required-arguments_6">Required arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#optional-arguments_6">Optional arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#batch-file-format_6">Batch file format</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#usage_6">Usage</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#azureautomate-move-folder">AzureAutomate move folder</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#required-arguments_7">Required arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#optional-arguments_7">Optional arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#batch-file-format_7">Batch file format</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#usage_7">Usage</a>
+    </li>
+        </ul>
+    </li>
+    <li class="toctree-l2"><a class="reference internal" href="#azureautomate-download">AzureAutomate download</a>
+        <ul>
+    <li class="toctree-l3"><a class="reference internal" href="#general-usage_4">General usage</a>
+    </li>
+        </ul>
+    </li>
+    <li class="toctree-l2"><a class="reference internal" href="#azureautomate-download-container">AzureAutomate download container</a>
+        <ul>
+    <li class="toctree-l3"><a class="reference internal" href="#required-arguments_8">Required arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#optional-arguments_8">Optional arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#batch-file-format_8">Batch file format</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#usage_8">Usage</a>
+    </li>
+        </ul>
+    </li>
+    <li class="toctree-l2"><a class="reference internal" href="#azureautomate-download-file">AzureAutomate download file</a>
+        <ul>
+    <li class="toctree-l3"><a class="reference internal" href="#required-arguments_9">Required arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#optional-arguments_9">Optional arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#batch-file-format_9">Batch file format</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#usage_9">Usage</a>
+    </li>
+        </ul>
+    </li>
+    <li class="toctree-l2"><a class="reference internal" href="#azureautomate-download-folder">AzureAutomate download folder</a>
+        <ul>
+    <li class="toctree-l3"><a class="reference internal" href="#required-arguments_10">Required arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#optional-arguments_10">Optional arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#batch-file-format_10">Batch file format</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#usage_10">Usage</a>
+    </li>
+        </ul>
+    </li>
+    <li class="toctree-l2"><a class="reference internal" href="#azureautomate-tier">AzureAutomate tier</a>
+        <ul>
+    <li class="toctree-l3"><a class="reference internal" href="#general-usage_5">General usage</a>
+    </li>
+        </ul>
+    </li>
+    <li class="toctree-l2"><a class="reference internal" href="#azureautomate-tier-container">AzureAutomate tier container</a>
+        <ul>
+    <li class="toctree-l3"><a class="reference internal" href="#required-arguments_11">Required arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#optional-arguments_11">Optional arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#batch-file-format_11">Batch file format</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#usage_11">Usage</a>
+    </li>
+        </ul>
+    </li>
+    <li class="toctree-l2"><a class="reference internal" href="#azureautomate-tier-file">AzureAutomate tier file</a>
+        <ul>
+    <li class="toctree-l3"><a class="reference internal" href="#required-arguments_12">Required arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#optional-arguments_12">Optional arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#batch-file-format_12">Batch file format</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#usage_12">Usage</a>
+    </li>
+        </ul>
+    </li>
+    <li class="toctree-l2"><a class="reference internal" href="#azureautomate-tier-folder">AzureAutomate tier folder</a>
+        <ul>
+    <li class="toctree-l3"><a class="reference internal" href="#required-arguments_13">Required arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#optional-arguments_13">Optional arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#batch-file-format_13">Batch file format</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#usage_13">Usage</a>
+    </li>
+        </ul>
+    </li>
+    <li class="toctree-l2"><a class="reference internal" href="#azureautomate-delete">AzureAutomate delete</a>
+        <ul>
+    <li class="toctree-l3"><a class="reference internal" href="#general-usage_6">General usage</a>
+    </li>
+        </ul>
+    </li>
+    <li class="toctree-l2"><a class="reference internal" href="#azureautomate-delete-container">AzureAutomate delete container</a>
+        <ul>
+    <li class="toctree-l3"><a class="reference internal" href="#required-arguments_14">Required arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#optional-arguments_14">Optional arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#batch-file-format_14">Batch file format</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#usage_14">Usage</a>
+    </li>
+        </ul>
+    </li>
+    <li class="toctree-l2"><a class="reference internal" href="#azureautomate-delete-file">AzureAutomate delete file</a>
+        <ul>
+    <li class="toctree-l3"><a class="reference internal" href="#required-arguments_15">Required arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#optional-arguments_15">Optional arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#batch-file-format_15">Batch file format</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#usage_15">Usage</a>
+    </li>
+        </ul>
+    </li>
+    <li class="toctree-l2"><a class="reference internal" href="#azureautomate-delete-folder">AzureAutomate delete folder</a>
+        <ul>
+    <li class="toctree-l3"><a class="reference internal" href="#required-arguments_16">Required arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#optional-arguments_16">Optional arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#batch-file-format_16">Batch file format</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#usage_16">Usage</a>
+    </li>
+        </ul>
+    </li>
+    <li class="toctree-l2"><a class="reference internal" href="#azureautomate-batch">AzureAutomate batch</a>
+    </li>
+    <li class="toctree-l2"><a class="reference internal" href="#batch-file-format_17">Batch file format</a>
+    </li>
+    <li class="toctree-l2"><a class="reference internal" href="#usage_17">Usage</a>
+    </li>
+    </ul>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="../list/">List</a>
+                    </li>
+                </ul>
+      </div>
+    </div>
+    </nav>
+
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+        <a href="..">OLC Bioinformatics Azure Storage</a>
+      </nav>
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+  <ul class="wy-breadcrumbs">
+    <li><a href="..">Docs</a> &raquo;</li>
+    
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+    <li class="wy-breadcrumbs-aside">
+      
+        <a href="https://github.com/OLC-LOC-Bioinformatics/AzureStorage/edit/main/docs/automate.md"
+          class="icon icon-github"> Edit on GitHub</a>
+      
+    </li>
+  </ul>
+  
+  <hr/>
+</div>
+          <div role="main">
+            <div class="section">
+              
+                <h2 id="azureautomate">AzureAutomate</h2>
+<p>Perform multiple upload, SAS URL creation, move, download, storage tier setting, or delete actions. Alternatively, perform multiple actions in a single call</p>
+<p>Choose either the <a href="#azureautomate-upload"><code>upload</code></a>, <a href="#azureautomate-sas"><code>sas</code></a>, <a href="#azureautomate-move"><code>move</code></a>, <a href="#azureautomate-download"><code>download</code></a>, <a href="#azureautomate-tier"><code>tier</code></a>, <a href="#azureautomate-delete"><code>delete</code></a>, or <a href="#azureautomate-batch"><code>batch</code></a> functionality</p>
+<h4 id="general-usage">General usage</h4>
+<pre><code>usage: AzureAutomate [-h] {upload,sas,move,download,tier,delete,batch} ...
+
+Automate the submission of multiple AzureStorage commands
+
+optional arguments:
+  -h, --help            show this help message and exit
+
+Available functionality:
+  {upload,sas,move,download,tier,delete,batch}
+    upload              Upload files/folders to Azure storage
+    sas                 Create SAS URLs for containers/files/folders in Azure storage
+    move                Move containers/files/folders in Azure storage
+    download            Download containers/files/folders in Azure storage
+    tier                Set the storage tier of containers/files/folders in Azure storage
+    delete              Delete containers/files/folders in Azure storage
+    batch               Perform multiple different operations in batch
+</code></pre>
+
+<h3 id="azureautomate-upload">AzureAutomate upload</h3>
+<p>Choose either the <a href="#azureautomate-upload-file"><code>file</code></a> or <a href="#azureautomate-upload-folder"><code>folder</code></a> functionality</p>
+<h4 id="general-usage_1">General usage</h4>
+<pre><code>usage: AzureAutomate upload [-h] {file,folder} ...
+
+Upload files/folders to Azure storage
+
+optional arguments:
+  -h, --help     show this help message and exit
+
+Upload functionality:
+  {file,folder}
+    file         Upload files to Azure storage
+    folder       Upload folders to Azure storage
+</code></pre>
+
+<h3 id="azureautomate-upload-file">AzureAutomate upload file</h3>
+<p>Automate the upload of multiple files to your Azure storage account</p>
+<h4 id="required-arguments">Required arguments:</h4>
+<ul>
+<li>container name</li>
+<li>account name</li>
+<li>name and path of batch file</li>
+</ul>
+<h4 id="optional-arguments">Optional arguments:</h4>
+<ul>
+<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
+<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
+</ul>
+<h4 id="batch-file-format">Batch file format</h4>
+<p>Tab-separated file with the following fields:</p>
+<p><code>container name, file name, destination path (optional), storage tier (optional)</code></p>
+<p>For additional details on running file uploads, please see the <a href="../upload/#azureupload-file"><code>AzureUpload file</code></a> section</p>
+<h4 id="usage">Usage</h4>
+<pre><code>usage: AzureAutomate upload file [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Upload files to Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file with the following fields:
+                         container name, file name, destination path (optional), storage tier (optional)
+</code></pre>
+
+<h3 id="azureautomate-upload-folder">AzureAutomate upload folder</h3>
+<p>Automate the upload of multiple folders to your Azure storage account</p>
+<h4 id="required-arguments_1">Required arguments:</h4>
+<ul>
+<li>container name</li>
+<li>account name</li>
+<li>name and path of batch file</li>
+</ul>
+<h4 id="optional-arguments_1">Optional arguments:</h4>
+<ul>
+<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
+<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
+</ul>
+<h4 id="batch-file-format_1">Batch file format</h4>
+<p>Tab-separated file with the following fields:</p>
+<p><code>container name, folder name, destination path (optional), storage tier (optional)</code></p>
+<p>For additional details on running folder uploads, please see the <a href="../upload/#azureupload-folder"><code>AzureUpload folder</code></a> section</p>
+<h4 id="usage_1">Usage</h4>
+<pre><code>usage: AzureAutomate upload folder [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Upload folders to Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file with the following fields (one entry per line):
+                         container name, folder name, destination path (optional), storage tier (optional)
+</code></pre>
+
+<h3 id="azureautomate-sas">AzureAutomate sas</h3>
+<p>Choose either the <a href="#azureautomate-sas-container"><code>container</code></a>, <a href="#azureautomate-sas-file"><code>file</code></a>, or <a href="#azureautomate-sas-folder"><code>folder</code></a> functionality</p>
+<h4 id="general-usage_2">General usage</h4>
+<pre><code>usage: AzureAutomate sas [-h] {container,file,folder} ...
+
+Create SAS URLs for containers/files/folders in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+
+SAS URL creation functionality:
+  {container,file,folder}
+    container           Create SAS URLs for containers in Azure storage
+    file                Create SAS URLs for files in Azure storage
+    folder              Create SAS URLs for folders in Azure storage
+</code></pre>
+
+<h4 id="azureautomate-sas-container">AzureAutomate sas container</h4>
+<p>Automate the creation of SAS URLs for multiple containers in your Azure storage account</p>
+<h4 id="required-arguments_2">Required arguments:</h4>
+<ul>
+<li>container name</li>
+<li>account name</li>
+<li>name and path of batch file</li>
+</ul>
+<h4 id="optional-arguments_2">Optional arguments:</h4>
+<ul>
+<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
+<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
+</ul>
+<h4 id="batch-file-format_2">Batch file format</h4>
+<p>Tab-separated file with the following fields:</p>
+<p><code>container name, expiry (optional), output file (optional)</code></p>
+<p>For additional details on creating SAS URLs for containers, please see the <a href="../sas_url/#azuresas-container"><code>AzureSAS container</code></a> section</p>
+<h4 id="usage_2">Usage</h4>
+<pre><code>usage: AzureAutomate sas container [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Create SAS URLs for containers in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file with the following fields:
+                        container name, expiry (optional), output file (optional)
+</code></pre>
+
+<h4 id="azureautomate-sas-file">AzureAutomate sas file</h4>
+<p>Automate the creation of SAS URLs for multiple files in your Azure storage account</p>
+<h4 id="required-arguments_3">Required arguments:</h4>
+<ul>
+<li>container name</li>
+<li>account name</li>
+<li>name and path of batch file</li>
+</ul>
+<h4 id="optional-arguments_3">Optional arguments:</h4>
+<ul>
+<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
+<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
+</ul>
+<h4 id="batch-file-format_3">Batch file format</h4>
+<p>Tab-separated file with the following fields:</p>
+<p><code>container name, file name and path, expiry (optional), output file (optional)</code></p>
+<p>For additional details on creating SAS URLs for files, please see the <a href="../sas_url/#azuresas-file"><code>AzureSAS file</code></a> section</p>
+<h4 id="usage_3">Usage</h4>
+<pre><code>usage: AzureAutomate sas file [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Create SAS URLs for files in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file with the following fields:
+                         container name, file name and path, expiry (optional), output file (optional)
+</code></pre>
+
+<h4 id="azureautomate-sas-folder">AzureAutomate sas folder</h4>
+<p>Automate the creation of SAS URLs for multiple folders in your Azure storage account</p>
+<h4 id="required-arguments_4">Required arguments:</h4>
+<ul>
+<li>container name</li>
+<li>account name</li>
+<li>name and path of batch file</li>
+</ul>
+<h4 id="optional-arguments_4">Optional arguments:</h4>
+<ul>
+<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
+<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
+</ul>
+<h4 id="batch-file-format_4">Batch file format</h4>
+<p>Tab-separated file with the following fields:</p>
+<p><code>container name, folder name and path, expiry (optional), output file (optional)</code></p>
+<p>For additional details on creating SAS URLs for folders, please see the <a href="../sas_url/#azuresas-folder"><code>AzureSAS folder</code></a> section</p>
+<h4 id="usage_4">Usage</h4>
+<pre><code>usage: AzureAutomate sas folder [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Create SAS URLs for folders in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file with the following fields:
+                         container name, folder name and path, expiry (optional), output file (optional)
+</code></pre>
+
+<h3 id="azureautomate-move">AzureAutomate move</h3>
+<p>Choose either the <a href="#azureautomate-move-container"><code>container</code></a>, <a href="#azureautomate-move-file"><code>file</code></a>, or <a href="#azureautomate-move-folder"><code>folder</code></a> functionality</p>
+<h4 id="general-usage_3">General usage</h4>
+<pre><code>usage: AzureAutomate move [-h] {container,file,folder} ...
+
+Move containers/files/folders in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+
+Move functionality:
+  {container,file,folder}
+    container           Move containers in Azure storage
+    file                Move files in Azure storage
+    folder              Move folders in Azure storage
+</code></pre>
+
+<h4 id="azureautomate-move-container">AzureAutomate move container</h4>
+<p>Automate the moving of multiple containers in your Azure storage account</p>
+<h4 id="required-arguments_5">Required arguments:</h4>
+<ul>
+<li>container name</li>
+<li>account name</li>
+<li>name and path of batch file</li>
+</ul>
+<h4 id="optional-arguments_5">Optional arguments:</h4>
+<ul>
+<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
+<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
+</ul>
+<h4 id="batch-file-format_5">Batch file format</h4>
+<p>Tab-separated file with the following fields:</p>
+<p><code>container name, target container, destination path (optional), storage tier (optional)</code></p>
+<p>For additional details on moving containers, please see the <a href="../move/#azuremove-container"><code>AzureMove container</code></a> section</p>
+<h4 id="usage_5">Usage</h4>
+<pre><code>usage: AzureAutomate move container [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Move containers in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file with the following fields:
+                         container name, target container, destination path (optional), storage tier (optional)
+</code></pre>
+
+<h4 id="azureautomate-move-file">AzureAutomate move file</h4>
+<p>Automate the moving of multiple files in your Azure storage account</p>
+<h4 id="required-arguments_6">Required arguments:</h4>
+<ul>
+<li>container name</li>
+<li>account name</li>
+<li>name and path of batch file</li>
+</ul>
+<h4 id="optional-arguments_6">Optional arguments:</h4>
+<ul>
+<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
+<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
+</ul>
+<h4 id="batch-file-format_6">Batch file format</h4>
+<p>Tab-separated file with the following fields:</p>
+<p><code>container name, target container, file name, destination path (optional), storage tier (optional)</code></p>
+<p>For additional details on moving files, please see the <a href="../move/#azuremove-file"><code>AzureMove file</code></a> section</p>
+<h4 id="usage_6">Usage</h4>
+<pre><code>usage: AzureAutomate move file [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Move files in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file with the following fields:
+                         container name, target container, file name, destination path (optional), storage tier (optional)
+</code></pre>
+
+<h4 id="azureautomate-move-folder">AzureAutomate move folder</h4>
+<p>Automate the moving of multiple folders in your Azure storage account</p>
+<h4 id="required-arguments_7">Required arguments:</h4>
+<ul>
+<li>container name</li>
+<li>account name</li>
+<li>name and path of batch file</li>
+</ul>
+<h4 id="optional-arguments_7">Optional arguments:</h4>
+<ul>
+<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
+<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
+</ul>
+<h4 id="batch-file-format_7">Batch file format</h4>
+<p>Tab-separated file with the following fields:</p>
+<p><code>container name, target container, folder name, destination path (optional), storage tier (optional)</code></p>
+<p>For additional details on moving folders, please see the <a href="../move/#azuremove-folder"><code>AzureMove folder</code></a> section</p>
+<h4 id="usage_7">Usage</h4>
+<pre><code>usage: AzureAutomate move folder [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Move folders in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file with the following fields:
+                         container name, target container, folder name, destination path (optional), storage tier (optional)
+
+</code></pre>
+
+<h3 id="azureautomate-download">AzureAutomate download</h3>
+<p>Choose either the <a href="#azureautomate-download-container"><code>container</code></a>, <a href="#azureautomate-download-file"><code>file</code></a>, or <a href="#azureautomate-download-folder"><code>folder</code></a> functionality</p>
+<h4 id="general-usage_4">General usage</h4>
+<pre><code>usage: AzureAutomate download [-h] {container,file,folder} ...
+
+Download containers/files/folders in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+
+Download functionality:
+  {container,file,folder}
+    container           Download containers from Azure storage
+    file                Download files from Azure storage
+    folder              Download folders from Azure storage
+</code></pre>
+
+<h3 id="azureautomate-download-container">AzureAutomate download container</h3>
+<p>Automate the downloading of multiple containers from your Azure storage account</p>
+<h4 id="required-arguments_8">Required arguments:</h4>
+<ul>
+<li>container name</li>
+<li>account name</li>
+<li>name and path of batch file</li>
+</ul>
+<h4 id="optional-arguments_8">Optional arguments:</h4>
+<ul>
+<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
+<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
+</ul>
+<h4 id="batch-file-format_8">Batch file format</h4>
+<p>Tab-separated file with the following fields:</p>
+<p><code>container name, output path (optional)</code></p>
+<p>For additional details on downloading containers, please see the <a href="../download/#azuredownload-container"><code>AzureDownload container</code></a> section</p>
+<h4 id="usage_8">Usage</h4>
+<pre><code>usage: AzureAutomate download container [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Download containers from Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file with the following fields:
+                         container name, output path (optional)
+</code></pre>
+
+<h3 id="azureautomate-download-file">AzureAutomate download file</h3>
+<p>Automate the downloading of multiple files from your Azure storage account</p>
+<h4 id="required-arguments_9">Required arguments:</h4>
+<ul>
+<li>container name</li>
+<li>account name</li>
+<li>name and path of batch file</li>
+</ul>
+<h4 id="optional-arguments_9">Optional arguments:</h4>
+<ul>
+<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
+<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
+</ul>
+<h4 id="batch-file-format_9">Batch file format</h4>
+<p>Tab-separated file with the following fields:</p>
+<p><code>container name, file name, output path (optional)</code></p>
+<p>For additional details on downloading files, please see the <a href="../download/#azuredownload-file"><code>AzureDownload file</code></a> section</p>
+<h4 id="usage_9">Usage</h4>
+<pre><code>usage: AzureAutomate download file [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Download files from Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file with the following fields:
+                         container name, file name, output path (optional)
+</code></pre>
+
+<h3 id="azureautomate-download-folder">AzureAutomate download folder</h3>
+<p>Automate the downloading of multiple folders from your Azure storage account</p>
+<h4 id="required-arguments_10">Required arguments:</h4>
+<ul>
+<li>container name</li>
+<li>account name</li>
+<li>name and path of batch file</li>
+</ul>
+<h4 id="optional-arguments_10">Optional arguments:</h4>
+<ul>
+<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
+<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
+</ul>
+<h4 id="batch-file-format_10">Batch file format</h4>
+<p>Tab-separated file with the following fields:</p>
+<p><code>container name, folder name, output path (optional)</code></p>
+<p>For additional details on downloading folders, please see the <a href="../download/#azuredownload-folder"><code>AzureDownload folder</code></a> section</p>
+<h4 id="usage_10">Usage</h4>
+<pre><code>usage: AzureAutomate download folder [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Download folders from Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file with the following fields:
+                         container name, folder name, output path (optional)
+</code></pre>
+
+<h3 id="azureautomate-tier">AzureAutomate tier</h3>
+<p>Choose either the <a href="#azureautomate-tier-container"><code>container</code></a>, <a href="#azureautomate-tier-file"><code>file</code></a>, or <a href="#azureautomate-tier-folder"><code>folder</code></a> functionality</p>
+<h4 id="general-usage_5">General usage</h4>
+<pre><code>usage: AzureAutomate tier [-h] {container,file,folder} ...
+
+Set the storage tier of containers/files/folders in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+
+Storage tier setting functionality:
+  {container,file,folder}
+    container           Set the storage tier of containers in Azure storage
+    file                Set the storage tier of files in Azure storage
+    folder              Set the storage tier of folders in Azure storage
+</code></pre>
+
+<h3 id="azureautomate-tier-container">AzureAutomate tier container</h3>
+<p>Automate setting the storage tier for multiple containers in your Azure storage account</p>
+<h4 id="required-arguments_11">Required arguments:</h4>
+<ul>
+<li>container name</li>
+<li>account name</li>
+<li>name and path of batch file</li>
+</ul>
+<h4 id="optional-arguments_11">Optional arguments:</h4>
+<ul>
+<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
+<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
+</ul>
+<h4 id="batch-file-format_11">Batch file format</h4>
+<p>Tab-separated file with the following fields:</p>
+<p><code>container name, storage tier</code></p>
+<p>For additional details on setting the storage tier of containers, please see the <a href="../set_tier/#azuretier-container"><code>AzureTier container</code></a> section</p>
+<h4 id="usage_11">Usage</h4>
+<pre><code>usage: AzureAutomate tier container [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Set the storage tier of containers in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file with the following fields:
+                         container name, storage tier
+
+</code></pre>
+
+<h3 id="azureautomate-tier-file">AzureAutomate tier file</h3>
+<p>Automate setting the storage tier for multiple files in your Azure storage account</p>
+<h4 id="required-arguments_12">Required arguments:</h4>
+<ul>
+<li>container name</li>
+<li>account name</li>
+<li>name and path of batch file</li>
+</ul>
+<h4 id="optional-arguments_12">Optional arguments:</h4>
+<ul>
+<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
+<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
+</ul>
+<h4 id="batch-file-format_12">Batch file format</h4>
+<p>Tab-separated file with the following fields:</p>
+<p><code>container name, file name, storage tier</code></p>
+<p>For additional details on setting the storage tier of files, please see the <a href="../set_tier/#azuretier-file"><code>AzureTier file</code></a> section</p>
+<h4 id="usage_12">Usage</h4>
+<pre><code>usage: AzureAutomate tier file [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Set the storage tier of files in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file with the following fields:
+                         container name, file name, storage tier
+</code></pre>
+
+<h3 id="azureautomate-tier-folder">AzureAutomate tier folder</h3>
+<p>Automate setting the storage tier for multiple folders in your Azure storage account</p>
+<h4 id="required-arguments_13">Required arguments:</h4>
+<ul>
+<li>container name</li>
+<li>account name</li>
+<li>name and path of batch file</li>
+</ul>
+<h4 id="optional-arguments_13">Optional arguments:</h4>
+<ul>
+<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
+<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
+</ul>
+<h4 id="batch-file-format_13">Batch file format</h4>
+<p>Tab-separated file with the following fields:</p>
+<p><code>container name, folder name, storage tier</code></p>
+<p>For additional details on setting the storage tier of folders, please see the <a href="../set_tier/#azuretier-folder"><code>AzureTier folder</code></a> section</p>
+<h4 id="usage_13">Usage</h4>
+<pre><code>usage: AzureAutomate tier folder [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Set the storage tier of folders in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file with the following fields:
+                         container name, folder name, storage tier
+</code></pre>
+
+<h3 id="azureautomate-delete">AzureAutomate delete</h3>
+<p>Choose either the <a href="#azureautomate-delete-container"><code>container</code></a>, <a href="#azureautomate-delete-file"><code>file</code></a>, or <a href="#azureautomate-delete-folder"><code>folder</code></a> functionality</p>
+<h4 id="general-usage_6">General usage</h4>
+<pre><code>usage: AzureAutomate delete [-h] {container,file,folder} ...
+
+Delete containers/files/folders in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+
+Delete functionality:
+  {container,file,folder}
+    container           Delete containers in Azure storage
+    file                Delete files in Azure storage
+    folder              Delete folders in Azure storage
+</code></pre>
+
+<h3 id="azureautomate-delete-container">AzureAutomate delete container</h3>
+<p>Automate deleting multiple containers in your Azure storage account</p>
+<h4 id="required-arguments_14">Required arguments:</h4>
+<ul>
+<li>container name</li>
+<li>account name</li>
+<li>name and path of batch file</li>
+</ul>
+<h4 id="optional-arguments_14">Optional arguments:</h4>
+<ul>
+<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
+<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
+</ul>
+<h4 id="batch-file-format_14">Batch file format</h4>
+<p>File with the following field:</p>
+<p><code>container name</code></p>
+<p>For additional details on deleting containers, please see the <a href="../delete/#azuredelete-container"><code>AzureDelete container</code></a> section</p>
+<h4 id="usage_14">Usage</h4>
+<pre><code>usage: AzureAutomate delete container [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Delete containers in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        File with the following field:
+                         container name
+</code></pre>
+
+<h3 id="azureautomate-delete-file">AzureAutomate delete file</h3>
+<p>Automate deleting multiple files in your Azure storage account</p>
+<h4 id="required-arguments_15">Required arguments:</h4>
+<ul>
+<li>container name</li>
+<li>account name</li>
+<li>name and path of batch file</li>
+</ul>
+<h4 id="optional-arguments_15">Optional arguments:</h4>
+<ul>
+<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
+<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
+</ul>
+<h4 id="batch-file-format_15">Batch file format</h4>
+<p>Tab-separated file with the following fields:</p>
+<p><code>container name, file name, retention time (optional)</code></p>
+<p>For additional details on deleting files, please see the <a href="../delete/#azuredelete-file"><code>AzureDelete file</code></a> section</p>
+<h4 id="usage_15">Usage</h4>
+<pre><code>usage: AzureAutomate delete file [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Delete files in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file with the following fields:
+                         container name, file name, retention time (optional)
+
+</code></pre>
+
+<h3 id="azureautomate-delete-folder">AzureAutomate delete folder</h3>
+<p>Automate deleting multiple folders in your Azure storage account</p>
+<h4 id="required-arguments_16">Required arguments:</h4>
+<ul>
+<li>container name</li>
+<li>account name</li>
+<li>name and path of batch file</li>
+</ul>
+<h4 id="optional-arguments_16">Optional arguments:</h4>
+<ul>
+<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
+<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
+</ul>
+<h4 id="batch-file-format_16">Batch file format</h4>
+<p>Tab-separated file with the following fields:</p>
+<p><code>container name, folder name, retention time (optional)</code></p>
+<p>For additional details on deleting folders, please see the <a href="../delete/#azuredelete-folder"><code>AzureDelete folder</code></a> section</p>
+<h4 id="usage_16">Usage</h4>
+<pre><code>usage: AzureAutomate delete folder [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Delete folders in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file with the following fields:
+                         container name, folder name, retention time (optional)
+</code></pre>
+
+<h3 id="azureautomate-batch">AzureAutomate batch</h3>
+<p>Automate multiple operations</p>
+<h3 id="batch-file-format_17">Batch file format</h3>
+<p>Tab-separated file in the following format:</p>
+<p><code>command, sub-command, command:subcommand-specific arguments</code></p>
+<p>Please review the <a href="#azureautomate"><code>AzureAutomate</code></a> documentation for all the possible operations</p>
+<h3 id="usage_17">Usage</h3>
+<pre><code>usage: AzureAutomate batch [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -b BATCH_FILE
+
+Perform multiple different operations in batch
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -b BATCH_FILE, --batch_file BATCH_FILE
+                        Tab-separated file in the following format:
+                        command, sub-command, arguments
+
+                        Below is the complete list of functionalities:
+                        upload, file, container name, file name, destination path (optional), storage tier (optional)
+                        upload, folder, container name, folder name, destination path (optional), storage tier (optional)
+                        sas, container, container name, expiry (optional), output file (optional)
+                        sas, file, container name, file name and path, expiry (optional), output file (optional)
+                        sas, folder, container name, folder name and path, expiry (optional), output file (optional)
+                        move, container, container name, target container, destination path (optional), storage tier (optional)
+                        move, file, container name, target container, file name, destination path (optional), storage tier (optional)
+                        move, folder, container name, target container, folder name, destination path (optional), storage tier (optional)
+                        download, container, container name, output path (optional)
+                        download, file, container name, file name, output path (optional)
+                        download, folder, container name, folder name, output path (optional)
+                        tier, container, container name, storage tier
+                        tier, file, container name, file name, storage tier
+                        tier, folder, container name, folder name, storage tier
+                        delete, container, container name
+                        delete, file, container name, file name, retention time (optional)
+                        delete, folder, container name, folder name, retention time (optional)
+</code></pre>
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+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="..">Home</a>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="../install/">Installation</a>
+                    </li>
+                </ul>
+                <ul class="current">
+                    <li class="toctree-l1 current"><a class="reference internal current" href="./">Credentials</a>
+    <ul class="current">
+    <li class="toctree-l2"><a class="reference internal" href="#general-usage">General Usage</a>
+    </li>
+    <li class="toctree-l2"><a class="reference internal" href="#azure-credentials-store">Azure credentials store</a>
+        <ul>
+    <li class="toctree-l3"><a class="reference internal" href="#required-arguments">Required arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#optional-arguments">Optional arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#example-commands">Example commands:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#usage">Usage</a>
+    </li>
+        </ul>
+    </li>
+    <li class="toctree-l2"><a class="reference internal" href="#azure-credentials-delete">Azure credentials delete</a>
+        <ul>
+    <li class="toctree-l3"><a class="reference internal" href="#required-arguments_1">Required arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#optional-arguments_1">Optional arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#example-command">Example command:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#usage_1">Usage</a>
+    </li>
+        </ul>
+    </li>
+    </ul>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="../upload/">Upload</a>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="../sas_url/">SAS URL</a>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="../move/">Move</a>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="../download/">Download</a>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="../set_tier/">Set Tier</a>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="../delete/">Delete</a>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="../automate/">Automate</a>
+                    </li>
+                </ul>
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+          class="icon icon-github"> Edit on GitHub</a>
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+  
+  <hr/>
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+          <div role="main">
+            <div class="section">
+              
+                <h2 id="azurecredentials">AzureCredentials</h2>
+<p>AzureCredentials allows you to store, modify, or delete your Azure account name and connection string in the system keyring</p>
+<p>Choose either the <a href="#azure-credentials-store"><code>store</code></a> or <a href="#azure-credentials-delete"><code>delete</code></a> functionality</p>
+<p><a href="https://docs.microsoft.com/en-us/azure/storage/common/storage-configure-connection-string#:~:text=You%20can%20find%20your%20storage,primary%20and%20secondary%20access%20keys.">Find your connection string</a></p>
+<p><a href="https://www.zenko.io/blog/how-to-find-keys-and-account-info-for-aws-azure-and-google/#:~:text=Azure%20Account%20Name%C2%A0%3D%20the%20name%20of%20your%20Azure%20storage%20account%20located%20on%20the%20top%20of%20the%20Azure%20Portal%20(screenshot%20below%20%E2%80%93%20%E2%80%9Cscalitydemo%E2%80%9D%20is%20Azure%20Account%20Name).">Find your account key</a></p>
+<h4 id="general-usage">General Usage</h4>
+<pre><code>usage: AzureCredentials [-h] {store,delete} ...
+
+Set, modify, or delete Azure storage credentials in the system keyring
+
+optional arguments:
+  -h, --help      show this help message and exit
+
+Available functionality:
+  {store,delete}
+    store         Store or update Azure storage credentials in the system keyring
+    delete        Delete Azure storage credentials in the system keyring
+
+</code></pre>
+
+<h3 id="azure-credentials-store">Azure credentials store</h3>
+<p>Store or modify your account name and connection string in the system keyring</p>
+<h4 id="required-arguments">Required arguments:</h4>
+<ul>
+<li>account name</li>
+</ul>
+<h4 id="optional-arguments">Optional arguments:</h4>
+<ul>
+<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
+<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
+</ul>
+<h4 id="example-commands">Example commands:</h4>
+<p>To store the account name <code>account_name</code> and your connection string in the system keyring</p>
+<p><code>AzureCredentials store -a account_name</code></p>
+<p>NOTE: You will be prompted to enter your connection string by the script. Note that, as a security precaution, you will not see the text you entered.</p>
+<p>To store the account name <code>account_name</code> and your connection string in the system keyring using the passphrase <code>passphrase</code></p>
+<p><code>AzureCredentials store -a account_name -p passphrase</code></p>
+<p>NOTE: You will be prompted to enter your connection string by the script. Note that, as a security precaution, you will not see the text you entered. </p>
+<h4 id="usage">Usage</h4>
+<pre><code>usage: AzureCredentials store [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY]
+
+Store or update Azure storage credentials in the system keyring
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+</code></pre>
+
+<h3 id="azure-credentials-delete">Azure credentials delete</h3>
+<p>Delete your account name and connection string from the system keyring</p>
+<h4 id="required-arguments_1">Required arguments:</h4>
+<ul>
+<li>account name</li>
+</ul>
+<h4 id="optional-arguments_1">Optional arguments:</h4>
+<ul>
+<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
+<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
+</ul>
+<h4 id="example-command">Example command:</h4>
+<p>To delete the account name <code>account_name</code> and your connection string from the system keyring</p>
+<p><code>AzureCredentials delete -a account_name</code></p>
+<p>NOTE: You will be prompted to enter your connection string by the script. Note that, as a security precaution, you will not see the text you entered.</p>
+<p>To delete the account name <code>account_name</code> and your connection string from the system keyring stored using the passphrase <code>passphrase</code></p>
+<p><code>AzureCredentials delete -a account_name -p passphrase</code></p>
+<p>NOTE: You will be prompted to enter your connection string by the script. Note that, as a security precaution, you will not see the text you entered.</p>
+<h4 id="usage_1">Usage</h4>
+<pre><code>usage: AzureCredentials delete [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY]
+
+Delete Azure storage credentials in the system keyring
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+</code></pre>
+              
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Azure/AzureStorage/site/css/theme_extra.css

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+/*
+ * Wrap inline code samples otherwise they shoot of the side and
+ * can't be read at all.
+ *
+ * https://github.com/mkdocs/mkdocs/issues/313
+ * https://github.com/mkdocs/mkdocs/issues/233
+ * https://github.com/mkdocs/mkdocs/issues/834
+ */
+.rst-content code {
+    white-space: pre-wrap;
+    word-wrap: break-word;
+    padding: 2px 5px;
+}
+
+/**
+ * Make code blocks display as blocks and give them the appropriate
+ * font size and padding.
+ *
+ * https://github.com/mkdocs/mkdocs/issues/855
+ * https://github.com/mkdocs/mkdocs/issues/834
+ * https://github.com/mkdocs/mkdocs/issues/233
+ */
+.rst-content pre code {
+  white-space: pre;
+  word-wrap: normal;
+  display: block;
+  padding: 12px;
+  font-size: 12px;
+}
+
+/**
+ * Fix code colors
+ *
+ * https://github.com/mkdocs/mkdocs/issues/2027
+ */
+.rst-content code {
+    color: #E74C3C;
+}
+
+.rst-content pre code {
+    color: #000;
+    background: #f8f8f8;
+}
+
+/*
+ * Fix link colors when the link text is inline code.
+ *
+ * https://github.com/mkdocs/mkdocs/issues/718
+ */
+a code {
+    color: #2980B9;
+}
+a:hover code {
+    color: #3091d1;
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+a:visited code {
+    color: #9B59B6;
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+
+/*
+ * The CSS classes from highlight.js seem to clash with the
+ * ReadTheDocs theme causing some code to be incorrectly made
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+ * https://github.com/mkdocs/mkdocs/issues/411
+ */
+pre .cs, pre .c {
+    font-weight: inherit;
+    font-style: inherit;
+}
+
+/*
+ * Fix some issues with the theme and non-highlighted code
+ * samples. Without and highlighting styles attached the
+ * formatting is broken.
+ *
+ * https://github.com/mkdocs/mkdocs/issues/319
+ */
+.rst-content .no-highlight {
+  display: block;
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+
+
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+ * Additions specific to the search functionality provided by MkDocs
+ */
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+    border-top: none;
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+
+form .search-query {
+    width: 100%;
+    border-radius: 50px;
+    padding: 6px 12px;  /* csslint allow: box-model */
+    border-color: #D1D4D5;
+}
+
+/*
+ * Improve inline code blocks within admonitions.
+ *
+ * https://github.com/mkdocs/mkdocs/issues/656
+ */
+ .rst-content .admonition code {
+  color: #404040;
+  border: 1px solid #c7c9cb;
+  border: 1px solid rgba(0, 0, 0, 0.2);
+  background: #f8fbfd;
+  background: rgba(255, 255, 255, 0.7);
+}
+
+/*
+ * Account for wide tables which go off the side.
+ * Override borders to avoid wierdness on narrow tables.
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+ * https://github.com/mkdocs/mkdocs/issues/834
+ * https://github.com/mkdocs/mkdocs/pull/1034
+ */
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+
+td, th {
+   border: 1px solid #e1e4e5 !important; /* csslint allow: important */
+   border-collapse: collapse;
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Azure/AzureStorage/site/delete/index.html

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+<!DOCTYPE html>
+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
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+                    </li>
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+                    </li>
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+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="../move/">Move</a>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="../download/">Download</a>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="../set_tier/">Set Tier</a>
+                    </li>
+                </ul>
+                <ul class="current">
+                    <li class="toctree-l1 current"><a class="reference internal current" href="./">Delete</a>
+    <ul class="current">
+    <li class="toctree-l2"><a class="reference internal" href="#general-usage">General usage</a>
+    </li>
+    <li class="toctree-l2"><a class="reference internal" href="#azuredelete-container">AzureDelete container</a>
+        <ul>
+    <li class="toctree-l3"><a class="reference internal" href="#required-arguments">Required arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#optional-arguments">Optional arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#example-command">Example command:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#usage">Usage</a>
+    </li>
+        </ul>
+    </li>
+    <li class="toctree-l2"><a class="reference internal" href="#azuredelete-file">AzureDelete file</a>
+        <ul>
+    <li class="toctree-l3"><a class="reference internal" href="#required-arguments_1">Required arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#optional-arguments_1">Optional arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#example-commands">Example commands:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#usage_1">Usage</a>
+    </li>
+        </ul>
+    </li>
+    <li class="toctree-l2"><a class="reference internal" href="#azuredelete-folder">AzureDelete folder</a>
+        <ul>
+    <li class="toctree-l3"><a class="reference internal" href="#required-arguments_2">Required arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#optional-arguments_2">Optional arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#example-commands_1">Example commands:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#usage_2">Usage</a>
+    </li>
+        </ul>
+    </li>
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+      
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+          class="icon icon-github"> Edit on GitHub</a>
+      
+    </li>
+  </ul>
+  
+  <hr/>
+</div>
+          <div role="main">
+            <div class="section">
+              
+                <h2 id="azuredelete">AzureDelete</h2>
+<p>Delete containers, files, or folders from your Azure storage account</p>
+<p>Choose either the <a href="#azuredelete-container"><code>container</code></a>, <a href="#azuredelete-file"><code>file</code></a>, or  <a href="#azuredelete-folder"><code>folder</code></a> functionality</p>
+<h4 id="general-usage">General usage</h4>
+<pre><code>usage: AzureDelete [-h] {container,file,folder} ...
+
+Move and/or delete containers, files, or folders in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+
+Available functionality:
+  {container,file,folder}
+    container           Delete a container in Azure storage
+    file                Delete a file in Azure storage
+    folder              Delete a folder in Azure storage
+</code></pre>
+
+<h3 id="azuredelete-container">AzureDelete container</h3>
+<p>Delete a container from your Azure storage account</p>
+<h4 id="required-arguments">Required arguments:</h4>
+<ul>
+<li>container name</li>
+<li>account name</li>
+</ul>
+<h4 id="optional-arguments">Optional arguments:</h4>
+<ul>
+<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
+<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
+</ul>
+<h4 id="example-command">Example command:</h4>
+<p>These commands will use <code>container-name</code> as the name of the container and <code>account_name</code> as the name of the storage account</p>
+<p>To delete a container from your Azure storage account</p>
+<p><code>AzureDelete container -a account_name -c container-name</code></p>
+<h4 id="usage">Usage</h4>
+<pre><code>usage: AzureDelete container [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY]
+
+Delete a container in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -c CONTAINER_NAME, --container_name CONTAINER_NAME
+                        Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted.
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+</code></pre>
+
+<h3 id="azuredelete-file">AzureDelete file</h3>
+<p>Delete a file from your Azure storage account</p>
+<h4 id="required-arguments_1">Required arguments:</h4>
+<ul>
+<li>container name</li>
+<li>account name</li>
+<li>file name</li>
+</ul>
+<h4 id="optional-arguments_1">Optional arguments:</h4>
+<ul>
+<li>retention time: time to retain deleted files. Default is 8 days</li>
+<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
+<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
+</ul>
+<h4 id="example-commands">Example commands:</h4>
+<p>These commands will use <code>container-name</code> as the name of the container and <code>account_name</code> as the name of the storage account</p>
+<p>To delete the file <code>file_name.gz</code> from your Azure storage account</p>
+<p><code>AzureDelete file -a account_name -c container-name -f file_name.gz</code></p>
+<p>To delete the file <code>file_name.gz</code> nested in folder outputs from your Azure storage account, and retain it for 10 days</p>
+<p><code>AzureDelete file -a account_name -c container-name -f outputs/file_name.gz -r 10</code></p>
+<h4 id="usage_1">Usage</h4>
+<pre><code>usage: AzureDelete file [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -f FILE [-r RETENTION_TIME]
+
+Delete a file in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -c CONTAINER_NAME, --container_name CONTAINER_NAME
+                        Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted.
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -f FILE, --file FILE  Name of blob file to delete in Azure storage. e.g. 2022-SEQ-0001_S1_L001_R1_001.fastq.gz
+  -r RETENTION_TIME, --retention_time RETENTION_TIME
+                        Retention time for deleted files. Default is 8 days. Must be between 1 and 365
+</code></pre>
+
+<h3 id="azuredelete-folder">AzureDelete folder</h3>
+<p>Delete a folder from your Azure storage account</p>
+<h4 id="required-arguments_2">Required arguments:</h4>
+<ul>
+<li>container name</li>
+<li>account name</li>
+<li>folder name</li>
+</ul>
+<h4 id="optional-arguments_2">Optional arguments:</h4>
+<ul>
+<li>retention time: time to retain deleted files in the folder. Default is 8 days</li>
+<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
+<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
+</ul>
+<h4 id="example-commands_1">Example commands:</h4>
+<p>These commands will use <code>container-name</code> as the name of the container and <code>account_name</code> as the name of the storage account</p>
+<p>To delete the folder <code>folder_name</code> from your Azure storage account</p>
+<p><code>AzureDelete folder -a account_name -c container-name -f folder_name</code></p>
+<p>To delete the folder <code>folder_name</code> nested in folder outputs from your Azure storage account, and retain it for 10 days</p>
+<p><code>AzureDelete folder -a account_name -c container-name -f outputs/folder_name -r 10</code></p>
+<h4 id="usage_2">Usage</h4>
+<pre><code>usage: AzureDelete folder [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -f FOLDER [-r RETENTION_TIME]
+
+Delete a folder in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -c CONTAINER_NAME, --container_name CONTAINER_NAME
+                        Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted.
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -f FOLDER, --folder FOLDER
+                        Name of folder to delete in Azure storage. e.g. InterOp
+  -r RETENTION_TIME, --retention_time RETENTION_TIME
+                        Retention time for deleted files. Default is 8 days
+</code></pre>
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Azure/AzureStorage/site/download/index.html

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+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="../move/">Move</a>
+                    </li>
+                </ul>
+                <ul class="current">
+                    <li class="toctree-l1 current"><a class="reference internal current" href="./">Download</a>
+    <ul class="current">
+    <li class="toctree-l2"><a class="reference internal" href="#general-usage">General usage</a>
+    </li>
+    <li class="toctree-l2"><a class="reference internal" href="#azuredownload-container">AzureDownload container</a>
+        <ul>
+    <li class="toctree-l3"><a class="reference internal" href="#required-arguments">Required arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#optional-arguments">Optional arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#example-commands">Example commands:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#usage">Usage</a>
+    </li>
+        </ul>
+    </li>
+    <li class="toctree-l2"><a class="reference internal" href="#azuredownload-file">AzureDownload file</a>
+        <ul>
+    <li class="toctree-l3"><a class="reference internal" href="#required-arguments_1">Required arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#optional-arguments_1">Optional arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#example-commands_1">Example commands:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#usage_1">Usage</a>
+    </li>
+        </ul>
+    </li>
+    <li class="toctree-l2"><a class="reference internal" href="#azuredownload-folder">AzureDownload folder</a>
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+    <li class="toctree-l3"><a class="reference internal" href="#required-arguments_2">Required arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#optional-arguments_2">Optional arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#example-commands_2">Example commands:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#usage_2">Usage</a>
+    </li>
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+    </li>
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+            <div class="section">
+              
+                <h2 id="azuredownload">AzureDownload</h2>
+<p>Download containers, files, or folders from your Azure storage account</p>
+<p>Choose either the <a href="#azuredownload-container"><code>container</code></a>, <a href="#azuredownload-file"><code>file</code></a>, or  <a href="#azuredownload-folder"><code>folder</code></a> functionality</p>
+<h4 id="general-usage">General usage</h4>
+<pre><code>usage: AzureDownload [-h] {container,file,folder} ...
+
+Download containers/files/folders from Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+
+Available functionality:
+  {container,file,folder}
+    container           Download a container from Azure storage
+    file                Download a file from Azure storage
+    folder              Download a folder from Azure storage
+</code></pre>
+
+<h3 id="azuredownload-container">AzureDownload container</h3>
+<p>Download a container from your Azure storage account</p>
+<h4 id="required-arguments">Required arguments:</h4>
+<ul>
+<li>container name</li>
+<li>account name</li>
+</ul>
+<h4 id="optional-arguments">Optional arguments:</h4>
+<ul>
+<li>output path: local path where container is to be saved. Default is your current working directory</li>
+<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
+<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
+</ul>
+<h4 id="example-commands">Example commands:</h4>
+<p>These commands will use <code>container-name</code> as the name of the container and <code>account_name</code> as the name of the storage account</p>
+<p>To perform a basic container download (download to your current working directory)</p>
+<p><code>AzureDownload container -a account name -c container-name</code></p>
+<p>To download a container to the folder <code>outputs</code> in your current working directory</p>
+<p><code>AzureDownload container -a account name -c container-name -o outputs</code></p>
+<p>To download a container to the folder <code>/home/users/outputs</code> </p>
+<p><code>AzureDownload container -a account name -c container-name -o /home/users/outputs</code></p>
+<h4 id="usage">Usage</h4>
+<pre><code>usage: AzureDownload container [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] [-o OUTPUT_PATH]
+
+Download a container from Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -c CONTAINER_NAME, --container_name CONTAINER_NAME
+                        Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted.
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -o OUTPUT_PATH, --output_path OUTPUT_PATH
+                        Name and path of directory in which the outputs are to be saved. Default is your $CWD
+</code></pre>
+
+<h3 id="azuredownload-file">AzureDownload file</h3>
+<p>Download a file from your Azure storage account</p>
+<h4 id="required-arguments_1">Required arguments:</h4>
+<ul>
+<li>container name</li>
+<li>account name</li>
+<li>file name</li>
+</ul>
+<h4 id="optional-arguments_1">Optional arguments:</h4>
+<ul>
+<li>output path: local path where container is to be saved. Default is your current working directory</li>
+<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
+<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
+</ul>
+<h4 id="example-commands_1">Example commands:</h4>
+<p>These commands will use <code>container-name</code> as the name of the container and <code>account_name</code> as the name of the storage account</p>
+<p>To download the file <code>file_name.gz</code> to your current working directory</p>
+<p><code>AzureDownload file -a account name -c container-name -f file_name.gz</code></p>
+<p>To download the file <code>file_name.gz</code> nested in the <code>outputs</code> folder to your current working directory</p>
+<p><code>AzureDownload file -a account name -c container-name -f outputs/file_name.gz</code></p>
+<p>To download the file <code>file_name.gz</code> nested in the <code>outputs</code> folder to the folder <code>files</code> in your current working directory</p>
+<p><code>AzureDownload file -a account name -c container-name -f outputs/file_name.gz -o files</code></p>
+<p>To download the file <code>file_name.gz</code> to the folder <code>/home/users/outputs</code> </p>
+<p><code>AzureDownload file -a account name -c container-name -f file_name.gz -o /home/users/outputs</code></p>
+<h4 id="usage_1">Usage</h4>
+<pre><code>usage: AzureDownload file [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] [-o OUTPUT_PATH] -f FILE
+
+Download a file from Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -c CONTAINER_NAME, --container_name CONTAINER_NAME
+                        Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted.
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -o OUTPUT_PATH, --output_path OUTPUT_PATH
+                        Name and path of directory in which the outputs are to be saved. Default is your $CWD
+  -f FILE, --file FILE  Name of file to download from Azure storage.e.g. 2022-SEQ-0001_S1_L001_R1_001.fastq.gz
+</code></pre>
+
+<h3 id="azuredownload-folder">AzureDownload folder</h3>
+<p>Download a folder from your Azure storage account</p>
+<h4 id="required-arguments_2">Required arguments:</h4>
+<ul>
+<li>container name</li>
+<li>account name</li>
+<li>folder name</li>
+</ul>
+<h4 id="optional-arguments_2">Optional arguments:</h4>
+<ul>
+<li>output path: local path where container is to be saved. Default is your current working directory</li>
+<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
+<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
+</ul>
+<h4 id="example-commands_2">Example commands:</h4>
+<p>These commands will use <code>container-name</code> as the name of the container and <code>account_name</code> as the name of the storage account</p>
+<p>To download the folder <code>folder_name</code> to your current working directory</p>
+<p><code>AzureDownload folder -a account name -c container-name -f folder_name</code></p>
+<p>To download the folder <code>folder_name</code> nested in the <code>outputs</code> folder to your current working directory</p>
+<p><code>AzureDownload folder -a account name -c container-name -f outputs/folder_name</code></p>
+<p>To download the folder <code>folder_name</code> nested in the <code>outputs</code> folder to the folder <code>folders</code> in your current working directory</p>
+<p><code>AzureDownload folder -a account name -c container-name -f outputs/folder_name -o folders</code></p>
+<p>To download the folder <code>folder_name</code> to the folder <code>/home/users/outputs</code> </p>
+<p><code>AzureDownload folder -a account name -c container-name -f folder_name -o /home/users/outputs</code></p>
+<h4 id="usage_2">Usage</h4>
+<pre><code>usage: AzureDownload folder [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] [-o OUTPUT_PATH] -f FOLDER
+
+Download a folder from Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -c CONTAINER_NAME, --container_name CONTAINER_NAME
+                        Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted.
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -o OUTPUT_PATH, --output_path OUTPUT_PATH
+                        Name and path of directory in which the outputs are to be saved. Default is your $CWD
+  -f FOLDER, --folder FOLDER
+                        Name of the folder to download from Azure storage e.g. InterOp
+</code></pre>
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Azure/AzureStorage/site/index.html

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+                    <li class="toctree-l1"><a class="reference internal" href="upload/">Upload</a>
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+                    <li class="toctree-l1"><a class="reference internal" href="sas_url/">SAS URL</a>
+                    </li>
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+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="move/">Move</a>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="download/">Download</a>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="set_tier/">Set Tier</a>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="delete/">Delete</a>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="automate/">Automate</a>
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+              
+                <h2 id="olc-bioinformatics-azurestorage-tools">OLC Bioinformatics AzureStorage tools</h2>
+<p>This suite of tools (written in Python) allows you to manipulate containers/files/folders in your Azure storage account.</p>
+<p>There are nine scripts in this package:</p>
+<ol>
+<li><a href="credentials/"><code>AzureCredentials</code></a>: enter, modify, or delete your Azure connection string and account name into your system keyring, avoiding storing plain text passwords, environmental variables, and entering the connection string every time you run one of the scripts in the package</li>
+<li><a href="upload/"><code>AzureUpload</code></a>: upload a file or folder to a container in your Azure storage account</li>
+<li><a href="sas_url/"><code>AzureSAS</code></a>: create SAS (shared access signature) URLs for a file, a folder, or an entire container in your Azure storage account.</li>
+<li><a href="move/"><code>AzureMove</code></a>: move a file, folder, or an entire container within your Azure storage account</li>
+<li><a href="download/"><code>AzureDownload</code></a>: download a file, folder, or an entire container from your Azure storage account</li>
+<li><a href="set_tier/"><code>AzureTier</code></a>: set the storage tier of a file, folder, or an entire container from your Azure storage account</li>
+<li><a href="delete/"><code>AzureDelete</code></a>: delete a file, folder, or an entire container from your Azure storage account</li>
+<li><a href="automate/"><code>AzureAutomate</code></a>: run upload, sas, move, download, set_tier, and/or delete in batch</li>
+<li><a href="list/"><code>AzureList</code></a>: List and optionally filter containers and/or files in your Azure storage account</li>
+</ol>
+<h3 id="feedback">Feedback</h3>
+<p>If you encounter any issues installing or running AzureStorage, have feature requests, or need assistance, please <a href="https://github.com/OLC-LOC-Bioinformatics/AzureStorage/issues/new/choose">open an issue on GitHub</a>, or email me at <code>adam.koziol@inspection.gc.ca</code>  </p>
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Azure/AzureStorage/site/install/index.html

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+    <li class="toctree-l2"><a class="reference internal" href="#conda">Conda</a>
+    </li>
+    <li class="toctree-l2"><a class="reference internal" href="#azurestorage">AzureStorage</a>
+        <ul>
+    <li class="toctree-l3"><a class="reference internal" href="#create-new-conda-environment">Create new conda environment</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#install-in-existing-python-385-environment">Install in existing Python 3.8.5 environment</a>
+    </li>
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+    </li>
+    <li class="toctree-l2"><a class="reference internal" href="#credentials">Credentials</a>
+    </li>
+    <li class="toctree-l2"><a class="reference internal" href="#tests">Tests</a>
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+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="../upload/">Upload</a>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="../sas_url/">SAS URL</a>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="../move/">Move</a>
+                    </li>
+                </ul>
+                <ul>
+                    <li class="toctree-l1"><a class="reference internal" href="../download/">Download</a>
+                    </li>
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+                    </li>
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+              
+                <h2 id="installation">Installation</h2>
+<p>AzureStorage is available as a conda package, so conda must be installed on your system.</p>
+<h3 id="conda">Conda</h3>
+<p>Skip this step if you have already installed conda</p>
+<pre><code>wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+bash miniconda.sh -b -p $HOME/miniconda
+conda update -q conda
+</code></pre>
+
+<h3 id="azurestorage">AzureStorage</h3>
+<h4 id="create-new-conda-environment">Create new conda environment</h4>
+<p><code>conda create -n azure_storage -c olcbioinformatics azure_storage</code></p>
+<h4 id="install-in-existing-python-385-environment">Install in existing Python 3.8.5 environment</h4>
+<p>Install the AzureStorage package:</p>
+<p><code>conda install -c olcbioinformatics azure_storage</code></p>
+<h3 id="credentials">Credentials</h3>
+<p>You must enter your Azure storage connection string and account name into the system keyring before running any of the other scripts</p>
+<p><a href="https://docs.microsoft.com/en-us/azure/storage/common/storage-configure-connection-string#:~:text=You%20can%20find%20your%20storage,primary%20and%20secondary%20access%20keys.">Find your connection string</a></p>
+<p><a href="https://www.zenko.io/blog/how-to-find-keys-and-account-info-for-aws-azure-and-google/#:~:text=Azure%20Account%20Name%C2%A0%3D%20the%20name%20of%20your%20Azure%20storage%20account%20located%20on%20the%20top%20of%20the%20Azure%20Portal%20(screenshot%20below%20%E2%80%93%20%E2%80%9Cscalitydemo%E2%80%9D%20is%20Azure%20Account%20Name).">Find your account key</a></p>
+<p>Once you know your account key and connection string, run:</p>
+<p><code>AzureCredentials store</code></p>
+<p>Your credentials will be securely stored in the system keyring</p>
+<h3 id="tests">Tests</h3>
+<p>If you encounter issues with the AzureStorage package, tests are available to ensure that the installation was successful and your credentials are valid.</p>
+<p>You will need to clone this repository and run the tests with pytest</p>
+<p><code>git clone https://github.com/OLC-LOC-Bioinformatics/AzureStorage.git</code></p>
+<p><code>cd AzureStorage</code></p>
+<p><code>python -m pytest tests/ --cov=azure_storage --cov-config=.coveragec</code></p>
+              
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Azure/AzureStorage/site/list/index.html

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+    <li class="toctree-l2"><a class="reference internal" href="#azurelist-container">AzureList container</a>
+        <ul>
+    <li class="toctree-l3"><a class="reference internal" href="#azurelist-container-required-arguments">AzureList container required arguments</a>
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+    <li class="toctree-l3"><a class="reference internal" href="#azurelist-container-optional-arguments">AzureList container optional arguments</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#azurelist-container-example-commands">AzureList container example commands</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#azurelist-container-usage">AzureList container usage</a>
+    </li>
+        </ul>
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+    <li class="toctree-l2"><a class="reference internal" href="#azurelist-search">AzureList search</a>
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+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#azurelist-search-example-commands">AzureList search example commands</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#azurelist-search-usage">AzureList search usage</a>
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+              
+                <h2 id="azurelist">AzureList</h2>
+<p>List and optionally filter containers and/or files in your Azure storage account</p>
+<p>Choose either the <a href="#azurelist-container"><code>container</code></a>, or the <a href="#azurelist-search"><code>search</code></a> functionality</p>
+<p>This script allows you to filter using regular expressions, so make sure you <a href="https://docs.python.org/3/howto/regex.html">know what you're doing</a>, <a href="https://docs.python.org/3/howto/regex.html">check out a tutorial</a>, <a href="https://www.dataquest.io/blog/regex-cheatsheet/">look at a cheatsheet</a>, and/or <a href="https://pythex.org/">test your expressions</a></p>
+<p><strong>Important:</strong> since the regular expressions are being entered on the command line, you will need to escape certain characters e.g. ! should be !</p>
+<h4 id="general-usage">General Usage</h4>
+<pre><code>usage: AzureList [-h] {container,search} ...
+
+Explore your Azure storage account
+
+optional arguments:
+  -h, --help          show this help message and exit
+
+Available functionality:
+  {container,search}
+    container         Filter and list containers in your Azure storage account
+    search            Search files in a container (or containers) in Azure storage
+</code></pre>
+
+<h3 id="azurelist-container">AzureList container</h3>
+<p>List and optionally filter containers in your Azure storage account</p>
+<h4 id="azurelist-container-required-arguments">AzureList container required arguments</h4>
+<ul>
+<li>account name</li>
+</ul>
+<h4 id="azurelist-container-optional-arguments">AzureList container optional arguments</h4>
+<ul>
+<li>expression: expression to use to filter the containers. Regular expressions are supported. Note that since the regular expression is being entered on the command line, you may need to escape certain characters e.g. ! should be \!</li>
+<li>output_file: name and path of file in which the outputs are to be saved.</li>
+<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
+<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
+</ul>
+<h4 id="azurelist-container-example-commands">AzureList container example commands</h4>
+<p>These commands will use <code>account_name</code> as the name of the storage account</p>
+<p>To list all containers in your Azure storage account</p>
+<p><code>AzureList container -a account_name</code></p>
+<p>To confirm the container <code>191216-dar</code> is present in your account</p>
+<p><code>AzureList container -a account_name 191216-dar</code></p>
+<p>To filter the list of containers to those starting with <code>19</code></p>
+<p><code>AzureList container -a account_name 19*</code></p>
+<p>To filter the list of container to those starting with <code>19</code> and four additional digits followed by a dash</p>
+<p><code>AzureList container -a account_name 19d{4}-*</code></p>
+<p>To filter the list of containers to those starting with six digits, a dash, and three digits</p>
+<p><code>AzureList container -a account_name \\d{6}-\\D{3}</code></p>
+<p>To filter the list of containers to those ending with <code>outputs</code></p>
+<p><code>AzureList container -a account_name *outputs\$</code></p>
+<p>To filter the list of containers to those that start with <code>19</code> and four additional digits, followed by a dash, three letters, and does not contain the word <code>outputs</code></p>
+<p><code>AzureList container -a account_name 1912\\d{2}-\\D{3}\(\?\!*output\)</code></p>
+<h4 id="azurelist-container-usage">AzureList container usage</h4>
+<pre><code>usage: AzureList container [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] [-o OUTPUT_FILE]
+                           [expression]
+
+Filter and list containers in your Azure storage account
+
+positional arguments:
+  expression            Expression to search. This command supports regular expressions. e.g. 1912* will return all containers starting with 1912, including 191216-dar Note that since the regular expression is being entered on the command line, you may need to escape certain characters e.g. ! should be \!
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -o OUTPUT_FILE, --output_file OUTPUT_FILE
+                        Optionally provide the name and path of file in which the outputs are to be saved.
+</code></pre>
+
+<h3 id="azurelist-search">AzureList search</h3>
+<p>Filter files in a container (or containers) in Azure storage</p>
+<h4 id="azurelist-search-required-arguments">AzureList search required arguments</h4>
+<ul>
+<li>account name</li>
+</ul>
+<h4 id="azurelist-search-optional-arguments">AzureList search optional arguments</h4>
+<ul>
+<li>container_name: name of the Azure storage container. Regular expressions are supported. Note that since the regular expression is being entered on the command line, you may need to escape certain characters e.g. ! should be \!</li>
+<li>expression: expression to use to filter the containers. Regular expressions are supported. Note that since the regular expression is being entered on the command line, you may need to escape certain characters e.g. ! should be \!</li>
+<li>output_file: name and path of file in which the outputs are to be saved.</li>
+<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
+<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
+</ul>
+<h4 id="azurelist-search-example-commands">AzureList search example commands</h4>
+<p>These commands will use <code>account_name</code> as the name of the storage account. Note that all the regex examples used in <a href="#azurelist-container-example-commands"><code>AzureList container</code></a> can be used here</p>
+<p>To list all files in all containers in your storage account</p>
+<p><code>AzureList search -a account_name</code></p>
+<p>To list all files in all containers ending with <code>.gz</code></p>
+<p><code>AzureList search -a account_name \*.gz</code></p>
+<p>To list all files in the container <code>container-name</code></p>
+<p><code>AzureList search -a account_name -c container_name</code></p>
+<p>To list all files in the container <code>container-name</code> starting with <code>reports</code></p>
+<p><code>AzureList search -a account_name -c container_name reports*</code></p>
+<p>To list all files in the container <code>container-name</code> ending with <code>.gz</code></p>
+<p><code>AzureList search -a account_name -c container-name \*.gz</code></p>
+<p>To list all files in the container <code>container-name</code> that contain <code>.gz</code> </p>
+<p><code>AzureList search -a account_name -c container-name \*.gz*</code></p>
+<p>To list all files in the container <code>container-name</code> that contain <code>.gz</code> (but not at the end)</p>
+<p><code>AzureList search -a account_name -c container-name \*.gz.+</code></p>
+<h4 id="azurelist-search-usage">AzureList search usage</h4>
+<pre><code>usage: AzureList search [-h] -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] [-o OUTPUT_FILE]
+                        [-c [CONTAINER_NAME]]
+                        [expression]
+
+Filter files in a container (or containers) in Azure storage
+
+positional arguments:
+  expression            Expression to search. This command supports regular expressions. e.g. 1912* will return all containers starting with 1912, including 191216-dar Note that since the regular expression is being entered on the command line, you may need to escape certain characters e.g. ! should be \!
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -o OUTPUT_FILE, --output_file OUTPUT_FILE
+                        Optionally provide the name and path of file in which the outputs are to be saved.
+  -c [CONTAINER_NAME], --container_name [CONTAINER_NAME]
+                        Name of the Azure storage container. This command supports regular expressions e.g. 1912* will return all containers starting with 1912.Note that since the regular expression is being entered on the command line, you may need to escape certain characters e.g. ! should be \! You can make your queries as complex as you wish: 1912\d{2}-\D{3}\(\?\!*output\) will only return containers that start with 1912, and have two additional digits. If the word output is present, any matches are ignored. There also have to be exactly three letters following a dash and the first six numbers e.g. 191216-dar and 191227-dar will be returned but not 191216-dar-outputs 191202-test, 191216dar, 1912162-dar, 191203-m05722, 191114-gta, or 200105-dar (and many others)
+</code></pre>
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Azure/AzureStorage/site/move/index.html

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+    </li>
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+          class="icon icon-github"> Edit on GitHub</a>
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+  
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+</div>
+          <div role="main">
+            <div class="section">
+              
+                <h2 id="azuremove">AzureMove</h2>
+<p>Move containers, files, or folders within your Azure storage account.</p>
+<p>Choose either the <a href="#azuremove-container"><code>container</code></a>, <a href="#azuremove-file"><code>file</code></a>, or  <a href="#azuremove-folder"><code>folder</code></a> functionality</p>
+<h4 id="general-usage">General usage</h4>
+<pre><code>usage: AzureMove [-h] {container,file,folder} ...
+
+Move containers, files, or folders in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+
+Available functionality:
+  {container,file,folder}
+    container           Move a container in Azure storage
+    file                Move a file within Azure storage 
+    folder              Move a folder within Azure storage
+
+</code></pre>
+
+<h3 id="azuremove-container">AzureMove container</h3>
+<p>Move a container within your Azure storage account</p>
+<h4 id="required-arguments">Required arguments:</h4>
+<ul>
+<li>container name</li>
+<li>account name</li>
+</ul>
+<h4 id="optional-arguments">Optional arguments:</h4>
+<ul>
+<li>target container: name of the container into which the container is to be moved</li>
+<li>path to store the container: nest the container within the target container</li>
+<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
+<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
+<li>storage tier: set the storage tier of the file in Azure storage. Options are Hot, Cool, Archive. Default is Hot</li>
+</ul>
+<h4 id="example-commands">Example commands:</h4>
+<p>These commands will use <code>container-name</code> as the name of the container, <code>target-container</code> as the name of the target container, and <code>account_name</code> as the name of the storage account</p>
+<p>To perform a basic move (this also renames a container):</p>
+<p><code>AzureMove container -a account_name -c container-name -t target-container</code></p>
+<p>To move a container, and set the storage tier to <code>Cool</code></p>
+<p><code>AzureMove container -a account_name -c container-name -t target-container -s Cool</code></p>
+<p>To move a container and nest it into folder <code>outputs</code>:</p>
+<p><code>AzureMove container -a account_name -c container-name -t target-container -r outputs</code></p>
+<h4 id="usage">Usage</h4>
+<pre><code>usage: AzureMove container [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -t TARGET_CONTAINER [-r RESET_PATH]
+                           [-s STORAGE_TIER]
+
+Move a container in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -c CONTAINER_NAME, --container_name CONTAINER_NAME
+                        Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted.
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -t TARGET_CONTAINER, --target_container TARGET_CONTAINER
+                        The target container to which the container/file/folder is to be moved (this can be the same as the container_name if you want to move a file/folder within a container
+  -r RESET_PATH, --reset_path RESET_PATH
+                        Set the path of the container/file/folder within a folder in the target container e.g. sequence_data/220202-m05722. If you want to place it directly in the container without any nesting, use or ''
+  -s STORAGE_TIER, --storage_tier STORAGE_TIER
+                        Set the storage tier for the container/file/folder to be moved. Options are &quot;Hot&quot;, &quot;Cool&quot;, and &quot;Archive&quot;. Default is Hot
+</code></pre>
+
+<h3 id="azuremove-file">AzureMove file</h3>
+<p>Move a file within your Azure storage account</p>
+<h4 id="required-arguments_1">Required arguments:</h4>
+<ul>
+<li>container name</li>
+<li>account name</li>
+<li>file name</li>
+</ul>
+<h4 id="optional-arguments_1">Optional arguments:</h4>
+<ul>
+<li>target container: name of the container into which the container is to be moved</li>
+<li>path to store the container: nest the container within the target container</li>
+<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
+<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
+<li>storage tier: set the storage tier of the file in Azure storage. Options are Hot, Cool, Archive. Default is Hot</li>
+</ul>
+<h4 id="example-commands_1">Example commands:</h4>
+<p>These commands will use <code>container-name</code> as the name of the container, <code>target-container</code> as the name of the target container, and <code>account_name</code> as the name of the storage account</p>
+<p>To move the file <code>file_name.gz</code></p>
+<p><code>AzureMove file -a account_name -c container-name -t target-container -f file_name.gz</code></p>
+<p>To move the file <code>file_name.gz</code>, and set the storage tier to <code>Cool</code></p>
+<p><code>AzureMove file -a account_name -c container-name -t target-container -f file_name.gz -s Cool</code></p>
+<p>To move the file <code>file_name.gz</code> nested in folder <code>outputs</code></p>
+<p><code>AzureMove file -a account_name -c container-name -t target-container -f outputs/file_name.gz</code></p>
+<p>To move the file <code>file_name.gz</code> nested in folder <code>outputs</code> to the root of the source container</p>
+<p><code>AzureMove file -a account_name -c container-name -t container-name -f outputs/file_name.gz -r ""</code></p>
+<p>To move the file <code>file_name.gz</code> nested in folder <code>outputs</code> to folder <code>results</code> in the source container</p>
+<p><code>AzureMove file -a account_name -c container-name -t container-name -f outputs/file_name.gz -r results</code></p>
+<p>To move the file <code>file_name.gz</code> nested in folder <code>outputs</code> to the root of the target container</p>
+<p><code>AzureMove file -a account_name -c container-name -t target-container -f outputs/file_name.gz -r ""</code></p>
+<p>To move the file <code>file_name.gz</code> nested in folder <code>outputs</code> to folder <code>results</code> in the target container</p>
+<p><code>AzureMove file -a account_name -c container-name -t target-container -f outputs/file_name.gz -r results</code></p>
+<h4 id="usage_1">Usage</h4>
+<pre><code>usage: AzureMove file [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -t TARGET_CONTAINER [-r RESET_PATH]
+                      [-s STORAGE_TIER] -f FILE
+
+Move a file within Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -c CONTAINER_NAME, --container_name CONTAINER_NAME
+                        Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted.
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -t TARGET_CONTAINER, --target_container TARGET_CONTAINER
+                        The target container to which the container/file/folder is to be moved (this can be the same as the container_name if you want to move a file/folder within a container
+  -r RESET_PATH, --reset_path RESET_PATH
+                        Set the path of the container/file/folder within a folder in the target container e.g. sequence_data/220202-m05722. If you want to place it directly in the container without any nesting, use or ''
+  -s STORAGE_TIER, --storage_tier STORAGE_TIER
+                        Set the storage tier for the container/file/folder to be moved. Options are &quot;Hot&quot;, &quot;Cool&quot;, and &quot;Archive&quot;. Default is Hot
+  -f FILE, --file FILE  Name of blob file to move in Azure storage. e.g. 2022-SEQ-0001_S1_L001_R1_001.fastq.gz
+</code></pre>
+
+<h3 id="azuremove-folder">AzureMove folder</h3>
+<p>Move a folder within your Azure storage account</p>
+<h4 id="required-arguments_2">Required arguments:</h4>
+<ul>
+<li>container name</li>
+<li>account name</li>
+<li>folder name</li>
+</ul>
+<h4 id="optional-arguments_2">Optional arguments:</h4>
+<ul>
+<li>target container: name of the container into which the container is to be moved</li>
+<li>path to store the container: nest the container within the target container</li>
+<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
+<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
+<li>storage tier: set the storage tier of the file in Azure storage. Options are Hot, Cool, Archive. Default is Hot</li>
+</ul>
+<h4 id="example-commands_2">Example commands:</h4>
+<p>These commands will use <code>container-name</code> as the name of the container, <code>target-container</code> as the name of the target container, and <code>account_name</code> as the name of the storage account</p>
+<p>To move the folder <code>folder_name</code></p>
+<p><code>AzureMove folder -a account_name -c container-name -t target-container -f folder_name</code></p>
+<p>To move the folder <code>folder_name</code>, and set the storage tier to <code>Cool</code></p>
+<p><code>AzureMove folder -a account_name -c container-name -t target-container -f folder_name -s Cool</code></p>
+<p>To move the folder <code>folder_name</code> nested in folder <code>outputs</code></p>
+<p><code>AzureMove folder -a account_name -c container-name -t target-container -f outputs/folder_name</code></p>
+<p>To move the folder <code>folder_name</code> nested in folder <code>outputs</code> to the root of the source container</p>
+<p><code>AzureMove folder -a account_name -c container-name -t container-name -f outputs/folder_name -r ""</code></p>
+<p>To move the folder <code>folder_name</code> nested in folder <code>outputs</code> to folder <code>results</code> in the source container</p>
+<p><code>AzureMove folder -a account_name -c container-name -t container-name -f outputs/folder_name -r results</code></p>
+<p>To move the folder <code>folder_name</code> nested in folder <code>outputs</code> to the root of the target container</p>
+<p><code>AzureMove folder -a account_name -c container-name -t target-container -f outputs/folder_name -r ""</code></p>
+<p>To move the folder <code>folder_name</code> nested in folder <code>outputs</code> to folder <code>results</code> in the target container</p>
+<p><code>AzureMove folder -a account_name -c container-name -t target-container -f outputs/folder_name -r results</code></p>
+<h4 id="usage_2">Usage</h4>
+<pre><code>usage: AzureMove folder [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] -t TARGET_CONTAINER [-r RESET_PATH]
+                        [-s STORAGE_TIER] -f FOLDER
+
+Move a folder within Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -c CONTAINER_NAME, --container_name CONTAINER_NAME
+                        Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted.
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -t TARGET_CONTAINER, --target_container TARGET_CONTAINER
+                        The target container to which the container/file/folder is to be moved (this can be the same as the container_name if you want to move a file/folder within a container
+  -r RESET_PATH, --reset_path RESET_PATH
+                        Set the path of the container/file/folder within a folder in the target container e.g. sequence_data/220202-m05722. If you want to place it directly in the container without any nesting, use or ''
+  -s STORAGE_TIER, --storage_tier STORAGE_TIER
+                        Set the storage tier for the container/file/folder to be moved. Options are &quot;Hot&quot;, &quot;Cool&quot;, and &quot;Archive&quot;. Default is Hot
+  -f FOLDER, --folder FOLDER
+                        Name of folder to move in Azure storage. e.g. InterOp
+</code></pre>
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+    <li class="toctree-l2"><a class="reference internal" href="#general-usage">General usage</a>
+    </li>
+    <li class="toctree-l2"><a class="reference internal" href="#azuresas-container">AzureSAS container</a>
+        <ul>
+    <li class="toctree-l3"><a class="reference internal" href="#required-arguments">Required arguments:</a>
+    </li>
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+    </li>
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+    </li>
+        </ul>
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+        <ul>
+    <li class="toctree-l3"><a class="reference internal" href="#required-arguments_1">Required arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#optional-arguments_1">Optional arguments:</a>
+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#example-commands_1">Example commands:</a>
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+    </li>
+        </ul>
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+        <ul>
+    <li class="toctree-l3"><a class="reference internal" href="#required-arguments_2">Required arguments:</a>
+    </li>
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+    </li>
+    <li class="toctree-l3"><a class="reference internal" href="#example-commands_2">Example commands:</a>
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+  
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+</div>
+          <div role="main">
+            <div class="section">
+              
+                <h2 id="azuresas">AzureSAS</h2>
+<p>Create shared access signatures (SAS) URLs for containers, files, folders in your Azure storage account.</p>
+<p>Note that each file in a container/folder has to be downloaded separately, so if there are 1000 files in the container, 1000 SAS URLs will be provided</p>
+<p>Choose either the <a href="#azuresas-container"><code>container</code></a>, <a href="#azuresas-file"><code>file</code></a>, or  <a href="#azuresas-folder"><code>folder</code></a> functionality</p>
+<h4 id="general-usage">General usage</h4>
+<pre><code>usage: AzureSAS [-h] {container,file,folder} ...
+
+Create shared access signatures (SAS) for containers/files/folders from Azure storage.
+Note that each file in the container/folder has to be downloaded separately, so if
+there are 1000 files in the container, 1000 SAS will be provided
+
+optional arguments:
+  -h, --help            show this help message and exit
+
+Available functionality:
+  {container,file,folder}
+    container           Create SAS for all files in a container in Azure storage
+    file                Create a SAS for a file in Azure storage
+    folder              Create SAS for all files in a folder in Azure storage
+</code></pre>
+
+<h3 id="azuresas-container">AzureSAS container</h3>
+<p>Create SAS URLs for all files in a container in your Azure storage account</p>
+<h4 id="required-arguments">Required arguments:</h4>
+<ul>
+<li>container name</li>
+<li>account name</li>
+</ul>
+<h4 id="optional-arguments">Optional arguments:</h4>
+<ul>
+<li>output file: file in which the SAS URLs are to be written. Default is <code>sas.txt</code> in your current working directory</li>
+<li>expiry: the number of days the SAS URL with be valid. Minimum is 1, maximum is 365. Default is 10</li>
+<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
+<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
+</ul>
+<h4 id="example-commands">Example commands:</h4>
+<p>These commands will use <code>container-name</code> as the name of the container, and <code>account_name</code> as the name of the storage account</p>
+<p>To create SAS URLs with default settings:</p>
+<p><code>AzureSAS container -a account_name -c container-name</code></p>
+<p>To create SAS URLs with an expiry of 15 days:</p>
+<p><code>AzureSAS container -a account_name -c container-name -e 15</code></p>
+<p>To create SAS URLs, and save them to the file <code>sas_urls.txt</code> in your current working directory:</p>
+<p><code>AzureSAS container -a account_name -c container-name -o sas_urls.txt</code></p>
+<p>To create SAS URLs, and save them to the file <code>sas_urls.txt</code> nested in folder <code>outputs</code> in your current working directory:</p>
+<p><code>AzureSAS container -a account_name -c container-name -o outputs/sas_urls.txt</code></p>
+<h4 id="usage">Usage</h4>
+<pre><code>usage: AzureSAS container [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] [-e EXPIRY] [-o OUTPUT_FILE]
+
+Create SAS URLs for all files in a container in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -c CONTAINER_NAME, --container_name CONTAINER_NAME
+                        Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted.
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -e EXPIRY, --expiry EXPIRY
+                        The number of days that the SAS URL will be valid. The minimum is 1, and the maximum is 365. The default is 10.
+  -o OUTPUT_FILE, --output_file OUTPUT_FILE
+                        Name and path of file in which the SAS URLs are to be saved. Default is $CWD/sas.txt
+</code></pre>
+
+<h3 id="azuresas-file">AzureSAS file</h3>
+<p>Create a SAS URL for a file in a container in your Azure storage account</p>
+<h4 id="required-arguments_1">Required arguments:</h4>
+<ul>
+<li>container name</li>
+<li>account name</li>
+<li>file name</li>
+</ul>
+<h4 id="optional-arguments_1">Optional arguments:</h4>
+<ul>
+<li>output file: file in which the SAS URLs are to be written. Default is <code>sas.txt</code> in your current working directory</li>
+<li>expiry: the number of days the SAS URL with be valid. Minimum is 1, maximum is 365. Default is 10</li>
+<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
+<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
+</ul>
+<h4 id="example-commands_1">Example commands:</h4>
+<p>These commands will use <code>container-name</code> as the name of the container, and <code>account_name</code> as the name of the storage account</p>
+<p>To create a SAS URL for file <code>file_name.gz</code> with default settings:</p>
+<p><code>AzureSAS file -a account_name -c container-name -f file_name.gz</code></p>
+<p>To create a SAS URL for file <code>file_name.gz</code> nested in folder <code>outputs</code> with default settings:</p>
+<p><code>AzureSAS file -a account_name -c container-name -f outputs/file_name.gz</code></p>
+<p>To create a SAS URL for file <code>file_name.gz</code> with an expiry of 15 days:</p>
+<p><code>AzureSAS file -a account_name -c container-name f file_name.gz -e 15</code></p>
+<p>To create a SAS URL for file <code>file_name.gz</code>, and save it to the file <code>sas_urls.txt</code> in your current working directory:</p>
+<p><code>AzureSAS file -a account_name -c container-name -f file_name.gz -o sas_urls.txt</code></p>
+<p>To create a SAS URL for file <code>file_name.gz</code>, and save it to the file <code>sas_urls.txt</code> nested in folder <code>outputs</code> in your current working directory:</p>
+<p><code>AzureSAS file -a account_name -c container-name -f file_name.gz -o outputs/sas_urls.txt</code></p>
+<h4 id="usage_1">Usage</h4>
+<pre><code>usage: AzureSAS file [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] [-e EXPIRY] [-o OUTPUT_FILE] -f FILE
+
+Create a SAS URL for a file in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -c CONTAINER_NAME, --container_name CONTAINER_NAME
+                        Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted.
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -e EXPIRY, --expiry EXPIRY
+                        The number of days that the SAS URL will be valid. The minimum is 1, and the maximum is 365. The default is 10.
+  -o OUTPUT_FILE, --output_file OUTPUT_FILE
+                        Name and path of file in which the SAS URLs are to be saved. Default is $CWD/sas.txt
+  -f FILE, --file FILE  Path of file in Azure storage from which a SAS URL is to be created. e.g. 2022-SEQ-0001_S1_L001_R1_001.fastq.gz
+</code></pre>
+
+<h3 id="azuresas-folder">AzureSAS folder</h3>
+<p>Create SAS URLs for all files in a folder in your Azure storage account</p>
+<h4 id="required-arguments_2">Required arguments:</h4>
+<ul>
+<li>container name</li>
+<li>account name</li>
+<li>folder name</li>
+</ul>
+<h4 id="optional-arguments_2">Optional arguments:</h4>
+<ul>
+<li>output file: file in which the SAS URLs are to be written. Default is <code>sas.txt</code> in your current working directory</li>
+<li>expiry: the number of days the SAS URL with be valid. Minimum is 1, maximum is 365. Default is 10</li>
+<li>passphrase used to store your connection string in the system keyring (default is AzureStorage)</li>
+<li>verbosity: set the logging level. Options are debug,info,warning,error,critical. Default is info</li>
+</ul>
+<h4 id="example-commands_2">Example commands:</h4>
+<p>These commands will use <code>container-name</code> as the name of the container, and <code>account_name</code> as the name of the storage account</p>
+<p>To create SAS URLs for all files in folder <code>folder_name</code> with default settings:</p>
+<p><code>AzureSAS folder -a account_name -c container-name -f folder_name</code></p>
+<p>To create SAS URLs for all files in folder <code>folder_name</code> nested in folder <code>outputs</code> with default settings:</p>
+<p><code>AzureSAS folder -a account_name -c container-name -f outputs/folder_name</code></p>
+<p>To create SAS URLs for all files in folder <code>folder_name</code> with an expiry of 15 days:</p>
+<p><code>AzureSAS folder -a account_name -c container-name f folder_name -e 15</code></p>
+<p>To create SAS URLs for all files in folder <code>folder_name</code>, and save them to the file <code>sas_urls.txt</code> in your current working directory:</p>
+<p><code>AzureSAS folder -a account_name -c container-name -f folder_name -o sas_urls.txt</code></p>
+<p>To create SAS URLs for all files in folder <code>folder_name</code>, and save them to the file <code>sas_urls.txt</code> nested in folder <code>outputs</code> in your current working directory:</p>
+<p><code>AzureSAS folder -a account_name -c container-name -f folder_name -o outputs/sas_urls.txt</code></p>
+<h4 id="usage_2">Usage</h4>
+<pre><code>usage: AzureSAS folder [-h] -c CONTAINER_NAME -a ACCOUNT_NAME [-p PASSPHRASE] [-v VERBOSITY] [-e EXPIRY] [-o OUTPUT_FILE] -f FOLDER
+
+Create SAS URLs for all files in a folder in Azure storage
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -c CONTAINER_NAME, --container_name CONTAINER_NAME
+                        Name of the Azure storage container. Note that container names must be lowercase, between 3 and 63 characters, start with a letter or number, and can contain only letters, numbers, and the dash (-) character. Consecutive dashes are not permitted.
+  -a ACCOUNT_NAME, --account_name ACCOUNT_NAME
+                        Name of the Azure storage account
+  -p PASSPHRASE, --passphrase PASSPHRASE
+                        The passphrase to use when encrypting the azure storage-specific connection string to the system keyring. Default is &quot;AzureStorage&quot;.
+  -v VERBOSITY, --verbosity VERBOSITY
+                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
+  -e EXPIRY, --expiry EXPIRY
+                        The number of days that the SAS URL will be valid. The minimum is 1, and the maximum is 365. The default is 10.
+  -o OUTPUT_FILE, --output_file OUTPUT_FILE
+                        Name and path of file in which the SAS URLs are to be saved. Default is $CWD/sas.txt
+  -f FOLDER, --folder FOLDER
+                        Name of the folder for which SAS URLs are to be created for all files. e.g. InterOp
+</code></pre>
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Azure/AzureStorage/site/search/lunr.js

@@ -0,0 +1,3475 @@
+/**
+ * lunr - http://lunrjs.com - A bit like Solr, but much smaller and not as bright - 2.3.8
+ * Copyright (C) 2019 Oliver Nightingale
+ * @license MIT
+ */
+
+;(function(){
+
+/**
+ * A convenience function for configuring and constructing
+ * a new lunr Index.
+ *
+ * A lunr.Builder instance is created and the pipeline setup
+ * with a trimmer, stop word filter and stemmer.
+ *
+ * This builder object is yielded to the configuration function
+ * that is passed as a parameter, allowing the list of fields
+ * and other builder parameters to be customised.
+ *
+ * All documents _must_ be added within the passed config function.
+ *
+ * @example
+ * var idx = lunr(function () {
+ *   this.field('title')
+ *   this.field('body')
+ *   this.ref('id')
+ *
+ *   documents.forEach(function (doc) {
+ *     this.add(doc)
+ *   }, this)
+ * })
+ *
+ * @see {@link lunr.Builder}
+ * @see {@link lunr.Pipeline}
+ * @see {@link lunr.trimmer}
+ * @see {@link lunr.stopWordFilter}
+ * @see {@link lunr.stemmer}
+ * @namespace {function} lunr
+ */
+var lunr = function (config) {
+  var builder = new lunr.Builder
+
+  builder.pipeline.add(
+    lunr.trimmer,
+    lunr.stopWordFilter,
+    lunr.stemmer
+  )
+
+  builder.searchPipeline.add(
+    lunr.stemmer
+  )
+
+  config.call(builder, builder)
+  return builder.build()
+}
+
+lunr.version = "2.3.8"
+/*!
+ * lunr.utils
+ * Copyright (C) 2019 Oliver Nightingale
+ */
+
+/**
+ * A namespace containing utils for the rest of the lunr library
+ * @namespace lunr.utils
+ */
+lunr.utils = {}
+
+/**
+ * Print a warning message to the console.
+ *
+ * @param {String} message The message to be printed.
+ * @memberOf lunr.utils
+ * @function
+ */
+lunr.utils.warn = (function (global) {
+  /* eslint-disable no-console */
+  return function (message) {
+    if (global.console && console.warn) {
+      console.warn(message)
+    }
+  }
+  /* eslint-enable no-console */
+})(this)
+
+/**
+ * Convert an object to a string.
+ *
+ * In the case of `null` and `undefined` the function returns
+ * the empty string, in all other cases the result of calling
+ * `toString` on the passed object is returned.
+ *
+ * @param {Any} obj The object to convert to a string.
+ * @return {String} string representation of the passed object.
+ * @memberOf lunr.utils
+ */
+lunr.utils.asString = function (obj) {
+  if (obj === void 0 || obj === null) {
+    return ""
+  } else {
+    return obj.toString()
+  }
+}
+
+/**
+ * Clones an object.
+ *
+ * Will create a copy of an existing object such that any mutations
+ * on the copy cannot affect the original.
+ *
+ * Only shallow objects are supported, passing a nested object to this
+ * function will cause a TypeError.
+ *
+ * Objects with primitives, and arrays of primitives are supported.
+ *
+ * @param {Object} obj The object to clone.
+ * @return {Object} a clone of the passed object.
+ * @throws {TypeError} when a nested object is passed.
+ * @memberOf Utils
+ */
+lunr.utils.clone = function (obj) {
+  if (obj === null || obj === undefined) {
+    return obj
+  }
+
+  var clone = Object.create(null),
+      keys = Object.keys(obj)
+
+  for (var i = 0; i < keys.length; i++) {
+    var key = keys[i],
+        val = obj[key]
+
+    if (Array.isArray(val)) {
+      clone[key] = val.slice()
+      continue
+    }
+
+    if (typeof val === 'string' ||
+        typeof val === 'number' ||
+        typeof val === 'boolean') {
+      clone[key] = val
+      continue
+    }
+
+    throw new TypeError("clone is not deep and does not support nested objects")
+  }
+
+  return clone
+}
+lunr.FieldRef = function (docRef, fieldName, stringValue) {
+  this.docRef = docRef
+  this.fieldName = fieldName
+  this._stringValue = stringValue
+}
+
+lunr.FieldRef.joiner = "/"
+
+lunr.FieldRef.fromString = function (s) {
+  var n = s.indexOf(lunr.FieldRef.joiner)
+
+  if (n === -1) {
+    throw "malformed field ref string"
+  }
+
+  var fieldRef = s.slice(0, n),
+      docRef = s.slice(n + 1)
+
+  return new lunr.FieldRef (docRef, fieldRef, s)
+}
+
+lunr.FieldRef.prototype.toString = function () {
+  if (this._stringValue == undefined) {
+    this._stringValue = this.fieldName + lunr.FieldRef.joiner + this.docRef
+  }
+
+  return this._stringValue
+}
+/*!
+ * lunr.Set
+ * Copyright (C) 2019 Oliver Nightingale
+ */
+
+/**
+ * A lunr set.
+ *
+ * @constructor
+ */
+lunr.Set = function (elements) {
+  this.elements = Object.create(null)
+
+  if (elements) {
+    this.length = elements.length
+
+    for (var i = 0; i < this.length; i++) {
+      this.elements[elements[i]] = true
+    }
+  } else {
+    this.length = 0
+  }
+}
+
+/**
+ * A complete set that contains all elements.
+ *
+ * @static
+ * @readonly
+ * @type {lunr.Set}
+ */
+lunr.Set.complete = {
+  intersect: function (other) {
+    return other
+  },
+
+  union: function (other) {
+    return other
+  },
+
+  contains: function () {
+    return true
+  }
+}
+
+/**
+ * An empty set that contains no elements.
+ *
+ * @static
+ * @readonly
+ * @type {lunr.Set}
+ */
+lunr.Set.empty = {
+  intersect: function () {
+    return this
+  },
+
+  union: function (other) {
+    return other
+  },
+
+  contains: function () {
+    return false
+  }
+}
+
+/**
+ * Returns true if this set contains the specified object.
+ *
+ * @param {object} object - Object whose presence in this set is to be tested.
+ * @returns {boolean} - True if this set contains the specified object.
+ */
+lunr.Set.prototype.contains = function (object) {
+  return !!this.elements[object]
+}
+
+/**
+ * Returns a new set containing only the elements that are present in both
+ * this set and the specified set.
+ *
+ * @param {lunr.Set} other - set to intersect with this set.
+ * @returns {lunr.Set} a new set that is the intersection of this and the specified set.
+ */
+
+lunr.Set.prototype.intersect = function (other) {
+  var a, b, elements, intersection = []
+
+  if (other === lunr.Set.complete) {
+    return this
+  }
+
+  if (other === lunr.Set.empty) {
+    return other
+  }
+
+  if (this.length < other.length) {
+    a = this
+    b = other
+  } else {
+    a = other
+    b = this
+  }
+
+  elements = Object.keys(a.elements)
+
+  for (var i = 0; i < elements.length; i++) {
+    var element = elements[i]
+    if (element in b.elements) {
+      intersection.push(element)
+    }
+  }
+
+  return new lunr.Set (intersection)
+}
+
+/**
+ * Returns a new set combining the elements of this and the specified set.
+ *
+ * @param {lunr.Set} other - set to union with this set.
+ * @return {lunr.Set} a new set that is the union of this and the specified set.
+ */
+
+lunr.Set.prototype.union = function (other) {
+  if (other === lunr.Set.complete) {
+    return lunr.Set.complete
+  }
+
+  if (other === lunr.Set.empty) {
+    return this
+  }
+
+  return new lunr.Set(Object.keys(this.elements).concat(Object.keys(other.elements)))
+}
+/**
+ * A function to calculate the inverse document frequency for
+ * a posting. This is shared between the builder and the index
+ *
+ * @private
+ * @param {object} posting - The posting for a given term
+ * @param {number} documentCount - The total number of documents.
+ */
+lunr.idf = function (posting, documentCount) {
+  var documentsWithTerm = 0
+
+  for (var fieldName in posting) {
+    if (fieldName == '_index') continue // Ignore the term index, its not a field
+    documentsWithTerm += Object.keys(posting[fieldName]).length
+  }
+
+  var x = (documentCount - documentsWithTerm + 0.5) / (documentsWithTerm + 0.5)
+
+  return Math.log(1 + Math.abs(x))
+}
+
+/**
+ * A token wraps a string representation of a token
+ * as it is passed through the text processing pipeline.
+ *
+ * @constructor
+ * @param {string} [str=''] - The string token being wrapped.
+ * @param {object} [metadata={}] - Metadata associated with this token.
+ */
+lunr.Token = function (str, metadata) {
+  this.str = str || ""
+  this.metadata = metadata || {}
+}
+
+/**
+ * Returns the token string that is being wrapped by this object.
+ *
+ * @returns {string}
+ */
+lunr.Token.prototype.toString = function () {
+  return this.str
+}
+
+/**
+ * A token update function is used when updating or optionally
+ * when cloning a token.
+ *
+ * @callback lunr.Token~updateFunction
+ * @param {string} str - The string representation of the token.
+ * @param {Object} metadata - All metadata associated with this token.
+ */
+
+/**
+ * Applies the given function to the wrapped string token.
+ *
+ * @example
+ * token.update(function (str, metadata) {
+ *   return str.toUpperCase()
+ * })
+ *
+ * @param {lunr.Token~updateFunction} fn - A function to apply to the token string.
+ * @returns {lunr.Token}
+ */
+lunr.Token.prototype.update = function (fn) {
+  this.str = fn(this.str, this.metadata)
+  return this
+}
+
+/**
+ * Creates a clone of this token. Optionally a function can be
+ * applied to the cloned token.
+ *
+ * @param {lunr.Token~updateFunction} [fn] - An optional function to apply to the cloned token.
+ * @returns {lunr.Token}
+ */
+lunr.Token.prototype.clone = function (fn) {
+  fn = fn || function (s) { return s }
+  return new lunr.Token (fn(this.str, this.metadata), this.metadata)
+}
+/*!
+ * lunr.tokenizer
+ * Copyright (C) 2019 Oliver Nightingale
+ */
+
+/**
+ * A function for splitting a string into tokens ready to be inserted into
+ * the search index. Uses `lunr.tokenizer.separator` to split strings, change
+ * the value of this property to change how strings are split into tokens.
+ *
+ * This tokenizer will convert its parameter to a string by calling `toString` and
+ * then will split this string on the character in `lunr.tokenizer.separator`.
+ * Arrays will have their elements converted to strings and wrapped in a lunr.Token.
+ *
+ * Optional metadata can be passed to the tokenizer, this metadata will be cloned and
+ * added as metadata to every token that is created from the object to be tokenized.
+ *
+ * @static
+ * @param {?(string|object|object[])} obj - The object to convert into tokens
+ * @param {?object} metadata - Optional metadata to associate with every token
+ * @returns {lunr.Token[]}
+ * @see {@link lunr.Pipeline}
+ */
+lunr.tokenizer = function (obj, metadata) {
+  if (obj == null || obj == undefined) {
+    return []
+  }
+
+  if (Array.isArray(obj)) {
+    return obj.map(function (t) {
+      return new lunr.Token(
+        lunr.utils.asString(t).toLowerCase(),
+        lunr.utils.clone(metadata)
+      )
+    })
+  }
+
+  var str = obj.toString().toLowerCase(),
+      len = str.length,
+      tokens = []
+
+  for (var sliceEnd = 0, sliceStart = 0; sliceEnd <= len; sliceEnd++) {
+    var char = str.charAt(sliceEnd),
+        sliceLength = sliceEnd - sliceStart
+
+    if ((char.match(lunr.tokenizer.separator) || sliceEnd == len)) {
+
+      if (sliceLength > 0) {
+        var tokenMetadata = lunr.utils.clone(metadata) || {}
+        tokenMetadata["position"] = [sliceStart, sliceLength]
+        tokenMetadata["index"] = tokens.length
+
+        tokens.push(
+          new lunr.Token (
+            str.slice(sliceStart, sliceEnd),
+            tokenMetadata
+          )
+        )
+      }
+
+      sliceStart = sliceEnd + 1
+    }
+
+  }
+
+  return tokens
+}
+
+/**
+ * The separator used to split a string into tokens. Override this property to change the behaviour of
+ * `lunr.tokenizer` behaviour when tokenizing strings. By default this splits on whitespace and hyphens.
+ *
+ * @static
+ * @see lunr.tokenizer
+ */
+lunr.tokenizer.separator = /[\s\-]+/
+/*!
+ * lunr.Pipeline
+ * Copyright (C) 2019 Oliver Nightingale
+ */
+
+/**
+ * lunr.Pipelines maintain an ordered list of functions to be applied to all
+ * tokens in documents entering the search index and queries being ran against
+ * the index.
+ *
+ * An instance of lunr.Index created with the lunr shortcut will contain a
+ * pipeline with a stop word filter and an English language stemmer. Extra
+ * functions can be added before or after either of these functions or these
+ * default functions can be removed.
+ *
+ * When run the pipeline will call each function in turn, passing a token, the
+ * index of that token in the original list of all tokens and finally a list of
+ * all the original tokens.
+ *
+ * The output of functions in the pipeline will be passed to the next function
+ * in the pipeline. To exclude a token from entering the index the function
+ * should return undefined, the rest of the pipeline will not be called with
+ * this token.
+ *
+ * For serialisation of pipelines to work, all functions used in an instance of
+ * a pipeline should be registered with lunr.Pipeline. Registered functions can
+ * then be loaded. If trying to load a serialised pipeline that uses functions
+ * that are not registered an error will be thrown.
+ *
+ * If not planning on serialising the pipeline then registering pipeline functions
+ * is not necessary.
+ *
+ * @constructor
+ */
+lunr.Pipeline = function () {
+  this._stack = []
+}
+
+lunr.Pipeline.registeredFunctions = Object.create(null)
+
+/**
+ * A pipeline function maps lunr.Token to lunr.Token. A lunr.Token contains the token
+ * string as well as all known metadata. A pipeline function can mutate the token string
+ * or mutate (or add) metadata for a given token.
+ *
+ * A pipeline function can indicate that the passed token should be discarded by returning
+ * null, undefined or an empty string. This token will not be passed to any downstream pipeline
+ * functions and will not be added to the index.
+ *
+ * Multiple tokens can be returned by returning an array of tokens. Each token will be passed
+ * to any downstream pipeline functions and all will returned tokens will be added to the index.
+ *
+ * Any number of pipeline functions may be chained together using a lunr.Pipeline.
+ *
+ * @interface lunr.PipelineFunction
+ * @param {lunr.Token} token - A token from the document being processed.
+ * @param {number} i - The index of this token in the complete list of tokens for this document/field.
+ * @param {lunr.Token[]} tokens - All tokens for this document/field.
+ * @returns {(?lunr.Token|lunr.Token[])}
+ */
+
+/**
+ * Register a function with the pipeline.
+ *
+ * Functions that are used in the pipeline should be registered if the pipeline
+ * needs to be serialised, or a serialised pipeline needs to be loaded.
+ *
+ * Registering a function does not add it to a pipeline, functions must still be
+ * added to instances of the pipeline for them to be used when running a pipeline.
+ *
+ * @param {lunr.PipelineFunction} fn - The function to check for.
+ * @param {String} label - The label to register this function with
+ */
+lunr.Pipeline.registerFunction = function (fn, label) {
+  if (label in this.registeredFunctions) {
+    lunr.utils.warn('Overwriting existing registered function: ' + label)
+  }
+
+  fn.label = label
+  lunr.Pipeline.registeredFunctions[fn.label] = fn
+}
+
+/**
+ * Warns if the function is not registered as a Pipeline function.
+ *
+ * @param {lunr.PipelineFunction} fn - The function to check for.
+ * @private
+ */
+lunr.Pipeline.warnIfFunctionNotRegistered = function (fn) {
+  var isRegistered = fn.label && (fn.label in this.registeredFunctions)
+
+  if (!isRegistered) {
+    lunr.utils.warn('Function is not registered with pipeline. This may cause problems when serialising the index.\n', fn)
+  }
+}
+
+/**
+ * Loads a previously serialised pipeline.
+ *
+ * All functions to be loaded must already be registered with lunr.Pipeline.
+ * If any function from the serialised data has not been registered then an
+ * error will be thrown.
+ *
+ * @param {Object} serialised - The serialised pipeline to load.
+ * @returns {lunr.Pipeline}
+ */
+lunr.Pipeline.load = function (serialised) {
+  var pipeline = new lunr.Pipeline
+
+  serialised.forEach(function (fnName) {
+    var fn = lunr.Pipeline.registeredFunctions[fnName]
+
+    if (fn) {
+      pipeline.add(fn)
+    } else {
+      throw new Error('Cannot load unregistered function: ' + fnName)
+    }
+  })
+
+  return pipeline
+}
+
+/**
+ * Adds new functions to the end of the pipeline.
+ *
+ * Logs a warning if the function has not been registered.
+ *
+ * @param {lunr.PipelineFunction[]} functions - Any number of functions to add to the pipeline.
+ */
+lunr.Pipeline.prototype.add = function () {
+  var fns = Array.prototype.slice.call(arguments)
+
+  fns.forEach(function (fn) {
+    lunr.Pipeline.warnIfFunctionNotRegistered(fn)
+    this._stack.push(fn)
+  }, this)
+}
+
+/**
+ * Adds a single function after a function that already exists in the
+ * pipeline.
+ *
+ * Logs a warning if the function has not been registered.
+ *
+ * @param {lunr.PipelineFunction} existingFn - A function that already exists in the pipeline.
+ * @param {lunr.PipelineFunction} newFn - The new function to add to the pipeline.
+ */
+lunr.Pipeline.prototype.after = function (existingFn, newFn) {
+  lunr.Pipeline.warnIfFunctionNotRegistered(newFn)
+
+  var pos = this._stack.indexOf(existingFn)
+  if (pos == -1) {
+    throw new Error('Cannot find existingFn')
+  }
+
+  pos = pos + 1
+  this._stack.splice(pos, 0, newFn)
+}
+
+/**
+ * Adds a single function before a function that already exists in the
+ * pipeline.
+ *
+ * Logs a warning if the function has not been registered.
+ *
+ * @param {lunr.PipelineFunction} existingFn - A function that already exists in the pipeline.
+ * @param {lunr.PipelineFunction} newFn - The new function to add to the pipeline.
+ */
+lunr.Pipeline.prototype.before = function (existingFn, newFn) {
+  lunr.Pipeline.warnIfFunctionNotRegistered(newFn)
+
+  var pos = this._stack.indexOf(existingFn)
+  if (pos == -1) {
+    throw new Error('Cannot find existingFn')
+  }
+
+  this._stack.splice(pos, 0, newFn)
+}
+
+/**
+ * Removes a function from the pipeline.
+ *
+ * @param {lunr.PipelineFunction} fn The function to remove from the pipeline.
+ */
+lunr.Pipeline.prototype.remove = function (fn) {
+  var pos = this._stack.indexOf(fn)
+  if (pos == -1) {
+    return
+  }
+
+  this._stack.splice(pos, 1)
+}
+
+/**
+ * Runs the current list of functions that make up the pipeline against the
+ * passed tokens.
+ *
+ * @param {Array} tokens The tokens to run through the pipeline.
+ * @returns {Array}
+ */
+lunr.Pipeline.prototype.run = function (tokens) {
+  var stackLength = this._stack.length
+
+  for (var i = 0; i < stackLength; i++) {
+    var fn = this._stack[i]
+    var memo = []
+
+    for (var j = 0; j < tokens.length; j++) {
+      var result = fn(tokens[j], j, tokens)
+
+      if (result === null || result === void 0 || result === '') continue
+
+      if (Array.isArray(result)) {
+        for (var k = 0; k < result.length; k++) {
+          memo.push(result[k])
+        }
+      } else {
+        memo.push(result)
+      }
+    }
+
+    tokens = memo
+  }
+
+  return tokens
+}
+
+/**
+ * Convenience method for passing a string through a pipeline and getting
+ * strings out. This method takes care of wrapping the passed string in a
+ * token and mapping the resulting tokens back to strings.
+ *
+ * @param {string} str - The string to pass through the pipeline.
+ * @param {?object} metadata - Optional metadata to associate with the token
+ * passed to the pipeline.
+ * @returns {string[]}
+ */
+lunr.Pipeline.prototype.runString = function (str, metadata) {
+  var token = new lunr.Token (str, metadata)
+
+  return this.run([token]).map(function (t) {
+    return t.toString()
+  })
+}
+
+/**
+ * Resets the pipeline by removing any existing processors.
+ *
+ */
+lunr.Pipeline.prototype.reset = function () {
+  this._stack = []
+}
+
+/**
+ * Returns a representation of the pipeline ready for serialisation.
+ *
+ * Logs a warning if the function has not been registered.
+ *
+ * @returns {Array}
+ */
+lunr.Pipeline.prototype.toJSON = function () {
+  return this._stack.map(function (fn) {
+    lunr.Pipeline.warnIfFunctionNotRegistered(fn)
+
+    return fn.label
+  })
+}
+/*!
+ * lunr.Vector
+ * Copyright (C) 2019 Oliver Nightingale
+ */
+
+/**
+ * A vector is used to construct the vector space of documents and queries. These
+ * vectors support operations to determine the similarity between two documents or
+ * a document and a query.
+ *
+ * Normally no parameters are required for initializing a vector, but in the case of
+ * loading a previously dumped vector the raw elements can be provided to the constructor.
+ *
+ * For performance reasons vectors are implemented with a flat array, where an elements
+ * index is immediately followed by its value. E.g. [index, value, index, value]. This
+ * allows the underlying array to be as sparse as possible and still offer decent
+ * performance when being used for vector calculations.
+ *
+ * @constructor
+ * @param {Number[]} [elements] - The flat list of element index and element value pairs.
+ */
+lunr.Vector = function (elements) {
+  this._magnitude = 0
+  this.elements = elements || []
+}
+
+
+/**
+ * Calculates the position within the vector to insert a given index.
+ *
+ * This is used internally by insert and upsert. If there are duplicate indexes then
+ * the position is returned as if the value for that index were to be updated, but it
+ * is the callers responsibility to check whether there is a duplicate at that index
+ *
+ * @param {Number} insertIdx - The index at which the element should be inserted.
+ * @returns {Number}
+ */
+lunr.Vector.prototype.positionForIndex = function (index) {
+  // For an empty vector the tuple can be inserted at the beginning
+  if (this.elements.length == 0) {
+    return 0
+  }
+
+  var start = 0,
+      end = this.elements.length / 2,
+      sliceLength = end - start,
+      pivotPoint = Math.floor(sliceLength / 2),
+      pivotIndex = this.elements[pivotPoint * 2]
+
+  while (sliceLength > 1) {
+    if (pivotIndex < index) {
+      start = pivotPoint
+    }
+
+    if (pivotIndex > index) {
+      end = pivotPoint
+    }
+
+    if (pivotIndex == index) {
+      break
+    }
+
+    sliceLength = end - start
+    pivotPoint = start + Math.floor(sliceLength / 2)
+    pivotIndex = this.elements[pivotPoint * 2]
+  }
+
+  if (pivotIndex == index) {
+    return pivotPoint * 2
+  }
+
+  if (pivotIndex > index) {
+    return pivotPoint * 2
+  }
+
+  if (pivotIndex < index) {
+    return (pivotPoint + 1) * 2
+  }
+}
+
+/**
+ * Inserts an element at an index within the vector.
+ *
+ * Does not allow duplicates, will throw an error if there is already an entry
+ * for this index.
+ *
+ * @param {Number} insertIdx - The index at which the element should be inserted.
+ * @param {Number} val - The value to be inserted into the vector.
+ */
+lunr.Vector.prototype.insert = function (insertIdx, val) {
+  this.upsert(insertIdx, val, function () {
+    throw "duplicate index"
+  })
+}
+
+/**
+ * Inserts or updates an existing index within the vector.
+ *
+ * @param {Number} insertIdx - The index at which the element should be inserted.
+ * @param {Number} val - The value to be inserted into the vector.
+ * @param {function} fn - A function that is called for updates, the existing value and the
+ * requested value are passed as arguments
+ */
+lunr.Vector.prototype.upsert = function (insertIdx, val, fn) {
+  this._magnitude = 0
+  var position = this.positionForIndex(insertIdx)
+
+  if (this.elements[position] == insertIdx) {
+    this.elements[position + 1] = fn(this.elements[position + 1], val)
+  } else {
+    this.elements.splice(position, 0, insertIdx, val)
+  }
+}
+
+/**
+ * Calculates the magnitude of this vector.
+ *
+ * @returns {Number}
+ */
+lunr.Vector.prototype.magnitude = function () {
+  if (this._magnitude) return this._magnitude
+
+  var sumOfSquares = 0,
+      elementsLength = this.elements.length
+
+  for (var i = 1; i < elementsLength; i += 2) {
+    var val = this.elements[i]
+    sumOfSquares += val * val
+  }
+
+  return this._magnitude = Math.sqrt(sumOfSquares)
+}
+
+/**
+ * Calculates the dot product of this vector and another vector.
+ *
+ * @param {lunr.Vector} otherVector - The vector to compute the dot product with.
+ * @returns {Number}
+ */
+lunr.Vector.prototype.dot = function (otherVector) {
+  var dotProduct = 0,
+      a = this.elements, b = otherVector.elements,
+      aLen = a.length, bLen = b.length,
+      aVal = 0, bVal = 0,
+      i = 0, j = 0
+
+  while (i < aLen && j < bLen) {
+    aVal = a[i], bVal = b[j]
+    if (aVal < bVal) {
+      i += 2
+    } else if (aVal > bVal) {
+      j += 2
+    } else if (aVal == bVal) {
+      dotProduct += a[i + 1] * b[j + 1]
+      i += 2
+      j += 2
+    }
+  }
+
+  return dotProduct
+}
+
+/**
+ * Calculates the similarity between this vector and another vector.
+ *
+ * @param {lunr.Vector} otherVector - The other vector to calculate the
+ * similarity with.
+ * @returns {Number}
+ */
+lunr.Vector.prototype.similarity = function (otherVector) {
+  return this.dot(otherVector) / this.magnitude() || 0
+}
+
+/**
+ * Converts the vector to an array of the elements within the vector.
+ *
+ * @returns {Number[]}
+ */
+lunr.Vector.prototype.toArray = function () {
+  var output = new Array (this.elements.length / 2)
+
+  for (var i = 1, j = 0; i < this.elements.length; i += 2, j++) {
+    output[j] = this.elements[i]
+  }
+
+  return output
+}
+
+/**
+ * A JSON serializable representation of the vector.
+ *
+ * @returns {Number[]}
+ */
+lunr.Vector.prototype.toJSON = function () {
+  return this.elements
+}
+/* eslint-disable */
+/*!
+ * lunr.stemmer
+ * Copyright (C) 2019 Oliver Nightingale
+ * Includes code from - http://tartarus.org/~martin/PorterStemmer/js.txt
+ */
+
+/**
+ * lunr.stemmer is an english language stemmer, this is a JavaScript
+ * implementation of the PorterStemmer taken from http://tartarus.org/~martin
+ *
+ * @static
+ * @implements {lunr.PipelineFunction}
+ * @param {lunr.Token} token - The string to stem
+ * @returns {lunr.Token}
+ * @see {@link lunr.Pipeline}
+ * @function
+ */
+lunr.stemmer = (function(){
+  var step2list = {
+      "ational" : "ate",
+      "tional" : "tion",
+      "enci" : "ence",
+      "anci" : "ance",
+      "izer" : "ize",
+      "bli" : "ble",
+      "alli" : "al",
+      "entli" : "ent",
+      "eli" : "e",
+      "ousli" : "ous",
+      "ization" : "ize",
+      "ation" : "ate",
+      "ator" : "ate",
+      "alism" : "al",
+      "iveness" : "ive",
+      "fulness" : "ful",
+      "ousness" : "ous",
+      "aliti" : "al",
+      "iviti" : "ive",
+      "biliti" : "ble",
+      "logi" : "log"
+    },
+
+    step3list = {
+      "icate" : "ic",
+      "ative" : "",
+      "alize" : "al",
+      "iciti" : "ic",
+      "ical" : "ic",
+      "ful" : "",
+      "ness" : ""
+    },
+
+    c = "[^aeiou]",          // consonant
+    v = "[aeiouy]",          // vowel
+    C = c + "[^aeiouy]*",    // consonant sequence
+    V = v + "[aeiou]*",      // vowel sequence
+
+    mgr0 = "^(" + C + ")?" + V + C,               // [C]VC... is m>0
+    meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$",  // [C]VC[V] is m=1
+    mgr1 = "^(" + C + ")?" + V + C + V + C,       // [C]VCVC... is m>1
+    s_v = "^(" + C + ")?" + v;                   // vowel in stem
+
+  var re_mgr0 = new RegExp(mgr0);
+  var re_mgr1 = new RegExp(mgr1);
+  var re_meq1 = new RegExp(meq1);
+  var re_s_v = new RegExp(s_v);
+
+  var re_1a = /^(.+?)(ss|i)es$/;
+  var re2_1a = /^(.+?)([^s])s$/;
+  var re_1b = /^(.+?)eed$/;
+  var re2_1b = /^(.+?)(ed|ing)$/;
+  var re_1b_2 = /.$/;
+  var re2_1b_2 = /(at|bl|iz)$/;
+  var re3_1b_2 = new RegExp("([^aeiouylsz])\\1$");
+  var re4_1b_2 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+
+  var re_1c = /^(.+?[^aeiou])y$/;
+  var re_2 = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
+
+  var re_3 = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
+
+  var re_4 = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
+  var re2_4 = /^(.+?)(s|t)(ion)$/;
+
+  var re_5 = /^(.+?)e$/;
+  var re_5_1 = /ll$/;
+  var re3_5 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+
+  var porterStemmer = function porterStemmer(w) {
+    var stem,
+      suffix,
+      firstch,
+      re,
+      re2,
+      re3,
+      re4;
+
+    if (w.length < 3) { return w; }
+
+    firstch = w.substr(0,1);
+    if (firstch == "y") {
+      w = firstch.toUpperCase() + w.substr(1);
+    }
+
+    // Step 1a
+    re = re_1a
+    re2 = re2_1a;
+
+    if (re.test(w)) { w = w.replace(re,"$1$2"); }
+    else if (re2.test(w)) { w = w.replace(re2,"$1$2"); }
+
+    // Step 1b
+    re = re_1b;
+    re2 = re2_1b;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      re = re_mgr0;
+      if (re.test(fp[1])) {
+        re = re_1b_2;
+        w = w.replace(re,"");
+      }
+    } else if (re2.test(w)) {
+      var fp = re2.exec(w);
+      stem = fp[1];
+      re2 = re_s_v;
+      if (re2.test(stem)) {
+        w = stem;
+        re2 = re2_1b_2;
+        re3 = re3_1b_2;
+        re4 = re4_1b_2;
+        if (re2.test(w)) { w = w + "e"; }
+        else if (re3.test(w)) { re = re_1b_2; w = w.replace(re,""); }
+        else if (re4.test(w)) { w = w + "e"; }
+      }
+    }
+
+    // Step 1c - replace suffix y or Y by i if preceded by a non-vowel which is not the first letter of the word (so cry -> cri, by -> by, say -> say)
+    re = re_1c;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      w = stem + "i";
+    }
+
+    // Step 2
+    re = re_2;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      suffix = fp[2];
+      re = re_mgr0;
+      if (re.test(stem)) {
+        w = stem + step2list[suffix];
+      }
+    }
+
+    // Step 3
+    re = re_3;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      suffix = fp[2];
+      re = re_mgr0;
+      if (re.test(stem)) {
+        w = stem + step3list[suffix];
+      }
+    }
+
+    // Step 4
+    re = re_4;
+    re2 = re2_4;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = re_mgr1;
+      if (re.test(stem)) {
+        w = stem;
+      }
+    } else if (re2.test(w)) {
+      var fp = re2.exec(w);
+      stem = fp[1] + fp[2];
+      re2 = re_mgr1;
+      if (re2.test(stem)) {
+        w = stem;
+      }
+    }
+
+    // Step 5
+    re = re_5;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = re_mgr1;
+      re2 = re_meq1;
+      re3 = re3_5;
+      if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) {
+        w = stem;
+      }
+    }
+
+    re = re_5_1;
+    re2 = re_mgr1;
+    if (re.test(w) && re2.test(w)) {
+      re = re_1b_2;
+      w = w.replace(re,"");
+    }
+
+    // and turn initial Y back to y
+
+    if (firstch == "y") {
+      w = firstch.toLowerCase() + w.substr(1);
+    }
+
+    return w;
+  };
+
+  return function (token) {
+    return token.update(porterStemmer);
+  }
+})();
+
+lunr.Pipeline.registerFunction(lunr.stemmer, 'stemmer')
+/*!
+ * lunr.stopWordFilter
+ * Copyright (C) 2019 Oliver Nightingale
+ */
+
+/**
+ * lunr.generateStopWordFilter builds a stopWordFilter function from the provided
+ * list of stop words.
+ *
+ * The built in lunr.stopWordFilter is built using this generator and can be used
+ * to generate custom stopWordFilters for applications or non English languages.
+ *
+ * @function
+ * @param {Array} token The token to pass through the filter
+ * @returns {lunr.PipelineFunction}
+ * @see lunr.Pipeline
+ * @see lunr.stopWordFilter
+ */
+lunr.generateStopWordFilter = function (stopWords) {
+  var words = stopWords.reduce(function (memo, stopWord) {
+    memo[stopWord] = stopWord
+    return memo
+  }, {})
+
+  return function (token) {
+    if (token && words[token.toString()] !== token.toString()) return token
+  }
+}
+
+/**
+ * lunr.stopWordFilter is an English language stop word list filter, any words
+ * contained in the list will not be passed through the filter.
+ *
+ * This is intended to be used in the Pipeline. If the token does not pass the
+ * filter then undefined will be returned.
+ *
+ * @function
+ * @implements {lunr.PipelineFunction}
+ * @params {lunr.Token} token - A token to check for being a stop word.
+ * @returns {lunr.Token}
+ * @see {@link lunr.Pipeline}
+ */
+lunr.stopWordFilter = lunr.generateStopWordFilter([
+  'a',
+  'able',
+  'about',
+  'across',
+  'after',
+  'all',
+  'almost',
+  'also',
+  'am',
+  'among',
+  'an',
+  'and',
+  'any',
+  'are',
+  'as',
+  'at',
+  'be',
+  'because',
+  'been',
+  'but',
+  'by',
+  'can',
+  'cannot',
+  'could',
+  'dear',
+  'did',
+  'do',
+  'does',
+  'either',
+  'else',
+  'ever',
+  'every',
+  'for',
+  'from',
+  'get',
+  'got',
+  'had',
+  'has',
+  'have',
+  'he',
+  'her',
+  'hers',
+  'him',
+  'his',
+  'how',
+  'however',
+  'i',
+  'if',
+  'in',
+  'into',
+  'is',
+  'it',
+  'its',
+  'just',
+  'least',
+  'let',
+  'like',
+  'likely',
+  'may',
+  'me',
+  'might',
+  'most',
+  'must',
+  'my',
+  'neither',
+  'no',
+  'nor',
+  'not',
+  'of',
+  'off',
+  'often',
+  'on',
+  'only',
+  'or',
+  'other',
+  'our',
+  'own',
+  'rather',
+  'said',
+  'say',
+  'says',
+  'she',
+  'should',
+  'since',
+  'so',
+  'some',
+  'than',
+  'that',
+  'the',
+  'their',
+  'them',
+  'then',
+  'there',
+  'these',
+  'they',
+  'this',
+  'tis',
+  'to',
+  'too',
+  'twas',
+  'us',
+  'wants',
+  'was',
+  'we',
+  'were',
+  'what',
+  'when',
+  'where',
+  'which',
+  'while',
+  'who',
+  'whom',
+  'why',
+  'will',
+  'with',
+  'would',
+  'yet',
+  'you',
+  'your'
+])
+
+lunr.Pipeline.registerFunction(lunr.stopWordFilter, 'stopWordFilter')
+/*!
+ * lunr.trimmer
+ * Copyright (C) 2019 Oliver Nightingale
+ */
+
+/**
+ * lunr.trimmer is a pipeline function for trimming non word
+ * characters from the beginning and end of tokens before they
+ * enter the index.
+ *
+ * This implementation may not work correctly for non latin
+ * characters and should either be removed or adapted for use
+ * with languages with non-latin characters.
+ *
+ * @static
+ * @implements {lunr.PipelineFunction}
+ * @param {lunr.Token} token The token to pass through the filter
+ * @returns {lunr.Token}
+ * @see lunr.Pipeline
+ */
+lunr.trimmer = function (token) {
+  return token.update(function (s) {
+    return s.replace(/^\W+/, '').replace(/\W+$/, '')
+  })
+}
+
+lunr.Pipeline.registerFunction(lunr.trimmer, 'trimmer')
+/*!
+ * lunr.TokenSet
+ * Copyright (C) 2019 Oliver Nightingale
+ */
+
+/**
+ * A token set is used to store the unique list of all tokens
+ * within an index. Token sets are also used to represent an
+ * incoming query to the index, this query token set and index
+ * token set are then intersected to find which tokens to look
+ * up in the inverted index.
+ *
+ * A token set can hold multiple tokens, as in the case of the
+ * index token set, or it can hold a single token as in the
+ * case of a simple query token set.
+ *
+ * Additionally token sets are used to perform wildcard matching.
+ * Leading, contained and trailing wildcards are supported, and
+ * from this edit distance matching can also be provided.
+ *
+ * Token sets are implemented as a minimal finite state automata,
+ * where both common prefixes and suffixes are shared between tokens.
+ * This helps to reduce the space used for storing the token set.
+ *
+ * @constructor
+ */
+lunr.TokenSet = function () {
+  this.final = false
+  this.edges = {}
+  this.id = lunr.TokenSet._nextId
+  lunr.TokenSet._nextId += 1
+}
+
+/**
+ * Keeps track of the next, auto increment, identifier to assign
+ * to a new tokenSet.
+ *
+ * TokenSets require a unique identifier to be correctly minimised.
+ *
+ * @private
+ */
+lunr.TokenSet._nextId = 1
+
+/**
+ * Creates a TokenSet instance from the given sorted array of words.
+ *
+ * @param {String[]} arr - A sorted array of strings to create the set from.
+ * @returns {lunr.TokenSet}
+ * @throws Will throw an error if the input array is not sorted.
+ */
+lunr.TokenSet.fromArray = function (arr) {
+  var builder = new lunr.TokenSet.Builder
+
+  for (var i = 0, len = arr.length; i < len; i++) {
+    builder.insert(arr[i])
+  }
+
+  builder.finish()
+  return builder.root
+}
+
+/**
+ * Creates a token set from a query clause.
+ *
+ * @private
+ * @param {Object} clause - A single clause from lunr.Query.
+ * @param {string} clause.term - The query clause term.
+ * @param {number} [clause.editDistance] - The optional edit distance for the term.
+ * @returns {lunr.TokenSet}
+ */
+lunr.TokenSet.fromClause = function (clause) {
+  if ('editDistance' in clause) {
+    return lunr.TokenSet.fromFuzzyString(clause.term, clause.editDistance)
+  } else {
+    return lunr.TokenSet.fromString(clause.term)
+  }
+}
+
+/**
+ * Creates a token set representing a single string with a specified
+ * edit distance.
+ *
+ * Insertions, deletions, substitutions and transpositions are each
+ * treated as an edit distance of 1.
+ *
+ * Increasing the allowed edit distance will have a dramatic impact
+ * on the performance of both creating and intersecting these TokenSets.
+ * It is advised to keep the edit distance less than 3.
+ *
+ * @param {string} str - The string to create the token set from.
+ * @param {number} editDistance - The allowed edit distance to match.
+ * @returns {lunr.Vector}
+ */
+lunr.TokenSet.fromFuzzyString = function (str, editDistance) {
+  var root = new lunr.TokenSet
+
+  var stack = [{
+    node: root,
+    editsRemaining: editDistance,
+    str: str
+  }]
+
+  while (stack.length) {
+    var frame = stack.pop()
+
+    // no edit
+    if (frame.str.length > 0) {
+      var char = frame.str.charAt(0),
+          noEditNode
+
+      if (char in frame.node.edges) {
+        noEditNode = frame.node.edges[char]
+      } else {
+        noEditNode = new lunr.TokenSet
+        frame.node.edges[char] = noEditNode
+      }
+
+      if (frame.str.length == 1) {
+        noEditNode.final = true
+      }
+
+      stack.push({
+        node: noEditNode,
+        editsRemaining: frame.editsRemaining,
+        str: frame.str.slice(1)
+      })
+    }
+
+    if (frame.editsRemaining == 0) {
+      continue
+    }
+
+    // insertion
+    if ("*" in frame.node.edges) {
+      var insertionNode = frame.node.edges["*"]
+    } else {
+      var insertionNode = new lunr.TokenSet
+      frame.node.edges["*"] = insertionNode
+    }
+
+    if (frame.str.length == 0) {
+      insertionNode.final = true
+    }
+
+    stack.push({
+      node: insertionNode,
+      editsRemaining: frame.editsRemaining - 1,
+      str: frame.str
+    })
+
+    // deletion
+    // can only do a deletion if we have enough edits remaining
+    // and if there are characters left to delete in the string
+    if (frame.str.length > 1) {
+      stack.push({
+        node: frame.node,
+        editsRemaining: frame.editsRemaining - 1,
+        str: frame.str.slice(1)
+      })
+    }
+
+    // deletion
+    // just removing the last character from the str
+    if (frame.str.length == 1) {
+      frame.node.final = true
+    }
+
+    // substitution
+    // can only do a substitution if we have enough edits remaining
+    // and if there are characters left to substitute
+    if (frame.str.length >= 1) {
+      if ("*" in frame.node.edges) {
+        var substitutionNode = frame.node.edges["*"]
+      } else {
+        var substitutionNode = new lunr.TokenSet
+        frame.node.edges["*"] = substitutionNode
+      }
+
+      if (frame.str.length == 1) {
+        substitutionNode.final = true
+      }
+
+      stack.push({
+        node: substitutionNode,
+        editsRemaining: frame.editsRemaining - 1,
+        str: frame.str.slice(1)
+      })
+    }
+
+    // transposition
+    // can only do a transposition if there are edits remaining
+    // and there are enough characters to transpose
+    if (frame.str.length > 1) {
+      var charA = frame.str.charAt(0),
+          charB = frame.str.charAt(1),
+          transposeNode
+
+      if (charB in frame.node.edges) {
+        transposeNode = frame.node.edges[charB]
+      } else {
+        transposeNode = new lunr.TokenSet
+        frame.node.edges[charB] = transposeNode
+      }
+
+      if (frame.str.length == 1) {
+        transposeNode.final = true
+      }
+
+      stack.push({
+        node: transposeNode,
+        editsRemaining: frame.editsRemaining - 1,
+        str: charA + frame.str.slice(2)
+      })
+    }
+  }
+
+  return root
+}
+
+/**
+ * Creates a TokenSet from a string.
+ *
+ * The string may contain one or more wildcard characters (*)
+ * that will allow wildcard matching when intersecting with
+ * another TokenSet.
+ *
+ * @param {string} str - The string to create a TokenSet from.
+ * @returns {lunr.TokenSet}
+ */
+lunr.TokenSet.fromString = function (str) {
+  var node = new lunr.TokenSet,
+      root = node
+
+  /*
+   * Iterates through all characters within the passed string
+   * appending a node for each character.
+   *
+   * When a wildcard character is found then a self
+   * referencing edge is introduced to continually match
+   * any number of any characters.
+   */
+  for (var i = 0, len = str.length; i < len; i++) {
+    var char = str[i],
+        final = (i == len - 1)
+
+    if (char == "*") {
+      node.edges[char] = node
+      node.final = final
+
+    } else {
+      var next = new lunr.TokenSet
+      next.final = final
+
+      node.edges[char] = next
+      node = next
+    }
+  }
+
+  return root
+}
+
+/**
+ * Converts this TokenSet into an array of strings
+ * contained within the TokenSet.
+ *
+ * This is not intended to be used on a TokenSet that
+ * contains wildcards, in these cases the results are
+ * undefined and are likely to cause an infinite loop.
+ *
+ * @returns {string[]}
+ */
+lunr.TokenSet.prototype.toArray = function () {
+  var words = []
+
+  var stack = [{
+    prefix: "",
+    node: this
+  }]
+
+  while (stack.length) {
+    var frame = stack.pop(),
+        edges = Object.keys(frame.node.edges),
+        len = edges.length
+
+    if (frame.node.final) {
+      /* In Safari, at this point the prefix is sometimes corrupted, see:
+       * https://github.com/olivernn/lunr.js/issues/279 Calling any
+       * String.prototype method forces Safari to "cast" this string to what
+       * it's supposed to be, fixing the bug. */
+      frame.prefix.charAt(0)
+      words.push(frame.prefix)
+    }
+
+    for (var i = 0; i < len; i++) {
+      var edge = edges[i]
+
+      stack.push({
+        prefix: frame.prefix.concat(edge),
+        node: frame.node.edges[edge]
+      })
+    }
+  }
+
+  return words
+}
+
+/**
+ * Generates a string representation of a TokenSet.
+ *
+ * This is intended to allow TokenSets to be used as keys
+ * in objects, largely to aid the construction and minimisation
+ * of a TokenSet. As such it is not designed to be a human
+ * friendly representation of the TokenSet.
+ *
+ * @returns {string}
+ */
+lunr.TokenSet.prototype.toString = function () {
+  // NOTE: Using Object.keys here as this.edges is very likely
+  // to enter 'hash-mode' with many keys being added
+  //
+  // avoiding a for-in loop here as it leads to the function
+  // being de-optimised (at least in V8). From some simple
+  // benchmarks the performance is comparable, but allowing
+  // V8 to optimize may mean easy performance wins in the future.
+
+  if (this._str) {
+    return this._str
+  }
+
+  var str = this.final ? '1' : '0',
+      labels = Object.keys(this.edges).sort(),
+      len = labels.length
+
+  for (var i = 0; i < len; i++) {
+    var label = labels[i],
+        node = this.edges[label]
+
+    str = str + label + node.id
+  }
+
+  return str
+}
+
+/**
+ * Returns a new TokenSet that is the intersection of
+ * this TokenSet and the passed TokenSet.
+ *
+ * This intersection will take into account any wildcards
+ * contained within the TokenSet.
+ *
+ * @param {lunr.TokenSet} b - An other TokenSet to intersect with.
+ * @returns {lunr.TokenSet}
+ */
+lunr.TokenSet.prototype.intersect = function (b) {
+  var output = new lunr.TokenSet,
+      frame = undefined
+
+  var stack = [{
+    qNode: b,
+    output: output,
+    node: this
+  }]
+
+  while (stack.length) {
+    frame = stack.pop()
+
+    // NOTE: As with the #toString method, we are using
+    // Object.keys and a for loop instead of a for-in loop
+    // as both of these objects enter 'hash' mode, causing
+    // the function to be de-optimised in V8
+    var qEdges = Object.keys(frame.qNode.edges),
+        qLen = qEdges.length,
+        nEdges = Object.keys(frame.node.edges),
+        nLen = nEdges.length
+
+    for (var q = 0; q < qLen; q++) {
+      var qEdge = qEdges[q]
+
+      for (var n = 0; n < nLen; n++) {
+        var nEdge = nEdges[n]
+
+        if (nEdge == qEdge || qEdge == '*') {
+          var node = frame.node.edges[nEdge],
+              qNode = frame.qNode.edges[qEdge],
+              final = node.final && qNode.final,
+              next = undefined
+
+          if (nEdge in frame.output.edges) {
+            // an edge already exists for this character
+            // no need to create a new node, just set the finality
+            // bit unless this node is already final
+            next = frame.output.edges[nEdge]
+            next.final = next.final || final
+
+          } else {
+            // no edge exists yet, must create one
+            // set the finality bit and insert it
+            // into the output
+            next = new lunr.TokenSet
+            next.final = final
+            frame.output.edges[nEdge] = next
+          }
+
+          stack.push({
+            qNode: qNode,
+            output: next,
+            node: node
+          })
+        }
+      }
+    }
+  }
+
+  return output
+}
+lunr.TokenSet.Builder = function () {
+  this.previousWord = ""
+  this.root = new lunr.TokenSet
+  this.uncheckedNodes = []
+  this.minimizedNodes = {}
+}
+
+lunr.TokenSet.Builder.prototype.insert = function (word) {
+  var node,
+      commonPrefix = 0
+
+  if (word < this.previousWord) {
+    throw new Error ("Out of order word insertion")
+  }
+
+  for (var i = 0; i < word.length && i < this.previousWord.length; i++) {
+    if (word[i] != this.previousWord[i]) break
+    commonPrefix++
+  }
+
+  this.minimize(commonPrefix)
+
+  if (this.uncheckedNodes.length == 0) {
+    node = this.root
+  } else {
+    node = this.uncheckedNodes[this.uncheckedNodes.length - 1].child
+  }
+
+  for (var i = commonPrefix; i < word.length; i++) {
+    var nextNode = new lunr.TokenSet,
+        char = word[i]
+
+    node.edges[char] = nextNode
+
+    this.uncheckedNodes.push({
+      parent: node,
+      char: char,
+      child: nextNode
+    })
+
+    node = nextNode
+  }
+
+  node.final = true
+  this.previousWord = word
+}
+
+lunr.TokenSet.Builder.prototype.finish = function () {
+  this.minimize(0)
+}
+
+lunr.TokenSet.Builder.prototype.minimize = function (downTo) {
+  for (var i = this.uncheckedNodes.length - 1; i >= downTo; i--) {
+    var node = this.uncheckedNodes[i],
+        childKey = node.child.toString()
+
+    if (childKey in this.minimizedNodes) {
+      node.parent.edges[node.char] = this.minimizedNodes[childKey]
+    } else {
+      // Cache the key for this node since
+      // we know it can't change anymore
+      node.child._str = childKey
+
+      this.minimizedNodes[childKey] = node.child
+    }
+
+    this.uncheckedNodes.pop()
+  }
+}
+/*!
+ * lunr.Index
+ * Copyright (C) 2019 Oliver Nightingale
+ */
+
+/**
+ * An index contains the built index of all documents and provides a query interface
+ * to the index.
+ *
+ * Usually instances of lunr.Index will not be created using this constructor, instead
+ * lunr.Builder should be used to construct new indexes, or lunr.Index.load should be
+ * used to load previously built and serialized indexes.
+ *
+ * @constructor
+ * @param {Object} attrs - The attributes of the built search index.
+ * @param {Object} attrs.invertedIndex - An index of term/field to document reference.
+ * @param {Object<string, lunr.Vector>} attrs.fieldVectors - Field vectors
+ * @param {lunr.TokenSet} attrs.tokenSet - An set of all corpus tokens.
+ * @param {string[]} attrs.fields - The names of indexed document fields.
+ * @param {lunr.Pipeline} attrs.pipeline - The pipeline to use for search terms.
+ */
+lunr.Index = function (attrs) {
+  this.invertedIndex = attrs.invertedIndex
+  this.fieldVectors = attrs.fieldVectors
+  this.tokenSet = attrs.tokenSet
+  this.fields = attrs.fields
+  this.pipeline = attrs.pipeline
+}
+
+/**
+ * A result contains details of a document matching a search query.
+ * @typedef {Object} lunr.Index~Result
+ * @property {string} ref - The reference of the document this result represents.
+ * @property {number} score - A number between 0 and 1 representing how similar this document is to the query.
+ * @property {lunr.MatchData} matchData - Contains metadata about this match including which term(s) caused the match.
+ */
+
+/**
+ * Although lunr provides the ability to create queries using lunr.Query, it also provides a simple
+ * query language which itself is parsed into an instance of lunr.Query.
+ *
+ * For programmatically building queries it is advised to directly use lunr.Query, the query language
+ * is best used for human entered text rather than program generated text.
+ *
+ * At its simplest queries can just be a single term, e.g. `hello`, multiple terms are also supported
+ * and will be combined with OR, e.g `hello world` will match documents that contain either 'hello'
+ * or 'world', though those that contain both will rank higher in the results.
+ *
+ * Wildcards can be included in terms to match one or more unspecified characters, these wildcards can
+ * be inserted anywhere within the term, and more than one wildcard can exist in a single term. Adding
+ * wildcards will increase the number of documents that will be found but can also have a negative
+ * impact on query performance, especially with wildcards at the beginning of a term.
+ *
+ * Terms can be restricted to specific fields, e.g. `title:hello`, only documents with the term
+ * hello in the title field will match this query. Using a field not present in the index will lead
+ * to an error being thrown.
+ *
+ * Modifiers can also be added to terms, lunr supports edit distance and boost modifiers on terms. A term
+ * boost will make documents matching that term score higher, e.g. `foo^5`. Edit distance is also supported
+ * to provide fuzzy matching, e.g. 'hello~2' will match documents with hello with an edit distance of 2.
+ * Avoid large values for edit distance to improve query performance.
+ *
+ * Each term also supports a presence modifier. By default a term's presence in document is optional, however
+ * this can be changed to either required or prohibited. For a term's presence to be required in a document the
+ * term should be prefixed with a '+', e.g. `+foo bar` is a search for documents that must contain 'foo' and
+ * optionally contain 'bar'. Conversely a leading '-' sets the terms presence to prohibited, i.e. it must not
+ * appear in a document, e.g. `-foo bar` is a search for documents that do not contain 'foo' but may contain 'bar'.
+ *
+ * To escape special characters the backslash character '\' can be used, this allows searches to include
+ * characters that would normally be considered modifiers, e.g. `foo\~2` will search for a term "foo~2" instead
+ * of attempting to apply a boost of 2 to the search term "foo".
+ *
+ * @typedef {string} lunr.Index~QueryString
+ * @example <caption>Simple single term query</caption>
+ * hello
+ * @example <caption>Multiple term query</caption>
+ * hello world
+ * @example <caption>term scoped to a field</caption>
+ * title:hello
+ * @example <caption>term with a boost of 10</caption>
+ * hello^10
+ * @example <caption>term with an edit distance of 2</caption>
+ * hello~2
+ * @example <caption>terms with presence modifiers</caption>
+ * -foo +bar baz
+ */
+
+/**
+ * Performs a search against the index using lunr query syntax.
+ *
+ * Results will be returned sorted by their score, the most relevant results
+ * will be returned first.  For details on how the score is calculated, please see
+ * the {@link https://lunrjs.com/guides/searching.html#scoring|guide}.
+ *
+ * For more programmatic querying use lunr.Index#query.
+ *
+ * @param {lunr.Index~QueryString} queryString - A string containing a lunr query.
+ * @throws {lunr.QueryParseError} If the passed query string cannot be parsed.
+ * @returns {lunr.Index~Result[]}
+ */
+lunr.Index.prototype.search = function (queryString) {
+  return this.query(function (query) {
+    var parser = new lunr.QueryParser(queryString, query)
+    parser.parse()
+  })
+}
+
+/**
+ * A query builder callback provides a query object to be used to express
+ * the query to perform on the index.
+ *
+ * @callback lunr.Index~queryBuilder
+ * @param {lunr.Query} query - The query object to build up.
+ * @this lunr.Query
+ */
+
+/**
+ * Performs a query against the index using the yielded lunr.Query object.
+ *
+ * If performing programmatic queries against the index, this method is preferred
+ * over lunr.Index#search so as to avoid the additional query parsing overhead.
+ *
+ * A query object is yielded to the supplied function which should be used to
+ * express the query to be run against the index.
+ *
+ * Note that although this function takes a callback parameter it is _not_ an
+ * asynchronous operation, the callback is just yielded a query object to be
+ * customized.
+ *
+ * @param {lunr.Index~queryBuilder} fn - A function that is used to build the query.
+ * @returns {lunr.Index~Result[]}
+ */
+lunr.Index.prototype.query = function (fn) {
+  // for each query clause
+  // * process terms
+  // * expand terms from token set
+  // * find matching documents and metadata
+  // * get document vectors
+  // * score documents
+
+  var query = new lunr.Query(this.fields),
+      matchingFields = Object.create(null),
+      queryVectors = Object.create(null),
+      termFieldCache = Object.create(null),
+      requiredMatches = Object.create(null),
+      prohibitedMatches = Object.create(null)
+
+  /*
+   * To support field level boosts a query vector is created per
+   * field. An empty vector is eagerly created to support negated
+   * queries.
+   */
+  for (var i = 0; i < this.fields.length; i++) {
+    queryVectors[this.fields[i]] = new lunr.Vector
+  }
+
+  fn.call(query, query)
+
+  for (var i = 0; i < query.clauses.length; i++) {
+    /*
+     * Unless the pipeline has been disabled for this term, which is
+     * the case for terms with wildcards, we need to pass the clause
+     * term through the search pipeline. A pipeline returns an array
+     * of processed terms. Pipeline functions may expand the passed
+     * term, which means we may end up performing multiple index lookups
+     * for a single query term.
+     */
+    var clause = query.clauses[i],
+        terms = null,
+        clauseMatches = lunr.Set.complete
+
+    if (clause.usePipeline) {
+      terms = this.pipeline.runString(clause.term, {
+        fields: clause.fields
+      })
+    } else {
+      terms = [clause.term]
+    }
+
+    for (var m = 0; m < terms.length; m++) {
+      var term = terms[m]
+
+      /*
+       * Each term returned from the pipeline needs to use the same query
+       * clause object, e.g. the same boost and or edit distance. The
+       * simplest way to do this is to re-use the clause object but mutate
+       * its term property.
+       */
+      clause.term = term
+
+      /*
+       * From the term in the clause we create a token set which will then
+       * be used to intersect the indexes token set to get a list of terms
+       * to lookup in the inverted index
+       */
+      var termTokenSet = lunr.TokenSet.fromClause(clause),
+          expandedTerms = this.tokenSet.intersect(termTokenSet).toArray()
+
+      /*
+       * If a term marked as required does not exist in the tokenSet it is
+       * impossible for the search to return any matches. We set all the field
+       * scoped required matches set to empty and stop examining any further
+       * clauses.
+       */
+      if (expandedTerms.length === 0 && clause.presence === lunr.Query.presence.REQUIRED) {
+        for (var k = 0; k < clause.fields.length; k++) {
+          var field = clause.fields[k]
+          requiredMatches[field] = lunr.Set.empty
+        }
+
+        break
+      }
+
+      for (var j = 0; j < expandedTerms.length; j++) {
+        /*
+         * For each term get the posting and termIndex, this is required for
+         * building the query vector.
+         */
+        var expandedTerm = expandedTerms[j],
+            posting = this.invertedIndex[expandedTerm],
+            termIndex = posting._index
+
+        for (var k = 0; k < clause.fields.length; k++) {
+          /*
+           * For each field that this query term is scoped by (by default
+           * all fields are in scope) we need to get all the document refs
+           * that have this term in that field.
+           *
+           * The posting is the entry in the invertedIndex for the matching
+           * term from above.
+           */
+          var field = clause.fields[k],
+              fieldPosting = posting[field],
+              matchingDocumentRefs = Object.keys(fieldPosting),
+              termField = expandedTerm + "/" + field,
+              matchingDocumentsSet = new lunr.Set(matchingDocumentRefs)
+
+          /*
+           * if the presence of this term is required ensure that the matching
+           * documents are added to the set of required matches for this clause.
+           *
+           */
+          if (clause.presence == lunr.Query.presence.REQUIRED) {
+            clauseMatches = clauseMatches.union(matchingDocumentsSet)
+
+            if (requiredMatches[field] === undefined) {
+              requiredMatches[field] = lunr.Set.complete
+            }
+          }
+
+          /*
+           * if the presence of this term is prohibited ensure that the matching
+           * documents are added to the set of prohibited matches for this field,
+           * creating that set if it does not yet exist.
+           */
+          if (clause.presence == lunr.Query.presence.PROHIBITED) {
+            if (prohibitedMatches[field] === undefined) {
+              prohibitedMatches[field] = lunr.Set.empty
+            }
+
+            prohibitedMatches[field] = prohibitedMatches[field].union(matchingDocumentsSet)
+
+            /*
+             * Prohibited matches should not be part of the query vector used for
+             * similarity scoring and no metadata should be extracted so we continue
+             * to the next field
+             */
+            continue
+          }
+
+          /*
+           * The query field vector is populated using the termIndex found for
+           * the term and a unit value with the appropriate boost applied.
+           * Using upsert because there could already be an entry in the vector
+           * for the term we are working with. In that case we just add the scores
+           * together.
+           */
+          queryVectors[field].upsert(termIndex, clause.boost, function (a, b) { return a + b })
+
+          /**
+           * If we've already seen this term, field combo then we've already collected
+           * the matching documents and metadata, no need to go through all that again
+           */
+          if (termFieldCache[termField]) {
+            continue
+          }
+
+          for (var l = 0; l < matchingDocumentRefs.length; l++) {
+            /*
+             * All metadata for this term/field/document triple
+             * are then extracted and collected into an instance
+             * of lunr.MatchData ready to be returned in the query
+             * results
+             */
+            var matchingDocumentRef = matchingDocumentRefs[l],
+                matchingFieldRef = new lunr.FieldRef (matchingDocumentRef, field),
+                metadata = fieldPosting[matchingDocumentRef],
+                fieldMatch
+
+            if ((fieldMatch = matchingFields[matchingFieldRef]) === undefined) {
+              matchingFields[matchingFieldRef] = new lunr.MatchData (expandedTerm, field, metadata)
+            } else {
+              fieldMatch.add(expandedTerm, field, metadata)
+            }
+
+          }
+
+          termFieldCache[termField] = true
+        }
+      }
+    }
+
+    /**
+     * If the presence was required we need to update the requiredMatches field sets.
+     * We do this after all fields for the term have collected their matches because
+     * the clause terms presence is required in _any_ of the fields not _all_ of the
+     * fields.
+     */
+    if (clause.presence === lunr.Query.presence.REQUIRED) {
+      for (var k = 0; k < clause.fields.length; k++) {
+        var field = clause.fields[k]
+        requiredMatches[field] = requiredMatches[field].intersect(clauseMatches)
+      }
+    }
+  }
+
+  /**
+   * Need to combine the field scoped required and prohibited
+   * matching documents into a global set of required and prohibited
+   * matches
+   */
+  var allRequiredMatches = lunr.Set.complete,
+      allProhibitedMatches = lunr.Set.empty
+
+  for (var i = 0; i < this.fields.length; i++) {
+    var field = this.fields[i]
+
+    if (requiredMatches[field]) {
+      allRequiredMatches = allRequiredMatches.intersect(requiredMatches[field])
+    }
+
+    if (prohibitedMatches[field]) {
+      allProhibitedMatches = allProhibitedMatches.union(prohibitedMatches[field])
+    }
+  }
+
+  var matchingFieldRefs = Object.keys(matchingFields),
+      results = [],
+      matches = Object.create(null)
+
+  /*
+   * If the query is negated (contains only prohibited terms)
+   * we need to get _all_ fieldRefs currently existing in the
+   * index. This is only done when we know that the query is
+   * entirely prohibited terms to avoid any cost of getting all
+   * fieldRefs unnecessarily.
+   *
+   * Additionally, blank MatchData must be created to correctly
+   * populate the results.
+   */
+  if (query.isNegated()) {
+    matchingFieldRefs = Object.keys(this.fieldVectors)
+
+    for (var i = 0; i < matchingFieldRefs.length; i++) {
+      var matchingFieldRef = matchingFieldRefs[i]
+      var fieldRef = lunr.FieldRef.fromString(matchingFieldRef)
+      matchingFields[matchingFieldRef] = new lunr.MatchData
+    }
+  }
+
+  for (var i = 0; i < matchingFieldRefs.length; i++) {
+    /*
+     * Currently we have document fields that match the query, but we
+     * need to return documents. The matchData and scores are combined
+     * from multiple fields belonging to the same document.
+     *
+     * Scores are calculated by field, using the query vectors created
+     * above, and combined into a final document score using addition.
+     */
+    var fieldRef = lunr.FieldRef.fromString(matchingFieldRefs[i]),
+        docRef = fieldRef.docRef
+
+    if (!allRequiredMatches.contains(docRef)) {
+      continue
+    }
+
+    if (allProhibitedMatches.contains(docRef)) {
+      continue
+    }
+
+    var fieldVector = this.fieldVectors[fieldRef],
+        score = queryVectors[fieldRef.fieldName].similarity(fieldVector),
+        docMatch
+
+    if ((docMatch = matches[docRef]) !== undefined) {
+      docMatch.score += score
+      docMatch.matchData.combine(matchingFields[fieldRef])
+    } else {
+      var match = {
+        ref: docRef,
+        score: score,
+        matchData: matchingFields[fieldRef]
+      }
+      matches[docRef] = match
+      results.push(match)
+    }
+  }
+
+  /*
+   * Sort the results objects by score, highest first.
+   */
+  return results.sort(function (a, b) {
+    return b.score - a.score
+  })
+}
+
+/**
+ * Prepares the index for JSON serialization.
+ *
+ * The schema for this JSON blob will be described in a
+ * separate JSON schema file.
+ *
+ * @returns {Object}
+ */
+lunr.Index.prototype.toJSON = function () {
+  var invertedIndex = Object.keys(this.invertedIndex)
+    .sort()
+    .map(function (term) {
+      return [term, this.invertedIndex[term]]
+    }, this)
+
+  var fieldVectors = Object.keys(this.fieldVectors)
+    .map(function (ref) {
+      return [ref, this.fieldVectors[ref].toJSON()]
+    }, this)
+
+  return {
+    version: lunr.version,
+    fields: this.fields,
+    fieldVectors: fieldVectors,
+    invertedIndex: invertedIndex,
+    pipeline: this.pipeline.toJSON()
+  }
+}
+
+/**
+ * Loads a previously serialized lunr.Index
+ *
+ * @param {Object} serializedIndex - A previously serialized lunr.Index
+ * @returns {lunr.Index}
+ */
+lunr.Index.load = function (serializedIndex) {
+  var attrs = {},
+      fieldVectors = {},
+      serializedVectors = serializedIndex.fieldVectors,
+      invertedIndex = Object.create(null),
+      serializedInvertedIndex = serializedIndex.invertedIndex,
+      tokenSetBuilder = new lunr.TokenSet.Builder,
+      pipeline = lunr.Pipeline.load(serializedIndex.pipeline)
+
+  if (serializedIndex.version != lunr.version) {
+    lunr.utils.warn("Version mismatch when loading serialised index. Current version of lunr '" + lunr.version + "' does not match serialized index '" + serializedIndex.version + "'")
+  }
+
+  for (var i = 0; i < serializedVectors.length; i++) {
+    var tuple = serializedVectors[i],
+        ref = tuple[0],
+        elements = tuple[1]
+
+    fieldVectors[ref] = new lunr.Vector(elements)
+  }
+
+  for (var i = 0; i < serializedInvertedIndex.length; i++) {
+    var tuple = serializedInvertedIndex[i],
+        term = tuple[0],
+        posting = tuple[1]
+
+    tokenSetBuilder.insert(term)
+    invertedIndex[term] = posting
+  }
+
+  tokenSetBuilder.finish()
+
+  attrs.fields = serializedIndex.fields
+
+  attrs.fieldVectors = fieldVectors
+  attrs.invertedIndex = invertedIndex
+  attrs.tokenSet = tokenSetBuilder.root
+  attrs.pipeline = pipeline
+
+  return new lunr.Index(attrs)
+}
+/*!
+ * lunr.Builder
+ * Copyright (C) 2019 Oliver Nightingale
+ */
+
+/**
+ * lunr.Builder performs indexing on a set of documents and
+ * returns instances of lunr.Index ready for querying.
+ *
+ * All configuration of the index is done via the builder, the
+ * fields to index, the document reference, the text processing
+ * pipeline and document scoring parameters are all set on the
+ * builder before indexing.
+ *
+ * @constructor
+ * @property {string} _ref - Internal reference to the document reference field.
+ * @property {string[]} _fields - Internal reference to the document fields to index.
+ * @property {object} invertedIndex - The inverted index maps terms to document fields.
+ * @property {object} documentTermFrequencies - Keeps track of document term frequencies.
+ * @property {object} documentLengths - Keeps track of the length of documents added to the index.
+ * @property {lunr.tokenizer} tokenizer - Function for splitting strings into tokens for indexing.
+ * @property {lunr.Pipeline} pipeline - The pipeline performs text processing on tokens before indexing.
+ * @property {lunr.Pipeline} searchPipeline - A pipeline for processing search terms before querying the index.
+ * @property {number} documentCount - Keeps track of the total number of documents indexed.
+ * @property {number} _b - A parameter to control field length normalization, setting this to 0 disabled normalization, 1 fully normalizes field lengths, the default value is 0.75.
+ * @property {number} _k1 - A parameter to control how quickly an increase in term frequency results in term frequency saturation, the default value is 1.2.
+ * @property {number} termIndex - A counter incremented for each unique term, used to identify a terms position in the vector space.
+ * @property {array} metadataWhitelist - A list of metadata keys that have been whitelisted for entry in the index.
+ */
+lunr.Builder = function () {
+  this._ref = "id"
+  this._fields = Object.create(null)
+  this._documents = Object.create(null)
+  this.invertedIndex = Object.create(null)
+  this.fieldTermFrequencies = {}
+  this.fieldLengths = {}
+  this.tokenizer = lunr.tokenizer
+  this.pipeline = new lunr.Pipeline
+  this.searchPipeline = new lunr.Pipeline
+  this.documentCount = 0
+  this._b = 0.75
+  this._k1 = 1.2
+  this.termIndex = 0
+  this.metadataWhitelist = []
+}
+
+/**
+ * Sets the document field used as the document reference. Every document must have this field.
+ * The type of this field in the document should be a string, if it is not a string it will be
+ * coerced into a string by calling toString.
+ *
+ * The default ref is 'id'.
+ *
+ * The ref should _not_ be changed during indexing, it should be set before any documents are
+ * added to the index. Changing it during indexing can lead to inconsistent results.
+ *
+ * @param {string} ref - The name of the reference field in the document.
+ */
+lunr.Builder.prototype.ref = function (ref) {
+  this._ref = ref
+}
+
+/**
+ * A function that is used to extract a field from a document.
+ *
+ * Lunr expects a field to be at the top level of a document, if however the field
+ * is deeply nested within a document an extractor function can be used to extract
+ * the right field for indexing.
+ *
+ * @callback fieldExtractor
+ * @param {object} doc - The document being added to the index.
+ * @returns {?(string|object|object[])} obj - The object that will be indexed for this field.
+ * @example <caption>Extracting a nested field</caption>
+ * function (doc) { return doc.nested.field }
+ */
+
+/**
+ * Adds a field to the list of document fields that will be indexed. Every document being
+ * indexed should have this field. Null values for this field in indexed documents will
+ * not cause errors but will limit the chance of that document being retrieved by searches.
+ *
+ * All fields should be added before adding documents to the index. Adding fields after
+ * a document has been indexed will have no effect on already indexed documents.
+ *
+ * Fields can be boosted at build time. This allows terms within that field to have more
+ * importance when ranking search results. Use a field boost to specify that matches within
+ * one field are more important than other fields.
+ *
+ * @param {string} fieldName - The name of a field to index in all documents.
+ * @param {object} attributes - Optional attributes associated with this field.
+ * @param {number} [attributes.boost=1] - Boost applied to all terms within this field.
+ * @param {fieldExtractor} [attributes.extractor] - Function to extract a field from a document.
+ * @throws {RangeError} fieldName cannot contain unsupported characters '/'
+ */
+lunr.Builder.prototype.field = function (fieldName, attributes) {
+  if (/\//.test(fieldName)) {
+    throw new RangeError ("Field '" + fieldName + "' contains illegal character '/'")
+  }
+
+  this._fields[fieldName] = attributes || {}
+}
+
+/**
+ * A parameter to tune the amount of field length normalisation that is applied when
+ * calculating relevance scores. A value of 0 will completely disable any normalisation
+ * and a value of 1 will fully normalise field lengths. The default is 0.75. Values of b
+ * will be clamped to the range 0 - 1.
+ *
+ * @param {number} number - The value to set for this tuning parameter.
+ */
+lunr.Builder.prototype.b = function (number) {
+  if (number < 0) {
+    this._b = 0
+  } else if (number > 1) {
+    this._b = 1
+  } else {
+    this._b = number
+  }
+}
+
+/**
+ * A parameter that controls the speed at which a rise in term frequency results in term
+ * frequency saturation. The default value is 1.2. Setting this to a higher value will give
+ * slower saturation levels, a lower value will result in quicker saturation.
+ *
+ * @param {number} number - The value to set for this tuning parameter.
+ */
+lunr.Builder.prototype.k1 = function (number) {
+  this._k1 = number
+}
+
+/**
+ * Adds a document to the index.
+ *
+ * Before adding fields to the index the index should have been fully setup, with the document
+ * ref and all fields to index already having been specified.
+ *
+ * The document must have a field name as specified by the ref (by default this is 'id') and
+ * it should have all fields defined for indexing, though null or undefined values will not
+ * cause errors.
+ *
+ * Entire documents can be boosted at build time. Applying a boost to a document indicates that
+ * this document should rank higher in search results than other documents.
+ *
+ * @param {object} doc - The document to add to the index.
+ * @param {object} attributes - Optional attributes associated with this document.
+ * @param {number} [attributes.boost=1] - Boost applied to all terms within this document.
+ */
+lunr.Builder.prototype.add = function (doc, attributes) {
+  var docRef = doc[this._ref],
+      fields = Object.keys(this._fields)
+
+  this._documents[docRef] = attributes || {}
+  this.documentCount += 1
+
+  for (var i = 0; i < fields.length; i++) {
+    var fieldName = fields[i],
+        extractor = this._fields[fieldName].extractor,
+        field = extractor ? extractor(doc) : doc[fieldName],
+        tokens = this.tokenizer(field, {
+          fields: [fieldName]
+        }),
+        terms = this.pipeline.run(tokens),
+        fieldRef = new lunr.FieldRef (docRef, fieldName),
+        fieldTerms = Object.create(null)
+
+    this.fieldTermFrequencies[fieldRef] = fieldTerms
+    this.fieldLengths[fieldRef] = 0
+
+    // store the length of this field for this document
+    this.fieldLengths[fieldRef] += terms.length
+
+    // calculate term frequencies for this field
+    for (var j = 0; j < terms.length; j++) {
+      var term = terms[j]
+
+      if (fieldTerms[term] == undefined) {
+        fieldTerms[term] = 0
+      }
+
+      fieldTerms[term] += 1
+
+      // add to inverted index
+      // create an initial posting if one doesn't exist
+      if (this.invertedIndex[term] == undefined) {
+        var posting = Object.create(null)
+        posting["_index"] = this.termIndex
+        this.termIndex += 1
+
+        for (var k = 0; k < fields.length; k++) {
+          posting[fields[k]] = Object.create(null)
+        }
+
+        this.invertedIndex[term] = posting
+      }
+
+      // add an entry for this term/fieldName/docRef to the invertedIndex
+      if (this.invertedIndex[term][fieldName][docRef] == undefined) {
+        this.invertedIndex[term][fieldName][docRef] = Object.create(null)
+      }
+
+      // store all whitelisted metadata about this token in the
+      // inverted index
+      for (var l = 0; l < this.metadataWhitelist.length; l++) {
+        var metadataKey = this.metadataWhitelist[l],
+            metadata = term.metadata[metadataKey]
+
+        if (this.invertedIndex[term][fieldName][docRef][metadataKey] == undefined) {
+          this.invertedIndex[term][fieldName][docRef][metadataKey] = []
+        }
+
+        this.invertedIndex[term][fieldName][docRef][metadataKey].push(metadata)
+      }
+    }
+
+  }
+}
+
+/**
+ * Calculates the average document length for this index
+ *
+ * @private
+ */
+lunr.Builder.prototype.calculateAverageFieldLengths = function () {
+
+  var fieldRefs = Object.keys(this.fieldLengths),
+      numberOfFields = fieldRefs.length,
+      accumulator = {},
+      documentsWithField = {}
+
+  for (var i = 0; i < numberOfFields; i++) {
+    var fieldRef = lunr.FieldRef.fromString(fieldRefs[i]),
+        field = fieldRef.fieldName
+
+    documentsWithField[field] || (documentsWithField[field] = 0)
+    documentsWithField[field] += 1
+
+    accumulator[field] || (accumulator[field] = 0)
+    accumulator[field] += this.fieldLengths[fieldRef]
+  }
+
+  var fields = Object.keys(this._fields)
+
+  for (var i = 0; i < fields.length; i++) {
+    var fieldName = fields[i]
+    accumulator[fieldName] = accumulator[fieldName] / documentsWithField[fieldName]
+  }
+
+  this.averageFieldLength = accumulator
+}
+
+/**
+ * Builds a vector space model of every document using lunr.Vector
+ *
+ * @private
+ */
+lunr.Builder.prototype.createFieldVectors = function () {
+  var fieldVectors = {},
+      fieldRefs = Object.keys(this.fieldTermFrequencies),
+      fieldRefsLength = fieldRefs.length,
+      termIdfCache = Object.create(null)
+
+  for (var i = 0; i < fieldRefsLength; i++) {
+    var fieldRef = lunr.FieldRef.fromString(fieldRefs[i]),
+        fieldName = fieldRef.fieldName,
+        fieldLength = this.fieldLengths[fieldRef],
+        fieldVector = new lunr.Vector,
+        termFrequencies = this.fieldTermFrequencies[fieldRef],
+        terms = Object.keys(termFrequencies),
+        termsLength = terms.length
+
+
+    var fieldBoost = this._fields[fieldName].boost || 1,
+        docBoost = this._documents[fieldRef.docRef].boost || 1
+
+    for (var j = 0; j < termsLength; j++) {
+      var term = terms[j],
+          tf = termFrequencies[term],
+          termIndex = this.invertedIndex[term]._index,
+          idf, score, scoreWithPrecision
+
+      if (termIdfCache[term] === undefined) {
+        idf = lunr.idf(this.invertedIndex[term], this.documentCount)
+        termIdfCache[term] = idf
+      } else {
+        idf = termIdfCache[term]
+      }
+
+      score = idf * ((this._k1 + 1) * tf) / (this._k1 * (1 - this._b + this._b * (fieldLength / this.averageFieldLength[fieldName])) + tf)
+      score *= fieldBoost
+      score *= docBoost
+      scoreWithPrecision = Math.round(score * 1000) / 1000
+      // Converts 1.23456789 to 1.234.
+      // Reducing the precision so that the vectors take up less
+      // space when serialised. Doing it now so that they behave
+      // the same before and after serialisation. Also, this is
+      // the fastest approach to reducing a number's precision in
+      // JavaScript.
+
+      fieldVector.insert(termIndex, scoreWithPrecision)
+    }
+
+    fieldVectors[fieldRef] = fieldVector
+  }
+
+  this.fieldVectors = fieldVectors
+}
+
+/**
+ * Creates a token set of all tokens in the index using lunr.TokenSet
+ *
+ * @private
+ */
+lunr.Builder.prototype.createTokenSet = function () {
+  this.tokenSet = lunr.TokenSet.fromArray(
+    Object.keys(this.invertedIndex).sort()
+  )
+}
+
+/**
+ * Builds the index, creating an instance of lunr.Index.
+ *
+ * This completes the indexing process and should only be called
+ * once all documents have been added to the index.
+ *
+ * @returns {lunr.Index}
+ */
+lunr.Builder.prototype.build = function () {
+  this.calculateAverageFieldLengths()
+  this.createFieldVectors()
+  this.createTokenSet()
+
+  return new lunr.Index({
+    invertedIndex: this.invertedIndex,
+    fieldVectors: this.fieldVectors,
+    tokenSet: this.tokenSet,
+    fields: Object.keys(this._fields),
+    pipeline: this.searchPipeline
+  })
+}
+
+/**
+ * Applies a plugin to the index builder.
+ *
+ * A plugin is a function that is called with the index builder as its context.
+ * Plugins can be used to customise or extend the behaviour of the index
+ * in some way. A plugin is just a function, that encapsulated the custom
+ * behaviour that should be applied when building the index.
+ *
+ * The plugin function will be called with the index builder as its argument, additional
+ * arguments can also be passed when calling use. The function will be called
+ * with the index builder as its context.
+ *
+ * @param {Function} plugin The plugin to apply.
+ */
+lunr.Builder.prototype.use = function (fn) {
+  var args = Array.prototype.slice.call(arguments, 1)
+  args.unshift(this)
+  fn.apply(this, args)
+}
+/**
+ * Contains and collects metadata about a matching document.
+ * A single instance of lunr.MatchData is returned as part of every
+ * lunr.Index~Result.
+ *
+ * @constructor
+ * @param {string} term - The term this match data is associated with
+ * @param {string} field - The field in which the term was found
+ * @param {object} metadata - The metadata recorded about this term in this field
+ * @property {object} metadata - A cloned collection of metadata associated with this document.
+ * @see {@link lunr.Index~Result}
+ */
+lunr.MatchData = function (term, field, metadata) {
+  var clonedMetadata = Object.create(null),
+      metadataKeys = Object.keys(metadata || {})
+
+  // Cloning the metadata to prevent the original
+  // being mutated during match data combination.
+  // Metadata is kept in an array within the inverted
+  // index so cloning the data can be done with
+  // Array#slice
+  for (var i = 0; i < metadataKeys.length; i++) {
+    var key = metadataKeys[i]
+    clonedMetadata[key] = metadata[key].slice()
+  }
+
+  this.metadata = Object.create(null)
+
+  if (term !== undefined) {
+    this.metadata[term] = Object.create(null)
+    this.metadata[term][field] = clonedMetadata
+  }
+}
+
+/**
+ * An instance of lunr.MatchData will be created for every term that matches a
+ * document. However only one instance is required in a lunr.Index~Result. This
+ * method combines metadata from another instance of lunr.MatchData with this
+ * objects metadata.
+ *
+ * @param {lunr.MatchData} otherMatchData - Another instance of match data to merge with this one.
+ * @see {@link lunr.Index~Result}
+ */
+lunr.MatchData.prototype.combine = function (otherMatchData) {
+  var terms = Object.keys(otherMatchData.metadata)
+
+  for (var i = 0; i < terms.length; i++) {
+    var term = terms[i],
+        fields = Object.keys(otherMatchData.metadata[term])
+
+    if (this.metadata[term] == undefined) {
+      this.metadata[term] = Object.create(null)
+    }
+
+    for (var j = 0; j < fields.length; j++) {
+      var field = fields[j],
+          keys = Object.keys(otherMatchData.metadata[term][field])
+
+      if (this.metadata[term][field] == undefined) {
+        this.metadata[term][field] = Object.create(null)
+      }
+
+      for (var k = 0; k < keys.length; k++) {
+        var key = keys[k]
+
+        if (this.metadata[term][field][key] == undefined) {
+          this.metadata[term][field][key] = otherMatchData.metadata[term][field][key]
+        } else {
+          this.metadata[term][field][key] = this.metadata[term][field][key].concat(otherMatchData.metadata[term][field][key])
+        }
+
+      }
+    }
+  }
+}
+
+/**
+ * Add metadata for a term/field pair to this instance of match data.
+ *
+ * @param {string} term - The term this match data is associated with
+ * @param {string} field - The field in which the term was found
+ * @param {object} metadata - The metadata recorded about this term in this field
+ */
+lunr.MatchData.prototype.add = function (term, field, metadata) {
+  if (!(term in this.metadata)) {
+    this.metadata[term] = Object.create(null)
+    this.metadata[term][field] = metadata
+    return
+  }
+
+  if (!(field in this.metadata[term])) {
+    this.metadata[term][field] = metadata
+    return
+  }
+
+  var metadataKeys = Object.keys(metadata)
+
+  for (var i = 0; i < metadataKeys.length; i++) {
+    var key = metadataKeys[i]
+
+    if (key in this.metadata[term][field]) {
+      this.metadata[term][field][key] = this.metadata[term][field][key].concat(metadata[key])
+    } else {
+      this.metadata[term][field][key] = metadata[key]
+    }
+  }
+}
+/**
+ * A lunr.Query provides a programmatic way of defining queries to be performed
+ * against a {@link lunr.Index}.
+ *
+ * Prefer constructing a lunr.Query using the {@link lunr.Index#query} method
+ * so the query object is pre-initialized with the right index fields.
+ *
+ * @constructor
+ * @property {lunr.Query~Clause[]} clauses - An array of query clauses.
+ * @property {string[]} allFields - An array of all available fields in a lunr.Index.
+ */
+lunr.Query = function (allFields) {
+  this.clauses = []
+  this.allFields = allFields
+}
+
+/**
+ * Constants for indicating what kind of automatic wildcard insertion will be used when constructing a query clause.
+ *
+ * This allows wildcards to be added to the beginning and end of a term without having to manually do any string
+ * concatenation.
+ *
+ * The wildcard constants can be bitwise combined to select both leading and trailing wildcards.
+ *
+ * @constant
+ * @default
+ * @property {number} wildcard.NONE - The term will have no wildcards inserted, this is the default behaviour
+ * @property {number} wildcard.LEADING - Prepend the term with a wildcard, unless a leading wildcard already exists
+ * @property {number} wildcard.TRAILING - Append a wildcard to the term, unless a trailing wildcard already exists
+ * @see lunr.Query~Clause
+ * @see lunr.Query#clause
+ * @see lunr.Query#term
+ * @example <caption>query term with trailing wildcard</caption>
+ * query.term('foo', { wildcard: lunr.Query.wildcard.TRAILING })
+ * @example <caption>query term with leading and trailing wildcard</caption>
+ * query.term('foo', {
+ *   wildcard: lunr.Query.wildcard.LEADING | lunr.Query.wildcard.TRAILING
+ * })
+ */
+
+lunr.Query.wildcard = new String ("*")
+lunr.Query.wildcard.NONE = 0
+lunr.Query.wildcard.LEADING = 1
+lunr.Query.wildcard.TRAILING = 2
+
+/**
+ * Constants for indicating what kind of presence a term must have in matching documents.
+ *
+ * @constant
+ * @enum {number}
+ * @see lunr.Query~Clause
+ * @see lunr.Query#clause
+ * @see lunr.Query#term
+ * @example <caption>query term with required presence</caption>
+ * query.term('foo', { presence: lunr.Query.presence.REQUIRED })
+ */
+lunr.Query.presence = {
+  /**
+   * Term's presence in a document is optional, this is the default value.
+   */
+  OPTIONAL: 1,
+
+  /**
+   * Term's presence in a document is required, documents that do not contain
+   * this term will not be returned.
+   */
+  REQUIRED: 2,
+
+  /**
+   * Term's presence in a document is prohibited, documents that do contain
+   * this term will not be returned.
+   */
+  PROHIBITED: 3
+}
+
+/**
+ * A single clause in a {@link lunr.Query} contains a term and details on how to
+ * match that term against a {@link lunr.Index}.
+ *
+ * @typedef {Object} lunr.Query~Clause
+ * @property {string[]} fields - The fields in an index this clause should be matched against.
+ * @property {number} [boost=1] - Any boost that should be applied when matching this clause.
+ * @property {number} [editDistance] - Whether the term should have fuzzy matching applied, and how fuzzy the match should be.
+ * @property {boolean} [usePipeline] - Whether the term should be passed through the search pipeline.
+ * @property {number} [wildcard=lunr.Query.wildcard.NONE] - Whether the term should have wildcards appended or prepended.
+ * @property {number} [presence=lunr.Query.presence.OPTIONAL] - The terms presence in any matching documents.
+ */
+
+/**
+ * Adds a {@link lunr.Query~Clause} to this query.
+ *
+ * Unless the clause contains the fields to be matched all fields will be matched. In addition
+ * a default boost of 1 is applied to the clause.
+ *
+ * @param {lunr.Query~Clause} clause - The clause to add to this query.
+ * @see lunr.Query~Clause
+ * @returns {lunr.Query}
+ */
+lunr.Query.prototype.clause = function (clause) {
+  if (!('fields' in clause)) {
+    clause.fields = this.allFields
+  }
+
+  if (!('boost' in clause)) {
+    clause.boost = 1
+  }
+
+  if (!('usePipeline' in clause)) {
+    clause.usePipeline = true
+  }
+
+  if (!('wildcard' in clause)) {
+    clause.wildcard = lunr.Query.wildcard.NONE
+  }
+
+  if ((clause.wildcard & lunr.Query.wildcard.LEADING) && (clause.term.charAt(0) != lunr.Query.wildcard)) {
+    clause.term = "*" + clause.term
+  }
+
+  if ((clause.wildcard & lunr.Query.wildcard.TRAILING) && (clause.term.slice(-1) != lunr.Query.wildcard)) {
+    clause.term = "" + clause.term + "*"
+  }
+
+  if (!('presence' in clause)) {
+    clause.presence = lunr.Query.presence.OPTIONAL
+  }
+
+  this.clauses.push(clause)
+
+  return this
+}
+
+/**
+ * A negated query is one in which every clause has a presence of
+ * prohibited. These queries require some special processing to return
+ * the expected results.
+ *
+ * @returns boolean
+ */
+lunr.Query.prototype.isNegated = function () {
+  for (var i = 0; i < this.clauses.length; i++) {
+    if (this.clauses[i].presence != lunr.Query.presence.PROHIBITED) {
+      return false
+    }
+  }
+
+  return true
+}
+
+/**
+ * Adds a term to the current query, under the covers this will create a {@link lunr.Query~Clause}
+ * to the list of clauses that make up this query.
+ *
+ * The term is used as is, i.e. no tokenization will be performed by this method. Instead conversion
+ * to a token or token-like string should be done before calling this method.
+ *
+ * The term will be converted to a string by calling `toString`. Multiple terms can be passed as an
+ * array, each term in the array will share the same options.
+ *
+ * @param {object|object[]} term - The term(s) to add to the query.
+ * @param {object} [options] - Any additional properties to add to the query clause.
+ * @returns {lunr.Query}
+ * @see lunr.Query#clause
+ * @see lunr.Query~Clause
+ * @example <caption>adding a single term to a query</caption>
+ * query.term("foo")
+ * @example <caption>adding a single term to a query and specifying search fields, term boost and automatic trailing wildcard</caption>
+ * query.term("foo", {
+ *   fields: ["title"],
+ *   boost: 10,
+ *   wildcard: lunr.Query.wildcard.TRAILING
+ * })
+ * @example <caption>using lunr.tokenizer to convert a string to tokens before using them as terms</caption>
+ * query.term(lunr.tokenizer("foo bar"))
+ */
+lunr.Query.prototype.term = function (term, options) {
+  if (Array.isArray(term)) {
+    term.forEach(function (t) { this.term(t, lunr.utils.clone(options)) }, this)
+    return this
+  }
+
+  var clause = options || {}
+  clause.term = term.toString()
+
+  this.clause(clause)
+
+  return this
+}
+lunr.QueryParseError = function (message, start, end) {
+  this.name = "QueryParseError"
+  this.message = message
+  this.start = start
+  this.end = end
+}
+
+lunr.QueryParseError.prototype = new Error
+lunr.QueryLexer = function (str) {
+  this.lexemes = []
+  this.str = str
+  this.length = str.length
+  this.pos = 0
+  this.start = 0
+  this.escapeCharPositions = []
+}
+
+lunr.QueryLexer.prototype.run = function () {
+  var state = lunr.QueryLexer.lexText
+
+  while (state) {
+    state = state(this)
+  }
+}
+
+lunr.QueryLexer.prototype.sliceString = function () {
+  var subSlices = [],
+      sliceStart = this.start,
+      sliceEnd = this.pos
+
+  for (var i = 0; i < this.escapeCharPositions.length; i++) {
+    sliceEnd = this.escapeCharPositions[i]
+    subSlices.push(this.str.slice(sliceStart, sliceEnd))
+    sliceStart = sliceEnd + 1
+  }
+
+  subSlices.push(this.str.slice(sliceStart, this.pos))
+  this.escapeCharPositions.length = 0
+
+  return subSlices.join('')
+}
+
+lunr.QueryLexer.prototype.emit = function (type) {
+  this.lexemes.push({
+    type: type,
+    str: this.sliceString(),
+    start: this.start,
+    end: this.pos
+  })
+
+  this.start = this.pos
+}
+
+lunr.QueryLexer.prototype.escapeCharacter = function () {
+  this.escapeCharPositions.push(this.pos - 1)
+  this.pos += 1
+}
+
+lunr.QueryLexer.prototype.next = function () {
+  if (this.pos >= this.length) {
+    return lunr.QueryLexer.EOS
+  }
+
+  var char = this.str.charAt(this.pos)
+  this.pos += 1
+  return char
+}
+
+lunr.QueryLexer.prototype.width = function () {
+  return this.pos - this.start
+}
+
+lunr.QueryLexer.prototype.ignore = function () {
+  if (this.start == this.pos) {
+    this.pos += 1
+  }
+
+  this.start = this.pos
+}
+
+lunr.QueryLexer.prototype.backup = function () {
+  this.pos -= 1
+}
+
+lunr.QueryLexer.prototype.acceptDigitRun = function () {
+  var char, charCode
+
+  do {
+    char = this.next()
+    charCode = char.charCodeAt(0)
+  } while (charCode > 47 && charCode < 58)
+
+  if (char != lunr.QueryLexer.EOS) {
+    this.backup()
+  }
+}
+
+lunr.QueryLexer.prototype.more = function () {
+  return this.pos < this.length
+}
+
+lunr.QueryLexer.EOS = 'EOS'
+lunr.QueryLexer.FIELD = 'FIELD'
+lunr.QueryLexer.TERM = 'TERM'
+lunr.QueryLexer.EDIT_DISTANCE = 'EDIT_DISTANCE'
+lunr.QueryLexer.BOOST = 'BOOST'
+lunr.QueryLexer.PRESENCE = 'PRESENCE'
+
+lunr.QueryLexer.lexField = function (lexer) {
+  lexer.backup()
+  lexer.emit(lunr.QueryLexer.FIELD)
+  lexer.ignore()
+  return lunr.QueryLexer.lexText
+}
+
+lunr.QueryLexer.lexTerm = function (lexer) {
+  if (lexer.width() > 1) {
+    lexer.backup()
+    lexer.emit(lunr.QueryLexer.TERM)
+  }
+
+  lexer.ignore()
+
+  if (lexer.more()) {
+    return lunr.QueryLexer.lexText
+  }
+}
+
+lunr.QueryLexer.lexEditDistance = function (lexer) {
+  lexer.ignore()
+  lexer.acceptDigitRun()
+  lexer.emit(lunr.QueryLexer.EDIT_DISTANCE)
+  return lunr.QueryLexer.lexText
+}
+
+lunr.QueryLexer.lexBoost = function (lexer) {
+  lexer.ignore()
+  lexer.acceptDigitRun()
+  lexer.emit(lunr.QueryLexer.BOOST)
+  return lunr.QueryLexer.lexText
+}
+
+lunr.QueryLexer.lexEOS = function (lexer) {
+  if (lexer.width() > 0) {
+    lexer.emit(lunr.QueryLexer.TERM)
+  }
+}
+
+// This matches the separator used when tokenising fields
+// within a document. These should match otherwise it is
+// not possible to search for some tokens within a document.
+//
+// It is possible for the user to change the separator on the
+// tokenizer so it _might_ clash with any other of the special
+// characters already used within the search string, e.g. :.
+//
+// This means that it is possible to change the separator in
+// such a way that makes some words unsearchable using a search
+// string.
+lunr.QueryLexer.termSeparator = lunr.tokenizer.separator
+
+lunr.QueryLexer.lexText = function (lexer) {
+  while (true) {
+    var char = lexer.next()
+
+    if (char == lunr.QueryLexer.EOS) {
+      return lunr.QueryLexer.lexEOS
+    }
+
+    // Escape character is '\'
+    if (char.charCodeAt(0) == 92) {
+      lexer.escapeCharacter()
+      continue
+    }
+
+    if (char == ":") {
+      return lunr.QueryLexer.lexField
+    }
+
+    if (char == "~") {
+      lexer.backup()
+      if (lexer.width() > 0) {
+        lexer.emit(lunr.QueryLexer.TERM)
+      }
+      return lunr.QueryLexer.lexEditDistance
+    }
+
+    if (char == "^") {
+      lexer.backup()
+      if (lexer.width() > 0) {
+        lexer.emit(lunr.QueryLexer.TERM)
+      }
+      return lunr.QueryLexer.lexBoost
+    }
+
+    // "+" indicates term presence is required
+    // checking for length to ensure that only
+    // leading "+" are considered
+    if (char == "+" && lexer.width() === 1) {
+      lexer.emit(lunr.QueryLexer.PRESENCE)
+      return lunr.QueryLexer.lexText
+    }
+
+    // "-" indicates term presence is prohibited
+    // checking for length to ensure that only
+    // leading "-" are considered
+    if (char == "-" && lexer.width() === 1) {
+      lexer.emit(lunr.QueryLexer.PRESENCE)
+      return lunr.QueryLexer.lexText
+    }
+
+    if (char.match(lunr.QueryLexer.termSeparator)) {
+      return lunr.QueryLexer.lexTerm
+    }
+  }
+}
+
+lunr.QueryParser = function (str, query) {
+  this.lexer = new lunr.QueryLexer (str)
+  this.query = query
+  this.currentClause = {}
+  this.lexemeIdx = 0
+}
+
+lunr.QueryParser.prototype.parse = function () {
+  this.lexer.run()
+  this.lexemes = this.lexer.lexemes
+
+  var state = lunr.QueryParser.parseClause
+
+  while (state) {
+    state = state(this)
+  }
+
+  return this.query
+}
+
+lunr.QueryParser.prototype.peekLexeme = function () {
+  return this.lexemes[this.lexemeIdx]
+}
+
+lunr.QueryParser.prototype.consumeLexeme = function () {
+  var lexeme = this.peekLexeme()
+  this.lexemeIdx += 1
+  return lexeme
+}
+
+lunr.QueryParser.prototype.nextClause = function () {
+  var completedClause = this.currentClause
+  this.query.clause(completedClause)
+  this.currentClause = {}
+}
+
+lunr.QueryParser.parseClause = function (parser) {
+  var lexeme = parser.peekLexeme()
+
+  if (lexeme == undefined) {
+    return
+  }
+
+  switch (lexeme.type) {
+    case lunr.QueryLexer.PRESENCE:
+      return lunr.QueryParser.parsePresence
+    case lunr.QueryLexer.FIELD:
+      return lunr.QueryParser.parseField
+    case lunr.QueryLexer.TERM:
+      return lunr.QueryParser.parseTerm
+    default:
+      var errorMessage = "expected either a field or a term, found " + lexeme.type
+
+      if (lexeme.str.length >= 1) {
+        errorMessage += " with value '" + lexeme.str + "'"
+      }
+
+      throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)
+  }
+}
+
+lunr.QueryParser.parsePresence = function (parser) {
+  var lexeme = parser.consumeLexeme()
+
+  if (lexeme == undefined) {
+    return
+  }
+
+  switch (lexeme.str) {
+    case "-":
+      parser.currentClause.presence = lunr.Query.presence.PROHIBITED
+      break
+    case "+":
+      parser.currentClause.presence = lunr.Query.presence.REQUIRED
+      break
+    default:
+      var errorMessage = "unrecognised presence operator'" + lexeme.str + "'"
+      throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)
+  }
+
+  var nextLexeme = parser.peekLexeme()
+
+  if (nextLexeme == undefined) {
+    var errorMessage = "expecting term or field, found nothing"
+    throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)
+  }
+
+  switch (nextLexeme.type) {
+    case lunr.QueryLexer.FIELD:
+      return lunr.QueryParser.parseField
+    case lunr.QueryLexer.TERM:
+      return lunr.QueryParser.parseTerm
+    default:
+      var errorMessage = "expecting term or field, found '" + nextLexeme.type + "'"
+      throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end)
+  }
+}
+
+lunr.QueryParser.parseField = function (parser) {
+  var lexeme = parser.consumeLexeme()
+
+  if (lexeme == undefined) {
+    return
+  }
+
+  if (parser.query.allFields.indexOf(lexeme.str) == -1) {
+    var possibleFields = parser.query.allFields.map(function (f) { return "'" + f + "'" }).join(', '),
+        errorMessage = "unrecognised field '" + lexeme.str + "', possible fields: " + possibleFields
+
+    throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)
+  }
+
+  parser.currentClause.fields = [lexeme.str]
+
+  var nextLexeme = parser.peekLexeme()
+
+  if (nextLexeme == undefined) {
+    var errorMessage = "expecting term, found nothing"
+    throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)
+  }
+
+  switch (nextLexeme.type) {
+    case lunr.QueryLexer.TERM:
+      return lunr.QueryParser.parseTerm
+    default:
+      var errorMessage = "expecting term, found '" + nextLexeme.type + "'"
+      throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end)
+  }
+}
+
+lunr.QueryParser.parseTerm = function (parser) {
+  var lexeme = parser.consumeLexeme()
+
+  if (lexeme == undefined) {
+    return
+  }
+
+  parser.currentClause.term = lexeme.str.toLowerCase()
+
+  if (lexeme.str.indexOf("*") != -1) {
+    parser.currentClause.usePipeline = false
+  }
+
+  var nextLexeme = parser.peekLexeme()
+
+  if (nextLexeme == undefined) {
+    parser.nextClause()
+    return
+  }
+
+  switch (nextLexeme.type) {
+    case lunr.QueryLexer.TERM:
+      parser.nextClause()
+      return lunr.QueryParser.parseTerm
+    case lunr.QueryLexer.FIELD:
+      parser.nextClause()
+      return lunr.QueryParser.parseField
+    case lunr.QueryLexer.EDIT_DISTANCE:
+      return lunr.QueryParser.parseEditDistance
+    case lunr.QueryLexer.BOOST:
+      return lunr.QueryParser.parseBoost
+    case lunr.QueryLexer.PRESENCE:
+      parser.nextClause()
+      return lunr.QueryParser.parsePresence
+    default:
+      var errorMessage = "Unexpected lexeme type '" + nextLexeme.type + "'"
+      throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end)
+  }
+}
+
+lunr.QueryParser.parseEditDistance = function (parser) {
+  var lexeme = parser.consumeLexeme()
+
+  if (lexeme == undefined) {
+    return
+  }
+
+  var editDistance = parseInt(lexeme.str, 10)
+
+  if (isNaN(editDistance)) {
+    var errorMessage = "edit distance must be numeric"
+    throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)
+  }
+
+  parser.currentClause.editDistance = editDistance
+
+  var nextLexeme = parser.peekLexeme()
+
+  if (nextLexeme == undefined) {
+    parser.nextClause()
+    return
+  }
+
+  switch (nextLexeme.type) {
+    case lunr.QueryLexer.TERM:
+      parser.nextClause()
+      return lunr.QueryParser.parseTerm
+    case lunr.QueryLexer.FIELD:
+      parser.nextClause()
+      return lunr.QueryParser.parseField
+    case lunr.QueryLexer.EDIT_DISTANCE:
+      return lunr.QueryParser.parseEditDistance
+    case lunr.QueryLexer.BOOST:
+      return lunr.QueryParser.parseBoost
+    case lunr.QueryLexer.PRESENCE:
+      parser.nextClause()
+      return lunr.QueryParser.parsePresence
+    default:
+      var errorMessage = "Unexpected lexeme type '" + nextLexeme.type + "'"
+      throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end)
+  }
+}
+
+lunr.QueryParser.parseBoost = function (parser) {
+  var lexeme = parser.consumeLexeme()
+
+  if (lexeme == undefined) {
+    return
+  }
+
+  var boost = parseInt(lexeme.str, 10)
+
+  if (isNaN(boost)) {
+    var errorMessage = "boost must be numeric"
+    throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)
+  }
+
+  parser.currentClause.boost = boost
+
+  var nextLexeme = parser.peekLexeme()
+
+  if (nextLexeme == undefined) {
+    parser.nextClause()
+    return
+  }
+
+  switch (nextLexeme.type) {
+    case lunr.QueryLexer.TERM:
+      parser.nextClause()
+      return lunr.QueryParser.parseTerm
+    case lunr.QueryLexer.FIELD:
+      parser.nextClause()
+      return lunr.QueryParser.parseField
+    case lunr.QueryLexer.EDIT_DISTANCE:
+      return lunr.QueryParser.parseEditDistance
+    case lunr.QueryLexer.BOOST:
+      return lunr.QueryParser.parseBoost
+    case lunr.QueryLexer.PRESENCE:
+      parser.nextClause()
+      return lunr.QueryParser.parsePresence
+    default:
+      var errorMessage = "Unexpected lexeme type '" + nextLexeme.type + "'"
+      throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end)
+  }
+}
+
+  /**
+   * export the module via AMD, CommonJS or as a browser global
+   * Export code from https://github.com/umdjs/umd/blob/master/returnExports.js
+   */
+  ;(function (root, factory) {
+    if (typeof define === 'function' && define.amd) {
+      // AMD. Register as an anonymous module.
+      define(factory)
+    } else if (typeof exports === 'object') {
+      /**
+       * Node. Does not work with strict CommonJS, but
+       * only CommonJS-like enviroments that support module.exports,
+       * like Node.
+       */
+      module.exports = factory()
+    } else {
+      // Browser globals (root is window)
+      root.lunr = factory()
+    }
+  }(this, function () {
+    /**
+     * Just return a value to define the module export.
+     * This example returns an object, but the module
+     * can return a function as the exported value.
+     */
+    return lunr
+  }))
+})();