refactor: move xmodule folder to root

- Moving xmodule folder to root as we're dissolving sub-projects of common folder in edx-platform
    - More info: https://openedx.atlassian.net/browse/BOM-2579
- -e common/lib/xmodule has been removed from the requirements as xmodule has itself become the part of edx-platform and not being installed through requirements
- The test files common/lib/xmodule/test_files/ have been removed as they are not being used anymore

xmodule/mongo_utils.py

@@ -0,0 +1,104 @@
+"""
+Common MongoDB connection functions.
+"""
+
+
+import logging
+
+import pymongo
+from mongodb_proxy import MongoProxy
+from pymongo.read_preferences import (  # lint-amnesty, pylint: disable=unused-import
+    ReadPreference,
+    _MONGOS_MODES,
+    _MODES
+)
+
+
+logger = logging.getLogger(__name__)  # pylint: disable=invalid-name
+
+# This will yeld a map of all available Mongo modes and their name
+MONGO_READ_PREFERENCE_MAP = dict(zip(_MONGOS_MODES, _MODES))
+
+
+def connect_to_mongodb(
+    db, host,
+    port=27017, tz_aware=True, user=None, password=None,
+    retry_wait_time=0.1, proxy=True, **kwargs
+):
+    """
+    Returns a MongoDB Database connection, optionally wrapped in a proxy. The proxy
+    handles AutoReconnect errors by retrying read operations, since these exceptions
+    typically indicate a temporary step-down condition for MongoDB.
+    """
+    # If the MongoDB server uses a separate authentication database that should be specified here
+    auth_source = kwargs.get('authsource', '') or None
+
+    # sanitize a kwarg which may be present and is no longer expected
+    # AED 2020-03-02 TODO: Remove this when 'auth_source' will no longer exist in kwargs
+    if 'auth_source' in kwargs:
+        kwargs.pop('auth_source')
+
+    # If read_preference is given as a name of a valid ReadPreference.<NAME>
+    # constant such as "SECONDARY_PREFERRED" or a mongo mode such as
+    # "secondaryPreferred", convert it. Otherwise pass it through unchanged.
+    if 'read_preference' in kwargs:
+        read_preference = MONGO_READ_PREFERENCE_MAP.get(
+            kwargs['read_preference'],
+            kwargs['read_preference']
+        )
+
+        read_preference = getattr(ReadPreference, read_preference, None)
+        if read_preference is not None:
+            kwargs['read_preference'] = read_preference
+
+    mongo_conn = pymongo.database.Database(
+        pymongo.MongoClient(
+            host=host,
+            port=port,
+            tz_aware=tz_aware,
+            document_class=dict,
+            **kwargs
+        ),
+        db
+    )
+
+    if proxy:
+        mongo_conn = MongoProxy(
+            mongo_conn,
+            wait_time=retry_wait_time
+        )
+    # If credentials were provided, authenticate the user.
+    if user is not None and password is not None:
+        mongo_conn.authenticate(user, password, source=auth_source)
+
+    return mongo_conn
+
+
+def create_collection_index(
+    collection, keys,
+    ignore_created=True, ignore_created_opts=True, **kwargs
+):
+    """
+    Create a MongoDB index in a collection. Optionally,
+    ignore errors related to the index already existing.
+    """
+    # For an explanation of the error codes:
+    # https://github.com/mongodb/mongo/blob/v3.0/src/mongo/db/catalog/index_catalog.cpp#L542-L583
+    # https://github.com/mongodb/mongo/blob/v3.0/src/mongo/base/error_codes.err#L70-L87
+    # pylint: disable=invalid-name
+    INDEX_ALREADY_EXISTS = 68
+    INDEX_OPTIONS_CONFLICT = 85
+    try:
+        collection.create_index(keys, **kwargs)
+    except pymongo.errors.OperationFailure as exc:
+        errors_to_ignore = []
+        if ignore_created:
+            errors_to_ignore.append(INDEX_ALREADY_EXISTS)
+        if ignore_created_opts:
+            errors_to_ignore.append(INDEX_OPTIONS_CONFLICT)
+        if exc.code in errors_to_ignore:
+            logger.warning("Existing index in collection '{}' remained unchanged!: {}".format(
+                collection.full_name, exc.details['errmsg'])
+            )
+        else:
+            raise exc