WIP: Get API_Keys from Database

functions/db/connector.py

@@ -156,14 +156,14 @@ def get_persisted_results(obj: Union[Review, Query], page: int = 0, page_length:
         list of results
     """
 
-    if(isinstance(obj, Query)):
+    if (isinstance(obj, Query)):
         result_collection = obj.parent_review.result_collection
 
     elif (isinstance(obj, Review)):
         result_collection = obj.result_collection
 
     with switch_collection(Result, result_collection):
-        if(isinstance(obj, Query)):
+        if (isinstance(obj, Query)):
             result_ids = obj.results
             results = Result.objects.raw({"_id": {"$in": result_ids}})
 
@@ -238,7 +238,7 @@ def get_result_by_doi(review: Review, doi: str):
         result object
     """
     with switch_collection(Result, review.result_collection):
-        return Result.objects.raw({"_id":  doi}).first()
+        return Result.objects.raw({"_id": doi}).first()
 
 
 def calc_start_at(page, page_length):
@@ -486,6 +486,37 @@ def get_reviews(user: User) -> list:
     return [review.to_son().to_dict() for review in list(reviews)],
 
 
+def get_api_keys_from_user(username: None) -> dict:
+    """Gets dict of api_keys for specific user from database
+
+    Args:
+        username: string of username, if username is None (e.g. dry_query), the username will be admin
+
+    Returns:
+         dictionary of all api_keys for specific user
+    """
+    if username is None:
+        username = "admin"
+    api_keys = dict()
+    user = get_user_by_username(username)
+    for data in user.databases:
+        api_keys[data.db_name] = data.api_key
+    return api_keys
+
+
+def get_username_by_review_id(review_id: str) -> str:
+    """Gets username by review_id
+
+    Args:
+        review_id: string is review_id
+
+    Returns:
+        username as string
+    """
+    review = get_review_by_id(review_id)
+    return review.owner.username
+
+
 if __name__ == "__main__":
     new_user = User(username="my_new_user").save()
     other_user = User(username="my_other_user").save()

functions/slr.py

@@ -10,39 +10,29 @@
 db_wrappers = list()
 
 
-def get_api_keys():
+def get_api_keys(username: None):
     """Get api keys.
 
-    TODO: get from user collection in mongodb
+    Args:
+        username: username as string
 
     Returns:
         dict of api-keys.
         dictionary keys are the same as the wrapper names defined in the wrapper module.
     """
+    return connector.get_api_keys_from_user(username)
 
-    api_keys = dict()
-    for wrapper_class in ALL_WRAPPERS:
-        # remove Wrapper suffix from class name
-        var_name = wrapper_class.__name__
-        if var_name.endswith('Wrapper'):
-            var_name = var_name[:-7]
-
-        # bring in env var format
-        var_name = var_name.upper()
-        var_name += "_API_KEY"
-
-        api_keys[wrapper_class.__name__] = os.getenv(var_name)
 
-    return api_keys
-
-
-def instantiate_wrappers():
+def instantiate_wrappers(username: None):
     """Instantiate wrappers with api keys.
 
+    Args:
+        username: username as string
+
     Returns:
         list of instantiated wrapper objects, each for each data base wrapper
     """
-    api_keys = get_api_keys()
+    api_keys = get_api_keys(username)
 
     instantiated_wrappers = []
     for wrapper_class in ALL_WRAPPERS:
@@ -74,7 +64,7 @@ def call_api(db_wrapper, search: dict, page: int, page_length: int):
     return db_wrapper.call_api(search)
 
 
-def conduct_query(search: dict, page: int, page_length="max") -> list:
+def conduct_query(search: dict, page: int, page_length="max", username=None) -> list:
     """Get page of specific length. Aggregates results from all available literature data bases.
 
     The number of results from each data base will be n/page_length with n being the number of data bases.
@@ -84,6 +74,7 @@ def conduct_query(search: dict, page: int, page_length="max") -> list:
         page: page number
         page_length: length of page. If set to "max", the respective maxmimum number of results
             results is returned by each wrapper.
+        username: id of the user that is using this function
 
     Returns:
         list of results in format https://github.com/DaWeSys/backend/blob/simple_persistance/wrapper/output_format.py.
@@ -93,7 +84,7 @@ def conduct_query(search: dict, page: int, page_length="max") -> list:
     results = []
 
     if not db_wrappers:
-        db_wrappers = instantiate_wrappers()
+        db_wrappers = instantiate_wrappers(username)
 
     if len(db_wrappers) == 0:
         print("No wrappers existing.")
@@ -189,11 +180,11 @@ def persistent_query(query: models.Query, review: models.Review, max_num_results
         "match": "AND"
     }
     # sample usage of dry search
-    #results = conduct_query(search, 1, 100)
+    # results = conduct_query(search, 1, 100)
     pass
 
     # sample usage of persistent query
-    from functions.db.connector import add_review, new_query
+    from functions.db.connector import add_review, new_query, get_api_keys_from_user, test111
 
     review = add_review("test REVIEW")
     query = new_query(review, search)

handler.py

@@ -233,6 +233,7 @@ def persist_pages_of_query(event, *args):
 
     review_id = event.get('pathParameters').get('review_id')
     review = connector.get_review_by_id(review_id)
+    username = connector.get_username_by_review_id(review_id)
 
     search = body.get('search')
     query = connector.new_query(review, search)
@@ -243,7 +244,7 @@ def persist_pages_of_query(event, *args):
 
     num_persisted = 0
     for page in pages:
-        results = slr.conduct_query(search, page, page_length)
+        results = slr.conduct_query(search, page, page_length, username)
         for wrapper_results in results:
             connector.save_results(
                 wrapper_results.get('records'), review, query)