fix: query filter in list task endpoint (#178)

docker-compose.yaml

@@ -36,7 +36,7 @@ services:
       - "5672:5672"
 
   mongodb:
-    image: mongo:3.2
+    image: mongo:3.6
     restart: unless-stopped
     volumes:
       - ${PROTES_DATA_DIR:-../data/pro_tes}/db:/data/db

pro_tes/ga4gh/tes/task_runs.py

@@ -272,15 +272,17 @@ def list_tasks(self, **kwargs) -> dict:
         )
         page_token = kwargs.get("page_token")
         filter_dict = {}
-        filter_dict["user_id"] = kwargs.get("user_id")
+
+        user_id = kwargs.get("user_id")
+        if user_id is not None:
+            filter_dict["user_id"] = user_id
 
         if page_token is not None:
             filter_dict["_id"] = {"$lt": ObjectId(page_token)}
         view = kwargs.get("view", "BASIC")
         projection = self._set_projection(view=view)
 
-        name_prefix: str = str(kwargs.get("name_prefix"))
-
+        name_prefix = kwargs.get("name_prefix")
         if name_prefix is not None:
             filter_dict["task_original.name"] = {"$regex": f"^{name_prefix}"}
 
@@ -437,7 +439,7 @@ def _write_doc_to_db(
             )
             document.worker_id = uuid()
             try:
-                self.db_client.insert(document.dict(exclude_none=True))
+                self.db_client.insert_one(document.dict(exclude_none=True))
             except DuplicateKeyError:
                 continue
             assert document is not None

pro_tes/utils/db.py

@@ -2,9 +2,7 @@
 
 import logging
 from typing import Mapping, Optional
-from pymongo.collection import ReturnDocument  # type: ignore
-from pymongo import collection as Collection  # type: ignore
-
+from pymongo.collection import ReturnDocument, Collection
 from pro_tes.ga4gh.tes.models import DbDocument, TesState
 
 logger = logging.getLogger(__name__)
@@ -56,7 +54,7 @@ def get_document(
             projection=projection,
         )
         try:
-            document: DbDocument = DbDocument(**document_unvalidated)
+            document: DbDocument = DbDocument(**(document_unvalidated or {}))
         except Exception as exc:
             raise ValueError(
                 "Database document does not conform to schema: "
@@ -110,8 +108,8 @@ def upsert_fields_in_root_object(
             {"worker_id": self.worker_id},
             {
                 "$set": {
-                    ".".join([root, key]): value
-                    for (key, value) in kwargs.items()
+                    ".".join([root, key]): value for (key, value) in
+                    kwargs.items()
                 }
             },
             projection=projection,