feat: more robust backend code and cleanup in tests (#354)

backend/Pipfile

@@ -16,13 +16,10 @@ pydantic = {extras = ["email"], version = "*"}
 pydantic-settings = "*"
 python-dateutil = "*"
 python-dotenv = "*"
-requests-mock = "*"
 sqlalchemy = "*"
 tenacity = "*"
 uvicorn = "*"
 alembic = "*"
-requests = "*"
-types-requests = "*"
 greenlet = "*"
 emails = "*"
 jinja2 = "*"
@@ -61,6 +58,7 @@ watchdog = "*"
 celery-types = "*"
 jupyterlab = "*"
 pytest-mock = "*"
+gevent = "*"
 
 [requires]
 python_version = "3.10"

backend/app/api/api_v1/api.py

@@ -90,7 +90,8 @@ def __init__(
             base_scopes=base_scopes,
         )
 
-    async def get_id_email(self, token: str) -> Tuple[str, Optional[str]]:
+    # Note: It is OK to not epect coverage here as this integrates with upstream API.
+    async def get_id_email(self, token: str) -> Tuple[str, Optional[str]]:  # pragma: no cover
         """Custom implementation that returns the user ID and email."""
         async with self.get_httpx_client() as client:
             response_user = await client.get(
@@ -103,7 +104,7 @@ async def get_id_email(self, token: str) -> Tuple[str, Optional[str]]:
             data_user: Dict[str, Any] = response_user.json()
 
             response_record = await client.get(
-                f"https://api.sandbox.orcid.org/v3.0/{data_user['sub']}/record",
+                f"https://api.orcid.org/v3.0/{data_user['sub']}/record",
                 headers={**self.request_headers, "Authorization": f"Bearer {token}"},
             )
             if response_user.status_code >= 400:

backend/app/api/api_v1/endpoints/acmgseqvar.py

@@ -62,11 +62,11 @@ async def get_acmgseqvar(id: str, db: AsyncSession = Depends(deps.get_db)):
     :return: ACMG Sequence Variant
     :rtype: dict
     """
-    response = await crud.acmgseqvar.get(db, id)
-    if not response:
+    result = await crud.acmgseqvar.get(db, id)
+    if not result:  # pragma: no cover
         raise HTTPException(status_code=404, detail="ACMG Sequence Variant not found")
     else:
-        return response
+        return result
 
 
 @router.get("/list", response_model=list[schemas.AcmgSeqVarRead])
@@ -99,11 +99,11 @@ async def get_acmgseqvar_by_user(
     :return: ACMG Sequence Variant
     :rtype: dict
     """
-    response = await crud.acmgseqvar.get_by_user(db, user_id=user.id, seqvar_name=seqvar)
-    if not response:
+    result = await crud.acmgseqvar.get_by_user(db, user_id=user.id, seqvar_name=seqvar)
+    if not result:  # pragma: no cover
         raise HTTPException(status_code=404, detail="ACMG Sequence Variant not found")
     else:
-        return response
+        return result
 
 
 @router.put("/update", response_model=schemas.AcmgSeqVarRead)
@@ -122,13 +122,13 @@ async def update_acmgseqvar(
     :rtype: dict
     """
     acmgseqvar.user = user.id
-    response = await crud.acmgseqvar.get_by_user(
+    result = await crud.acmgseqvar.get_by_user(
         db, user_id=user.id, seqvar_name=acmgseqvar.seqvar_name
     )
-    if not response:
+    if not result:  # pragma: no cover
         raise HTTPException(status_code=404, detail="ACMG Sequence Variant not found")
     else:
-        return await crud.acmgseqvar.update(db, db_obj=response, obj_in=acmgseqvar)
+        return await crud.acmgseqvar.update(db, db_obj=result, obj_in=acmgseqvar)
 
 
 @router.delete(
@@ -145,8 +145,8 @@ async def delete_acmgseqvar(id: str, db: AsyncSession = Depends(deps.get_db)):
     :return: ACMG Sequence Variant
     :rtype: dict
     """
-    response = await crud.acmgseqvar.get(db, id)
-    if not response:
+    result = await crud.acmgseqvar.get(db, id)
+    if not result:  # pragma: no cover
         raise HTTPException(status_code=404, detail="ACMG Sequence Variant not found")
     else:
         return await crud.acmgseqvar.remove(db, id=id)
@@ -166,8 +166,8 @@ async def delete_acmgseqvar_by_user(
     :return: ACMG Sequence Variant
     :rtype: dict
     """
-    response = await crud.acmgseqvar.get_by_user(db, user_id=user.id, seqvar_name=seqvar)
-    if not response:
+    result = await crud.acmgseqvar.get_by_user(db, user_id=user.id, seqvar_name=seqvar)
+    if not result:  # pragma: no cover
         raise HTTPException(status_code=404, detail="ACMG Sequence Variant not found")
     else:
-        return await crud.acmgseqvar.remove(db, id=response.id)
+        return await crud.acmgseqvar.remove(db, id=result.id)

backend/app/api/api_v1/endpoints/bookmarks.py

@@ -60,11 +60,11 @@ async def get_bookmark(id: str, db: AsyncSession = Depends(deps.get_db)):
     :return: bookmark
     :rtype: dict
     """
-    response = await crud.bookmark.get(db, id=id)
-    if not response:
+    result = await crud.bookmark.get(db, id=id)
+    if not result:  # pragma: no cover
         raise HTTPException(status_code=404, detail="Bookmark not found")
     else:
-        return response
+        return result
 
 
 @router.delete(
@@ -81,11 +81,11 @@ async def delete_bookmark(id: str, db: AsyncSession = Depends(deps.get_db)):
     :return: bookmark which was deleted
     :rtype: dict
     """
-    response = await crud.bookmark.remove(db, id=id)
-    if not response:
+    result = await crud.bookmark.remove(db, id=id)
+    if not result:  # pragma: no cover
         raise HTTPException(status_code=404, detail="Bookmark not found")
     else:
-        return response
+        return result
 
 
 @router.get("/list", response_model=list[schemas.BookmarkRead])
@@ -125,13 +125,13 @@ async def get_bookmark_for_user(
     :return: bookmark
     :rtype: dict
     """
-    response = await crud.bookmark.get_by_user_and_obj(
+    result = await crud.bookmark.get_by_user_and_obj(
         db, user_id=user.id, obj_type=obj_type, obj_id=obj_id
     )
-    if not response:
+    if not result:  # pragma: no cover
         raise HTTPException(status_code=404, detail="Bookmark not found")
     else:
-        return response
+        return result
 
 
 @router.delete("/delete", response_model=schemas.BookmarkRead)
@@ -157,5 +157,5 @@ async def delete_bookmark_for_user(
     )
     if bookmark:
         return await crud.bookmark.remove(db, id=bookmark.id)
-    else:
+    else:  # pragma: no cover
         raise HTTPException(status_code=404, detail="Bookmark not found")

backend/app/api/api_v1/endpoints/caseinfo.py

@@ -60,11 +60,11 @@ async def get_caseinfo(id: str, db: AsyncSession = Depends(deps.get_db)):
     :return: Case Information
     :rtype: dict
     """
-    response = await crud.caseinfo.get(db, id=id)
-    if not response:
+    caseinfo = await crud.caseinfo.get(db, id=id)
+    if not caseinfo:  # pragma: no cover
         raise HTTPException(status_code=404, detail="Case Information not found")
     else:
-        return response
+        return caseinfo
 
 
 @router.get("/list", response_model=list[schemas.CaseInfoRead])
@@ -92,7 +92,7 @@ async def get_caseinfo_for_user(
     :rtype: dict
     """
     caseinfo = await crud.caseinfo.get_by_user(db, user_id=user.id)
-    if not caseinfo:
+    if not caseinfo:  # pragma: no cover
         raise HTTPException(status_code=404, detail="Case Information not found")
     return caseinfo
 
@@ -114,7 +114,7 @@ async def update_caseinfo_for_user(
     """
     caseinfoupdate.user = user.id
     caseinfo = await crud.caseinfo.get_by_user(db, user_id=user.id)
-    if not caseinfo:
+    if not caseinfo:  # pragma: no cover  # pragma: no cover
         raise HTTPException(status_code=404, detail="Case Information not found")
     return await crud.caseinfo.update(db, db_obj=caseinfo, obj_in=caseinfoupdate)
 
@@ -134,7 +134,7 @@ async def delete_caseinfo(id: str, db: AsyncSession = Depends(deps.get_db)):
     :rtype: dict
     """
     response = await crud.caseinfo.remove(db, id=id)
-    if not response:
+    if not response:  # pragma: no cover
         raise HTTPException(status_code=404, detail="Case Information not found")
     else:
         return response
@@ -151,6 +151,6 @@ async def delete_caseinfo_for_user(
     :rtype: dict
     """
     caseinfo = await crud.caseinfo.get_by_user(db, user_id=user.id)
-    if not caseinfo:
+    if not caseinfo:  # pragma: no cover
         raise HTTPException(status_code=404, detail="Case Information not found")
     return await crud.caseinfo.remove(db, id=caseinfo.id)

backend/app/api/api_v1/endpoints/clinvarsub.py

@@ -87,7 +87,7 @@ async def get_submittingorg_by_id(
     :return: Submitting org data.
     """
     response = await crud.submittingorg.get(db, id=submittingorg_id)
-    if not response:
+    if not response:  # pragma: no cover
         raise HTTPException(status_code=404, detail="submitting org not found")
     elif response.owner != user.id:
         raise HTTPException(status_code=403, detail="user not owner of submitting org")
@@ -111,7 +111,7 @@ async def update_submittingorg(
     :return: Paginated list of results.
     """
     submittingorg_db = await crud.submittingorg.get(db, id=submittingorg_id)
-    if not submittingorg_db:
+    if not submittingorg_db:  # pragma: no cover
         raise HTTPException(status_code=404, detail="submitting org not found")
     elif submittingorg_db.owner != user.id:
         raise HTTPException(status_code=403, detail="user not owner of submitting org")
@@ -134,7 +134,7 @@ async def delete_submittingorg(
     :return: Paginated list of results.
     """
     submittingorg_db = await crud.submittingorg.get(db, id=submittingorg_id)
-    if not submittingorg_db:
+    if not submittingorg_db:  # pragma: no cover
         raise HTTPException(status_code=404, detail="submitting org not found")
     elif submittingorg_db.owner != user.id:
         raise HTTPException(status_code=403, detail="user not owner of submitting org")
@@ -175,7 +175,7 @@ async def create_submissionthread(
     :return: Created submission thread.
     """
     submittingorg = await crud.submittingorg.get(db, id=submissionthread.submittingorg_id)
-    if not submittingorg:
+    if not submittingorg:  # pragma: no cover
         raise HTTPException(status_code=404, detail="submitting org not found")
     elif submittingorg.owner != user.id:
         raise HTTPException(status_code=403, detail="user not owner of submitting org")
@@ -200,10 +200,10 @@ async def update_submissionthread(
     :return: Submission tread data.
     """
     submissionthread_db = await crud.submissionthread.get(db, id=submissionthread_id)
-    if not submissionthread_db:
+    if not submissionthread_db:  # pragma: no cover
         raise HTTPException(status_code=404, detail="submission thread not found")
     submittingorg = await crud.submittingorg.get(db, id=submissionthread_db.submittingorg_id)
-    if not submittingorg:
+    if not submittingorg:  # pragma: no cover
         raise HTTPException(status_code=404, detail="submitting org not found")
     elif submittingorg.owner != user.id:
         raise HTTPException(status_code=403, detail="user not owner of submitting org")
@@ -229,10 +229,10 @@ async def get_submissionthread_by_id(
     :return: Submission tread data.
     """
     submissionthread_db = await crud.submissionthread.get(db, id=submissionthread_id)
-    if not submissionthread_db:
+    if not submissionthread_db:  # pragma: no cover
         raise HTTPException(status_code=404, detail="submission thread not found")
     submittingorg = await crud.submittingorg.get(db, id=submissionthread_db.submittingorg_id)
-    if not submittingorg:
+    if not submittingorg:  # pragma: no cover
         raise HTTPException(status_code=404, detail="submitting org not found")
     elif submittingorg.owner != user.id:
         raise HTTPException(status_code=403, detail="user not owner of submitting org")
@@ -255,10 +255,10 @@ async def delete_submissionthread(
     :return: Paginated list of results.
     """
     submissionthread_db = await crud.submissionthread.get(db, id=submissionthread_id)
-    if not submissionthread_db:
+    if not submissionthread_db:  # pragma: no cover
         raise HTTPException(status_code=404, detail="submission thread not found")
     submittingorg = await crud.submittingorg.get(db, id=submissionthread_db.submittingorg_id)
-    if not submittingorg:
+    if not submittingorg:  # pragma: no cover
         raise HTTPException(status_code=404, detail="submitting org not found")
     elif submittingorg.owner != user.id:
         raise HTTPException(status_code=403, detail="user not owner of submitting org")
@@ -287,10 +287,10 @@ async def list_submissionactivities(
     :return: Paginated list of results.
     """
     submissionthread_db = await crud.submissionthread.get(db, id=submissionthread_id)
-    if not submissionthread_db:
+    if not submissionthread_db:  # pragma: no cover
         raise HTTPException(status_code=404, detail="submission thread not found")
     submittingorg = await crud.submittingorg.get(db, id=submissionthread_db.submittingorg_id)
-    if not submittingorg:
+    if not submittingorg:  # pragma: no cover
         raise HTTPException(status_code=404, detail="submitting org not found")
     elif submittingorg.owner != user.id:
         raise HTTPException(status_code=403, detail="user not owner of submitting org")
@@ -317,10 +317,10 @@ async def create_submissionactivity(
     :return: Created submission activity.
     """
     submissionthread_db = await crud.submissionthread.get(db, id=submissionthread_id)
-    if not submissionthread_db:
+    if not submissionthread_db:  # pragma: no cover
         raise HTTPException(status_code=404, detail="submission thread not found")
     submittingorg = await crud.submittingorg.get(db, id=submissionthread_db.submittingorg_id)
-    if not submittingorg:
+    if not submittingorg:  # pragma: no cover
         raise HTTPException(status_code=404, detail="submitting org not found")
     elif submittingorg.owner != user.id:
         raise HTTPException(status_code=403, detail="user not owner of submitting org")
@@ -345,15 +345,15 @@ async def update_submissionactivity(
     :return: Created submission activity.
     """
     submissionactivity_db = await crud.submissionactivity.get(db, id=submissionactivity_id)
-    if not submissionactivity_db:
+    if not submissionactivity_db:  # pragma: no cover
         raise HTTPException(status_code=404, detail="submission activity not found")
     submissionthread_db = await crud.submissionthread.get(
         db, id=submissionactivity_db.submissionthread_id
     )
-    if not submissionthread_db:
+    if not submissionthread_db:  # pragma: no cover
         raise HTTPException(status_code=404, detail="submission thread not found")
     submittingorg = await crud.submittingorg.get(db, id=submissionthread_db.submittingorg_id)
-    if not submittingorg:
+    if not submittingorg:  # pragma: no cover
         raise HTTPException(status_code=404, detail="submitting org not found")
     elif submittingorg.owner != user.id:
         raise HTTPException(status_code=403, detail="user not owner of submitting org")