MyPy fixes for bumped dependency type regressions

src/mavedb/routers/experiments.py

@@ -2,7 +2,6 @@
 from operator import attrgetter
 from typing import Any, Optional
 
-import pydantic
 import requests
 from fastapi import APIRouter, Depends, HTTPException
 from fastapi.encoders import jsonable_encoder
@@ -71,7 +70,7 @@ def list_experiments(
         query = query.filter(
             or_(
                 Experiment.created_by_id == user_data.user.id,
-                Experiment.contributors.any(Contributor.orcid_id == user_data.user.username)
+                Experiment.contributors.any(Contributor.orcid_id == user_data.user.username),
             )
         )
 
@@ -225,10 +224,7 @@ async def create_experiment(
         ]
     except NonexistentOrcidUserError as e:
         logger.error(msg="Could not find ORCID user with the provided user ID.", extra=logging_context())
-        raise pydantic.ValidationError(
-            [pydantic.error_wrappers.ErrorWrapper(ValidationError(str(e)), loc="contributors")],
-            model=experiment.ExperimentCreate,
-        )
+        raise HTTPException(status_code=422, detail=str(e))
 
     try:
         doi_identifiers = [
@@ -369,10 +365,7 @@ async def update_experiment(
         ]
     except NonexistentOrcidUserError as e:
         logger.error(msg="Could not find ORCID user with the provided user ID.", extra=logging_context())
-        raise pydantic.ValidationError(
-            [pydantic.error_wrappers.ErrorWrapper(ValidationError(str(e)), loc="contributors")],
-            model=experiment.ExperimentUpdate,
-        )
+        raise HTTPException(status_code=422, detail=str(e))
 
     doi_identifiers = [
         await find_or_create_doi_identifier(db, identifier.identifier)

src/mavedb/routers/score_sets.py

@@ -3,7 +3,6 @@
 from typing import Any, List, Optional
 
 import pandas as pd
-import pydantic
 from arq import ArqRedis
 from fastapi import APIRouter, Depends, File, Query, UploadFile, status
 from fastapi.encoders import jsonable_encoder
@@ -23,7 +22,7 @@
     RoleRequirer,
 )
 from mavedb.lib.contributors import find_or_create_contributor
-from mavedb.lib.exceptions import MixedTargetError, NonexistentOrcidUserError, ValidationError
+from mavedb.lib.exceptions import MixedTargetError, NonexistentOrcidUserError
 from mavedb.lib.identifiers import (
     create_external_gene_identifier_offset,
     find_or_create_doi_identifier,
@@ -502,10 +501,7 @@ async def create_score_set(
         ]
     except NonexistentOrcidUserError as e:
         logger.error(msg="Could not find ORCID user with the provided user ID.", extra=logging_context())
-        raise pydantic.ValidationError(
-            [pydantic.error_wrappers.ErrorWrapper(ValidationError(str(e)), loc="contributors")],
-            model=score_set.ScoreSetCreate,
-        )
+        raise HTTPException(status_code=422, detail=str(e))
 
     doi_identifiers = [
         await find_or_create_doi_identifier(db, identifier.identifier)
@@ -739,7 +735,7 @@ async def update_score_set_calibration_data(
 
     assert_permission(user_data, item, Action.UPDATE)
 
-    item.score_calibrations = {k: v.dict() for k, v in calibration_update.items()}
+    item.score_calibrations = calibration_update
     db.add(item)
     db.commit()
     db.refresh(item)
@@ -832,10 +828,7 @@ async def update_score_set(
         ]
     except NonexistentOrcidUserError as e:
         logger.error(msg="Could not find ORCID user with the provided user ID.", extra=logging_context())
-        raise pydantic.ValidationError(
-            [pydantic.error_wrappers.ErrorWrapper(ValidationError(str(e)), loc="contributors")],
-            model=score_set.ScoreSetUpdate,
-        )
+        raise HTTPException(status_code=422, detail=str(e))
 
     # Score set has not been published and attributes affecting scores may still be edited.
     if item.private:

tests/helpers/util.py

@@ -11,6 +11,7 @@
 
 from mavedb.lib.score_sets import columns_for_dataset, create_variants, create_variants_data, csv_data_to_df
 from mavedb.lib.validation.dataframe import validate_and_standardize_dataframe_pair
+from mavedb.lib.exceptions import NonexistentOrcidUserError
 from mavedb.models.contributor import Contributor
 from mavedb.models.enums.processing_state import ProcessingState
 from mavedb.models.score_set import ScoreSet as ScoreSetDbModel
@@ -297,6 +298,10 @@ async def awaitable_exception():
     return Exception()
 
 
+def callable_nonexistent_orcid_user_exception():
+    raise NonexistentOrcidUserError()
+
+
 def update_expected_response_for_created_resources(expected_response, created_experiment, created_score_set):
     expected_response.update({"urn": created_score_set["urn"]})
     expected_response["experiment"].update(

tests/routers/test_experiments.py

@@ -8,6 +8,7 @@
 import requests
 import requests_mock
 
+from mavedb.lib.exceptions import NonexistentOrcidUserError
 from mavedb.lib.validation.urn_re import MAVEDB_TMP_URN_RE
 from mavedb.models.experiment import Experiment as ExperimentDbModel
 from mavedb.models.experiment_set import ExperimentSet as ExperimentSetDbModel
@@ -85,6 +86,22 @@ def test_create_experiment_with_contributor(client, setup_router_db):
         assert (key, expected_response[key]) == (key, response_data[key])
 
 
+def test_cannot_create_experiment_with_nonexistent_contributor(client, setup_router_db):
+    experiment = deepcopy(TEST_MINIMAL_EXPERIMENT)
+    experiment.update({"contributors": [{"orcid_id": TEST_ORCID_ID}]})
+
+    with patch(
+        "mavedb.lib.orcid.fetch_orcid_user",
+        side_effect=NonexistentOrcidUserError(f"No ORCID user was found for ORCID ID {TEST_ORCID_ID}."),
+    ):
+        response = client.post("/api/v1/experiments/", json=experiment)
+
+    assert response.status_code == 422
+    response_data = response.json()
+
+    assert "No ORCID user was found for ORCID ID 1111-1111-1111-1111." in response_data["detail"]
+
+
 def test_create_experiment_with_keywords(session, client, setup_router_db):
     response = client.post("/api/v1/experiments/", json=TEST_EXPERIMENT_WITH_KEYWORD)
     assert response.status_code == 200
@@ -586,6 +603,50 @@ def test_can_edit_private_experiment(client, setup_router_db, test_field, test_v
     assert (test_field, response_data[test_field]) == (test_field, test_value)
 
 
+def test_can_add_contributor_to_own_private_experiment(client, setup_router_db):
+    experiment = create_experiment(client)
+    experiment_post_payload = experiment.copy()
+    experiment_post_payload.update({"contributors": [{"orcid_id": TEST_ORCID_ID}]})
+
+    with patch(
+        "mavedb.lib.orcid.fetch_orcid_user",
+        lambda orcid_id: OrcidUser(orcid_id=orcid_id, given_name="ORCID", family_name="User"),
+    ):
+        response = client.put(f"/api/v1/experiments/{experiment['urn']}", json=experiment_post_payload)
+
+    assert response.status_code == 200
+    response_data = response.json()
+    jsonschema.validate(instance=response_data, schema=Experiment.model_json_schema())
+    assert ("contributors", response_data["contributors"]) == (
+        "contributors",
+        [
+            {
+                "recordType": "Contributor",
+                "orcidId": TEST_ORCID_ID,
+                "givenName": "ORCID",
+                "familyName": "User",
+            }
+        ],
+    )
+
+
+def test_cannot_add_nonexistent_contributor_to_experiment(client, setup_router_db):
+    experiment = create_experiment(client)
+    experiment_post_payload = experiment.copy()
+    experiment_post_payload.update({"contributors": [{"orcid_id": TEST_ORCID_ID}]})
+
+    with patch(
+        "mavedb.lib.orcid.fetch_orcid_user",
+        side_effect=NonexistentOrcidUserError(f"No ORCID user was found for ORCID ID {TEST_ORCID_ID}."),
+    ):
+        response = client.put(f"/api/v1/experiments/{experiment['urn']}", json=experiment_post_payload)
+
+    assert response.status_code == 422
+    response_data = response.json()
+
+    assert "No ORCID user was found for ORCID ID 1111-1111-1111-1111." in response_data["detail"]
+
+
 @pytest.mark.parametrize(
     "test_field,test_value",
     [

tests/routers/test_score_set.py

@@ -10,6 +10,7 @@
 from sqlalchemy import select
 
 from mavedb.lib.validation.urn_re import MAVEDB_TMP_URN_RE, MAVEDB_SCORE_SET_URN_RE, MAVEDB_EXPERIMENT_URN_RE
+from mavedb.lib.exceptions import NonexistentOrcidUserError
 from mavedb.models.enums.processing_state import ProcessingState
 from mavedb.models.enums.target_category import TargetCategory
 from mavedb.models.experiment import Experiment as ExperimentDbModel
@@ -132,6 +133,23 @@ def test_create_score_set_with_contributor(client, setup_router_db):
     assert response.status_code == 200
 
 
+def test_cannot_create_score_set_with_nonexistent_contributor(client, setup_router_db):
+    experiment = create_experiment(client)
+    score_set = deepcopy(TEST_MINIMAL_SEQ_SCORESET)
+    score_set["experimentUrn"] = experiment["urn"]
+    score_set.update({"contributors": [{"orcid_id": TEST_ORCID_ID}]})
+
+    with patch(
+        "mavedb.lib.orcid.fetch_orcid_user",
+        side_effect=NonexistentOrcidUserError(f"No ORCID user was found for ORCID ID {TEST_ORCID_ID}."),
+    ):
+        response = client.post("/api/v1/score-sets/", json=score_set)
+
+    assert response.status_code == 422
+    response_data = response.json()
+    assert "No ORCID user was found for ORCID ID 1111-1111-1111-1111." in response_data["detail"]
+
+
 def test_create_score_set_with_score_range(client, setup_router_db):
     experiment = create_experiment(client)
     score_set = deepcopy(TEST_MINIMAL_SEQ_SCORESET)
@@ -381,6 +399,27 @@ def test_cannot_update_score_set_target_data_after_publication(
         assert camelize(attribute) not in response_data.keys()
 
 
+def test_cannot_update_score_set_with_nonexistent_contributor(
+    client,
+    setup_router_db,
+):
+    experiment = create_experiment(client)
+    score_set = create_seq_score_set(client, experiment["urn"])
+
+    score_set_update_payload = deepcopy(TEST_MINIMAL_SEQ_SCORESET)
+    score_set_update_payload.update({"contributors": [{"orcid_id": TEST_ORCID_ID}]})
+
+    with patch(
+        "mavedb.lib.orcid.fetch_orcid_user",
+        side_effect=NonexistentOrcidUserError(f"No ORCID user was found for ORCID ID {TEST_ORCID_ID}."),
+    ):
+        response = client.put(f"/api/v1/score-sets/{score_set['urn']}", json=score_set_update_payload)
+
+    assert response.status_code == 422
+    response_data = response.json()
+    assert "No ORCID user was found for ORCID ID 1111-1111-1111-1111." in response_data["detail"]
+
+
 ########################################################################################################################
 # Score set fetching
 ########################################################################################################################