Replace deprecated json method

Author: pkalita-lbl

nmdc_server/fakes.py

@@ -1,5 +1,5 @@
 from collections import OrderedDict
-from datetime import datetime
+from datetime import UTC, datetime
 from typing import Dict, List, Optional
 from uuid import UUID, uuid4
 
@@ -342,7 +342,8 @@ class Meta:
     status = "In Progress"
     study_name = Faker("word")
     templates = Faker("pylist", nb_elements=2, value_types=[str])
-    created = datetime.utcnow()
+    created = datetime.now(tz=UTC)
+    date_last_modified = created
     # TODO specify all fields!
     metadata_submission = {
         "sampleData": {},
@@ -400,6 +401,7 @@ class Meta:
     }
     locked_by = None
     lock_updated = None
+    is_test_submission = False
 
 
 class SubmissionRoleFactory(SQLAlchemyModelFactory):

nmdc_server/schemas_submission.py

@@ -126,6 +126,8 @@ class SubmissionMetadataSchemaCreate(BaseModel):
 
 
 class SubmissionMetadataSchemaPatch(BaseModel):
+    model_config = ConfigDict(from_attributes=True)
+
     metadata_submission: PartialMetadataSubmissionRecord
     status: Optional[str] = None
     # Map of ORCID iD to permission level

tests/test_submission.py

@@ -1,8 +1,8 @@
-import json
 from csv import DictReader
 from datetime import UTC, datetime, timedelta
 
 import pytest
+from fastapi.encoders import jsonable_encoder
 from sqlalchemy.orm.session import Session
 from starlette.testclient import TestClient
 
@@ -154,7 +154,6 @@ def test_get_metadata_submissions_report_as_admin(
         author=logged_in_user,
         author_orcid=logged_in_user.orcid,
         created=now,
-        date_last_modified=datetime.now(tz=UTC),
         is_test_submission=False,
     )
     fakes.SubmissionRoleFactory(
@@ -168,7 +167,6 @@ def test_get_metadata_submissions_report_as_admin(
         author=other_user,
         author_orcid=other_user.orcid,
         created=now + timedelta(seconds=1),
-        date_last_modified=datetime.now(tz=UTC),
         # TODO: Omit some optional fields in order to simplify the test data.
         # See: `class MetadataSubmissionRecordCreate` in `schema_submission.py`
         # See: https://microbiomedata.github.io/submission-schema/SampleData/
@@ -467,7 +465,6 @@ def test_cannot_release_other_users_submission_lock(
         author_orcid=logged_in_user.orcid,
         locked_by=locking_user,
         lock_updated=datetime.now(tz=UTC),
-        date_last_modified=datetime.now(tz=UTC),
     )
     fakes.SubmissionRoleFactory(
         submission=submission,
@@ -492,21 +489,20 @@ def test_try_edit_locked_submission(db: Session, client: TestClient, logged_in_u
         author_orcid=logged_in_user.orcid,
         locked_by=fakes.UserFactory(),
         lock_updated=datetime.now(tz=UTC),
-        date_last_modified=datetime.now(tz=UTC),
     )
     fakes.SubmissionRoleFactory(
         submission=submission,
         submission_id=submission.id,
         user_orcid=logged_in_user.orcid,
         role=SubmissionEditorRole.owner,
     )
-    payload = SubmissionMetadataSchema(**submission.__dict__).json(exclude_unset=True)
+    payload = SubmissionMetadataSchema.model_validate(submission)
     db.commit()
 
     response = client.request(
         method="patch",
         url=f"/api/metadata_submission/{submission.id}",
-        json=json.loads(payload),
+        json=jsonable_encoder(payload, exclude_unset=True),
     )
     assert response.status_code == 400
 
@@ -518,19 +514,20 @@ def test_try_edit_expired_locked_submission(db: Session, client: TestClient, log
         author_orcid=logged_in_user.orcid,
         locked_by=fakes.UserFactory(),
         lock_updated=datetime.now(tz=UTC) - timedelta(hours=1),
-        date_last_modified=datetime.now(tz=UTC),
     )
     fakes.SubmissionRoleFactory(
         submission=submission,
         submission_id=submission.id,
         user_orcid=logged_in_user.orcid,
         role=SubmissionEditorRole.owner,
     )
-    payload = SubmissionMetadataSchema(**submission.__dict__).json(exclude_unset=True)
+    payload = SubmissionMetadataSchema.model_validate(submission)
     db.commit()
 
     response = client.request(
-        method="patch", url=f"/api/metadata_submission/{submission.id}", json=json.loads(payload)
+        method="patch",
+        url=f"/api/metadata_submission/{submission.id}",
+        json=jsonable_encoder(payload, exclude_unset=True),
     )
     assert response.status_code == 200
 
@@ -543,36 +540,32 @@ def test_try_edit_locked_by_current_user_submission(
         author_orcid=logged_in_user.orcid,
         locked_by=logged_in_user,
         lock_updated=datetime.now(tz=UTC),
-        date_last_modified=datetime.now(tz=UTC),
     )
     fakes.SubmissionRoleFactory(
         submission=submission,
         submission_id=submission.id,
         user_orcid=logged_in_user.orcid,
         role=SubmissionEditorRole.owner,
     )
-    payload = SubmissionMetadataSchema(**submission.__dict__).json(exclude_unset=True)
+    payload = SubmissionMetadataSchema.model_validate(submission)
     db.commit()
 
     response = client.request(
-        method="patch", url=f"/api/metadata_submission/{submission.id}", json=json.loads(payload)
+        method="patch",
+        url=f"/api/metadata_submission/{submission.id}",
+        json=jsonable_encoder(payload, exclude_unset=True),
     )
     assert response.status_code == 200
 
 
 def test_submission_list_with_roles(db: Session, client: TestClient, logged_in_user):
     user_a = fakes.UserFactory()
-    submission_a = fakes.MetadataSubmissionFactory(
-        author=user_a, author_orcid=user_a.orcid, date_last_modified=datetime.now(tz=UTC)
-    )
+    submission_a = fakes.MetadataSubmissionFactory(author=user_a, author_orcid=user_a.orcid)
     fakes.MetadataSubmissionFactory(
         author=logged_in_user,
         author_orcid=logged_in_user.orcid,
-        date_last_modified=datetime.now(tz=UTC),
-    )
-    fakes.MetadataSubmissionFactory(
-        author=user_a, author_orcid=user_a.orcid, date_last_modified=datetime.now(tz=UTC)
     )
+    fakes.MetadataSubmissionFactory(author=user_a, author_orcid=user_a.orcid)
     db.commit()
     fakes.SubmissionRoleFactory(
         submission=submission_a,
@@ -593,13 +586,13 @@ def test_submission_list_with_roles(db: Session, client: TestClient, logged_in_u
 @pytest.mark.parametrize("role,code", [(SubmissionEditorRole.owner, 200), (None, 403)])
 def test_get_submission_with_roles(db: Session, client: TestClient, logged_in_user, role, code):
     if role == SubmissionEditorRole.owner:
-        submission = fakes.MetadataSubmissionFactory(date_last_modified=datetime.now(tz=UTC))
+        submission = fakes.MetadataSubmissionFactory()
         db.commit()
         role = fakes.SubmissionRoleFactory(
             submission=submission, submission_id=submission.id, user_orcid=logged_in_user.orcid
         )
     else:
-        submission = fakes.MetadataSubmissionFactory(date_last_modified=datetime.now(tz=UTC))
+        submission = fakes.MetadataSubmissionFactory()
     db.commit()
     response = client.request(method="get", url=f"/api/metadata_submission/{submission.id}")
     assert response.status_code == code
@@ -608,20 +601,22 @@ def test_get_submission_with_roles(db: Session, client: TestClient, logged_in_us
 @pytest.mark.parametrize("role,code", [(SubmissionEditorRole.owner, 200), (None, 403)])
 def test_edit_submission_with_roles(db: Session, client: TestClient, logged_in_user, role, code):
     if role == SubmissionEditorRole.owner:
-        submission = fakes.MetadataSubmissionFactory(date_last_modified=datetime.now(tz=UTC))
-        payload = SubmissionMetadataSchema(**submission.__dict__).json()
+        submission = fakes.MetadataSubmissionFactory()
+        payload = SubmissionMetadataSchema.model_validate(submission)
         db.commit()
         role = fakes.SubmissionRoleFactory(
             submission=submission,
             submission_id=submission.id,
             user_orcid=logged_in_user.orcid,
         )
     else:
-        submission = fakes.MetadataSubmissionFactory(date_last_modified=datetime.now(tz=UTC))
-        payload = SubmissionMetadataSchema(**submission.__dict__).json()
+        submission = fakes.MetadataSubmissionFactory()
+        payload = SubmissionMetadataSchema.model_validate(submission)
     db.commit()
     response = client.request(
-        method="patch", url=f"/api/metadata_submission/{submission.id}", json=json.loads(payload)
+        method="patch",
+        url=f"/api/metadata_submission/{submission.id}",
+        json=jsonable_encoder(payload),
     )
     assert response.status_code == code
 
@@ -641,7 +636,7 @@ def test_create_role_on_patch(db: Session, client: TestClient, logged_in_user):
     response = client.request(
         method="patch",
         url=f"/api/metadata_submission/{submission.id}",
-        json=json.loads(payload.json()),
+        json=jsonable_encoder(payload),
     )
     assert response.status_code == 200
 
@@ -667,22 +662,24 @@ def test_piecewise_patch_metadata_contributor(
         user_orcid=logged_in_user.orcid,
         role=SubmissionEditorRole.metadata_contributor,
     )
-    full_payload = SubmissionMetadataSchemaPatch(**submission.__dict__)
+    full_payload = SubmissionMetadataSchemaPatch.model_validate(submission)
     db.commit()
 
     if samples_only:
         request_dict = {
             "metadata_submission": {"sampleData": full_payload.metadata_submission.sampleData}
         }
-        request_payload = SubmissionMetadataSchemaPatch(**request_dict).json(exclude_unset=True)
+        request_payload = jsonable_encoder(
+            SubmissionMetadataSchemaPatch.model_validate(request_dict), exclude_unset=True
+        )
     else:
-        request_payload = full_payload.json()
+        request_payload = jsonable_encoder(full_payload)
 
     # Logged in user should not be able to submit full payload because it contains non-sample data
     response = client.request(
         method="patch",
         url=f"/api/metadata_submission/{submission.id}",
-        json=json.loads(request_payload),
+        json=request_payload,
     )
     assert response.status_code == code
 
@@ -709,15 +706,15 @@ def test_delete_role_on_patch(db: Session, client: TestClient, logged_in_user):
         user_orcid=user_orcid,
         role=SubmissionEditorRole.viewer,
     )
-    payload = SubmissionMetadataSchemaPatch(**submission.__dict__)
+    payload = SubmissionMetadataSchemaPatch.model_validate(submission)
     db.commit()
 
     payload.permissions = {}
 
     response = client.request(
         method="patch",
         url=f"/api/metadata_submission/{submission.id}",
-        json=json.loads(payload.json()),
+        json=jsonable_encoder(payload),
     )
     assert response.status_code == 200
     roles = db.query(SubmissionRole)
@@ -742,14 +739,14 @@ def test_update_role_on_patch(db: Session, client: TestClient, logged_in_user):
         user_orcid=user_orcid,
         role=SubmissionEditorRole.viewer,
     )
-    payload = SubmissionMetadataSchemaPatch(**submission.__dict__)
+    payload = SubmissionMetadataSchemaPatch.model_validate(submission)
     db.commit()
 
     payload.permissions = {str(user_orcid): SubmissionEditorRole.editor.value}
     response = client.request(
         method="patch",
         url=f"/api/metadata_submission/{submission.id}",
-        json=json.loads(payload.json()),
+        json=jsonable_encoder(payload),
     )
     assert response.status_code == 200
     roles = db.query(SubmissionRole).filter(SubmissionRole.user_orcid == str(user_orcid))
@@ -844,8 +841,8 @@ def test_sync_submission_templates(db: Session, client: TestClient, logged_in_us
         user_orcid=logged_in_user.orcid,
         role=SubmissionEditorRole.owner,
     )
-    payload = json.loads(
-        SubmissionMetadataSchemaPatch(**submission.__dict__).json(exclude_unset=True)
+    payload = jsonable_encoder(
+        SubmissionMetadataSchemaPatch.model_validate(submission), exclude_unset=True
     )
     payload["metadata_submission"]["templates"] = [template]
     db.commit()
@@ -873,8 +870,8 @@ def test_sync_submission_study_name(db: Session, client: TestClient, logged_in_u
         user_orcid=logged_in_user.orcid,
         role=SubmissionEditorRole.owner,
     )
-    payload = json.loads(
-        SubmissionMetadataSchemaPatch(**submission.__dict__).json(exclude_unset=True)
+    payload = jsonable_encoder(
+        SubmissionMetadataSchemaPatch.model_validate(submission), exclude_unset=True
     )
     payload["metadata_submission"]["studyForm"]["studyName"] = expected_val
     db.commit()