Merge pull request #1395 from microbiomedata/1392-sync-submission-templates

Ensure template props are synced on PATCH

Author: naglepuff

nmdc_server/api.py

@@ -825,8 +825,12 @@ async def update_submission(
     submission.metadata_submission = (
         submission.metadata_submission | body_dict["metadata_submission"]
     )
+    # TODO: remove the child properties "studyName" and "templates" in favor of the top-
+    # level property. Requires some coordination between this API and its clients.
     if "studyForm" in body_dict["metadata_submission"]:
         submission.study_name = body_dict["metadata_submission"]["studyForm"]["studyName"]
+    if "templates" in body_dict["metadata_submission"]:
+        submission.templates = body_dict["metadata_submission"]["templates"]
     # Update permissions and status iff the user is an "owner"
     if current_user_role and current_user_role.role == models.SubmissionEditorRole.owner:
         new_permissions = body_dict.get("permissions", None)

nmdc_server/migrations/versions/ff4e651c3007_migrate_templates.py

@@ -0,0 +1,49 @@
+"""Migrate study templates
+
+Revision ID: ff4e651c3007
+Revises: 317274ad8137
+Create Date: 2024-09-18 17:21:05.171525
+
+"""
+
+from typing import Optional
+
+import sqlalchemy as sa
+from alembic import op
+from sqlalchemy.dialects.postgresql import JSONB
+from sqlalchemy.sql import column, table
+
+# revision identifiers, used by Alembic.
+revision: str = "ff4e651c3007"
+down_revision: Optional[str] = "317274ad8137"
+branch_labels: Optional[str] = None
+depends_on: Optional[str] = None
+
+
+def upgrade():
+    submission_metadata = table(
+        "submission_metadata",
+        column("id", sa.String),
+        column("metadata_submission", JSONB),
+        column("templates", JSONB),
+    )
+
+    connection = op.get_bind()
+    submissions = connection.execute(
+        sa.select([submission_metadata.c.id, submission_metadata.c.metadata_submission])
+    )
+
+    for submission in submissions:
+        templates = submission.metadata_submission.get("templates")
+        if templates:
+            connection.execute(
+                submission_metadata.update()
+                .where(submission_metadata.c.id == submission.id)
+                .values(templates=templates)
+            )
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    pass
+    # ### end Alembic commands ###

tests/test_submission.py

@@ -553,3 +553,60 @@ def test_delete_submission_while_locked(db: Session, client: TestClient, logged_
     # Verify that it is still there
     response = client.request(method="GET", url=f"/api/metadata_submission/{submission.id}")
     assert response.status_code == 200
+
+
+def test_sync_submission_templates(db: Session, client: TestClient, logged_in_user):
+    template = "foo"
+    submission = fakes.MetadataSubmissionFactory(
+        author=logged_in_user,
+        author_orcid=logged_in_user.orcid,
+        locked_by=logged_in_user,
+        lock_updated=datetime.utcnow(),
+    )
+    fakes.SubmissionRoleFactory(
+        submission=submission,
+        submission_id=submission.id,
+        user_orcid=logged_in_user.orcid,
+        role=SubmissionEditorRole.owner,
+    )
+    payload = json.loads(
+        SubmissionMetadataSchemaPatch(**submission.__dict__).json(exclude_unset=True)
+    )
+    payload["metadata_submission"]["templates"] = [template]
+    db.commit()
+
+    _ = client.request(
+        method="PATCH", url=f"/api/metadata_submission/{submission.id}", json=payload
+    )
+    response = client.request(method="GET", url=f"/api/metadata_submission/{submission.id}")
+    assert response.status_code == 200
+    assert len(response.json()["templates"]) == 1
+    assert response.json()["templates"][0] == template
+
+
+def test_sync_submission_study_name(db: Session, client: TestClient, logged_in_user):
+    expected_val = "my study"
+    submission = fakes.MetadataSubmissionFactory(
+        author=logged_in_user,
+        author_orcid=logged_in_user.orcid,
+        locked_by=logged_in_user,
+        lock_updated=datetime.utcnow(),
+    )
+    fakes.SubmissionRoleFactory(
+        submission=submission,
+        submission_id=submission.id,
+        user_orcid=logged_in_user.orcid,
+        role=SubmissionEditorRole.owner,
+    )
+    payload = json.loads(
+        SubmissionMetadataSchemaPatch(**submission.__dict__).json(exclude_unset=True)
+    )
+    payload["metadata_submission"]["studyForm"]["studyName"] = expected_val
+    db.commit()
+
+    _ = client.request(
+        method="PATCH", url=f"/api/metadata_submission/{submission.id}", json=payload
+    )
+    response = client.request(method="GET", url=f"/api/metadata_submission/{submission.id}")
+    assert response.status_code == 200
+    assert response.json()["study_name"] == expected_val