removed attempts at loading nmdc_schema in api.py and models.py

Author: samobermiller

nmdc_server/api.py

@@ -34,8 +34,6 @@
 from nmdc_server.pagination import Pagination
 from nmdc_server.table import Table
 
-from nmdc_schema.nmdc import SubmissionStatusEnum
-
 router = APIRouter()
 
 logger = get_logger(__name__)
@@ -769,7 +767,7 @@ async def get_metadata_submissions_mixs(
 ):
     r"""
     Generate a TSV-formatted report of biosamples belonging to submissions
-    that have a status of "Submitted- Pending Review".
+    that have a status of "Submitted - Pending Review".
 
     The report indicates which environmental package/extension, broad scale,
     local scale, and medium are specified for each biosample. The report is
@@ -1184,8 +1182,8 @@ async def update_submission(
 
     # Create GitHub issue when metadata is being submitted and not a test submission
     if (
-        submission.status == SubmissionStatusEnum.InProgress.text
-        and body_dict.get("status", None) == SubmissionStatusEnum.SubmittedPendingReview.text
+        submission.status == "In Progress"
+        and body_dict.get("status", None) == "Submitted - Pending Review"
         and submission.is_test_submission is False
     ):
         submission_model = schemas_submission.SubmissionMetadataSchema.model_validate(submission)
@@ -1212,7 +1210,7 @@ async def update_submission(
 
         if body_dict.get("status", None):
             if (
-                body_dict.get("status", None) == "Submitted- Pending Review"
+                body_dict.get("status", None) == "Submitted - Pending Review"
                 and submission.is_test_submission is False
             ):
                 submission.status = body_dict["status"]
@@ -1265,7 +1263,7 @@ def create_github_issue(submission: schemas_submission.SubmissionMetadataSchema,
         f"Has data been generated: {data_generated}",
         f"PI name: {pi_name}",
         f"PI orcid: {pi_orcid}",
-        "Status: Submitted- Pending Review",
+        "Status: Submitted - Pending Review",
         f"Data types: {omics_processing_types}",
         f"Sample type: {sample_types}",
         f"Number of samples: {num_samples}",
@@ -1489,4 +1487,4 @@ async def update_user(
 ):
     if body.id != id:
         raise HTTPException(status_code=400, detail="Invalid id")
-    return crud.update_user(db, body)
+    return crud.update_user(db, body)

nmdc_server/fakes.py

@@ -12,7 +12,7 @@
 from nmdc_server.database import SessionLocal
 from nmdc_server.schemas import AnnotationValue
 
-from nmdc_schema.nmdc import SubmissionStatusEnum
+from nmdc_schema.nmdc_materialized_patterns import SubmissionStatusEnum
 
 
 class DoiProvider(BaseProvider):
@@ -341,7 +341,7 @@ class Meta:
     id: UUID = Faker("uuid")
     author = SubFactory(UserFactory)
     author_orcid = Faker("pystr")
-    status = SubmissionStatusEnum.InProgress.text
+    status = SubmissionStatusEnum.InProgress.title
     study_name = Faker("word")
     templates = Faker("pylist", nb_elements=2, value_types=[str])
     created = datetime.utcnow()

nmdc_server/models.py

@@ -30,8 +30,6 @@
 
 from nmdc_server.database import Base, update_multiomics_sql
 
-from nmdc_schema.nmdc import SubmissionStatusEnum
-
 # The models in the file are a specialized representation of the domain objects
 # described by https://microbiomedata.github.io/nmdc-schema/.
 
@@ -923,7 +921,7 @@ class SubmissionMetadata(Base):
     id = Column(UUID(as_uuid=True), primary_key=True, default=uuid4)
     author_orcid = Column(String, nullable=False)
     created = Column(DateTime, nullable=False, default=datetime.utcnow)
-    status = Column(String, nullable=False, default=SubmissionStatusEnum.InProgress.text)
+    status = Column(String, nullable=False, default="In Progress")
     metadata_submission = Column(JSONB, nullable=False)
     author_id = Column(UUID(as_uuid=True), ForeignKey(User.id))
     study_name = Column(String, nullable=True)
@@ -1017,4 +1015,4 @@ class AuthorizationCode(Base):
 class InvalidatedToken(Base):
     __tablename__ = "invalidated_token"
 
-    token = Column(String, primary_key=True)
+    token = Column(String, primary_key=True)

tests/test_submission.py

@@ -10,6 +10,8 @@
 from nmdc_server.models import SubmissionEditorRole, SubmissionRole
 from nmdc_server.schemas_submission import SubmissionMetadataSchema, SubmissionMetadataSchemaPatch
 
+from nmdc_schema.nmdc import SubmissionStatusEnum
+
 @pytest.fixture
 def suggest_payload():
     return [
@@ -43,11 +45,19 @@ def test_get_metadata_submissions_mixs_as_non_admin(
     response = client.request(method="GET", url="/api/metadata_submission/mixs_report")
     assert response.status_code == 403
 
-def test_submission_enum(db: Session, client: TestClient, logged_in_user):
+def test_print_submission_enum(db: Session, client: TestClient, logged_in_user):
     submission = fakes.MetadataSubmissionFactory(
         author=logged_in_user, author_orcid=logged_in_user.orcid
     )
-    print(submission.__dict__)
+    print("Available submission status enum values:")
+    for attr_name in dir(SubmissionStatusEnum):
+        attr_value = getattr(SubmissionStatusEnum, attr_name)
+        if hasattr(attr_value, 'text'):
+            print(attr_value.text)
+    
+    print('\nSpecific enum value string')
+    print(SubmissionStatusEnum.InProgress.text)
+
     assert not submission
 
 def test_get_metadata_submissions_mixs_as_admin(
@@ -64,7 +74,7 @@ def test_get_metadata_submissions_mixs_as_admin(
         author=logged_in_user,
         author_orcid=logged_in_user.orcid,
         created=now,
-        status=SubmissionStatusEnum.SubmittedPendingReview,
+        status=SubmissionStatusEnum.SubmittedPendingReview.text,
         metadata_submission={
             "sampleData": {
                 "built_env_data": [
@@ -116,7 +126,7 @@ def test_get_metadata_submissions_mixs_as_admin(
 
     data_row = rows[1]  # first data row (data about Sample A in submission1)
     assert data_row["Submission ID"] == str(submission1.id)
-    assert data_row["Status"] == SubmissionStatusEnum.SubmittedPendingReview
+    assert data_row["Status"] == SubmissionStatusEnum.SubmittedPendingReview.text
     assert data_row["Sample Name"] == "Sample A"
     assert data_row["Environmental Package/Extension"] == "Env Pkg 1"
     assert data_row["Environmental Broad Scale"] == "Broad Scale A"
@@ -129,7 +139,7 @@ def test_get_metadata_submissions_mixs_as_admin(
 
     data_row = rows[2]  # second data row (data about Sample B in submission1)
     assert data_row["Submission ID"] == str(submission1.id)
-    assert data_row["Status"] == SubmissionStatusEnum.SubmittedPendingReview
+    assert data_row["Status"] == SubmissionStatusEnum.SubmittedPendingReview.text
     assert data_row["Sample Name"] == "Sample B"
     assert data_row["Environmental Package/Extension"] == "Env Pkg 1"
     assert data_row["Environmental Broad Scale"] == "Broad Scale B"
@@ -311,7 +321,7 @@ def test_get_metadata_submissions_report_as_admin(
             "packageName": [],
         },
         is_test_submission=True,
-        status=SubmissionStatusEnum.InProgress,
+        status=SubmissionStatusEnum.InProgress.text,
         source_client="field_notes",
     )
     db.commit()
@@ -352,7 +362,7 @@ def test_get_metadata_submissions_report_as_admin(
     assert data_row["PI Name"] == "My PI name"
     assert data_row["PI Email"] == "My PI email"
     assert data_row["Source Client"] == "field_notes"
-    assert data_row["Status"] == SubmissionStatusEnum.InProgress
+    assert data_row["Status"] == SubmissionStatusEnum.InProgress.text
     assert data_row["Is Test Submission"] == "True"
     assert data_row["Number of Samples"] == "4"
     assert isinstance(data_row["Date Last Modified"], str)
@@ -366,7 +376,7 @@ def test_get_metadata_submissions_report_as_admin(
     assert data_row["PI Name"] == ""
     assert data_row["PI Email"] == ""
     assert data_row["Source Client"] == ""  # upstream faker lacks `source_client` attribute
-    assert data_row["Status"] == SubmissionStatusEnum.InProgress  # matches value in upstream faker
+    assert data_row["Status"] == SubmissionStatusEnum.InProgress.text  # matches value in upstream faker
     assert data_row["Is Test Submission"] == "False"
     assert data_row["Number of Samples"] == "0"
     assert isinstance(data_row["Date Last Modified"], str)

web/src/views/SubmissionPortal/store/index.ts

@@ -60,6 +60,9 @@ const isSubmissionStatus = (str: any): str is SubmissionStatusTitle => Object.va
 const status = ref(submissionStatus.InProgress);
 const isTestSubmission = ref(false);
 
+// Helper function to check if current status is valid for saving
+const isValidStatusForSaving = (): boolean => isSubmissionStatus(status.value);
+
 /**
  * Submission record locking information
  */
@@ -399,6 +402,11 @@ async function incrementalSaveRecord(id: string): Promise<number | void> {
     return Promise.resolve();
   }
 
+  // Check if current status is valid before saving
+  if (!isValidStatusForSaving()) {
+    throw new Error(`Cannot save record: current status "${status.value}" is not a valid status`);
+  }
+
   let payload: Partial<MetadataSubmission> = {};
   let permissions: Record<string, PermissionLevelValues> | undefined;
   if (isOwner()) {