found a way to pull in schema enum in api.py and models.py

Author: samobermiller

nmdc_server/api.py

@@ -12,6 +12,7 @@
 from fastapi import APIRouter, Depends, Header, HTTPException, Query, Response, status
 from fastapi.responses import JSONResponse
 from linkml_runtime.utils.schemaview import SchemaView
+from nmdc_schema.nmdc_data import get_nmdc_schema_definition
 from sqlalchemy.orm import Session
 from starlette.responses import StreamingResponse
 
@@ -39,6 +40,15 @@
 logger = get_logger(__name__)
 
 
+def get_submission_status_enum():
+    """Get SubmissionStatusEnum from the NMDC schema definition."""
+    schema = get_nmdc_schema_definition()
+    return schema.enums["SubmissionStatusEnum"].permissible_values
+
+
+SubmissionStatusEnum = get_submission_status_enum()
+
+
 # get application settings
 @router.get("/settings", name="Get application settings")
 async def get_settings() -> Dict[str, Any]:
@@ -1183,7 +1193,7 @@ async def update_submission(
     # Create GitHub issue when metadata is being submitted and not a test submission
     if (
         submission.status == "In Progress"
-        and body_dict.get("status", None) == "Submitted - Pending Review"
+        and body_dict.get("status", None) == SubmissionStatusEnum["SubmittedPendingReview"].title
         and submission.is_test_submission is False
     ):
         submission_model = schemas_submission.SubmissionMetadataSchema.model_validate(submission)
@@ -1210,7 +1220,8 @@ async def update_submission(
 
         if body_dict.get("status", None):
             if (
-                body_dict.get("status", None) == "Submitted - Pending Review"
+                body_dict.get("status", None)
+                == SubmissionStatusEnum["SubmittedPendingReview"].title
                 and submission.is_test_submission is False
             ):
                 submission.status = body_dict["status"]
@@ -1263,7 +1274,7 @@ 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",
+        f"{SubmissionStatusEnum["SubmittedPendingReview"].title}",
         f"Data types: {omics_processing_types}",
         f"Sample type: {sample_types}",
         f"Number of samples: {num_samples}",
@@ -1487,4 +1498,4 @@ 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

@@ -6,13 +6,21 @@
 from factory import Faker, SubFactory, lazy_attribute, post_generation
 from factory.alchemy import SQLAlchemyModelFactory
 from faker.providers import BaseProvider, date_time, geo, internet, lorem, misc, person, python
+from nmdc_schema.nmdc_data import get_nmdc_schema_definition
 from sqlalchemy.orm.scoping import scoped_session
 
 from nmdc_server import models
 from nmdc_server.database import SessionLocal
 from nmdc_server.schemas import AnnotationValue
 
-from nmdc_schema.nmdc_materialized_patterns import SubmissionStatusEnum
+
+def get_submission_status_enum():
+    """Get SubmissionStatusEnum from the NMDC schema definition."""
+    schema = get_nmdc_schema_definition()
+    return schema.enums["SubmissionStatusEnum"].permissible_values
+
+
+SubmissionStatusEnum = get_submission_status_enum()
 
 
 class DoiProvider(BaseProvider):
@@ -341,7 +349,7 @@ class Meta:
     id: UUID = Faker("uuid")
     author = SubFactory(UserFactory)
     author_orcid = Faker("pystr")
-    status = SubmissionStatusEnum.InProgress.title
+    status = SubmissionStatusEnum["InProgress"].title
     study_name = Faker("word")
     templates = Faker("pylist", nb_elements=2, value_types=[str])
     created = datetime.utcnow()

nmdc_server/models.py

@@ -3,6 +3,7 @@
 from typing import Any, Dict, Iterator, List, Optional, Type, Union
 from uuid import uuid4
 
+from nmdc_schema.nmdc_data import get_nmdc_schema_definition
 from sqlalchemy import (
     BigInteger,
     Boolean,
@@ -34,6 +35,15 @@
 # described by https://microbiomedata.github.io/nmdc-schema/.
 
 
+def get_submission_status_enum():
+    """Get SubmissionStatusEnum from the NMDC schema definition."""
+    schema = get_nmdc_schema_definition()
+    return schema.enums["SubmissionStatusEnum"].permissible_values
+
+
+SubmissionStatusEnum = get_submission_status_enum()
+
+
 def gold_url(base: str, id: str, gold_identifiers: Optional[list[str]] = None) -> Optional[str]:
     if id.startswith("gold:"):
         return f"{base}{id[5:]}"
@@ -1015,4 +1025,4 @@ 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

@@ -3,14 +3,23 @@
 from datetime import datetime, timedelta
 
 import pytest
+from nmdc_schema.nmdc_data import get_nmdc_schema_definition
 from sqlalchemy.orm.session import Session
 from starlette.testclient import TestClient
 
 from nmdc_server import fakes
 from nmdc_server.models import SubmissionEditorRole, SubmissionRole
 from nmdc_server.schemas_submission import SubmissionMetadataSchema, SubmissionMetadataSchemaPatch
 
-from nmdc_schema.nmdc import SubmissionStatusEnum
+
+def get_submission_status_enum():
+    """Get SubmissionStatusEnum from the NMDC schema definition."""
+    schema = get_nmdc_schema_definition()
+    return schema.enums["SubmissionStatusEnum"].permissible_values
+
+
+SubmissionStatusEnum = get_submission_status_enum()
+
 
 @pytest.fixture
 def suggest_payload():
@@ -45,20 +54,18 @@ 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_print_submission_enum(db: Session, client: TestClient, logged_in_user):
     submission = fakes.MetadataSubmissionFactory(
         author=logged_in_user, author_orcid=logged_in_user.orcid
     )
     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)
+    print(SubmissionStatusEnum)
+    print("\nSpecific enum value string")
+    print(SubmissionStatusEnum["InProgress"].title)
+
+    assert submission
 
-    assert not submission
 
 def test_get_metadata_submissions_mixs_as_admin(
     db: Session, client: TestClient, logged_in_admin_user
@@ -74,7 +81,7 @@ def test_get_metadata_submissions_mixs_as_admin(
         author=logged_in_user,
         author_orcid=logged_in_user.orcid,
         created=now,
-        status=SubmissionStatusEnum.SubmittedPendingReview.text,
+        status=SubmissionStatusEnum["SubmittedPendingReview"].title,
         metadata_submission={
             "sampleData": {
                 "built_env_data": [
@@ -126,7 +133,7 @@ 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.text
+    assert data_row["Status"] == SubmissionStatusEnum["SubmittedPendingReview"].title
     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"
@@ -139,7 +146,7 @@ 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.text
+    assert data_row["Status"] == SubmissionStatusEnum["SubmittedPendingReview"].title
     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"
@@ -321,7 +328,7 @@ def test_get_metadata_submissions_report_as_admin(
             "packageName": [],
         },
         is_test_submission=True,
-        status=SubmissionStatusEnum.InProgress.text,
+        status=SubmissionStatusEnum["InProgress"].title,
         source_client="field_notes",
     )
     db.commit()
@@ -362,7 +369,7 @@ 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.text
+    assert data_row["Status"] == SubmissionStatusEnum["InProgress"].title
     assert data_row["Is Test Submission"] == "True"
     assert data_row["Number of Samples"] == "4"
     assert isinstance(data_row["Date Last Modified"], str)
@@ -376,7 +383,9 @@ 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.text  # matches value in upstream faker
+    assert (
+        data_row["Status"] == SubmissionStatusEnum["InProgress"].title
+    )  # 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)