linter fixes

Author: samobermiller

nmdc_server/api.py

@@ -1244,8 +1244,10 @@ async def update_submission(
         if body_dict.get("status", None):
             new_status = body_dict["status"]
             allowed_transitions = {
-                SubmissionStatusEnum.UpdatesRequired.text: SubmissionStatusEnum.InProgress.text,
-                SubmissionStatusEnum.InProgress.text: SubmissionStatusEnum.SubmittedPendingReview.text
+                SubmissionStatusEnum.UpdatesRequired.text:
+                    SubmissionStatusEnum.InProgress.text,
+                SubmissionStatusEnum.InProgress.text:
+                    SubmissionStatusEnum.SubmittedPendingReview.text,
             }
             current_status = submission.status
             if (
@@ -1266,15 +1268,18 @@ def create_github_issue(submission: schemas_submission.SubmissionMetadataSchema,
     # If the settings for issue creation weren't supplied return, no need to do anything further
     if gh_url is None or token is None:
         return None
-    
+
     headers = {"Authorization": f"Bearer {token}", "Content-Type": "text/plain; charset=utf-8"}
 
     # Check for existing issues first
     existing_issue = check_existing_github_issue(submission.id, headers, gh_url, user)
     if existing_issue:
-        logging.info(f"GitHub issue already exists for submission {submission.id}: {existing_issue['html_url']}")
+        logging.info(
+            f"GitHub issue already exists for submission {submission.id}: \
+                {existing_issue['html_url']}"
+        )
         return existing_issue
-    
+
     else:
 
         # Gathering the fields we want to display in the issue
@@ -1333,6 +1338,7 @@ def create_github_issue(submission: schemas_submission.SubmissionMetadataSchema,
 
         return res
 
+
 def update_github_issue_for_resubmission(existing_issue, user, headers):
     """
     Update an existing GitHub issue to note that the submission was resubmitted.
@@ -1341,78 +1347,73 @@ def update_github_issue_for_resubmission(existing_issue, user, headers):
     try:
         issue_number = existing_issue.get("number")
         issue_url = existing_issue.get("url")  # API URL for the issue
-        
+
         if not issue_number or not issue_url:
             logging.error("Could not find issue number or URL for existing GitHub issue")
             return existing_issue
-        
+
         # Create a comment noting the resubmission
         from datetime import datetime
+
         timestamp = datetime.utcnow().strftime("%Y-%m-%d %H:%M:%S UTC")
-        
+
         comment_body = f"""
 ## 🔄 Submission Resubmitted
 
-**Resubmitted by:** {user.name} ({user.orcid})  
-**Timestamp:** {timestamp}  
+**Resubmitted by:** {user.name} ({user.orcid})
+**Timestamp:** {timestamp}
 **Status:** {SubmissionStatusEnum.SubmittedPendingReview.text}
 
 The submission has been updated and resubmitted for review.
         """.strip()
-        
+
         # Add comment to the issue
         comment_url = f"{issue_url}/comments"
         comment_payload = {"body": comment_body}
-        
+
         comment_response = requests.post(
-            comment_url, 
-            headers=headers, 
-            data=json.dumps(comment_payload)
+            comment_url, headers=headers, data=json.dumps(comment_payload)
         )
-        
+
         if comment_response.status_code == 201:
             logging.info(f"Successfully added resubmission comment to GitHub issue #{issue_number}")
         else:
             logging.error(f"Failed to add comment to GitHub issue: {comment_response.status_code}")
-        
+
         # If the issue is closed, reopen it
         if existing_issue.get("state") == "closed":
-            reopen_payload = {
-                "state": "open",
-                "state_reason": "reopened"
-            }
-            
+            reopen_payload = {"state": "open", "state_reason": "reopened"}
+
             reopen_response = requests.patch(
-                issue_url,
-                headers=headers,
-                data=json.dumps(reopen_payload)
+                issue_url, headers=headers, data=json.dumps(reopen_payload)
             )
-            
+
             if reopen_response.status_code == 200:
                 logging.info(f"Successfully reopened GitHub issue #{issue_number}")
             else:
                 logging.error(f"Failed to reopen GitHub issue: {reopen_response.status_code}")
-        
+
         return existing_issue
-        
+
     except Exception as e:
         logging.error(f"Error updating GitHub issue for resubmission: {str(e)}")
         return existing_issue
 
-def check_existing_github_issue(submission_id: str, headers: dict, gh_base_url:str, user):
+
+def check_existing_github_issue(submission_id: str, headers: dict, gh_base_url: str, user):
     """
     Check if a GitHub issue already exists for the given submission ID using GitHub's search API.
     """
     try:
-        repo_url = gh_base_url.replace('/issues', '')
+        repo_url = gh_base_url.replace("/issues", "")
         search_url = f"{repo_url}/issues"
         expected_title = f"NMDC Submission: {submission_id}"
         params = {
             "state": "all",
             "per_page": 100,
         }
         response = requests.get(search_url, headers=headers, params=params)
-        
+
         if response.status_code == 200:
             issues = response.json()
 
@@ -1428,11 +1429,12 @@ def check_existing_github_issue(submission_id: str, headers: dict, gh_base_url:s
         else:
             logging.warning(f"Failed to search GitHub issues: {response.status_code}")
             return None
-            
+
     except Exception as e:
         logging.error(f"Error searching GitHub issues: {str(e)}")
         return None
 
+
 @router.delete(
     "/metadata_submission/{id}",
     tags=["metadata_submission"],

tests/test_submission.py

@@ -1,8 +1,8 @@
+import json
 from csv import DictReader
 from datetime import UTC, datetime, timedelta
-
-import json
 from unittest.mock import Mock, patch
+
 import pytest
 from fastapi.encoders import jsonable_encoder
 from nmdc_schema.nmdc import SubmissionStatusEnum
@@ -1433,8 +1433,9 @@ def test_delete_submission_study_images_success(
 def test_github_issue_resubmission_creates_comment_only(
     db: Session, client: TestClient, logged_in_user
 ):
-    """Test that when a GitHub issue already exists for a submission, only a comment is created (no new issue)."""
-    
+    """Test that when a GitHub issue already exists for a submission,
+    only a comment is created (no new issue)."""
+
     # Create a submission
     submission = fakes.MetadataSubmissionFactory(
         author=logged_in_user,
@@ -1456,72 +1457,72 @@ def test_github_issue_resubmission_creates_comment_only(
         "url": "https://api.github.com/repos/owner/repo/issues/123",
         "html_url": "https://github.com/owner/repo/issues/123",
         "title": f"NMDC Submission: {submission.id}",
-        "state": "open"
+        "state": "open",
     }
 
     # Mock responses for the GitHub API calls
     mock_responses = []
-    
+
     # Mock the search for existing issues (returns the existing issue)
     search_response = Mock()
     search_response.status_code = 200
     search_response.json.return_value = [existing_issue]  # List of issues from repo issues endpoint
     mock_responses.append(search_response)
-    
+
     # Mock the comment creation response
     comment_response = Mock()
     comment_response.status_code = 201
     comment_response.json.return_value = {"id": 456, "body": "comment content"}
     mock_responses.append(comment_response)
-    
+
     # Patch the requests.get and requests.post calls
-    with patch('nmdc_server.api.requests.get') as mock_get, \
-         patch('nmdc_server.api.requests.post') as mock_post, \
-         patch('nmdc_server.api.settings') as mock_settings:
-        
+    with patch("nmdc_server.api.requests.get") as mock_get, patch(
+        "nmdc_server.api.requests.post"
+    ) as mock_post, patch("nmdc_server.api.settings") as mock_settings:
+
         # Configure settings
         mock_settings.github_issue_url = "https://api.github.com/repos/owner/repo/issues"
         mock_settings.github_authentication_token = "fake_token"
         mock_settings.github_issue_assignee = "assignee"
         mock_settings.host = "test-host"
-        
+
         # Set up the mock responses
         mock_get.return_value = search_response
         mock_post.return_value = comment_response
-        
+
         # Update submission status to trigger GitHub issue creation/update
         payload = {
             "status": SubmissionStatusEnum.SubmittedPendingReview.text,
-            "metadata_submission": {}
+            "metadata_submission": {},
         }
-        
+
         response = client.request(
             method="PATCH",
             url=f"/api/metadata_submission/{submission.id}",
             json=payload,
         )
-        
+
         assert response.status_code == 200
-        
+
         # Verify that requests.get was called to search for existing issues
         assert mock_get.call_count == 1
         get_call = mock_get.call_args
         assert "https://api.github.com/repos/owner/repo/issues" in get_call[0][0]
-        
+
         # Verify that requests.post was called to create a comment (not a new issue)
         assert mock_post.call_count == 1
         post_call = mock_post.call_args
-        
+
         # Verify the comment endpoint was called
         assert post_call[0][0] == "https://api.github.com/repos/owner/repo/issues/123/comments"
-        
+
         # Verify the comment content includes resubmission information
-        comment_data = json.loads(post_call[1]['data'])
-        assert "Submission Resubmitted" in comment_data['body']
-        assert logged_in_user.name in comment_data['body']
-        assert logged_in_user.orcid in comment_data['body']
-        assert SubmissionStatusEnum.SubmittedPendingReview.text in comment_data['body']
-        
+        comment_data = json.loads(post_call[1]["data"])
+        assert "Submission Resubmitted" in comment_data["body"]
+        assert logged_in_user.name in comment_data["body"]
+        assert logged_in_user.orcid in comment_data["body"]
+        assert SubmissionStatusEnum.SubmittedPendingReview.text in comment_data["body"]
+
         # Verify headers include authorization
-        headers = post_call[1]['headers']
-        assert headers['Authorization'] == "Bearer fake_token"
+        headers = post_call[1]["headers"]
+        assert headers["Authorization"] == "Bearer fake_token"