[db/models] Deduplicate repos by repo_src_id on CLI add

augur/application/db/models/augur_data.py

@@ -954,7 +954,7 @@ def is_valid_github_repo(gh_session, url: str) -> bool:
 
                 return False, {"status": f"Github Error: {data['message']}"}
 
-            return True, {"status": "Valid repo", "repo_type": data["owner"]["type"]}
+            return True, {"status": "Valid repo", "repo_type": data["owner"]["type"], "repo_src_id": data["id"]}
 
         return False, {"status": "Failed to validate repo after multiple attempts"}
 
@@ -1145,6 +1145,15 @@ def insert_github_repo(session, url: str, repo_group_id: int, tool_source, repo_
         if not owner or not repo:
             return None
 
+        # If we know the numeric source ID, check whether this repo is already
+        # tracked under a different URL (e.g. after a GitHub rename/transfer).
+        # This prevents duplicate rows when the same repo is added twice with
+        # different URLs (issue #3056).
+        if repo_src_id is not None:
+            existing = session.query(Repo).filter(Repo.repo_src_id == repo_src_id).first()
+            if existing:
+                return existing.repo_id
+
         repo_data = {
             "repo_group_id": repo_group_id,
             "repo_git": url,

augur/util/repo_load_controller.py

@@ -49,6 +49,8 @@ def add_cli_repo(self, repo_data: Dict[str, Any], from_org_list=False, repo_type
         url = repo_data["url"]
         repo_group_id = repo_data["repo_group_id"]
 
+        repo_src_id = None
+
         # if it is from not from an org list then we need to check its validity, and get the repo type
         if not from_org_list:
             if "gitlab" in url:
@@ -57,19 +59,24 @@ def add_cli_repo(self, repo_data: Dict[str, Any], from_org_list=False, repo_type
                 result = Repo.is_valid_github_repo(self.session, url)
             if not result[0]:
                 return False, {"status": result[1]["status"], "repo_url": url}
-            
+
             try:
                 repo_type = result[1]["repo_type"]
             except KeyError:
                 print("Skipping repo type...")
 
+            # Capture the source ID so we can deduplicate by it (issue #3056).
+            # Repos that were renamed keep the same numeric src ID even though
+            # their URL changes, so using src_id prevents double-ingestion.
+            repo_src_id = result[1].get("repo_src_id")
+
 
         # if the repo doesn't exist it adds it
         if "gitlab" in url:
-            repo_id = Repo.insert_gitlab_repo(self.session, url, repo_group_id, "CLI")
+            repo_id = Repo.insert_gitlab_repo(self.session, url, repo_group_id, "CLI", repo_src_id=repo_src_id)
             CollectionStatus.insert(self.session, logger, repo_id)
         else:
-            repo_id = Repo.insert_github_repo(self.session, url, repo_group_id, "CLI", repo_type)
+            repo_id = Repo.insert_github_repo(self.session, url, repo_group_id, "CLI", repo_type, repo_src_id=repo_src_id)
             CollectionStatus.insert(self.session, logger, repo_id)
 
         if not repo_id: