Merge pull request #183 from OpenUpSA/indexing

added jobs monitor

Author: michaelglenister

app.py

@@ -341,6 +341,20 @@ def delete(self, pathogen_id):
 
             with get_db_cursor() as cursor:
                 if hard_delete:
+
+                    # Check if there are associated schemas
+                    cursor.execute("""
+                        SELECT COUNT(*) as count FROM schemas 
+                        WHERE pathogen_id = %s
+                    """, (pathogen_id,))
+                    
+                    schema_count = cursor.fetchone()['count']
+                    
+                    if schema_count > 0:
+                        return {
+                            'error': f'Cannot delete pathogen: {schema_count} schema(s) are still associated with it. Delete schemas first or use soft delete.'
+                        }, 400
+
                     # Hard delete - permanently remove from database
                     cursor.execute("""
                         DELETE FROM pathogens 
@@ -2672,11 +2686,6 @@ def post(self):
         try:
             data = request.get_json()
 
-            print('========================================')
-            print("Incoming search query:")
-            print(data)
-            print('========================================')
-
             # convert json data to string and replace all .keyword with ''
             data_str = json.dumps(data).replace('.keyword', '')
             data = json.loads(data_str)
@@ -2731,10 +2740,6 @@ def post(self):
             if not data:
                 return {'error': 'No JSON data provided'}, 400
 
-            print("Final Query ========================")
-            print(data['query'])
-            print("===================================")
-
             results = query_elastic(data)
 
             print(results)
@@ -2830,6 +2835,41 @@ def post(self):
             logger.exception(f"Error during reindexing: {str(e)}")
             return {'error': f'Reindexing error: {str(e)}'}, 500
 
+##########################
+### JOBS MONITORING
+##########################
+
+jobs_ns = api.namespace('jobs', description='Job monitoring endpoints')
+
+@jobs_ns.route('/')
+class JobsList(Resource):
+
+    ### GET /jobs ###
+
+    @jobs_ns.doc('list_jobs')
+    @require_auth(keycloak_auth)
+    @require_permission('system_admin_access')
+    def get(self):
+        """List all jobs from the jobs table"""
+        
+        try:
+            with get_db_cursor() as cursor:
+                cursor.execute("""
+                    SELECT * FROM jobs
+                    ORDER BY created_at DESC
+                """)
+                
+                jobs = cursor.fetchall()
+                
+                return {
+                    'jobs': jobs,
+                    'total': len(jobs)
+                }
+                
+        except Exception as e:
+            logger.exception(f"Error retrieving jobs: {str(e)}")
+            return {'error': f'Database error: {str(e)}'}, 500
+
 
 
 ##########################

helpers.py

@@ -739,11 +739,11 @@ async def check_for_sequence_data(isolate, split_on_fasta_headers=True):
                     """
                     SELECT object_id 
                     FROM submission_files 
-                    WHERE filename = %s AND file_type = 'fasta'
+                    WHERE filename = %s AND file_type = 'fasta' AND submission_id = %s
                     ORDER BY created_at DESC 
                     LIMIT 1
                     """,
-                    (fasta_file,),
+                    (fasta_file, isolate['submission_id']),
                 )
                 file_record = cursor.fetchone()
 
@@ -763,11 +763,11 @@ async def check_for_sequence_data(isolate, split_on_fasta_headers=True):
                 """
                 SELECT object_id 
                 FROM submission_files 
-                WHERE filename = %s AND file_type = 'fasta'
+                WHERE filename = %s AND file_type = 'fasta' AND submission_id = %s
                 ORDER BY created_at DESC 
                 LIMIT 1
                 """,
-                (fasta_file,),
+                (fasta_file, isolate['submission_id']),
             )
             file_record = cursor.fetchone()