Fix error handling

ena-submission/flyway/sql/V1__Initial_Schema.sql

@@ -34,7 +34,7 @@ CREATE TABLE sample_table (
     status text not null,
     started_at timestamp not null,
     finished_at timestamp,
-    sample_metadata jsonb,
+    result jsonb,
     primary key (accession, version)
 );
 
@@ -46,6 +46,6 @@ CREATE TABLE assembly_table (
     status text not null,
     started_at timestamp not null,
     finished_at timestamp,
-    assembly_metadata jsonb,
+    result jsonb,
     primary key (accession, version)
 );

ena-submission/scripts/create_project.py

@@ -55,6 +55,9 @@ class Config:
     ena_submission_url: str
     ena_submission_password: str
     ena_submission_username: str
+    slack_hook: str
+    slack_token: str
+    slack_channel_id: str
 
 
 def construct_project_set_object(
@@ -250,16 +253,17 @@ def project_table_create(db_config, config, retry_number=3):
             number_rows_updated = 0
             tries = 0
             while number_rows_updated != 1 and tries < retry_number:
+                if tries > 0:
+                    # If state not correctly added retry
+                    logger.warning(
+                        f"Project created but DB update failed - reentry DB update #{tries}."
+                    )
                 number_rows_updated = update_db_where_conditions(
                     db_config,
                     table_name="project_table",
                     conditions=group_key,
                     update_values=update_values,
                 )
-                # If state not correctly added retry
-                logger.warning(
-                    f"Project created but DB update failed - reentry DB update #{tries}."
-                )
                 tries += 1
             if number_rows_updated == 1:
                 logger.info(f"Project creation for group_id {row["group_id"]} succeeded!")
@@ -271,16 +275,17 @@ def project_table_create(db_config, config, retry_number=3):
             number_rows_updated = 0
             tries = 0
             while number_rows_updated != 1 and tries < retry_number:
+                if tries > 0:
+                    # If state not correctly added retry
+                    logger.warning(
+                        f"Project creation failed and DB update failed - reentry DB update #{tries}."
+                    )
                 number_rows_updated = update_db_where_conditions(
                     db_config,
                     table_name="project_table",
                     conditions=group_key,
                     update_values=update_values,
                 )
-                # If state not correctly added retry
-                logger.warning(
-                    f"Project creation failed and DB update failed - reentry DB update #{tries}."
-                )
                 tries += 1
 
 
@@ -295,10 +300,10 @@ def project_table_handle_errors(db_config, config, time_threshold=15, slack_time
     entries_with_errors = find_errors_in_db(
         db_config, "project_table", time_threshold=time_threshold
     )
-    if len(entries_with_errors) > 1:
+    if len(entries_with_errors) > 0:
         error_msg = (
-            f"Found {len(entries_with_errors)} entries in project_table in status HAS_ERRORS",
-            f" for {time_threshold}m",
+            f"Found {len(entries_with_errors)} entries in project_table in status HAS_ERRORS"
+            f"of SUBMITTING for over {time_threshold}m"
         )
         logger.warning(error_msg)
         send_slack_notification(