Clean up logging for testing

ena-submission/scripts/create_sample.py

@@ -106,15 +106,24 @@ def get_sample_attributes(config, sample_metadata, row):
 
 
 def construct_sample_set_object(
-    config, organism_metadata, sample_metadata, center_name, row, organism
+    config,
+    organism_metadata,
+    sample_metadata,
+    center_name,
+    row,
+    organism,
+    test=False,
 ):
+    if test:
+        alias = XmlAttribute(
+            f"{row["accession"]}:{organism}:{config.unique_project_suffix}:{datetime.now(tz=pytz.utc)}"
+        )  # TODO(https://github.com/loculus-project/loculus/issues/2425): remove in production
+    else:
+        alias = XmlAttribute(f"{row["accession"]}:{organism}:{config.unique_project_suffix}")
     list_sample_attributes = get_sample_attributes(config, sample_metadata, row)
     sample_type = SampleType(
         center_name=XmlAttribute(center_name),
-        alias=XmlAttribute(f"{row["accession"]}:{organism}:{config.unique_project_suffix}"),
-        # alias=XmlAttribute(
-        #     f"{row["accession"]}:{organism}:{config.unique_project_suffix}:{datetime.now(tz=pytz.utc)}"  # For testing
-        # ),
+        alias=alias,
         title=f"{organism_metadata["scientific_name"]}: Genome sequencing",
         description=(
             f"Automated upload of {organism_metadata["scientific_name"]} sequences submitted by {center_name} from {config.db_name}",
@@ -148,6 +157,7 @@ def send_slack_notification(config: Config, comment: str, time: datetime, time_t
         not _last_notification_sent
         or time - timedelta(hours=time_threshold) > _last_notification_sent
     ):
+        logger.warning(comment)
         comment = f"{config.backend_url}: " + comment
         notify(slack_config, comment)
         _last_notification_sent = time
@@ -275,7 +285,7 @@ def sample_table_create(db_config, config, retry_number=3):
         organism_metadata = config.organisms[organism]["ingest"]
 
         sample_set = construct_sample_set_object(
-            config, organism_metadata, sample_metadata, center_name, row, organism
+            config, organism_metadata, sample_metadata, center_name, row, organism, test=True
         )
         update_values = {"status": Status.SUBMITTING}
         number_rows_updated = update_db_where_conditions(
@@ -353,7 +363,6 @@ def sample_table_handle_errors(db_config, config, time_threshold=15, slack_time_
             f"ENA Submission pipeline found {len(entries_with_errors)} entries in sample_table in "
             f"status HAS_ERRORS or SUBMITTING for over {time_threshold}m"
         )
-        logger.warning(error_msg)
         send_slack_notification(
             config, error_msg, time=datetime.now(tz=pytz.utc), time_threshold=slack_time_threshold
         )