Bug fixes for 0.2.1

lib/workload/components/icav2-copy-files/check_or_launch_job_lambda_py/check_or_launch_job_lambda.py

@@ -29,20 +29,27 @@
 # Standard imports
 from pathlib import Path
 from typing import List
+from urllib.parse import urlunparse, urlparse
 import boto3
 from os import environ
 import typing
+import logging
 
 # Wrapica imports
+from wrapica.libica_models import ProjectData
 from wrapica.job import get_job
 from wrapica.project_data import (
-    convert_uri_to_project_data_obj, project_data_copy_batch_handler
+    convert_uri_to_project_data_obj, project_data_copy_batch_handler, delete_project_data
 )
 
 if typing.TYPE_CHECKING:
     from mypy_boto3_ssm import SSMClient
     from mypy_boto3_secretsmanager import SecretsManagerClient
 
+# Set logging
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
 # Globals
 SUCCESS_STATES = [
     "SUCCEEDED"
@@ -63,6 +70,7 @@
 DEFAULT_WAIT_TIME_SECONDS = 10
 DEFAULT_WAIT_TIME_SECONDS_EXT = 10
 
+# Globals
 ICAV2_BASE_URL = "https://ica.illumina.com/ica/rest"
 
 
@@ -222,6 +230,64 @@ def handler(event, context):
 
     # Handle successful job
     if job_status is True:
+        # Confirm source uris have made it to the destination successfully
+        # Get dest folder
+        dest_project_folder_data_obj: ProjectData = convert_uri_to_project_data_obj(dest_uri)
+
+        # Iterate through each source uri
+        has_errors = False
+        for source_uri in source_uris:
+            # Get the source project data object
+            source_project_data_obj: ProjectData = convert_uri_to_project_data_obj(source_uri)
+
+            # Get the dest uri file name
+            dest_file_uri = str(
+                urlunparse(
+                    (
+                        urlparse(dest_uri).scheme,
+                        urlparse(dest_uri).netloc,
+                        str(Path(dest_project_folder_data_obj.data.details.path) / source_project_data_obj.data.details.name),
+                        None, None, None
+                    )
+                )
+            )
+            # Get the dest project data object
+            dest_project_data_file_obj = convert_uri_to_project_data_obj(
+                dest_file_uri
+            )
+
+            # Compare the source and dest project data objects etags
+            if source_project_data_obj.data.details.file_size_in_bytes != dest_project_data_file_obj.data.details.file_size_in_bytes:
+                # Set has errors to true
+                has_errors = True
+                logger.error("Data size mismatch between source and dest project data objects")
+                logger.error(f"Data {source_uri} was transferred to {dest_file_uri} but the file sizes do not match")
+                logger.error(f"Source file size: {source_project_data_obj.data.details.file_size_in_bytes}")
+                logger.error(f"Dest file size: {dest_project_data_file_obj.data.details.file_size_in_bytes}")
+                logger.error("Purging the dest uri file and starting again")
+                # Purge the dest uri file and start again
+                delete_project_data(
+                    project_id=dest_project_data_file_obj.project_id,
+                    data_id=dest_project_data_file_obj.data.id
+                )
+
+        # If we have errors, we need to rerun the job
+        if has_errors:
+            # Add this job id to the failed job list
+            failed_job_list.append(job_id)
+            return {
+                "dest_uri": dest_uri,
+                "source_uris": source_uris,
+                "job_id": submit_copy_job(
+                    dest_uri=dest_uri,
+                    source_uris=source_uris,
+                ),
+                "failed_job_list": failed_job_list,  # Empty list or list of failed jobs
+                "job_status": "RUNNING",
+                "wait_time_seconds": DEFAULT_WAIT_TIME_SECONDS
+            }
+
+        # If we don't have errors, we can return the job as successful
         return {
             "dest_uri": dest_uri,
             "source_uris": source_uris,

lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/check_success_py/check_success.py

@@ -284,12 +284,14 @@ def handler(event, context):
 
 # Failed workflow
 # if __name__ == "__main__":
+#     environ['AWS_PROFILE'] = 'umccr-production'
+#     environ['AWS_REGION'] = 'ap-southeast-2'
 #     environ['ICAV2_ACCESS_TOKEN_SECRET_ID'] = "ICAv2JWTKey-umccr-prod-service-production"
 #     print(
 #         json.dumps(
 #             handler(
 #                 {
-#                     "output_uri": "s3://pipeline-prod-cache-503977275616-ap-southeast-2/byob-icav2/production/analysis/cttsov2/202409156f4e1c52/"
+#                     "output_uri": "s3://pipeline-prod-cache-503977275616-ap-southeast-2/byob-icav2/production/analysis/cttsov2/20240922130c78be/"
 #                 },
 #                 None
 #             ),
@@ -299,10 +301,10 @@ def handler(event, context):
 #
 #     # {
 #     #     "success": false,
-#     #     "message": "Workflow failed at 'DragenCaller' step"
+#     #     "message": "Workflow failed at 'FastqValidation' step"
 #     # }
 
-# Passing workflow
+# # Passing workflow
 # if __name__ == "__main__":
 #     environ['ICAV2_ACCESS_TOKEN_SECRET_ID'] = "ICAv2JWTKey-umccr-prod-service-production"
 #     print(

lib/workload/stateless/stacks/cttso-v2-pipeline-manager/step_functions_templates/set_cttso_v2_nf_outputs.asl.json

@@ -81,7 +81,7 @@
               ],
               "ResultSelector": {
                 "workflow_success.$": "$.Payload.success",
-                "error_message.$": "$.Payload.error_message"
+                "error_message.$": "$.Payload.message"
               },
               "ResultPath": "$.check_successful_analysis_step",
               "Next": "Is successful analysis"

lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/jb-weld/part_1/initialise-cttsov2-instrument-dbs/step_functions_templates/initialise_cttsov2_instrument_run_db_sfn_template.asl.json

@@ -21,9 +21,6 @@
           },
           "id_type": {
             "S": "${__instrument_run_partition_name__}"
-          },
-          "library_set": {
-            "SS": []
           }
         }
       },

lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/kwik/part_1/initialise-wgts-instrument-run-db/step_functions_templates/initialise_wgts_instrument_run_db_sfn_template.asl.json

@@ -21,9 +21,6 @@
           },
           "id_type": {
             "S": "${__instrument_run_partition_name__}"
-          },
-          "library_set": {
-            "SS": []
           }
         }
       },