Setup to rearrange the outputs for the ora compression manager

lib/workload/stateless/stacks/ora-compression-manager/deploy/index.ts

@@ -227,7 +227,7 @@ export class OraCompressionIcav2PipelineManagerStack extends cdk.Stack {
       environment: {
         ICAV2_ACCESS_TOKEN_SECRET_ID: icav2AccessTokenSecretObj.secretName,
       },
-      timeout: Duration.seconds(60),
+      timeout: Duration.seconds(120),
       memorySize: 1024,
     });
     // Give the lambda function access to the secret
@@ -248,6 +248,8 @@ export class OraCompressionIcav2PipelineManagerStack extends cdk.Stack {
           )
         ),
         definitionSubstitutions: {
+          __event_bus_name__: eventBusObj.eventBusName,
+          __detail_type__: this.globals.outputCompressionDetailType,
           __merge_sizes_lambda_function_arn__: setMergeSizesLambdaObj.currentVersion.functionArn,
         },
       }

lib/workload/stateless/stacks/ora-compression-manager/lambdas/set_outputs_json_py/set_outputs_json.py

@@ -76,7 +76,7 @@ def handler(events, context):
 
     # Get analysis uri
     analysis_uri = events.get("analysis_output_uri")
-    instrument_run_id = events.get("instrument_run_id")
+    portal_run_id = events.get("portal_run_id")
 
     # Convert analysis uri to project folder object
     analysis_project_data_obj = convert_uri_to_project_data_obj(analysis_uri)
@@ -87,19 +87,19 @@ def handler(events, context):
         parent_folder_id=analysis_project_data_obj.data.id,
     )
 
-    # Get multiqc directory
+    # Get instrument run id
     try:
         instrument_run_id_project_data_obj: ProjectData = next(
             filter(
                 lambda project_data_iter: (
-                    project_data_iter.data.details.name == instrument_run_id and
+                    project_data_iter.data.details.name == portal_run_id and
                     DataType[project_data_iter.data.details.data_type] == DataType.FOLDER
                 ),
                 analysis_top_level_data_list
             )
         )
     except StopIteration:
-        raise ValueError(f"instrument run id directory '{instrument_run_id}' not found in '{analysis_uri}'")
+        raise ValueError(f"output directory '{portal_run_id}' not found in '{analysis_uri}'")
 
     return {
         "instrument_run_ora_output_uri": convert_project_data_obj_to_uri(instrument_run_id_project_data_obj, UriType.S3),

lib/workload/stateless/stacks/ora-compression-manager/step_functions_templates/fastq_list_row_compression_event.asl.json

@@ -5,7 +5,6 @@
     "Get fastq files from fastq list csv": {
       "Type": "Task",
       "Resource": "arn:aws:states:::lambda:invoke",
-      "OutputPath": "$.Payload",
       "Parameters": {
         "Payload": {
           "output_dir_uri.$": "$.payload.data.outputs.instrumentRunOraOutputUri"

lib/workload/stateless/stacks/ora-compression-manager/step_functions_templates/set_compression_inputs.asl.json

@@ -57,7 +57,7 @@
         "input_json": {
           "instrument_run_directory": {
             "class": "Directory",
-            "basename.$": "$.get_input_parameters_from_event.inputs.instrumentRunId",
+            "basename.$": "$.portal_run_id",
             "location.$": "$.get_input_parameters_from_event.inputs.instrumentRunDirectoryUri"
           },
           "ora_reference": {

lib/workload/stateless/stacks/ora-compression-manager/step_functions_templates/set_compression_outputs.asl.json

@@ -25,7 +25,7 @@
       "Parameters": {
         "FunctionName": "${__set_outputs_json_lambda_function_arn__}",
         "Payload": {
-          "instrument_run_id.$": "$.get_db_attributes_step.ready_event_data_inputs.instrumentRunId",
+          "portal_run_id.$": "$.portal_run_id",
           "analysis_output_uri.$": "$.get_db_attributes_step.analysis_output_uri"
         }
       },