Large stacky changes to fix linked libraries

Added linked libraries for each of the workflow inputs / outputs

Fixes to umccrise inputs (and outputs)

Refactor fastq list row ids, now uses rgid as the fastq list row id (which has the instrument run id and library id)

Added project level data functions

Author: alexiswl

lib/workload/components/dynamodb-icav2-handle-event-change-sfn/step_functions_templates/icav2_get_workflow_status_and_raise_internal_event.asl.json

@@ -159,6 +159,7 @@
         "workflow_name": "${__workflow_type__}",
         "workflow_version": "${__workflow_version__}",
         "workflow_run_name.$": "$.Item.workflow_run_name.S",
+        "linked_libraries.$": "$.Item.linked_libraries.S",
         "payload_version": "${__service_version__}",
         "payload_inputs.$": "States.StringToJson($.Item.ready_event_data_inputs.S)",
         "payload_tags.$": "States.StringToJson($.Item.tags.S)",
@@ -216,6 +217,7 @@
               "workflowName.$": "$.get_event_data_step.workflow_name",
               "workflowVersion.$": "$.get_event_data_step.workflow_version",
               "workflowRunName.$": "$.get_event_data_step.workflow_run_name",
+              "linkedLibraries.$": "$.get_event_data_step.linked_libraries",
               "payload": {
                 "version": "${__service_version__}",
                 "data.$": "$.set_data_event_outputs"

lib/workload/components/dynamodb-icav2-ready-event-handler-sfn/index.ts

@@ -164,7 +164,7 @@ export class WfmWorkflowStateChangeIcav2ReadyEventHandlerConstruct extends Const
         source: [props.triggerLaunchSource],
         detailType: [props.detailType],
         detail: {
-          status: ['ready'],
+          status: ['READY'],
           workflowName: [{ 'equals-ignore-case': props.workflowName }],
         },
       },

lib/workload/components/dynamodb-icav2-ready-event-handler-sfn/step_functions_templates/icav2_launch_workflow_and_raise_internal_event.asl.json

@@ -76,6 +76,9 @@
                   "workflow_run_name": {
                     "S.$": "$.workflow_inputs.workflowRunName"
                   },
+                  "linked_libraries": {
+                    "S.$": "States.JsonToString($.workflow_inputs.linkedLibraries)"
+                  },
                   "workflow_version": {
                     "S.$": "$.workflow_inputs.workflowVersion"
                   },
@@ -502,6 +505,7 @@
         "workflowName": "${__workflow_type__}",
         "workflowVersion": "${__workflow_version__}",
         "workflowRunName.$": "$.Item.workflow_run_name.S",
+        "linkedLibraries.$": "States.StringToJson($.Item.linked_libraries.S)",
         "payload": {
           "version": "${__service_version__}",
           "data": {

lib/workload/components/event-workflowdraftrunstatechange-to-workflowrunstatechange-ready/step_functions_templates/workflowrunstatechange_draft_to_ready_step_function_template.asl.json

@@ -131,7 +131,7 @@
                 "UpdateExpression": "SET analysis_status = :analysis_status",
                 "ExpressionAttributeValues": {
                   ":analysis_status": {
-                    "S": "ready"
+                    "S": "READY"
                   }
                 }
               },
@@ -179,12 +179,12 @@
             "Detail": {
               "portalRunId.$": "$.input_event_detail.portalRunId",
               "timestamp.$": "$$.State.EnteredTime",
-              "status": "ready",
+              "status": "READY",
               "workflowName.$": "$.input_event_detail.workflowName",
               "workflowVersion.$": "$.input_event_detail.workflowVersion",
               "workflowRunName.$": "$.input_event_detail.workflowRunName",
+              "linkedLibraries.$": "$.input_event_detail.linkedLibraries",
               "payload": {
-                "refId": null,
                 "version": "${__payload_version__}",
                 "data": {
                   "inputs.$": "$.get_event_data_output_step.inputs",

lib/workload/components/python-lambda-b64gz-translator/index.ts

@@ -15,7 +15,7 @@ export class LambdaB64GzTranslatorConstruct extends Construct {
 
     // UUID 7 Generator lambda
     this.lambdaObj = new PythonFunction(this, 'b64_gzip_translator_obj', {
-      functionName: `${props.functionNamePrefix}-b64gz-translator`,
+      functionName: `${props.functionNamePrefix}-b64gz-t`,
       entry: path.join(__dirname, 'b64gz_translator_py'),
       runtime: lambda.Runtime.PYTHON_3_12,
       architecture: lambda.Architecture.ARM_64,

lib/workload/stateless/stacks/umccrise-pipeline-manager/lambdas/get_cwl_object_from_s3_inputs_py/get_cwl_object_from_s3_inputs.py lib/workload/components/python-lambda-get-cwl-object-from-s3-inputs-py/get_cwl_object_from_s3_inputs_py/get_cwl_object_from_s3_inputs.py

@@ -0,0 +1,23 @@
+import { Construct } from 'constructs';
+import * as lambda_python from '@aws-cdk/aws-lambda-python-alpha';
+import * as lambda from 'aws-cdk-lib/aws-lambda';
+import path from 'path';
+import { Duration } from 'aws-cdk-lib';
+
+export class PythonLambdaGetCwlObjectFromS3InputsConstruct extends Construct {
+  public readonly lambdaObj: lambda_python.PythonFunction;
+
+  constructor(scope: Construct, id: string) {
+    super(scope, id);
+
+    this.lambdaObj = new lambda_python.PythonFunction(this, 'get_cwl_object_from_s3_inputs_py', {
+      runtime: lambda.Runtime.PYTHON_3_12,
+      architecture: lambda.Architecture.ARM_64,
+      entry: path.join(__dirname, 'get_cwl_object_from_s3_inputs_py'),
+      index: 'get_cwl_object_from_s3_inputs.py',
+      handler: 'handler',
+      memorySize: 1024,
+      timeout: Duration.seconds(10),
+    });
+  }
+}