Stacky updates for generating umccrise events

config/constants.ts

@@ -403,8 +403,8 @@ export const mockInputMakerTableName = 'stacky-input-maker-table';
 export const mockCttsov2InputGlueTableName = 'stacky-cttsov2-workflow-glue-table';
 export const mockWgtsQcGlueTableName = 'stacky-wgts-qc-glue-table';
 export const mockTnGlueTableName = 'stacky-tn-glue-table';
-
 export const mockWtsGlueTableName = 'stacky-wts-glue-table';
+export const mockUmccriseGlueTableName = 'stacky-umccrise-glue-table';
 
 export const mockWorkflowManagerTableName = 'stacky-workflow-manager-table';
 

config/stacks/stackyMcStackFace.ts

@@ -14,6 +14,7 @@ import {
   AppStage,
   mockTnGlueTableName,
   mockWtsGlueTableName,
+  mockUmccriseGlueTableName,
 } from '../constants';
 import { GlueStackConfig } from '../../lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs';
 import { StackyStatefulTablesConfig } from '../../lib/workload/stateful/stacks/stacky-mcstackface-dynamodb';
@@ -36,6 +37,7 @@ export const getGlueStackProps = (stage: AppStage): GlueStackConfig => {
     wgtsQcGlueTableName: mockWgtsQcGlueTableName,
     tnGlueTableName: mockTnGlueTableName,
     wtsGlueTableName: mockWtsGlueTableName,
+    umccriseGlueTableName: mockUmccriseGlueTableName,
     /* Secrets */
     icav2AccessTokenSecretName: icav2AccessTokenSecretName[stage],
   };
@@ -50,5 +52,6 @@ export const getStatefulGlueStackProps = (): StackyStatefulTablesConfig => {
     dynamodbWgtsQcGlueTableName: mockWgtsQcGlueTableName,
     dynamodbTnGlueTableName: mockTnGlueTableName,
     dynamodbWtsGlueTableName: mockWtsGlueTableName,
+    dynamodbUmccriseGlueTableName: mockUmccriseGlueTableName,
   };
 };

lib/workload/stateful/stacks/stacky-mcstackface-dynamodb/index.ts

@@ -12,6 +12,7 @@ export interface StackyStatefulTablesConfig {
   dynamodbWgtsQcGlueTableName: string;
   dynamodbTnGlueTableName: string;
   dynamodbWtsGlueTableName: string;
+  dynamodbUmccriseGlueTableName: string;
   removalPolicy?: RemovalPolicy;
 }
 
@@ -25,6 +26,7 @@ export class StackyStatefulTablesStack extends Stack {
   public readonly wgtsQcGlueTable: dynamodb.ITableV2;
   public readonly tnGlueTable: dynamodb.ITableV2;
   public readonly wtsGlueTable: dynamodb.ITableV2;
+  public readonly umccriseGlueTable: dynamodb.ITableV2;
   constructor(scope: Construct, id: string, props: StackProps & StackyStatefulTablesStackProps) {
     super(scope, id, props);
 
@@ -95,5 +97,13 @@ export class StackyStatefulTablesStack extends Stack {
       tableName: props.dynamodbWtsGlueTableName,
       removalPolicy: props.removalPolicy,
     }).tableObj;
+
+    /*
+    Initialise dynamodb table for the umccrise glue service
+    */
+    this.umccriseGlueTable = new DynamodbPartitionedPipelineConstruct(this, 'umccriseGlueTable', {
+      tableName: props.dynamodbUmccriseGlueTableName,
+      removalPolicy: props.removalPolicy,
+    }).tableObj;
   }
 }

lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/index.ts

@@ -11,6 +11,7 @@ import { Cttsov2GlueHandlerConstruct } from './jb-weld';
 import { WgtsQcGlueHandlerConstruct } from './kwik';
 import { TnGlueHandlerConstruct } from './loctite';
 import { WtsGlueHandlerConstruct } from './mod-podge';
+import { UmccriseGlueHandlerConstruct } from './pva';
 
 /*
 Provide the glue to get from the bclconvertmanager success event
@@ -28,6 +29,7 @@ export interface GlueConstructProps {
   wgtsQcGlueTableObj: dynamodb.ITableV2;
   tnGlueTableObj: dynamodb.ITableV2;
   wtsGlueTableObj: dynamodb.ITableV2;
+  umccriseGlueTableObj: dynamodb.ITableV2;
   /* SSM Parameters */
   icav2ProjectIdSsmParameterObj: ssm.IStringParameter;
   bsshOutputFastqCopyOutputUriSsmParameterObj: ssm.IStringParameter;
@@ -43,8 +45,8 @@ export class GlueConstruct extends Construct {
     super(scope, id);
 
     /*
-        Part A: Send 'showered' events if a new samplesheet arrives or new fastq list rows arrive
-        */
+    Part A: Send 'showered' events if a new samplesheet arrives or new fastq list rows arrive
+    */
     const clag = new showerGlueHandlerConstruct(this, 'clag', {
       /* Event Bus */
       eventBusObj: props.eventBusObj,
@@ -67,8 +69,8 @@ export class GlueConstruct extends Construct {
     });
 
     /*
-        Part C: Connect the bclconvert interop qc
-        */
+    Part C: Connect the bclconvert interop qc
+    */
     const gorilla = new BsshFastqCopyToBclconvertInteropQcConstruct(this, 'gorilla', {
       /* Event Objects */
       eventBusObj: props.eventBusObj,
@@ -101,8 +103,8 @@ export class GlueConstruct extends Construct {
     });
 
     /*
-        Part E: Plumber-up the WGTS QC Execution Service to the shower services
-        */
+    Part E: Plumber-up the WGTS QC Execution Service to the shower services
+    */
     const kwik = new WgtsQcGlueHandlerConstruct(this, 'kwik', {
       /* Event Bus */
       eventBusObj: props.eventBusObj,
@@ -153,6 +155,24 @@ export class GlueConstruct extends Construct {
       /* Secrets */
       icav2AccessTokenSecretObj: props.icav2AccessTokenSecretObj,
     });
+
+    /*
+    Part H: Plumber-up the UMCCRise Execution Service to the shower services
+    */
+    const pva = new UmccriseGlueHandlerConstruct(this, 'pva', {
+      /* Event Bus */
+      eventBusObj: props.eventBusObj,
+      /* Tables */
+      inputMakerTableObj: props.inputMakerTableObj,
+      umccriseGlueTableObj: props.umccriseGlueTableObj,
+      /* SSM Parameters */
+      icav2ProjectIdSsmParameterObj: props.icav2ProjectIdSsmParameterObj,
+      analysisOutputUriSsmParameterObj: props.analysisOutputUriSsmParameterObj,
+      analysisLogsUriSsmParameterObj: props.analysisLogsUriSsmParameterObj,
+      analysisCacheUriSsmParameterObj: props.analysisCacheUriSsmParameterObj,
+      /* Secrets */
+      icav2AccessTokenSecretObj: props.icav2AccessTokenSecretObj,
+    });
   }
 }
 
@@ -167,6 +187,7 @@ export interface GlueStackConfig {
   wgtsQcGlueTableName: string;
   tnGlueTableName: string;
   wtsGlueTableName: string;
+  umccriseGlueTableName: string;
   /* SSM Parameters */
   icav2ProjectIdSsmParameterName: string;
   bsshOutputFastqCopyUriSsmParameterName: string;
@@ -230,6 +251,11 @@ export class GlueStack extends cdk.Stack {
       'wtsGlueTableObj',
       props.wtsGlueTableName
     );
+    const umccriseGlueTableObj = dynamodb.Table.fromTableName(
+      this,
+      'umccriseGlueTableObj',
+      props.umccriseGlueTableName
+    );
 
     /*
         Get the SSM Parameters
@@ -285,6 +311,7 @@ export class GlueStack extends cdk.Stack {
       cttsov2GlueTableObj: cttsov2GlueTableObj,
       tnGlueTableObj: tnGlueTableObj,
       wtsGlueTableObj: wtsGlueTableObj,
+      umccriseGlueTableObj: umccriseGlueTableObj,
       /* SSM Parameters */
       icav2ProjectIdSsmParameterObj: icav2ProjectIdSsmParameterObj,
       bsshOutputFastqCopyOutputUriSsmParameterObj: bsshOutputFastqCopyUriSsmParameterObj,

lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/loctite/part_5/library-qc-complete-db-to-tn-draft/lambdas/generate_draft_event_payload_py/generate_draft_event_payload.py

@@ -29,6 +29,7 @@ def handler(event, context) -> Dict:
     :param event: event object
     :return: draft event payload
     """
+    subject_id = event['subject_id']
 
     tumor_library_id = event['tumor_library_id']
     normal_library_id = event['normal_library_id']
@@ -52,8 +53,9 @@ def handler(event, context) -> Dict:
             "dragenReferenceVersion": DEFAULT_DRAGEN_REFERENCE_VERSION
         },
         "event_tags": {
+            "subjectId": subject_id,
             "tumorLibraryId": tumor_library_id,
-            "normalLibrary_id": normal_library_id,
+            "normalLibraryId": normal_library_id,
             "tumorFastqListRowIds": tumor_fastq_list_row_ids,
             "normalFastqListRowIds": fastq_list_row_ids
         }

lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/loctite/part_5/library-qc-complete-db-to-tn-draft/step_functions_templates/add_library_qc_complete_to_tn_draft_sfn_template.asl.json

@@ -340,6 +340,7 @@
       "Parameters": {
         "FunctionName": "${__generate_draft_event_payload_lambda_function_arn__}",
         "Payload": {
+          "subject_id.$": "$.get_library_item_step.Item.subject_id.S",
           "tumor_library_id.$": "$.get_tn_pair_step.tumor_library.id",
           "normal_library_id.$": "$.get_tn_pair_step.normal_library.id",
           "tumor_fastq_list_rows.$": "$.get_parameters_step.tumor_fastq_list_rows",

lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/mod-podge/part_4/library-qc-complete-to-wts-draft/lambdas/generate_draft_event_payload_py/generate_draft_event_payload.py

@@ -1,12 +1,5 @@
 #!/usr/bin/env python3
 
-
-# Set the fastq list rows
-
-# Set the output file prefix
-
-#!/usr/bin/env python3
-
 """
 Generate draft event payload for the event
 

lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/mod-podge/part_4/library-qc-complete-to-wts-draft/step_functions_templates/add_library_qc_complete_to_wts_draft_sfn_template.asl.json

@@ -136,7 +136,8 @@
       "ResultPath": "$.generate_draft_event_payload_data_step",
       "Next": "Push WTS Draft Event",
       "ResultSelector": {
-        "input_event_data.$": "$.Payload.input_event_data"
+        "input_event_data.$": "$.Payload.input_event_data",
+        "event_tags.$": "$.Payload.event_tags"
       }
     },
     "Push WTS Draft Event": {

lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/pva/index.ts

@@ -0,0 +1,148 @@
+import { Construct } from 'constructs';
+import * as events from 'aws-cdk-lib/aws-events';
+import * as dynamodb from 'aws-cdk-lib/aws-dynamodb';
+import * as ssm from 'aws-cdk-lib/aws-ssm';
+import * as secretsManager from 'aws-cdk-lib/aws-secretsmanager';
+import { UmccriseInitialiseSubjectDbRowConstruct } from './part_1/initialise-umccrise-subject-dbs';
+import { UmccriseInitialiseLibraryAndFastqListRowConstruct } from './part_2/initialise-umccrise-library-dbs';
+import { UmccrisePopulateFastqListRowConstruct } from './part_3/update-fastq-list-rows-dbs';
+import { TnCompleteToUmccriseDraftConstruct } from './part_4/tn-complete-to-umccrise-draft';
+import { UmccriseInputMakerConstruct } from './part_5/umccrise-draft-to-ready';
+
+/*
+Provide the glue to get from the bssh fastq copy manager to submitting wgts qc analyses
+*/
+
+export interface umccriseGlueHandlerConstructProps {
+  /* General */
+  eventBusObj: events.IEventBus;
+  /* Tables */
+  umccriseGlueTableObj: dynamodb.ITableV2;
+  inputMakerTableObj: dynamodb.ITableV2;
+  /* SSM Parameters */
+  analysisOutputUriSsmParameterObj: ssm.IStringParameter;
+  analysisLogsUriSsmParameterObj: ssm.IStringParameter;
+  analysisCacheUriSsmParameterObj: ssm.IStringParameter;
+  icav2ProjectIdSsmParameterObj: ssm.IStringParameter;
+  /* Secrets */
+  icav2AccessTokenSecretObj: secretsManager.ISecret;
+}
+
+export class UmccriseGlueHandlerConstruct extends Construct {
+  constructor(scope: Construct, id: string, props: umccriseGlueHandlerConstructProps) {
+    super(scope, id);
+
+    /*
+    Part 1
+
+    Input Event Source: `orcabus.instrumentrunmanager`
+    Input Event DetailType: `SamplesheetMetadataUnion`
+    Input Event status: `SubjectInSamplesheet`
+
+    * Initialise umccrise instrument db construct
+    */
+    const umccrise_initialise_subject = new UmccriseInitialiseSubjectDbRowConstruct(
+      this,
+      'umccrise_initialise_subject',
+      {
+        eventBusObj: props.eventBusObj,
+        tableObj: props.umccriseGlueTableObj,
+      }
+    );
+
+    /*
+    Part 2
+
+    Input Event Source: `orcabus.instrumentrunmanager`
+    Input Event DetailType: `SamplesheetMetadataUnion`
+    Input Event status: `LibraryInSamplesheet`
+
+    * Initialise umccrise instrument db construct
+    */
+    const umccrise_initialise_library_and_fastq_list_row =
+      new UmccriseInitialiseLibraryAndFastqListRowConstruct(
+        this,
+        'umccrise_initialise_library_and_fastq_list_row',
+        {
+          eventBusObj: props.eventBusObj,
+          tableObj: props.umccriseGlueTableObj,
+        }
+      );
+
+    /*
+    Part 3
+
+    Input Event Source: `orcabus.instrumentrunmanager`
+    Input Event DetailType: `FastqListRowStateChange`
+    Input Event status: `newFastqListRow`
+
+    * Populate the fastq list row attributes for the rgid for this workflow
+    */
+
+    const umccrise_populate_fastq_list_row = new UmccrisePopulateFastqListRowConstruct(
+      this,
+      'umccrise_populate_fastq_list_row',
+      {
+        eventBusObj: props.eventBusObj,
+        tableObj: props.umccriseGlueTableObj,
+      }
+    );
+
+    /*
+    Part 4
+
+    Input Event Source: `orcabus.workflowmanager`
+    Input Event DetailType: `WorkflowRunStateChange`
+    Input Event status: `succeeded`
+
+    Output Event source: `orcabus.umccriseinputeventglue`
+    Output Event DetailType: `WorkflowDraftRunStateChange`
+    Output Event status: `draft`
+
+    * Populate the fastq list row attributes for the rgid for this workflow
+    */
+
+    const tn_to_umccrise_draft = new TnCompleteToUmccriseDraftConstruct(
+      this,
+      'tn_to_umccrise_draft',
+      {
+        eventBusObj: props.eventBusObj,
+        tableObj: props.umccriseGlueTableObj,
+        workflowsTableObj: props.inputMakerTableObj,
+      }
+    );
+
+    /*
+    Part 5
+
+    Input Event source: `orcabus.umccriseinputeventglue`
+    Input Event DetailType: `WorkflowDraftRunStateChange`
+    Input Event status: `draft`
+
+    Output Event source: `orcabus.umccriseinputeventglue`
+    Output Event DetailType: `WorkflowRunStateChange`
+    Output Event status: `ready`
+
+    * The umccriseInputMaker, subscribes to the umccrise input event glue (itself) and generates a ready event for the umccriseReadySfn
+      * However, in order to be 'ready' we need to use a few more variables such as
+        * icaLogsUri,
+        * analysisOutputUri
+        * cacheUri
+        * projectId
+        * userReference
+    */
+    const umccriseInputMaker = new UmccriseInputMakerConstruct(this, 'fastq_list_row_qc_complete', {
+      /* Event bus */
+      eventBusObj: props.eventBusObj,
+      /* Tables */
+      inputMakerTableObj: props.inputMakerTableObj,
+      /* SSM Param objects */
+      icav2ProjectIdSsmParameterObj: props.icav2ProjectIdSsmParameterObj,
+      outputUriSsmParameterObj: props.analysisOutputUriSsmParameterObj,
+      cacheUriSsmParameterObj: props.analysisCacheUriSsmParameterObj,
+      logsUriSsmParameterObj: props.analysisLogsUriSsmParameterObj,
+      /* Secrets Manager */
+      icav2AccessTokenSecretObj: props.icav2AccessTokenSecretObj,
+    });
+  }
+}