From d0340338080e90ce7d723862b05e7194207e8044 Mon Sep 17 00:00:00 2001 From: Alexis Lucattini Date: Sun, 1 Sep 2024 15:43:15 +1000 Subject: [PATCH] Various stacky fixes for umccrise + rnasum * Use portal_run_id over ref id for database id (since refId isn't always propagated) * Use idempotency key (set to portal run id) to prevent duplicate analyses * Various fixes for linkedLibraries * Various fixes for using new fastqListRow object syntax (and using rgid as the key) * Add subjectId to wts tags (required by umccrise) * Fixes to umccrise glue after testing * Fixes to rnasum glue after testing * Use new output_prefix syntax for dragen inputs --- config/constants.ts | 10 +- config/stacks/umccrisePipelineManager.ts | 4 +- ...w_status_and_raise_internal_event.asl.json | 26 +- .../icav2_launch_pipeline_lambda.py | 5 +- .../requirements.txt | 2 +- ...workflow_and_raise_internal_event.asl.json | 93 ++---- .../dynamodb-nonpartitioned-table/index.ts | 2 +- .../index.ts | 2 + .../requirements.txt | 2 +- .../requirements.txt | 2 +- .../requirements.txt | 2 +- .../index.ts | 19 +- .../set_outputs_json_py/requirements.txt | 2 +- ...convert_interop_qc_cwl_inputs_sfn.asl.json | 10 +- ...onvert_interop_qc_cwl_outputs_sfn.asl.json | 10 +- .../bclconvert-manager/deps/requirements.txt | 2 +- .../bs-runs-upload-manager/layers/poetry.lock | 294 +++++++++--------- .../layers/pyproject.toml | 2 +- .../layers/poetry.lock | 286 ++++++++--------- .../layers/pyproject.toml | 2 +- .../delete_cache_uri_py/requirements.txt | 2 +- .../find_all_vcf_files_py/requirements.txt | 2 +- .../requirements.txt | 2 +- .../set_outputs_json_py/requirements.txt | 2 +- .../requirements.txt | 2 +- .../set_cttso_v2_nf_inputs.asl.json | 18 +- .../set_cttso_v2_nf_outputs.asl.json | 10 +- .../rnasum-pipeline-manager/deploy/index.ts | 5 +- .../set_rnasum_cwl_inputs_sfn.asl.json | 10 +- .../set_rnasum_cwl_outputs_sfn.asl.json | 15 +- .../index.ts | 1 + .../index.ts | 1 + .../initialise-cttsov2-library-dbs/index.ts | 1 + .../part_5/cttsov2-draft-to-ready/index.ts | 1 + .../initialise-wgts-library-dbs/index.ts | 1 + ...ete_to_wgts_qc_draft_sfn_template.asl.json | 5 +- .../part_5/wgts-qc-draft-to-ready/index.ts | 1 + .../requirements.txt | 2 +- .../part_2/initialise-tn-library-dbs/index.ts | 1 + ...d_fastq_list_rows_db_sfn_template.asl.json | 2 +- ...complete_to_tn_draft_sfn_template.asl.json | 10 +- .../loctite/part_6/tn-draft-to-ready/index.ts | 1 + .../initialise-wts-library-dbs/index.ts | 1 + ...alise_wts_library_db_sfn_template.asl.json | 2 +- .../generate_draft_event_payload.py | 2 + ...omplete_to_wts_draft_sfn_template.asl.json | 9 +- .../part_5/wts-draft-to-ready/index.ts | 1 + .../initialise-umccrise-library-dbs/index.ts | 1 + ..._umccrise_library_db_sfn_template.asl.json | 2 +- .../tn-complete-to-umccrise-draft/index.ts | 6 +- ...te_to_umccrise_draft_sfn_template.asl.json | 6 +- .../part_5/umccrise-draft-to-ready/index.ts | 1 + ..._and_wts_complete_to_rnasum_draft.asl.json | 47 +-- .../part_3/rnasum-draft-to-ready/index.ts | 1 + .../set_outputs_json_py/requirements.txt | 2 +- .../set_outputs_json_py/set_outputs_json.py | 24 +- .../set_wts_cwl_inputs_sfn.asl.json | 11 +- .../set_wts_cwl_outputs_sfn.asl.json | 8 +- .../set_outputs_json_py/requirements.txt | 2 +- .../set_tn_cwl_inputs_sfn.asl.json | 14 +- .../set_tn_cwl_outputs_sfn.asl.json | 8 +- .../umccrise-pipeline-manager/deploy/index.ts | 5 +- .../lambdas/get_outputs_py/get_outputs.py | 6 +- .../set_umccrise_cwl_inputs_sfn.asl.json | 15 +- .../set_umccrise_cwl_outputs_sfn.asl.json | 9 +- .../set_outputs_json_py/requirements.txt | 2 +- ..._wgts_alignment_qc_cwl_inputs_sfn.asl.json | 11 +- ...wgts_alignment_qc_cwl_outputs_sfn.asl.json | 8 +- 68 files changed, 542 insertions(+), 534 deletions(-) diff --git a/config/constants.ts b/config/constants.ts index 36c71dc04..a8f22e87e 100644 --- a/config/constants.ts +++ b/config/constants.ts @@ -268,7 +268,7 @@ External resources required by the wgtsqc Stack */ // Deployed under dev/stg/prod -export const wgtsQcIcav2PipelineIdSSMParameterPath = '/icav2/umccr-prod/wgts_qc_4.2.4_pipeline_id'; // 413b3c60-a3f5-42eb-a9df-8a77768a8328 +export const wgtsQcIcav2PipelineIdSSMParameterPath = '/icav2/umccr-prod/wgts_qc_4.2.4_pipeline_id'; // 03689516-b7f8-4dca-bba9-8405b85fae45 export const wgtsQcIcav2PipelineWorkflowType = 'wgtsQc'; export const wgtsQcIcav2PipelineWorkflowTypeVersion = '4.2.4'; @@ -302,7 +302,7 @@ TN Stateless stack */ // Deployed under dev/stg/prod -export const tnIcav2PipelineIdSSMParameterPath = '/icav2/umccr-prod/tumor_normal_4.2.4_pipeline_id'; // fc82a668-4a60-4acf-a528-38f5ee3ffdf5 +export const tnIcav2PipelineIdSSMParameterPath = '/icav2/umccr-prod/tumor_normal_4.2.4_pipeline_id'; // 0f5575bc-6cf8-4a90-a80e-05088aae8ed7 export const tnIcav2PipelineWorkflowType = 'tumor_normal'; export const tnIcav2PipelineWorkflowTypeVersion = '4.2.4'; export const tnIcav2ServiceVersion = '2024.07.01'; @@ -378,7 +378,7 @@ WTS Stateless stack */ // Deployed under dev/stg/prod -export const wtsIcav2PipelineIdSSMParameterPath = '/icav2/umccr-prod/wts_4.2.4_pipeline_id'; // 66c89437-ec33-4138-8a92-9c018ee533af +export const wtsIcav2PipelineIdSSMParameterPath = '/icav2/umccr-prod/wts_4.2.4_pipeline_id'; // 1e53ae07-08a6-458b-9fa3-9cf7430409a0 export const wtsIcav2PipelineWorkflowType = 'wts'; export const wtsIcav2PipelineWorkflowTypeVersion = '4.2.4'; export const wtsIcav2ServiceVersion = '2024.07.01'; @@ -469,9 +469,9 @@ UMCCRise Stateless stack */ // Deployed in dev/stg/prod -export const rnasumIcav2PipelineIdSSMParameterPath = '/icav2/umccr-prod/rnasum_1.0.0_pipeline_id'; // bd6e5690-3ccf-4ac4-997d-59462f852f65 +export const rnasumIcav2PipelineIdSSMParameterPath = '/icav2/umccr-prod/rnasum_1.1.0_pipeline_id'; // 69362d8e-8f6f-4d87-84b5-a8c6205b7032 export const rnasumIcav2PipelineWorkflowType = 'rnasum'; -export const rnasumIcav2PipelineWorkflowTypeVersion = '2.3.1'; +export const rnasumIcav2PipelineWorkflowTypeVersion = '1.1.0'; export const rnasumIcav2ServiceVersion = '2024.07.01'; export const rnasumIcav2ReadyEventSource = 'orcabus.workflowmanager'; export const rnasumIcav2EventSource = 'orcabus.rnasum'; diff --git a/config/stacks/umccrisePipelineManager.ts b/config/stacks/umccrisePipelineManager.ts index b253645b8..9dffba917 100644 --- a/config/stacks/umccrisePipelineManager.ts +++ b/config/stacks/umccrisePipelineManager.ts @@ -3,7 +3,6 @@ import { eventBusName, icaEventPipeStackName, icav2AccessTokenSecretName, - dragenIcav2ReferenceUriMappingSSMParameterPath, umccriseIcav2PipelineIdSSMParameterPath, umccriseIcav2PipelineManagerDynamodbTableName, umccriseIcav2PipelineWorkflowType, @@ -16,6 +15,7 @@ import { umccriseDefaultGenomeVersion, umccriseDynamoDbTableSSMArn, umccriseDynamoDbTableSSMName, + icav2UmccriseGenomesReferenceUriMappingSSMParameterPath, } from '../constants'; import { UmccriseIcav2PipelineManagerConfig } from '../../lib/workload/stateless/stacks/umccrise-pipeline-manager/deploy'; import { UmccriseIcav2PipelineTableConfig } from '../../lib/workload/stateful/stacks/umccrise-pipeline-dynamo-db/deploy/stack'; @@ -53,6 +53,6 @@ export const getUmccriseIcav2PipelineManagerStackProps = ( stateMachinePrefix: umccriseStateMachinePrefix, /* SSM Workflow Parameters */ defaultReferenceVersion: umccriseDefaultGenomeVersion, - referenceUriSsmPath: dragenIcav2ReferenceUriMappingSSMParameterPath, + referenceUriSsmPath: icav2UmccriseGenomesReferenceUriMappingSSMParameterPath, }; }; diff --git a/lib/workload/components/dynamodb-icav2-handle-event-change-sfn/step_functions_templates/icav2_get_workflow_status_and_raise_internal_event.asl.json b/lib/workload/components/dynamodb-icav2-handle-event-change-sfn/step_functions_templates/icav2_get_workflow_status_and_raise_internal_event.asl.json index 0705efbf9..ce23b33c7 100644 --- a/lib/workload/components/dynamodb-icav2-handle-event-change-sfn/step_functions_templates/icav2_get_workflow_status_and_raise_internal_event.asl.json +++ b/lib/workload/components/dynamodb-icav2-handle-event-change-sfn/step_functions_templates/icav2_get_workflow_status_and_raise_internal_event.asl.json @@ -50,8 +50,8 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.get_analysis_id_in_db_step.db_response.Item.db_uuid.S", - "id_type": "db_uuid" + "id.$": "$.get_analysis_id_in_db_step.db_response.Item.portal_run_id.S", + "id_type": "portal_run_id" }, "UpdateExpression": "SET analysis_status = :analysis_status", "ExpressionAttributeValues": { @@ -74,7 +74,7 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.get_analysis_id_in_db_step.db_response.Item.db_uuid.S", + "id.$": "$.get_analysis_id_in_db_step.db_response.Item.portal_run_id.S", "id_type": "event_logger" }, "UpdateExpression": "SET analysis_status_list = list_append(analysis_status_list, :status), event_timestamp_list = list_append(event_timestamp_list, :event_timestamp)", @@ -120,7 +120,7 @@ "Parameters": { "StateMachineArn": "${__sfn_get_outputs_json__}", "Input": { - "db_uuid.$": "$.get_analysis_id_in_db_step.db_response.Item.db_uuid.S" + "portal_run_id.$": "$.get_analysis_id_in_db_step.db_response.Item.portal_run_id.S" } }, "Next": "Pass", @@ -140,26 +140,26 @@ "Wait (database - updates)": { "Type": "Wait", "Seconds": 1, - "Next": "Get UUID Row For Payload" + "Next": "Get Portal Run ID For Payload" }, - "Get UUID Row For Payload": { + "Get Portal Run ID For Payload": { "Type": "Task", "Resource": "arn:aws:states:::dynamodb:getItem", "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.get_analysis_id_in_db_step.db_response.Item.db_uuid.S", - "id_type": "db_uuid" + "id.$": "$.get_analysis_id_in_db_step.db_response.Item.portal_run_id.S", + "id_type": "portal_run_id" } }, "ResultSelector": { - "portal_run_id.$": "$.Item.portal_run_id.S", + "portal_run_id.$": "$.Item.id.S", "timestamp.$": "$$.State.EnteredTime", "status.$": "$.Item.analysis_status.S", "workflow_name": "${__workflow_type__}", "workflow_version": "${__workflow_version__}", "workflow_run_name.$": "$.Item.workflow_run_name.S", - "linked_libraries.$": "$.Item.linked_libraries.S", + "linked_libraries.$": "States.StringToJson($.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)", @@ -196,8 +196,9 @@ "Next": "Push Event to Orcabus", "Parameters": { "inputs.$": "$.get_event_data_step.payload_inputs", + "outputs.$": "$.get_event_data_step.payload_outputs", "engineParameters.$": "$.get_event_data_step.payload_engine_parameters", - "outputs.$": "$.get_event_data_step.payload_outputs" + "tags.$": "$.get_event_data_step.payload_tags" }, "ResultPath": "$.set_data_event_outputs" }, @@ -221,8 +222,7 @@ "payload": { "version": "${__service_version__}", "data.$": "$.set_data_event_outputs" - }, - "tags.$": "$.get_event_data_step.payload_tags" + } } } ] diff --git a/lib/workload/components/dynamodb-icav2-ready-event-handler-sfn/icav2_launch_pipeline_lambda_py/icav2_launch_pipeline_lambda.py b/lib/workload/components/dynamodb-icav2-ready-event-handler-sfn/icav2_launch_pipeline_lambda_py/icav2_launch_pipeline_lambda.py index 4728d515a..877b5eced 100644 --- a/lib/workload/components/dynamodb-icav2-ready-event-handler-sfn/icav2_launch_pipeline_lambda_py/icav2_launch_pipeline_lambda.py +++ b/lib/workload/components/dynamodb-icav2-ready-event-handler-sfn/icav2_launch_pipeline_lambda_py/icav2_launch_pipeline_lambda.py @@ -199,6 +199,7 @@ def handler(event, context): project_id = event.get("project_id", None) user_reference = event.get("user_reference", None) input_json = json.loads(event.get("input_json", {})) + idempotency_key = event.get("idempotency_key", None) # Get the output uris analysis_output_uri = event.get("analysis_output_uri", None) @@ -303,7 +304,9 @@ def handler(event, context): # Generate the inputs and analysis object # Call the object to launch it logger.info("Launching the ICAv2 Analysis") - analysis_launch_obj: Analysis = analysis_obj() + analysis_launch_obj: Analysis = analysis_obj( + idempotency_key=idempotency_key + ) # Save the analysis logger.info("Saving the analysis") diff --git a/lib/workload/components/dynamodb-icav2-ready-event-handler-sfn/icav2_launch_pipeline_lambda_py/requirements.txt b/lib/workload/components/dynamodb-icav2-ready-event-handler-sfn/icav2_launch_pipeline_lambda_py/requirements.txt index 8e96e580b..f3272963d 100644 --- a/lib/workload/components/dynamodb-icav2-ready-event-handler-sfn/icav2_launch_pipeline_lambda_py/requirements.txt +++ b/lib/workload/components/dynamodb-icav2-ready-event-handler-sfn/icav2_launch_pipeline_lambda_py/requirements.txt @@ -1,2 +1,2 @@ -wrapica>=2.27.1.post20240806222234,<2.28.0 +wrapica>=2.27.1.post20240830140737,<2.28.0 boto3>=1.28 diff --git a/lib/workload/components/dynamodb-icav2-ready-event-handler-sfn/step_functions_templates/icav2_launch_workflow_and_raise_internal_event.asl.json b/lib/workload/components/dynamodb-icav2-ready-event-handler-sfn/step_functions_templates/icav2_launch_workflow_and_raise_internal_event.asl.json index 0feffb31b..b523599dc 100644 --- a/lib/workload/components/dynamodb-icav2-ready-event-handler-sfn/step_functions_templates/icav2_launch_workflow_and_raise_internal_event.asl.json +++ b/lib/workload/components/dynamodb-icav2-ready-event-handler-sfn/step_functions_templates/icav2_launch_workflow_and_raise_internal_event.asl.json @@ -41,7 +41,7 @@ "Next": "Add Technical Tags" } ], - "Default": "Get PortalRunId DataBase Entry" + "Default": "Get Push Event Info From DB" }, "Add Technical Tags": { "Type": "Pass", @@ -60,19 +60,16 @@ "Next": "Wait 1 Second (pre-input-generation)", "Branches": [ { - "StartAt": "Initialise DB Item", + "StartAt": "Initialise Portal Run Id Item", "States": { - "Initialise DB Item": { + "Initialise Portal Run Id Item": { "Type": "Task", "Resource": "arn:aws:states:::dynamodb:putItem", "Parameters": { "TableName": "${__table_name__}", "Item": { - "id.$": "$.workflow_inputs.payload.refId", - "id_type": "db_uuid", - "portal_run_id": { - "S.$": "$.workflow_inputs.portalRunId" - }, + "id.$": "$.workflow_inputs.portalRunId", + "id_type": "portal_run_id", "workflow_run_name": { "S.$": "$.workflow_inputs.workflowRunName" }, @@ -145,8 +142,8 @@ "Item": { "id.$": "$.workflow_inputs.workflowRunName", "id_type": "workflow_run_name", - "db_uuid": { - "S.$": "$.workflow_inputs.payload.refId" + "portal_run_id": { + "S.$": "$.workflow_inputs.portalRunId" } } }, @@ -155,27 +152,6 @@ } } }, - { - "StartAt": "Put Portal Partition Key Item", - "States": { - "Put Portal Partition Key Item": { - "Type": "Task", - "Resource": "arn:aws:states:::dynamodb:putItem", - "Parameters": { - "TableName": "${__table_name__}", - "Item": { - "id.$": "$.workflow_inputs.portalRunId", - "id_type": "portal_run_id", - "db_uuid": { - "S.$": "$.workflow_inputs.payload.refId" - } - } - }, - "ResultPath": "$.dynamo_db_put_item_step", - "End": true - } - } - }, { "StartAt": "Add Event Logger Item", "States": { @@ -185,10 +161,10 @@ "Parameters": { "TableName": "${__table_name__}", "Item": { - "id.$": "$.workflow_inputs.payload.refId", + "id.$": "$.workflow_inputs.portalRunId", "id_type": "event_logger", - "db_uuid": { - "S.$": "$.workflow_inputs.payload.refId" + "portal_run_id": { + "S.$": "$.workflow_inputs.portalRunId" }, "event_timestamp_list": { "L": [ @@ -231,7 +207,7 @@ "Parameters": { "StateMachineArn": "${__set_input_json_state_machine_arn__}", "Input": { - "db_uuid.$": "$.workflow_inputs.payload.refId" + "portal_run_id.$": "$.workflow_inputs.portalRunId" } }, "ResultPath": null, @@ -279,8 +255,8 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.workflow_inputs.payload.refId", - "id_type": "db_uuid" + "id.$": "$.workflow_inputs.portalRunId", + "id_type": "portal_run_id" }, "UpdateExpression": "SET analysis_pipeline_id = :analysis_pipeline_id, engine_parameters = :engine_parameters", "ExpressionAttributeValues": { @@ -319,8 +295,8 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.workflow_inputs.payload.refId", - "id_type": "db_uuid" + "id.$": "$.workflow_inputs.portalRunId", + "id_type": "portal_run_id" } }, "ResultSelector": { @@ -358,7 +334,8 @@ "analysis_output_uri.$": "$.get_parameters_from_payload.analysis_output_uri", "ica_logs_uri.$": "$.get_parameters_from_payload.ica_logs_uri", "technical_tags.$": "$.add_technical_tags_step.technical_tags", - "user_tags.$": "$.get_parameters_from_payload.user_tags" + "user_tags.$": "$.get_parameters_from_payload.user_tags", + "idempotency_key.$": "$.workflow_inputs.portalRunId" }, "FunctionName": "${__launch_icav2_pipeline_lambda_function_name__}" }, @@ -389,18 +366,16 @@ "Type": "Parallel", "Branches": [ { - "StartAt": "Update Db Uuid Item", + "StartAt": "Update Portal Run ID Item", "States": { - "Update Db Uuid Item": { + "Update Portal Run ID Item": { "Type": "Task", "Resource": "arn:aws:states:::dynamodb:updateItem", "Parameters": { "TableName": "${__table_name__}", "Key": { - "id": { - "S.$": "$.workflow_inputs.payload.refId" - }, - "id_type": "db_uuid" + "id.$": "$.workflow_inputs.portalRunId", + "id_type": "portal_run_id" }, "UpdateExpression": "SET analysis_id = :analysis_id, analysis_status = :analysis_status, analysis_return_payload = :analysis_return_payload, analysis_launch_payload = :analysis_launch_payload, engine_parameters = :engine_parameters", "ExpressionAttributeValues": { @@ -437,8 +412,8 @@ "Item": { "id.$": "$.launch_nextflow_object_step.analysis_id", "id_type": "icav2_analysis_id", - "db_uuid": { - "S.$": "$.workflow_inputs.payload.refId" + "portal_run_id": { + "S.$": "$.workflow_inputs.portalRunId" } } }, @@ -469,9 +444,9 @@ "Type": "Wait", "Seconds": 1, "Comment": "Wait for databases to sync before continuing", - "Next": "Get PortalRunId DataBase Entry" + "Next": "Get Push Event Info From DB" }, - "Get PortalRunId DataBase Entry": { + "Get Push Event Info From DB": { "Type": "Task", "Resource": "arn:aws:states:::dynamodb:getItem", "Parameters": { @@ -481,25 +456,9 @@ "id_type": "portal_run_id" } }, - "Next": "Get Push Event Info From DB", - "ResultPath": "$.database_event_data", - "ResultSelector": { - "db_uuid.$": "$.Item.db_uuid.S" - } - }, - "Get Push Event Info From DB": { - "Type": "Task", - "Resource": "arn:aws:states:::dynamodb:getItem", - "Parameters": { - "TableName": "${__table_name__}", - "Key": { - "id.$": "$.database_event_data.db_uuid", - "id_type": "db_uuid" - } - }, "Next": "Push event to orcabus", "ResultSelector": { - "portalRunId.$": "$.Item.portal_run_id.S", + "portalRunId.$": "$.Item.id.S", "timestamp.$": "$$.State.EnteredTime", "status.$": "$.Item.analysis_status.S", "workflowName": "${__workflow_type__}", diff --git a/lib/workload/components/dynamodb-nonpartitioned-table/index.ts b/lib/workload/components/dynamodb-nonpartitioned-table/index.ts index c0258f74c..38560f07b 100644 --- a/lib/workload/components/dynamodb-nonpartitioned-table/index.ts +++ b/lib/workload/components/dynamodb-nonpartitioned-table/index.ts @@ -15,7 +15,7 @@ export class DynamodbNonPartitionedPipelineConstruct extends Construct { super(scope, id); this.tableObj = new dynamodb.TableV2(this, 'dynamodb_partitioned_pipeline_table', { - /* Either a db_uuid or an icav2 analysis id or a portal run id */ + /* Either a portal run id or an icav2 analysis id */ partitionKey: { name: 'id', type: dynamodb.AttributeType.STRING, diff --git a/lib/workload/components/event-workflowdraftrunstatechange-to-workflowrunstatechange-ready/index.ts b/lib/workload/components/event-workflowdraftrunstatechange-to-workflowrunstatechange-ready/index.ts index 4c1dd8ca1..d14033b58 100644 --- a/lib/workload/components/event-workflowdraftrunstatechange-to-workflowrunstatechange-ready/index.ts +++ b/lib/workload/components/event-workflowdraftrunstatechange-to-workflowrunstatechange-ready/index.ts @@ -22,6 +22,7 @@ export interface WorkflowRunStateChangeInternalInputMakerProps { /* Object name prefixes */ stateMachinePrefix: string; lambdaPrefix: string; + rulePrefix: string; /* Table configs */ tableObj: dynamodb.ITableV2; tablePartitionName: string; @@ -204,6 +205,7 @@ export class WorkflowDraftRunStateChangeToWorkflowRunStateChangeReadyConstruct e Part 4 - Set up a rule to trigger the state machine */ const rule = new events.Rule(this, 'workflowrunstatechangeparser_event_rule', { + ruleName: `${props.rulePrefix}-rule`, eventBus: props.eventBusObj, eventPattern: { source: [props.triggerSource], diff --git a/lib/workload/components/event-workflowdraftrunstatechange-to-workflowrunstatechange-ready/lambdas/fill_placeholders_in_event_payload_data_py/requirements.txt b/lib/workload/components/event-workflowdraftrunstatechange-to-workflowrunstatechange-ready/lambdas/fill_placeholders_in_event_payload_data_py/requirements.txt index 77ef47ad4..9afec8ad8 100644 --- a/lib/workload/components/event-workflowdraftrunstatechange-to-workflowrunstatechange-ready/lambdas/fill_placeholders_in_event_payload_data_py/requirements.txt +++ b/lib/workload/components/event-workflowdraftrunstatechange-to-workflowrunstatechange-ready/lambdas/fill_placeholders_in_event_payload_data_py/requirements.txt @@ -1,2 +1,2 @@ -wrapica>=2.27.1.post20240806222234 +wrapica>=2.27.1.post20240830140737 boto3>=1.34.0 \ No newline at end of file diff --git a/lib/workload/components/icav2-copy-files/check_or_launch_job_lambda_py/requirements.txt b/lib/workload/components/icav2-copy-files/check_or_launch_job_lambda_py/requirements.txt index ca362fea6..368c71346 100644 --- a/lib/workload/components/icav2-copy-files/check_or_launch_job_lambda_py/requirements.txt +++ b/lib/workload/components/icav2-copy-files/check_or_launch_job_lambda_py/requirements.txt @@ -1,2 +1,2 @@ -wrapica>=2.27.1.post20240806222234 +wrapica>=2.27.1.post20240830140737 boto3>=1.34 \ No newline at end of file diff --git a/lib/workload/components/python-lambda-get-cwl-object-from-s3-inputs-py/get_cwl_object_from_s3_inputs_py/requirements.txt b/lib/workload/components/python-lambda-get-cwl-object-from-s3-inputs-py/get_cwl_object_from_s3_inputs_py/requirements.txt index f2ac9700e..51fdef847 100644 --- a/lib/workload/components/python-lambda-get-cwl-object-from-s3-inputs-py/get_cwl_object_from_s3_inputs_py/requirements.txt +++ b/lib/workload/components/python-lambda-get-cwl-object-from-s3-inputs-py/get_cwl_object_from_s3_inputs_py/requirements.txt @@ -1 +1 @@ -wrapica == 2.27.1.post20240806222234 +wrapica == 2.27.1.post20240830140737 diff --git a/lib/workload/components/python-lambda-get-cwl-object-from-s3-inputs-py/index.ts b/lib/workload/components/python-lambda-get-cwl-object-from-s3-inputs-py/index.ts index 37f9e63bc..44873fb35 100644 --- a/lib/workload/components/python-lambda-get-cwl-object-from-s3-inputs-py/index.ts +++ b/lib/workload/components/python-lambda-get-cwl-object-from-s3-inputs-py/index.ts @@ -3,11 +3,20 @@ 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'; +import * as dynamodb from 'aws-cdk-lib/aws-dynamodb'; +import * as events from 'aws-cdk-lib/aws-events'; +import * as ssm from 'aws-cdk-lib/aws-ssm'; +import * as secretsManager from 'aws-cdk-lib/aws-secretsmanager'; + +export interface PythonLambdaGetCwlObjectFromS3InputsProps { + /* Secrets */ + icav2AccessTokenSecretObj: secretsManager.ISecret; +} export class PythonLambdaGetCwlObjectFromS3InputsConstruct extends Construct { public readonly lambdaObj: lambda_python.PythonFunction; - constructor(scope: Construct, id: string) { + constructor(scope: Construct, id: string, props: PythonLambdaGetCwlObjectFromS3InputsProps) { super(scope, id); this.lambdaObj = new lambda_python.PythonFunction(this, 'get_cwl_object_from_s3_inputs_py', { @@ -17,7 +26,13 @@ export class PythonLambdaGetCwlObjectFromS3InputsConstruct extends Construct { index: 'get_cwl_object_from_s3_inputs.py', handler: 'handler', memorySize: 1024, - timeout: Duration.seconds(10), + timeout: Duration.seconds(60), + environment: { + ICAV2_ACCESS_TOKEN_SECRET_ID: props.icav2AccessTokenSecretObj.secretName, + }, }); + + /* Give the Lambda permission to access the icav2 secret */ + props.icav2AccessTokenSecretObj.grantRead(this.lambdaObj.currentVersion); } } diff --git a/lib/workload/stateless/stacks/bclconvert-interop-qc-pipeline-manager/lambdas/set_outputs_json_py/requirements.txt b/lib/workload/stateless/stacks/bclconvert-interop-qc-pipeline-manager/lambdas/set_outputs_json_py/requirements.txt index 77ef47ad4..9afec8ad8 100644 --- a/lib/workload/stateless/stacks/bclconvert-interop-qc-pipeline-manager/lambdas/set_outputs_json_py/requirements.txt +++ b/lib/workload/stateless/stacks/bclconvert-interop-qc-pipeline-manager/lambdas/set_outputs_json_py/requirements.txt @@ -1,2 +1,2 @@ -wrapica>=2.27.1.post20240806222234 +wrapica>=2.27.1.post20240830140737 boto3>=1.34.0 \ No newline at end of file diff --git a/lib/workload/stateless/stacks/bclconvert-interop-qc-pipeline-manager/step_functions_templates/set_bclconvert_interop_qc_cwl_inputs_sfn.asl.json b/lib/workload/stateless/stacks/bclconvert-interop-qc-pipeline-manager/step_functions_templates/set_bclconvert_interop_qc_cwl_inputs_sfn.asl.json index 75e65c01a..a594135c1 100644 --- a/lib/workload/stateless/stacks/bclconvert-interop-qc-pipeline-manager/step_functions_templates/set_bclconvert_interop_qc_cwl_inputs_sfn.asl.json +++ b/lib/workload/stateless/stacks/bclconvert-interop-qc-pipeline-manager/step_functions_templates/set_bclconvert_interop_qc_cwl_inputs_sfn.asl.json @@ -8,8 +8,8 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.db_uuid", - "id_type": "db_uuid" + "id.$": "$.portal_run_id", + "id_type": "portal_run_id" } }, "ResultSelector": { @@ -43,10 +43,8 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id": { - "S.$": "$.db_uuid" - }, - "id_type": "db_uuid" + "id.$": "$.portal_run_id", + "id_type": "portal_run_id" }, "UpdateExpression": "SET input_json = :input_json", "ExpressionAttributeValues": { diff --git a/lib/workload/stateless/stacks/bclconvert-interop-qc-pipeline-manager/step_functions_templates/set_bclconvert_interop_qc_cwl_outputs_sfn.asl.json b/lib/workload/stateless/stacks/bclconvert-interop-qc-pipeline-manager/step_functions_templates/set_bclconvert_interop_qc_cwl_outputs_sfn.asl.json index 0bc7ff1ed..597d724f8 100644 --- a/lib/workload/stateless/stacks/bclconvert-interop-qc-pipeline-manager/step_functions_templates/set_bclconvert_interop_qc_cwl_outputs_sfn.asl.json +++ b/lib/workload/stateless/stacks/bclconvert-interop-qc-pipeline-manager/step_functions_templates/set_bclconvert_interop_qc_cwl_outputs_sfn.asl.json @@ -8,8 +8,8 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.db_uuid", - "id_type": "db_uuid" + "id.$": "$.portal_run_id", + "id_type": "portal_run_id" } }, "ResultSelector": { @@ -57,10 +57,8 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id": { - "S.$": "$.db_uuid" - }, - "id_type": "db_uuid" + "id.$": "$.portal_run_id", + "id_type": "portal_run_id" }, "UpdateExpression": "SET analysis_output = :output_json", "ExpressionAttributeValues": { diff --git a/lib/workload/stateless/stacks/bclconvert-manager/deps/requirements.txt b/lib/workload/stateless/stacks/bclconvert-manager/deps/requirements.txt index 5e80d75ea..477366077 100644 --- a/lib/workload/stateless/stacks/bclconvert-manager/deps/requirements.txt +++ b/lib/workload/stateless/stacks/bclconvert-manager/deps/requirements.txt @@ -1,6 +1,6 @@ uuid6>=2024.1.12 v2-samplesheet-maker>=4.2.4.post20240528161300 -wrapica==2.27.1.post20240806222234 +wrapica==2.27.1.post20240830140737 xmltodict==0.13.0 mypy_boto3_ssm>=1.16.0 mypy_boto3_secretsmanager>=1.16.0 diff --git a/lib/workload/stateless/stacks/bs-runs-upload-manager/layers/poetry.lock b/lib/workload/stateless/stacks/bs-runs-upload-manager/layers/poetry.lock index 5a735ee1b..b70157ed7 100644 --- a/lib/workload/stateless/stacks/bs-runs-upload-manager/layers/poetry.lock +++ b/lib/workload/stateless/stacks/bs-runs-upload-manager/layers/poetry.lock @@ -48,17 +48,17 @@ lxml = ["lxml"] [[package]] name = "boto3" -version = "1.34.154" +version = "1.35.9" description = "The AWS SDK for Python" optional = false python-versions = ">=3.8" files = [ - {file = "boto3-1.34.154-py3-none-any.whl", hash = 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"wrapica-2.27.1.post20240806222234.tar.gz", hash = "sha256:f13ea1fc0cf5975aa5a6d60b7c053447c79c04e5da9218a8d2da00255ff59b44"}, + {file = "wrapica-2.27.1.post20240830140737-py3-none-any.whl", hash = "sha256:620aa8e800677111b72e4ea2a2bf23d6942a2d861366dcb6ad3b6c059bf1ad76"}, + {file = "wrapica-2.27.1.post20240830140737.tar.gz", hash = "sha256:e4a9226ebeba9f3a9b860fa51e6c3ff4bd2ed521b07e193c20c8eab619557bf1"}, ] [package.dependencies] @@ -1311,4 +1317,4 @@ files = [ [metadata] lock-version = "2.0" python-versions = "^3.12, <3.13" -content-hash = "c90e3d2e41930e64b6d18fafb7d9203a07fbbe6f2ae293327a411ba050857599" +content-hash = "639b7a39de072ddfb6257ba9ccf48fce24554929f1d615449920793d000d9f21" diff --git a/lib/workload/stateless/stacks/bssh-icav2-fastq-copy-manager/layers/pyproject.toml b/lib/workload/stateless/stacks/bssh-icav2-fastq-copy-manager/layers/pyproject.toml index 05c16c742..bd448ec3f 100644 --- a/lib/workload/stateless/stacks/bssh-icav2-fastq-copy-manager/layers/pyproject.toml +++ b/lib/workload/stateless/stacks/bssh-icav2-fastq-copy-manager/layers/pyproject.toml @@ -23,7 +23,7 @@ aws_requests_auth = "^0.4.3" xmltodict = "^0.13.0" pandas = "^2.2.0" v2_samplesheet_maker = "^4.2.4" -wrapica = "^2.27.1.post20240806222234, <2.28.0" +wrapica = "^2.27.1.post20240830140737, <2.28.0" [tool.poetry.group.dev] optional = true diff --git a/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/delete_cache_uri_py/requirements.txt b/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/delete_cache_uri_py/requirements.txt index 035e4f833..da6e0f5eb 100644 --- a/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/delete_cache_uri_py/requirements.txt +++ b/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/delete_cache_uri_py/requirements.txt @@ -1 +1 @@ -wrapica>=2.27.1.post20240806222234 \ No newline at end of file +wrapica>=2.27.1.post20240830140737 \ No newline at end of file diff --git a/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/find_all_vcf_files_py/requirements.txt b/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/find_all_vcf_files_py/requirements.txt index 035e4f833..da6e0f5eb 100644 --- a/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/find_all_vcf_files_py/requirements.txt +++ b/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/find_all_vcf_files_py/requirements.txt @@ -1 +1 @@ -wrapica>=2.27.1.post20240806222234 \ No newline at end of file +wrapica>=2.27.1.post20240830140737 \ No newline at end of file diff --git a/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/generate_copy_manifest_dict_py/requirements.txt b/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/generate_copy_manifest_dict_py/requirements.txt index 035e4f833..da6e0f5eb 100644 --- a/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/generate_copy_manifest_dict_py/requirements.txt +++ b/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/generate_copy_manifest_dict_py/requirements.txt @@ -1 +1 @@ -wrapica>=2.27.1.post20240806222234 \ No newline at end of file +wrapica>=2.27.1.post20240830140737 \ No newline at end of file diff --git a/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/set_outputs_json_py/requirements.txt b/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/set_outputs_json_py/requirements.txt index 035e4f833..da6e0f5eb 100644 --- a/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/set_outputs_json_py/requirements.txt +++ b/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/set_outputs_json_py/requirements.txt @@ -1 +1 @@ -wrapica>=2.27.1.post20240806222234 \ No newline at end of file +wrapica>=2.27.1.post20240830140737 \ No newline at end of file diff --git a/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/upload_samplesheet_to_cache_dir_py/requirements.txt b/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/upload_samplesheet_to_cache_dir_py/requirements.txt index 89f9fa686..7f3a02f5d 100644 --- a/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/upload_samplesheet_to_cache_dir_py/requirements.txt +++ b/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/lambdas/upload_samplesheet_to_cache_dir_py/requirements.txt @@ -1,2 +1,2 @@ -wrapica>=2.27.1.post20240806222234 +wrapica>=2.27.1.post20240830140737 v2-samplesheet-maker>=4.2.4.post20240528161300 diff --git a/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/step_functions_templates/set_cttso_v2_nf_inputs.asl.json b/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/step_functions_templates/set_cttso_v2_nf_inputs.asl.json index 869302ef7..4f1b13bd1 100644 --- a/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/step_functions_templates/set_cttso_v2_nf_inputs.asl.json +++ b/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/step_functions_templates/set_cttso_v2_nf_inputs.asl.json @@ -8,8 +8,8 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.db_uuid", - "id_type": "db_uuid" + "id.$": "$.portal_run_id", + "id_type": "portal_run_id" } }, "ResultPath": "$.get_ready_event_step", @@ -25,8 +25,8 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.db_uuid", - "id_type": "db_uuid" + "id.$": "$.portal_run_id", + "id_type": "portal_run_id" }, "UpdateExpression": "SET analysis_status = :analysis_status", "ExpressionAttributeValues": { @@ -145,8 +145,8 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.db_uuid", - "id_type": "db_uuid" + "id.$": "$.portal_run_id", + "id_type": "portal_run_id" }, "UpdateExpression": "SET analysis_status = :analysis_status", "ExpressionAttributeValues": { @@ -177,10 +177,8 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id": { - "S.$": "$.db_uuid" - }, - "id_type": "db_uuid" + "id.$": "$.portal_run_id", + "id_type": "portal_run_id" }, "UpdateExpression": "SET input_json = :input_json", "ExpressionAttributeValues": { diff --git a/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/step_functions_templates/set_cttso_v2_nf_outputs.asl.json b/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/step_functions_templates/set_cttso_v2_nf_outputs.asl.json index 571c0dec5..f4f5e201f 100644 --- a/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/step_functions_templates/set_cttso_v2_nf_outputs.asl.json +++ b/lib/workload/stateless/stacks/cttso-v2-pipeline-manager/step_functions_templates/set_cttso_v2_nf_outputs.asl.json @@ -8,8 +8,8 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.db_uuid", - "id_type": "db_uuid" + "id.$": "$.portal_run_id", + "id_type": "portal_run_id" } }, "Next": "Delete Cache and Set Outputs JSON", @@ -98,10 +98,8 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id": { - "S.$": "$.db_uuid" - }, - "id_type": "db_uuid" + "id.$": "$.portal_run_id", + "id_type": "portal_run_id" }, "UpdateExpression": "SET analysis_output = :output_json", "ExpressionAttributeValues": { diff --git a/lib/workload/stateless/stacks/rnasum-pipeline-manager/deploy/index.ts b/lib/workload/stateless/stacks/rnasum-pipeline-manager/deploy/index.ts index af40e8874..76685b473 100644 --- a/lib/workload/stateless/stacks/rnasum-pipeline-manager/deploy/index.ts +++ b/lib/workload/stateless/stacks/rnasum-pipeline-manager/deploy/index.ts @@ -82,7 +82,10 @@ export class RnasumIcav2PipelineManagerStack extends cdk.Stack { // Convert Fastq List Rows to Lambda Object const getCwlObjectFromS3InputsLambdaObj = new PythonLambdaGetCwlObjectFromS3InputsConstruct( this, - 'get_cwl_object_from_s3_inputs_lambda' + 'get_cwl_object_from_s3_inputs_lambda', + { + icav2AccessTokenSecretObj: this.icav2AccessTokenSecretObj, + } ).lambdaObj; // Add permissions to lambda diff --git a/lib/workload/stateless/stacks/rnasum-pipeline-manager/step_functions_templates/set_rnasum_cwl_inputs_sfn.asl.json b/lib/workload/stateless/stacks/rnasum-pipeline-manager/step_functions_templates/set_rnasum_cwl_inputs_sfn.asl.json index 28ce6df5c..eed877617 100644 --- a/lib/workload/stateless/stacks/rnasum-pipeline-manager/step_functions_templates/set_rnasum_cwl_inputs_sfn.asl.json +++ b/lib/workload/stateless/stacks/rnasum-pipeline-manager/step_functions_templates/set_rnasum_cwl_inputs_sfn.asl.json @@ -8,8 +8,8 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.db_uuid", - "id_type": "db_uuid" + "id.$": "$.portal_run_id", + "id_type": "portal_run_id" } }, "ResultSelector": { @@ -201,13 +201,13 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.db_uuid", - "id_type": "db_uuid" + "id.$": "$.portal_run_id", + "id_type": "portal_run_id" }, "UpdateExpression": "SET input_json = :input_json", "ExpressionAttributeValues": { ":input_json": { - "S.$": "States.JsonToString($.merge_boolean_enable_parameters_step.input_json)" + "S.$": "States.JsonToString($.merge_data_inputs_step.input_json)" } } }, diff --git a/lib/workload/stateless/stacks/rnasum-pipeline-manager/step_functions_templates/set_rnasum_cwl_outputs_sfn.asl.json b/lib/workload/stateless/stacks/rnasum-pipeline-manager/step_functions_templates/set_rnasum_cwl_outputs_sfn.asl.json index eeb6d3765..df9f95b99 100644 --- a/lib/workload/stateless/stacks/rnasum-pipeline-manager/step_functions_templates/set_rnasum_cwl_outputs_sfn.asl.json +++ b/lib/workload/stateless/stacks/rnasum-pipeline-manager/step_functions_templates/set_rnasum_cwl_outputs_sfn.asl.json @@ -8,8 +8,8 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.db_uuid", - "id_type": "db_uuid" + "id.$": "$.portal_run_id", + "id_type": "portal_run_id" } }, "Next": "Set outputs from analysis uri", @@ -25,8 +25,8 @@ "Parameters": { "FunctionName": "${__set_outputs_json_lambda_function_arn__}", "Payload": { - "output_directory_name.$": "States.Format('{}__{}', $.get_input_parameters_from_event_step.inputs.subjectId, $.get_input_parameters_from_event_step.inputs.wtsTumorLibraryId)", - "wts_tumor_library_id.$": "$.get_input_parameters_from_event_step.inputs.wtsTumorLibraryId", + "output_directory_name.$": "States.Format('{}__{}', $.get_db_attributes_step.ready_event_data_inputs.subjectId, $.get_db_attributes_step.ready_event_data_inputs.wtsTumorLibraryId)", + "wts_tumor_library_id.$": "$.get_db_attributes_step.ready_event_data_inputs.wtsTumorLibraryId", "analysis_output_uri.$": "$.get_db_attributes_step.engine_parameters.outputUri" } }, @@ -46,7 +46,8 @@ "TimeoutSeconds": 60, "ResultSelector": { "output_json": { - "outputDirectoryUri.$": "$.Payload.output_uri" + "outputDirectoryUri.$": "$.Payload.output_directory_uri", + "htmlReportUri.$": "$.Payload.html_report_uri" } }, "ResultPath": "$.analysis_outputs_step", @@ -58,8 +59,8 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.db_uuid", - "id_type": "db_uuid" + "id.$": "$.portal_run_id", + "id_type": "portal_run_id" }, "UpdateExpression": "SET analysis_output = :output_json", "ExpressionAttributeValues": { diff --git a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/elmer/part_2/bssh-fastq-copy-manager-draft-to-ready/index.ts b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/elmer/part_2/bssh-fastq-copy-manager-draft-to-ready/index.ts index 786438e47..35827cd76 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/elmer/part_2/bssh-fastq-copy-manager-draft-to-ready/index.ts +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/elmer/part_2/bssh-fastq-copy-manager-draft-to-ready/index.ts @@ -62,6 +62,7 @@ export class BsshFastqCopyManagerDraftToReadyMakerConstruct extends Construct { lambdaPrefix: this.bsshFastqCopyManagerDraftToReadyMakerEventMap.prefix, payloadVersion: this.bsshFastqCopyManagerDraftToReadyMakerEventMap.payloadVersion, stateMachinePrefix: this.bsshFastqCopyManagerDraftToReadyMakerEventMap.prefix, + rulePrefix: `stacky-${this.bsshFastqCopyManagerDraftToReadyMakerEventMap.prefix}`, /* Table objects diff --git a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/gorilla/part_2/bclconvert-interop-qc-input-maker/index.ts b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/gorilla/part_2/bclconvert-interop-qc-input-maker/index.ts index 13dc657c5..28964b963 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/gorilla/part_2/bclconvert-interop-qc-input-maker/index.ts +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/gorilla/part_2/bclconvert-interop-qc-input-maker/index.ts @@ -65,6 +65,7 @@ export class BclconvertInteropQcDraftToReadyMakerConstruct extends Construct { lambdaPrefix: this.bclconvertInteropQcDraftToReadyMakerEventMap.prefix, payloadVersion: this.bclconvertInteropQcDraftToReadyMakerEventMap.payloadVersion, stateMachinePrefix: this.bclconvertInteropQcDraftToReadyMakerEventMap.prefix, + rulePrefix: `stacky-${this.bclconvertInteropQcDraftToReadyMakerEventMap.prefix}-rule`, /* Table objects diff --git a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/jb-weld/part_2/initialise-cttsov2-library-dbs/index.ts b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/jb-weld/part_2/initialise-cttsov2-library-dbs/index.ts index 4b73a2895..c231795fb 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/jb-weld/part_2/initialise-cttsov2-library-dbs/index.ts +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/jb-weld/part_2/initialise-cttsov2-library-dbs/index.ts @@ -83,6 +83,7 @@ export class Cttsov2InitialiseLibraryAndFastqListRowConstruct extends Construct Part 4: Subscribe to the library events from the event bus where the library assay type is cttsov2 */ const rule = new events.Rule(this, 'initialise_library_assay', { + ruleName: `stacky-${this.Cttsov2InitialiseLibraryAndFastqListRowMap.prefix}-rule`, eventBus: props.eventBusObj, eventPattern: { source: [this.Cttsov2InitialiseLibraryAndFastqListRowMap.triggerSource], diff --git a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/jb-weld/part_5/cttsov2-draft-to-ready/index.ts b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/jb-weld/part_5/cttsov2-draft-to-ready/index.ts index 88464f406..4a8eae4cb 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/jb-weld/part_5/cttsov2-draft-to-ready/index.ts +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/jb-weld/part_5/cttsov2-draft-to-ready/index.ts @@ -73,6 +73,7 @@ export class Cttsov2InputMakerConstruct extends Construct { lambdaPrefix: this.cttsov2InputMakerEventMap.prefix, payloadVersion: this.cttsov2InputMakerEventMap.payloadVersion, stateMachinePrefix: this.cttsov2InputMakerEventMap.prefix, + rulePrefix: this.cttsov2InputMakerEventMap.prefix, /* Table objects diff --git a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/kwik/part_2/initialise-wgts-library-dbs/index.ts b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/kwik/part_2/initialise-wgts-library-dbs/index.ts index af2f36d67..a5625d562 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/kwik/part_2/initialise-wgts-library-dbs/index.ts +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/kwik/part_2/initialise-wgts-library-dbs/index.ts @@ -88,6 +88,7 @@ export class WgtsQcInitialiseLibraryAndFastqListRowConstruct extends Construct { is WGS or WTS and the workflow is QC, RESEARCH or CLINICAL */ const rule = new events.Rule(this, 'initialise_library_assay', { + ruleName: `stacky-${this.WgtsQcInitialiseLibraryAndFastqListRowMap.prefix}-rule`, eventBus: props.eventBusObj, eventPattern: { source: [this.WgtsQcInitialiseLibraryAndFastqListRowMap.triggerSource], diff --git a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/kwik/part_4/fastq-list-rows-shower-complete-to-wgts-qc-draft/step_functions_templates/fastq_list_rows_shower_complete_to_wgts_qc_draft_sfn_template.asl.json b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/kwik/part_4/fastq-list-rows-shower-complete-to-wgts-qc-draft/step_functions_templates/fastq_list_rows_shower_complete_to_wgts_qc_draft_sfn_template.asl.json index d09606865..4737ca0b2 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/kwik/part_4/fastq-list-rows-shower-complete-to-wgts-qc-draft/step_functions_templates/fastq_list_rows_shower_complete_to_wgts_qc_draft_sfn_template.asl.json +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/kwik/part_4/fastq-list-rows-shower-complete-to-wgts-qc-draft/step_functions_templates/fastq_list_rows_shower_complete_to_wgts_qc_draft_sfn_template.asl.json @@ -228,10 +228,11 @@ "status": "${__output_status__}", "workflowName": "${__workflow_name__}", "workflowVersion": "${__workflow_version__}", + "workflowRunName.$": "$.get_per_workflow_run_inputs_step.workflow_run_name", "linkedLibraries": [ { - "libraryId.$": "$.get_fastq_list_row_ids_step.library_id", - "orcabusId.$": "$.get_fastq_list_row_ids_step.orcabus_id" + "libraryId.$": "$.library_id", + "orcabusId.$": "$.orcabus_id" } ], "payload": { diff --git a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/kwik/part_5/wgts-qc-draft-to-ready/index.ts b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/kwik/part_5/wgts-qc-draft-to-ready/index.ts index b324b8293..46b3984bd 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/kwik/part_5/wgts-qc-draft-to-ready/index.ts +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/kwik/part_5/wgts-qc-draft-to-ready/index.ts @@ -70,6 +70,7 @@ export class WgtsQcInputMakerConstruct extends Construct { lambdaPrefix: this.wgtsQcInputMakerEventMap.prefix, payloadVersion: this.wgtsQcInputMakerEventMap.payloadVersion, stateMachinePrefix: this.wgtsQcInputMakerEventMap.prefix, + rulePrefix: `stacky-${this.wgtsQcInputMakerEventMap.prefix}`, /* Table objects diff --git a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/kwik/part_6/push-fastq-list-row-qc-complete-event/lambdas/collect_qc_metrics_from_alignment_directory_py/requirements.txt b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/kwik/part_6/push-fastq-list-row-qc-complete-event/lambdas/collect_qc_metrics_from_alignment_directory_py/requirements.txt index c69ec13fd..0a4dc278e 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/kwik/part_6/push-fastq-list-row-qc-complete-event/lambdas/collect_qc_metrics_from_alignment_directory_py/requirements.txt +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/kwik/part_6/push-fastq-list-row-qc-complete-event/lambdas/collect_qc_metrics_from_alignment_directory_py/requirements.txt @@ -1,3 +1,3 @@ -wrapica==2.27.1.post20240806222234 +wrapica==2.27.1.post20240830140737 pandas>=2.2.2 boto3>=1.34.0 diff --git a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/loctite/part_2/initialise-tn-library-dbs/index.ts b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/loctite/part_2/initialise-tn-library-dbs/index.ts index 6b683671d..453894c98 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/loctite/part_2/initialise-tn-library-dbs/index.ts +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/loctite/part_2/initialise-tn-library-dbs/index.ts @@ -89,6 +89,7 @@ export class TnInitialiseLibraryAndFastqListRowConstruct extends Construct { and where the phenotype is NORMAL or TUMOR */ const rule = new events.Rule(this, 'initialise_library_assay', { + ruleName: `stacky-${this.TnInitialiseLibraryAndFastqListRowMap.prefix}-rule`, eventBus: props.eventBusObj, eventPattern: { source: [this.TnInitialiseLibraryAndFastqListRowMap.triggerSource], diff --git a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/loctite/part_3/update-fastq-list-rows-dbs/step_functions_templates/add_fastq_list_rows_db_sfn_template.asl.json b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/loctite/part_3/update-fastq-list-rows-dbs/step_functions_templates/add_fastq_list_rows_db_sfn_template.asl.json index e5cdfae90..cac3f0eec 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/loctite/part_3/update-fastq-list-rows-dbs/step_functions_templates/add_fastq_list_rows_db_sfn_template.asl.json +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/loctite/part_3/update-fastq-list-rows-dbs/step_functions_templates/add_fastq_list_rows_db_sfn_template.asl.json @@ -40,7 +40,7 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.payload_data.id", + "id.$": "$.payload_data.fastqListRow.rgid", "id_type": "${__fastq_list_row_partition_name__}" }, "UpdateExpression": "SET fastq_list_row_json = :fastq_list_row_json", diff --git a/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 b/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 index e1386ea06..7bc89329a 100644 --- a/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 +++ b/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 @@ -122,7 +122,7 @@ "type.$": "$.get_library_map_step.Item.type.S", "assay.$": "$.get_library_map_step.Item.assay.S", "subject_id.$": "$.get_library_map_step.Item.subject_id.S", - "orcabus_id.$": "$.get_library_item_step.Item.orcabus_id.S", + "orcabus_id.$": "$.get_library_map_step.Item.orcabus_id.S", "fastq_list_row_id_set.$": "$.get_library_map_step.Item.fastq_list_row_id_set.SS" } } @@ -386,12 +386,12 @@ "workflowRunName.$": "$.get_parameters_step.workflow_run_name", "linkedLibraries": [ { - "libraryId": "$.get_tn_pair_step.tumor_library.id", - "orcabusId": "$.get_tn_pair_step.tumor_library.orcabus_id" + "libraryId.$": "$.get_tn_pair_step.tumor_library.id", + "orcabusId.$": "$.get_tn_pair_step.tumor_library.orcabus_id" }, { - "libraryId": "$.get_tn_pair_step.normal_library.id", - "orcabusId": "$.get_tn_pair_step.normal_library.orcabus_id" + "libraryId.$": "$.get_tn_pair_step.normal_library.id", + "orcabusId.$": "$.get_tn_pair_step.normal_library.orcabus_id" } ], "payload": { diff --git a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/loctite/part_6/tn-draft-to-ready/index.ts b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/loctite/part_6/tn-draft-to-ready/index.ts index ca36d079d..7e533d704 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/loctite/part_6/tn-draft-to-ready/index.ts +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/loctite/part_6/tn-draft-to-ready/index.ts @@ -69,6 +69,7 @@ export class TnInputMakerConstruct extends Construct { lambdaPrefix: this.tnInputMakerEventMap.prefix, payloadVersion: this.tnInputMakerEventMap.payloadVersion, stateMachinePrefix: this.tnInputMakerEventMap.prefix, + rulePrefix: `stacky-${this.tnInputMakerEventMap.prefix}`, /* Table objects diff --git a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/mod-podge/part_1/initialise-wts-library-dbs/index.ts b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/mod-podge/part_1/initialise-wts-library-dbs/index.ts index d82566589..eccd96169 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/mod-podge/part_1/initialise-wts-library-dbs/index.ts +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/mod-podge/part_1/initialise-wts-library-dbs/index.ts @@ -85,6 +85,7 @@ export class WtsInitialiseLibraryAndFastqListRowConstruct extends Construct { and where the phenotype is NORMAL or TUMOR */ const rule = new events.Rule(this, 'initialise_library_assay', { + ruleName: `stacky-${this.WtsInitialiseLibraryAndFastqListRowMap.prefix}-rule`, eventBus: props.eventBusObj, eventPattern: { source: [this.WtsInitialiseLibraryAndFastqListRowMap.triggerSource], diff --git a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/mod-podge/part_1/initialise-wts-library-dbs/step_functions_templates/initialise_wts_library_db_sfn_template.asl.json b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/mod-podge/part_1/initialise-wts-library-dbs/step_functions_templates/initialise_wts_library_db_sfn_template.asl.json index 8dafc1cf3..3861f91b2 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/mod-podge/part_1/initialise-wts-library-dbs/step_functions_templates/initialise_wts_library_db_sfn_template.asl.json +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/mod-podge/part_1/initialise-wts-library-dbs/step_functions_templates/initialise_wts_library_db_sfn_template.asl.json @@ -85,7 +85,7 @@ "Type": "Pass", "Next": "Initialise Fastq List Row and Update Library", "Parameters": { - "fastq_list_row_id.$": "States.ArrayGetItem($.fastq_list_row_objs[*].fastqListRowId, $.index)" + "fastq_list_row_id.$": "States.ArrayGetItem($.fastq_list_row_objs[*].fastqListRowRgId, $.index)" }, "ResultPath": "$.get_fastq_list_row_id_step" }, diff --git a/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 b/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 index 0c8eb659e..c44bf094e 100644 --- a/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 +++ b/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 @@ -24,6 +24,7 @@ def handler(event, context) -> Dict: """ tumor_library_id = event['tumor_library_id'] + subject_id = event['subject_id'] tumor_fastq_list_rows: List[Dict] = event['tumor_fastq_list_rows'] tumor_fastq_list_row_ids: List[str] = event['tumor_fastq_list_row_ids'] @@ -33,6 +34,7 @@ def handler(event, context) -> Dict: "tumorFastqListRows": tumor_fastq_list_rows, }, "event_tags": { + "subjectId": subject_id, "tumorLibraryId": tumor_library_id, "tumorFastqListRowIds": tumor_fastq_list_row_ids } diff --git a/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 b/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 index 3d6593f44..c755fba5c 100644 --- a/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 +++ b/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 @@ -63,7 +63,7 @@ } }, "ResultSelector": { - "fastq_list_row_id.$": "$.Item.id", + "fastq_list_row_id.$": "$.Item.id.S", "fastq_list_row_obj.$": "States.StringToJson($.Item.fastq_list_row_json.S)" }, "ResultPath": "$.get_tumor_fastq_list_row_obj", @@ -117,7 +117,8 @@ "Payload": { "tumor_library_id.$": "$.payload_data.libraryId", "tumor_fastq_list_rows.$": "$.get_parameters_step.tumor_fastq_list_rows", - "tumor_fastq_list_row_ids.$": "$.get_parameters_step.tumor_fastq_list_row_ids" + "tumor_fastq_list_row_ids.$": "$.get_parameters_step.tumor_fastq_list_row_ids", + "subject_id.$": "$.get_library_item_step.Item.subject_id.S" } }, "Retry": [ @@ -158,8 +159,8 @@ "workflowRunName.$": "$.get_parameters_step.workflow_run_name", "linkedLibraries": [ { - "libraryId.$": "$.get_library_item_step.id", - "orcabusId.$": "$.get_library_item_step.orcabus_id" + "libraryId.$": "$.get_library_item_step.Item.id.S", + "orcabusId.$": "$.get_library_item_step.Item.orcabus_id.S" } ], "payload": { diff --git a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/mod-podge/part_5/wts-draft-to-ready/index.ts b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/mod-podge/part_5/wts-draft-to-ready/index.ts index 1c1cb3ae7..570dfb022 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/mod-podge/part_5/wts-draft-to-ready/index.ts +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/mod-podge/part_5/wts-draft-to-ready/index.ts @@ -69,6 +69,7 @@ export class WtsInputMakerConstruct extends Construct { lambdaPrefix: this.wtsInputMakerEventMap.prefix, payloadVersion: this.wtsInputMakerEventMap.payloadVersion, stateMachinePrefix: this.wtsInputMakerEventMap.prefix, + rulePrefix: `stacky-${this.wtsInputMakerEventMap.prefix}`, /* Table objects diff --git a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/pva/part_2/initialise-umccrise-library-dbs/index.ts b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/pva/part_2/initialise-umccrise-library-dbs/index.ts index 2657edf6d..c70a0cc2d 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/pva/part_2/initialise-umccrise-library-dbs/index.ts +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/pva/part_2/initialise-umccrise-library-dbs/index.ts @@ -89,6 +89,7 @@ export class UmccriseInitialiseLibraryAndFastqListRowConstruct extends Construct and where the phenotype is NORMAL or TUMOR */ const rule = new events.Rule(this, 'initialise_library_assay', { + ruleName: `stacky-${this.UmccriseInitialiseLibraryAndFastqListRowMap.prefix}-rule`, eventBus: props.eventBusObj, eventPattern: { source: [this.UmccriseInitialiseLibraryAndFastqListRowMap.triggerSource], diff --git a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/pva/part_2/initialise-umccrise-library-dbs/step_functions_templates/initialise_umccrise_library_db_sfn_template.asl.json b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/pva/part_2/initialise-umccrise-library-dbs/step_functions_templates/initialise_umccrise_library_db_sfn_template.asl.json index b28d8857e..81ee404b2 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/pva/part_2/initialise-umccrise-library-dbs/step_functions_templates/initialise_umccrise_library_db_sfn_template.asl.json +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/pva/part_2/initialise-umccrise-library-dbs/step_functions_templates/initialise_umccrise_library_db_sfn_template.asl.json @@ -126,7 +126,7 @@ "Type": "Pass", "Next": "Initialise Fastq List Row and Update Library", "Parameters": { - "fastq_list_row_id.$": "States.ArrayGetItem($.fastq_list_row_objs[*].fastqListRowId, $.index)" + "fastq_list_row_id.$": "States.ArrayGetItem($.fastq_list_row_objs[*].fastqListRowRgId, $.index)" }, "ResultPath": "$.get_fastq_list_row_id_step" }, diff --git a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/pva/part_4/tn-complete-to-umccrise-draft/index.ts b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/pva/part_4/tn-complete-to-umccrise-draft/index.ts index b2f7ae5c6..3916e8010 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/pva/part_4/tn-complete-to-umccrise-draft/index.ts +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/pva/part_4/tn-complete-to-umccrise-draft/index.ts @@ -45,7 +45,8 @@ export class TnCompleteToUmccriseDraftConstruct extends Construct { outputStatus: 'DRAFT', payloadVersion: '2024.07.23', workflowName: 'umccrise', - workflowVersion: '4.2.4', + workflowVersion: '2.3.1', + tablePartitionName: 'subject', }; constructor(scope: Construct, id: string, props: TnCompleteToUmccriseDraftConstructProps) { @@ -108,6 +109,9 @@ export class TnCompleteToUmccriseDraftConstruct extends Construct { /* Tables */ __table_name__: props.tableObj.tableName, + /* Table Partitions */ + __subject_table_partition_name__: this.UmccriseDraftMap.tablePartitionName, + // State Machines __sfn_preamble_state_machine_arn__: sfn_preamble.stateMachineArn, }, diff --git a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/pva/part_4/tn-complete-to-umccrise-draft/step_functions_templates/tn_complete_to_umccrise_draft_sfn_template.asl.json b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/pva/part_4/tn-complete-to-umccrise-draft/step_functions_templates/tn_complete_to_umccrise_draft_sfn_template.asl.json index 603a7f1dc..756332981 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/pva/part_4/tn-complete-to-umccrise-draft/step_functions_templates/tn_complete_to_umccrise_draft_sfn_template.asl.json +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/pva/part_4/tn-complete-to-umccrise-draft/step_functions_templates/tn_complete_to_umccrise_draft_sfn_template.asl.json @@ -17,7 +17,7 @@ "TableName": "${__table_name__}", "Key": { "id.$": "$.payload_data.tags.subjectId", - "id_type": "${__subject_partition_name__}" + "id_type": "${__subject_table_partition_name__}" } }, "ResultPath": "$.get_subject_item_step", @@ -91,12 +91,12 @@ "Entries": [ { "Detail": { - "portalRunId.$": "$.get_parameters_step.portal_run_id", + "portalRunId.$": "$.get_portal_and_run_name_step.portal_run_id", "timestamp.$": "$$.State.EnteredTime", "status": "${__output_status__}", "workflowName": "${__workflow_name__}", "workflowVersion": "${__workflow_version__}", - "workflowRunName.$": "$.get_parameters_step.workflow_run_name", + "workflowRunName.$": "$.get_portal_and_run_name_step.workflow_run_name", "linkedLibraries.$": "$.linked_libraries", "payload": { "version": "${__payload_version__}", diff --git a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/pva/part_5/umccrise-draft-to-ready/index.ts b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/pva/part_5/umccrise-draft-to-ready/index.ts index 9b272b85e..41aa3cc1d 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/pva/part_5/umccrise-draft-to-ready/index.ts +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/pva/part_5/umccrise-draft-to-ready/index.ts @@ -69,6 +69,7 @@ export class UmccriseInputMakerConstruct extends Construct { lambdaPrefix: this.umccriseInputMakerEventMap.prefix, payloadVersion: this.umccriseInputMakerEventMap.payloadVersion, stateMachinePrefix: this.umccriseInputMakerEventMap.prefix, + rulePrefix: this.umccriseInputMakerEventMap.prefix, /* Table objects diff --git a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/roket/part_2/umccrise-and-wts-complete-to-rnasum-draft/step_functions_templates/umccrise_and_wts_complete_to_rnasum_draft.asl.json b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/roket/part_2/umccrise-and-wts-complete-to-rnasum-draft/step_functions_templates/umccrise_and_wts_complete_to_rnasum_draft.asl.json index ae5140398..7dc3c1e47 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/roket/part_2/umccrise-and-wts-complete-to-rnasum-draft/step_functions_templates/umccrise_and_wts_complete_to_rnasum_draft.asl.json +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/roket/part_2/umccrise-and-wts-complete-to-rnasum-draft/step_functions_templates/umccrise_and_wts_complete_to_rnasum_draft.asl.json @@ -15,7 +15,7 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.workflow_inputs.data.tags.subjectId", + "id.$": "$.workflow_inputs.payload.data.tags.subjectId", "id_type": "${__subject_table_partition_name__}" } }, @@ -47,25 +47,25 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.workflow_inputs.data.tags.subjectId", + "id.$": "$.workflow_inputs.payload.data.tags.subjectId", "id_type": "${__subject_table_partition_name__}" }, - "UpdateExpression": "SET wts_workflow_status = :wts_workflow_status, wts_tumor_library_id = :wts_tumor_library_id, wts_tumor_fastq_list_row_ids =: wts_tumor_fastq_list_row_ids, arriba_output_uri = :arriba_output_uri, dragen_wts_output_uri = :dragen_wts_output_uri", + "UpdateExpression": "SET wts_workflow_status = :wts_workflow_status, wts_tumor_library_id = :wts_tumor_library_id, wts_tumor_fastq_list_row_ids = :wts_tumor_fastq_list_row_ids, arriba_output_uri = :arriba_output_uri, dragen_wts_output_uri = :dragen_wts_output_uri", "ExpressionAttributeValues": { ":wts_workflow_status": { "S.$": "$.workflow_inputs.status" }, ":wts_tumor_library_id": { - "S": "$.workflow_inputs.data.tags.libraryId" + "S.$": "$.workflow_inputs.payload.data.tags.tumorLibraryId" }, ":arriba_output_uri": { - "S.$": "$.workflow_inputs.data.outputs.arribaOutputUri" + "S.$": "$.workflow_inputs.payload.data.outputs.arribaOutputUri" }, ":dragen_wts_output_uri": { - "S.$": "$.workflow_inputs.data.outputs.dragenTranscriptomeOutputUri" + "S.$": "$.workflow_inputs.payload.data.outputs.dragenTranscriptomeOutputUri" }, ":wts_tumor_fastq_list_row_ids": { - "S.$": "$.workflow_inputs.data.tags.tumorLibraryId" + "S.$": "States.JsonToString($.workflow_inputs.payload.data.tags.tumorFastqListRowIds)" } } }, @@ -78,7 +78,7 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.workflow_inputs.data.tags.subjectId", + "id.$": "$.workflow_inputs.payload.data.tags.subjectId", "id_type": "${__subject_table_partition_name__}" }, "UpdateExpression": "SET umccrise_workflow_status = :umccrise_workflow_status, umccrise_tumor_library_id = :umccrise_tumor_library_id, umccrise_normal_library_id = :umccrise_normal_library_id, umccrise_output_uri = :umccrise_output_uri, umccrise_tumor_fastq_list_row_ids = :umccrise_tumor_fastq_list_row_ids, umccrise_normal_fastq_list_row_ids = :umccrise_normal_fastq_list_row_ids", @@ -87,19 +87,19 @@ "S.$": "$.workflow_inputs.status" }, ":umccrise_tumor_library_id": { - "S.$": "$.workflow_inputs.data.tags.tumorLibraryId" + "S.$": "$.workflow_inputs.payload.data.tags.tumorLibraryId" }, ":umccrise_normal_library_id": { - "S.$": "$.workflow_inputs.data.tags.normalLibraryId" + "S.$": "$.workflow_inputs.payload.data.tags.normalLibraryId" }, ":umccrise_output_uri": { - "S.$": "$.workflow_inputs.data.outputs.outputDirectoryUri" + "S.$": "$.workflow_inputs.payload.data.outputs.outputDirectoryUri" }, ":umccrise_tumor_fastq_list_row_ids": { - "S.$": "States.JsonToString($.workflow_inputs.data.tags.tumorFastqListRowIds)" + "S.$": "States.JsonToString($.workflow_inputs.payload.data.tags.tumorFastqListRowIds)" }, ":umccrise_normal_fastq_list_row_ids": { - "S.$": "States.JsonToString($.workflow_inputs.data.tags.normalFastqListRowIds)" + "S.$": "States.JsonToString($.workflow_inputs.payload.data.tags.normalFastqListRowIds)" } } }, @@ -120,7 +120,7 @@ "Type": "Map", "ItemsPath": "$.workflow_inputs.linkedLibraries", "ItemSelector": { - "subject_id.$": "$.workflow_inputs.data.tags.subjectId", + "subject_id.$": "$.workflow_inputs.payload.data.tags.subjectId", "linked_library.$": "$$.Map.Item.Value" }, "ItemProcessor": { @@ -150,13 +150,13 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.subject_id", + "id.$": "$.workflow_inputs.payload.data.tags.subjectId", "id_type": "${__subject_table_partition_name__}" }, - "UpdateExpression": "ADD linked_libraries_set = :linked_libraries_set", + "UpdateExpression": "ADD linked_libraries_set :linked_libraries_set", "ExpressionAttributeValues": { ":linked_libraries_set": { - "SS.$": "$.linked_libraries_str_list" + "SS.$": "$.get_linked_libraries_as_str.linked_libraries_str_list" } } }, @@ -165,7 +165,8 @@ } } } - ] + ], + "ResultPath": null }, "Get Subject Item": { "Type": "Task", @@ -173,7 +174,7 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.workflow_inputs.data.tags.subjectId", + "id.$": "$.workflow_inputs.payload.data.tags.subjectId", "id_type": "${__subject_table_partition_name__}" } }, @@ -226,9 +227,9 @@ "wts_tumor_library_id.$": "$.get_subject_item_step.Item.wts_tumor_library_id.S", "wgs_tumor_library_id.$": "$.get_subject_item_step.Item.umccrise_tumor_library_id.S", "wgs_normal_library_id.$": "$.get_subject_item_step.Item.umccrise_normal_library_id.S", - "wts_tumor_fastq_list_row_ids.$": "$.get_subject_item_step.Item.wts_tumor_library_id.S", - "wgs_tumor_fastq_list_row_ids.$": "$.get_subject_item_step.Item.umccrise_tumor_fastq_list_row_ids.S", - "wgs_normal_fastq_list_row_ids.$": "$.get_subject_item_step.Item.umccrise_normal_fastq_list_row_ids.S", + "wts_tumor_fastq_list_row_ids.$": "States.StringToJson($.get_subject_item_step.Item.wts_tumor_fastq_list_row_ids.S)", + "wgs_tumor_fastq_list_row_ids.$": "States.StringToJson($.get_subject_item_step.Item.umccrise_tumor_fastq_list_row_ids.S)", + "wgs_normal_fastq_list_row_ids.$": "States.StringToJson($.get_subject_item_step.Item.umccrise_normal_fastq_list_row_ids.S)", "subject_id.$": "$.get_subject_item_step.Item.id.S" } }, @@ -278,7 +279,7 @@ "Type": "Map", "ItemsPath": "$.get_subject_item_step.Item.linked_libraries_set.SS", "ItemSelector": { - "linked_library_str": "$$.Map.Item.Value" + "linked_library_str.$": "$$.Map.Item.Value" }, "ItemProcessor": { "ProcessorConfig": { diff --git a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/roket/part_3/rnasum-draft-to-ready/index.ts b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/roket/part_3/rnasum-draft-to-ready/index.ts index c09191191..da6073b94 100644 --- a/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/roket/part_3/rnasum-draft-to-ready/index.ts +++ b/lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/roket/part_3/rnasum-draft-to-ready/index.ts @@ -69,6 +69,7 @@ export class RnasumInputMakerConstruct extends Construct { lambdaPrefix: this.rnasumInputMakerEventMap.prefix, payloadVersion: this.rnasumInputMakerEventMap.payloadVersion, stateMachinePrefix: this.rnasumInputMakerEventMap.prefix, + rulePrefix: `stacky-${this.rnasumInputMakerEventMap.prefix}`, /* Table objects diff --git a/lib/workload/stateless/stacks/transcriptome-pipeline-manager/lambdas/set_outputs_json_py/requirements.txt b/lib/workload/stateless/stacks/transcriptome-pipeline-manager/lambdas/set_outputs_json_py/requirements.txt index fc8f437f4..10dfd16fd 100644 --- a/lib/workload/stateless/stacks/transcriptome-pipeline-manager/lambdas/set_outputs_json_py/requirements.txt +++ b/lib/workload/stateless/stacks/transcriptome-pipeline-manager/lambdas/set_outputs_json_py/requirements.txt @@ -1,2 +1,2 @@ -wrapica==2.27.0 +wrapica>=2.27.1.post20240830140737 boto3>=1.34.0 diff --git a/lib/workload/stateless/stacks/transcriptome-pipeline-manager/lambdas/set_outputs_json_py/set_outputs_json.py b/lib/workload/stateless/stacks/transcriptome-pipeline-manager/lambdas/set_outputs_json_py/set_outputs_json.py index c076233c7..bbcc1e5d8 100644 --- a/lib/workload/stateless/stacks/transcriptome-pipeline-manager/lambdas/set_outputs_json_py/set_outputs_json.py +++ b/lib/workload/stateless/stacks/transcriptome-pipeline-manager/lambdas/set_outputs_json_py/set_outputs_json.py @@ -285,8 +285,8 @@ def handler(event, context): # json.dumps( # handler( # { -# "output_prefix": "L2400195", -# "analysis_output_uri": "icav2://ea19a3f5-ec7c-4940-a474-c31cd91dbad4/analysis/wts/202407237e0fd947/" +# "output_prefix": "L2400255", +# "analysis_output_uri": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/analysis/wts/2024083105106d48/" # }, # None # ), @@ -295,15 +295,13 @@ def handler(event, context): # ) # # # { -# # "dragen_germline_output": "icav2://ea19a3f5-ec7c-4940-a474-c31cd91dbad4/analysis/tumor_normal/202407237e0fd947/L2400191_dragen_germline/", -# # "dragen_somatic_output": "icav2://ea19a3f5-ec7c-4940-a474-c31cd91dbad4/analysis/tumor_normal/202407237e0fd947/L2400195_dragen_somatic/", -# # "multiqc_output": "icav2://ea19a3f5-ec7c-4940-a474-c31cd91dbad4/analysis/tumor_normal/202407237e0fd947/L2400195__L2400191_dragen_somatic_and_germline_multiqc/", -# # "dragen_germline_snv_vcf": "icav2://ea19a3f5-ec7c-4940-a474-c31cd91dbad4/analysis/tumor_normal/202407237e0fd947/L2400191_dragen_germline/L2400191.vcf.gz", -# # "dragen_germline_snv_vcf_hard_filtered": "icav2://ea19a3f5-ec7c-4940-a474-c31cd91dbad4/analysis/tumor_normal/202407237e0fd947/L2400191_dragen_germline/L2400191.hard-filtered.vcf.gz", -# # "dragen_germline_bam": "icav2://ea19a3f5-ec7c-4940-a474-c31cd91dbad4/analysis/tumor_normal/202407237e0fd947/L2400195_dragen_somatic/L2400191_normal.bam", -# # "dragen_somatic_snv_vcf": "icav2://ea19a3f5-ec7c-4940-a474-c31cd91dbad4/analysis/tumor_normal/202407237e0fd947/L2400195_dragen_somatic/L2400195.vcf.gz", -# # "dragen_somatic_snv_vcf_hard_filtered": "icav2://ea19a3f5-ec7c-4940-a474-c31cd91dbad4/analysis/tumor_normal/202407237e0fd947/L2400195_dragen_somatic/L2400195.hard-filtered.vcf.gz", -# # "dragen_somatic_sv_vcf": "icav2://ea19a3f5-ec7c-4940-a474-c31cd91dbad4/analysis/tumor_normal/202407237e0fd947/L2400195_dragen_somatic/L2400195.sv.vcf.gz", -# # "dragen_somatic_bam": "icav2://ea19a3f5-ec7c-4940-a474-c31cd91dbad4/analysis/tumor_normal/202407237e0fd947/L2400195_dragen_somatic/L2400195_tumor.bam", -# # "multiqc_html_report": "icav2://ea19a3f5-ec7c-4940-a474-c31cd91dbad4/analysis/tumor_normal/202407237e0fd947/L2400195__L2400191_dragen_somatic_and_germline_multiqc/L2400195__L2400191_dragen_somatic_and_germline_multiqc.html" +# # "arriba_output": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/analysis/wts/2024083105106d48/L2400255_arriba/", +# # "dragen_transcriptome_output": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/analysis/wts/2024083105106d48/L2400255_dragen_transcriptome/", +# # "qualimap_output": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/analysis/wts/2024083105106d48/L2400255_qualimap/", +# # "multiqc_output": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/analysis/wts/2024083105106d48/L2400255_dragen_transcriptome_multiqc/", +# # "dragen_transcriptome_bam": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/analysis/wts/2024083105106d48/L2400255_dragen_transcriptome/L2400255.bam", +# # "dragen_transcriptome_fusion_candidates_vcf": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/analysis/wts/2024083105106d48/L2400255_dragen_transcriptome/L2400255.fusion_candidates.vcf.gz", +# # "qualimap_html_report": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/analysis/wts/2024083105106d48/L2400255_qualimap/qualimapReport.html", +# # "arriba_fusions_tsv": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/analysis/wts/2024083105106d48/L2400255_arriba/fusions.tsv", +# # "multiqc_html_report": "s3://pipeline-dev-cache-503977275616-ap-southeast-2/byob-icav2/development/analysis/wts/2024083105106d48/L2400255_dragen_transcriptome_multiqc/L2400255_dragen_transcriptome_multiqc.html" # # } diff --git a/lib/workload/stateless/stacks/transcriptome-pipeline-manager/step_functions_templates/set_wts_cwl_inputs_sfn.asl.json b/lib/workload/stateless/stacks/transcriptome-pipeline-manager/step_functions_templates/set_wts_cwl_inputs_sfn.asl.json index f2ca1ce22..a5beadc81 100644 --- a/lib/workload/stateless/stacks/transcriptome-pipeline-manager/step_functions_templates/set_wts_cwl_inputs_sfn.asl.json +++ b/lib/workload/stateless/stacks/transcriptome-pipeline-manager/step_functions_templates/set_wts_cwl_inputs_sfn.asl.json @@ -8,8 +8,8 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.db_uuid", - "id_type": "db_uuid" + "id.$": "$.portal_run_id", + "id_type": "portal_run_id" } }, "ResultSelector": { @@ -433,8 +433,7 @@ "cl_config.$": "States.JsonToString($.configure_inputs_step.cl_config_sample_names_replace)", "cytobands.$": "$.configure_inputs_step.cytobands_uri", "fastq_list_rows.$": "$.configure_inputs_step.tumor_fastq_list_rows_cwl", - "output_file_prefix.$": "$.get_input_parameters_from_event_step.inputs.outputPrefix", - "output_directory.$": "States.Format('{}_dragen_transcriptome', $.get_input_parameters_from_event_step.inputs.outputPrefix)", + "output_prefix.$": "$.get_input_parameters_from_event_step.inputs.outputPrefix", "protein_domains.$": "$.configure_inputs_step.protein_domains_uri", "qc_reference_samples.$": "$.configure_inputs_step.qc_reference_samples_list", "reference_fasta.$": "$.configure_inputs_step.reference_fasta_uri", @@ -457,8 +456,8 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.db_uuid", - "id_type": "db_uuid" + "id.$": "$.portal_run_id", + "id_type": "portal_run_id" }, "UpdateExpression": "SET input_json = :input_json", "ExpressionAttributeValues": { diff --git a/lib/workload/stateless/stacks/transcriptome-pipeline-manager/step_functions_templates/set_wts_cwl_outputs_sfn.asl.json b/lib/workload/stateless/stacks/transcriptome-pipeline-manager/step_functions_templates/set_wts_cwl_outputs_sfn.asl.json index e420d8ce6..97450adae 100644 --- a/lib/workload/stateless/stacks/transcriptome-pipeline-manager/step_functions_templates/set_wts_cwl_outputs_sfn.asl.json +++ b/lib/workload/stateless/stacks/transcriptome-pipeline-manager/step_functions_templates/set_wts_cwl_outputs_sfn.asl.json @@ -8,8 +8,8 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.db_uuid", - "id_type": "db_uuid" + "id.$": "$.portal_run_id", + "id_type": "portal_run_id" } }, "Next": "Set outputs from analysis uri", @@ -65,8 +65,8 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.db_uuid", - "id_type": "db_uuid" + "id.$": "$.portal_run_id", + "id_type": "portal_run_id" }, "UpdateExpression": "SET analysis_output = :output_json", "ExpressionAttributeValues": { diff --git a/lib/workload/stateless/stacks/tumor-normal-pipeline-manager/lambdas/set_outputs_json_py/requirements.txt b/lib/workload/stateless/stacks/tumor-normal-pipeline-manager/lambdas/set_outputs_json_py/requirements.txt index e85f37f20..94c02ba6d 100644 --- a/lib/workload/stateless/stacks/tumor-normal-pipeline-manager/lambdas/set_outputs_json_py/requirements.txt +++ b/lib/workload/stateless/stacks/tumor-normal-pipeline-manager/lambdas/set_outputs_json_py/requirements.txt @@ -1,2 +1,2 @@ -wrapica>=2.27.1.post20240806222234,<2.28.0 +wrapica>=2.27.1.post20240830140737,<2.28.0 boto3>=1.34 diff --git a/lib/workload/stateless/stacks/tumor-normal-pipeline-manager/step_functions_templates/set_tn_cwl_inputs_sfn.asl.json b/lib/workload/stateless/stacks/tumor-normal-pipeline-manager/step_functions_templates/set_tn_cwl_inputs_sfn.asl.json index fed5a13e5..8401e5271 100644 --- a/lib/workload/stateless/stacks/tumor-normal-pipeline-manager/step_functions_templates/set_tn_cwl_inputs_sfn.asl.json +++ b/lib/workload/stateless/stacks/tumor-normal-pipeline-manager/step_functions_templates/set_tn_cwl_inputs_sfn.asl.json @@ -8,8 +8,8 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.db_uuid", - "id_type": "db_uuid" + "id.$": "$.portal_run_id", + "id_type": "portal_run_id" } }, "ResultSelector": { @@ -357,10 +357,8 @@ "Next": "Merge Data Inputs", "Parameters": { "input_json": { - "output_directory_germline.$": "States.Format('{}_dragen_germline', $.get_input_parameters_from_event_step.inputs.outputPrefixGermline)", - "output_directory_somatic.$": "States.Format('{}_dragen_somatic', $.get_input_parameters_from_event_step.inputs.outputPrefixSomatic)", - "output_file_prefix_germline.$": "$.get_input_parameters_from_event_step.inputs.outputPrefixGermline", - "output_file_prefix_somatic.$": "$.get_input_parameters_from_event_step.inputs.outputPrefixSomatic", + "output_prefix_germline.$": "$.get_input_parameters_from_event_step.inputs.outputPrefixGermline", + "output_prefix_somatic.$": "$.get_input_parameters_from_event_step.inputs.outputPrefixSomatic", "reference_tar": { "class": "File", "location.$": "$.configure_inputs_step.reference_uri" @@ -391,8 +389,8 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.db_uuid", - "id_type": "db_uuid" + "id.$": "$.portal_run_id", + "id_type": "portal_run_id" }, "UpdateExpression": "SET input_json = :input_json", "ExpressionAttributeValues": { diff --git a/lib/workload/stateless/stacks/tumor-normal-pipeline-manager/step_functions_templates/set_tn_cwl_outputs_sfn.asl.json b/lib/workload/stateless/stacks/tumor-normal-pipeline-manager/step_functions_templates/set_tn_cwl_outputs_sfn.asl.json index 4990680c2..9708b5411 100644 --- a/lib/workload/stateless/stacks/tumor-normal-pipeline-manager/step_functions_templates/set_tn_cwl_outputs_sfn.asl.json +++ b/lib/workload/stateless/stacks/tumor-normal-pipeline-manager/step_functions_templates/set_tn_cwl_outputs_sfn.asl.json @@ -8,8 +8,8 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.db_uuid", - "id_type": "db_uuid" + "id.$": "$.portal_run_id", + "id_type": "portal_run_id" } }, "Next": "Set outputs from analysis uri", @@ -68,8 +68,8 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.db_uuid", - "id_type": "db_uuid" + "id.$": "$.portal_run_id", + "id_type": "portal_run_id" }, "UpdateExpression": "SET analysis_output = :output_json", "ExpressionAttributeValues": { diff --git a/lib/workload/stateless/stacks/umccrise-pipeline-manager/deploy/index.ts b/lib/workload/stateless/stacks/umccrise-pipeline-manager/deploy/index.ts index 762d6049f..539b2b4b1 100644 --- a/lib/workload/stateless/stacks/umccrise-pipeline-manager/deploy/index.ts +++ b/lib/workload/stateless/stacks/umccrise-pipeline-manager/deploy/index.ts @@ -91,7 +91,10 @@ export class UmccriseIcav2PipelineManagerStack extends cdk.Stack { // Convert Fastq List Rows to Lambda Object const getCwlObjectFromS3InputsLambdaObj = new PythonLambdaGetCwlObjectFromS3InputsConstruct( this, - 'get_cwl_object_from_s3_inputs_lambda' + 'get_cwl_object_from_s3_inputs_lambda', + { + icav2AccessTokenSecretObj: this.icav2AccessTokenSecretObj, + } ).lambdaObj; // Add permissions to lambda diff --git a/lib/workload/stateless/stacks/umccrise-pipeline-manager/lambdas/get_outputs_py/get_outputs.py b/lib/workload/stateless/stacks/umccrise-pipeline-manager/lambdas/get_outputs_py/get_outputs.py index 59499196f..93c72bdd6 100644 --- a/lib/workload/stateless/stacks/umccrise-pipeline-manager/lambdas/get_outputs_py/get_outputs.py +++ b/lib/workload/stateless/stacks/umccrise-pipeline-manager/lambdas/get_outputs_py/get_outputs.py @@ -21,6 +21,7 @@ def handler(event, context): { "analysis_output_uri": "s3://umccr-raw-data/analysis/2019/2019-06-04/2019-06-04_1", "output_directory_name": "TUMOR_LIBRARY_ID__NORMAL_LIBRARY_ID" + "output_subdirectory_name": "SUBJECT_ID__TUMOR_LIBRARY_ID" } :param event: @@ -28,8 +29,9 @@ def handler(event, context): :return: """ - analysis_output_uri = event["analysis_output_uri"] output_directory_name = event["output_directory_name"] + output_subdirectory_name = event['output_subdirectory_name'] + analysis_output_uri = event["analysis_output_uri"] # Parse the analysis output uri parsed_uri = urlparse(analysis_output_uri) @@ -42,7 +44,7 @@ def handler(event, context): # Extend the path with the output directory name # Then add in the trailing slash str( - Path(parsed_uri.path) / output_directory_name + Path(parsed_uri.path) / output_directory_name / output_subdirectory_name ) + "/", None, None, None ) diff --git a/lib/workload/stateless/stacks/umccrise-pipeline-manager/step_functions_templates/set_umccrise_cwl_inputs_sfn.asl.json b/lib/workload/stateless/stacks/umccrise-pipeline-manager/step_functions_templates/set_umccrise_cwl_inputs_sfn.asl.json index ce36f258e..3a0493af6 100644 --- a/lib/workload/stateless/stacks/umccrise-pipeline-manager/step_functions_templates/set_umccrise_cwl_inputs_sfn.asl.json +++ b/lib/workload/stateless/stacks/umccrise-pipeline-manager/step_functions_templates/set_umccrise_cwl_inputs_sfn.asl.json @@ -8,8 +8,8 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.db_uuid", - "id_type": "db_uuid" + "id.$": "$.portal_run_id", + "id_type": "portal_run_id" } }, "ResultSelector": { @@ -161,8 +161,7 @@ "ResultPath": "$.configure_inputs_step", "ResultSelector": { "cwl_data_inputs.$": "$.[0].cwl_data_inputs", - "reference_uri.$": "$.[1].get_reference_version_uri_step.reference_uri", - "boolean_parameters.$": "$.[2].get_boolean_parameters_step.boolean_parameters" + "reference_uri.$": "$.[1].get_reference_version_uri_step.reference_uri" } }, "Set Input JSON": { @@ -174,7 +173,7 @@ "dragen_normal_id.$": "$.get_input_parameters_from_event_step.inputs.dragenGermlineLibraryId", "dragen_tumor_id.$": "$.get_input_parameters_from_event_step.inputs.dragenSomaticLibraryId", "subject_identifier.$": "$.get_input_parameters_from_event_step.inputs.subjectId", - "reference_tar": { + "genomes_tar": { "class": "File", "location.$": "$.configure_inputs_step.reference_uri" } @@ -196,13 +195,13 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.db_uuid", - "id_type": "db_uuid" + "id.$": "$.portal_run_id", + "id_type": "portal_run_id" }, "UpdateExpression": "SET input_json = :input_json", "ExpressionAttributeValues": { ":input_json": { - "S.$": "States.JsonToString($.merge_boolean_enable_parameters_step.input_json)" + "S.$": "States.JsonToString($.merge_data_inputs_step.input_json)" } } }, diff --git a/lib/workload/stateless/stacks/umccrise-pipeline-manager/step_functions_templates/set_umccrise_cwl_outputs_sfn.asl.json b/lib/workload/stateless/stacks/umccrise-pipeline-manager/step_functions_templates/set_umccrise_cwl_outputs_sfn.asl.json index e2efe06d5..46cd76c50 100644 --- a/lib/workload/stateless/stacks/umccrise-pipeline-manager/step_functions_templates/set_umccrise_cwl_outputs_sfn.asl.json +++ b/lib/workload/stateless/stacks/umccrise-pipeline-manager/step_functions_templates/set_umccrise_cwl_outputs_sfn.asl.json @@ -8,8 +8,8 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.db_uuid", - "id_type": "db_uuid" + "id.$": "$.portal_run_id", + "id_type": "portal_run_id" } }, "Next": "Set outputs from analysis uri", @@ -26,6 +26,7 @@ "FunctionName": "${__set_outputs_json_lambda_function_arn__}", "Payload": { "output_directory_name.$": "States.Format('{}__{}', $.get_db_attributes_step.ready_event_data_inputs.dragenSomaticLibraryId, $.get_db_attributes_step.ready_event_data_inputs.dragenGermlineLibraryId)", + "output_subdirectory_name.$": "States.Format('{}__{}', $.get_db_attributes_step.ready_event_data_inputs.subjectId, $.get_db_attributes_step.ready_event_data_inputs.dragenSomaticLibraryId)", "analysis_output_uri.$": "$.get_db_attributes_step.engine_parameters.outputUri" } }, @@ -57,8 +58,8 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.db_uuid", - "id_type": "db_uuid" + "id.$": "$.portal_run_id", + "id_type": "portal_run_id" }, "UpdateExpression": "SET analysis_output = :output_json", "ExpressionAttributeValues": { diff --git a/lib/workload/stateless/stacks/wgts-alignment-qc-pipeline-manager/lambdas/set_outputs_json_py/requirements.txt b/lib/workload/stateless/stacks/wgts-alignment-qc-pipeline-manager/lambdas/set_outputs_json_py/requirements.txt index 56ae47e68..9976297e1 100644 --- a/lib/workload/stateless/stacks/wgts-alignment-qc-pipeline-manager/lambdas/set_outputs_json_py/requirements.txt +++ b/lib/workload/stateless/stacks/wgts-alignment-qc-pipeline-manager/lambdas/set_outputs_json_py/requirements.txt @@ -1,2 +1,2 @@ -wrapica>=2.27.1.post20240806222234,<2.28.0 +wrapica>=2.27.1.post20240830140737,<2.28.0 boto3 \ No newline at end of file diff --git a/lib/workload/stateless/stacks/wgts-alignment-qc-pipeline-manager/step_functions_templates/set_wgts_alignment_qc_cwl_inputs_sfn.asl.json b/lib/workload/stateless/stacks/wgts-alignment-qc-pipeline-manager/step_functions_templates/set_wgts_alignment_qc_cwl_inputs_sfn.asl.json index d5e40d67d..108a32580 100644 --- a/lib/workload/stateless/stacks/wgts-alignment-qc-pipeline-manager/step_functions_templates/set_wgts_alignment_qc_cwl_inputs_sfn.asl.json +++ b/lib/workload/stateless/stacks/wgts-alignment-qc-pipeline-manager/step_functions_templates/set_wgts_alignment_qc_cwl_inputs_sfn.asl.json @@ -8,8 +8,8 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.db_uuid", - "id_type": "db_uuid" + "id.$": "$.portal_run_id", + "id_type": "portal_run_id" } }, "ResultSelector": { @@ -180,8 +180,7 @@ "enable_rna": false, "enable_sort": true, "fastq_list_rows.$": "$.configure_inputs_step.fastq_list_rows_cwl", - "output_directory.$": "States.Format('{}_dragen_alignment', $.get_input_parameters_from_event_step.inputs.outputPrefix)", - "output_file_prefix.$": "$.get_input_parameters_from_event_step.inputs.outputPrefix", + "output_prefix.$": "$.get_input_parameters_from_event_step.inputs.outputPrefix", "reference_tar": { "class": "File", "location.$": "$.configure_inputs_step.reference_uri" @@ -232,8 +231,8 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.db_uuid", - "id_type": "db_uuid" + "id.$": "$.portal_run_id", + "id_type": "portal_run_id" }, "UpdateExpression": "SET input_json = :input_json", "ExpressionAttributeValues": { diff --git a/lib/workload/stateless/stacks/wgts-alignment-qc-pipeline-manager/step_functions_templates/set_wgts_alignment_qc_cwl_outputs_sfn.asl.json b/lib/workload/stateless/stacks/wgts-alignment-qc-pipeline-manager/step_functions_templates/set_wgts_alignment_qc_cwl_outputs_sfn.asl.json index 69672e79b..cdabf4d7c 100644 --- a/lib/workload/stateless/stacks/wgts-alignment-qc-pipeline-manager/step_functions_templates/set_wgts_alignment_qc_cwl_outputs_sfn.asl.json +++ b/lib/workload/stateless/stacks/wgts-alignment-qc-pipeline-manager/step_functions_templates/set_wgts_alignment_qc_cwl_outputs_sfn.asl.json @@ -8,8 +8,8 @@ "Parameters": { "TableName": "${__table_name__}", "Key": { - "id.$": "$.db_uuid", - "id_type": "db_uuid" + "id.$": "$.portal_run_id", + "id_type": "portal_run_id" } }, "Next": "Set outputs from analysis uri", @@ -60,9 +60,9 @@ "TableName": "${__table_name__}", "Key": { "id": { - "S.$": "$.db_uuid" + "S.$": "$.portal_run_id" }, - "id_type": "db_uuid" + "id_type": "portal_run_id" }, "UpdateExpression": "SET analysis_output = :output_json", "ExpressionAttributeValues": {