Update nails stack to collect project id from library orcabus id (#1039)

Author: alexiswl

lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/nails/part_1/initialise-library-db/index.ts

@@ -21,6 +21,16 @@ import path from 'path';
 import * as sfn from 'aws-cdk-lib/aws-stepfunctions';
 import * as events from 'aws-cdk-lib/aws-events';
 import * as eventsTargets from 'aws-cdk-lib/aws-events-targets';
+import * as ssm from 'aws-cdk-lib/aws-ssm';
+import * as secretsmanager from 'aws-cdk-lib/aws-secretsmanager';
+import * as lambda from 'aws-cdk-lib/aws-lambda';
+import { MetadataToolsPythonLambdaLayer } from '../../../../../../../components/python-metadata-tools-layer';
+import {
+  hostedZoneNameParameterPath,
+  jwtSecretName,
+} from '../../../../../../../../../config/constants';
+import { PythonFunction } from '@aws-cdk/aws-lambda-python-alpha';
+import { Duration } from 'aws-cdk-lib';
 
 export interface PieriandxInitialiseLibraryConstructProps {
   tableObj: dynamodb.ITableV2;
@@ -45,6 +55,51 @@ export class PieriandxInitialiseLibraryConstruct extends Construct {
   constructor(scope: Construct, id: string, props: PieriandxInitialiseLibraryConstructProps) {
     super(scope, id);
 
+    /*
+    Part 0: Get the metadata layer
+   */
+    // Get the metadata layer object
+    const metadataLayerObj = new MetadataToolsPythonLambdaLayer(this, 'metadata-tools-layer', {
+      layerPrefix: 'nails-get-library',
+    });
+
+    /*
+    Collect the required secret and ssm parameters for getting metadata
+    */
+    const hostnameSsmParameterObj = ssm.StringParameter.fromStringParameterName(
+      this,
+      'hostname_ssm_parameter',
+      hostedZoneNameParameterPath
+    );
+    const orcabusTokenSecretObj = secretsmanager.Secret.fromSecretNameV2(
+      this,
+      'orcabus_token_secret',
+      jwtSecretName
+    );
+
+    // Get library objects
+    const lambdaObj = new PythonFunction(this, 'get_project_id_from_library_id_py', {
+      entry: path.join(__dirname, 'lambdas', 'get_project_id_from_library_id_py'),
+      runtime: lambda.Runtime.PYTHON_3_12,
+      architecture: lambda.Architecture.ARM_64,
+      index: 'get_project_id_from_library_id.py',
+      handler: 'handler',
+      memorySize: 1024,
+      layers: [metadataLayerObj.lambdaLayerVersionObj],
+      environment: {
+        HOSTNAME_SSM_PARAMETER: hostnameSsmParameterObj.parameterName,
+        ORCABUS_TOKEN_SECRET_ID: orcabusTokenSecretObj.secretName,
+      },
+      // We dont know how big the database will get so will may need a longer timeout
+      timeout: Duration.seconds(120),
+    });
+
+    // Allow the lambda to read the secret
+    orcabusTokenSecretObj.grantRead(lambdaObj.currentVersion);
+
+    // Allow the lambda to read the ssm parameter
+    hostnameSsmParameterObj.grantRead(lambdaObj.currentVersion);
+
     /*
     Part 1: Build the internal sfn
     */
@@ -61,6 +116,10 @@ export class PieriandxInitialiseLibraryConstruct extends Construct {
         /* General */
         __table_name__: props.tableObj.tableName,
 
+        /* Lambdas */
+        __get_project_id_from_library_id_lambda_function_arn__:
+          lambdaObj.currentVersion.functionArn,
+
         /* Table Partitions */
         __library_partition_name__: this.PieriandxInitialiseLibrary.tablePartition.library,
       },
@@ -70,7 +129,9 @@ export class PieriandxInitialiseLibraryConstruct extends Construct {
     Part 2: Grant the sfn permissions
     */
     // access the dynamodb table
-    props.tableObj.grantReadWriteData(inputMakerSfn.role);
+    props.tableObj.grantReadWriteData(inputMakerSfn);
+    // invoke the lambda
+    lambdaObj.currentVersion.grantInvoke(inputMakerSfn);
 
     /*
     Part 3: Subscribe to the library events from the event bus where the library assay type

lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/nails/part_1/initialise-library-db/lambdas/get_project_id_from_library_id_py/get_project_id_from_library_id.py

@@ -0,0 +1,40 @@
+#!/usr/bin/env python3
+
+"""
+Given the following
+
+* libraryOrcabusId
+
+Get the library object, and return the projectId
+
+* projectId
+"""
+
+import boto3
+import typing
+
+from metadata_tools import get_library_from_library_orcabus_id
+
+if typing.TYPE_CHECKING:
+    from mypy_boto3_ssm import SSMClient
+    from mypy_boto3_secretsmanager import SecretsManagerClient
+
+
+def handler(event, context):
+    """
+
+    :param event:
+    :param context:
+    :return:
+    """
+
+    # Inputs
+    library_orcabus_id = event.get("libraryOrcabusId")
+
+    # Get the library object
+    library_obj = get_library_from_library_orcabus_id(library_orcabus_id)
+
+    # Return the projectId
+    return {
+        "projectId": library_obj['projectSet'][0]['projectId']
+    }

lib/workload/stateless/stacks/stacky-mcstackface/glue-constructs/nails/part_1/initialise-library-db/step_functions_templates/store_cttsov2_metadata_sfn_template.asl.json

@@ -1,48 +1,77 @@
 {
   "Comment": "A description of my state machine",
-  "StartAt": "Move Inputs",
+  "StartAt": "Save input vars",
   "States": {
-    "Move Inputs": {
+    "Save input vars": {
       "Type": "Pass",
-      "Next": "Initialise Library ID",
-      "Parameters": {
-        "inputs.$": "$",
-        "input_payload_data.$": "$.payload.data"
+      "Next": "Get project id from library id",
+      "Assign": {
+        "inputPayloadData": "{% $states.input.payload.data %}"
       }
     },
-    "Initialise Library ID": {
+    "Get project id from library id": {
+      "Type": "Task",
+      "Resource": "arn:aws:states:::lambda:invoke",
+      "Output": "{% $states.result.Payload %}",
+      "Arguments": {
+        "FunctionName": "${__get_project_id_from_library_id_lambda_function_arn__}",
+        "Payload": {
+          "libraryOrcabusId": "{% $inputPayloadData.library.orcabusId %}"
+        }
+      },
+      "Retry": [
+        {
+          "ErrorEquals": [
+            "Lambda.ServiceException",
+            "Lambda.AWSLambdaException",
+            "Lambda.SdkClientException",
+            "Lambda.TooManyRequestsException"
+          ],
+          "IntervalSeconds": 1,
+          "MaxAttempts": 3,
+          "BackoffRate": 2,
+          "JitterStrategy": "FULL"
+        }
+      ],
+      "Next": "Initialise Library Id",
+      "Assign": {
+        "projectId": "{% $states.result.Payload.projectId %}"
+      }
+    },
+    "Initialise Library Id": {
       "Type": "Task",
       "Resource": "arn:aws:states:::dynamodb:putItem",
-      "Parameters": {
+      "Arguments": {
         "TableName": "${__table_name__}",
         "Item": {
           "id": {
-            "S.$": "$.input_payload_data.library.orcabusId"
+            "S": "{% $inputPayloadData.library.orcabusId %}"
           },
           "id_type": {
             "S": "${__library_partition_name__}"
           },
           "library_id": {
-            "S.$": "$.input_payload_data.library.libraryId"
+            "S": "{% $inputPayloadData.library.libraryId %}"
           },
           "library_obj": {
-            "S.$": "States.JsonToString($.input_payload_data.library)"
+            "S": "{% $string($inputPayloadData.library) %}"
           },
           "project_id": {
-            "S.$": "$.input_payload_data.projectSet[0].projectId"
+            "S": "{% $projectId %}"
           },
           "external_sample_id": {
-            "S.$": "$.input_payload_data.sample.externalSampleId"
+            "S": "{% $inputPayloadData.sample.externalSampleId %}"
           },
           "external_subject_id": {
-            "S.$": "$.input_payload_data.subject.subjectId"
+            "S": "{% $inputPayloadData.subject.subjectId %}"
           },
           "instrument_run_id": {
-            "S.$": "$.input_payload_data.instrumentRunId"
+            "S": "{% $inputPayloadData.instrumentRunId %}"
           }
         }
       },
       "End": true
     }
-  }
+  },
+  "QueryLanguage": "JSONata"
 }