@orcabus/platform-cdk-constructs 0.0.28 → 0.0.29

package/.jsii

@@ -6740,6 +6740,6 @@
       "symbolId": "shared-config/slack:SlackAlerts"
     }
   },
-  "version": "0.0.28",
-  "fingerprint": "3HtbqKnwW4YrMNvfhWD3vgT0u6E0rtGMf60tZDj+OeE="
+  "version": "0.0.29",
+  "fingerprint": "to2qJ4qhRMxIu8FDi+dQkfjTFHOmV0JnqoO4A+JpGGY="
 }

package/api-gateway/api-gateway.js

@@ -15,7 +15,7 @@ const aws_lambda_1 = require("aws-cdk-lib/aws-lambda");
 const aws_route53_targets_1 = require("aws-cdk-lib/aws-route53-targets");
 const config_1 = require("./config");
 class OrcaBusApiGateway extends constructs_1.Construct {
-    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.apigateway.OrcaBusApiGateway", version: "0.0.28" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.apigateway.OrcaBusApiGateway", version: "0.0.29" };
     /**
      * The AWS region where the API Gateway is deployed.
      */

package/deployment-stack-pipeline/artifact-bucket.js

@@ -13,7 +13,7 @@ exports.CROSS_DEPLOYMENT_ARTIFACT_BUCKET_NAME = "orcabus-cross-deployment-codepi
 exports.CROSS_DEPLOYMENT_ARTIFACT_KMS_ALIAS = "orcabus-cross-deployment-codepipeline-artifact";
 exports.CROSS_DEPLOYMENT_ARTIFACT_KMS_ARN_SSM_PARAMETER_NAME = "/orcabus/deployment-stack-pipeline/artifact-bucket/kms-key-arn";
 class CrossDeploymentArtifactBucket extends constructs_1.Construct {
-    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.deploymentPipeline.CrossDeploymentArtifactBucket", version: "0.0.28" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.deploymentPipeline.CrossDeploymentArtifactBucket", version: "0.0.29" };
     /**
      * The S3 bucket used to store artifacts for cross-deployment pipelines.
      */

package/deployment-stack-pipeline/pipeline.js

@@ -31,7 +31,7 @@ exports.DEFAULT_SYNTH_STEP_PARTIAL_BUILD_SPEC = {
  * before using this construct.
  */
 class DeploymentStackPipeline extends constructs_1.Construct {
-    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.deploymentPipeline.DeploymentStackPipeline", version: "0.0.28" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.deploymentPipeline.DeploymentStackPipeline", version: "0.0.29" };
     /**
      * The code pipeline construct that is created.
      */

package/dynamodb/index.js

@@ -40,7 +40,7 @@ const dynamodb = __importStar(require("aws-cdk-lib/aws-dynamodb"));
 const aws_cdk_lib_1 = require("aws-cdk-lib");
 const config_1 = require("./config");
 class DynamoDbPartitionedConstruct extends constructs_1.Construct {
-    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.dynamodb.DynamoDbPartitionedConstruct", version: "0.0.28" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.dynamodb.DynamoDbPartitionedConstruct", version: "0.0.29" };
     table;
     constructor(scope, id, props) {
         super(scope, id);
@@ -75,7 +75,7 @@ class DynamoDbPartitionedConstruct extends constructs_1.Construct {
 }
 exports.DynamoDbPartitionedConstruct = DynamoDbPartitionedConstruct;
 class DynamoDbNonPartitionedConstruct extends constructs_1.Construct {
-    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.dynamodb.DynamoDbNonPartitionedConstruct", version: "0.0.28" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.dynamodb.DynamoDbNonPartitionedConstruct", version: "0.0.29" };
     table;
     constructor(scope, id, props) {
         super(scope, id);

package/ecs/index.js

@@ -55,7 +55,7 @@ exports.LAMBDA_ARCHITECTURE_MAP = {
     ['ARM64']: lambda.Architecture.ARM_64
 };
 class EcsFargateTaskConstruct extends constructs_1.Construct {
-    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.ecs.EcsFargateTaskConstruct", version: "0.0.28" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.ecs.EcsFargateTaskConstruct", version: "0.0.29" };
     cluster;
     taskDefinition;
     taskExecutionRole;

package/lambda/index.js

@@ -56,7 +56,7 @@ function getPythonUvDockerImage() {
     return aws_cdk_lib_1.DockerImage.fromBuild(path_1.default.join(__dirname, 'build_python'));
 }
 class PythonUvFunction extends aws_lambda_python_alpha_1.PythonFunction {
-    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.lambda.PythonUvFunction", version: "0.0.28" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.lambda.PythonUvFunction", version: "0.0.29" };
     // Class constructs, to be used for caching the layers
     // This means that if there are multiple lambdas throughout the stack
     // They will all use the same layer

package/lambda/layers/orcabus_api_tools/src/orcabus_api_tools/fastq_decompression/models.py

@@ -12,21 +12,62 @@
 """
 
 from typing import (
-    TypedDict, NotRequired, Literal, List
+    TypedDict, NotRequired, Literal, List, Union
 )
 
 JobType = Literal['FASTQ_DECOMPRESSION']
 JobStatus = Literal['PENDING', 'RUNNING', 'FAILED', 'ABORTED', 'SUCCEEDED']
 
+# Output jobs
+class DecompressionJobOutputObjectItem(TypedDict):
+    ingestId: str
+    gzipFileUri: str
 
-class JobOutput(TypedDict):
-    index: str
-    lane: str
-    libraryId: str
-    instrumentRunId: str
-    read1FileUriDecompressed: str
-    read2FileUriDecompressed: NotRequired[str]
 
+class DecompressionJobOutputObjectFastqId(TypedDict):
+    fastqId: str
+    decompressedFileUriByOraFileIngestIdList: List[DecompressionJobOutputObjectItem]
+
+
+class GzipFileSizeCalculationOutputObjectItem(TypedDict):
+    ingestId: str
+    gzipFileSize: int
+
+
+class GzipFileSizeCalculationOutputsFastqId(TypedDict):
+    fastqId: str
+    gzipFileSizeByOraFileIngestIdList: List[GzipFileSizeCalculationOutputObjectItem]
+
+
+class RawMd5sumCalculationOutputsObjectItem(TypedDict):
+    ingestId: str
+    rawMd5sum: str
+
+
+class RawMd5sumCalculationOutputsFastqId(TypedDict):
+    fastqId: str
+    rawMd5sumByOraFileIngestIdList: List[RawMd5sumCalculationOutputsObjectItem]
+
+
+class DecompressionJobOutputObject(TypedDict):
+   # Decompressed file URI by ORA file ingest ID list
+   decompressedFileList: List[DecompressionJobOutputObjectFastqId]
+
+class GzipFileSizeCalculationOutputObject(TypedDict):
+    # Gzip file size by ORA file ingest ID list
+    gzipFileSizeList: List[GzipFileSizeCalculationOutputsFastqId]
+
+
+class RawMd5sumCalculationOutputObject(TypedDict):
+    # Raw md5sum by ORA file ingest ID list
+    rawMd5sumList: List[RawMd5sumCalculationOutputsFastqId]
+
+
+JobOutputType = Union[
+  DecompressionJobOutputObject |
+  GzipFileSizeCalculationOutputObject |
+  RawMd5sumCalculationOutputObject
+]
 
 class Job(TypedDict):
     id: str
@@ -36,7 +77,7 @@ class Job(TypedDict):
     startTime: str
     endTime: str
     errorMessages: NotRequired[str]
-    outputs: NotRequired[List[JobOutput]]
+    outputs: NotRequired[JobOutputType]
 
 
 class JobQueryParameters(TypedDict):

package/lambda/layers/orcabus_api_tools/src/orcabus_api_tools/fastq_decompression/update_helpers.py

@@ -5,12 +5,12 @@ Update helpers for the update script.
 """
 
 # Standard imports
-from typing import Optional, Dict
+from typing import Optional, Dict, Any
 
 # Local imports
 from . import fastq_decompression_patch_request
 from .globals import JOB_ENDPOINT
-from .models import Job, JobStatus
+from .models import Job, JobStatus, JobOutputType
 
 
 def update_status(
@@ -18,13 +18,15 @@ def update_status(
         job_status: JobStatus,
         steps_execution_arn: Optional[str] = None,
         error_message: Optional[str] = None,
-        output: Optional[Dict[str, Any]] = None
+        output: Optional[Dict[str, JobOutputType]] = None
 ) -> Job:
     """
     Add QC stats to a fastq_id.
 
     :param job_id: The job id
     :param job_status: Dictionary of QC stats
+    :param steps_execution_arn:
+    :param output:
     :param error_message: Optional error message
     """
     return fastq_decompression_patch_request(

package/lambda/layers/orcabus_api_tools/src/orcabus_api_tools/filemanager/file_helpers.py

@@ -337,5 +337,8 @@ def update_ingest_id(s3_object_id: str, new_ingest_id: str) -> Dict:
     }
     return file_manager_patch_request(
         endpoint=f"{S3_LIST_ENDPOINT}/{s3_object_id}",
-        params=json_data
+        json_data=json_data,
+        params = {
+            "updateTag": json.dumps(True)
+        }
     )

package/monitored-queue/index.js

@@ -12,7 +12,7 @@ const aws_cloudwatch_actions_1 = require("aws-cdk-lib/aws-cloudwatch-actions");
  * SNS topic.
  */
 class MonitoredQueue extends constructs_1.Construct {
-    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.monitoredQueue.MonitoredQueue", version: "0.0.28" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.monitoredQueue.MonitoredQueue", version: "0.0.29" };
     queue;
     deadLetterQueue;
     alarm;

package/named-lambda-role/index.js

@@ -7,7 +7,7 @@ const aws_iam_1 = require("aws-cdk-lib/aws-iam");
  * A construct which represents a named role that a Lambda function can assume.
  */
 class NamedLambdaRole extends aws_iam_1.Role {
-    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.namedLambdaRole.NamedLambdaRole", version: "0.0.28" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.namedLambdaRole.NamedLambdaRole", version: "0.0.29" };
     constructor(scope, id, props) {
         super(scope, id, {
             assumedBy: new aws_iam_1.ServicePrincipal("lambda.amazonaws.com"),

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@orcabus/platform-cdk-constructs",
-  "version": "0.0.28",
+  "version": "0.0.29",
   "description": "CDK Package for OrcaBus infrastructure.",
   "main": "index.ts",
   "types": "index.d.ts",

package/provider-function/index.js

@@ -15,7 +15,7 @@ const aws_cdk_lib_1 = require("aws-cdk-lib");
  * to the provider framework.
  */
 class ProviderFunction extends constructs_1.Construct {
-    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.provider.ProviderFunction", version: "0.0.28" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.provider.ProviderFunction", version: "0.0.29" };
     _function;
     _response;
     constructor(scope, id, props) {

package/shared-config/networking.js

@@ -23,7 +23,7 @@ exports.VPC_LOOKUP_PROPS = {
  * Helper for looking up the shared OrcaBus VPC.
  */
 class OrcaBusVpc {
-    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.networking.OrcaBusVpc", version: "0.0.28" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.networking.OrcaBusVpc", version: "0.0.29" };
     /**
      * The shared VPC that is used by OrcaBus.
      * @param scope
@@ -42,7 +42,7 @@ exports.SHARED_SECURITY_GROUP_NAME = "OrcaBusSharedComputeSecurityGroup";
  * Helper for looking up the shared compute security group by name.
  */
 class OrcaBusSharedComputeSecurityGroup {
-    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.networking.OrcaBusSharedComputeSecurityGroup", version: "0.0.28" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.networking.OrcaBusSharedComputeSecurityGroup", version: "0.0.29" };
     /**
      * The shared security group that is used by compute resources to access the database.
      * @param scope

package/shared-config/slack.js

@@ -11,7 +11,7 @@ exports.SLACK_ALERTS_SNS_TOPIC = "AwsChatBotTopic-alerts";
  * A helper class to construct the arn for the slack SNS topic.
  */
 class SlackAlerts {
-    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.slack.SlackAlerts", version: "0.0.28" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.slack.SlackAlerts", version: "0.0.29" };
     /**
      * Format the ARN for the slack alerts SNS topic for the current stack.
      * @param stack