@orcabus/platform-cdk-constructs 0.0.44 → 0.0.46

package/.jsii

@@ -6756,6 +6756,6 @@
       "symbolId": "shared-config/slack:SlackAlerts"
     }
   },
-  "version": "0.0.44",
-  "fingerprint": "arsb/LGcRULLZhW7yVeQPPrQ6Xufpe98A6X9G62fzCM="
+  "version": "0.0.46",
+  "fingerprint": "wq/3vu0Z5vehQmydjFGp9Xs6zhtw4bSqWMa+sy2zW+0="
 }

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: "0.0.44" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.apigateway.OrcaBusApiGateway", version: "0.0.46" };
     /**
      * 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: "0.0.44" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.deploymentPipeline.CrossDeploymentArtifactBucket", version: "0.0.46" };
     /**
      * The S3 bucket used to store artifacts for cross-deployment pipelines.
      */

package/deployment-stack-pipeline/pipeline.js

@@ -32,7 +32,7 @@ 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: "0.0.44" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.deploymentPipeline.DeploymentStackPipeline", version: "0.0.46" };
     /**
      * 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: "0.0.44" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.dynamodb.DynamoDbPartitionedConstruct", version: "0.0.46" };
     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: "0.0.44" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.dynamodb.DynamoDbNonPartitionedConstruct", version: "0.0.46" };
     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: "0.0.44" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.ecs.EcsFargateTaskConstruct", version: "0.0.46" };
     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: "0.0.44" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.lambda.PythonUvFunction", version: "0.0.46" };
     // 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/data_sharing/__init__.py

@@ -59,12 +59,21 @@ def data_sharing_post_request(
     )
 
 
+from .query_helpers import (
+    get_package,
+    get_push_job
+)
+
 from .update_helpers import (
     update_package_status,
     update_push_job_status,
 )
 
 __all__ = [
+    # Get helpers
+    "get_package",
+    "get_push_job",
+    # Push job helpers
     "update_package_status",
     "update_push_job_status",
 ]

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

@@ -1,3 +1,4 @@
+from datetime import datetime
 from typing import Literal, TypedDict, NotRequired, Union
 
 PackageStatusType = Literal[
@@ -17,7 +18,7 @@ PushJobStatusType = Literal[
 ]
 
 
-class PackageObject(TypedDict):
+class PackageObjectDict(TypedDict):
     id: str
     packageName: str
     stepsExecutionArn: str
@@ -27,6 +28,18 @@ class PackageObject(TypedDict):
     hasExpired: NotRequired[bool]
 
 
+class PushJobObjectDict(TypedDict):
+    id: str
+    stepFunctionsExecutionArn: str
+    status: PushJobStatusType
+    startTime: str
+    packageId: str
+    shareDestination: str
+    logUri: NotRequired[str]
+    endTime: NotRequired[str]
+    errorMessages: NotRequired[str]
+
+
 class JobPatchParameters(TypedDict):
     status: Union[PackageStatusType, PushJobStatusType]
     errorMessage: NotRequired[str]

package/lambda/layers/orcabus_api_tools/src/orcabus_api_tools/data_sharing/query_helpers.py

@@ -0,0 +1,32 @@
+#!/usr/bin/env python3
+from .globals import PACKAGE_ENDPOINT, PUSH_ENDPOINT
+from .models import PackageObjectDict, PushJobObjectDict
+from . import get_data_sharing_request
+
+def get_package(
+        package_id: str,
+) -> PackageObjectDict:
+    """
+    Add QC stats to a fastq_id.
+
+    :param package_id: The package id
+    :param kwargs: JobPatchParameters to update the package with.
+    """
+    return get_data_sharing_request(
+        f"{PACKAGE_ENDPOINT}/{package_id}"
+    )
+
+
+def get_push_job(
+        push_job_id: str,
+) -> PushJobObjectDict:
+    """
+    Add push job status to a push job.
+
+    :param push_job_id: The push job id
+    :param push_job_status: The push job status to set
+    :param error_message: Optional error message
+    """
+    return get_data_sharing_request(
+        f"{PUSH_ENDPOINT}/{push_job_id}",
+    )

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

@@ -2,13 +2,13 @@ from typing import Unpack
 
 from . import data_sharing_patch_request
 from .globals import PACKAGE_ENDPOINT, PUSH_ENDPOINT
-from .models import PackageObject, JobPatchParameters
+from .models import PackageObjectDict, JobPatchParameters, PushJobObjectDict
 
 
 def update_package_status(
         package_id: str,
         **kwargs: Unpack[JobPatchParameters]
-) -> PackageObject:
+) -> PackageObjectDict:
     """
     Add QC stats to a fastq_id.
 
@@ -32,7 +32,7 @@ def update_package_status(
 def update_push_job_status(
         push_job_id: str,
         **kwargs: Unpack[JobPatchParameters]
-) -> PackageObject:
+) -> PushJobObjectDict:
     """
     Add push job status to a push job.
 

package/lambda/layers/orcabus_api_tools/src/orcabus_api_tools/fastq/multiqc_helpers.py

@@ -28,7 +28,8 @@ def update_multiqc_job_status(
         job_id: str,
         status: str,
         steps_execution_arn: Optional[str] = None,
-        output_uri: Optional[str] = None
+        html_output_uri: Optional[str] = None,
+        parquet_output_uri: Optional[str] = None
 ):
     """
     Update the status of a MultiQC job.
@@ -36,7 +37,8 @@ def update_multiqc_job_status(
     :param job_id: The unique identifier of the MultiQC job.
     :param status: The new status of the job (e.g., "running", "completed", "failed").
     :param steps_execution_arn: (Optional) The ARN of the step function execution associated with the job.
-    :param output_uri: (Optional) The URI of the output MultiQC report.
+    :param html_output_uri: (Optional) The URI of the output MultiQC report.
+    :param parquet_output_uri: (Optional) The URI of the output MultiQC parquet file.
     :return: The response from the fastq_patch_request function.
     """
     return fastq_patch_request(
@@ -46,7 +48,12 @@ def update_multiqc_job_status(
             {
                 "status": status,
                 "stepsExecutionArn": steps_execution_arn,
-                "multiqcOutputHtmlUri": output_uri
+                "multiqcHtml": ({
+                    "s3Uri": html_output_uri
+                }) if html_output_uri else None,
+                "multiqcParquet": ({
+                    "s3Uri": parquet_output_uri
+                }) if parquet_output_uri else None
             }.items())
         )
     )

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

@@ -15,6 +15,8 @@ from typing import (
     TypedDict, NotRequired, Literal, List, Union
 )
 
+from app.interface.jobs_api.models import ReadCountCalculationOutputObject
+
 JobType = Literal['FASTQ_DECOMPRESSION']
 JobStatusType = Literal['PENDING', 'RUNNING', 'FAILED', 'ABORTED', 'SUCCEEDED']
 
@@ -66,7 +68,8 @@ class RawMd5sumCalculationOutputObject(TypedDict):
 JobOutputType = Union[
   DecompressionJobOutputObject |
   GzipFileSizeCalculationOutputObject |
-  RawMd5sumCalculationOutputObject
+  RawMd5sumCalculationOutputObject |
+  ReadCountCalculationOutputObject
 ]
 
 class Job(TypedDict):
@@ -86,6 +89,7 @@ class JobCreateParameters(TypedDict):
     maxReads: NotRequired[int]
     outputUriPrefix: NotRequired[str]
     sampling: NotRequired[bool]
+    noSplitByLane: NotRequired[bool]
 
 
 class JobQueryParameters(TypedDict):

package/monitored-queue/index.js

@@ -13,7 +13,7 @@ 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: "0.0.44" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.monitoredQueue.MonitoredQueue", version: "0.0.46" };
     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: "0.0.44" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.namedLambdaRole.NamedLambdaRole", version: "0.0.46" };
     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": "0.0.44",
+  "version": "0.0.46",
   "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: "0.0.44" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.provider.ProviderFunction", version: "0.0.46" };
     _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: "0.0.44" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.networking.OrcaBusVpc", version: "0.0.46" };
     /**
      * 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: "0.0.44" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.networking.OrcaBusSharedComputeSecurityGroup", version: "0.0.46" };
     /**
      * 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: "0.0.44" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.slack.SlackAlerts", version: "0.0.46" };
     /**
      * Format the ARN for the slack alerts SNS topic for the current stack.
      * @param stack