@orcabus/platform-cdk-constructs 0.0.43 → 0.0.44

package/.jsii

@@ -6756,6 +6756,6 @@
       "symbolId": "shared-config/slack:SlackAlerts"
     }
   },
-  "version": "0.0.43",
-  "fingerprint": "YSlLcVlXhkJ2rWV9TD1SfBIOuMH4gCYXv6HSkM9za/g="
+  "version": "0.0.44",
+  "fingerprint": "arsb/LGcRULLZhW7yVeQPPrQ6Xufpe98A6X9G62fzCM="
 }

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: "0.0.43" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.apigateway.OrcaBusApiGateway", version: "0.0.44" };
     /**
      * 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: "0.0.43" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.deploymentPipeline.CrossDeploymentArtifactBucket", version: "0.0.44" };
     /**
      * 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: "0.0.43" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.deploymentPipeline.DeploymentStackPipeline", version: "0.0.44" };
     /**
      * 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: "0.0.43" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.dynamodb.DynamoDbPartitionedConstruct", version: "0.0.44" };
     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: "0.0.43" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.dynamodb.DynamoDbNonPartitionedConstruct", version: "0.0.44" };
     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: "0.0.43" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.ecs.EcsFargateTaskConstruct", version: "0.0.44" };
     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: "0.0.43" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.lambda.PythonUvFunction", version: "0.0.44" };
     // 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/__init__.py

@@ -141,7 +141,8 @@ from .workflow_helpers import (
 
 # Multiqc
 from .multiqc_helpers import (
-    run_multiqc
+    run_multiqc,
+    update_multiqc_job_status
 )
 
 
@@ -199,5 +200,6 @@ __all__ = [
     "to_fastq_list_rows",
     # Multiqc
     "run_multiqc",
+    "update_multiqc_job_status",
 ]
 

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

@@ -92,6 +92,17 @@ class SequaliReportsDict(TypedDict):
     multiqcParquet: FileStorageObject
 
 
+class QcStats(TypedDict):
+    insertSizeEstimate: int
+    rawWgsCoverageEstimate: int
+    r1Q20Fraction: float
+    r2Q20Fraction: float
+    r1GcFraction: float
+    r2GcFraction: float
+    duplicationFractionEstimate: float
+    sequaliReports: Optional[SequaliReportsDict]
+
+
 # Deprecated: Use FastqCreate instead
 class FastqListRowCreate(TypedDict):
     fastqSetId: Optional[str]
@@ -140,7 +151,7 @@ class Fastq(TypedDict):
     center: Optional[str]
     date: Optional[datetime]
     readSet: Optional[ReadSet]
-    qc: Optional[Dict]
+    qc: Optional[QcStats]
     readCount: Optional[int]
     baseCountEst: Optional[int]
     isValid: Optional[bool]
@@ -157,7 +168,7 @@ class FastqCreate(TypedDict):
     center: Optional[str]
     date: Optional[datetime]
     readSet: Optional[ReadSet]
-    qc: Optional[Dict]
+    qc: Optional[QcStats]
     readCount: Optional[int]
     baseCountEst: Optional[int]
     isValid: Optional[bool]
@@ -179,17 +190,6 @@ class FastqSet(TypedDict):
     isCurrentFastqSet: bool
 
 
-class QcStats(TypedDict):
-    insertSizeEstimate: int
-    rawWgsCoverageEstimate: int
-    r1Q20Fraction: float
-    r2Q20Fraction: float
-    r1GcFraction: float
-    r2GcFraction: float
-    duplicationFractionEstimate: float
-    sequaliReports: Optional[SequaliReportsDict]
-
-
 class ReadCount(TypedDict):
     readCount: int
     baseCountEst: int

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

@@ -3,8 +3,11 @@
 """
 Run MultiQC on a list of fastq ids
 """
-from typing import List
 
+# Standard imports
+from typing import List, Optional
+
+# Custom imports
 from orcabus_api_tools.fastq import fastq_patch_request
 from orcabus_api_tools.fastq.globals import MULTIQC_ENDPOINT
 
@@ -19,3 +22,31 @@ def run_multiqc(fastq_id_list: List[str]) -> str:
         f"{MULTIQC_ENDPOINT}",
         json_data=fastq_id_list
     )
+
+
+def update_multiqc_job_status(
+        job_id: str,
+        status: str,
+        steps_execution_arn: Optional[str] = None,
+        output_uri: Optional[str] = None
+):
+    """
+    Update the status of a MultiQC job.
+
+    :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.
+    :return: The response from the fastq_patch_request function.
+    """
+    return fastq_patch_request(
+        f"{MULTIQC_ENDPOINT}/{job_id}",
+        json_data=dict(filter(
+            lambda kv_iter_: kv_iter_[1] is not None,
+            {
+                "status": status,
+                "stepsExecutionArn": steps_execution_arn,
+                "multiqcOutputHtmlUri": output_uri
+            }.items())
+        )
+    )

package/lambda/layers/orcabus_api_tools/src/orcabus_api_tools/fastq_unarchiving/create_helpers.py

@@ -20,7 +20,7 @@ def create_job(fastq_ids: List[str], job_type: Optional[JobType] = None) -> Job:
 
     return fastq_unarchiving_post_request(
         JOB_ENDPOINT,
-        params={
+        json_data={
             "fastqIds": fastq_ids,
             "jobType": job_type
         }

package/lambda/layers/orcabus_api_tools/src/orcabus_api_tools/metadata/__init__.py

@@ -50,7 +50,7 @@ def get_item_objs_from_item_id_list(
             }
         )
     except HTTPError as e:
-        raise HTTPError(f"Could not get item from item id list {item_id_list} from endpoint {endpoint}") from e
+        raise ValueError(f"Could not get item from item id list {item_id_list} from endpoint {endpoint}") from e
 
     # Accept missing
     if accept_missing:

package/lambda/layers/orcabus_api_tools/src/orcabus_api_tools/metadata/project_helpers.py

@@ -92,7 +92,8 @@ def get_project_from_project_orcabus_id(project_orcabus_id: str) -> Project:
 def get_projects_list_from_project_orcabus_id_list(project_orcabus_id_list: List[str], accept_missing: bool = False) -> List[Project]:
     """
     Get project from the project id
-    :param project_id:
+    :param project_orcabus_id_list:
+    :param accept_missing:
     :return:
     """
     # We have an internal id, convert to int

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: "0.0.43" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.monitoredQueue.MonitoredQueue", version: "0.0.44" };
     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: "0.0.43" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.namedLambdaRole.NamedLambdaRole", version: "0.0.44" };
     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": "0.0.43",
+  "version": "0.0.44",
   "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: "0.0.43" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.provider.ProviderFunction", version: "0.0.44" };
     _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: "0.0.43" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.networking.OrcaBusVpc", version: "0.0.44" };
     /**
      * 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: "0.0.43" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.networking.OrcaBusSharedComputeSecurityGroup", version: "0.0.44" };
     /**
      * 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: "0.0.43" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.slack.SlackAlerts", version: "0.0.44" };
     /**
      * Format the ARN for the slack alerts SNS topic for the current stack.
      * @param stack