@orcabus/platform-cdk-constructs 0.0.38 → 0.0.40

package/.jsii

@@ -6756,6 +6756,6 @@
       "symbolId": "shared-config/slack:SlackAlerts"
     }
   },
-  "version": "0.0.38",
-  "fingerprint": "4FjPVQ7u4dRTAh4I76FF/w9EfDixVRbUKYR3r1wD8kg="
+  "version": "0.0.40",
+  "fingerprint": "ischMi4D/qAlGXofBjJIHsN2yNBJY4fISqc+SVhvE7M="
 }

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: "0.0.38" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.apigateway.OrcaBusApiGateway", version: "0.0.40" };
     /**
      * 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: "0.0.38" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.deploymentPipeline.CrossDeploymentArtifactBucket", version: "0.0.40" };
     /**
      * 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: "0.0.38" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.deploymentPipeline.DeploymentStackPipeline", version: "0.0.40" };
     /**
      * 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: "0.0.38" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.dynamodb.DynamoDbPartitionedConstruct", version: "0.0.40" };
     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: "0.0.38" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.dynamodb.DynamoDbNonPartitionedConstruct", version: "0.0.40" };
     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: "0.0.38" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.ecs.EcsFargateTaskConstruct", version: "0.0.40" };
     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: "0.0.38" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.lambda.PythonUvFunction", version: "0.0.40" };
     // 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/models.py

@@ -1,4 +1,4 @@
-from typing import Literal, TypedDict, NotRequired
+from typing import Literal, TypedDict, NotRequired, Union
 
 PackageStatusType = Literal[
     "PENDING",
@@ -28,5 +28,5 @@ class PackageObject(TypedDict):
 
 
 class JobPatchParameters(TypedDict):
-    status: str
+    status: Union[PackageStatusType, PushJobStatusType]
     errorMessage: NotRequired[str]

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

@@ -104,7 +104,7 @@ from .query_helpers import (
     get_fastqs_in_project,
     get_fastq_list_rows_in_fastq_set,
     get_fastqs_in_fastq_set,
-    get_fastq_jobs,
+    get_fastq_jobs, get_fastq_by_rgid,
 )
 
 # Updaters
@@ -165,6 +165,7 @@ __all__ = [
     "get_fastqs_in_subject",
     "get_fastqs_in_individual",
     "get_fastqs_in_project",
+    "get_fastq_by_rgid",
     "get_fastq_list_rows_in_fastq_set",
     "get_fastqs_in_fastq_set",
     "get_fastq_jobs",

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

@@ -8,6 +8,7 @@ FASTQ_SUBDOMAIN_NAME = "fastq"
 # API ENDPOINTS
 FASTQ_ENDPOINT = "api/v1/fastq"
 FASTQ_SET_ENDPOINT = "api/v1/fastqSet"
+RGID_ENDPOINT = "api/v1/rgid"
 
 # REGEX
 ORCABUS_ULID_REGEX_MATCH = re.compile(r'^[a-z0-9]{3}\.[A-Z0-9]{26}$')

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

@@ -15,7 +15,7 @@ get_fastqs_in_individual
 
 get_fastqs_in_project
 
-get_fastq_by_rgid_and_instrument_run_id
+get_fastq_by_rgid
 
 """
 from functools import reduce
@@ -25,7 +25,7 @@ from typing import List, Unpack
 from fastapi.encoders import jsonable_encoder
 
 from . import get_fastq_request_response_results, get_fastq_request
-from .globals import FASTQ_ENDPOINT, FASTQ_SET_ENDPOINT
+from .globals import FASTQ_ENDPOINT, FASTQ_SET_ENDPOINT, RGID_ENDPOINT
 from .models import (
     FastqSet, Job, FastqParameters, FastqSetQueryParameters,
     FastqGetResponseParameters, VALID_BATCH_KEYS, Fastq
@@ -58,7 +58,7 @@ def get_fastq_set(
     """
     # Raise error if any of the kwargs are not in the FastqSetQueryParameters
     for key in kwargs.keys():
-        if key not in FastqSetQueryParameters.__annotations__:
+        if key not in FastqGetResponseParameters.__annotations__:
             raise ValueError(f"Invalid parameter: {key}")
 
     return FastqSet(
@@ -230,6 +230,24 @@ def get_fastqs_in_project(project_id):
     )
 
 
+def get_fastq_by_rgid(
+        rgid: str,
+        **kwargs: Unpack[FastqGetResponseParameters]
+) -> Fastq:
+    # Raise error if any of the kwargs are not in the FastqGetResponseParameters
+    for key in kwargs.keys():
+        if key not in FastqGetResponseParameters.__annotations__:
+            raise ValueError(f"Invalid parameter: {key}")
+
+    return get_fastq_request(
+        f"{RGID_ENDPOINT}/{rgid}",
+        params=dict(filter(
+            lambda kv_iter_: kv_iter_[1] is not None,
+            kwargs.items()
+        ))
+    )
+
+
 def get_fastq_list_rows_in_fastq_set(fastq_set_id):
     """
     DEPRECATED: Use get_fastqs_in_fastq_set instead

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

@@ -144,7 +144,7 @@ def invalidate_fastq(fastq_id: str) -> Fastq:
 
 def link_fastq_list_row_to_fastq_set(fastq_id: str, fastq_set_id: str) -> FastqSet:
     """
-    Deprecated: Use `link_fastq_to_fast_set` instead.
+    Deprecated: Use `link_fastq_to_fastq_set` instead.
     Link a fastq id to a fastq set.
 
     :param fastq_id:

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

@@ -85,6 +85,7 @@ class JobCreateParameters(TypedDict):
     jobType: JobType
     maxReads: NotRequired[int]
     outputUriPrefix: NotRequired[str]
+    sampling: NotRequired[bool]
 
 
 class JobQueryParameters(TypedDict):

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

@@ -23,7 +23,7 @@ from . import (
 from .globals import (
     S3_LIST_ENDPOINT,
     S3_BUCKETS_BY_ACCOUNT_ID,
-    S3_PREFIXES_BY_ACCOUNT_ID
+    S3_PREFIXES_BY_ACCOUNT_ID, S3_ATTRIBUTES_LIST_ENDPOINT
 )
 
 if typing.TYPE_CHECKING:
@@ -108,27 +108,22 @@ def get_file_object_from_ingest_id(ingest_id: str, **kwargs) -> FileObject:
 
 def list_files_from_portal_run_id(
         portal_run_id: str,
-        workflow_name: str,
-        **kwargs
+        remove_log_files: bool = True,
 ) -> List[FileObject]:
-    portal_run_id_date_str = datetime.strptime(portal_run_id[:8], "%Y%m%d")
 
     # Get files from cache
-    cache_response = get_file_manager_request_response_results(S3_LIST_ENDPOINT, {
-        "bucket": get_cache_bucket_from_account_id(),
-        "key": f"{get_analysis_cache_prefix_from_account_id()}/{workflow_name}/{portal_run_id}/*",
-        **kwargs
+    all_files_list = get_file_manager_request_response_results(S3_ATTRIBUTES_LIST_ENDPOINT, {
+        "portalRunId": portal_run_id,
+        "currentState": json.dumps(True)
     })
 
-    # Get files from archive
-    archive_response = get_file_manager_request_response_results(S3_LIST_ENDPOINT, {
-        "bucket": get_archive_analysis_bucket_from_account_id(),
-        "key": f"v1/year={portal_run_id_date_str.year}/month={str(portal_run_id_date_str.month).zfill(2)}/{portal_run_id}/*",
-        **kwargs
-    })
+    if not remove_log_files:
+        return all_files_list
 
-    # Return as a list of FileObject models
-    return [FileObject(**file) for file in cache_response + archive_response]
+    return list(filter(
+        lambda file_iter_: not '/ica_logs/' in file_iter_['key'],
+        all_files_list
+    ))
 
 
 def get_presigned_url(s3_object_id: str) -> str:
@@ -137,7 +132,6 @@ def get_presigned_url(s3_object_id: str) -> str:
     :param s3_object_id:
     :return:
     """
-
     response = get_file_manager_request(f"{S3_LIST_ENDPOINT}/presign/{s3_object_id}")
 
     return str(response)

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: "0.0.38" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.monitoredQueue.MonitoredQueue", version: "0.0.40" };
     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: "0.0.38" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.namedLambdaRole.NamedLambdaRole", version: "0.0.40" };
     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": "0.0.38",
+  "version": "0.0.40",
   "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: "0.0.38" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.provider.ProviderFunction", version: "0.0.40" };
     _function;
     _response;
     constructor(scope, id, props) {

package/shared-config/file-manager.js

@@ -10,22 +10,25 @@ const secrets_1 = require("./secrets");
 exports.FILE_MANAGER_BUCKETS = {
     BETA: [
         "umccr-temp-dev",
-        `ntsm-fingerprints-${deployment_stack_pipeline_1.BETA_ENVIRONMENT.account}-ap-southeast-2`,
-        `data-sharing-artifacts-${deployment_stack_pipeline_1.BETA_ENVIRONMENT.account}-ap-southeast-2`,
+        `ntsm-fingerprints-${deployment_stack_pipeline_1.BETA_ENVIRONMENT.account}-${deployment_stack_pipeline_1.BETA_ENVIRONMENT.region}`,
+        `fastq-manager-sequali-outputs-${deployment_stack_pipeline_1.BETA_ENVIRONMENT.account}-${deployment_stack_pipeline_1.BETA_ENVIRONMENT.region}`,
+        `data-sharing-artifacts-${deployment_stack_pipeline_1.BETA_ENVIRONMENT.account}-${deployment_stack_pipeline_1.BETA_ENVIRONMENT.region}`,
         "filemanager-inventory-test",
     ],
     GAMMA: [
         "umccr-temp-stg",
-        `ntsm-fingerprints-${deployment_stack_pipeline_1.GAMMA_ENVIRONMENT.account}-ap-southeast-2`,
-        `data-sharing-artifacts-${deployment_stack_pipeline_1.GAMMA_ENVIRONMENT.account}-ap-southeast-2`,
+        `ntsm-fingerprints-${deployment_stack_pipeline_1.GAMMA_ENVIRONMENT.account}-${deployment_stack_pipeline_1.GAMMA_ENVIRONMENT.region}`,
+        `fastq-manager-sequali-outputs-${deployment_stack_pipeline_1.GAMMA_ENVIRONMENT.account}-${deployment_stack_pipeline_1.GAMMA_ENVIRONMENT.region}`,
+        `data-sharing-artifacts-${deployment_stack_pipeline_1.GAMMA_ENVIRONMENT.account}-${deployment_stack_pipeline_1.GAMMA_ENVIRONMENT.region}`,
     ],
     PROD: [
         "org.umccr.data.oncoanalyser",
         "archive-prod-analysis-503977275616-ap-southeast-2",
         "archive-prod-fastq-503977275616-ap-southeast-2",
-        `ntsm-fingerprints-${deployment_stack_pipeline_1.PROD_ENVIRONMENT.account}-ap-southeast-2`,
-        `data-sharing-artifacts-${deployment_stack_pipeline_1.PROD_ENVIRONMENT.account}-ap-southeast-2`,
-        "pipeline-montauk-977251586657-ap-southeast-2",
+        `ntsm-fingerprints-${deployment_stack_pipeline_1.PROD_ENVIRONMENT.account}-${deployment_stack_pipeline_1.PROD_ENVIRONMENT.region}`,
+        `fastq-manager-sequali-outputs-${deployment_stack_pipeline_1.GAMMA_ENVIRONMENT.account}-${deployment_stack_pipeline_1.PROD_ENVIRONMENT.region}`,
+        `data-sharing-artifacts-${deployment_stack_pipeline_1.PROD_ENVIRONMENT.account}-${deployment_stack_pipeline_1.PROD_ENVIRONMENT.region}`,
+        `pipeline-montauk-977251586657-${deployment_stack_pipeline_1.PROD_ENVIRONMENT.region}`,
     ],
 };
 exports.FILE_MANAGER_CACHE_BUCKETS = {
@@ -43,4 +46,4 @@ exports.FILE_MANAGER_ACCESS_KEY_ARNS = {
 exports.FILE_MANAGER_INGEST_ROLE = "orcabus-file-manager-ingest-role";
 exports.FILE_MANAGER_PRESIGN_USER = "orcabus-file-manager-presign-user"; // pragma: allowlist secret
 exports.FILE_MANAGER_DOMAIN_PREFIX = "file";
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+//# 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

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: "0.0.38" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.networking.OrcaBusVpc", version: "0.0.40" };
     /**
      * 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: "0.0.38" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.networking.OrcaBusSharedComputeSecurityGroup", version: "0.0.40" };
     /**
      * 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: "0.0.38" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.slack.SlackAlerts", version: "0.0.40" };
     /**
      * Format the ARN for the slack alerts SNS topic for the current stack.
      * @param stack