@orcabus/platform-cdk-constructs 0.0.96 → 0.0.98

package/.jsii

@@ -7163,6 +7163,6 @@
       "symbolId": "shared-config/slack:SlackAlerts"
     }
   },
-  "version": "0.0.96",
-  "fingerprint": "Re6bzpleDW744afYQA2WMtPW+LFjfQUMhVTC1NUS/cM="
+  "version": "0.0.98",
+  "fingerprint": "rvUu4EFizvs1v4SixWCFt+FunEo4NBzVMRNVRUmnt78="
 }

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: "0.0.96" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.apigateway.OrcaBusApiGateway", version: "0.0.98" };
     /**
      * 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: "0.0.96" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.deploymentPipeline.CrossDeploymentArtifactBucket", version: "0.0.98" };
     /**
      * 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: "0.0.96" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.deploymentPipeline.DeploymentStackPipeline", version: "0.0.98" };
     /**
      * 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: "0.0.96" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.dynamodb.DynamoDbPartitionedConstruct", version: "0.0.98" };
     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: "0.0.96" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.dynamodb.DynamoDbNonPartitionedConstruct", version: "0.0.98" };
     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: "0.0.96" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.ecs.EcsFargateTaskConstruct", version: "0.0.98" };
     cluster;
     taskDefinition;
     taskExecutionRole;

package/eventbridge-rules/sfn-slack-notification.js

@@ -17,7 +17,7 @@ var SfnEventStatus;
     SfnEventStatus["ABORTED"] = "ABORTED";
 })(SfnEventStatus || (exports.SfnEventStatus = SfnEventStatus = {}));
 class SfnSlackNotification extends constructs_1.Construct {
-    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.eventbridgeRule.SfnSlackNotification", version: "0.0.96" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.eventbridgeRule.SfnSlackNotification", version: "0.0.98" };
     rule;
     constructor(scope, id, props) {
         super(scope, id);

package/lambda/index.js

@@ -57,7 +57,7 @@ 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: "0.0.96" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.lambda.PythonUvFunction", version: "0.0.98" };
     // 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

@@ -83,7 +83,8 @@ from .job_helpers import (
     run_qc_stats,
     run_ntsm,
     run_file_compression_stats,
-    run_read_count_stats
+    run_read_count_stats,
+    run_extract_fingerprint
 )
 
 # Query
@@ -114,6 +115,7 @@ from .update_helpers import (
     add_file_compression_information,
     add_ntsm_storage_object,
     add_read_set,
+    add_somalier_fingerprint,
     detach_read_set,
     validate_fastq,
     invalidate_fastq,
@@ -156,6 +158,7 @@ __all__ = [
     "run_ntsm",
     "run_file_compression_stats",
     "run_read_count_stats",
+    "run_extract_fingerprint",
     # Query
     "get_fastq",
     "get_fastq_set",
@@ -184,6 +187,7 @@ __all__ = [
     "detach_read_set",
     "validate_fastq",
     "invalidate_fastq",
+    "add_somalier_fingerprint",
     "link_fastq_list_row_to_fastq_set",
     "link_fastq_to_fastq_set",
     "unlink_fastq_list_row_from_fastq_set",

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

@@ -7,11 +7,13 @@ Update helpers for the update script.
 - run_ntsm
 - run_file_compression_information
 """
+from typing import Dict, Any
+
 # Standard imports
 
 # Local imports
 from . import fastq_patch_request
-from .globals import FASTQ_ENDPOINT
+from .globals import FASTQ_ENDPOINT, FASTQ_SET_ENDPOINT
 from .models import Job
 
 
@@ -63,3 +65,25 @@ def run_read_count_stats(fastq_id: str) -> Job:
             f"{FASTQ_ENDPOINT}/{fastq_id}:runReadCountInformation"
         )
     )
+
+def run_extract_fingerprint(
+        fastq_set_id: str,
+        reference_name: str,
+        bam_uri: str
+) -> Dict[str, Any]:
+    """
+    Run extract fingerprint for a fastq_set_id.
+
+    :param bam_uri:
+    :param reference_name:
+    :param fastq_set_id: Fastq set id
+    """
+    return fastq_patch_request(
+        f"{FASTQ_SET_ENDPOINT}/{fastq_set_id}:runExtractFingerprint",
+        params={
+            "referenceName": reference_name
+        },
+        json_data={
+            "s3Uri": bam_uri
+        }
+    )

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

@@ -237,3 +237,21 @@ def set_is_not_current_fastq_set(fastq_set_id: str) -> FastqSet:
     return fastq_patch_request(
         f"{FASTQ_SET_ENDPOINT}/{fastq_set_id}/notCurrentFastqSet"
     )
+
+
+def add_somalier_fingerprint(
+    fastq_set_id: str,
+    s3_uri: str
+) -> FastqSet:
+    """
+    Add a Somalier storage object to a fastq set id.
+
+    :param fastq_set_id: Fastq str
+    :param s3_uri: Somalier s3 uri
+    """
+    return fastq_patch_request(
+        f"{FASTQ_SET_ENDPOINT}/{fastq_set_id}:addFingerprint",
+        json_data={
+            "s3Uri": s3_uri
+        }
+    )

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

@@ -104,7 +104,7 @@ def get_file_object_from_ingest_id(ingest_id: str, **kwargs) -> FileObject:
     file_objects_list.sort(
         key=lambda file_obj_iter_: (
             StorageClassPriority[file_obj_iter_['storageClass']],
-            -datetime.fromisoformat(file_obj_iter_['eventTime']).timestamp()
+            -datetime.fromisoformat(file_obj_iter_['lastModifiedDate']).timestamp()
         )
     )
 
@@ -157,7 +157,7 @@ def get_portal_run_id_root_prefix(portal_run_id: str) -> str:
 
     # Sort by most recent output
     all_portal_run_id_files.sort(
-        key=lambda file_iter_: datetime.fromisoformat(file_iter_['eventTime']).timestamp(),
+        key=lambda file_iter_: datetime.fromisoformat(file_iter_['lastModifiedDate']).timestamp(),
         reverse=True
     )
 
@@ -277,7 +277,9 @@ def get_presigned_url_expiry(s3_presigned_url: str) -> datetime:
     return (creation_time + expiry_ext).astimezone(tz=timezone.utc)
 
 
-def get_s3_objs_from_ingest_ids_map(ingest_ids: List[str], **kwargs) -> List[Dict[str, Union[FileObject, str]]]:
+def get_s3_objs_from_ingest_ids_map(
+        ingest_ids: List[str], **kwargs
+) -> List[Dict[str, Union[FileObject, str]]]:
     # Check if the list is empty
     if len(ingest_ids) == 0:
         return []
@@ -322,7 +324,7 @@ def get_s3_objs_from_ingest_ids_map(ingest_ids: List[str], **kwargs) -> List[Dic
         s3_objects_match.sort(
             key=lambda s3_object_iter_: (
                 StorageClassPriority[s3_object_iter_['fileObject']['storageClass']],
-                -datetime.fromisoformat(s3_object_iter_['fileObject']['eventTime']).timestamp()
+                -datetime.fromisoformat(s3_object_iter_['fileObject']['lastModifiedDate']).timestamp()
             )
         )
 

package/lambda/layers/orcabus_api_tools/src/orcabus_api_tools/icav2_wes/update_helpers.py

@@ -17,9 +17,12 @@ def update_icav2_wes_analysis_status(
     # Confirm param keys are valid
     for key in kwargs.keys():
         if key not in WESPatchRequest.__annotations__:
-            raise ValueError(f"Invalid parameter key: {key}. Valid keys are: {', '.join(WESPatchRequest.__annotations__.keys())}")
-
+            raise ValueError(
+                f"Invalid parameter key: {key}. "
+                f"Valid keys are: {', '.join(WESPatchRequest.__annotations__.keys())}"
+            )
 
+    # Return the patch request
     return icav2_wes_patch_request(
         f"{ANALYSES_ENDPOINT}/{icav2_wes_orcabus_id}",
         json_data=dict(filter(

package/lambda/layers/orcabus_api_tools/src/orcabus_api_tools/utils/miscell.py

@@ -1,6 +1,11 @@
+#!/usr/bin/env python3
+
+# Imports
+from typing import Tuple
 from urllib.parse import urlparse
 
-def get_bucket_key_pair_from_uri(s3_uri: str) -> (str, str):
+
+def get_bucket_key_pair_from_uri(s3_uri: str) -> Tuple[str, str]:
     """
     Get the bucket and key from an s3 uri
     :param s3_uri:

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

@@ -39,7 +39,8 @@ from .create_helpers import (
 
 from .metadata_helpers import (
     get_workflows_from_library_id,
-    get_workflows_from_library_id_list
+    get_workflows_from_library_id_list,
+    get_workflow_runs_from_metadata,
 )
 
 from .query_helpers import (
@@ -47,6 +48,7 @@ from .query_helpers import (
     get_workflows_from_analysis_run_id,
     list_workflow_runs_by_workflow_name,
     list_workflow_runs_from_analysis_run_id,
+    list_workflow_runs,
 )
 
 from .workflow_helpers import (
@@ -75,12 +77,14 @@ __all__ = [
     # Metadata
     "get_workflows_from_library_id",
     "get_workflows_from_library_id_list",
+    "get_workflow_runs_from_metadata",
     # Query
     # Deprecated
     "get_workflow_by_workflow_name",
     "get_workflows_from_analysis_run_id",
-    # New
     "list_workflow_runs_by_workflow_name",
+    # New
+    "list_workflow_runs",
     "list_workflow_runs_from_analysis_run_id",
     # Payload
     "get_payload",

package/lambda/layers/orcabus_api_tools/src/orcabus_api_tools/workflow/metadata_helpers.py

@@ -5,7 +5,7 @@ Get workflows from library id
 """
 
 # Standard imports
-from typing import List
+from typing import List, Optional
 
 # Local imports
 from . import get_workflow_request_response_results
@@ -57,4 +57,123 @@ def get_workflows_from_library_id_list(library_id_list: List[str]) -> List[Workf
             workflows_for_library
         ))
 
-    return all_workflows_intersected
+    return all_workflows_intersected
+
+
+def get_workflows_from_rgid_list(
+        rgid_list: List[str]
+) -> List[WorkflowRunDetail]:
+    """
+    Use the query libraries__rgid to get workflows from a list of rgids
+    However, we only collect the workflows that are associated will all rgids in the list,
+    This may be useful if given a tumor normal pair and you want to find all workflows associated
+    with that specific tumor normal pair
+    :param rgid_list:
+    :return:
+    """
+    from ..fastq import get_fastq_by_rgid
+
+    fastq_id_list = list(map(
+        lambda rgid_: get_fastq_by_rgid(rgid_)['id'],
+        rgid_list
+    ))
+
+    if len(fastq_id_list) < 1:
+        return []
+
+    all_workflows_intersected = get_workflow_request_response_results(
+        WORKFLOW_RUN_ENDPOINT,
+        params={
+            "readsets": fastq_id_list[0]
+        }
+    )
+
+    if len(fastq_id_list) == 1:
+        return all_workflows_intersected
+
+    for fastq_id in fastq_id_list[1:]:
+        workflows_for_fastq_id = get_workflow_request_response_results(
+            WORKFLOW_RUN_ENDPOINT,
+            params={
+                "readsets": fastq_id
+            }
+        )
+        all_workflows_intersected = list(filter(
+            lambda workflow_iter_: workflow_iter_['orcabusId'] in list(map(
+                lambda all_workflows_iter_: all_workflows_iter_['orcabusId'],
+                all_workflows_intersected
+            )),
+            workflows_for_fastq_id
+        ))
+
+    return all_workflows_intersected
+
+
+def get_workflow_runs_from_metadata(
+        workflow_name: str,
+        workflow_version: Optional[str] = None,
+        code_version: Optional[str] = None,
+        analysis_run_id: Optional[str] = None,
+        current_status: Optional[str] = None,
+        library_id_list: Optional[List[str]] = None,
+        rgid_list: Optional[List[str]] = None,
+) -> List[WorkflowRunDetail]:
+    """
+    Get workflow runs from metadata such as library ids or rgids
+    but allow filtering on standard workflow run metadata such as workflow name, version, analysis run id, and current status
+    :param workflow_name:
+    :param workflow_version:
+    :param code_version:
+    :param analysis_run_id:
+    :param current_status:
+    :param library_id_list:
+    :param rgid_list:
+    :return:
+    """
+
+    # Local relative imports
+    from .query_helpers import (
+        list_workflow_runs
+    )
+
+    # Get all workflows for a given workflow name and version
+    workflow_run_list = list_workflow_runs(
+        workflow_name=workflow_name,
+        workflow_version=workflow_version,
+        code_version=code_version,
+        analysis_run_id=analysis_run_id,
+        current_status=current_status,
+    )
+
+    # Filter by library id list if provided
+    if library_id_list is not None:
+        workflow_library_id_list = get_workflows_from_library_id_list(
+            library_id_list=library_id_list,
+        )
+        workflow_run_list = list(filter(
+            lambda workflow_run_iter_: (
+                workflow_run_iter_['orcabusId'] in list(map(
+                    lambda workflow_iter_: workflow_iter_['orcabusId'],
+                    workflow_library_id_list
+                ))
+            ),
+            workflow_run_list
+        ))
+
+    # Filter by rgid list if provided
+    if rgid_list is not None:
+        workflow_rgid_list = get_workflows_from_rgid_list(
+            rgid_list=rgid_list,
+        )
+        workflow_run_list = list(filter(
+            lambda workflow_run_iter_: (
+                workflow_run_iter_['orcabusId'] in list(map(
+                    lambda workflow_iter_: workflow_iter_['orcabusId'],
+                    workflow_rgid_list
+                ))
+            ),
+            workflow_run_list
+        ))
+
+    # Return the filtered list of workflow runs
+    return workflow_run_list

package/lambda/layers/orcabus_api_tools/src/orcabus_api_tools/workflow/payload_helpers.py

@@ -13,14 +13,14 @@ from .globals import PAYLOAD_ENDPOINT
 from .models import Payload
 
 
-def get_payload(payload_id: str) -> Payload:
+def get_payload(payload_id: str) -> Optional[Payload]:
     """
     Get payload from the payload id
     :param payload_id:
     :return:
     """
     # Get payload
-    return Payload(**get_workflow_request(f"{PAYLOAD_ENDPOINT}/{payload_id}"))
+    return cast(Payload, get_workflow_request(f"{PAYLOAD_ENDPOINT}/{payload_id}"))
 
 
 def get_payload_from_state_orcabus_id(workflow_run_orcabus_id: str, state_orcabus_id: str) -> Optional[Payload]:

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

@@ -5,7 +5,7 @@ Get workflows from library id
 """
 # Standard imports
 import warnings
-from typing import List
+from typing import List, Optional
 
 # Local imports
 from . import get_workflow_request_response_results
@@ -13,20 +13,37 @@ from .globals import WORKFLOW_RUN_ENDPOINT
 from .models import WorkflowRunDetail
 
 
-def list_workflow_runs_from_analysis_run_id(analysis_run_id: str) -> List[WorkflowRunDetail]:
+def list_workflow_runs(
+        workflow_name: Optional[str] = None,
+        workflow_version: Optional[str] = None,
+        code_version: Optional[str] = None,
+        current_status: Optional[str] = None,
+        analysis_run_id: Optional[str] = None,
+) -> List[WorkflowRunDetail]:
     """
-    Use the query analysisRuns__analysisRunId to get workflows from an analysis run id
-    :param analysis_run_id:
+    Use the query name to get workflows
+    :param workflow_name:
+    :param workflow_version:
+    :param code_version:
+    :param current_status:
     :return:
     """
     return get_workflow_request_response_results(
         WORKFLOW_RUN_ENDPOINT,
-        params={
-            "analysisRun__orcabusId": analysis_run_id
-        }
+        params=dict(filter(
+            lambda item: item[1] is not None,
+            {
+                "workflow__name": workflow_name,
+                "workflow__version": workflow_version,
+                "workflow__codeVersion": code_version,
+                "currentState__status": current_status,
+                "analysisRun__orcabusId": analysis_run_id
+            }.items()
+        ))
     )
 
 
+# Deprecated
 def list_workflow_runs_by_workflow_name(
         workflow_name: str,
 ) -> List[WorkflowRunDetail]:
@@ -35,27 +52,47 @@ def list_workflow_runs_by_workflow_name(
     :param workflow_name:
     :return:
     """
-
+    warnings.warn(DeprecationWarning(
+        "This function is deprecated, "
+        "please use list_workflow_runs instead"
+    ))
     return get_workflow_request_response_results(
         WORKFLOW_RUN_ENDPOINT,
-        params={
-            "workflow__name": workflow_name
-        }
+        params=dict(filter(
+            lambda item: item[1] is not None,
+            {
+                "workflow__name": workflow_name,
+            }.items()
+        ))
     )
 
 
-# Deprecated
 def get_workflow_by_workflow_name(workflow_name: str) -> List[WorkflowRunDetail]:
     warnings.warn(DeprecationWarning(
         "This function is deprecated, "
-        "please use list_workflow_runs_by_workflow_name instead"
+        "please use list_workflow_runs(workflow_name=workflow_name) instead"
     ))
-    return list_workflow_runs_by_workflow_name(workflow_name)
+    return list_workflow_runs(workflow_name=workflow_name)
 
 
 def get_workflows_from_analysis_run_id(analysis_run_id: str) -> List[WorkflowRunDetail]:
     warnings.warn(DeprecationWarning(
         "This function is deprecated, "
-        "please use list_workflow_runs_from_analysis_run_id instead"
+        "please use list_workflow_runs(analysis_run_id=analysis_run_id) instead"
     ))
-    return list_workflow_runs_from_analysis_run_id(analysis_run_id)
+    return list_workflow_runs(analysis_run_id=analysis_run_id)
+
+
+def list_workflow_runs_from_analysis_run_id(analysis_run_id: str) -> List[WorkflowRunDetail]:
+    """
+    Use the query analysisRuns__analysisRunId to get workflows from an analysis run id
+    :param analysis_run_id:
+    :return:
+    """
+    warnings.warn(DeprecationWarning(
+        "This function is deprecated, "
+        "please use list_workflow_runs(analysis_run_id=analysis_run_id) instead"
+    ))
+    return list_workflow_runs(
+        analysis_run_id=analysis_run_id
+    )

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: "0.0.96" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.monitoredQueue.MonitoredQueue", version: "0.0.98" };
     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: "0.0.96" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.namedLambdaRole.NamedLambdaRole", version: "0.0.98" };
     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": "0.0.96",
+  "version": "0.0.98",
   "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: "0.0.96" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.provider.ProviderFunction", version: "0.0.98" };
     _function;
     _response;
     constructor(scope, id, props) {

package/shared-config/file-manager.d.ts

@@ -2,6 +2,7 @@
  * Shared config for the FileManager.
  */
 import { StageName } from "./accounts";
+export declare const FILE_MANAGER_INVENTORY_BUCKET = "filemanager-inventory-test";
 export declare const FILE_MANAGER_BUCKETS: Record<StageName, string[]>;
 export declare const FILE_MANAGER_CACHE_BUCKETS: Record<StageName, string[]>;
 export declare const FILE_MANAGER_CROSS_ACCOUNT_BUCKETS: string[];

package/shared-config/file-manager.js

@@ -3,18 +3,20 @@
  * Shared config for the FileManager.
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.FILE_MANAGER_DOMAIN_PREFIX = exports.FILE_MANAGER_PRESIGN_USER = exports.FILE_MANAGER_INGEST_ROLE = exports.FILE_MANAGER_ACCESS_KEY_ARNS = exports.FILE_MANAGER_PRESIGN_USER_SECRET = exports.FILE_MANAGER_CROSS_ACCOUNT_BUCKETS = exports.FILE_MANAGER_CACHE_BUCKETS = exports.FILE_MANAGER_BUCKETS = void 0;
+exports.FILE_MANAGER_DOMAIN_PREFIX = exports.FILE_MANAGER_PRESIGN_USER = exports.FILE_MANAGER_INGEST_ROLE = exports.FILE_MANAGER_ACCESS_KEY_ARNS = exports.FILE_MANAGER_PRESIGN_USER_SECRET = exports.FILE_MANAGER_CROSS_ACCOUNT_BUCKETS = exports.FILE_MANAGER_CACHE_BUCKETS = exports.FILE_MANAGER_BUCKETS = exports.FILE_MANAGER_INVENTORY_BUCKET = void 0;
 const deployment_stack_pipeline_1 = require("../deployment-stack-pipeline");
 const s3_1 = require("./s3");
 const secrets_1 = require("./secrets");
+// The inventory bucket used for testing filemanager.
+exports.FILE_MANAGER_INVENTORY_BUCKET = "filemanager-inventory-test";
 // Regular buckets where all data is available and ingested.
 exports.FILE_MANAGER_BUCKETS = {
     BETA: [
         s3_1.ONCOANALYSER_BUCKET.BETA,
+        exports.FILE_MANAGER_INVENTORY_BUCKET,
         `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: [
         s3_1.ONCOANALYSER_BUCKET.GAMMA,
@@ -57,4 +59,4 @@ 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: "0.0.96" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.networking.OrcaBusVpc", version: "0.0.98" };
     /**
      * 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: "0.0.96" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.networking.OrcaBusSharedComputeSecurityGroup", version: "0.0.98" };
     /**
      * The shared security group that is used by compute resources to access the database.
      * @param scope

package/shared-config/s3.js

@@ -41,4 +41,4 @@ exports.ANALYSIS_ARCHIVE_BUCKET = "archive-prod-analysis-503977275616-ap-southea
  * The fastq archive bucket.
  */
 exports.FASTQ_ARCHIVE_BUCKET = "archive-prod-fastq-503977275616-ap-southeast-2";
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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: "0.0.96" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.slack.SlackAlerts", version: "0.0.98" };
     /**
      * Format the ARN for the slack alerts SNS topic for the current stack.
      * @param stack