@orcabus/platform-cdk-constructs 0.0.37 → 0.0.39

package/.jsii

@@ -6756,6 +6756,6 @@
       "symbolId": "shared-config/slack:SlackAlerts"
     }
   },
-  "version": "0.0.37",
-  "fingerprint": "WJnxu31JCGx88czmTm4wEcOiYLDLTbs658r/FyyoErY="
+  "version": "0.0.39",
+  "fingerprint": "qjgprLux9UbUIiorobtrlx7b3YD70Zoe6UAFDPpxrKg="
 }

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: "0.0.37" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.apigateway.OrcaBusApiGateway", version: "0.0.39" };
     /**
      * 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: "0.0.37" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.deploymentPipeline.CrossDeploymentArtifactBucket", version: "0.0.39" };
     /**
      * 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: "0.0.37" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.deploymentPipeline.DeploymentStackPipeline", version: "0.0.39" };
     /**
      * 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: "0.0.37" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.dynamodb.DynamoDbPartitionedConstruct", version: "0.0.39" };
     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: "0.0.37" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.dynamodb.DynamoDbNonPartitionedConstruct", version: "0.0.39" };
     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: "0.0.37" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.ecs.EcsFargateTaskConstruct", version: "0.0.39" };
     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: "0.0.37" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.lambda.PythonUvFunction", version: "0.0.39" };
     // 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/mart_tools/src/mart_tools/mart/models.py

@@ -1,8 +1,6 @@
 #!/usr/bin/env python
 
 from enum import Enum
-from typing import Literal
-
 
 class AthenaDMLTypes(Enum):
     # https://docs.aws.amazon.com/athena/latest/ug/data-types.html

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

@@ -41,21 +41,21 @@ def get_data_sharing_request_response_results(
 
 def data_sharing_patch_request(
     endpoint: str,
-    params: Optional[Dict] = None,
+    json_data: Optional[Dict] = None,
 ):
     return patch_request(
         url=get_data_sharing_url(endpoint),
-        params=params
+        json_data=json_data
     )
 
 
 def data_sharing_post_request(
     endpoint: str,
-    params: Optional[Dict] = None,
+    json_data: Optional[Dict] = None,
 ):
     return patch_request(
         url=get_data_sharing_url(endpoint),
-        params=params
+        json_data=json_data
     )
 
 

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

@@ -1,6 +1,5 @@
 # Imports
 import re
-from typing import Literal
 
 # AWS PARAMETERS
 DATA_SHARING_SUBDOMAIN_NAME = "data-sharing"

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",
@@ -17,7 +17,6 @@ PushJobStatusType = Literal[
 ]
 
 
-
 class PackageObject(TypedDict):
     id: str
     packageName: str
@@ -26,3 +25,8 @@ class PackageObject(TypedDict):
     requestTime: str
     completionTime: NotRequired[str]
     hasExpired: NotRequired[bool]
+
+
+class JobPatchParameters(TypedDict):
+    status: Union[PackageStatusType, PushJobStatusType]
+    errorMessage: NotRequired[str]

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

@@ -1,38 +1,37 @@
-from typing import Optional
+from typing import Unpack
 
 from . import data_sharing_patch_request
 from .globals import PACKAGE_ENDPOINT, PUSH_ENDPOINT
-from .models import PackageStatusType, PackageObject, PushJobStatusType
+from .models import PackageObject, JobPatchParameters
 
 
 def update_package_status(
         package_id: str,
-        package_status: PackageStatusType,
-        error_message: Optional[str] = None
+        **kwargs: Unpack[JobPatchParameters]
 ) -> PackageObject:
     """
     Add QC stats to a fastq_id.
 
     :param package_id: The package id
-    :param package_status: The package status to set
-    :param error_message: Optional error message
+    :param kwargs: JobPatchParameters to update the package with.
     """
+    # Raise error if any of the kwargs are not in the FastqListRowQueryParameters
+    for key in kwargs.keys():
+        if key not in JobPatchParameters.__annotations__:
+            raise ValueError(f"Invalid parameter: {key}")
+
     return data_sharing_patch_request(
         f"{PACKAGE_ENDPOINT}/{package_id}",
-        params=dict(filter(
+        json_data=dict(filter(
             lambda x: x[1] is not None,
-            {
-                "status": package_status,
-                "error_message": error_message
-            }.items()
+            kwargs.items()
         ))
     )
 
 
 def update_push_job_status(
         push_job_id: str,
-        push_job_status: PushJobStatusType,
-        error_message: Optional[str] = None
+        **kwargs: Unpack[JobPatchParameters]
 ) -> PackageObject:
     """
     Add push job status to a push job.
@@ -43,11 +42,8 @@ def update_push_job_status(
     """
     return data_sharing_patch_request(
         f"{PUSH_ENDPOINT}/{push_job_id}",
-        params=dict(filter(
+        json_data=dict(filter(
             lambda x: x[1] is not None,
-            {
-                "status": push_job_status,
-                "error_message": error_message
-            }.items()
+            kwargs.items()
         ))
     )

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

@@ -40,27 +40,31 @@ def get_fastq_request_response_results(
 ):
     return get_request_response_results(
         url=get_fastq_url(endpoint),
-        params=params
+        params=params,
     )
 
 
 def fastq_patch_request(
     endpoint: str,
     params: Optional[Dict] = None,
+    json_data: Optional[Dict] = None,
 ):
     return patch_request(
         url=get_fastq_url(endpoint),
-        params=params
+        params=params,
+        json_data=json_data,
     )
 
 
 def fastq_post_request(
     endpoint: str,
     params: Optional[Dict] = None,
+    json_data: Optional[Dict] = None,
 ):
     return post_request(
         url=get_fastq_url(endpoint),
-        params=params
+        params=params,
+        json_data=json_data,
     )
 
 
@@ -100,7 +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
@@ -161,6 +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/create_helpers.py

@@ -41,7 +41,7 @@ def create_fastq_object(**kwargs: Unpack[FastqCreate]) -> Fastq:
     return Fastq(
         **fastq_post_request(
             endpoint=FASTQ_ENDPOINT,
-            params=dict(kwargs)
+            json_data=dict(kwargs)
         )
     )
 
@@ -59,6 +59,6 @@ def create_fastq_set_object(**kwargs: Unpack[FastqSetCreate]) -> FastqSet:
     return FastqSet(
         **fastq_post_request(
             endpoint=FASTQ_SET_ENDPOINT,
-            params=dict(kwargs)
+            json_data=dict(kwargs)
         )
     )

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/models.py

@@ -35,7 +35,6 @@
 }
 """
 
-from enum import Enum
 from typing import (
     TypedDict,
     Optional,

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

@@ -37,7 +37,7 @@ def add_qc_stats(fastq_id: str, qc_stats: QcStats) -> Fastq:
 
     return fastq_patch_request(
         f"{FASTQ_ENDPOINT}/{fastq_id}/addQcStats",
-        params=dict(qc_stats)
+        json_data=dict(qc_stats)
     )
 
 
@@ -54,7 +54,7 @@ def add_read_count(fastq_id: str, read_count: ReadCount) -> Fastq:
 
     return fastq_patch_request(
         f"{FASTQ_ENDPOINT}/{fastq_id}/addReadCount",
-        params=dict(read_count)
+        json_data=dict(read_count)
     )
 
 
@@ -71,7 +71,7 @@ def add_file_compression_information(fastq_id: str, file_compression_information
 
     return fastq_patch_request(
         f"{FASTQ_ENDPOINT}/{fastq_id}/addFileCompressionInformation",
-        params=dict(file_compression_information)
+        json_data=dict(file_compression_information)
     )
 
 
@@ -88,7 +88,7 @@ def add_ntsm_storage_object(fastq_id: str, ntsm_fastq_storage_object: FileStorag
 
     return fastq_patch_request(
         f"{FASTQ_ENDPOINT}/{fastq_id}/addNtsmStorageObject",
-        params=dict(ntsm_fastq_storage_object)
+        json_data=dict(ntsm_fastq_storage_object)
     )
 
 
@@ -105,7 +105,7 @@ def add_read_set(fastq_id: str, read_set: ReadSet) -> Fastq:
 
     return fastq_patch_request(
         f"{FASTQ_ENDPOINT}/{fastq_id}/addFastqPairStorageObject",
-        params=dict(read_set)
+        json_data=dict(read_set)
     )
 
 
@@ -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/globals.py

@@ -1,7 +1,6 @@
 #!/usr/bin/env python3
 
 import re
-from enum import Enum
 
 # AWS PARAMETERS
 FASTQ_DECOMPRESSION_SUBDOMAIN_NAME = "fastq-decompression"

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

@@ -5,7 +5,7 @@ Update helpers for the update script.
 """
 
 # Standard imports
-from typing import Optional, Dict, Any, Unpack
+from typing import Unpack
 
 # Local imports
 from . import fastq_decompression_patch_request

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/lambda/layers/orcabus_api_tools/src/orcabus_api_tools/icav2_wes/__init__.py

@@ -4,7 +4,7 @@
 from typing import Optional, Dict
 
 from .globals import ICAV2_WES_SUBDOMAIN_NAME
-from .models import WESRequest
+from .models import WESPostRequest
 from ..utils.requests_helpers import (
     get_request, get_url, patch_request, get_request_response_results, post_request
 )
@@ -45,22 +45,22 @@ def get_icav2_wes_request_response_results(
 
 def icav2_wes_patch_request(
     endpoint: str,
-    params: Optional[Dict] = None,
+    json_data: Optional[Dict] = None,
 ):
     return patch_request(
         url=get_icav2_wes_url(endpoint),
-        params=params
+        json_data=json_data
     )
 
 
 def icav2_wes_post_request(
     endpoint: str,
-    params: Dict
+    json_data: Dict
 ):
     # Confirm param keys are valid
     return post_request(
         url=get_icav2_wes_url(endpoint),
-        params=params
+        json_data=json_data
     )
 
 

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

@@ -8,22 +8,22 @@ from typing import Unpack
 
 from . import icav2_wes_post_request
 from .globals import ANALYSES_ENDPOINT
-from .models import WESRequest, WESResponse
+from .models import WESPostRequest, WESResponse
 
 
 def create_icav2_wes_analysis(
-    **kwargs: Unpack[WESRequest]
+    **kwargs: Unpack[WESPostRequest]
 ) -> WESResponse:
     """
     Launch an icav2 analysis in the ICAV2 WES API.
     """
     # Confirm param keys are valid
     for key in kwargs.keys():
-        if key not in WESRequest.__annotations__:
-            raise ValueError(f"Invalid parameter key: {key}. Valid keys are: {', '.join(WESRequest.__annotations__.keys())}")
+        if key not in WESPostRequest.__annotations__:
+            raise ValueError(f"Invalid parameter key: {key}. Valid keys are: {', '.join(WESPostRequest.__annotations__.keys())}")
 
     # Confirm param values are valid
     return icav2_wes_post_request(
         ANALYSES_ENDPOINT,
-        params=dict(**kwargs)
+        json_data=dict(**kwargs)
     )

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

@@ -25,7 +25,7 @@ class EngineParameters(TypedDict):
     logsUri: str
 
 
-class WESRequest(TypedDict):
+class WESPostRequest(TypedDict):
     """WES request object."""
     name: str
     inputs: Dict[str, Any]
@@ -33,6 +33,11 @@ class WESRequest(TypedDict):
     tags: NotRequired[Dict[str, Any]]
 
 
+class WESPatchRequest(TypedDict):
+    status: str
+    icav2AnalysisId: NotRequired[str]
+
+
 class WESResponse(TypedDict):
     """WES response object."""
     id: str

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

@@ -1,26 +1,29 @@
 #!/usr/bin/env python3
-from typing import Optional
+from typing import Unpack
 
 from . import icav2_wes_patch_request
 from .globals import ANALYSES_ENDPOINT
-from .models import WESResponse
+from .models import WESResponse, WESPatchRequest
+
 
 # Get the icav2 wes analysis by analysis name
 def update_icav2_wes_analysis_status(
         icav2_wes_orcabus_id: str,
-        status: str,
-        icav2_analysis_id: Optional[str] = None
+        **kwargs: Unpack[WESPatchRequest]
 ) -> WESResponse:
     """
     Get the icav2 wes analysis by analysis name
     """
+    # 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())}")
+
+
     return icav2_wes_patch_request(
         f"{ANALYSES_ENDPOINT}/{icav2_wes_orcabus_id}",
-        params=dict(filter(
+        json_data=dict(filter(
             lambda kv_iter_: kv_iter_[1] is not None,
-            {
-                "status": status,
-                "icav2AnalysisId": icav2_analysis_id
-            }.items()
+            kwargs.items()
         ))
     )

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

@@ -1,8 +1,6 @@
 #!/usr/bin/env python
 
 from enum import Enum
-from typing import Literal
-
 
 class AthenaDMLTypes(Enum):
     # https://docs.aws.amazon.com/athena/latest/ug/data-types.html

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

@@ -42,7 +42,7 @@ def get_project_from_project_id(project_id: str) -> Project:
 def get_projects_list_from_project_id_list(project_id_list: List[str], accept_missing: bool = False) -> List[Project]:
     """
     Get project from the project id
-    :param project_id:
+    :param project_id_list:
     :return:
     """
     # We have an internal id, convert to int

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

@@ -44,7 +44,7 @@ def get_sample_from_sample_id(sample_id: str) -> Sample:
 def get_samples_list_from_sample_id_list(sample_id_list: List[str], accept_missing: bool = False) -> List[Sample]:
     """
     Get sample from the sample id
-    :param sample_id:
+    :param sample_id_list:
     :return:
     """
     # We have an internal id, convert to int
@@ -88,7 +88,7 @@ def get_sample_from_sample_orcabus_id(sample_orcabus_id: str) -> Sample:
 def get_samples_list_from_sample_orcabus_id_list(sample_orcabus_id_list: List[str], accept_missing: bool = False) -> List[Project]:
     """
     Get sample from the sample id
-    :param sample_id:
+    :param sample_orcabus_id_list:
     :return:
     """
     # We have an internal id, convert to int

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

@@ -40,8 +40,8 @@ def get_subject_from_subject_id(subject_id: str) -> Subject:
 
 def get_subjects_list_from_subject_id_list(subject_id_list: List[str], accept_missing: bool = False) -> List[Sample]:
     """
-    Get sample from the sample id
-    :param sample_id:
+    Get subject objects from subject id list
+    :param subject_id_list:
     :return:
     """
     # We have an internal id, convert to int
@@ -74,8 +74,8 @@ def get_subject_orcabus_id_from_subject_id(subject_id: str) -> str:
 
 def get_subjects_list_from_subject_orcabus_id_list(subject_orcabus_id_list: List[str], accept_missing: bool = False) -> List[Sample]:
     """
-    Get sample from the sample id
-    :param sample_id:
+    Get subject objects from subject orcabus id list
+    :param subject_orcabus_id_list:
     :return:
     """
     # We have an internal id, convert to int

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

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-from typing import TypedDict, Literal, NotRequired, Optional, Dict
+from typing import TypedDict, Literal, Optional, Dict
 
 statusLiteral = Literal['STARTED', 'FAILED', 'SUCCEEDED', 'ABORTED', 'RESOLVED']
 

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

@@ -9,8 +9,6 @@ from copy import deepcopy
 
 from requests import HTTPError
 
-from fastapi.encoders import jsonable_encoder
-
 # Locals
 from .aws_helpers import (
     get_orcabus_token, get_hostname

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: "0.0.37" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.monitoredQueue.MonitoredQueue", version: "0.0.39" };
     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: "0.0.37" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.namedLambdaRole.NamedLambdaRole", version: "0.0.39" };
     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": "0.0.37",
+  "version": "0.0.39",
   "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: "0.0.37" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.provider.ProviderFunction", version: "0.0.39" };
     _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: "0.0.37" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.networking.OrcaBusVpc", version: "0.0.39" };
     /**
      * 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: "0.0.37" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.networking.OrcaBusSharedComputeSecurityGroup", version: "0.0.39" };
     /**
      * 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: "0.0.37" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.slack.SlackAlerts", version: "0.0.39" };
     /**
      * Format the ARN for the slack alerts SNS topic for the current stack.
      * @param stack