@orcabus/platform-cdk-constructs 0.0.35 → 0.0.37

package/.jsii

@@ -6756,6 +6756,6 @@
       "symbolId": "shared-config/slack:SlackAlerts"
     }
   },
-  "version": "0.0.35",
-  "fingerprint": "dgr8YQrliJh0hWpEcsepSzBVhIznw5JYimaBU1p7VKg="
+  "version": "0.0.37",
+  "fingerprint": "WJnxu31JCGx88czmTm4wEcOiYLDLTbs658r/FyyoErY="
 }

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: "0.0.35" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.apigateway.OrcaBusApiGateway", version: "0.0.37" };
     /**
      * 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: "0.0.35" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.deploymentPipeline.CrossDeploymentArtifactBucket", version: "0.0.37" };
     /**
      * 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: "0.0.35" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.deploymentPipeline.DeploymentStackPipeline", version: "0.0.37" };
     /**
      * 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: "0.0.35" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.dynamodb.DynamoDbPartitionedConstruct", version: "0.0.37" };
     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: "0.0.35" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.dynamodb.DynamoDbNonPartitionedConstruct", version: "0.0.37" };
     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: "0.0.35" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.ecs.EcsFargateTaskConstruct", version: "0.0.37" };
     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: "0.0.35" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.lambda.PythonUvFunction", version: "0.0.37" };
     // 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/models.py

@@ -180,6 +180,7 @@ class QcStats(TypedDict):
     r2Q20Fraction: float
     r1GcFraction: float
     r2GcFraction: float
+    duplicationFractionEstimate: float
 
 
 class ReadCount(TypedDict):
@@ -218,12 +219,6 @@ class Job(TypedDict):
     startTime: datetime
     endTime: Optional[datetime]
 
-# Deprecated: Use BoolLiteral instead
-class BoolAllEnum(Enum):
-    ALL = "ALL"
-    true = True
-    false = False
-
 BoolLiteral = Literal[
     'ALL',
     True,
@@ -232,7 +227,7 @@ BoolLiteral = Literal[
 
 
 class FastqGetResponseParameters(TypedDict):
-    includeS3Details: NotRequired[BoolLiteral]
+    includeS3Details: NotRequired[bool]
 
 
 class StandardQueryParameters(TypedDict):

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

@@ -6,7 +6,7 @@ from typing import Dict, Optional
 # Local imports
 from .globals import FASTQ_DECOMPRESSION_SUBDOMAIN_NAME
 from ..utils.requests_helpers import (
-    get_request_response_results, get_url, patch_request, get_request
+    get_request_response_results, get_url, patch_request, get_request, post_request
 )
 
 
@@ -46,21 +46,21 @@ def get_fastq_decompression_request_response_results(
 
 def fastq_decompression_patch_request(
     endpoint: str,
-    params: Optional[Dict] = None,
+    json_data: Optional[Dict] = None,
 ):
     return patch_request(
         url=get_fastq_decompression_url(endpoint),
-        params=params
+        json_data=json_data
     )
 
 
 def fastq_decompression_post_request(
     endpoint: str,
-    params: Optional[Dict] = None,
+    json_data: Optional[Dict] = None,
 ):
-    return patch_request(
+    return post_request(
         url=get_fastq_decompression_url(endpoint),
-        params=params
+        json_data=json_data
     )
 
 # Create imports

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

@@ -4,31 +4,31 @@
 Create the job
 """
 
-from typing import List, Optional
+from typing import Unpack
 
 from . import fastq_decompression_post_request
 from .globals import JOB_ENDPOINT
-from .models import Job, JobType
+from .models import Job, JobCreateParameters
 
 
 def create_job(
-        fastq_id_list: List[str],
-        output_uri_prefix: str = None,
-        job_type: Optional[JobType] = None,
+    **kwargs: Unpack[JobCreateParameters]
 ) -> Job:
     """
     Create the job
     """
-    if job_type is None:
-        job_type = 'FASTQ_DECOMPRESSION'
+
+    # Raise error if any of the kwargs are not in the FastqListRowQueryParameters
+    for key in kwargs.keys():
+        if key not in JobCreateParameters.__annotations__:
+            raise ValueError(f"Invalid parameter: {key}")
+
+    non_null_kwargs = dict(filter(
+        lambda kv_iter_: kv_iter_[1] is not None,
+        kwargs.items()
+    ))
 
     return fastq_decompression_post_request(
         JOB_ENDPOINT,
-        params={
-            "fastqIdList": fastq_id_list,
-            "jobType": job_type,
-            "outputUriPrefix": output_uri_prefix,
-        }
+        json_data=non_null_kwargs
     )
-
-

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

@@ -16,7 +16,7 @@ from typing import (
 )
 
 JobType = Literal['FASTQ_DECOMPRESSION']
-JobStatus = Literal['PENDING', 'RUNNING', 'FAILED', 'ABORTED', 'SUCCEEDED']
+JobStatusType = Literal['PENDING', 'RUNNING', 'FAILED', 'ABORTED', 'SUCCEEDED']
 
 # Output jobs
 class DecompressionJobOutputObjectItem(TypedDict):
@@ -73,20 +73,34 @@ class Job(TypedDict):
     id: str
     jobType: JobType
     stepsExecutionArn: str
-    status: JobStatus
+    status: JobStatusType
     startTime: str
     endTime: str
     errorMessages: NotRequired[str]
     outputs: NotRequired[JobOutputType]
 
 
+class JobCreateParameters(TypedDict):
+    fastqIdList: List[str]
+    jobType: JobType
+    maxReads: NotRequired[int]
+    outputUriPrefix: NotRequired[str]
+
+
 class JobQueryParameters(TypedDict):
     fastqId: NotRequired[str]
     fastqSetId: NotRequired[str]
-    status: NotRequired[JobStatus]
+    status: NotRequired[JobStatusType]
     createdAfter: NotRequired[str]
     createdBefore: NotRequired[str]
     completedAfter: NotRequired[str]
     completedBefore: NotRequired[str]
     page: NotRequired[int]
     rowsPerPage: NotRequired[int]
+
+
+class JobUpdateParameters(TypedDict):
+    status: JobStatusType
+    errorMessage: NotRequired[str]
+    stepsExecutionArn: NotRequired[str]
+    output: NotRequired[JobOutputType]

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

@@ -10,11 +10,11 @@ get_unarchiving_job_list
 """
 
 # Type hints
-from typing import List, Unpack
+from typing import List, Unpack, Optional
 
 # Local imports
 from . import get_fastq_decompression_request_response_results
-from .models import Job, JobStatus, JobQueryParameters
+from .models import Job, JobStatusType, JobQueryParameters
 from .globals import JOB_ENDPOINT
 
 
@@ -39,13 +39,16 @@ def get_decompression_job_list(**kwargs: Unpack[JobQueryParameters]) -> List[Job
 
 def get_job_list_for_fastq(
         fastq_id: str,
-        job_status: JobStatus
+        status: Optional[JobStatusType] = None
 ) -> List[Job]:
     """
     Check if fastq in job list
     :return:
     """
-    return get_decompression_job_list(
-        fastqId=fastq_id,
-        status=job_status
-    )
+    return get_decompression_job_list(**dict(filter(
+        lambda kv_iter_: kv_iter_[1] is not None,
+        {
+            "fastqId": fastq_id,
+            "status": status
+        }.items()
+    )))

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

@@ -5,39 +5,33 @@ Update helpers for the update script.
 """
 
 # Standard imports
-from typing import Optional, Dict, Any
+from typing import Optional, Dict, Any, Unpack
 
 # Local imports
 from . import fastq_decompression_patch_request
 from .globals import JOB_ENDPOINT
-from .models import Job, JobStatus, JobOutputType
+from .models import Job, JobUpdateParameters
 
 
 def update_status(
         job_id: str,
-        job_status: JobStatus,
-        steps_execution_arn: Optional[str] = None,
-        error_message: Optional[str] = None,
-        output: Optional[Dict[str, JobOutputType]] = None
+        **kwargs: Unpack[JobUpdateParameters]
 ) -> Job:
     """
     Add QC stats to a fastq_id.
 
-    :param job_id: The job id
-    :param job_status: Dictionary of QC stats
-    :param steps_execution_arn:
-    :param output:
-    :param error_message: Optional error message
+    :param job_id:
+    :param kwargs: JobUpdateStatusParameters
     """
+    # Raise error if any of the kwargs are not in the JobUpdateParameters
+    for key in kwargs.keys():
+        if key not in JobUpdateParameters.__annotations__:
+            raise ValueError(f"Invalid parameter: {key}")
+
     return fastq_decompression_patch_request(
         f"{JOB_ENDPOINT}/{job_id}",
-        params=dict(filter(
-            lambda x: x[1] is not None,
-            {
-                "status": job_status,
-                "errorMessage": error_message,
-                "stepsExecutionArn": steps_execution_arn,
-                "output": output
-            }.items()
+        json_data=dict(filter(
+            lambda kv_iter_: kv_iter_[1] is not None,
+            kwargs.items()
         ))
     )

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

@@ -9,7 +9,7 @@ from ..utils.requests_helpers import (
     get_request_response_results,
     get_url,
     patch_request,
-    get_request
+    get_request, post_request
 )
 
 
@@ -49,21 +49,21 @@ def get_fastq_unarchiving_request_response_results(
 
 def fastq_unarchiving_patch_request(
     endpoint: str,
-    params: Optional[Dict] = None,
+    json_data: Optional[Dict] = None,
 ):
     return patch_request(
         url=get_fastq_unarchiving_url(endpoint),
-        params=params
+        json_data=json_data
     )
 
 
 def fastq_unarchiving_post_request(
     endpoint: str,
-    params: Optional[Dict] = None,
+    json_data: Optional[Dict] = None,
 ):
-    return patch_request(
+    return post_request(
         url=get_fastq_unarchiving_url(endpoint),
-        params=params
+        json_data=json_data
     )
 
 # Create imports

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

@@ -35,7 +35,7 @@ def update_status(
     """
     return fastq_unarchiving_patch_request(
         f"{JOB_ENDPOINT}/{job_id}",
-        params=dict(filter(
+        json_data=dict(filter(
             lambda x: x[1] is not None,
             {
                 "status": job_status,

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

@@ -1,4 +1,9 @@
-from typing import Optional, TypedDict, Dict, Literal
+from typing import (
+    Optional,
+    TypedDict,
+    Dict,
+    Literal
+)
 
 """
 Example File Object response

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

@@ -115,17 +115,16 @@ def patch_request(
         "Authorization": f"Bearer {get_orcabus_token()}"
     }
 
-    req_params = deepcopy(DEFAULT_REQUEST_PARAMS)
-
-    req_params.update(
-        params if params is not None else {}
-    )
+    if json_data is not None:
+       headers.update({
+           "Content-Type": "application/json"
+       })
 
     # Make the request
     response = requests.patch(
         url,
         headers=headers,
-        params=req_params,
+        params=params,
         json=json_data
     )
 
@@ -137,29 +136,34 @@ def patch_request(
     return response.json()
 
 
-def post_request(url: str, params: Optional[Dict] = None) -> Dict:
+def post_request(
+        url: str,
+        json_data: Optional[Dict] = None,
+        params: Optional[Dict] = None
+) -> Dict:
     """
     Run post request against the fastq endpoint
+    :param json_data:
     :param url:
     :param params:
     :return:
     """
     # Get authorization header
     headers = {
-        "Authorization": f"Bearer {get_orcabus_token()}"
+        "Authorization": f"Bearer {get_orcabus_token()}",
     }
 
-    req_params = deepcopy(DEFAULT_REQUEST_PARAMS)
-
-    req_params.update(
-        params if params is not None else {}
-    )
+    if json_data is not None:
+       headers.update({
+           "Content-Type": "application/json"
+       })
 
     # Make the request
     response = requests.post(
         url,
         headers=headers,
-        json=req_params
+        json=json_data,
+        params=params
     )
 
     try:

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: "0.0.35" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.monitoredQueue.MonitoredQueue", version: "0.0.37" };
     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: "0.0.35" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.namedLambdaRole.NamedLambdaRole", version: "0.0.37" };
     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": "0.0.35",
+  "version": "0.0.37",
   "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: "0.0.35" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.provider.ProviderFunction", version: "0.0.37" };
     _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: "0.0.35" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.networking.OrcaBusVpc", version: "0.0.37" };
     /**
      * 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: "0.0.35" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.networking.OrcaBusSharedComputeSecurityGroup", version: "0.0.37" };
     /**
      * 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: "0.0.35" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.slack.SlackAlerts", version: "0.0.37" };
     /**
      * Format the ARN for the slack alerts SNS topic for the current stack.
      * @param stack