@orcabus/platform-cdk-constructs 0.0.15 → 0.0.17

package/.jsii

@@ -6394,6 +6394,6 @@
       "symbolId": "shared-config/networking:OrcaBusVpc"
     }
   },
-  "version": "0.0.15",
-  "fingerprint": "CZcXrboaQo0Ige4emPXo7d215wrsEhYAgaPp/iMU5hk="
+  "version": "0.0.17",
+  "fingerprint": "JOiC6iKaNG6BMY7XsewmVTAEHSHX+qV3ybXaUWTW6s4="
 }

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: "0.0.15" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.apigateway.OrcaBusApiGateway", version: "0.0.17" };
     /**
      * 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: "0.0.15" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.deploymentPipeline.CrossDeploymentArtifactBucket", version: "0.0.17" };
     /**
      * The S3 bucket used to store artifacts for cross-deployment pipelines.
      */

package/deployment-stack-pipeline/pipeline.js

@@ -31,7 +31,7 @@ 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: "0.0.15" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.deploymentPipeline.DeploymentStackPipeline", version: "0.0.17" };
     /**
      * 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: "0.0.15" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.dynamodb.DynamoDbPartitionedConstruct", version: "0.0.17" };
     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: "0.0.15" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.dynamodb.DynamoDbNonPartitionedConstruct", version: "0.0.17" };
     table;
     constructor(scope, id, props) {
         super(scope, id);

package/ecs/index.js

@@ -52,7 +52,7 @@ 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: "0.0.15" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.ecs.EcsFargateTaskConstruct", version: "0.0.17" };
     cluster;
     taskDefinition;
     securityGroup;

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: "0.0.15" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.lambda.PythonUvFunction", version: "0.0.17" };
     // 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/update_helpers.py

@@ -109,20 +109,14 @@ def add_read_set(fastq_id: str, read_set: ReadSet) -> FastqListRow:
     )
 
 
-def detach_read_set(fastq_id: str, read_set: ReadSet) -> FastqListRow:
+def detach_read_set(fastq_id: str) -> FastqListRow:
     """
     Detach a read set to a fastq id.
 
     :param fastq_id: Fastq str
-    :param read_set: ReadSet str
     """
-    for key in read_set.keys():
-        if key not in ReadSet.__annotations__:
-            raise ValueError(f"Invalid parameter: {key}")
-
     return fastq_patch_request(
-        f"{FASTQ_LIST_ROW_ENDPOINT}/{fastq_id}/detachFastqPairStorageObject",
-        params=dict(read_set)
+        f"{FASTQ_LIST_ROW_ENDPOINT}/{fastq_id}/detachFastqPairStorageObject"
     )
 
 

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

@@ -75,7 +75,7 @@ def get_item_from_item_id_list_batched(
         endpoint: str,
         accept_missing: bool = False,
         batch_size: int = 50
-) -> List[Dict[str: Any]]:
+) -> List[Dict[str, Any]]:
     """
     Get items from a list of item ids
     We batch the requests to avoid hitting the API limits

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

@@ -16,8 +16,7 @@ from requests.exceptions import HTTPError
 from . import get_metadata_request_response_results, get_item_objs_from_item_id_list
 from .errors import SampleNotFoundError
 from .globals import SAMPLE_ENDPOINT, ORCABUS_ULID_REGEX_MATCH
-from .models import Sample, LibraryDetail
-
+from .models import Sample, LibraryDetail, Project
 
 
 def get_sample_from_sample_id(sample_id: str) -> Sample:

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

@@ -0,0 +1,73 @@
+#!/usr/bin/env python3
+from typing import Optional, Dict
+
+from orcabus_api_tools.utils.requests_helpers import get_url, get_request_response_results, get_request
+from orcabus_api_tools.workflow.globals import WORKFLOW_SUBDOMAIN_NAME
+
+
+def get_workflow_url(endpoint: str) -> str:
+    """
+    Get the URL for the Metadata endpoint
+    :param endpoint:
+    :return:
+    """
+    return get_url(
+        endpoint,
+        WORKFLOW_SUBDOMAIN_NAME
+    )
+
+
+def get_workflow_request(
+        endpoint: str,
+        params: Optional[Dict] = None,
+):
+    return get_request(get_workflow_url(endpoint), params=params)
+
+
+def get_workflow_request_response_results(
+        endpoint: str,
+        params: Optional[Dict] = None,
+):
+    return get_request_response_results(get_workflow_url(endpoint), params=params)
+
+
+# Now 'import all'
+from .create_helpers import (
+    create_portal_run_id,
+    create_workflow_run_name_from_workflow_name_workflow_version_and_portal_run_id,
+)
+
+from .metadata_helpers import (
+    get_workflows_from_library_id
+)
+
+from .payload_helpers import (
+    get_payload,
+    get_payload_from_state,
+    get_latest_payload_from_workflow_run,
+    get_latest_payload_from_portal_run_id,
+)
+
+from .workflow_run_helpers import (
+    get_workflow_run,
+    get_workflow_run_from_portal_run_id,
+    get_workflow_run_state,
+)
+
+
+__all__ = [
+    # Create
+    "create_portal_run_id",
+    "create_workflow_run_name_from_workflow_name_workflow_version_and_portal_run_id",
+    # Metadata
+    "get_workflows_from_library_id",
+    # Payload
+    "get_payload",
+    "get_payload_from_state",
+    "get_latest_payload_from_workflow_run",
+    "get_latest_payload_from_portal_run_id",
+    # Workflow Run
+    "get_workflow_run",
+    "get_workflow_run_from_portal_run_id",
+    "get_workflow_run_state",
+]

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

@@ -0,0 +1,30 @@
+from datetime import datetime, timezone
+import random
+
+from orcabus_api_tools.workflow.globals import WORKFLOW_RUN_PREFIX
+
+
+def generate_rand_hex_string(length: int = 8) -> str:
+    """
+    Generate a random hexadecimal string of a given length.
+    :param length: Length of the hexadecimal string to generate.
+    :return: Random hexadecimal string.
+    """
+    return ''.join(random.choices('0123456789abcdef', k=length))
+
+
+def create_portal_run_id():
+    return datetime.now(timezone.utc).strftime("%Y%m%d") + str(generate_rand_hex_string())[0:8]
+
+
+def create_workflow_run_name_from_workflow_name_workflow_version_and_portal_run_id(
+        workflow_name: str,
+        workflow_version: str,
+        portal_run_id: str
+):
+    return '--'.join([
+        WORKFLOW_RUN_PREFIX,
+        workflow_name.lower(),
+        workflow_version.replace(".", "-"),
+        portal_run_id
+    ])

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

@@ -0,0 +1,7 @@
+# Run name for sequence run manager
+WORKFLOW_SUBDOMAIN_NAME = 'workflow'
+
+WORKFLOW_RUN_ENDPOINT = 'api/v1/workflowrun'
+PAYLOAD_ENDPOINT = 'api/v1/payload'
+
+WORKFLOW_RUN_PREFIX = 'umccr--automated'

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

@@ -7,9 +7,8 @@ Get workflows from library id
 # Standard imports
 from typing import List
 
-
 # Local imports
-from .requests_helpers import get_request_response_results
+from . import get_workflow_request_response_results
 from .globals import WORKFLOW_RUN_ENDPOINT
 from .models import WorkflowRunDetail
 
@@ -20,7 +19,7 @@ def get_workflows_from_library_id(library_id: str) -> List[WorkflowRunDetail]:
     :param library_id:
     :return:
     """
-    return get_request_response_results(
+    return get_workflow_request_response_results(
         WORKFLOW_RUN_ENDPOINT,
         params={
             "libraries__libraryId": library_id

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

@@ -7,9 +7,9 @@ Getting the payload helpers
 # Standard imports
 from typing import Dict
 
+from . import get_workflow_request
 # Local imports
 from .globals import PAYLOAD_ENDPOINT
-from .requests_helpers import get_request_results
 from .models import Payload
 
 
@@ -20,7 +20,7 @@ def get_payload(payload_id: str) -> Dict:
     :return:
     """
     # Get subject
-    return get_request_results(PAYLOAD_ENDPOINT, payload_id)
+    return get_workflow_request(f"{PAYLOAD_ENDPOINT}/{payload_id}")
 
 
 def get_payload_from_state(workflow_run_orcabus_id: str, status: str):
@@ -51,7 +51,7 @@ def get_latest_payload_from_workflow_run(workflow_run_orcabus_id: str) -> Payloa
     workflow_run = get_workflow_run(workflow_run_orcabus_id)
 
     # Get the payload
-    return get_payload_from_state(workflow_run_orcabus_id, workflow_run['currentState']['orcabusId'])
+    return Payload(**get_payload_from_state(workflow_run_orcabus_id, workflow_run['currentState']['orcabusId']))
 
 
 def get_latest_payload_from_portal_run_id(portal_run_id: str) -> Payload:
@@ -61,4 +61,4 @@ def get_latest_payload_from_portal_run_id(portal_run_id: str) -> Payload:
     workflow_run = get_workflow_run_from_portal_run_id(portal_run_id)
 
     # Get the payload
-    return get_payload_from_state(workflow_run['orcabusId'], workflow_run['currentState']['orcabusId'])
+    return Payload(**get_payload_from_state(workflow_run['orcabusId'], workflow_run['currentState']['orcabusId']))

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

@@ -5,14 +5,12 @@ Helpers for using the contact API endpoint
 """
 
 # Standard imports
-from typing import Dict
 from requests import HTTPError
+from . import get_workflow_request_response_results, get_workflow_request
 
 # Local imports
 from .globals import WORKFLOW_RUN_ENDPOINT
-from .requests_helpers import get_request_response_results, get_request_results_ext, get_request_results
 from .models import WorkflowRun, State
-from .. import WorkflowRunNotFoundError
 
 
 def get_workflow_run(workflow_run_orcabus_id: str) -> WorkflowRun:
@@ -23,7 +21,7 @@ def get_workflow_run(workflow_run_orcabus_id: str) -> WorkflowRun:
     """
     # Get workflow run
     try:
-        return get_request_results(WORKFLOW_RUN_ENDPOINT, workflow_run_orcabus_id)
+        return get_workflow_request(f"{WORKFLOW_RUN_ENDPOINT}/{workflow_run_orcabus_id}")
     except HTTPError as e:
         from .errors import WorkflowRunNotFoundError
         raise WorkflowRunNotFoundError(workflow_run_id=workflow_run_orcabus_id) from e
@@ -42,13 +40,13 @@ def get_workflow_run_from_portal_run_id(portal_run_id: str) -> WorkflowRun:
         "portalRunId": portal_run_id
     }
 
-    workflow_runs_list = get_request_response_results(WORKFLOW_RUN_ENDPOINT, params)
+    workflow_runs_list = get_workflow_request_response_results(WORKFLOW_RUN_ENDPOINT, params)
 
     if len(workflow_runs_list) == 0:
         raise WorkflowRunNotFoundError(portal_run_id=portal_run_id)
 
     try:
-        return get_request_results(
+        return get_workflow_request_response_results(
             WORKFLOW_RUN_ENDPOINT,
             workflow_runs_list[0]["orcabusId"],
         )
@@ -68,7 +66,7 @@ def get_workflow_run_state(workflow_run_orcabus_id: str, status: str) -> State:
         return next(
             filter(
                 lambda workflow_state_iter_: workflow_state_iter_["status"] == status,
-                get_request_results_ext(WORKFLOW_RUN_ENDPOINT, workflow_run_orcabus_id, "state")
+                get_workflow_request_response_results(f"{WORKFLOW_RUN_ENDPOINT}/{workflow_run_orcabus_id}/{status}")
             )
         )
     except HTTPError as e:

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: "0.0.15" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.namedLambdaRole.NamedLambdaRole", version: "0.0.17" };
     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": "0.0.15",
+  "version": "0.0.17",
   "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: "0.0.15" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.provider.ProviderFunction", version: "0.0.17" };
     _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: "0.0.15" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.networking.OrcaBusVpc", version: "0.0.17" };
     /**
      * 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: "0.0.15" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.networking.OrcaBusSharedComputeSecurityGroup", version: "0.0.17" };
     /**
      * The shared security group that is used by compute resources to access the database.
      * @param scope