@orcabus/platform-cdk-constructs 0.0.101 → 0.0.102

package/.jsii

@@ -7163,6 +7163,6 @@
       "symbolId": "shared-config/slack:SlackAlerts"
     }
   },
-  "version": "0.0.101",
-  "fingerprint": "zvLwqJtTziHgrpFnG4EL5SxYV18znkqslm91rEBOpXI="
+  "version": "0.0.102",
+  "fingerprint": "Hef5eUEuQANqtuVO8TDAnwhrGFM8+86Cdr6Nu/QQycw="
 }

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: "0.0.101" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.apigateway.OrcaBusApiGateway", version: "0.0.102" };
     /**
      * 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: "0.0.101" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.deploymentPipeline.CrossDeploymentArtifactBucket", version: "0.0.102" };
     /**
      * 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: "0.0.101" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.deploymentPipeline.DeploymentStackPipeline", version: "0.0.102" };
     /**
      * 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: "0.0.101" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.dynamodb.DynamoDbPartitionedConstruct", version: "0.0.102" };
     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: "0.0.101" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.dynamodb.DynamoDbNonPartitionedConstruct", version: "0.0.102" };
     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: "0.0.101" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.ecs.EcsFargateTaskConstruct", version: "0.0.102" };
     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: "0.0.101" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.eventbridgeRule.SfnSlackNotification", version: "0.0.102" };
     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: "0.0.101" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.lambda.PythonUvFunction", version: "0.0.102" };
     // 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/query_helpers.py

@@ -149,7 +149,8 @@ def get_fastqs_batched(
                     rowsPerPage=100
                 ),
                 item_lists
-            ))
+            )),
+            []
         ))
     except TypeError as e:
         # TypeError: reduce() of empty iterable with no initial value

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

@@ -245,7 +245,8 @@ def get_presigned_urls_from_ingest_ids(ingest_ids: List[str]) -> List[Dict[str,
                 })
             ),
             ingest_id_batches
-        ))
+        )),
+        []
     ))
 
     s3_object_list = get_s3_objs_from_ingest_ids_map(ingest_ids)
@@ -303,7 +304,8 @@ def get_s3_objs_from_ingest_ids_map(
                             **kwargs
                         }),
                     ingest_id_batches
-                ))
+                )),
+                []
             ))
         ))
     except TypeError as e:

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

@@ -102,7 +102,8 @@ def get_item_from_item_id_list_batched(
                     )
                 ),
                 item_id_lists
-            ))
+            )),
+            []
         ))
     except TypeError as e:
         # TypeError: reduce() of empty sequence with no initial value
@@ -119,6 +120,8 @@ from .contact_helpers import (
     get_contacts_list_from_contact_orcabus_id_list,
     coerce_contact_id_or_orcabus_id_to_contact_orcabus_id,
     get_all_contacts,
+    list_libraries_for_contact_id,
+    list_libraries_for_contact_orcabus_id,
 )
 
 from .individual_helpers import (
@@ -145,7 +148,11 @@ from .library_helpers import (
     get_library_assay_type,
     get_library_phenotype,
     get_library_workflow,
-    get_all_libraries
+    get_all_libraries,
+    get_project_list_from_library_orcabus_id,
+    get_project_list_from_library_id,
+    get_contact_list_from_library_orcabus_id,
+    get_contact_list_from_library_id
 )
 
 from .project_helpers import (
@@ -191,6 +198,8 @@ __all__ = [
     "get_contacts_list_from_contact_orcabus_id_list",
     "coerce_contact_id_or_orcabus_id_to_contact_orcabus_id",
     "get_all_contacts",
+    "list_libraries_for_contact_id",
+    "list_libraries_for_contact_orcabus_id",
 
     # Individual Helpers
     "get_individual_from_individual_id",
@@ -216,6 +225,10 @@ __all__ = [
     "get_library_phenotype",
     "get_library_workflow",
     "get_all_libraries",
+    "get_project_list_from_library_orcabus_id",
+    "get_project_list_from_library_id",
+    "get_contact_list_from_library_orcabus_id",
+    "get_contact_list_from_library_id",
 
     # Project Helpers
     "get_project_from_project_id",

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

@@ -3,15 +3,16 @@
 """
 Helpers for using the contact API endpoint
 """
-
 # Standard imports
+from functools import reduce
+from operator import concat
 from typing import List
 from requests import HTTPError
 
 # Local imports
 from . import get_metadata_request_response_results, get_item_objs_from_item_id_list
 from .globals import CONTACT_ENDPOINT, ORCABUS_ULID_REGEX_MATCH
-from .models import Contact
+from .models import Contact, Library
 from .errors import ContactNotFoundError
 
 
@@ -107,3 +108,41 @@ def get_all_contacts() -> List[Contact]:
     :return:
     """
     return get_metadata_request_response_results(CONTACT_ENDPOINT)
+
+
+def list_libraries_for_contact_orcabus_id(contact_orcabus_id: str) -> List[Library]:
+    """
+    Given a contact orcabus id, get libraries associated with projects, associated with the contact
+    :param contact_orcabus_id:
+    :return:
+    """
+    from .project_helpers import list_libraries_in_project
+
+    # Get the contact object
+    contact_obj = get_contact_from_contact_orcabus_id(contact_orcabus_id)
+
+    # For each project in the projectSet, get the libraries in the project
+    library_object_list = list(reduce(
+        concat,
+        list(map(
+            lambda project_iter_: list_libraries_in_project(project_iter_['orcabusId']),
+            contact_obj.get('projectSet', [])
+        )),
+        []
+    ))
+
+    # Remove duplicates by library orcabus id
+    library_object_list = list({lib['orcabusId']: lib for lib in library_object_list}.values())
+
+    return library_object_list
+
+
+def list_libraries_for_contact_id(contact_id: str) -> List[Library]:
+    """
+    Get libraries associated with a contact id
+    :param contact_id:
+    :return:
+    """
+    return list_libraries_for_contact_orcabus_id(
+        get_contact_orcabus_id_from_contact_id(contact_id)
+    )

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

@@ -135,5 +135,6 @@ def list_libraries_in_individual(individual_orcabus_id: str) -> List[LibraryDeta
             lambda subject_iter_: list_libraries_in_subject(subject_iter_['orcabusId']),
             # Get list of subject orcabus ids
             get_individual_from_individual_orcabus_id(individual_orcabus_id)["subjectSet"]
-        ))
+        )),
+        []
     ))

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

@@ -1,11 +1,15 @@
 #!/usr/bin/env python
+from functools import reduce
+from operator import concat
 from typing import Union, List
 
 from requests import HTTPError
 
 from .globals import LIBRARY_ENDPOINT, ORCABUS_ULID_REGEX_MATCH
-from .models import Library, Subject
-from . import get_metadata_request_response_results, get_item_objs_from_item_id_list
+from .models import Library, Subject, Contact, Project
+from . import (
+    get_metadata_request_response_results, get_item_objs_from_item_id_list
+)
 from .errors import LibraryNotFoundError
 
 
@@ -166,31 +170,77 @@ def get_library_workflow(library_id: str) -> Union[str | None]:
     return library.get("workflow")
 
 
-# def get_library_project_owner(library_id: str) -> Union[str | None]:
-#     """
-#     Given a library id, collect the library project owner
-#     :param library_id:
-#     :return:
-#     """
-#     library = get_library_from_library_id(library_id)
-#
-#     return library.get("projectOwner")
-#
-#
-# def get_library_project_name(library_id: str) -> Union[str | None]:
-#     """
-#     Given a library id, collect the library workflow
-#     :param library_id:
-#     :return:
-#     """
-#     library = get_library_from_library_id(library_id)
-#
-#     return library.get("projectName")
-
-
 def get_all_libraries() -> List[Library]:
     """
     Collect all libraries from the database
     :return:
     """
     return get_metadata_request_response_results(LIBRARY_ENDPOINT)
+
+
+def get_project_list_from_library_orcabus_id(library_orcabus_id: str) -> List[Project]:
+    """
+    Given a library orcabus id, collect the project list
+    :param library_orcabus_id:
+    :return:
+    """
+    # Local imports
+    from .project_helpers import get_project_from_project_orcabus_id
+
+    # For each project in the projectSet, get the project (convert from ProjectDetail to Project)
+    # Then return the list
+    return list(map(
+        lambda project_iter_: get_project_from_project_orcabus_id(project_iter_['orcabusId']),
+        get_library_from_library_orcabus_id(library_orcabus_id).get("projectSet", [])
+    ))
+
+
+def get_project_list_from_library_id(library_id: str) -> List[Project]:
+    """
+    Given a library id, collect the project list
+    :param library_id:
+    :return:
+    """
+    return get_project_list_from_library_orcabus_id(get_library_orcabus_id_from_library_id(library_id))
+
+
+def get_contact_list_from_library_orcabus_id(library_orcabus_id: str) -> List[Contact]:
+    """
+    Given a library orcabus id, collect the contact list
+    :param library_orcabus_id:
+    :return:
+    """
+    # Local imports
+    from .project_helpers import get_project_from_project_orcabus_id
+    from .contact_helpers import get_contact_from_contact_orcabus_id
+
+    # For each project in the projectSet,
+    # Get the contact set, then we reduce to a single list
+    contact_list = list(reduce(
+        concat,
+        list(map(
+            lambda project_iter_: get_project_from_project_orcabus_id(project_iter_['orcabusId']).get('contactSet', []),
+            get_library_from_library_orcabus_id(library_orcabus_id).get("projectSet", [])
+        )),
+        []
+    ))
+
+    # We need to deduplicate the contact list
+    contact_list = list({contact_iter_['orcabusId']: contact_iter_ for contact_iter_ in contact_list}.values())
+
+    # Then convert from ContactDetail to Contact objects by fetching each contact
+    contact_list = list(map(
+        lambda contact_iter_: get_contact_from_contact_orcabus_id(contact_iter_['orcabusId']),
+        contact_list
+    ))
+
+    return contact_list
+
+
+def get_contact_list_from_library_id(library_id: str) -> List[Contact]:
+    """
+    Given a library id, collect the contact list
+    :param library_id:
+    :return:
+    """
+    return get_contact_list_from_library_orcabus_id(get_library_orcabus_id_from_library_id(library_id))

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

@@ -135,13 +135,13 @@ def add_samplesheet(
     """
     Add a sample sheet to the sequence run.
     :param instrument_run_id: The instrument run identifier for which the sample sheet is being added.
-    :param samplesheet: Path to the sample sheet file to be uploaded.
+    :param samplesheet_path: Path to the sample sheet file to be uploaded.
     :param created_by: The user who is adding the sample sheet.
     :param comment: A comment describing the sample sheet or the reason for adding it.
     :return: Response from the API containing the updated sequence information.
     """
     # Open the sample sheet file
-    with open(samplesheet, 'r') as ss_file:
+    with open(samplesheet_path, 'r') as ss_file:
         ss_content = ss_file.read()
 
     return sequence_post_request(

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: "0.0.101" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.monitoredQueue.MonitoredQueue", version: "0.0.102" };
     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: "0.0.101" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.namedLambdaRole.NamedLambdaRole", version: "0.0.102" };
     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": "0.0.101",
+  "version": "0.0.102",
   "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: "0.0.101" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.provider.ProviderFunction", version: "0.0.102" };
     _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: "0.0.101" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.networking.OrcaBusVpc", version: "0.0.102" };
     /**
      * 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: "0.0.101" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.networking.OrcaBusSharedComputeSecurityGroup", version: "0.0.102" };
     /**
      * 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: "0.0.101" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.slack.SlackAlerts", version: "0.0.102" };
     /**
      * Format the ARN for the slack alerts SNS topic for the current stack.
      * @param stack