@orcabus/platform-cdk-constructs 0.0.46 → 0.0.48

package/.jsii

@@ -6756,6 +6756,6 @@
       "symbolId": "shared-config/slack:SlackAlerts"
     }
   },
-  "version": "0.0.46",
-  "fingerprint": "wq/3vu0Z5vehQmydjFGp9Xs6zhtw4bSqWMa+sy2zW+0="
+  "version": "0.0.48",
+  "fingerprint": "2o+clcDs/L5F1h+iDeYKodwO0D2DU26xdnQrBgLLPDc="
 }

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: "0.0.46" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.apigateway.OrcaBusApiGateway", version: "0.0.48" };
     /**
      * 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: "0.0.46" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.deploymentPipeline.CrossDeploymentArtifactBucket", version: "0.0.48" };
     /**
      * 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: "0.0.46" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.deploymentPipeline.DeploymentStackPipeline", version: "0.0.48" };
     /**
      * 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: "0.0.46" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.dynamodb.DynamoDbPartitionedConstruct", version: "0.0.48" };
     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: "0.0.46" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.dynamodb.DynamoDbNonPartitionedConstruct", version: "0.0.48" };
     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: "0.0.46" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.ecs.EcsFargateTaskConstruct", version: "0.0.48" };
     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: "0.0.46" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.lambda.PythonUvFunction", version: "0.0.48" };
     // 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_decompression/models.py

@@ -15,8 +15,6 @@ from typing import (
     TypedDict, NotRequired, Literal, List, Union
 )
 
-from app.interface.jobs_api.models import ReadCountCalculationOutputObject
-
 JobType = Literal['FASTQ_DECOMPRESSION']
 JobStatusType = Literal['PENDING', 'RUNNING', 'FAILED', 'ABORTED', 'SUCCEEDED']
 
@@ -51,10 +49,16 @@ class RawMd5sumCalculationOutputsFastqId(TypedDict):
     rawMd5sumByOraFileIngestIdList: List[RawMd5sumCalculationOutputsObjectItem]
 
 
+class ReadCountCalculationOutputsFastqId(TypedDict):
+    fastqId: str
+    readCount: int
+
+
 class DecompressionJobOutputObject(TypedDict):
    # Decompressed file URI by ORA file ingest ID list
    decompressedFileList: List[DecompressionJobOutputObjectFastqId]
 
+
 class GzipFileSizeCalculationOutputObject(TypedDict):
     # Gzip file size by ORA file ingest ID list
     gzipFileSizeList: List[GzipFileSizeCalculationOutputsFastqId]
@@ -65,6 +69,11 @@ class RawMd5sumCalculationOutputObject(TypedDict):
     rawMd5sumList: List[RawMd5sumCalculationOutputsFastqId]
 
 
+class ReadCountCalculationOutputObject(TypedDict):
+    # Raw md5sum by ORA file ingest ID list
+    readCountList: List[ReadCountCalculationOutputsFastqId]
+
+
 JobOutputType = Union[
   DecompressionJobOutputObject |
   GzipFileSizeCalculationOutputObject |

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

@@ -1,15 +1,59 @@
 #!/usr/bin/env python3
 
+# Standard imports
+from typing import Dict
+
+# Local imports
+from ..utils.requests_helpers import (
+    get_request_response_results,
+    get_request,
+    get_url
+)
+from .globals import SEQUENCE_SUBDOMAIN_NAME
+from .models import Sequence, SequenceDetail, SampleSheet
+
+
+def get_sequence_url(endpoint: str) -> str:
+    """
+    Get the base URL for the sequence api
+    :param endpoint:
+    :return:
+    """
+    return get_url(
+        endpoint,
+        SEQUENCE_SUBDOMAIN_NAME
+    )
+
+
+def get_sequence_request(
+        endpoint: str,
+        params: Optional[Dict] = None,
+):
+    return get_request(get_sequence_url(endpoint), params=params)
+
+
+def get_sequence_request_response_results(
+        endpoint: str,
+        params: Optional[Dict] = None,
+):
+    return get_request_response_results(get_sequence_url(endpoint), params=params)
+
+
+
 from .sequence_helpers import (
     get_sequence_object_from_instrument_run_id,
+    get_libraries_from_instrument_run_id,
     get_sample_sheet_from_orcabus_id,
     get_library_ids_in_sequence,
+    get_sample_sheet_from_instrument_run_id
 )
 
 __all__ = [
     "get_sequence_object_from_instrument_run_id",
+    "get_libraries_from_instrument_run_id",
     "get_sample_sheet_from_orcabus_id",
     "get_library_ids_in_sequence",
+    "get_sample_sheet_from_instrument_run_id",
 ]
 
 

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

@@ -1,2 +1,6 @@
 # Run name for sequence run manager
-SEQUENCE_SUBDOMAIN_NAME = 'sequence'
+SEQUENCE_SUBDOMAIN_NAME = 'sequence'
+
+SEQUENCE_ENDPOINT = "api/v1/sequence"
+
+SEQUENCE_RUN_ENDPOINT = "api/v1/sequence_run"

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

@@ -1,8 +1,8 @@
 #!/usr/bin/env python3
 
-from typing import TypedDict, Literal, Optional, Dict
+from typing import TypedDict, Literal, Optional, Dict, List
 
-statusLiteral = Literal['STARTED', 'FAILED', 'SUCCEEDED', 'ABORTED', 'RESOLVED']
+StatusType = Literal['STARTED', 'FAILED', 'SUCCEEDED', 'ABORTED', 'RESOLVED']
 
 
 class SequenceDetail(TypedDict):
@@ -10,15 +10,15 @@ class SequenceDetail(TypedDict):
     instrumentRunId: str
     experimentName: str
     startTime: str
-    endTime: str
-    status: statusLiteral
+    endTime: Optional[str]
+    status: Optional[StatusType]
 
 
 class Sequence(TypedDict):
     orcabusId: str
-    libraries: str
+    libraries: List[str]
     sequenceRunId: str
-    status: statusLiteral
+    status: StatusType
     startTime: str
     sampleSheetName: str
     v1pre3Id: str

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

@@ -1,38 +1,82 @@
 #!/usr/bin/env python3
-from .globals import SEQUENCE_SUBDOMAIN_NAME
-from .models import Sequence, SequenceDetail, SampleSheet
-from ..utils.requests_helpers import get_request_response_results, get_request, get_url
 
+# Standard imports
+from typing import Optional, cast, List
+import logging
 
-def get_sequence_url(endpoint: str) -> str:
+
+# Local imports
+from . import get_sequence_request
+from .globals import SEQUENCE_RUN_ENDPOINT, SEQUENCE_ENDPOINT
+from .models import SequenceDetail, SampleSheet, Sequence
+
+
+def get_sample_sheet_from_instrument_run_id(instrument_run_id: str) -> Optional[SampleSheet]:
+    samplesheet_dict_list = sorted(
+        get_sequence_request(endpoint=f"{SEQUENCE_ENDPOINT}/{instrument_run_id}/sample_sheets"),
+        key=lambda x: x.get("orcabusId")
+    )
+
+    if len(samplesheet_dict_list) == 0:
+        logging.warning("Could not find sample sheet for instrument run id: %s", instrument_run_id)
+        return None
+
+    # If there are multiple sample sheets, print to logs, but return the last one
+    if len(samplesheet_dict_list) > 1:
+        logging.warning(
+            f"Multiple sample sheets found for instrument run id {instrument_run_id}. "
+            f"Returning the last one."
+        )
+
+    return cast(SampleSheet, samplesheet_dict_list[-1])
+
+
+def get_libraries_from_instrument_run_id(instrument_run_id: str) -> List[str]:
     """
-    Get the URL for the Metadata endpoint
-    :param endpoint:
+    Get the sequence run object
+    :param instrument_run_id:
     :return:
     """
-    return get_url(
-        endpoint,
-        SEQUENCE_SUBDOMAIN_NAME
+    sequence_run_object = get_sequence_object_from_instrument_run_id(
+        instrument_run_id=instrument_run_id
     )
 
-def get_sequence_object_from_instrument_run_id(instrument_run_id: str) -> SequenceDetail:
+    if sequence_run_object is None:
+        logging.warning("Could not find sequence run for instrument run id: %s", instrument_run_id)
+        return []
+
+    return sequence_run_object.get('libraries', [])
+
+
+def get_sequence_object_from_instrument_run_id(instrument_run_id: str) -> Optional[Sequence]:
     """
     Get the sequence object from the instrument run id.
     :param instrument_run_id:
     :return:
     """
 
-    return Sequence(
-        **dict(
-            get_request_response_results(
-                get_sequence_url(endpoint="api/v1/sequence"),
-                params={
-                    "instrumentRunId": instrument_run_id,
-                }
-            )[0]
-        )
+    # Get the sequence run details from the instrument run id
+    sequence_run_dict_list = sorted(
+        get_sequence_request(endpoint=f"{SEQUENCE_ENDPOINT}/{instrument_run_id}/sequence_run"),
+        # Orcabus ids are ulids so they are sortable by timestamp
+        key=lambda x: x.get("orcabusId")
     )
 
+    # Check we have at least one sequence run
+    if len(sequence_run_dict_list) == 0:
+        logging.warning("Could not find sequence run for instrument run id: %s", instrument_run_id)
+        return None
+
+    # Check if there are multiple sequence runs
+    if len(sequence_run_dict_list) > 1:
+        logging.warning(
+            f"Multiple sequence runs found for instrument run id {instrument_run_id}. "
+            f"Returning the last one."
+        )
+
+    # Return the last sequence run
+    return cast(Sequence, sequence_run_dict_list[-1])
+
 
 def get_sample_sheet_from_orcabus_id(sequence_orcabus_id: str) -> SampleSheet:
     """
@@ -43,20 +87,15 @@ def get_sample_sheet_from_orcabus_id(sequence_orcabus_id: str) -> SampleSheet:
 
     return SampleSheet(
         **dict(
-            get_request(
-                get_sequence_url(endpoint=f"api/v1/sequence/{sequence_orcabus_id}/sample_sheet")
-            )
+            get_sequence_request(endpoint=f"{SEQUENCE_RUN_ENDPOINT}/{sequence_orcabus_id}/sample_sheet")
         )
     )
 
 
-def get_library_ids_in_sequence(sequence_orcabus_id: str) -> list[str]:
+def get_library_ids_in_sequence(sequence_orcabus_id: str) -> List[str]:
     """
     Get the library ids in the sequence run.
     :param sequence_orcabus_id:
     :return:
     """
-
-    return get_request(
-        get_sequence_url(endpoint=f"api/v1/sequence/{sequence_orcabus_id}")
-    )['libraries']
+    return get_sequence_request(endpoint=f"{SEQUENCE_RUN_ENDPOINT}/{sequence_orcabus_id}").get('libraries', [])

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: "0.0.46" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.monitoredQueue.MonitoredQueue", version: "0.0.48" };
     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: "0.0.46" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.namedLambdaRole.NamedLambdaRole", version: "0.0.48" };
     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": "0.0.46",
+  "version": "0.0.48",
   "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: "0.0.46" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.provider.ProviderFunction", version: "0.0.48" };
     _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: "0.0.46" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.networking.OrcaBusVpc", version: "0.0.48" };
     /**
      * 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: "0.0.46" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.networking.OrcaBusSharedComputeSecurityGroup", version: "0.0.48" };
     /**
      * 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: "0.0.46" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.slack.SlackAlerts", version: "0.0.48" };
     /**
      * Format the ARN for the slack alerts SNS topic for the current stack.
      * @param stack