@orcabus/platform-cdk-constructs 0.0.102 → 0.0.104

package/.jsii

@@ -7163,6 +7163,6 @@
       "symbolId": "shared-config/slack:SlackAlerts"
     }
   },
-  "version": "0.0.102",
-  "fingerprint": "Hef5eUEuQANqtuVO8TDAnwhrGFM8+86Cdr6Nu/QQycw="
+  "version": "0.0.104",
+  "fingerprint": "8AsqEKwEq47IHwU7uXbyWa7zxnJSt8IBwMi+dm3nfvs="
 }

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: "0.0.102" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.apigateway.OrcaBusApiGateway", version: "0.0.104" };
     /**
      * 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: "0.0.102" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.deploymentPipeline.CrossDeploymentArtifactBucket", version: "0.0.104" };
     /**
      * 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: "0.0.102" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.deploymentPipeline.DeploymentStackPipeline", version: "0.0.104" };
     /**
      * 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: "0.0.102" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.dynamodb.DynamoDbPartitionedConstruct", version: "0.0.104" };
     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: "0.0.102" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.dynamodb.DynamoDbNonPartitionedConstruct", version: "0.0.104" };
     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: "0.0.102" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.ecs.EcsFargateTaskConstruct", version: "0.0.104" };
     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: "0.0.102" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.eventbridgeRule.SfnSlackNotification", version: "0.0.104" };
     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: "0.0.102" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.lambda.PythonUvFunction", version: "0.0.104" };
     // 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/workflow_helpers.py

@@ -7,7 +7,7 @@ Workflow helpers - a collection of helper functions for the workflow
 """
 
 # Standard library imports
-from typing import List
+from typing import List, Optional
 
 # Local imports
 from . import get_fastq_request
@@ -15,12 +15,35 @@ from .globals import FASTQ_ENDPOINT, FASTQ_SET_ENDPOINT
 from .models import FastqListRowDict
 
 
-def to_fastq_list_row(fastq_id) -> FastqListRowDict:
+def to_fastq_list_row(
+        fastq_id: str,
+        bucket: Optional[str] = None,
+        key_prefix: Optional[str] = None,
+) -> FastqListRowDict:
     return get_fastq_request(
-        f"{FASTQ_ENDPOINT}/{fastq_id}/toFastqListRow"
+        f"{FASTQ_ENDPOINT}/{fastq_id}/toFastqListRow",
+        params=dict(filter(
+            lambda param_iter_: param_iter_[1] is not None,
+            {
+                "bucket": bucket,
+                "keyPrefix": key_prefix,
+            }.items()
+        ))
     )
 
-def to_fastq_list_rows(fastq_set_id: str) -> List[FastqListRowDict]:
+
+def to_fastq_list_rows(
+        fastq_set_id: str,
+        bucket: Optional[str] = None,
+        key_prefix: Optional[str] = None,
+) -> List[FastqListRowDict]:
     return get_fastq_request(
-        f"{FASTQ_SET_ENDPOINT}/{fastq_set_id}/toFastqListRows"
+        f"{FASTQ_SET_ENDPOINT}/{fastq_set_id}/toFastqListRows",
+        params=dict(filter(
+            lambda param_iter_: param_iter_[1] is not None,
+            {
+                "bucket": bucket,
+                "keyPrefix": key_prefix,
+            }.items()
+        ))
     )

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

@@ -5,7 +5,7 @@ import json
 from functools import reduce
 from operator import concat
 from pathlib import Path
-from typing import List, Dict, Union
+from typing import List, Dict, Union, Optional, Unpack
 import typing
 import boto3
 from datetime import datetime, timedelta, timezone
@@ -14,7 +14,7 @@ from itertools import batched
 
 # Local imports
 from .errors import S3FileNotFoundError, S3DuplicateFileCopyError
-from .models import FileObject, StorageClassPriority
+from .models import FileObject, StorageClassPriority, FileQueryParameters
 from ..utils.miscell import get_bucket_key_pair_from_uri
 from . import (
     get_file_manager_request_response_results,
@@ -84,7 +84,10 @@ def get_file_object_from_id(s3_object_id: str) -> FileObject:
     return FileObject(**response[0])
 
 
-def get_file_object_from_ingest_id(ingest_id: str, **kwargs) -> FileObject:
+def get_file_object_from_ingest_id(
+        ingest_id: str,
+        **kwargs: Unpack[FileQueryParameters]
+) -> FileObject:
     response = get_file_manager_request_response_results(S3_LIST_ENDPOINT, {
         "ingestId": ingest_id,
         **kwargs
@@ -199,8 +202,21 @@ def get_s3_uri_from_s3_object_id(s3_object_id: str) -> str:
     return f"s3://{file_object['bucket']}/{file_object['key']}"
 
 
-def get_s3_uri_from_ingest_id(ingest_id: str) -> str:
-    file_object: FileObject = get_file_object_from_ingest_id(ingest_id)
+def get_s3_uri_from_ingest_id(
+        ingest_id: str,
+        bucket: Optional[str] = None,
+        key_prefix: Optional[str] = None
+) -> str:
+    file_object: FileObject = get_file_object_from_ingest_id(
+        ingest_id=ingest_id,
+        **dict(filter(
+            lambda param_iter_: param_iter_[1] is not None,
+            {
+                "bucket": bucket,
+                "key": f"{key_prefix}*" if key_prefix else None
+            }.items()
+        ))
+    )
     return f"s3://{file_object['bucket']}/{file_object['key']}"
 
 

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

@@ -2,7 +2,9 @@ from typing import (
     Optional,
     TypedDict,
     Dict,
-    Literal
+    Literal,
+    NotRequired,
+    Any
 )
 
 """
@@ -49,6 +51,54 @@ StorageClassPriority: Dict[StorageClassType, int] = {
     "DeepArchive": 6,
 }
 
+EventType = Literal[
+    "Created",
+    "Deleted",
+    "Other"
+]
+
+ReasonType = Literal[
+    "CreatedPut",
+    "CreatedPost",
+    "CreatedCopy",
+    "CreatedCompleteMultipartUpload",
+    "Deleted",
+    "DeletedLifecycle",
+    "Restored",
+    "RestoreExpired",
+    "StorageClassChanged",
+    "Crawl",
+    "Unknown",
+    "CrawlRestored"
+]
+
+ArchiveStatusType = Literal[
+    "ArchiveAccess",
+    "DeepArchiveAccess"
+]
+
+
+class FileQueryParameters(TypedDict):
+    caseSensitive: NotRequired[bool]
+    currentState: NotRequired[bool]
+    eventType: NotRequired[EventType]
+    bucket: NotRequired[str]
+    key: NotRequired[str]
+    versionId: NotRequired[str]
+    eventTime: NotRequired[str]
+    size: NotRequired[int]
+    sha256: NotRequired[str]
+    lastModifiedDate: NotRequired[str]
+    eTag: NotRequired[str]
+    storageClass: NotRequired[StorageClassType]
+    isDeleteMarker: NotRequired[bool]
+    reason: NotRequired[ReasonType]
+    archiveStatus: NotRequired[ArchiveStatusType]
+    isAccessible: NotRequired[bool]
+    ingestId: NotRequired[str]
+    attributes: NotRequired[Dict[str, Any]]
+
+
 class FileObject(TypedDict):
     # Identifier
     s3ObjectId: str

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

@@ -1,7 +1,8 @@
 #!/usr/bin/env python3
 
 # Standard imports
-from typing import Dict, Optional
+from io import BufferedReader
+from typing import Dict, Optional, Tuple
 
 # Local imports
 from ..utils.requests_helpers import (
@@ -43,11 +44,20 @@ def get_sequence_request_response_results(
 def sequence_post_request(
         endpoint: str,
         json_data: Optional[Dict] = None,
+        files: Optional[Dict[str, Tuple[str, BufferedReader, str]]] = None,
 ) -> Dict:
+    """
+    Waap POST request with sequence base url
+    :param endpoint:
+    :param json_data:
+    :param files:
+    :return:
+    """
     return post_request(
         get_sequence_url(endpoint),
-        json_data=json_data
-)
+        json_data=json_data,
+        files=files,
+    )
 
 
 from .sequence_helpers import (

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

@@ -141,15 +141,13 @@ def add_samplesheet(
     :return: Response from the API containing the updated sequence information.
     """
     # Open the sample sheet file
-    with open(samplesheet_path, 'r') as ss_file:
-        ss_content = ss_file.read()
-
-    return sequence_post_request(
-        endpoint=f"{SEQUENCE_RUN_ENDPOINT}/action/add_samplesheet/",
-        json_data={
-            "file": ss_content,
-            "instrument_run_id": instrument_run_id,
-            "created_by": created_by,
-            "comment": comment
-        }
-    )
+    with open(samplesheet_path, 'rb') as file_data:
+        return sequence_post_request(
+            endpoint=f"{SEQUENCE_RUN_ENDPOINT}/action/add_samplesheet/",
+            files={
+                "file": ("SampleSheet.csv", file_data, 'text/csv'),
+                "instrument_run_id": (None, instrument_run_id),
+                "created_by": (None, created_by),
+                "comment": (None, comment),
+            }
+        )

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

@@ -1,13 +1,13 @@
 #!/usr/bin/env python3
-import json
-from typing import Dict, Optional, List, Union
-from urllib.parse import urlunparse, unquote, urlparse, parse_qs
 
 # Standard imports
+import json
 import requests
+from io import BufferedReader
+from typing import Dict, Optional, List, Union, Tuple
+from urllib.parse import urlunparse, unquote, urlparse, parse_qs
 import logging
 from copy import deepcopy
-
 from fastapi.encoders import jsonable_encoder
 from requests import HTTPError
 
@@ -159,13 +159,15 @@ def patch_request(
 def post_request(
         url: str,
         json_data: Optional[Dict] = None,
-        params: Optional[Dict] = None
+        params: Optional[Dict] = None,
+        files:  Optional[Dict[str, Tuple[str, BufferedReader, str]]] = None,
 ) -> Dict:
     """
     Run post request against the fastq endpoint
     :param json_data:
     :param url:
     :param params:
+    :param files:
     :return:
     """
     # Get authorization header
@@ -173,7 +175,11 @@ def post_request(
         "Authorization": f"Bearer {get_orcabus_token()}",
     }
 
-    if json_data is not None:
+    # Set content type headers
+    if files is not None:
+        # Let requests set the content type for multipart
+        pass
+    elif json_data is not None:
        headers.update({
            "Content-Type": "application/json"
        })
@@ -183,7 +189,8 @@ def post_request(
         url,
         headers=headers,
         json=json_data,
-        params=params
+        params=params,
+        files=files,
     )
 
     try:

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

@@ -28,7 +28,8 @@ def list_workflow_runs(
     :param current_status:
     :return:
     """
-    return get_workflow_request_response_results(
+    # Get workflow runs
+    workflow_runs = get_workflow_request_response_results(
         WORKFLOW_RUN_ENDPOINT,
         params=dict(filter(
             lambda item: item[1] is not None,
@@ -36,12 +37,21 @@ def list_workflow_runs(
                 "workflow__name": workflow_name,
                 "workflow__version": workflow_version,
                 "workflow__codeVersion": code_version,
-                "currentState__status": current_status,
                 "analysisRun__orcabusId": analysis_run_id
             }.items()
         ))
     )
 
+    # Check if status is set?
+    if current_status is None:
+        return workflow_runs
+
+    # Filter by status
+    return list(filter(
+        lambda workflow_run_iter_: workflow_run_iter_.get("currentState", {}).get("status") == current_status,
+        workflow_runs
+    ))
+
 
 # Deprecated
 def list_workflow_runs_by_workflow_name(

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: "0.0.102" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.monitoredQueue.MonitoredQueue", version: "0.0.104" };
     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: "0.0.102" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.namedLambdaRole.NamedLambdaRole", version: "0.0.104" };
     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": "0.0.102",
+  "version": "0.0.104",
   "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: "0.0.102" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.provider.ProviderFunction", version: "0.0.104" };
     _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: "0.0.102" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.networking.OrcaBusVpc", version: "0.0.104" };
     /**
      * 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: "0.0.102" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.networking.OrcaBusSharedComputeSecurityGroup", version: "0.0.104" };
     /**
      * 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: "0.0.102" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.slack.SlackAlerts", version: "0.0.104" };
     /**
      * Format the ARN for the slack alerts SNS topic for the current stack.
      * @param stack