@orcabus/platform-cdk-constructs 0.0.75 → 0.0.77

package/.jsii

@@ -7163,6 +7163,6 @@
       "symbolId": "shared-config/slack:SlackAlerts"
     }
   },
-  "version": "0.0.75",
-  "fingerprint": "Ykn25DM2HdYbzbNJH+RKV9bIbtU8XVh74ugP3ixEHug="
+  "version": "0.0.77",
+  "fingerprint": "lLOIvtH8+InIo5ZgIeSeOUN+PjQo/fJl6VcUDxnMo7k="
 }

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: "0.0.75" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.apigateway.OrcaBusApiGateway", version: "0.0.77" };
     /**
      * 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: "0.0.75" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.deploymentPipeline.CrossDeploymentArtifactBucket", version: "0.0.77" };
     /**
      * 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: "0.0.75" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.deploymentPipeline.DeploymentStackPipeline", version: "0.0.77" };
     /**
      * 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: "0.0.75" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.dynamodb.DynamoDbPartitionedConstruct", version: "0.0.77" };
     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: "0.0.75" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.dynamodb.DynamoDbNonPartitionedConstruct", version: "0.0.77" };
     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: "0.0.75" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.ecs.EcsFargateTaskConstruct", version: "0.0.77" };
     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: "0.0.75" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.eventbridgeRule.SfnSlackNotification", version: "0.0.77" };
     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: "0.0.75" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.lambda.PythonUvFunction", version: "0.0.77" };
     // 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/icav2_tools/src/icav2_tools/__init__.py

@@ -15,6 +15,14 @@ from .aws_helpers import (
 )
 from .globals import ICAV2_BASE_URL
 
+# We also want to set up our environment variables as global variables, so that future calls
+# On the same lambda do not need to re-initialize these variables
+# While we use the lambda params-and-secrets secret extension, this does not work
+# When we need to list params in a path
+STORAGE_CONFIGURATION_FILE = None
+PROJECT_TO_STORAGE_CONFIGURATION_MAPPING_FILE = None
+STORAGE_CREDENTIAL_FILE = None
+
 
 def create_storage_configuration_file() -> Path:
     storage_configuration_file = Path(NamedTemporaryFile(
@@ -31,6 +39,13 @@ def create_storage_configuration_file() -> Path:
     return storage_configuration_file
 
 
+def get_storage_configuration_file() -> Path:
+    global STORAGE_CONFIGURATION_FILE
+    if STORAGE_CONFIGURATION_FILE is None:
+        STORAGE_CONFIGURATION_FILE = create_storage_configuration_file()
+    return STORAGE_CONFIGURATION_FILE
+
+
 def create_project_to_storage_configuration_mapping_file() -> Path:
     project_to_storage_configuration_file = Path(NamedTemporaryFile(
         delete=False,
@@ -46,6 +61,13 @@ def create_project_to_storage_configuration_mapping_file() -> Path:
     return project_to_storage_configuration_file
 
 
+def get_project_to_storage_configuration_mapping_file() -> Path:
+    global PROJECT_TO_STORAGE_CONFIGURATION_MAPPING_FILE
+    if PROJECT_TO_STORAGE_CONFIGURATION_MAPPING_FILE is None:
+        PROJECT_TO_STORAGE_CONFIGURATION_MAPPING_FILE = create_project_to_storage_configuration_mapping_file()
+    return PROJECT_TO_STORAGE_CONFIGURATION_MAPPING_FILE
+
+
 def create_storage_credential_file() -> Path:
     storage_credential_file = Path(NamedTemporaryFile(
         delete=False,
@@ -61,6 +83,13 @@ def create_storage_credential_file() -> Path:
     return storage_credential_file
 
 
+def get_storage_credential_file() -> Path:
+    global STORAGE_CREDENTIAL_FILE
+    if STORAGE_CREDENTIAL_FILE is None:
+        STORAGE_CREDENTIAL_FILE = create_storage_credential_file()
+    return STORAGE_CREDENTIAL_FILE
+
+
 def set_icav2_env_vars():
     """
     Set the environment variables for the ICAV2 API
@@ -71,9 +100,9 @@ def set_icav2_env_vars():
     environ["ICAV2_ACCESS_TOKEN"] = get_icav2_access_token()
 
     # Configuration files needed to map storage configurations
-    environ["ICAV2_STORAGE_CONFIGURATION_LIST_FILE"] = str(create_storage_configuration_file())
-    environ["ICAV2_PROJECT_TO_STORAGE_CONFIGURATION_MAPPING_LIST_FILE"] = str(create_project_to_storage_configuration_mapping_file())
-    environ["ICAV2_STORAGE_CREDENTIAL_LIST_FILE"] = str(create_storage_credential_file())
+    environ["ICAV2_STORAGE_CONFIGURATION_LIST_FILE"] = str(get_storage_configuration_file())
+    environ["ICAV2_PROJECT_TO_STORAGE_CONFIGURATION_MAPPING_LIST_FILE"] = str(get_project_to_storage_configuration_mapping_file())
+    environ["ICAV2_STORAGE_CREDENTIAL_LIST_FILE"] = str(get_storage_credential_file())
 
 
 __all__ = [

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

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 import json
 from typing import Dict, Optional, List, Union
-from urllib.parse import urlunparse, unquote
+from urllib.parse import urlunparse, unquote, urlparse, parse_qs
 
 # Standard imports
 import requests
@@ -58,8 +58,16 @@ def get_request_response_results(url: str, params: Optional[Dict] = None) -> Lis
         "Authorization": f"Bearer {get_orcabus_token()}"
     }
 
+    # Get default request params
     req_params = deepcopy(DEFAULT_REQUEST_PARAMS)
 
+    # Drop any req params that are already in the url
+    req_params = dict(filter(
+        lambda kv_iter_: kv_iter_[0] not in parse_qs(urlparse(url).query).keys(),
+        req_params.items()
+    ))
+
+    # Update with params
     req_params.update(
         params if params is not None else {}
     )

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

@@ -50,8 +50,8 @@ def get_workflows_from_library_id_list(library_id_list: List[str]) -> List[Workf
     for library_id in library_id_list[1:]:
         workflows_for_library = get_workflows_from_library_id(library_id)
         all_workflows_intersected = list(filter(
-            lambda workflow_iter_: workflow_iter_.id in list(map(
-                lambda all_workflows_iter_: all_workflows_iter_.id,
+            lambda workflow_iter_: workflow_iter_['orcabusId'] in list(map(
+                lambda all_workflows_iter_: all_workflows_iter_['orcabusId'],
                 all_workflows_intersected
             )),
             workflows_for_library

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

@@ -41,8 +41,17 @@ Payload is
 """
 
 # Imports
-from typing import TypedDict, Optional, Dict, List
-
+from typing import TypedDict, Optional, Dict, List, NotRequired, Literal
+
+# Literals
+AnalysisStatusType = Literal[
+    'ACTIVE',
+    'INACTIVE',
+]
+ContextUseCaseType = Literal[
+    'COMPUTE',
+    'STORAGE',
+]
 
 # Classes
 class StateDetail(TypedDict):
@@ -63,6 +72,30 @@ class State(StateDetail):
     payload: str
 
 
+class Analysis(TypedDict):
+    orcabusId: str
+    analysisName: str
+    analysisVersion: str
+    status: AnalysisStatusType
+
+
+class Context(TypedDict):
+    orcabusId: str
+    name: str
+    usecase: ContextUseCaseType
+
+
+class AnalysisRun(TypedDict):
+    orcabusId: str
+    analysis: Analysis
+    storageContext: Context
+    computeContext: Context
+    analysisRunName: str
+    comment: NotRequired[str]
+    contexts: List[str]
+    readsets: List[str]
+
+
 class WorkflowRunDetail(TypedDict):
     orcabusId: str
     currentState: StateDetail
@@ -71,7 +104,9 @@ class WorkflowRunDetail(TypedDict):
     executionId: Optional[str]
     workflowRunName: str
     comment: Optional[str]
-    analysisRun: Optional[str]
+    analysisRun: Optional[AnalysisRun]
+    contexts: NotRequired[List[str]]
+    readsets: NotRequired[List[str]]
 
 
 class WorkflowRun(WorkflowRunDetail):

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: "0.0.75" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.monitoredQueue.MonitoredQueue", version: "0.0.77" };
     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: "0.0.75" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.namedLambdaRole.NamedLambdaRole", version: "0.0.77" };
     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": "0.0.75",
+  "version": "0.0.77",
   "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: "0.0.75" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.provider.ProviderFunction", version: "0.0.77" };
     _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: "0.0.75" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.networking.OrcaBusVpc", version: "0.0.77" };
     /**
      * 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: "0.0.75" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.networking.OrcaBusSharedComputeSecurityGroup", version: "0.0.77" };
     /**
      * 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: "0.0.75" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.slack.SlackAlerts", version: "0.0.77" };
     /**
      * Format the ARN for the slack alerts SNS topic for the current stack.
      * @param stack