@orcabus/platform-cdk-constructs 0.0.33 → 0.0.35

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

@@ -13,28 +13,27 @@
 
 from typing import (
     TypedDict, NotRequired,
+    Literal
 )
 
-from enum import Enum
+JobType = Literal[
+    "S3_UNARCHIVING",
+]
 
 
-class JobType(Enum):
-    S3_UNARCHIVING = "S3_UNARCHIVING"
-
-
-class JobStatus(Enum):
-    PENDING = "PENDING"
-    RUNNING = "RUNNING"
-    FAILED = "FAILED"
-    ABORTED = "ABORTED"
-    SUCCEEDED = "SUCCEEDED"
-
+JobStatusType = Literal[
+    "PENDING",
+    "RUNNING",
+    "FAILED",
+    "ABORTED",
+    "SUCCEEDED",
+]
 
 class Job(TypedDict):
     id: str
     jobType: JobType
     stepsExecutionArn: str
-    status: JobStatus
+    status: JobStatusType
     startTime: str
     endTime: str
     errorMessages: str
@@ -42,7 +41,7 @@ class Job(TypedDict):
 
 class JobQueryParameters(TypedDict):
     fastqId: NotRequired[str]
-    status: NotRequired[JobStatus]
+    status: NotRequired[JobStatusType]
     createdAfter: NotRequired[str]
     createdBefore: NotRequired[str]
     completedAfter: NotRequired[str]

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

@@ -14,7 +14,7 @@ from typing import List, Unpack
 
 # Local imports
 from . import get_fastq_unarchiving_request_response_results
-from .models import Job, JobStatus, JobQueryParameters
+from .models import Job, JobStatusType, JobQueryParameters
 
 from .globals import JOB_ENDPOINT
 
@@ -40,7 +40,7 @@ def get_unarchiving_job_list(**kwargs: Unpack[JobQueryParameters]) -> List[Job]:
 
 def get_job_list_for_fastq(
         fastq_id: str,
-        job_status: JobStatus
+        job_status: JobStatusType
 ) -> List[Job]:
     """
     Check if fastq in job list
@@ -48,5 +48,5 @@ def get_job_list_for_fastq(
     """
     return get_unarchiving_job_list(
         fastqId=fastq_id,
-        status=job_status.value
+        status=job_status
     )

package/lambda/layers/orcabus_api_tools/src/orcabus_api_tools/fastq_unarchiving/update_helpers.py

@@ -17,13 +17,13 @@ from typing import Optional
 
 # Local imports
 from . import fastq_unarchiving_patch_request
-from .globals import JobStatus, JOB_ENDPOINT
-from .models import Job
+from .globals import JOB_ENDPOINT
+from .models import Job, JobStatusType
 
 
 def update_status(
         job_id: str,
-        job_status: JobStatus,
+        job_status: JobStatusType,
         error_message: Optional[str] = None
 ) -> Job:
     """

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

@@ -40,10 +40,12 @@ def get_file_manager_request(
 
 def file_manager_patch_request(
         endpoint: str,
+        json_data: Optional[Dict] = None,
         params: Optional[Dict] = None
 ):
     return patch_request(
         get_file_manager_url(endpoint),
+        json_data=json_data,
         params=params
     )
 

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

@@ -1,24 +1,30 @@
 #!/usr/bin/env python3
+
+# Standard imports
+import json
 from functools import reduce
 from operator import concat
 from typing import List, Dict, Union
 import typing
-
 import boto3
+from datetime import datetime, timedelta, timezone
+from urllib.parse import urlparse
+from itertools import batched
 
+# Local imports
 from .errors import S3FileNotFoundError, S3DuplicateFileCopyError
-from .models import FileObject
+from .models import FileObject, StorageClassPriority
 from ..utils.miscell import get_bucket_key_pair_from_uri
-from . import get_file_manager_request_response_results, get_file_manager_request, file_manager_patch_request
+from . import (
+    get_file_manager_request_response_results,
+    get_file_manager_request,
+    file_manager_patch_request
+)
 from .globals import (
     S3_LIST_ENDPOINT,
     S3_BUCKETS_BY_ACCOUNT_ID,
-    S3_PREFIXES_BY_ACCOUNT_ID,
-    StorageEnum, StoragePriority,
+    S3_PREFIXES_BY_ACCOUNT_ID
 )
-from datetime import datetime, timedelta, timezone
-from urllib.parse import urlparse
-from itertools import batched
 
 if typing.TYPE_CHECKING:
     from mypy_boto3_sts import STSClient
@@ -94,7 +100,7 @@ def get_file_object_from_ingest_id(ingest_id: str, **kwargs) -> FileObject:
     ))
 
     # Order by storage class
-    file_objects_list.sort(key=lambda file_obj_iter_: StoragePriority[StorageEnum(file_obj_iter_['storageClass']).name].value)
+    file_objects_list.sort(key=lambda file_obj_iter_: StorageClassPriority[file_obj_iter_['storageClass']])
 
     # Return as a FileObject model
     return file_objects_list[0]
@@ -263,8 +269,9 @@ def get_s3_objs_from_ingest_ids_map(ingest_ids: List[str], **kwargs) -> List[Dic
             continue
 
         s3_objects_match.sort(
-            key=lambda s3_object_iter_: StoragePriority[
-                StorageEnum(s3_object_iter_['fileObject']['storageClass']).name].value
+            key=lambda s3_object_iter_: StorageClassPriority[
+                s3_object_iter_['fileObject']['storageClass']
+            ]
         )
 
         s3_objects_by_ingest_id_filtered.append(

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

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-from enum import Enum
 
 # AWS PARAMETERS
 FILEMANAGER_SUBDOMAIN_NAME = "file"
@@ -41,30 +40,3 @@ S3_PREFIXES_BY_ACCOUNT_ID = {
     },
 }
 
-# FROM FileManager Schema
-# "DeepArchive"
-# "Glacier"
-# "GlacierIr"
-# "IntelligentTiering"
-# "OnezoneIa"
-# "Outposts"
-# "ReducedRedundancy"
-# "Snow"
-# "Standard"
-# "StandardIa"
-class StorageEnum(Enum):
-    STANDARD = "Standard"
-    STANDARD_IA = "StandardIa"
-    INTELLIGENT_TIERING = "IntelligentTiering"
-    GLACIER_INSTANT_RETRIEVAL = "GlacierIr"
-    GLACIER = "Glacier"
-    DEEP_ARCHIVE = "DeepArchive"
-
-
-class StoragePriority(Enum):
-    STANDARD = 1
-    STANDARD_IA = 2
-    INTELLIGENT_TIERING = 3
-    GLACIER_INSTANT_RETRIEVAL = 4
-    GLACIER = 5
-    DEEP_ARCHIVE = 6

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

@@ -1,4 +1,4 @@
-from typing import Optional, TypedDict, Dict
+from typing import Optional, TypedDict, Dict, Literal
 
 """
 Example File Object response
@@ -26,6 +26,23 @@ Example File Object response
     }
 """
 
+StorageClassType = Literal[
+    "Standard",
+    "StandardIa",
+    "IntelligentTiering",
+    "GlacierIr",
+    "Glacier",
+    "DeepArchive",
+]
+
+StorageClassPriority: Dict[StorageClassType, int] = {
+    "Standard": 1,
+    "StandardIa": 2,
+    "IntelligentTiering": 3,
+    "GlacierIr": 4,
+    "Glacier": 5,
+    "DeepArchive": 6,
+}
 
 class FileObject(TypedDict):
     # Identifier
@@ -47,7 +64,7 @@ class FileObject(TypedDict):
     numberReordered: int
     sequencer: str
     size: int
-    storageClass: str
+    storageClass: StorageClassType
 
     # Attribute attributes
     attributes: Optional[Dict]

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

@@ -9,6 +9,8 @@ from copy import deepcopy
 
 from requests import HTTPError
 
+from fastapi.encoders import jsonable_encoder
+
 # Locals
 from .aws_helpers import (
     get_orcabus_token, get_hostname
@@ -103,7 +105,11 @@ def get_request(url: str, params: Optional[Dict] = None) -> Dict:
     return response.json()
 
 
-def patch_request(url: str, params: Optional[Dict] = None) -> Dict:
+def patch_request(
+        url: str,
+        json_data: Optional[Dict] = None,
+        params: Optional[Dict] = None
+) -> Dict:
     # Get authorization header
     headers = {
         "Authorization": f"Bearer {get_orcabus_token()}"
@@ -119,7 +125,8 @@ def patch_request(url: str, params: Optional[Dict] = None) -> Dict:
     response = requests.patch(
         url,
         headers=headers,
-        json=req_params
+        params=req_params,
+        json=json_data
     )
 
     try:

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: "0.0.33" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.monitoredQueue.MonitoredQueue", version: "0.0.35" };
     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: "0.0.33" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.namedLambdaRole.NamedLambdaRole", version: "0.0.35" };
     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": "0.0.33",
+  "version": "0.0.35",
   "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: "0.0.33" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.provider.ProviderFunction", version: "0.0.35" };
     _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: "0.0.33" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.networking.OrcaBusVpc", version: "0.0.35" };
     /**
      * 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: "0.0.33" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.networking.OrcaBusSharedComputeSecurityGroup", version: "0.0.35" };
     /**
      * 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: "0.0.33" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.sharedConfig.slack.SlackAlerts", version: "0.0.35" };
     /**
      * Format the ARN for the slack alerts SNS topic for the current stack.
      * @param stack