@orcabus/platform-cdk-constructs 0.0.34 → 0.0.36

package/.jsii

@@ -6756,6 +6756,6 @@
       "symbolId": "shared-config/slack:SlackAlerts"
     }
   },
-  "version": "0.0.34",
-  "fingerprint": "d+PMtKWVtmzS+P1omiV5f8tQJsCkfNLbBjjTeYDFmFM="
+  "version": "0.0.36",
+  "fingerprint": "AQT2JtcqQttpFxgpSQBleYyVLEKOYHPF4q1ii9wJBZ4="
 }

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: "0.0.34" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.apigateway.OrcaBusApiGateway", version: "0.0.36" };
     /**
      * 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: "0.0.34" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.deploymentPipeline.CrossDeploymentArtifactBucket", version: "0.0.36" };
     /**
      * 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: "0.0.34" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.deploymentPipeline.DeploymentStackPipeline", version: "0.0.36" };
     /**
      * 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: "0.0.34" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.dynamodb.DynamoDbPartitionedConstruct", version: "0.0.36" };
     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: "0.0.34" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.dynamodb.DynamoDbNonPartitionedConstruct", version: "0.0.36" };
     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: "0.0.34" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.ecs.EcsFargateTaskConstruct", version: "0.0.36" };
     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: "0.0.34" };
+    static [JSII_RTTI_SYMBOL_1] = { fqn: "@orcabus/platform-cdk-constructs.lambda.PythonUvFunction", version: "0.0.36" };
     // 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/data_sharing/__init__.py

@@ -0,0 +1,70 @@
+# FIMXE Implement the following imports
+from typing import Optional, Dict
+
+from .globals import DATA_SHARING_SUBDOMAIN_NAME
+from ..utils.requests_helpers import get_url, get_request, get_request_response_results, patch_request
+
+
+# Get url for the subdomain
+def get_data_sharing_url(endpoint: str) -> str:
+    """
+    Get the URL for the data sharing endpoint
+    :param endpoint:
+    :return:
+    """
+    return get_url(
+        endpoint=endpoint,
+        subdomain=DATA_SHARING_SUBDOMAIN_NAME,
+    )
+
+
+# Wrappers
+def get_data_sharing_request(
+        endpoint: str,
+        params: Optional[Dict] = None,
+):
+    return get_request(
+        url=get_data_sharing_url(endpoint),
+        params=params
+    )
+
+
+def get_data_sharing_request_response_results(
+        endpoint: str,
+        params: Optional[Dict] = None,
+):
+    return get_request_response_results(
+        url=get_data_sharing_url(endpoint),
+        params=params
+    )
+
+
+def data_sharing_patch_request(
+    endpoint: str,
+    params: Optional[Dict] = None,
+):
+    return patch_request(
+        url=get_data_sharing_url(endpoint),
+        params=params
+    )
+
+
+def data_sharing_post_request(
+    endpoint: str,
+    params: Optional[Dict] = None,
+):
+    return patch_request(
+        url=get_data_sharing_url(endpoint),
+        params=params
+    )
+
+
+from .update_helpers import (
+    update_package_status,
+    update_push_job_status,
+)
+
+__all__ = [
+    "update_package_status",
+    "update_push_job_status",
+]

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

@@ -0,0 +1,15 @@
+# Imports
+import re
+from typing import Literal
+
+# AWS PARAMETERS
+DATA_SHARING_SUBDOMAIN_NAME = "data-sharing"
+
+# API ENDPOINTS
+PACKAGE_ENDPOINT = "api/v1/package"
+PUSH_ENDPOINT = "api/v1/push"
+
+# REGEX
+ORCABUS_ULID_REGEX_MATCH = re.compile(r'^[a-z0-9]{3}\.[A-Z0-9]{26}$')
+
+

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

@@ -0,0 +1,28 @@
+from typing import Literal, TypedDict, NotRequired
+
+PackageStatusType = Literal[
+    "PENDING",
+    "RUNNING",
+    "FAILED",
+    "ABORTED",
+    "SUCCEEDED",
+]
+
+PushJobStatusType = Literal[
+    "PENDING",
+    "RUNNING",
+    "FAILED",
+    "ABORTED",
+    "SUCCEEDED",
+]
+
+
+
+class PackageObject(TypedDict):
+    id: str
+    packageName: str
+    stepsExecutionArn: str
+    status: PackageStatusType
+    requestTime: str
+    completionTime: NotRequired[str]
+    hasExpired: NotRequired[bool]

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

@@ -0,0 +1,53 @@
+from typing import Optional
+
+from . import data_sharing_patch_request
+from .globals import PACKAGE_ENDPOINT, PUSH_ENDPOINT
+from .models import PackageStatusType, PackageObject, PushJobStatusType
+
+
+def update_package_status(
+        package_id: str,
+        package_status: PackageStatusType,
+        error_message: Optional[str] = None
+) -> PackageObject:
+    """
+    Add QC stats to a fastq_id.
+
+    :param package_id: The package id
+    :param package_status: The package status to set
+    :param error_message: Optional error message
+    """
+    return data_sharing_patch_request(
+        f"{PACKAGE_ENDPOINT}/{package_id}",
+        params=dict(filter(
+            lambda x: x[1] is not None,
+            {
+                "status": package_status,
+                "error_message": error_message
+            }.items()
+        ))
+    )
+
+
+def update_push_job_status(
+        push_job_id: str,
+        push_job_status: PushJobStatusType,
+        error_message: Optional[str] = None
+) -> PackageObject:
+    """
+    Add push job status to a push job.
+
+    :param push_job_id: The push job id
+    :param push_job_status: The push job status to set
+    :param error_message: Optional error message
+    """
+    return data_sharing_patch_request(
+        f"{PUSH_ENDPOINT}/{push_job_id}",
+        params=dict(filter(
+            lambda x: x[1] is not None,
+            {
+                "status": push_job_status,
+                "error_message": error_message
+            }.items()
+        ))
+    )

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

@@ -70,14 +70,16 @@ def fastq_post_request(
 # Create
 from .create_helpers import (
     create_fastq_set_object,
-    create_fastq_list_row_object
+    create_fastq_list_row_object,
+    create_fastq_object,
 )
 
 # Job
 from .job_helpers import (
     run_qc_stats,
     run_ntsm,
-    run_file_compression_stats
+    run_file_compression_stats,
+    run_read_count_stats
 )
 
 # Query
@@ -97,6 +99,7 @@ from .query_helpers import (
     get_fastqs_in_individual,
     get_fastqs_in_project,
     get_fastq_list_rows_in_fastq_set,
+    get_fastqs_in_fastq_set,
     get_fastq_jobs,
 )
 
@@ -111,7 +114,9 @@ from .update_helpers import (
     validate_fastq,
     invalidate_fastq,
     link_fastq_list_row_to_fastq_set,
+    link_fastq_to_fastq_set,
     unlink_fastq_list_row_from_fastq_set,
+    unlink_fastq_from_fastq_set,
     allow_additional_fastqs_to_fastq_set,
     disallow_additional_fastqs_to_fastq_set,
     set_is_current_fastq_set,
@@ -135,10 +140,12 @@ __all__ = [
     # Create
     "create_fastq_set_object",
     "create_fastq_list_row_object",
+    "create_fastq_object",
     # Job
     "run_qc_stats",
     "run_ntsm",
     "run_file_compression_stats",
+    "run_read_count_stats",
     # Query
     "get_fastq",
     "get_fastq_set",
@@ -155,6 +162,7 @@ __all__ = [
     "get_fastqs_in_individual",
     "get_fastqs_in_project",
     "get_fastq_list_rows_in_fastq_set",
+    "get_fastqs_in_fastq_set",
     "get_fastq_jobs",
     # Updaters
     "add_qc_stats",
@@ -166,7 +174,9 @@ __all__ = [
     "validate_fastq",
     "invalidate_fastq",
     "link_fastq_list_row_to_fastq_set",
+    "link_fastq_to_fastq_set",
     "unlink_fastq_list_row_from_fastq_set",
+    "unlink_fastq_from_fastq_set",
     "allow_additional_fastqs_to_fastq_set",
     "disallow_additional_fastqs_to_fastq_set",
     "set_is_current_fastq_set",

package/lambda/layers/orcabus_api_tools/src/orcabus_api_tools/fastq/create_helpers.py

@@ -17,18 +17,30 @@ from typing import Unpack
 
 # Local imports
 from . import fastq_post_request
-from .globals import FASTQ_LIST_ROW_ENDPOINT, FASTQ_SET_ENDPOINT
-from .models import FastqListRow, FastqSet, FastqListRowCreate, FastqSetCreate
+from .globals import FASTQ_ENDPOINT, FASTQ_SET_ENDPOINT
+from .models import Fastq, FastqSet, FastqCreate, FastqSetCreate
 
 
-def create_fastq_list_row_object(**kwargs: Unpack[FastqListRowCreate]) -> FastqListRow:
+def create_fastq_list_row_object(**kwargs: Unpack[FastqCreate]) -> Fastq:
+    """
+    DEPRECATED: Use create_fastq_object instead.
+    """
+    return create_fastq_object(**kwargs)
+
+
+def create_fastq_object(**kwargs: Unpack[FastqCreate]) -> Fastq:
     """
     Add a fastq list row object to the database.
     Returns the created fastq list row object
     """
-    return FastqListRow(
+    # Raise error if any of the kwargs are not in the FastqCreate
+    for key in kwargs.keys():
+        if key not in FastqCreate.__annotations__:
+            raise ValueError(f"Invalid parameter: {key}")
+
+    return Fastq(
         **fastq_post_request(
-            endpoint=FASTQ_LIST_ROW_ENDPOINT,
+            endpoint=FASTQ_ENDPOINT,
             params=dict(kwargs)
         )
     )
@@ -39,6 +51,11 @@ def create_fastq_set_object(**kwargs: Unpack[FastqSetCreate]) -> FastqSet:
     Add a fastq set object to the database.
     Returns the created fastq set object
     """
+    # Raise error if any of the kwargs are not in the FastqCreate
+    for key in kwargs.keys():
+        if key not in FastqSetCreate.__annotations__:
+            raise ValueError(f"Invalid parameter: {key}")
+
     return FastqSet(
         **fastq_post_request(
             endpoint=FASTQ_SET_ENDPOINT,

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

@@ -6,7 +6,7 @@ import re
 FASTQ_SUBDOMAIN_NAME = "fastq"
 
 # API ENDPOINTS
-FASTQ_LIST_ROW_ENDPOINT = "api/v1/fastq"
+FASTQ_ENDPOINT = "api/v1/fastq"
 FASTQ_SET_ENDPOINT = "api/v1/fastqSet"
 
 # REGEX

package/lambda/layers/orcabus_api_tools/src/orcabus_api_tools/fastq/job_helpers.py

@@ -11,7 +11,7 @@ Update helpers for the update script.
 
 # Local imports
 from . import fastq_patch_request
-from .globals import FASTQ_LIST_ROW_ENDPOINT
+from .globals import FASTQ_ENDPOINT
 from .models import Job
 
 
@@ -23,7 +23,7 @@ def run_qc_stats(fastq_id: str) -> Job:
     """
     return Job(
         **fastq_patch_request(
-            f"{FASTQ_LIST_ROW_ENDPOINT}/{fastq_id}:runQcStats"
+            f"{FASTQ_ENDPOINT}/{fastq_id}:runQcStats"
         )
     )
 
@@ -36,7 +36,7 @@ def run_ntsm(fastq_id: str) -> Job:
     """
     return Job(
         **fastq_patch_request(
-            f"{FASTQ_LIST_ROW_ENDPOINT}/{fastq_id}:runNtsm"
+            f"{FASTQ_ENDPOINT}/{fastq_id}:runNtsm"
         )
     )
 
@@ -48,6 +48,18 @@ def run_file_compression_stats(fastq_id: str) -> Job:
     """
     return Job(
         **fastq_patch_request(
-            f"{FASTQ_LIST_ROW_ENDPOINT}/{fastq_id}:runFileCompressionInformation"
+            f"{FASTQ_ENDPOINT}/{fastq_id}:runFileCompressionInformation"
+        )
+    )
+
+def run_read_count_stats(fastq_id: str) -> Job:
+    """
+    Run file compression stats for a fastq_id.
+
+    :param fastq_id: Fastq str
+    """
+    return Job(
+        **fastq_patch_request(
+            f"{FASTQ_ENDPOINT}/{fastq_id}:runReadCountInformation"
         )
     )

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

@@ -40,22 +40,27 @@ from typing import (
     TypedDict,
     Optional,
     Dict,
-    List, NotRequired, Union, Literal
+    List, NotRequired, Union,
+    Literal
 )
 from datetime import datetime
 
 
-class JobType(Enum):
-    QC = 'QC'
-    FILE_COMPRESSION = 'FILE_COMPRESSION'
-    NTSM = 'NTSM'
+JobType = Literal[
+    'QC',
+    'FILE_COMPRESSION',
+    'NTSM',
+    'READ_COUNT',
+]
+
 
+JobStatus = Literal[
+    "PENDING",
+    "RUNNING",
+    "FAILED",
+    "SUCCEEDED",
+]
 
-class JobStatus(Enum):
-    PENDING = "PENDING"
-    RUNNING = "RUNNING"
-    FAILED = "FAILED"
-    SUCCEEDED = "SUCCEEDED"
 
 
 class FileStorageObject(TypedDict):
@@ -81,6 +86,7 @@ class Library(TypedDict):
     libraryId: str
 
 
+# Deprecated: Use FastqCreate instead
 class FastqListRowCreate(TypedDict):
     fastqSetId: Optional[str]
     index: str
@@ -98,6 +104,7 @@ class FastqListRowCreate(TypedDict):
     ntsm: Optional[FileStorageObject]
 
 
+# Deprecated: Use Fastq instead
 class FastqListRow(TypedDict):
     id: str
     fastqSetId: Optional[str]
@@ -116,9 +123,44 @@ class FastqListRow(TypedDict):
     ntsm: Optional[FileStorageObject]
 
 
+class Fastq(TypedDict):
+    id: str
+    fastqSetId: Optional[str]
+    index: str
+    lane: int
+    instrumentRunId: str
+    library: Library
+    platform: Optional[str]
+    center: Optional[str]
+    date: Optional[datetime]
+    readSet: Optional[ReadSet]
+    qc: Optional[Dict]
+    readCount: Optional[int]
+    baseCountEst: Optional[int]
+    isValid: Optional[bool]
+    ntsm: Optional[FileStorageObject]
+
+
+class FastqCreate(TypedDict):
+    fastqSetId: Optional[str]
+    index: str
+    lane: int
+    instrumentRunId: str
+    library: Library
+    platform: Optional[str]
+    center: Optional[str]
+    date: Optional[datetime]
+    readSet: Optional[ReadSet]
+    qc: Optional[Dict]
+    readCount: Optional[int]
+    baseCountEst: Optional[int]
+    isValid: Optional[bool]
+    ntsm: Optional[FileStorageObject]
+
+
 class FastqSetCreate(TypedDict):
     library: Library
-    fastqSet: List[Union[str, FastqListRow]]
+    fastqSet: List[Union[str, Fastq]]
     allowAdditionalFastq: bool
     isCurrentFastqSet: bool
 
@@ -126,7 +168,7 @@ class FastqSetCreate(TypedDict):
 class FastqSet(TypedDict):
     id: str
     library: Library
-    fastqSet: List[FastqListRow]
+    fastqSet: List[Fastq]
     allowAdditionalFastq: bool
     isCurrentFastqSet: bool
 
@@ -138,6 +180,7 @@ class QcStats(TypedDict):
     r2Q20Fraction: float
     r1GcFraction: float
     r2GcFraction: float
+    duplicationFractionEstimate: float
 
 
 class ReadCount(TypedDict):
@@ -176,15 +219,15 @@ class Job(TypedDict):
     startTime: datetime
     endTime: Optional[datetime]
 
-
-class BoolAllEnum(Enum):
-    ALL = "ALL"
-    true = True
-    false = False
+BoolLiteral = Literal[
+    'ALL',
+    True,
+    False
+]
 
 
 class FastqGetResponseParameters(TypedDict):
-    includeS3Details: NotRequired[BoolAllEnum]
+    includeS3Details: NotRequired[bool]
 
 
 class StandardQueryParameters(TypedDict):
@@ -224,15 +267,28 @@ InstrumentRunIdQueryParametersList = TypedDict(
 )
 
 
-class FastqListRowQueryParameters(
+# Deprecated: Use FastqQueryParameters instead
+class FastqParameters(
+    StandardQueryParameters,
+    MetadataQueryParameter,
+    InstrumentRunIdQueryParameters,
+    MetadataQueryParametersList,
+    InstrumentRunIdQueryParametersList
+):
+    valid: NotRequired[BoolLiteral]
+    includeS3Details: NotRequired[BoolLiteral]
+    fastqSetId: NotRequired[str]
+
+
+class FastqQueryParameters(
     StandardQueryParameters,
     MetadataQueryParameter,
     InstrumentRunIdQueryParameters,
     MetadataQueryParametersList,
     InstrumentRunIdQueryParametersList
 ):
-    valid: NotRequired[BoolAllEnum]
-    includeS3Details: NotRequired[BoolAllEnum]
+    valid: NotRequired[BoolLiteral]
+    includeS3Details: NotRequired[BoolLiteral]
     fastqSetId: NotRequired[str]
 
 
@@ -242,9 +298,9 @@ class FastqSetQueryParameters(
     MetadataQueryParametersList,
     InstrumentRunIdQueryParameters
 ):
-    currentFastqSet: NotRequired[BoolAllEnum]
-    allowAdditionalFastq: NotRequired[BoolAllEnum]
-    includeS3Details: NotRequired[BoolAllEnum]
+    currentFastqSet: NotRequired[BoolLiteral]
+    allowAdditionalFastq: NotRequired[BoolLiteral]
+    includeS3Details: NotRequired[BoolLiteral]
 
 # Additional types
 VALID_BATCH_KEYS = Literal[