@orcabus/platform-cdk-constructs 0.0.7-alpha.6 → 0.0.7-beta.2

package/lambda/layers/fastapi_tools/pyproject.toml

@@ -0,0 +1,32 @@
+[build-system]
+requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.poetry]
+name = "fastapi_tools"
+version = "1.0.0"
+description = "A collection of secondary-level functions to use to interact with the OrcaBus"
+license = "GPL-3.0-or-later"
+authors = [
+    "Alexis Lucattini"
+]
+homepage = "https://github.com/orcabus/platform-cdk-constructs"
+repository = "https://github.com/orcabus/platform-cdk-constructs"
+
+[tool.poetry.dependencies]
+python = "^3.12, <3.13"
+fastapi = {extras = ["standard"], version = ">=0.115.6"}
+pydantic = "^2.10.5"
+mangum = "^0.19.0"
+dyntastic = "^0.16.0"
+ulid-py = "^1.1.0"
+requests = "^2.32.3"
+
+[tool.poetry.group.dev]
+optional = true
+
+[tool.poetry.group.dev.dependencies]
+pytest = "^7.0.0"  # For testing only
+# For typehinting only, not required at runtime
+mypy-boto3-ssm = "^1.34"
+mypy-boto3-secretsmanager = "^1.34"

package/lambda/layers/fastapi_tools/src/fastapi_tools/__init__.py

@@ -0,0 +1,20 @@
+#!/usr/bin/env python3
+
+"""
+
+"""
+
+from .pagination_helpers import (
+    Links,
+    QueryPagination,
+    ResponsePagination,
+    QueryPaginatedResponse,
+)
+
+__all__ = [
+    # Pagination helpers
+    "Links",
+    "QueryPagination",
+    "ResponsePagination",
+    "QueryPaginatedResponse",
+]

package/lambda/layers/fastapi_tools/src/fastapi_tools/globals.py

@@ -0,0 +1,3 @@
+#!/usr/bin/env python3
+
+DEFAULT_ROWS_PER_PAGE = 100

package/lambda/layers/fastapi_tools/src/fastapi_tools/pagination_helpers.py

@@ -0,0 +1,102 @@
+import typing
+from typing import Optional, TypedDict, List, Any, ClassVar, Dict, Self
+from urllib.parse import urlparse, urlunparse
+
+from pydantic import BaseModel
+
+from .globals import DEFAULT_ROWS_PER_PAGE
+
+
+class Links(TypedDict):
+    previous: Optional[str]
+    next: Optional[str]
+
+
+class QueryPagination(TypedDict):
+    page: Optional[int]
+    rowsPerPage: Optional[int]
+
+
+class ResponsePagination(QueryPagination):
+    count: int
+
+
+class QueryPaginatedResponse(BaseModel):
+    """
+    Job Query Response, includes a list of jobs, the total
+    """
+    links: Links
+    pagination: ResponsePagination
+    results: List[Any]
+    # Implemented in subclass
+    url_placeholder: ClassVar[str] = None
+
+    def resolve_url_placeholder(self, **kwargs) -> str:
+        raise NotImplementedError
+
+    @classmethod
+    def from_results_list(cls, results: List[Any], query_pagination: QueryPagination, params_response: Dict, **kwargs) -> Self:
+        # From pagination calculate the links
+        if cls.url_placeholder is None:
+            raise ValueError("URL must be set for QueryPaginatedResponse")
+        url_obj = urlparse(cls.resolve_url_placeholder(**kwargs))
+
+        query_pagination = {
+            'page': query_pagination.get('page', 1),
+            'rowsPerPage': query_pagination.get('rowsPerPage', DEFAULT_ROWS_PER_PAGE)
+        }
+
+        response_pagination: ResponsePagination = ResponsePagination(
+            **dict(
+                **query_pagination,
+                # Add in count using the results length
+                **{
+                    'count': len(results)
+                }
+            )
+        )
+
+        if query_pagination['page'] == 1:
+            previous_page = None
+        else:
+            params_response_prev = params_response.copy()
+            params_response_prev['page'] = query_pagination['page'] - 1
+            params_str = "&".join([
+                f"{k}={v}"
+                for k, v in params_response_prev.items()
+            ])
+
+            previous_page = str(urlunparse(
+                (url_obj.scheme, url_obj.netloc, url_obj.path, None, params_str, None)
+            ))
+
+        if ( response_pagination['page'] * response_pagination['rowsPerPage'] ) >= response_pagination['count']:
+            next_page = None
+        else:
+            params_response_next = params_response.copy()
+            params_response_next['page'] = query_pagination['page'] + 1
+            params_str = "&".join([
+                f"{k}={v}"
+                for k, v in params_response_next.items()
+            ])
+            next_page = str(urlunparse(
+                (url_obj.scheme, url_obj.netloc, url_obj.path, None, params_str, None)
+            ))
+
+        # Calculate the start and end of the results
+        results_start = ( query_pagination['page'] - 1 ) * query_pagination['rowsPerPage']
+        results_end = results_start + query_pagination['rowsPerPage']
+
+        # Generate the response object
+        return cls(
+            links={
+                'previous': previous_page,
+                'next': next_page
+            },
+            pagination=response_pagination,
+            results=results[results_start:results_end]
+        )
+
+    if typing.TYPE_CHECKING:
+        def model_dump(self, **kwargs) -> 'Self':
+            pass

package/lambda/layers/icav2_tools/poetry.lock

@@ -0,0 +1,85 @@
+# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand.
+
+[[package]]
+name = "colorama"
+version = "0.4.6"
+description = "Cross-platform colored terminal text."
+optional = false
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
+files = [
+    {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"},
+    {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
+]
+
+[[package]]
+name = "iniconfig"
+version = "2.1.0"
+description = "brain-dead simple config-ini parsing"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "iniconfig-2.1.0-py3-none-any.whl", hash = "sha256:9deba5723312380e77435581c6bf4935c94cbfab9b1ed33ef8d238ea168eb760"},
+    {file = "iniconfig-2.1.0.tar.gz", hash = "sha256:3abbd2e30b36733fee78f9c7f7308f2d0050e88f0087fd25c2645f63c773e1c7"},
+]
+
+[[package]]
+name = "mypy-boto3-secretsmanager"
+version = "1.38.0"
+description = "Type annotations for boto3 SecretsManager 1.38.0 service generated with mypy-boto3-builder 8.10.1"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "mypy_boto3_secretsmanager-1.38.0-py3-none-any.whl", hash = "sha256:48d5057450ee307b132ce2d0976233a2c5331616fabdf423ecbc103f7431dd5e"},
+    {file = "mypy_boto3_secretsmanager-1.38.0.tar.gz", hash = "sha256:1666108e70f03e4dc1de449388d7facb77aba231a026bac0c3240fc27fd31a98"},
+]
+
+[[package]]
+name = "packaging"
+version = "25.0"
+description = "Core utilities for Python packages"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "packaging-25.0-py3-none-any.whl", hash = "sha256:29572ef2b1f17581046b3a2227d5c611fb25ec70ca1ba8554b24b0e69331a484"},
+    {file = "packaging-25.0.tar.gz", hash = "sha256:d443872c98d677bf60f6a1f2f8c1cb748e8fe762d2bf9d3148b5599295b0fc4f"},
+]
+
+[[package]]
+name = "pluggy"
+version = "1.6.0"
+description = "plugin and hook calling mechanisms for python"
+optional = false
+python-versions = ">=3.9"
+files = [
+    {file = "pluggy-1.6.0-py3-none-any.whl", hash = "sha256:e920276dd6813095e9377c0bc5566d94c932c33b27a3e3945d8389c374dd4746"},
+    {file = "pluggy-1.6.0.tar.gz", hash = "sha256:7dcc130b76258d33b90f61b658791dede3486c3e6bfb003ee5c9bfb396dd22f3"},
+]
+
+[package.extras]
+dev = ["pre-commit", "tox"]
+testing = ["coverage", "pytest", "pytest-benchmark"]
+
+[[package]]
+name = "pytest"
+version = "7.4.4"
+description = "pytest: simple powerful testing with Python"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "pytest-7.4.4-py3-none-any.whl", hash = "sha256:b090cdf5ed60bf4c45261be03239c2c1c22df034fbffe691abe93cd80cea01d8"},
+    {file = "pytest-7.4.4.tar.gz", hash = "sha256:2cf0005922c6ace4a3e2ec8b4080eb0d9753fdc93107415332f50ce9e7994280"},
+]
+
+[package.dependencies]
+colorama = {version = "*", markers = "sys_platform == \"win32\""}
+iniconfig = "*"
+packaging = "*"
+pluggy = ">=0.12,<2.0"
+
+[package.extras]
+testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
+
+[metadata]
+lock-version = "2.0"
+python-versions = "^3.12, <3.13"
+content-hash = "6d7f1b2b62e2f7ec2963e9cdc6621e96b3e6477b70c155a989cf09368378ae80"

package/lambda/layers/icav2_tools/pyproject.toml

@@ -0,0 +1,26 @@
+[build-system]
+requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.poetry]
+name = "icav2_tools"
+version = "1.0.0"
+description = "Useful layer for python lambdas that use ICAv2, smart-collection of the ICAv2 access token"
+license = "GPL-3.0-or-later"
+authors = [
+    "Alexis Lucattini"
+]
+homepage = "https://github.com/orcabus/platform-cdk-constructs"
+repository = "https://github.com/orcabus/platform-cdk-constructs"
+
+[tool.poetry.dependencies]
+python = "^3.12, <3.13"
+wrapica = "2.27.1.post20240830140737"
+
+[tool.poetry.group.dev]
+optional = true
+
+[tool.poetry.group.dev.dependencies]
+pytest = "^7.0.0"  # For testing only
+# For typehinting only, not required at runtime
+mypy-boto3-secretsmanager = "^1.34"

package/lambda/layers/icav2_tools/src/icav2_tools/__init__.py

@@ -0,0 +1,19 @@
+#!/usr/bin/env python
+
+from .aws_helpers import get_icav2_access_token
+from os import environ
+from .globals import ICAV2_BASE_URL
+
+
+def set_icav2_env_vars():
+    """
+    Set the environment variables for the ICAV2 API
+    :return:
+    """
+    environ["ICAV2_ACCESS_TOKEN"] = get_icav2_access_token()
+    environ["ICAV2_BASE_URL"] = ICAV2_BASE_URL
+
+
+__all__ = [
+    "set_icav2_env_vars"
+]

package/lambda/layers/icav2_tools/src/icav2_tools/aws_helpers.py

@@ -0,0 +1,116 @@
+#!/usr/bin/env python3
+
+# Standard imports
+import typing
+from typing import Optional
+import boto3
+import json
+from os import environ
+import urllib3
+from urllib.parse import urlunparse
+
+
+# Type hinting
+if typing.TYPE_CHECKING:
+    from mypy_boto3_secretsmanager import SecretsManagerClient
+    from mypy_boto3_ssm import SSMClient
+
+# Set globals
+from .globals import ICAV2_BASE_URL
+
+http = urllib3.PoolManager()
+
+LOCAL_HTTP_CACHE_PORT = 2773
+PARAMETER_URL = '/systemsmanager/parameters/get/'
+SECRETS_URL = '/secretsmanager/get/'
+
+def retrieve_extension_value(url, query):
+    url = str(urlunparse((
+        'http', f'localhost:{LOCAL_HTTP_CACHE_PORT}',
+        url, None,
+        "&".join(list(map(
+            lambda kv: f"{kv[0]}={kv[1]}",
+            query.items()
+        ))), None
+    )))
+    headers = {
+        "X-Aws-Parameters-Secrets-Token": environ.get('AWS_SESSION_TOKEN')
+    }
+    response = http.request("GET", url, headers=headers)
+    response = json.loads(response.data)
+    return response
+
+
+def get_ssm_value_from_cache(parameter_name: str) -> Optional[str]:
+    try:
+        return retrieve_extension_value(
+            PARAMETER_URL,
+            {
+                "name": parameter_name,
+            }
+        )['Parameter']['Value']
+    except Exception as e:
+        print("Got an exception while trying to get ssm value from cache")
+        print(e)
+        return None
+
+
+def get_secret_value_from_cache(secret_id: str) -> Optional[str]:
+    try:
+        return retrieve_extension_value(
+            SECRETS_URL,
+            {
+                "secretId": secret_id,
+            }
+        )['SecretString']
+    except Exception as e:
+        print("Got an exception while trying to get secret value from cache")
+        print(e)
+        return None
+
+def get_secretsmanager_client() -> 'SecretsManagerClient':
+    return boto3.client('secretsmanager')
+
+
+def get_ssm_client() -> 'SSMClient':
+    return boto3.client('ssm')
+
+
+def get_secret_value(secret_id) -> str:
+    """
+    Collect the secret value
+    :param secret_id:
+    :return:
+    """
+    secret_value_cached = get_secret_value_from_cache(secret_id)
+    if secret_value_cached is not None:
+        return secret_value_cached
+
+    # Get the boto3 response
+    get_secret_value_response = get_secretsmanager_client().get_secret_value(SecretId=secret_id)
+
+    return get_secret_value_response['SecretString']
+
+
+def get_ssm_value(parameter_name) -> str:
+    """
+    Collect the parameter from SSM
+    :param parameter_name:
+    :return:
+    """
+    ssm_parameter_cached = get_ssm_value_from_cache(parameter_name)
+    if ssm_parameter_cached is not None:
+        return ssm_parameter_cached
+
+    # Get the boto3 response
+    get_ssm_parameter_response = get_ssm_client().get_parameter(Name=parameter_name)
+
+    return get_ssm_parameter_response['Parameter']['Value']
+
+
+def get_icav2_access_token() -> str:
+    """
+    From the AWS Secrets Manager, retrieve the OrcaBus token.
+    :return:
+    """
+    return get_secret_value(environ.get("ICAV2_ACCESS_TOKEN_SECRET_ID"))

package/lambda/layers/icav2_tools/src/icav2_tools/globals.py

@@ -0,0 +1,2 @@
+# Set ICAV2 Base url
+ICAV2_BASE_URL = "https://ica.illumina.com/ica/rest"

package/lambda/layers/orcabus_api_tools/src/orcabus_api_tools/icav2_wes/__init__.py

@@ -0,0 +1,79 @@
+#!/usr/bin/env python3
+
+# Imports
+from typing import Optional, Dict
+
+from .globals import ICAV2_WES_SUBDOMAIN_NAME
+from .models import WESRequest
+from ..utils.requests_helpers import (
+    get_request, get_url, patch_request, get_request_response_results
+)
+
+
+# Wrappers
+def get_icav2_wes_url(endpoint: str) -> str:
+    """
+    Get the URL for the Metadata endpoint
+    :param endpoint:
+    :return:
+    """
+    return get_url(
+        endpoint=endpoint,
+        subdomain=ICAV2_WES_SUBDOMAIN_NAME,
+    )
+
+
+def get_icav2_wes_request(
+        endpoint: str,
+        params: Optional[Dict] = None,
+):
+    return get_request(
+        url=get_icav2_wes_url(endpoint),
+        params=params
+    )
+
+
+def get_icav2_wes_request_response_results(
+        endpoint: str,
+        params: Optional[Dict] = None,
+):
+    return get_request_response_results(
+        url=get_icav2_wes_url(endpoint),
+        params=params
+    )
+
+
+def icav2_wes_patch_request(
+    endpoint: str,
+    params: Optional[Dict] = None,
+):
+    return patch_request(
+        url=get_icav2_wes_url(endpoint),
+        params=params
+    )
+
+
+def icav2_wes_post_request(
+    endpoint: str,
+    params: Dict
+):
+    # Confirm param keys are valid
+    return patch_request(
+        url=get_icav2_wes_url(endpoint),
+        params=params
+    )
+
+
+# Set all
+from create_helpers import create_icav2_wes_analysis
+from query_helpers import get_icav2_wes_analysis_by_name
+from update_helpers import update_icav2_wes_analysis_status
+
+__all__ = [
+    # Launch helpers
+    'create_icav2_wes_analysis',
+    # Query helpers
+    'get_icav2_wes_analysis_by_name',
+    # Update helpers
+    'update_icav2_wes_analysis_status'
+]

package/lambda/layers/orcabus_api_tools/src/orcabus_api_tools/icav2_wes/create_helpers.py

@@ -0,0 +1,29 @@
+#!/usr/bin/env python3
+
+"""
+Create the job
+"""
+
+from typing import Unpack
+
+from . import icav2_wes_post_request
+from .globals import ANALYSES_ENDPOINT
+from .models import WESRequest, WESResponse
+
+
+def create_icav2_wes_analysis(
+    **kwargs: Unpack[WESRequest]
+) -> WESResponse:
+    """
+    Launch an icav2 analysis in the ICAV2 WES API.
+    """
+    # Confirm param keys are valid
+    for key in kwargs.keys():
+        if key not in WESRequest.__annotations__:
+            raise ValueError(f"Invalid parameter key: {key}. Valid keys are: {', '.join(WESRequest.__annotations__.keys())}")
+
+    # Confirm param values are valid
+    return icav2_wes_post_request(
+        ANALYSES_ENDPOINT,
+        params=dict(**kwargs)
+    )

package/lambda/layers/orcabus_api_tools/src/orcabus_api_tools/icav2_wes/globals.py

@@ -0,0 +1,6 @@
+
+# AWS PARAMETERS
+ICAV2_WES_SUBDOMAIN_NAME = "icav2-wes"
+
+# API ENDPOINTS
+ANALYSES_ENDPOINT = "api/v1/analyses"

package/lambda/layers/orcabus_api_tools/src/orcabus_api_tools/icav2_wes/models.py

@@ -0,0 +1,50 @@
+from typing import (
+    TypedDict, Dict, Any, Literal, NotRequired
+)
+
+AnalysisStorageSize = Literal['SMALL', 'MEDIUM', 'LARGE']
+STATUS = Literal[
+    'SUBMITTED',
+    'PENDING',
+    'RUNNABLE',
+    'STARTING',
+    'RUNNING',
+    'SUCCEEDED',
+    'FAILED',
+    'ABORTED',
+]
+
+
+class EngineParameters(TypedDict):
+    # Launch Configurations
+    pipelineId: str
+    projectId: str
+    analysisStorageSize: AnalysisStorageSize
+    # Locations
+    outputUri: str
+    logsUri: str
+
+
+class WESRequest(TypedDict):
+    """WES request object."""
+    name: str
+    inputs: Dict[str, Any]
+    engineParameters: EngineParameters
+    tags: NotRequired[Dict[str, Any]]
+
+
+class WESResponse(TypedDict):
+    """WES response object."""
+    id: str
+    name: str
+    state: str
+    inputs: Dict[str, Any]
+    outputs: NotRequired[Dict[str, Any]]
+    engineParameters: EngineParameters
+    tags: NotRequired[Dict[str, Any]]
+    createdAt: str
+    updatedAt: str
+    projectId: str
+    pipelineId: str
+    status: str
+    errorMessage: str

package/lambda/layers/orcabus_api_tools/src/orcabus_api_tools/icav2_wes/query_helpers.py

@@ -0,0 +1,20 @@
+#!/usr/bin/env python3
+
+from . import get_icav2_wes_request_response_results
+from .globals import ANALYSES_ENDPOINT
+from .models import WESResponse
+
+# Get the icav2 wes analysis by analysis name
+def get_icav2_wes_analysis_by_name(analysis_name: str) -> WESResponse:
+    """
+    Get the icav2 wes analysis by analysis name
+    """
+    response_results = get_icav2_wes_request_response_results(
+        ANALYSES_ENDPOINT,
+        params={"name": analysis_name}
+    )
+
+    if not len(response_results) == 1:
+        raise ValueError(f"Expected 1 result, got {len(response_results)}")
+
+    return response_results[0]

package/lambda/layers/orcabus_api_tools/src/orcabus_api_tools/icav2_wes/update_helpers.py

@@ -0,0 +1,23 @@
+#!/usr/bin/env python3
+
+from . import icav2_wes_patch_request
+from .globals import ANALYSES_ENDPOINT
+from .models import WESResponse
+
+# Get the icav2 wes analysis by analysis name
+def update_icav2_wes_analysis_status(
+        icav2_wes_orcabus_id: str,
+        status: str
+) -> WESResponse:
+    """
+    Get the icav2 wes analysis by analysis name
+    """
+    response_results = icav2_wes_patch_request(
+        f"{ANALYSES_ENDPOINT}/{icav2_wes_orcabus_id}",
+        params={"status": status}
+    )
+
+    if not len(response_results) == 1:
+        raise ValueError(f"Expected 1 result, got {len(response_results)}")
+
+    return response_results[0]

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@orcabus/platform-cdk-constructs",
-  "version": "0.0.7-alpha.6",
+  "version": "0.0.7-beta.2",
   "description": "CDK Package for OrcaBus infrastructure.",
   "main": "index.ts",
   "types": "index.d.ts",