diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 9b95418..459b996 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -12,12 +12,12 @@ jobs: test: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v1 + - uses: actions/checkout@v4 - name: Set up Python 3.9 - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: '3.9' - - uses: actions/cache@preview + - uses: actions/cache@v4 with: path: ~/.cache/pypoetry/virtualenvs key: ${{ runner.os }}-poetry-${{ hashFiles(format('{0}{1}', github.workspace, '/poetry.lock')) }} @@ -27,7 +27,6 @@ jobs: run: | python -m pip install --upgrade pip poetry poetry install - pip install . - name: Test with pytest run: | poetry run pytest test diff --git a/.github/workflows/labeler.yml b/.github/workflows/labeler.yml index 6d259b8..d2e02b9 100644 --- a/.github/workflows/labeler.yml +++ b/.github/workflows/labeler.yml @@ -7,6 +7,6 @@ jobs: triage: runs-on: ubuntu-latest steps: - - uses: actions/labeler@v3 + - uses: actions/labeler@v5 with: repo-token: "${{ secrets.GITHUB_TOKEN }}" diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml index 9ecca6d..3ad6329 100644 --- a/.github/workflows/lint.yaml +++ b/.github/workflows/lint.yaml @@ -8,18 +8,17 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Set up Python 3.9 - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: '3.9' + - name: Install dependencies run: | - python -m pip install --upgrade pip - pip install pylint python -m pip install --upgrade pip poetry poetry install - pip install . + - name: Analysing the code with pylint run: | - python -m pylint --fail-under=8 src/; + poetry run pylint --fail-under=8 src/; diff --git a/.github/workflows/test_coverage.yaml b/.github/workflows/test_coverage.yaml index 4e9fd2f..aa4f88c 100644 --- a/.github/workflows/test_coverage.yaml +++ b/.github/workflows/test_coverage.yaml @@ -7,9 +7,9 @@ jobs: build: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v1 + - uses: actions/checkout@v4 - name: Set up Python 3.9 - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: '3.9' @@ -17,8 +17,7 @@ jobs: run: | python -m pip install --upgrade pip poetry poetry install - pip install . - name: Get test coverage and fail if total coverage under 80 percent run: | - pytest --cov argowrapper test --cov-fail-under=80 + poetry run pytest --cov argowrapper test --cov-fail-under=80 diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index b2886cb..ad3c5a3 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,18 +1,18 @@ repos: -- repo: git@github.com:Yelp/detect-secrets - rev: v0.13.1 +- repo: https://github.com/Yelp/detect-secrets + rev: v1.5.0 hooks: - id: detect-secrets args: ['--baseline', '.secrets.baseline'] exclude: poetry.lock - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v2.5.0 + rev: v5.0.0 hooks: - id: trailing-whitespace - id: end-of-file-fixer - id: no-commit-to-branch args: [--branch, develop, --branch, master, --pattern, release/.*] - repo: https://github.com/psf/black - rev: 22.3.0 + rev: 24.10.0 hooks: - id: black diff --git a/.secrets.baseline b/.secrets.baseline index 21a6281..e7caf15 100644 --- a/.secrets.baseline +++ b/.secrets.baseline @@ -1,19 +1,18 @@ { - "exclude": { - "files": null, - "lines": null - }, - "generated_at": "2022-01-13T22:51:55Z", + "version": "1.5.0", "plugins_used": [ + { + "name": "ArtifactoryDetector" + }, { "name": "AWSKeyDetector" }, { - "name": "ArtifactoryDetector" + "name": "AzureStorageKeyDetector" }, { - "base64_limit": 4.5, - "name": "Base64HighEntropyString" + "name": "Base64HighEntropyString", + "limit": 4.5 }, { "name": "BasicAuthDetector" @@ -22,8 +21,17 @@ "name": "CloudantDetector" }, { - "hex_limit": 3, - "name": "HexHighEntropyString" + "name": "DiscordBotTokenDetector" + }, + { + "name": "GitHubTokenDetector" + }, + { + "name": "GitLabTokenDetector" + }, + { + "name": "HexHighEntropyString", + "limit": 3.0 }, { "name": "IbmCloudIamDetector" @@ -31,45 +39,93 @@ { "name": "IbmCosHmacDetector" }, + { + "name": "IPPublicDetector" + }, { "name": "JwtTokenDetector" }, { - "keyword_exclude": null, - "name": "KeywordDetector" + "name": "KeywordDetector", + "keyword_exclude": "" }, { "name": "MailchimpDetector" }, + { + "name": "NpmDetector" + }, + { + "name": "OpenAIDetector" + }, { "name": "PrivateKeyDetector" }, + { + "name": "PypiTokenDetector" + }, + { + "name": "SendGridDetector" + }, { "name": "SlackDetector" }, { "name": "SoftlayerDetector" }, + { + "name": "SquareOAuthDetector" + }, { "name": "StripeDetector" }, + { + "name": "TelegramBotTokenDetector" + }, { "name": "TwilioKeyDetector" } ], - "results": { - "poetry.lock": [ - { - "hashed_secret": "d3eec25983a67b9b1f2cc08ccac6689b73d040dd", - "is_verified": false, - "line_number": 289, - "type": "Hex High Entropy String" - } - ] - }, - "version": "0.13.1", - "word_list": { - "file": null, - "hash": null - } + "filters_used": [ + { + "path": "detect_secrets.filters.allowlist.is_line_allowlisted" + }, + { + "path": "detect_secrets.filters.common.is_baseline_file", + "filename": ".secrets.baseline" + }, + { + "path": "detect_secrets.filters.common.is_ignored_due_to_verification_policies", + "min_level": 2 + }, + { + "path": "detect_secrets.filters.heuristic.is_indirect_reference" + }, + { + "path": "detect_secrets.filters.heuristic.is_likely_id_string" + }, + { + "path": "detect_secrets.filters.heuristic.is_lock_file" + }, + { + "path": "detect_secrets.filters.heuristic.is_not_alphanumeric_string" + }, + { + "path": "detect_secrets.filters.heuristic.is_potential_uuid" + }, + { + "path": "detect_secrets.filters.heuristic.is_prefixed_with_dollar_sign" + }, + { + "path": "detect_secrets.filters.heuristic.is_sequential_string" + }, + { + "path": "detect_secrets.filters.heuristic.is_swagger_file" + }, + { + "path": "detect_secrets.filters.heuristic.is_templated_secret" + } + ], + "results": {}, + "generated_at": "2024-11-05T09:47:19Z" } diff --git a/Dockerfile b/Dockerfile index 8c6d9a9..25920c9 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,7 @@ ARG AZLINUX_BASE_VERSION=master FROM 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/python-build-base:${AZLINUX_BASE_VERSION} AS base +# FROM quay.io/cdis/python-build-base:${AZLINUX_BASE_VERSION} AS base ENV appname=argowrapper @@ -9,7 +10,7 @@ FROM base AS builder WORKDIR /$appname COPY poetry.lock pyproject.toml /$appname/ -RUN pip install --upgrade poetry \ +RUN pip install --upgrade pip poetry \ && poetry install --without dev --no-interaction COPY src /$appname/src diff --git a/poetry.lock b/poetry.lock index 4b2c514..efe3aa7 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,35 +1,47 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. + +[[package]] +name = "annotated-types" +version = "0.7.0" +description = "Reusable constraint types to use with typing.Annotated" +optional = false +python-versions = ">=3.8" +files = [ + {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"}, + {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"}, +] [[package]] name = "anyio" -version = "3.7.1" +version = "4.6.2.post1" description = "High level compatibility layer for multiple asynchronous event loop implementations" optional = false -python-versions = ">=3.7" +python-versions = ">=3.9" files = [ - 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"bbbe53072e442988cd895a68cb0067713965eab864db5496eabcc65e706dbd7c" diff --git a/pyproject.toml b/pyproject.toml index a323d6c..6faa46b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,27 +7,24 @@ repository = "https://github.com/uc-cdis/argo-wrapper" [tool.poetry.dependencies] python = "^3.9" -fastapi = "^0.71.0" -uvicorn = "^0.16.0" -gunicorn = "^20.0.4" -importlib-metadata = "^4.10.0" -PyYAML = "6.0.1" -pytest = "^6.2.5" -pytest-mock = "^3.6.1" -pytest-asyncio = "^0.20" +argo-workflows = "^6.5" cdislogging = "^1.1.1" -argo-workflows = "6.4.7" +fastapi = "^0.115" gen3authz = "^1.5.0" -importlib-resources = "^5.4.0" -requests = "^2.27.1" -PyJWT = "^2.4.0" -pytest-cov = "^3.0.0" -freezegun = "^1.2.2" - -[tool.poetry.dev-dependencies] -pytest = "^6.2.5" +gunicorn = "^23.0" +PyJWT = "^2.9" +PyYAML = "^6.0" +requests = "^2.32" +uvicorn = "^0.32" +[tool.poetry.group.dev.dependencies] +freezegun = "^1.5" +pylint = "^3.3" +pytest = "^6.2" +pytest-asyncio = "^0" +pytest-cov = "^5.0" +pytest-mock = "^3.6" [build-system] -requires = ["poetry-core>=1.0.0"] +requires = ["poetry-core"] build-backend = "poetry.core.masonry.api" diff --git a/src/argowrapper/__init__.py b/src/argowrapper/__init__.py index 901ad8b..5b71fe0 100644 --- a/src/argowrapper/__init__.py +++ b/src/argowrapper/__init__.py @@ -1,3 +1,3 @@ from cdislogging import get_logger -logger = get_logger("requestor", log_level="debug") +logger = get_logger("argo-wrapper", log_level="debug") diff --git a/src/argowrapper/auth/auth.py b/src/argowrapper/auth/auth.py index 063f27b..bbe3c4e 100644 --- a/src/argowrapper/auth/auth.py +++ b/src/argowrapper/auth/auth.py @@ -1,4 +1,4 @@ -import re +from typing import Optional from gen3authz.client.arborist.client import ArboristClient from gen3authz.client.arborist.errors import ArboristError @@ -27,7 +27,7 @@ def __init__(self): else: self.arborist_client = ArboristClient(logger=logger) - def _parse_jwt(self, token: str) -> str: + def _parse_jwt(self, token: Optional[str]) -> str: parsed_token = TOKEN_REGEX.sub("", token) parsed_token = parsed_token.replace(" ", "") @@ -37,7 +37,7 @@ def _parse_jwt(self, token: str) -> str: return parsed_token - def authenticate(self, token: str, team_project=None) -> bool: + def authenticate(self, token, team_project=None): """ jwt token authentication for mariner access diff --git a/src/argowrapper/constants.py b/src/argowrapper/constants.py index 0ae84c1..6fce4ae 100644 --- a/src/argowrapper/constants.py +++ b/src/argowrapper/constants.py @@ -47,14 +47,14 @@ class POD_COMPLETION_STRATEGY(Enum): - ONWORKFLOWSUCCESS: Final = "OnWorkflowSuccess" - ONPODSUCESS: Final = "OnPodSuccess" - ONPODCOMPLETION: Final = "OnPodCompletion" + ONWORKFLOWSUCCESS = "OnWorkflowSuccess" + ONPODSUCESS = "OnPodSuccess" + ONPODCOMPLETION = "OnPodCompletion" class WORKFLOW_ENTRYPOINT(Enum): - GWAS_ENTRYPOINT: Final = "gwas-workflow" + GWAS_ENTRYPOINT = "gwas-workflow" class WORKFLOW(Enum): - GWAS: Final = "GWAS" + GWAS = "GWAS" diff --git a/src/argowrapper/engine/argo_engine.py b/src/argowrapper/engine/argo_engine.py index c811976..43ca6b1 100644 --- a/src/argowrapper/engine/argo_engine.py +++ b/src/argowrapper/engine/argo_engine.py @@ -1,7 +1,6 @@ -import string import traceback from datetime import datetime -from typing import Dict, List, Literal +from typing import Any, Dict, List, Tuple, Union, Optional import argo_workflows from argo_workflows.api import ( @@ -76,7 +75,7 @@ def __init__(self, dry_run: bool = False): ) self.artifact_api_instance = artifact_service_api.ArtifactServiceApi(api_client) - def _get_workflow_details_dict(self, workflow_name: str) -> Dict: + def _get_workflow_details_dict(self, workflow_name: Optional[str]) -> Dict: return self.api_instance.get_workflow( namespace=ARGO_NAMESPACE, name=workflow_name, @@ -85,7 +84,7 @@ def _get_workflow_details_dict(self, workflow_name: str) -> Dict: _check_return_type=False, ).to_dict() - def _get_archived_workflow_details_dict(self, uid: str) -> Dict: + def _get_archived_workflow_details_dict(self, uid: Optional[str]) -> Dict: """ Queries the archived workflows api. Raises a argo_workflows.exceptions.NotFoundException if the workflow uid cannot be found @@ -142,7 +141,9 @@ def _find_first_failed_node(self, uid: str): else: return None - def _get_log_errors(self, uid: str, status_nodes_dict: Dict) -> List[Dict]: + def _get_log_errors( + self, uid: str, status_nodes_dict: Dict + ) -> List[Dict[str, Any]]: errors = [] first_failed_node = self._find_first_failed_node(uid) @@ -205,8 +206,8 @@ def _get_lock_for_user(self, username: str) -> Lock: return self.user_locks[username] def get_workflow_details( - self, workflow_name: str, uid: str = None - ) -> Dict[str, any]: + self, workflow_name: Optional[str], uid: Optional[str] = None + ) -> Union[Dict[str, Any], str]: """ Gets the workflow status @@ -215,7 +216,7 @@ def get_workflow_details( uid (str): uid of an archived workflow to get status of Returns: - Dict[str, any]: returns a dict that looks like the below + Union[Dict[str, Any], str]: returns a dict that looks like the below { "name": {workflow_name}, "arguments": {workflow_arguments}, @@ -334,7 +335,7 @@ def retry_workflow(self, workflow_name: str, uid: str) -> str: def _get_archived_workflow_wf_name_and_team_project( self, archived_workflow_uid - ) -> (str, str, str): + ) -> Tuple[str, str, str]: """ Gets the name and team project details for the given archived workflow @@ -368,7 +369,7 @@ def _get_archived_workflow_wf_name_and_team_project( return given_name, team_project, gen3username def get_workflows_for_team_projects_and_user( - self, team_projects: List[str], auth_header: str + self, team_projects: List[str], auth_header: Optional[str] ) -> List[Dict]: team_project_workflows = self.get_workflows_for_team_projects(team_projects) user_workflows = self.get_workflows_for_user(auth_header) @@ -405,7 +406,7 @@ def get_workflows_for_team_project(self, team_project: str) -> List[Dict]: workflows = self.get_workflows_for_label_selector(label_selector=label_selector) return workflows - def get_workflows_for_user(self, auth_header: str) -> List[Dict]: + def get_workflows_for_user(self, auth_header: Optional[str]) -> List[Dict]: """ Get the list of all workflows for the current user. Each item in the list contains the workflow name, its status, start and end time. @@ -529,7 +530,7 @@ def get_workflows_for_label_selector(self, label_selector: str) -> List[Dict]: ) raise exception - def get_workflow_logs(self, workflow_name: str, uid: str) -> List[Dict]: + def get_workflow_logs(self, workflow_name: str, uid: str) -> List[Dict[str, Any]]: """ Gets the workflow errors from failed workflow @@ -538,7 +539,7 @@ def get_workflow_logs(self, workflow_name: str, uid: str) -> List[Dict]: uid (str): uid of an archived workflow to get status of Returns: - Dict[str, any]: returns a list of dictionaries of errors of Retry nodes + List[Dict[str, Any]]: returns a list of dictionaries of errors of Retry nodes """ try: archived_workflow_dict = self._get_archived_workflow_details_dict(uid) @@ -589,7 +590,7 @@ def get_workflow_logs(self, workflow_name: str, uid: str) -> List[Dict]: f"could not get status of {workflow_name}, workflow does not exist" ) - def workflow_submission(self, request_body: Dict, auth_header: str): + def workflow_submission(self, request_body: Dict, auth_header: Optional[str]): # Lock function so only one can run at a time per user username = argo_engine_helper.get_username_from_token(auth_header) user_lock = self._get_lock_for_user(username) @@ -698,7 +699,10 @@ def check_user_info_for_billing_id_and_workflow_limit(self, request_token): return None, None def check_user_monthly_workflow_cap( - self, request_token, billing_id, custom_limit: int + self, + request_token: str, + billing_id: Optional[int] = None, + custom_limit: Optional[int] = None, ): """ Query Argo service to see how many workflow runs user already diff --git a/src/argowrapper/engine/helpers/argo_engine_helper.py b/src/argowrapper/engine/helpers/argo_engine_helper.py index b5d179f..2d9fc7c 100644 --- a/src/argowrapper/engine/helpers/argo_engine_helper.py +++ b/src/argowrapper/engine/helpers/argo_engine_helper.py @@ -2,7 +2,7 @@ import random import re import string -from typing import Callable, Dict, List +from typing import Any, Callable, Dict, List, Optional import jwt @@ -38,8 +38,8 @@ def _convert_request_body_to_parameter_dict(request_body: Dict) -> Dict: def parse_common_details( - workflow_details: Dict[str, any], workflow_type: str -) -> Dict[str, any]: + workflow_details: Dict[str, Any], workflow_type: str +) -> Dict[str, Any]: phase = workflow_details["status"].get("phase") if workflow_type == "active_workflow": shutdown = workflow_details["spec"].get("shutdown") @@ -68,8 +68,8 @@ def parse_common_details( def parse_details( - workflow_details: Dict[str, any], workflow_type: str -) -> Dict[str, any]: + workflow_details: Dict[str, Any], workflow_type: str +) -> Dict[str, Any]: result = parse_common_details( workflow_details=workflow_details, workflow_type=workflow_type ) @@ -95,10 +95,10 @@ def parse_details( def parse_list_item( - workflow_details: Dict[str, any], + workflow_details: Dict[str, Any], workflow_type: str, - get_archived_workflow_wf_name_and_team_project: Callable = None, -) -> Dict[str, any]: + get_archived_workflow_wf_name_and_team_project: Optional[Callable] = None, +) -> Dict[str, Any]: """Parse the return of workflow list view""" result = parse_common_details( workflow_details=workflow_details, workflow_type=workflow_type @@ -163,7 +163,7 @@ def _get_argo_config_dict() -> Dict: return data -def _convert_to_hex(special_character_match: str) -> str: +def _convert_to_hex(special_character_match: str) -> Optional[str]: if match := special_character_match.group(): hex_val = match.encode("utf-8").hex() return f"-{hex_val}" @@ -194,7 +194,7 @@ def convert_gen3teamproject_to_pod_label(team_project: str) -> str: return label -def convert_pod_label_to_gen3teamproject(pod_label: str) -> str: +def convert_pod_label_to_gen3teamproject(pod_label: str) -> Optional[str]: """ Reverse the conversion gen3teamproject to pod_label. """ @@ -216,7 +216,7 @@ def convert_string_to_pod_label(value: str) -> str: return label -def get_username_from_token(header_and_or_token: str) -> str: +def get_username_from_token(header_and_or_token: Optional[str]) -> str: """ Args: @@ -250,7 +250,7 @@ def convert_username_label_to_gen3username(label: str) -> str: return "" -def _convert_to_label(special_character_match: str) -> str: +def _convert_to_label(special_character_match: str) -> Optional[str]: if match := special_character_match.group(): match = match.strip("-") try: diff --git a/src/argowrapper/engine/helpers/workflow_factory.py b/src/argowrapper/engine/helpers/workflow_factory.py index f15f273..517d274 100644 --- a/src/argowrapper/engine/helpers/workflow_factory.py +++ b/src/argowrapper/engine/helpers/workflow_factory.py @@ -1,4 +1,4 @@ -from ast import Dict +from typing import Any, Dict, Optional from argowrapper.constants import WORKFLOW from argowrapper.workflows.argo_workflows.gwas import GWAS @@ -8,8 +8,8 @@ class WorkflowFactory: @staticmethod def _get_workflow( namespace: str, - request_body: Dict, - auth_header: str, + request_body: Dict[str, Any], + auth_header: Optional[str], workflow_type: WORKFLOW, ): workflows = {WORKFLOW.GWAS: GWAS} diff --git a/src/argowrapper/routes/routes.py b/src/argowrapper/routes/routes.py index da91431..eff0583 100644 --- a/src/argowrapper/routes/routes.py +++ b/src/argowrapper/routes/routes.py @@ -1,6 +1,6 @@ import traceback from functools import wraps -from typing import Dict, List, Any, Optional +from typing import Any, Dict, List, Optional, Union from fastapi import APIRouter, Request, Query from fastapi.responses import HTMLResponse @@ -220,7 +220,7 @@ def test(): def submit_workflow( request_body: Dict[Any, Any], request: Request, # pylint: disable=unused-argument -) -> str: +) -> Union[str, Any]: """route to submit workflow""" try: return argo_engine.workflow_submission( @@ -247,7 +247,7 @@ def get_workflow_details( workflow_name: str, uid: str, request: Request, # pylint: disable=unused-argument -) -> Dict[str, any]: +) -> Union[Dict[str, Any], str, Any]: """returns details of a workflow""" try: @@ -268,7 +268,7 @@ def retry_workflow( workflow_name: str, uid: str, request: Request, # pylint: disable=unused-argument -) -> str: +) -> Union[str, Any]: """retries a currently failed workflow""" workflow_details = argo_engine.get_workflow_details(workflow_name, uid) try: @@ -295,7 +295,7 @@ def retry_workflow( def cancel_workflow( workflow_name: str, request: Request, # pylint: disable=unused-argument -) -> str: +) -> Union[str, Any]: """cancels a currently running workflow""" try: @@ -315,7 +315,7 @@ def cancel_workflow( def get_workflows( request: Request, # pylint: disable=unused-argument team_projects: Optional[List[str]] = Query(default=None), -) -> List[str]: +) -> Union[List[Dict], Any]: """returns the list of workflows the user has ran""" try: @@ -344,7 +344,7 @@ def get_workflow_logs( workflow_name: str, uid: str, request: Request, # pylint: disable=unused-argument -) -> List[str]: +) -> Union[List[Dict], Any]: """returns the list of workflows the user has ran""" try: @@ -361,7 +361,7 @@ def get_workflow_logs( @router.get("/workflows/user-monthly", status_code=HTTP_200_OK) def get_user_monthly_workflow( request: Request, -) -> Dict[str, any]: +) -> Dict[str, Any]: """ Query Argo service to see how many successful run user already have in the current calendar month. Return workflow numbers and workflow cap diff --git a/src/argowrapper/workflows/argo_workflows/gwas.py b/src/argowrapper/workflows/argo_workflows/gwas.py index ac9ff05..bf68f9f 100644 --- a/src/argowrapper/workflows/argo_workflows/gwas.py +++ b/src/argowrapper/workflows/argo_workflows/gwas.py @@ -1,4 +1,4 @@ -from typing import Dict +from typing import Dict, List, Optional import argowrapper.engine.helpers.argo_engine_helper as argo_engine_helper from argowrapper import logger @@ -15,6 +15,16 @@ ) +def create_gds_files() -> str: + gds_files = [ + f'"/commons-data/gds/chr{chrom_num}.merged.vcf.gz.gds"' + for chrom_num in range(1, 23) + ] + # add chrX VCF + gds_files.append('"/commons-data/gds/chrX.merged.vcf.gz.gds"') + return f'[{", ".join(gds_files)}]' + + class GWAS(WorkflowBase): """A class to represent the gwas workflow @@ -25,15 +35,6 @@ class GWAS(WorkflowBase): _request_body (Dict): a dictionary of request parameters from the user """ - def __create_gds_files() -> str: - gds_files = [ - f'"/commons-data/gds/chr{chrom_num}.merged.vcf.gz.gds"' - for chrom_num in range(1, 23) - ] - # add chrX VCF - gds_files.append('"/commons-data/gds/chrX.merged.vcf.gz.gds"') - return f'[{", ".join(gds_files)}]' - HARD_CODED_PARAMETERS = { "genome_build": "hg19", "pca_file": "/commons-data/pcs.RData", @@ -44,7 +45,7 @@ def __create_gds_files() -> str: "segment_length": 2000, "variant_block_size": 100, "mac_threshold": 0, - "gds_files": __create_gds_files(), + "gds_files": create_gds_files(), } PARAMETER_TO_DEFAULT_VALS = { @@ -69,7 +70,11 @@ def __create_gds_files() -> str: METADATA_LABELS = {"workflows.argoproj.io/archive-strategy": "true"} def __init__( - self, namespace: str, request_body: Dict, auth_header: str, dry_run=False + self, + namespace: str, + request_body: Dict, + auth_header: Optional[str], + dry_run=False, ): self.username = argo_engine_helper.get_username_from_token(auth_header) self.gen3username_label = argo_engine_helper.convert_gen3username_to_pod_label(