galaxy/lib/galaxy_test/api/conftest.py

"""Fixtures for a version of API testing that relies more heavily on pytest injection."""

import os
from dataclasses import dataclass
from typing import (
    Any,
    Iterator,
    List,
    Optional,
)

import pytest

from galaxy.tool_util.verify.test_data import TestDataResolver
from galaxy_test.base.api import (
    AnonymousGalaxyInteractor,
    ApiTestInteractor,
)
from galaxy_test.base.api_util import (
    get_admin_api_key,
    get_user_api_key,
)
from galaxy_test.base.env import setup_keep_outdir
from galaxy_test.base.populators import (
    check_missing_tool,
    DatasetCollectionPopulator,
    DatasetPopulator,
    DescribeToolInputs,
    get_tool_ids,
    RequiredTool,
    TargetHistory,
)
from galaxy_test.base.testcase import host_port_and_url


@dataclass
class ApiConfigObject:
    host: str
    port: Optional[str]
    url: str
    user_api_key: Optional[str]
    admin_api_key: Optional[str]
    test_data_resolver: Any
    keepOutdir: Any


@pytest.fixture(scope="session")
def api_test_config_object(real_driver) -> ApiConfigObject:
    host, port, url = host_port_and_url(real_driver)
    user_api_key = get_user_api_key()
    admin_api_key = get_admin_api_key()
    test_data_resolver = TestDataResolver()
    keepOutdir = setup_keep_outdir()
    return ApiConfigObject(
        host,
        port,
        url,
        user_api_key,
        admin_api_key,
        test_data_resolver,
        keepOutdir,
    )


@pytest.fixture(scope="session")
def galaxy_interactor(api_test_config_object: ApiConfigObject) -> ApiTestInteractor:
    return ApiTestInteractor(api_test_config_object)


@pytest.fixture(scope="session")
def dataset_populator(galaxy_interactor: ApiTestInteractor) -> DatasetPopulator:
    return DatasetPopulator(galaxy_interactor)


@pytest.fixture(scope="session")
def dataset_collection_populator(galaxy_interactor: ApiTestInteractor) -> DatasetCollectionPopulator:
    return DatasetCollectionPopulator(galaxy_interactor)


@pytest.fixture(scope="session")
def anonymous_galaxy_interactor(api_test_config_object: ApiConfigObject) -> AnonymousGalaxyInteractor:
    return AnonymousGalaxyInteractor(api_test_config_object)


@pytest.fixture(autouse=True, scope="session")
def request_celery_app(celery_session_app, celery_config):
    try:
        yield
    finally:
        if os.environ.get("GALAXY_TEST_EXTERNAL") is None:
            from galaxy.celery import celery_app

            celery_app.fork_pool.stop()
            celery_app.fork_pool.join(timeout=5)


@pytest.fixture(autouse=True, scope="session")
def request_celery_worker(celery_session_worker, celery_config, celery_worker_parameters):
    yield


@pytest.fixture(scope="session", autouse=True)
def celery_worker_parameters():
    return {
        "queues": ("galaxy.internal", "galaxy.external"),
    }


@pytest.fixture(scope="session")
def celery_parameters():
    return {
        "task_create_missing_queues": True,
        "task_default_queue": "galaxy.internal",
    }


@pytest.fixture
def history_id(dataset_populator: DatasetPopulator, request) -> Iterator[str]:
    history_name = f"API Test History for {request.node.nodeid}"
    with dataset_populator.test_history(name=history_name) as history_id:
        yield history_id


@pytest.fixture
def target_history(
    dataset_populator: DatasetPopulator, dataset_collection_populator: DatasetCollectionPopulator, history_id: str
) -> TargetHistory:
    return TargetHistory(dataset_populator, dataset_collection_populator, history_id)


@pytest.fixture
def required_tools(
    dataset_populator: DatasetPopulator, history_id: str, required_tool_ids: List[str]
) -> List[RequiredTool]:
    tools = []
    for tool_id in required_tool_ids:
        tool = RequiredTool(dataset_populator, tool_id, history_id)
        tools.append(tool)
    return tools


@pytest.fixture
def required_tool(dataset_populator: DatasetPopulator, history_id: str, required_tool_ids: List[str]) -> RequiredTool:
    if len(required_tool_ids) != 1:
        raise AssertionError("required_tool fixture must only be used on methods that require a single tool")
    tool_id = required_tool_ids[0]
    tool = RequiredTool(dataset_populator, tool_id, history_id)
    return tool


@pytest.fixture(params=["legacy", "21.01"])
def tool_input_format(request) -> Iterator[DescribeToolInputs]:
    yield DescribeToolInputs(request.param)


@pytest.fixture(autouse=True)
def check_required_tools(anonymous_galaxy_interactor, request):
    for marker in request.node.iter_markers():
        if marker.name == "requires_tool_id":
            tool_id = _requires_marker_to_effective_tool_id(anonymous_galaxy_interactor, marker)
            check_missing_tool(tool_id not in get_tool_ids(anonymous_galaxy_interactor))


@pytest.fixture
def required_tool_ids(anonymous_galaxy_interactor, request) -> List[str]:
    tool_ids = []
    for marker in request.node.iter_markers():
        if marker.name == "requires_tool_id":
            tool_id = _requires_marker_to_effective_tool_id(anonymous_galaxy_interactor, marker)
            tool_ids.append(tool_id)
    return tool_ids


def _requires_marker_to_effective_tool_id(anonymous_galaxy_interactor, marker):
    tool_id = marker.args[0]
    if "|" in tool_id:
        any_of_tool_ids = tool_id.split("|")
        all_tool_ids = get_tool_ids(anonymous_galaxy_interactor)
        tool_id = [t for t in any_of_tool_ids if t in all_tool_ids][0]
    return tool_id