Commit 78da479d authored by John Chilton's avatar John Chilton
Browse files

typing fixes for integration testing framework stuff... 

I wonder if there is a better way to model mixins - seems heavy to annotate everything we need from the derived class.
parent 8412cb53

lib/galaxy_test/driver/driver_util.py

+1 −1
Original line number Diff line number Diff line
@@ -621,7 +621,7 @@ def setup_shed_tools_for_test(app, tmpdir, testing_migrated_tools, testing_insta 
        app.toolbox = tools.ToolBox(tool_configs, app.config.tool_path, app)





def build_galaxy_app(simple_kwargs):

def build_galaxy_app(simple_kwargs) -> GalaxyUniverseApplication:

    """Build a Galaxy app object from a simple keyword arguments.



    Construct paste style complex dictionary and use load_app_properties so

lib/galaxy_test/driver/integration_util.py

+8 −2
Original line number Diff line number Diff line
@@ -5,10 +5,12 @@ order to test something that cannot be tested with the default functional/api 
testing configuration.

"""

import os

from typing import ClassVar

from unittest import skip, SkipTest, TestCase



import pytest



from galaxy.app import UniverseApplication

from galaxy.tool_util.verify.test_data import TestDataResolver

from galaxy.util.commands import which

from galaxy_test.base.api import UsesApiTestCaseMixin
@@ -79,6 +81,8 @@ class IntegrationInstance(UsesApiTestCaseMixin): 
    """Unit test case with utilities for spinning up Galaxy."""

    _test_driver: GalaxyTestDriver  # Optional in parent class, but required for integration tests.



    _app_available: ClassVar[bool]



    prefer_template_database = True

    # Subclasses can override this to force uwsgi for tests.

    require_uwsgi = False
@@ -121,9 +125,11 @@ class IntegrationInstance(UsesApiTestCaseMixin): 
        self._configure_interactor()



    @property

    def _app(self):

    def _app(self) -> UniverseApplication:

        assert self._app_available, NO_APP_MESSAGE

        return self._test_driver.app

        app = self._test_driver.app

        assert app, NO_APP_MESSAGE

        return app



    @property

    def _tempdir(self):

setup.cfg

+0 −4
Original line number Diff line number Diff line
@@ -763,10 +763,6 @@ check_untyped_defs = False 
check_untyped_defs = False

[mypy-tool_shed.test.base.test_db_util]

check_untyped_defs = False

[mypy-galaxy_test.driver.integration_util]

check_untyped_defs = False

[mypy-integration.uses_shed]

check_untyped_defs = False

[mypy-integration.test_save_job_id_on_datasets]

check_untyped_defs = False

[mypy-integration.test_config_defaults]

test/integration/uses_shed.py

+16 −4
Original line number Diff line number Diff line
@@ -2,12 +2,16 @@ import os 
import shutil

import string

import tempfile

from typing import ClassVar



import pytest



from galaxy.app import UniverseApplication

from galaxy.tool_util.verify.interactor import GalaxyInteractorApi

from galaxy.util import unicodify

from galaxy_test.base.api_asserts import assert_status_code_is

from galaxy_test.base.populators import DEFAULT_TIMEOUT

from galaxy_test.driver.driver_util import FRAMEWORK_UPLOAD_TOOL_CONF

from galaxy_test.driver.driver_util import FRAMEWORK_UPLOAD_TOOL_CONF, GalaxyTestDriver





# Needs a longer timeout because of the conda_auto_install.
@@ -30,6 +34,14 @@ SHED_DATA_TABLES = """<?xml version="1.0"?> 




class UsesShed:

    @property

    def _app(self) -> UniverseApplication:

        ...

    shed_tools_dir: ClassVar[str]

    shed_tool_data_dir: ClassVar[str]

    conda_tmp_prefix: ClassVar[str]

    galaxy_interactor: GalaxyInteractorApi

    _test_driver: GalaxyTestDriver



    @classmethod

    def configure_shed(cls, config):
@@ -84,10 +96,10 @@ class UsesShed: 
        model.context.flush()



    def delete_repo_request(self, payload):

        return self._delete('/tool_shed_repositories', data=payload, admin=True)

        return self.galaxy_interactor._delete('/tool_shed_repositories', data=payload, admin=True)



    def install_repo_request(self, payload):

        return self._post('/tool_shed_repositories/new/install_repository_revision', data=payload, admin=True)

        return self.galaxy_interactor._post('/tool_shed_repositories/new/install_repository_revision', data=payload, admin=True)



    def repository_operation(self, operation, owner, name, changeset, tool_shed_url='https://toolshed.g2.bx.psu.edu'):

        payload = {
@@ -97,7 +109,7 @@ class UsesShed: 
            'changeset_revision': changeset

        }

        create_response = operation(payload)

        self._assert_status_code_is(create_response, 200)

        assert_status_code_is(create_response, 200)

        return create_response.json()



    def install_repository(self, owner, name, changeset, tool_shed_url='https://toolshed.g2.bx.psu.edu'):