Source code for galaxy_test.base.uses_shed

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, GalaxyTestDriver


# Needs a longer timeout because of the conda_auto_install.
CONDA_AUTO_INSTALL_JOB_TIMEOUT = DEFAULT_TIMEOUT * 3

SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
TOOL_SHEDS_CONF = os.path.join(SCRIPT_DIRECTORY, "tool_sheds_conf.xml")

SHED_TOOL_CONF = string.Template("""<?xml version="1.0"?>
<toolbox tool_path="$shed_tools_path">
</toolbox>""")

SHED_DATA_MANAGER_CONF = """<?xml version="1.0"?>
<data_managers>
</data_managers>"""

SHED_DATA_TABLES = """<?xml version="1.0"?>
<tables>
</tables>"""


[docs]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

[docs]    @classmethod
    def configure_shed(cls, config):
        cls.shed_tools_dir = tempfile.mkdtemp()
        cls.shed_tool_data_dir = tempfile.mkdtemp()
        cls._test_driver.temp_directories.extend([cls.shed_tool_data_dir, cls.shed_tools_dir])
        shed_tool_config = os.path.join(cls.shed_tools_dir, 'shed_tool_conf.xml')
        config["tool_sheds_config_file"] = TOOL_SHEDS_CONF
        config["tool_config_file"] = FRAMEWORK_UPLOAD_TOOL_CONF
        config["shed_tool_config_file"] = shed_tool_config
        config["shed_data_manager_config_file"] = os.path.join(cls.shed_tool_data_dir, 'shed_data_manager_config_file')
        config["shed_tool_data_table_config"] = os.path.join(cls.shed_tool_data_dir, 'shed_data_table_conf.xml')
        config["shed_tool_data_path"] = cls.shed_tool_data_dir
        with open(shed_tool_config, 'w') as tool_conf_file:
            tool_conf_file.write(SHED_TOOL_CONF.substitute(shed_tools_path=cls.shed_tools_dir))
        with open(config["shed_data_manager_config_file"], 'w') as shed_data_config:
            shed_data_config.write(SHED_DATA_MANAGER_CONF)
        with open(config["shed_tool_data_table_config"], 'w') as shed_data_table_config:
            shed_data_table_config.write(SHED_DATA_TABLES)

[docs]    @classmethod
    def configure_shed_and_conda(cls, config):
        cls.configure_shed(config)
        cls.conda_tmp_prefix = tempfile.mkdtemp()
        cls._test_driver.temp_directories.append(cls.conda_tmp_prefix)
        config["conda_auto_init"] = True
        config["conda_auto_install"] = True
        config["conda_prefix"] = os.environ.get('GALAXY_TEST_CONDA_PREFIX') or os.path.join(cls.conda_tmp_prefix, 'conda')

[docs]    def setup_shed_config(self):
        shutil.rmtree(self._app.config.shed_tools_dir, ignore_errors=True)
        os.makedirs(self._app.config.shed_tools_dir)
        self._app.config.shed_tools_dir = self.shed_tools_dir
        with open(self._app.config.shed_tool_config_file, "w") as tool_conf_file:
            tool_conf_file.write(SHED_TOOL_CONF.substitute(shed_tools_path=self._app.config.shed_tools_dir))
        # deleting the containing folder doesn't trigger a toolbox reload, so signal it now and wait until it's done
        self._app.queue_worker.send_control_task('reload_toolbox', get_response=True)

[docs]    def reset_shed_tools(self):
        self.setup_shed_config()
        model = self._app.install_model
        models_to_delete = [
            model.RepositoryRepositoryDependencyAssociation,
            model.RepositoryDependency,
            model.ToolVersion,
            model.ToolVersionAssociation,
            model.ToolDependency,
            model.ToolShedRepository,
        ]
        for item in models_to_delete:
            model.context.query(item).delete()
        model.context.flush()

[docs]    def delete_repo_request(self, payload):
        return self.galaxy_interactor._delete('tool_shed_repositories', data=payload, admin=True)

[docs]    def install_repo_request(self, payload):
        return self.galaxy_interactor._post('tool_shed_repositories/new/install_repository_revision', data=payload, admin=True)

[docs]    def repository_operation(self, operation, owner, name, changeset, tool_shed_url='https://toolshed.g2.bx.psu.edu'):
        payload = {
            'tool_shed_url': tool_shed_url,
            'name': name,
            'owner': owner,
            'changeset_revision': changeset
        }
        create_response = operation(payload)
        assert_status_code_is(create_response, 200)
        return create_response.json()

[docs]    def install_repository(self, owner, name, changeset, tool_shed_url='https://toolshed.g2.bx.psu.edu'):
        try:
            return self.repository_operation(operation=self.install_repo_request, owner=owner, name=name, changeset=changeset, tool_shed_url=tool_shed_url)
        except AssertionError as e:
            if "Error attempting to retrieve installation information from tool shed" in unicodify(e):
                pytest.skip("Toolshed '%s' unavailable" % tool_shed_url)
            raise

[docs]    def uninstall_repository(self, owner, name, changeset, tool_shed_url='https://toolshed.g2.bx.psu.edu'):
        return self.repository_operation(operation=self.delete_repo_request, owner=owner, name=name, changeset=changeset, tool_shed_url=tool_shed_url)