import os import shutil import string import tempfile import pytest from galaxy.util import unicodify from galaxy_test.base.populators import DEFAULT_TIMEOUT from galaxy_test.driver.driver_util import FRAMEWORK_UPLOAD_TOOL_CONF # 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(""" """) SHED_DATA_MANAGER_CONF = """ """ SHED_DATA_TABLES = """ """ class UsesShed(object): @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) @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') def reset_shed_tools(self): shutil.rmtree(self._app.config.shed_tools_dir, ignore_errors=True) os.makedirs(self._app.config.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) 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() def delete_repo_request(self, payload): return self._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) 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) self._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'): 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 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)