Source code for tool_shed.test.functional.test_1460_data_managers

import logging

from ..base.twilltestcase import common, ShedTwillTestCase

log = logging.getLogger(__name__)

category_name = 'Test 1460 Data Manager'
category_description = 'Test script 1460 for testing Data Managers'
data_manager_repository_name = 'data_manager_1460'
data_manager_repository_description = 'Repository that contains a Data Manager'
data_manager_repository_long_description = f'{data_manager_repository_name}: {data_manager_repository_description}'
data_manager_name = 'testing_data_manager'
data_manager_tar_file = '1460_files/data_manager_files/test_data_manager.tar'

'''
1. Add a Data Manager to toolshed

2. install Data Manager

3. Check that Data Manager tool

'''

# TODO: Allow testing actual Execution of installed Data Manager Tool.


[docs]class TestDataManagers(ShedTwillTestCase):
    '''Test installing a repository containing a Data Manager.'''

[docs]    def test_0000_initiate_users_and_category(self):
        """Create necessary user accounts and login as an admin user."""
        self.login(email=common.admin_email, username=common.admin_username)
        admin_user = self.test_db_util.get_user(common.admin_email)
        assert admin_user is not None, f'Problem retrieving user with email {common.admin_email} from the database'
        self.test_db_util.get_private_role(admin_user)
        self.create_category(name=category_name, description=category_description)
        self.login(email=common.test_user_2_email, username=common.test_user_2_name)
        test_user_2 = self.test_db_util.get_user(common.test_user_2_email)
        assert test_user_2 is not None, f'Problem retrieving user with email {common.test_user_2_email} from the database'
        self.test_db_util.get_private_role(test_user_2)
        self.login(email=common.test_user_1_email, username=common.test_user_1_name)
        test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
        assert test_user_1 is not None, f'Problem retrieving user with email {common.test_user_1_email} from the database'
        self.test_db_util.get_private_role(test_user_1)

[docs]    def test_0010_create_data_manager_repository(self):
        '''Create and populate data_manager_1460.

        This is step 1 - Create repository data_manager_1460.

        Create and populate a repository that contains a Data manager.
        '''
        category = self.test_db_util.get_category_by_name(category_name)
        repository = self.get_or_create_repository(name=data_manager_repository_name,
                                                   description=data_manager_repository_description,
                                                   long_description=data_manager_repository_long_description,
                                                   owner=common.test_user_1_name,
                                                   category_id=self.security.encode_id(category.id),
                                                   strings_displayed=[])
        # Upload the data manager files to the repository.
        self.upload_file(repository,
                         filename=data_manager_tar_file,
                         filepath=None,
                         valid_tools_only=True,
                         uncompress_file=True,
                         remove_repo_files_not_in_tar=False,
                         commit_message=f'Populate {data_manager_repository_name} with a data manager configuration.',
                         strings_displayed=[],
                         strings_not_displayed=[])

[docs]    def test_0020_install_data_manager_repository(self):
        '''Install the data_manager_1460 repository to galaxy.

        This is step 3 - Attempt to install the repository into a galaxy instance, verify that it is installed.
        '''
        self.galaxy_login(email=common.admin_email, username=common.admin_username)
        post_submit_strings_displayed = [data_manager_repository_name]
        self.install_repository(data_manager_repository_name,
                                common.test_user_1_name,
                                category_name,
                                install_tool_dependencies=True,
                                post_submit_strings_displayed=post_submit_strings_displayed)

[docs]    def test_0030_verify_data_manager_tool(self):
        '''Verify that the data_manager_1460 repository is installed and Data Manager tool appears in list in Galaxy.'''
        repository = self.test_db_util.get_installed_repository_by_name_owner(data_manager_repository_name, common.test_user_1_name)
        strings_displayed = ['status', 'jobs', data_manager_name]
        self.display_installed_jobs_list_page(repository, data_manager_names=data_manager_name, strings_displayed=strings_displayed)

[docs]    def test_0040_verify_data_manager_data_table(self):
        '''Verify that the installed repository populated shed_tool_data_table.xml and the sample files.'''
        self.verify_installed_repository_data_table_entries(required_data_table_entries=['data_manager_test_data_table'])