Source code for tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies

import logging
import os

from ..base.twilltestcase import common, ShedTwillTestCase

repository_name = 'freebayes_0010'
repository_description = "Galaxy's freebayes tool"
repository_long_description = "Long description of Galaxy's freebayes tool"
category_name = 'Test 0010 Repository With Tool Dependencies'
log = logging.getLogger(__name__)


[docs]class ToolWithToolDependencies(ShedTwillTestCase):
    '''Test installing a repository with tool dependencies.'''

[docs]    def test_0000_initiate_users(self):
        """Create necessary user accounts."""
        self.galaxy_login(email=common.admin_email, username=common.admin_username)
        admin_user = self.test_db_util.get_galaxy_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_galaxy_private_role(admin_user)
        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)
        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)

[docs]    def test_0005_ensure_repositories_and_categories_exist(self):
        '''Create the 0010 category and upload the freebayes repository to it, if necessary.'''
        category = self.create_category(name=category_name, description='Tests for a repository with tool dependencies.')
        self.login(email=common.test_user_1_email, username=common.test_user_1_name)
        repository = self.get_or_create_repository(name=repository_name,
                                                   description=repository_description,
                                                   long_description=repository_long_description,
                                                   owner=common.test_user_1_name,
                                                   category_id=self.security.encode_id(category.id))
        if self.repository_is_new(repository):
            self.upload_file(repository,
                             filename='freebayes/freebayes.xml',
                             filepath=None,
                             valid_tools_only=False,
                             uncompress_file=False,
                             remove_repo_files_not_in_tar=False,
                             commit_message='Uploaded the tool xml.',
                             strings_displayed=['Metadata may have been defined', 'This file requires an entry', 'tool_data_table_conf'],
                             strings_not_displayed=[])
            self.upload_file(repository,
                             filename='freebayes/tool_data_table_conf.xml.sample',
                             filepath=None,
                             valid_tools_only=False,
                             uncompress_file=False,
                             remove_repo_files_not_in_tar=False,
                             commit_message='Uploaded the tool data table sample file.',
                             strings_displayed=[],
                             strings_not_displayed=[])
            self.upload_file(repository,
                             filename='freebayes/sam_fa_indices.loc.sample',
                             filepath=None,
                             valid_tools_only=True,
                             uncompress_file=False,
                             remove_repo_files_not_in_tar=False,
                             commit_message='Uploaded tool data table .loc file.',
                             strings_displayed=[],
                             strings_not_displayed=[])
            self.upload_file(repository,
                             filename=os.path.join('freebayes', 'malformed_tool_dependencies', 'tool_dependencies.xml'),
                             filepath=None,
                             valid_tools_only=False,
                             uncompress_file=False,
                             remove_repo_files_not_in_tar=False,
                             commit_message='Uploaded malformed tool dependency XML.',
                             strings_displayed=['Exception attempting to parse', 'not well-formed'],
                             strings_not_displayed=[])
            self.upload_file(repository,
                             filename=os.path.join('freebayes', 'invalid_tool_dependencies', 'tool_dependencies.xml'),
                             filepath=None,
                             valid_tools_only=False,
                             uncompress_file=False,
                             remove_repo_files_not_in_tar=False,
                             commit_message='Uploaded invalid tool dependency XML.',
                             strings_displayed=['The settings for <b>name</b>, <b>version</b> and <b>type</b> from a contained tool configuration'],
                             strings_not_displayed=[])
            self.upload_file(repository,
                             filename=os.path.join('freebayes', 'tool_dependencies.xml'),
                             filepath=None,
                             valid_tools_only=True,
                             uncompress_file=False,
                             remove_repo_files_not_in_tar=False,
                             commit_message='Uploaded valid tool dependency XML.',
                             strings_displayed=[],
                             strings_not_displayed=[])

[docs]    def test_0010_browse_tool_shed(self):
        """Browse the available tool sheds in this Galaxy instance and preview the freebayes tool."""
        self.galaxy_login(email=common.admin_email, username=common.admin_username)
        self.browse_tool_shed(url=self.url, strings_displayed=[category_name])
        category = self.test_db_util.get_category_by_name(category_name)
        self.browse_category(category, strings_displayed=[repository_name])
        strings_displayed = [repository_name, 'Valid tools', 'Tool dependencies']
        self.preview_repository_in_tool_shed(repository_name, common.test_user_1_name, strings_displayed=strings_displayed)

[docs]    def test_0015_install_freebayes_repository(self):
        '''Install the freebayes repository without installing tool dependencies.'''
        strings_displayed = ['Never installed', 'install all needed dependencies', 'install Tool Shed managed', 'tool dependencies']
        strings_displayed.extend(['freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18'])
        self.install_repository(repository_name,
                                common.test_user_1_name,
                                category_name,
                                strings_displayed=strings_displayed,
                                install_tool_dependencies=False,
                                new_tool_panel_section_label='test_1010')
        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(repository_name, common.test_user_1_name)
        strings_displayed = ['freebayes_0010',
                             "Galaxy's freebayes tool",
                             'user1',
                             self.url.replace('http://', ''),
                             installed_repository.installed_changeset_revision]
        self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
        strings_displayed.extend(['Installed tool shed repository', 'Valid tools', 'FreeBayes'])
        self.display_installed_repository_manage_page(installed_repository, strings_displayed=strings_displayed)
        strings_displayed = ['freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18']
        self.check_installed_repository_tool_dependencies(installed_repository, strings_displayed=strings_displayed, dependencies_installed=False)
        self.verify_tool_metadata_for_installed_repository(installed_repository)

[docs]    def test_0020_verify_installed_repository_metadata(self):
        '''Verify that resetting the metadata on an installed repository does not change the metadata.'''
        self.verify_installed_repository_metadata_unchanged(repository_name, common.test_user_1_name)

[docs]    def test_0025_verify_sample_files(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=['sam_fa_indexes'])