Source code for tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies

from ..base.twilltestcase import common, ShedTwillTestCase

datatypes_repository_name = 'emboss_datatypes_0020'
datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools.  This repository contains no tools."

emboss_repository_name = 'emboss_0020'
emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools for test 0020'
emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools for test 0020'

base_datatypes_count = 0
repository_datatypes_count = 0


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

[docs]    def test_0000_initiate_users(self):
        """Create necessary user accounts."""
        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, 'Problem retrieving user with email %s from the database' % common.test_user_1_email
        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, 'Problem retrieving user with email %s from the database' % common.admin_email
        self.test_db_util.get_private_role(admin_user)
        self.galaxy_login(email=common.admin_email, username=common.admin_username)
        galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
        assert galaxy_admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email
        self.test_db_util.get_galaxy_private_role(galaxy_admin_user)

[docs]    def test_0005_ensure_repositories_and_categories_exist(self):
        '''Create the 0020 category and any missing repositories.'''
        global repository_datatypes_count
        category = self.create_category(name='Test 0020 Basic Repository Dependencies', description='Test 0020 Basic Repository Dependencies')
        self.login(email=common.test_user_1_email, username=common.test_user_1_name)
        datatypes_repository = self.get_or_create_repository(name=datatypes_repository_name,
                                                             description=datatypes_repository_description,
                                                             long_description=datatypes_repository_long_description,
                                                             owner=common.test_user_1_name,
                                                             category_id=self.security.encode_id(category.id),
                                                             strings_displayed=[])
        if self.repository_is_new(datatypes_repository):
            self.upload_file(datatypes_repository,
                             filename='emboss/datatypes/datatypes_conf.xml',
                             filepath=None,
                             valid_tools_only=True,
                             uncompress_file=False,
                             remove_repo_files_not_in_tar=False,
                             commit_message='Uploaded datatypes_conf.xml.',
                             strings_displayed=[],
                             strings_not_displayed=[])
            emboss_repository = self.get_or_create_repository(name=emboss_repository_name,
                                                              description=emboss_repository_description,
                                                              long_description=emboss_repository_long_description,
                                                              owner=common.test_user_1_name,
                                                              category_id=self.security.encode_id(category.id),
                                                              strings_displayed=[])
            self.upload_file(emboss_repository,
                             filename='emboss/emboss.tar',
                             filepath=None,
                             valid_tools_only=True,
                             uncompress_file=True,
                             remove_repo_files_not_in_tar=False,
                             commit_message='Uploaded emboss.tar',
                             strings_displayed=[],
                             strings_not_displayed=[])
            repository_dependencies_path = self.generate_temp_path('test_1020', additional_paths=['emboss', '5'])
            repository_tuple = (self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip(datatypes_repository))
            self.create_repository_dependency(repository=emboss_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path)
        repository_datatypes_count = int(self.get_repository_datatypes_count(datatypes_repository))

[docs]    def test_0010_browse_tool_shed(self):
        """Browse the available tool sheds in this Galaxy instance and preview the emboss tool."""
        global base_datatypes_count
        self.galaxy_login(email=common.admin_email, username=common.admin_username)
        base_datatypes_count = int(self.get_datatypes_count())
        self.browse_tool_shed(url=self.url, strings_displayed=['Test 0020 Basic Repository Dependencies'])
        category = self.test_db_util.get_category_by_name('Test 0020 Basic Repository Dependencies')
        self.browse_category(category, strings_displayed=['emboss_0020'])
        self.preview_repository_in_tool_shed('emboss_0020', common.test_user_1_name, strings_displayed=['emboss_0020', 'Valid tools'])

[docs]    def test_0015_install_emboss_repository(self):
        '''Install the emboss repository without installing tool dependencies.'''
        global repository_datatypes_count
        global base_datatypes_count
        strings_displayed = ['Handle', 'Never installed', 'tool dependencies', 'emboss', '5.0.0', 'package']
        self.install_repository('emboss_0020',
                                common.test_user_1_name,
                                'Test 0020 Basic Repository Dependencies',
                                strings_displayed=strings_displayed,
                                install_tool_dependencies=False,
                                new_tool_panel_section_label='test_1020')
        installed_repository = self.test_db_util.get_installed_repository_by_name_owner('emboss_0020', common.test_user_1_name)
        strings_displayed = ['emboss_0020',
                             'Galaxy wrappers for Emboss version 5.0.0 tools for test 0020',
                             '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', 'antigenic'])
        self.display_installed_repository_manage_page(installed_repository, strings_displayed=strings_displayed)
        strings_displayed = ['emboss', '5.0.0', 'package']
        self.check_installed_repository_tool_dependencies(installed_repository, strings_displayed=strings_displayed, dependencies_installed=False)
        self.verify_tool_metadata_for_installed_repository(installed_repository)
        current_datatypes = int(self.get_datatypes_count())
        assert current_datatypes > base_datatypes_count, 'Installing emboss did not add new datatypes. Expected: %d. Found: %d' % \
            (base_datatypes_count + repository_datatypes_count, current_datatypes)

[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('emboss_0020', common.test_user_1_name)

[docs]    def test_0025_deactivate_datatypes_repository(self):
        '''Deactivate the emboss_datatypes repository without removing it from disk.'''
        global repository_datatypes_count
        global base_datatypes_count
        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(datatypes_repository_name, common.test_user_1_name)
        old_datatypes_count = int(self.get_datatypes_count())
        self.deactivate_repository(installed_repository)
        current_datatypes = int(self.get_datatypes_count())
        assert current_datatypes < old_datatypes_count, 'Uninstalling emboss did not remove datatypes.'

[docs]    def test_0030_reactivate_datatypes_repository(self):
        '''Reactivate the datatypes repository and verify that the datatypes are again present.'''
        global repository_datatypes_count
        global base_datatypes_count
        installed_repository = self.test_db_util.get_installed_repository_by_name_owner(datatypes_repository_name, common.test_user_1_name)
        self.reactivate_repository(installed_repository)
        current_datatypes = int(self.get_datatypes_count())
        assert current_datatypes > base_datatypes_count, 'Reactivating emboss did not add new datatypes.'