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 ), 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) 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 ), f"Problem retrieving user with email {common.admin_email} from the database" 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) 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."