Source code for tool_shed.test.functional.test_1030_install_repository_with_dependency_revisions

from ..base.twilltestcase import (
    common,
    ShedTwillTestCase,
)

datatypes_repository_name = "emboss_datatypes_0030"
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_0030"
emboss_5_repository_name = "emboss_5_0030"
emboss_6_repository_name = "emboss_6_0030"
emboss_repository_description = "Galaxy wrappers for Emboss version 5.0.0 tools for test 0030"
emboss_repository_long_description = "Galaxy wrappers for Emboss version 5.0.0 tools for test 0030"

base_datatypes_count = 0
repository_datatypes_count = 0
running_standalone = False


[docs]class RepositoryWithDependencyRevisions(ShedTwillTestCase): """Test installing a repository with dependency revisions."""
[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 0030 category and add repositories to it, if necessary.""" global repository_datatypes_count global running_standalone category = self.create_category( name="Test 0030 Repository Dependency Revisions", description="Test 0030 Repository Dependency Revisions" ) 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): running_standalone = True 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_5_repository = self.get_or_create_repository( name=emboss_5_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_5_repository, filename="emboss/emboss.tar", filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message="Uploaded tool tarball.", strings_displayed=[], strings_not_displayed=[], ) repository_dependencies_path = self.generate_temp_path("test_1030", additional_paths=["emboss", "5"]) datatypes_tuple = ( self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip(datatypes_repository), ) self.create_repository_dependency( repository=emboss_5_repository, repository_tuples=[datatypes_tuple], filepath=repository_dependencies_path, ) emboss_6_repository = self.get_or_create_repository( name=emboss_6_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_6_repository, filename="emboss/emboss.tar", filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message="Uploaded tool tarball.", strings_displayed=[], strings_not_displayed=[], ) repository_dependencies_path = self.generate_temp_path("test_1030", additional_paths=["emboss", "6"]) datatypes_tuple = ( self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip(datatypes_repository), ) self.create_repository_dependency( repository=emboss_6_repository, repository_tuples=[datatypes_tuple], filepath=repository_dependencies_path, ) 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=False, remove_repo_files_not_in_tar=False, commit_message="Uploaded tool tarball.", strings_displayed=[], strings_not_displayed=[], ) repository_dependencies_path = self.generate_temp_path("test_1030", additional_paths=["emboss", "5"]) dependency_tuple = ( self.url, emboss_5_repository.name, emboss_5_repository.user.username, self.get_repository_tip(emboss_5_repository), ) self.create_repository_dependency( repository=emboss_repository, repository_tuples=[dependency_tuple], filepath=repository_dependencies_path, ) dependency_tuple = ( self.url, emboss_6_repository.name, emboss_6_repository.user.username, self.get_repository_tip(emboss_6_repository), ) self.create_repository_dependency( repository=emboss_repository, repository_tuples=[dependency_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.""" self.galaxy_login(email=common.admin_email, username=common.admin_username) self.browse_tool_shed(url=self.url, strings_displayed=["Test 0030 Repository Dependency Revisions"]) category = self.test_db_util.get_category_by_name("Test 0030 Repository Dependency Revisions") self.browse_category(category, strings_displayed=["emboss_0030"]) self.preview_repository_in_tool_shed( "emboss_0030", common.test_user_1_name, strings_displayed=["emboss_0030", "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 global running_standalone base_datatypes_count = int(self.get_datatypes_count()) strings_displayed = ["Handle", "Never installed", "tool dependencies", "emboss", "5.0.0", "package"] self.install_repository( "emboss_0030", common.test_user_1_name, "Test 0030 Repository Dependency Revisions", strings_displayed=strings_displayed, install_tool_dependencies=False, new_tool_panel_section_label="test_1030", ) installed_repository = self.test_db_util.get_installed_repository_by_name_owner( "emboss_0030", common.test_user_1_name ) strings_displayed = [ "emboss_0030", "Galaxy wrappers for Emboss version 5.0.0 tools for test 0030", "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) self.update_installed_repository(installed_repository, strings_displayed=["there are no updates available"]) current_datatypes = int(self.get_datatypes_count()) if running_standalone: assert ( current_datatypes == base_datatypes_count + repository_datatypes_count ), "Installing emboss did not add new datatypes." else: assert current_datatypes == base_datatypes_count, "Installing emboss added new datatypes."
[docs] def test_0025_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_0030", common.test_user_1_name)