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Source code for tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency

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

column_maker_repository_name = "column_maker_0110"
column_maker_repository_description = "A flexible aligner."
column_maker_repository_long_description = "A flexible aligner and methylation caller for Bisulfite-Seq applications."

emboss_repository_name = "emboss_0110"
emboss_repository_description = "Galaxy wrappers for Emboss version 5.0.0 tools"
emboss_repository_long_description = "Galaxy wrappers for Emboss version 5.0.0 tools"

category_name = "Test 0110 Invalid Repository Dependencies"
category_desc = "Test 0110 Invalid Repository Dependencies"
running_standalone = False


[docs]class TestBasicRepositoryDependencies(ShedTwillTestCase): """Testing emboss 5 with repository dependencies."""
[docs] def test_0000_initiate_users(self): """Create necessary user accounts and login as an admin user.""" self.login(email=common.test_user_1_email, username=common.test_user_1_name) self.login(email=common.admin_email, username=common.admin_username)
[docs] def test_0005_create_category(self): """Create a category for this test suite""" self.create_category(name=category_name, description=category_desc)
[docs] def test_0010_create_emboss_dependendent_column_maker_repository_and_upload_tarball(self): """Create and populate the column_maker repository.""" global running_standalone self.login(email=common.test_user_1_email, username=common.test_user_1_name) category = self.populator.get_category_with_name(category_name) column_maker_repository = self.get_or_create_repository( name=column_maker_repository_name, description=column_maker_repository_description, long_description=column_maker_repository_long_description, owner=common.test_user_1_name, category=category, strings_displayed=[], ) if self.repository_is_new(column_maker_repository): running_standalone = True self.upload_file( column_maker_repository, filename="column_maker/column_maker.tar", filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message="Uploaded column_maker tarball.", strings_displayed=[], strings_not_displayed=[], )
[docs] def test_0020_create_emboss_5_repository_and_upload_files(self): """Create and populate the emboss_5_0110 repository.""" global running_standalone if running_standalone: category = self.populator.get_category_with_name(category_name) 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=category, strings_displayed=[], ) self.upload_file( 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 tool tarball.", strings_displayed=[], strings_not_displayed=[], )
[docs] def test_0025_generate_repository_dependency_with_invalid_url(self): """Generate a repository dependency for emboss 5 with an invalid URL.""" global running_standalone if running_standalone: dependency_path = self.generate_temp_path("test_1110", additional_paths=["simple"]) column_maker_repository = self._get_repository_by_name_and_owner( column_maker_repository_name, common.test_user_1_name ) emboss_repository = self._get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name) url = "http://http://this is not an url!" name = column_maker_repository.name owner = column_maker_repository.owner changeset_revision = self.get_repository_tip(column_maker_repository) strings_displayed = ["Repository dependencies are currently supported only within the same tool shed"] repository_tuple = (url, name, owner, changeset_revision) self.create_repository_dependency( repository=emboss_repository, filepath=dependency_path, repository_tuples=[repository_tuple], strings_displayed=strings_displayed, complex=False, )
[docs] def test_0030_generate_repository_dependency_with_invalid_name(self): """Generate a repository dependency for emboss 5 with an invalid name.""" global running_standalone if running_standalone: dependency_path = self.generate_temp_path("test_1110", additional_paths=["simple"]) repository = self._get_repository_by_name_and_owner(column_maker_repository_name, common.test_user_1_name) emboss_repository = self._get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name) url = self.url name = "!?invalid?!" owner = repository.owner changeset_revision = self.get_repository_tip(repository) strings_displayed = ["because the name is invalid."] repository_tuple = (url, name, owner, changeset_revision) self.create_repository_dependency( repository=emboss_repository, filepath=dependency_path, repository_tuples=[repository_tuple], strings_displayed=strings_displayed, complex=False, )
[docs] def test_0035_generate_repository_dependency_with_invalid_owner(self): """Generate a repository dependency for emboss 5 with an invalid owner.""" global running_standalone if running_standalone: dependency_path = self.generate_temp_path("test_1110", additional_paths=["simple"]) repository = self._get_repository_by_name_and_owner(column_maker_repository_name, common.test_user_1_name) emboss_repository = self._get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name) url = self.url name = repository.name owner = "!?invalid?!" changeset_revision = self.get_repository_tip(repository) strings_displayed = ["because the owner is invalid."] repository_tuple = (url, name, owner, changeset_revision) self.create_repository_dependency( repository=emboss_repository, filepath=dependency_path, repository_tuples=[repository_tuple], strings_displayed=strings_displayed, complex=False, )
[docs] def test_0040_generate_repository_dependency_with_invalid_changeset_revision(self): """Generate a repository dependency for emboss 5 with an invalid changeset revision.""" global running_standalone if running_standalone: dependency_path = self.generate_temp_path("test_1110", additional_paths=["simple", "invalid"]) repository = self._get_repository_by_name_and_owner(column_maker_repository_name, common.test_user_1_name) emboss_repository = self._get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name) url = self.url name = repository.name owner = repository.owner changeset_revision = "!?invalid?!" strings_displayed = ["because the changeset revision is invalid."] repository_tuple = (url, name, owner, changeset_revision) self.create_repository_dependency( repository=emboss_repository, filepath=dependency_path, repository_tuples=[repository_tuple], strings_displayed=strings_displayed, complex=False, )
[docs] def test_0045_install_repository_with_invalid_repository_dependency(self): """Install the repository and verify that galaxy detects invalid repository dependencies.""" self.galaxy_login(email=common.admin_email, username=common.admin_username) repository = self._get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name) preview_strings_displayed = [ "emboss_0110", self.get_repository_tip(repository), "Ignoring repository dependency definition", ] self.install_repository( emboss_repository_name, common.test_user_1_name, category_name, install_tool_dependencies=False, install_repository_dependencies=True, preview_strings_displayed=preview_strings_displayed, ) installed_repository = self.test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name ) self.display_installed_repository_manage_page( installed_repository=installed_repository, strings_displayed=[], strings_not_displayed=["Repository dependencies"], )