Source code for tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies

from ..base import common
from ..base.twilltestcase import ShedTwillTestCase

freebayes_repository_name = "freebayes_0040"
freebayes_repository_description = "Galaxy's freebayes tool for test 0040"
freebayes_repository_long_description = "Long description of Galaxy's freebayes tool for test 0040"

filtering_repository_name = "filtering_0040"
filtering_repository_description = "Galaxy's filtering tool for test 0040"
filtering_repository_long_description = "Long description of Galaxy's filtering tool for test 0040"

category_name = "test_0040_repository_circular_dependencies"

running_standalone = False


[docs]class TestInstallingCircularDependencies(ShedTwillTestCase): """Verify that the code correctly handles installing repositories with circular dependencies.""" requires_galaxy = True
[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) self.login(email=common.admin_email, username=common.admin_username)
[docs] def test_0005_create_freebayes_repository(self): """Create and populate freebayes_0040.""" global running_standalone category = self.create_category( name=category_name, description="Testing handling of circular repository dependencies." ) self.login(email=common.test_user_1_email, username=common.test_user_1_name) repository = self.get_or_create_repository( name=freebayes_repository_name, description=freebayes_repository_description, long_description=freebayes_repository_long_description, owner=common.test_user_1_name, category=category, strings_displayed=[], ) if self.repository_is_new(repository): running_standalone = True self.commit_tar_to_repository( repository, "freebayes/freebayes.tar", commit_message="Uploaded the tool tarball.", )
[docs] def test_0015_create_filtering_repository(self): """Create and populate filtering_0040.""" global running_standalone category = self.create_category( name=category_name, description="Testing handling of circular repository dependencies." ) self.login(email=common.test_user_1_email, username=common.test_user_1_name) repository = self.get_or_create_repository( name=filtering_repository_name, description=filtering_repository_description, long_description=filtering_repository_long_description, owner=common.test_user_1_name, category=category, strings_displayed=[], ) if self.repository_is_new(repository): running_standalone = True self.commit_tar_to_repository( repository, "filtering/filtering_1.1.0.tar", commit_message="Uploaded the tool tarball for filtering 1.1.0.", )
[docs] def test_0020_create_repository_dependencies(self): """Set up the filtering and freebayes repository dependencies.""" # The dependency structure should look like: # Filtering revision 0 -> freebayes revision 0. # Freebayes revision 0 -> filtering revision 1. # Filtering will have two revisions, one with just the filtering tool, and one with the filtering tool and a dependency on freebayes. global running_standalone if running_standalone: freebayes_repository = self._get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) filtering_repository = self._get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name ) repository_dependencies_path = self.generate_temp_path("test_1040", additional_paths=["circular"]) repository_tuple = ( self.url, freebayes_repository.name, freebayes_repository.owner, self.get_repository_tip(freebayes_repository), ) self.create_repository_dependency( repository=filtering_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path, ) repository_tuple = ( self.url, filtering_repository.name, filtering_repository.owner, self.get_repository_tip(filtering_repository), ) self.create_repository_dependency( repository=freebayes_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path, )
[docs] def test_0025_install_freebayes_repository(self): """Install freebayes with blank tool panel section, without tool dependencies but with repository dependencies.""" self._install_repository( freebayes_repository_name, common.test_user_1_name, category_name, install_tool_dependencies=False, install_repository_dependencies=True, )
[docs] def test_0030_uninstall_filtering_repository(self): """Deactivate filtering, verify tool panel section and missing repository dependency.""" installed_freebayes_repository = self._get_installed_repository_by_name_owner( freebayes_repository_name, common.test_user_1_name ) installed_filtering_repository = self._get_installed_repository_by_name_owner( filtering_repository_name, common.test_user_1_name ) assert self._get_installed_repository_for( common.test_user_1, freebayes_repository_name, installed_freebayes_repository.installed_changeset_revision ) assert self._get_installed_repository_for( common.test_user_1, filtering_repository_name, installed_filtering_repository.installed_changeset_revision ) self.deactivate_repository(installed_filtering_repository) self._refresh_tool_shed_repository(installed_filtering_repository) self._assert_has_missing_dependency(installed_freebayes_repository, filtering_repository_name) self.check_galaxy_repository_db_status(filtering_repository_name, common.test_user_1_name, "Deactivated")
[docs] def test_0035_reactivate_filtering_repository(self): """Reinstall filtering into 'filtering' tool panel section.""" installed_filtering_repository = self._get_installed_repository_by_name_owner( freebayes_repository_name, common.test_user_1_name ) self.reinstall_repository_api( installed_filtering_repository, install_tool_dependencies=False, install_repository_dependencies=True, new_tool_panel_section_label="filtering", ) installed_freebayes_repository = self._get_installed_repository_by_name_owner( freebayes_repository_name, common.test_user_1_name ) self._assert_is_not_missing_dependency(installed_freebayes_repository, filtering_repository_name)
[docs] def test_0040_uninstall_freebayes_repository(self): """Deactivate freebayes, verify tool panel section and missing repository dependency.""" installed_freebayes_repository = self._get_installed_repository_by_name_owner( freebayes_repository_name, common.test_user_1_name ) installed_filtering_repository = self._get_installed_repository_by_name_owner( filtering_repository_name, common.test_user_1_name ) assert self._get_installed_repository_for( common.test_user_1, freebayes_repository_name, installed_freebayes_repository.installed_changeset_revision ) assert self._get_installed_repository_for( common.test_user_1, filtering_repository_name, installed_filtering_repository.installed_changeset_revision ) self.deactivate_repository(installed_freebayes_repository) assert not self._get_installed_repository_for( common.test_user_1, freebayes_repository_name, installed_freebayes_repository.installed_changeset_revision ) self._refresh_tool_shed_repository(installed_filtering_repository) self._assert_has_missing_dependency(installed_filtering_repository, freebayes_repository_name) self.check_galaxy_repository_db_status("freebayes_0040", "user1", "Deactivated")
[docs] def test_0045_deactivate_filtering_repository(self): """Deactivate filtering, verify tool panel section.""" installed_filtering_repository = self._get_installed_repository_by_name_owner( filtering_repository_name, common.test_user_1_name ) installed_freebayes_repository = self._get_installed_repository_by_name_owner( freebayes_repository_name, common.test_user_1_name ) assert self._get_installed_repository_for( common.test_user_1, filtering_repository_name, installed_filtering_repository.installed_changeset_revision ) self.deactivate_repository(installed_filtering_repository) assert not self._get_installed_repository_for( common.test_user_1, freebayes_repository_name, installed_freebayes_repository.installed_changeset_revision ) assert not self._get_installed_repository_for( common.test_user_1, filtering_repository_name, installed_filtering_repository.installed_changeset_revision ) self._refresh_tool_shed_repository(installed_freebayes_repository) self._assert_has_missing_dependency(installed_freebayes_repository, filtering_repository_name) self.check_galaxy_repository_db_status(filtering_repository_name, common.test_user_1_name, "Deactivated")