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Source code for tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies

from ..base.twilltestcase import (
    common,
    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."""
[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.upload_file( repository, filename="freebayes/freebayes.tar", filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message="Uploaded the tool tarball.", strings_displayed=[], strings_not_displayed=[], )
[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.upload_file( repository, filename="filtering/filtering_1.1.0.tar", filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message="Uploaded the tool tarball for filtering 1.1.0.", strings_displayed=[], strings_not_displayed=[], )
[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.test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name ) filtering_repository = self.test_db_util.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.user.username, 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.user.username, 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.galaxy_login(email=common.admin_email, username=common.admin_username) strings_displayed = ["Handle", "tool dependencies", "freebayes", "0.9.4_9696d0ce8a9", "samtools", "0.1.18"] self.install_repository( freebayes_repository_name, common.test_user_1_name, category_name, strings_displayed=strings_displayed, 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.test_db_util.get_installed_repository_by_name_owner( freebayes_repository_name, common.test_user_1_name ) installed_filtering_repository = self.test_db_util.get_installed_repository_by_name_owner( filtering_repository_name, common.test_user_1_name ) self.display_installed_repository_manage_page(installed_freebayes_repository) self.display_installed_repository_manage_page(installed_filtering_repository) self.deactivate_repository(installed_filtering_repository) self.test_db_util.ga_refresh(installed_filtering_repository) strings_displayed = [ "Missing repository", "filtering", "freebayes_0040", "user1", "Galaxy's freebayes tool for test 0040", ] self.display_installed_repository_manage_page( installed_freebayes_repository, strings_displayed=strings_displayed ) 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.test_db_util.get_installed_repository_by_name_owner( freebayes_repository_name, common.test_user_1_name ) self.reinstall_repository( installed_filtering_repository, install_tool_dependencies=False, install_repository_dependencies=True, new_tool_panel_section_label="filtering", no_changes=False, )
[docs] def test_0040_uninstall_freebayes_repository(self): """Deactivate freebayes, verify tool panel section and missing repository dependency.""" installed_freebayes_repository = self.test_db_util.get_installed_repository_by_name_owner( freebayes_repository_name, common.test_user_1_name ) installed_filtering_repository = self.test_db_util.get_installed_repository_by_name_owner( filtering_repository_name, common.test_user_1_name ) self.display_installed_repository_manage_page(installed_freebayes_repository) self.display_installed_repository_manage_page(installed_filtering_repository) self.deactivate_repository(installed_freebayes_repository) self.test_db_util.ga_refresh(installed_freebayes_repository) strings_displayed = [ "Missing repository", "freebayes", "filtering_0040", "user1", "Galaxy's filtering tool for test 0040", ] self.display_installed_repository_manage_page( installed_filtering_repository, strings_displayed=strings_displayed ) 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.test_db_util.get_installed_repository_by_name_owner( filtering_repository_name, common.test_user_1_name ) installed_freebayes_repository = self.test_db_util.get_installed_repository_by_name_owner( freebayes_repository_name, common.test_user_1_name ) self.display_installed_repository_manage_page(installed_freebayes_repository) self.display_installed_repository_manage_page(installed_filtering_repository) self.deactivate_repository(installed_filtering_repository) self.test_db_util.ga_refresh(installed_filtering_repository) strings_displayed = [ "Missing repository", "filtering", "freebayes_0040", "user1", "Galaxy's freebayes tool for test 0040", ] self.display_installed_repository_manage_page( installed_freebayes_repository, strings_displayed=strings_displayed ) self.check_galaxy_repository_db_status(filtering_repository_name, common.test_user_1_name, "Deactivated")