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Source code for tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies

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

column_maker_repository_name = "column_maker_0020"
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_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"


[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) self.login(email=common.admin_email, username=common.admin_username) self.galaxy_login(email=common.admin_email, username=common.admin_username)
[docs] def test_0005_ensure_repositories_and_categories_exist(self): """Create the 0020 category and any missing repositories.""" 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) 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): 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=[], ) 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=category, 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, column_maker_repository.name, column_maker_repository.user.username, self.get_repository_tip(column_maker_repository), ) self.create_repository_dependency( repository=emboss_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path, )
[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 0020 Basic Repository Dependencies"]) category = self.populator.get_category_with_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.""" 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)
[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.""" installed_repository = self.test_db_util.get_installed_repository_by_name_owner( column_maker_repository_name, common.test_user_1_name ) self.deactivate_repository(installed_repository)
[docs] def test_0030_reactivate_datatypes_repository(self): """Reactivate the datatypes repository and verify that the datatypes are again present.""" installed_repository = self.test_db_util.get_installed_repository_by_name_owner( column_maker_repository_name, common.test_user_1_name ) self.reactivate_repository(installed_repository)
# This used to reactive datatype repositories and verify counts... # test may be considerably less useful now.