Source code for tool_shed.test.functional.test_0030_repository_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"


[docs]class TestRepositoryDependencyRevisions(ShedTwillTestCase): """Test dependencies on different revisions of a repository."""
[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)
[docs] def test_0005_create_category(self): """Create a category for this test suite""" self.create_category( name="Test 0030 Repository Dependency Revisions", description="Testing repository dependencies by revision." )
[docs] def test_0010_create_emboss_5_repository(self): """Create and populate the emboss_5_0030 repository.""" self.login(email=common.test_user_1_email, username=common.test_user_1_name) category = self.test_db_util.get_category_by_name("Test 0030 Repository Dependency Revisions") 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), ) self.upload_file( 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=[], )
[docs] def test_0015_create_emboss_6_repository(self): """Create and populate the emboss_6_0030 repository.""" self.login(email=common.test_user_1_email, username=common.test_user_1_name) category = self.test_db_util.get_category_by_name("Test 0030 Repository Dependency Revisions") 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), ) self.upload_file( 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=[], )
[docs] def test_0020_create_emboss_datatypes_repository(self): """Create and populate the emboss_datatypes_0030 repository.""" self.login(email=common.test_user_1_email, username=common.test_user_1_name) category = self.test_db_util.get_category_by_name("Test 0030 Repository Dependency Revisions") repository = self.get_or_create_repository( name=datatypes_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), ) self.upload_file( 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=[], )
[docs] def test_0025_create_emboss_repository(self): """Create and populate the emboss_0030 repository.""" self.login(email=common.test_user_1_email, username=common.test_user_1_name) category = self.test_db_util.get_category_by_name("Test 0030 Repository Dependency Revisions") 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), ) self.upload_file( repository, filename="emboss/emboss.tar", filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message="Uploaded the tool tarball.", strings_displayed=[], strings_not_displayed=[], )
[docs] def test_0030_generate_repository_dependencies_for_emboss_5(self): """Generate a repository_dependencies.xml file specifying emboss_datatypes and upload it to the emboss_5 repository.""" datatypes_repository = self.test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) emboss_5_repository = self.test_db_util.get_repository_by_name_and_owner( emboss_5_repository_name, common.test_user_1_name ) repository_dependencies_path = self.generate_temp_path("test_0030", additional_paths=["emboss5"]) 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 )
[docs] def test_0035_generate_repository_dependencies_for_emboss_6(self): """Generate a repository_dependencies.xml file specifying emboss_datatypes and upload it to the emboss_6 repository.""" emboss_6_repository = self.test_db_util.get_repository_by_name_and_owner( emboss_6_repository_name, common.test_user_1_name ) datatypes_repository = self.test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) repository_dependencies_path = self.generate_temp_path("test_0030", additional_paths=["emboss6"]) 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 )
[docs] def test_0040_generate_repository_dependency_on_emboss_5(self): """Create and upload repository_dependencies.xml for the emboss_5_0030 repository.""" emboss_repository = self.test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) emboss_5_repository = self.test_db_util.get_repository_by_name_and_owner( emboss_5_repository_name, common.test_user_1_name ) repository_dependencies_path = self.generate_temp_path("test_0030", additional_paths=["emboss", "5"]) emboss_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=[emboss_tuple], filepath=repository_dependencies_path )
[docs] def test_0045_generate_repository_dependency_on_emboss_6(self): """Create and upload repository_dependencies.xml for the emboss_6_0030 repository.""" emboss_repository = self.test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) emboss_6_repository = self.test_db_util.get_repository_by_name_and_owner( emboss_6_repository_name, common.test_user_1_name ) repository_dependencies_path = self.generate_temp_path("test_0030", additional_paths=["emboss", "5"]) emboss_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=[emboss_tuple], filepath=repository_dependencies_path )
[docs] def test_0050_verify_repository_dependency_revisions(self): """Verify that different metadata revisions of the emboss repository have different repository dependencies.""" repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name) repository_metadata = [ (metadata.metadata, metadata.changeset_revision) for metadata in self.get_repository_metadata(repository) ] datatypes_repository = self.test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) datatypes_tip = self.get_repository_tip(datatypes_repository) strings_displayed = [] # Iterate through all metadata revisions and check for repository dependencies. for _metadata, changeset_revision in repository_metadata: # Add the dependency description and datatypes repository details to the strings to check. strings_displayed = ["emboss_datatypes_0030", "user1", datatypes_tip] strings_displayed.extend(["Tool dependencies", "emboss", "5.0.0", "package"]) self.display_manage_repository_page( repository, changeset_revision=changeset_revision, strings_displayed=strings_displayed )
[docs] def test_0055_verify_repository_metadata(self): """Verify that resetting the metadata does not change it.""" emboss_repository = self.test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) emboss_5_repository = self.test_db_util.get_repository_by_name_and_owner( emboss_5_repository_name, common.test_user_1_name ) emboss_6_repository = self.test_db_util.get_repository_by_name_and_owner( emboss_6_repository_name, common.test_user_1_name ) datatypes_repository = self.test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) for repository in [emboss_repository, emboss_5_repository, emboss_6_repository, datatypes_repository]: self.verify_unchanged_repository_metadata(repository)