Source code for tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies

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

datatypes_repository_name = "emboss_datatypes_0110"
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_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"


[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)
        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=category_name, description=category_desc)

[docs]    def test_0010_create_emboss_datatypes_repository_and_upload_tarball(self):
        """Create and populate the emboss_datatypes repository."""
        self.login(email=common.test_user_1_email, username=common.test_user_1_name)
        category = self.test_db_util.get_category_by_name(category_name)
        repository = self.get_or_create_repository(
            name=datatypes_repository_name,
            description=datatypes_repository_description,
            long_description=datatypes_repository_long_description,
            owner=common.test_user_1_name,
            category_id=self.security.encode_id(category.id),
            strings_displayed=[],
        )
        self.upload_file(
            repository,
            filename="emboss/datatypes/datatypes_conf.xml",
            filepath=None,
            valid_tools_only=True,
            uncompress_file=True,
            remove_repo_files_not_in_tar=False,
            commit_message="Uploaded datatypes_conf.xml.",
            strings_displayed=[],
            strings_not_displayed=[],
        )

[docs]    def test_0015_verify_datatypes_in_datatypes_repository(self):
        """Verify that the emboss_datatypes repository contains datatype entries."""
        repository = self.test_db_util.get_repository_by_name_and_owner(
            datatypes_repository_name, common.test_user_1_name
        )
        self.display_manage_repository_page(
            repository, strings_displayed=["Datatypes", "equicktandem", "hennig86", "vectorstrip"]
        )

[docs]    def test_0020_create_emboss_5_repository_and_upload_files(self):
        """Create and populate the emboss_5_0110 repository."""
        category = self.test_db_util.get_category_by_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_id=self.security.encode_id(category.id),
            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."""
        dependency_path = self.generate_temp_path("test_0110", additional_paths=["simple"])
        datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(
            datatypes_repository_name, common.test_user_1_name
        )
        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(
            emboss_repository_name, common.test_user_1_name
        )
        url = "http://http://this is not an url!"
        name = datatypes_repository.name
        owner = datatypes_repository.user.username
        changeset_revision = self.get_repository_tip(datatypes_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."""
        dependency_path = self.generate_temp_path("test_0110", additional_paths=["simple"])
        repository = self.test_db_util.get_repository_by_name_and_owner(
            datatypes_repository_name, common.test_user_1_name
        )
        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(
            emboss_repository_name, common.test_user_1_name
        )
        url = self.url
        name = "!?invalid?!"
        owner = repository.user.username
        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."""
        dependency_path = self.generate_temp_path("test_0110", additional_paths=["simple"])
        repository = self.test_db_util.get_repository_by_name_and_owner(
            datatypes_repository_name, common.test_user_1_name
        )
        emboss_repository = self.test_db_util.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."""
        dependency_path = self.generate_temp_path("test_0110", additional_paths=["simple", "invalid"])
        repository = self.test_db_util.get_repository_by_name_and_owner(
            datatypes_repository_name, common.test_user_1_name
        )
        emboss_repository = self.test_db_util.get_repository_by_name_and_owner(
            emboss_repository_name, common.test_user_1_name
        )
        url = self.url
        name = repository.name
        owner = repository.user.username
        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,
        )