from ..base.twilltestcase import (
common,
ShedTwillTestCase,
)
column_repository_name = "column_maker_1087"
column_repository_description = "Add column"
column_repository_long_description = "Compute an expression on every row"
convert_repository_name = "convert_chars_1087"
convert_repository_description = "Convert delimiters"
convert_repository_long_description = "Convert delimiters to tab"
category_name = "Test 1087 Advanced Circular Dependencies"
category_description = "Test circular dependency features"
[docs]class TestRepositoryDependencies(ShedTwillTestCase):
"""Test installing a repository, then updating it to include repository dependencies."""
[docs] def test_0000_create_or_login_admin_user(self):
"""Create necessary user accounts and login as an admin user."""
self.galaxy_login(email=common.admin_email, username=common.admin_username)
galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
assert (
galaxy_admin_user is not None
), f"Problem retrieving user with email {common.admin_email} from the database"
self.test_db_util.get_galaxy_private_role(galaxy_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_and_populate_column_repository(self):
"""Create a category for this test suite and add repositories to it."""
category = self.create_category(name=category_name, description=category_description)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
repository = self.get_or_create_repository(
name=column_repository_name,
description=column_repository_description,
long_description=column_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
strings_displayed=[],
)
if self.repository_is_new(repository):
self.upload_file(
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=[],
)
[docs] def test_0010_create_and_populate_convert_repository(self):
"""Create and populate the convert_chars repository."""
self.login(email=common.admin_email, username=common.admin_username)
category = self.create_category(name=category_name, description=category_description)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
repository = self.get_or_create_repository(
name=convert_repository_name,
description=convert_repository_description,
long_description=convert_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
strings_displayed=[],
)
if self.repository_is_new(repository):
self.upload_file(
repository,
filename="convert_chars/convert_chars.tar",
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message="Uploaded convert_chars tarball.",
strings_displayed=[],
strings_not_displayed=[],
)
[docs] def test_0015_install_and_uninstall_column_repository(self):
"""Install and uninstall the column_maker repository."""
self.galaxy_login(email=common.admin_email, username=common.admin_username)
self.install_repository(
column_repository_name,
common.test_user_1_name,
category_name,
install_tool_dependencies=False,
install_repository_dependencies=True,
new_tool_panel_section_label="column_maker",
strings_not_displayed=["install_repository_dependencies"],
)
installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(
column_repository_name, common.test_user_1_name
)
self.uninstall_repository(installed_column_repository)
[docs] def test_0020_upload_dependency_xml(self):
"""Upload a repository_dependencies.xml file to column_maker that specifies convert_chars."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
convert_repository = self.test_db_util.get_repository_by_name_and_owner(
convert_repository_name, common.test_user_1_name
)
column_repository = self.test_db_util.get_repository_by_name_and_owner(
column_repository_name, common.test_user_1_name
)
repository_dependencies_path = self.generate_temp_path("test_1085", additional_paths=["column"])
convert_tuple = (
self.url,
convert_repository.name,
convert_repository.user.username,
self.get_repository_tip(convert_repository),
)
self.create_repository_dependency(
repository=column_repository, repository_tuples=[convert_tuple], filepath=repository_dependencies_path
)
[docs] def test_0025_verify_repository_dependency(self):
"""Verify that the new revision of column_maker now depends on convert_chars."""
convert_repository = self.test_db_util.get_repository_by_name_and_owner(
convert_repository_name, common.test_user_1_name
)
column_repository = self.test_db_util.get_repository_by_name_and_owner(
column_repository_name, common.test_user_1_name
)
self.check_repository_dependency(column_repository, convert_repository)
[docs] def test_0030_reinstall_column_repository(self):
"""Reinstall column_maker and verify that it now shows repository dependencies."""
self.galaxy_login(email=common.admin_email, username=common.admin_username)
installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner(
column_repository_name, common.test_user_1_name
)
convert_repository = self.test_db_util.get_repository_by_name_and_owner(
convert_repository_name, common.test_user_1_name
)
strings_displayed = [
"Handle repository dependencies",
"convert_chars_1087",
self.get_repository_tip(convert_repository),
]
# Due to twill's limitations, only check for strings on the (redirected) reselect tool panel section page, don't actually reinstall.
params = dict(id=self.security.encode_id(installed_column_repository.id))
url = "/admin_toolshed/restore_repository"
self.visit_galaxy_url(url, params)
self.check_for_strings(strings_displayed)
strings_not_displayed = ["column_maker_1087"]
self.display_galaxy_browse_repositories_page(strings_not_displayed=strings_not_displayed)