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,
)