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Source code for tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
column_maker_repository_name = "column_maker_0110"
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_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"
running_standalone = False
[docs]class TestBasicRepositoryDependencies(ShedTwillTestCase):
"""Testing emboss 5 with repository dependencies."""
requires_galaxy = True
[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)
self.login(email=common.admin_email, username=common.admin_username)
[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_dependendent_column_maker_repository_and_upload_tarball(self):
"""Create and populate the column_maker repository."""
global running_standalone
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
category = self.populator.get_category_with_name(category_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):
running_standalone = True
self.commit_tar_to_repository(
column_maker_repository,
"column_maker/column_maker.tar",
commit_message="Uploaded column_maker tarball.",
)
[docs] def test_0020_create_emboss_5_repository_and_upload_files(self):
"""Create and populate the emboss_5_0110 repository."""
global running_standalone
if running_standalone:
category = self.populator.get_category_with_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=category,
strings_displayed=[],
)
self.commit_tar_to_repository(
repository,
"emboss/emboss.tar",
commit_message="Uploaded emboss tool tarball.",
)
[docs] def test_0025_generate_repository_dependency_with_invalid_url(self):
"""Generate a repository dependency for emboss 5 with an invalid URL."""
global running_standalone
if running_standalone:
dependency_path = self.generate_temp_path("test_1110", additional_paths=["simple"])
column_maker_repository = self._get_repository_by_name_and_owner(
column_maker_repository_name, common.test_user_1_name
)
emboss_repository = self._get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
url = "http://http://this is not an url!"
name = column_maker_repository.name
owner = column_maker_repository.owner
changeset_revision = self.get_repository_tip(column_maker_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."""
global running_standalone
if running_standalone:
dependency_path = self.generate_temp_path("test_1110", additional_paths=["simple"])
repository = self._get_repository_by_name_and_owner(column_maker_repository_name, common.test_user_1_name)
emboss_repository = self._get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
url = self.url
name = "!?invalid?!"
owner = repository.owner
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."""
global running_standalone
if running_standalone:
dependency_path = self.generate_temp_path("test_1110", additional_paths=["simple"])
repository = self._get_repository_by_name_and_owner(column_maker_repository_name, common.test_user_1_name)
emboss_repository = self._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."""
global running_standalone
if running_standalone:
dependency_path = self.generate_temp_path("test_1110", additional_paths=["simple", "invalid"])
repository = self._get_repository_by_name_and_owner(column_maker_repository_name, common.test_user_1_name)
emboss_repository = self._get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
url = self.url
name = repository.name
owner = repository.owner
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,
)
[docs] def test_0045_install_repository_with_invalid_repository_dependency(self):
"""Install the repository and verify that galaxy detects invalid repository dependencies."""
repository = self._get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
preview_strings_displayed = [
"emboss_0110",
self.get_repository_tip(repository),
"Ignoring repository dependency definition",
]
self._install_repository(
emboss_repository_name,
common.test_user_1_name,
category_name,
install_tool_dependencies=False,
install_repository_dependencies=True,
preview_strings_displayed=preview_strings_displayed,
)
installed_repository = self._get_installed_repository_by_name_owner(
emboss_repository_name, common.test_user_1_name
)
json = self.display_installed_repository_manage_json(installed_repository)
assert "repository_dependencies" not in json