from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
column_maker_repository_name = "column_maker_0030"
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_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"
running_standalone = False
[docs]class TestRepositoryWithDependencyRevisions(ShedTwillTestCase):
"""Test installing a repository with dependency revisions."""
requires_galaxy = True
[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)
self.login(email=common.admin_email, username=common.admin_username)
[docs] def test_0005_ensure_repositories_and_categories_exist(self):
"""Create the 0030 category and add repositories to it, if necessary."""
global running_standalone
category = self.create_category(
name="Test 0030 Repository Dependency Revisions", description="Test 0030 Repository Dependency Revisions"
)
self.login(email=common.test_user_1_email, username=common.test_user_1_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.",
)
emboss_5_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=category,
strings_displayed=[],
)
self.commit_tar_to_repository(
emboss_5_repository,
"emboss/emboss.tar",
commit_message="Uploaded tool tarball.",
)
repository_dependencies_path = self.generate_temp_path("test_1030", additional_paths=["emboss", "5"])
column_maker_tuple = (
self.url,
column_maker_repository.name,
column_maker_repository.owner,
self.get_repository_tip(column_maker_repository),
)
self.create_repository_dependency(
repository=emboss_5_repository,
repository_tuples=[column_maker_tuple],
filepath=repository_dependencies_path,
)
emboss_6_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=category,
strings_displayed=[],
)
self.commit_tar_to_repository(
emboss_6_repository,
"emboss/emboss.tar",
commit_message="Uploaded tool tarball.",
)
repository_dependencies_path = self.generate_temp_path("test_1030", additional_paths=["emboss", "6"])
column_maker_tuple = (
self.url,
column_maker_repository.name,
column_maker_repository.owner,
self.get_repository_tip(column_maker_repository),
)
self.create_repository_dependency(
repository=emboss_6_repository,
repository_tuples=[column_maker_tuple],
filepath=repository_dependencies_path,
)
emboss_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(
emboss_repository,
"emboss/emboss.tar",
commit_message="Uploaded tool tarball.",
)
repository_dependencies_path = self.generate_temp_path("test_1030", additional_paths=["emboss", "5"])
dependency_tuple = (
self.url,
emboss_5_repository.name,
emboss_5_repository.owner,
self.get_repository_tip(emboss_5_repository),
)
self.create_repository_dependency(
repository=emboss_repository,
repository_tuples=[dependency_tuple],
filepath=repository_dependencies_path,
)
dependency_tuple = (
self.url,
emboss_6_repository.name,
emboss_6_repository.owner,
self.get_repository_tip(emboss_6_repository),
)
self.create_repository_dependency(
repository=emboss_repository,
repository_tuples=[dependency_tuple],
filepath=repository_dependencies_path,
)
[docs] def test_0015_install_emboss_repository(self):
"""Install the emboss repository without installing tool dependencies."""
global running_standalone
self._install_repository(
emboss_repository_name,
common.test_user_1_name,
"Test 0030 Repository Dependency Revisions",
install_tool_dependencies=False,
new_tool_panel_section_label="test_1030",
)
installed_repository = self._get_installed_repository_by_name_owner(
emboss_repository_name, common.test_user_1_name
)
assert self._get_installed_repository_for(
common.test_user_1, emboss_repository_name, installed_repository.installed_changeset_revision
)
self._assert_repo_has_tool_with_id(installed_repository, "EMBOSS: antigenic1")
self._assert_has_valid_tool_with_name("antigenic")
self.update_installed_repository(installed_repository, verify_no_updates=True)