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Source code for tool_shed.test.functional.test_0040_repository_circular_dependencies
from ..base.twilltestcase import (
common,
ShedTwillTestCase,
)
freebayes_repository_name = "freebayes_0040"
freebayes_repository_description = "Galaxy's freebayes tool for test 0040"
freebayes_repository_long_description = "Long description of Galaxy's freebayes tool for test 0040"
filtering_repository_name = "filtering_0040"
filtering_repository_description = "Galaxy's filtering tool for test 0040"
filtering_repository_long_description = "Long description of Galaxy's filtering tool for test 0040"
CATEGORY_NAME = "test_0040_repository_circular_dependencies"
CATEGORY_DESC = "Testing handling of circular repository dependencies."
[docs]class TestRepositoryCircularDependencies(ShedTwillTestCase):
"""Verify that the code correctly displays repositories with circular repository dependencies."""
[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_create_category(self):
"""Create a category for this test suite"""
self.create_category(
name=CATEGORY_NAME,
description=CATEGORY_DESC,
)
[docs] def test_0010_create_freebayes_repository(self):
"""Create and populate freebayes_0040."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
category = self.populator.get_category_with_name(CATEGORY_NAME)
repository = self.get_or_create_repository(
name=freebayes_repository_name,
description=freebayes_repository_description,
long_description=freebayes_repository_long_description,
owner=common.test_user_1_name,
category=category,
strings_displayed=[],
)
self.upload_file(
repository,
filename="freebayes/freebayes.tar",
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message="Uploaded the tool tarball.",
strings_displayed=[],
strings_not_displayed=[],
)
[docs] def test_0015_create_filtering_repository(self):
"""Create and populate filtering_0040."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
category = self.populator.get_category_with_name(CATEGORY_NAME)
repository = self.get_or_create_repository(
name=filtering_repository_name,
description=filtering_repository_description,
long_description=filtering_repository_long_description,
owner=common.test_user_1_name,
category=category,
strings_displayed=[],
)
self.upload_file(
repository,
filename="filtering/filtering_1.1.0.tar",
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message="Uploaded the tool tarball for filtering 1.1.0.",
strings_displayed=[],
strings_not_displayed=[],
)
[docs] def test_0020_create_dependency_on_freebayes(self):
"""Upload a repository_dependencies.xml file that specifies the current revision of freebayes to the filtering_0040 repository."""
# The dependency structure should look like:
# Filtering revision 0 -> freebayes revision 0.
# Freebayes revision 0 -> filtering revision 1.
# Filtering will have two revisions, one with just the filtering tool, and one with the filtering tool and a dependency on freebayes.
repository = self._get_repository_by_name_and_owner(freebayes_repository_name, common.test_user_1_name)
filtering_repository = self._get_repository_by_name_and_owner(
filtering_repository_name, common.test_user_1_name
)
repository_dependencies_path = self.generate_temp_path("test_0040", additional_paths=["filtering"])
repository_tuple = (self.url, repository.name, repository.owner, self.get_repository_tip(repository))
self.create_repository_dependency(
repository=filtering_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path
)
[docs] def test_0025_create_dependency_on_filtering(self):
"""Upload a repository_dependencies.xml file that specifies the current revision of filtering to the freebayes_0040 repository."""
# The dependency structure should look like:
# Filtering revision 0 -> freebayes revision 0.
# Freebayes revision 0 -> filtering revision 1.
# Filtering will have two revisions, one with just the filtering tool, and one with the filtering tool and a dependency on freebayes.
repository = self._get_repository_by_name_and_owner(filtering_repository_name, common.test_user_1_name)
freebayes_repository = self._get_repository_by_name_and_owner(
freebayes_repository_name, common.test_user_1_name
)
repository_dependencies_path = self.generate_temp_path("test_0040", additional_paths=["freebayes"])
repository_tuple = (self.url, repository.name, repository.owner, self.get_repository_tip(repository))
self.create_repository_dependency(
repository=freebayes_repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path
)
[docs] def test_0030_verify_repository_dependencies(self):
"""Verify that each repository can depend on the other without causing an infinite loop."""
filtering_repository = self._get_repository_by_name_and_owner(
filtering_repository_name, common.test_user_1_name
)
freebayes_repository = self._get_repository_by_name_and_owner(
freebayes_repository_name, common.test_user_1_name
)
# The dependency structure should look like:
# Filtering revision 0 -> freebayes revision 0.
# Freebayes revision 0 -> filtering revision 1.
# Filtering will have two revisions, one with just the filtering tool, and one with the filtering tool and a dependency on freebayes.
# In this case, the displayed dependency will specify the tip revision, but this will not always be the case.
self.check_repository_dependency(
filtering_repository, freebayes_repository, self.get_repository_tip(freebayes_repository)
)
self.check_repository_dependency(
freebayes_repository, filtering_repository, self.get_repository_tip(filtering_repository)
)
[docs] def test_0035_verify_repository_metadata(self):
"""Verify that resetting the metadata does not change it."""
freebayes_repository = self._get_repository_by_name_and_owner(
freebayes_repository_name, common.test_user_1_name
)
filtering_repository = self._get_repository_by_name_and_owner(
filtering_repository_name, common.test_user_1_name
)
for repository in [freebayes_repository, filtering_repository]:
self.verify_unchanged_repository_metadata(repository)
[docs] def test_0040_verify_tool_dependencies(self):
"""Verify that freebayes displays tool dependencies."""
repository = self._get_repository_by_name_and_owner(freebayes_repository_name, common.test_user_1_name)
self.display_manage_repository_page(
repository,
strings_displayed=["freebayes", "0.9.4_9696d0ce8a9", "samtools", "0.1.18", "Valid tools", "package"],
strings_not_displayed=["Invalid tools"],
)