from ..base import common
from ..base.api import skip_if_api_v2
from ..base.twilltestcase import ShedTwillTestCase
column_maker_repository_name = "column_maker_0020"
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_0020"
emboss_repository_description = "Galaxy wrappers for Emboss version 5.0.0 tools for test 0020"
emboss_repository_long_description = "Galaxy wrappers for Emboss version 5.0.0 tools for test 0020"
[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)
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="Test 0020 Basic Repository Dependencies", description="Testing basic repository dependency features."
)
[docs] def test_0010_create_column_maker_repository(self):
"""Create and populate column_maker_0020."""
category = self.populator.get_category_with_name("Test 0020 Basic Repository Dependencies")
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=[],
)
self.commit_tar_to_repository(column_maker_repository, "column_maker/column_maker.tar")
[docs] def test_0020_create_emboss_5_repository_and_upload_files(self):
"""Create and populate the emboss_5_0020 repository."""
category = self.populator.get_category_with_name("Test 0020 Basic Repository Dependencies")
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")
[docs] def test_0025_generate_and_upload_repository_dependencies_xml(self):
"""Generate and upload the repository_dependencies.xml file"""
repository = self._get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
column_maker_repository = self._get_repository_by_name_and_owner(
column_maker_repository_name, common.test_user_1_name
)
repository_dependencies_path = self.generate_temp_path("test_0020", additional_paths=["emboss", "5"])
repository_tuple = (
self.url,
column_maker_repository.name,
column_maker_repository.owner,
self.get_repository_tip(column_maker_repository),
)
self.create_repository_dependency(
repository=repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path
)
[docs] @skip_if_api_v2
def test_0030_verify_emboss_5_dependencies(self):
"""Verify that the emboss_5 repository now depends on the emboss_datatypes repository with correct name, owner, and changeset revision."""
repository = self._get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
column_maker_repository = self._get_repository_by_name_and_owner(
column_maker_repository_name, common.test_user_1_name
)
changeset_revision = self.get_repository_tip(column_maker_repository)
strings_displayed = [
"Tool dependencies",
"emboss",
"5.0.0",
"package",
"user1",
changeset_revision,
"Repository dependencies",
]
self.display_manage_repository_page(repository, strings_displayed=strings_displayed)