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Source code for tool_shed.test.functional.test_0020_basic_repository_dependencies
from ..base.twilltestcase import common, ShedTwillTestCase
datatypes_repository_name = 'emboss_datatypes_0020'
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_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)
test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_1_email
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, 'Problem retrieving user with email %s from the database' % common.admin_email
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='Test 0020 Basic Repository Dependencies', description='Testing basic repository dependency features.')
[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('Test 0020 Basic Repository Dependencies')
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=False,
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_0020 repository.'''
category = self.test_db_util.get_category_by_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_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.tar',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0025_generate_and_upload_repository_dependencies_xml(self):
'''Generate and upload the repository_dependencies.xml file'''
repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
repository_dependencies_path = self.generate_temp_path('test_0020', additional_paths=['emboss', '5'])
repository_tuple = (self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip(datatypes_repository))
self.create_repository_dependency(repository=repository, repository_tuples=[repository_tuple], filepath=repository_dependencies_path)
[docs] 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.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
changeset_revision = self.get_repository_tip(datatypes_repository)
strings_displayed = ['Tool dependencies',
'emboss',
'5.0.0',
'package',
'emboss_datatypes_0020',
'user1',
changeset_revision,
'Repository dependencies']
self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
[docs] def test_0040_verify_repository_metadata(self):
'''Verify that resetting the metadata does not change it.'''
emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
self.verify_unchanged_repository_metadata(emboss_repository)
self.verify_unchanged_repository_metadata(datatypes_repository)