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Source code for tool_shed.test.functional.test_0030_repository_dependency_revisions
from ..base.twilltestcase import common, ShedTwillTestCase
datatypes_repository_name = 'emboss_datatypes_0030'
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_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'
[docs]class TestRepositoryDependencyRevisions(ShedTwillTestCase):
'''Test dependencies on different revisions of a repository.'''
[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)
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 0030 Repository Dependency Revisions', description='Testing repository dependencies by revision.')
[docs] def test_0010_create_emboss_5_repository(self):
'''Create and populate the emboss_5_0030 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 0030 Repository Dependency Revisions')
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_id=self.security.encode_id(category.id))
self.upload_file(repository,
filename='emboss/emboss.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded tool tarball.',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0015_create_emboss_6_repository(self):
'''Create and populate the emboss_6_0030 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 0030 Repository Dependency Revisions')
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_id=self.security.encode_id(category.id))
self.upload_file(repository,
filename='emboss/emboss.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded tool tarball.',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0020_create_emboss_datatypes_repository(self):
'''Create and populate the emboss_datatypes_0030 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 0030 Repository Dependency Revisions')
repository = self.get_or_create_repository(name=datatypes_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))
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_0025_create_emboss_repository(self):
'''Create and populate the emboss_0030 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 0030 Repository Dependency Revisions')
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))
self.upload_file(repository,
filename='emboss/emboss.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded the tool tarball.',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0030_generate_repository_dependencies_for_emboss_5(self):
'''Generate a repository_dependencies.xml file specifying emboss_datatypes and upload it to the emboss_5 repository.'''
datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
emboss_5_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_5_repository_name, common.test_user_1_name)
repository_dependencies_path = self.generate_temp_path('test_0030', additional_paths=['emboss5'])
datatypes_tuple = (self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip(datatypes_repository))
self.create_repository_dependency(repository=emboss_5_repository, repository_tuples=[datatypes_tuple], filepath=repository_dependencies_path)
[docs] def test_0035_generate_repository_dependencies_for_emboss_6(self):
'''Generate a repository_dependencies.xml file specifying emboss_datatypes and upload it to the emboss_6 repository.'''
emboss_6_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_6_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_0030', additional_paths=['emboss6'])
datatypes_tuple = (self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip(datatypes_repository))
self.create_repository_dependency(repository=emboss_6_repository, repository_tuples=[datatypes_tuple], filepath=repository_dependencies_path)
[docs] def test_0040_generate_repository_dependency_on_emboss_5(self):
'''Create and upload repository_dependencies.xml for the emboss_5_0030 repository.'''
emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
emboss_5_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_5_repository_name, common.test_user_1_name)
repository_dependencies_path = self.generate_temp_path('test_0030', additional_paths=['emboss', '5'])
emboss_tuple = (self.url, emboss_5_repository.name, emboss_5_repository.user.username, self.get_repository_tip(emboss_5_repository))
self.create_repository_dependency(repository=emboss_repository, repository_tuples=[emboss_tuple], filepath=repository_dependencies_path)
[docs] def test_0045_generate_repository_dependency_on_emboss_6(self):
'''Create and upload repository_dependencies.xml for the emboss_6_0030 repository.'''
emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
emboss_6_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_6_repository_name, common.test_user_1_name)
repository_dependencies_path = self.generate_temp_path('test_0030', additional_paths=['emboss', '5'])
emboss_tuple = (self.url, emboss_6_repository.name, emboss_6_repository.user.username, self.get_repository_tip(emboss_6_repository))
self.create_repository_dependency(repository=emboss_repository, repository_tuples=[emboss_tuple], filepath=repository_dependencies_path)
[docs] def test_0050_verify_repository_dependency_revisions(self):
'''Verify that different metadata revisions of the emboss repository have different repository dependencies.'''
repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
repository_metadata = [(metadata.metadata, metadata.changeset_revision) for metadata in self.get_repository_metadata(repository)]
datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
datatypes_tip = self.get_repository_tip(datatypes_repository)
strings_displayed = []
# Iterate through all metadata revisions and check for repository dependencies.
for _metadata, changeset_revision in repository_metadata:
# Add the dependency description and datatypes repository details to the strings to check.
strings_displayed = ['emboss_datatypes_0030', 'user1', datatypes_tip]
strings_displayed.extend(['Tool dependencies', 'emboss', '5.0.0', 'package'])
self.display_manage_repository_page(repository,
changeset_revision=changeset_revision,
strings_displayed=strings_displayed)
[docs] def test_0055_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)
emboss_5_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_5_repository_name, common.test_user_1_name)
emboss_6_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_6_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)
for repository in [emboss_repository, emboss_5_repository, emboss_6_repository, datatypes_repository]:
self.verify_unchanged_repository_metadata(repository)