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Source code for tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency
from ..base.twilltestcase import common, ShedTwillTestCase
datatypes_repository_name = 'emboss_datatypes_0110'
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_0110'
emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
category_name = 'Test 0110 Invalid Repository Dependencies'
category_desc = 'Test 0110 Invalid Repository Dependencies'
running_standalone = False
[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=category_name, description=category_desc)
[docs] def test_0010_create_emboss_datatypes_repository_and_upload_tarball(self):
'''Create and populate the emboss_datatypes repository.'''
global running_standalone
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
category = self.test_db_util.get_category_by_name(category_name)
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=[])
if self.repository_is_new(repository):
running_standalone = True
self.upload_file(repository,
filename='emboss/datatypes/datatypes_conf.xml',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
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_0110 repository.'''
global running_standalone
if running_standalone:
category = self.test_db_util.get_category_by_name(category_name)
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 tool tarball.',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0025_generate_repository_dependency_with_invalid_url(self):
'''Generate a repository dependency for emboss 5 with an invalid URL.'''
global running_standalone
if running_standalone:
dependency_path = self.generate_temp_path('test_1110', additional_paths=['simple'])
datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
url = 'http://http://this is not an url!'
name = datatypes_repository.name
owner = datatypes_repository.user.username
changeset_revision = self.get_repository_tip(datatypes_repository)
strings_displayed = ['Repository dependencies are currently supported only within the same tool shed']
repository_tuple = (url, name, owner, changeset_revision)
self.create_repository_dependency(repository=emboss_repository,
filepath=dependency_path,
repository_tuples=[repository_tuple],
strings_displayed=strings_displayed,
complex=False)
[docs] def test_0030_generate_repository_dependency_with_invalid_name(self):
'''Generate a repository dependency for emboss 5 with an invalid name.'''
global running_standalone
if running_standalone:
dependency_path = self.generate_temp_path('test_1110', additional_paths=['simple'])
repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
url = self.url
name = '!?invalid?!'
owner = repository.user.username
changeset_revision = self.get_repository_tip(repository)
strings_displayed = ['because the name is invalid.']
repository_tuple = (url, name, owner, changeset_revision)
self.create_repository_dependency(repository=emboss_repository,
filepath=dependency_path,
repository_tuples=[repository_tuple],
strings_displayed=strings_displayed,
complex=False)
[docs] def test_0035_generate_repository_dependency_with_invalid_owner(self):
'''Generate a repository dependency for emboss 5 with an invalid owner.'''
global running_standalone
if running_standalone:
dependency_path = self.generate_temp_path('test_1110', additional_paths=['simple'])
repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
url = self.url
name = repository.name
owner = '!?invalid?!'
changeset_revision = self.get_repository_tip(repository)
strings_displayed = ['because the owner is invalid.']
repository_tuple = (url, name, owner, changeset_revision)
self.create_repository_dependency(repository=emboss_repository,
filepath=dependency_path,
repository_tuples=[repository_tuple],
strings_displayed=strings_displayed,
complex=False)
[docs] def test_0040_generate_repository_dependency_with_invalid_changeset_revision(self):
'''Generate a repository dependency for emboss 5 with an invalid changeset revision.'''
global running_standalone
if running_standalone:
dependency_path = self.generate_temp_path('test_1110', additional_paths=['simple', 'invalid'])
repository = self.test_db_util.get_repository_by_name_and_owner(datatypes_repository_name, common.test_user_1_name)
emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
url = self.url
name = repository.name
owner = repository.user.username
changeset_revision = '!?invalid?!'
strings_displayed = ['because the changeset revision is invalid.']
repository_tuple = (url, name, owner, changeset_revision)
self.create_repository_dependency(repository=emboss_repository,
filepath=dependency_path,
repository_tuples=[repository_tuple],
strings_displayed=strings_displayed,
complex=False)
[docs] def test_0045_install_repository_with_invalid_repository_dependency(self):
'''Install the repository and verify that galaxy detects invalid repository dependencies.'''
self.galaxy_login(email=common.admin_email, username=common.admin_username)
repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
preview_strings_displayed = ['emboss_0110', self.get_repository_tip(repository), 'Ignoring repository dependency definition']
self.install_repository(emboss_repository_name,
common.test_user_1_name,
category_name,
install_tool_dependencies=False,
install_repository_dependencies=True,
preview_strings_displayed=preview_strings_displayed,
post_submit_strings_displayed=[repository.name, repository.name, 'New'],
includes_tools_for_display_in_tool_panel=True)
installed_repository = self.test_db_util.get_installed_repository_by_name_owner(emboss_repository_name, common.test_user_1_name)
self.display_installed_repository_manage_page(installed_repository=installed_repository,
strings_displayed=[],
strings_not_displayed=['Repository dependencies'])