Warning
This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.
Source code for tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies
import os
from ..base.twilltestcase import common, ShedTwillTestCase
bwa_base_repository_name = 'bwa_base_repository_0100'
bwa_base_repository_description = "BWA Base"
bwa_base_repository_long_description = "BWA tool that depends on bwa 0.5.9, with a complex repository dependency pointing at package_bwa_0_5_9_0100"
bwa_package_repository_name = 'package_bwa_0_5_9_0100'
bwa_package_repository_description = "BWA Package"
bwa_package_repository_long_description = "BWA repository with a package tool dependency defined to compile and install BWA 0.5.9."
category_name = 'Test 0100 Complex Repository Dependencies'
category_description = 'Test 0100 Complex Repository Dependencies'
running_standalone = False
[docs]class TestInstallingComplexRepositoryDependencies(ShedTwillTestCase):
'''Test features related to installing repositories with complex 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)
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_bwa_package_repository(self):
'''Create and populate package_bwa_0_5_9_0100.'''
global running_standalone
category = self.create_category(name=category_name, description=category_description)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
repository = self.get_or_create_repository(name=bwa_package_repository_name,
description=bwa_package_repository_description,
long_description=bwa_package_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
old_tool_dependency = self.get_filename(os.path.join('bwa', 'complex', 'tool_dependencies.xml'))
new_tool_dependency_path = self.generate_temp_path('test_1100', additional_paths=['tool_dependency'])
xml_filename = os.path.abspath(os.path.join(new_tool_dependency_path, 'tool_dependencies.xml'))
open(xml_filename, 'w').write(open(old_tool_dependency)
.read().replace('__PATH__', self.get_filename('bwa/complex')))
self.upload_file(repository,
filename=xml_filename,
filepath=new_tool_dependency_path,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded tool_dependencies.xml.',
strings_displayed=['This repository currently contains a single file named <b>tool_dependencies.xml</b>'],
strings_not_displayed=[])
self.display_manage_repository_page(repository, strings_displayed=['Tool dependencies', 'consider setting its type'])
[docs] def test_0010_create_bwa_base_repository(self):
'''Create and populate bwa_base_0100.'''
global running_standalone
if running_standalone:
category = self.create_category(name=category_name, description=category_description)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
repository = self.get_or_create_repository(name=bwa_base_repository_name,
description=bwa_base_repository_description,
long_description=bwa_base_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
strings_displayed=[])
self.test_db_util.get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name)
self.upload_file(repository,
filename='bwa/complex/bwa_base.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded bwa_base.tar with tool wrapper XML, but without tool dependency XML.',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0015_generate_complex_repository_dependency_invalid_shed_url(self):
'''Generate and upload a complex repository definition that specifies an invalid tool shed URL.'''
global running_standalone
if running_standalone:
dependency_path = self.generate_temp_path('test_0100', additional_paths=['complex', 'shed'])
base_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
tool_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name)
url = 'http://http://this is not an url!'
name = tool_repository.name
owner = tool_repository.user.username
changeset_revision = self.get_repository_tip(tool_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=base_repository,
filepath=dependency_path,
repository_tuples=[repository_tuple],
strings_displayed=strings_displayed,
complex=True,
package='bwa',
version='0.5.9')
[docs] def test_0020_generate_complex_repository_dependency_invalid_repository_name(self):
'''Generate and upload a complex repository definition that specifies an invalid repository name.'''
global running_standalone
if running_standalone:
dependency_path = self.generate_temp_path('test_0100', additional_paths=['complex', 'shed'])
base_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
tool_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name)
url = self.url
name = 'invalid_repository!?'
owner = tool_repository.user.username
changeset_revision = self.get_repository_tip(tool_repository)
strings_displayed = ['because the name is invalid.']
repository_tuple = (url, name, owner, changeset_revision)
self.create_repository_dependency(repository=base_repository,
filepath=dependency_path,
repository_tuples=[repository_tuple],
strings_displayed=strings_displayed,
complex=True,
package='bwa',
version='0.5.9')
[docs] def test_0025_generate_complex_repository_dependency_invalid_owner_name(self):
'''Generate and upload a complex repository definition that specifies an invalid owner.'''
global running_standalone
if running_standalone:
dependency_path = self.generate_temp_path('test_0100', additional_paths=['complex', 'shed'])
base_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
tool_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name)
url = self.url
name = tool_repository.name
owner = 'invalid_owner!?'
changeset_revision = self.get_repository_tip(tool_repository)
strings_displayed = ['because the owner is invalid.']
repository_tuple = (url, name, owner, changeset_revision)
self.create_repository_dependency(repository=base_repository,
filepath=dependency_path,
repository_tuples=[repository_tuple],
strings_displayed=strings_displayed,
complex=True,
package='bwa',
version='0.5.9')
[docs] def test_0030_generate_complex_repository_dependency_invalid_changeset_revision(self):
'''Generate and upload a complex repository definition that specifies an invalid changeset revision.'''
global running_standalone
if running_standalone:
dependency_path = self.generate_temp_path('test_0100', additional_paths=['complex', 'shed'])
base_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
tool_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name)
url = self.url
name = tool_repository.name
owner = tool_repository.user.username
changeset_revision = '1234abcd'
strings_displayed = ['because the changeset revision is invalid.']
repository_tuple = (url, name, owner, changeset_revision)
self.create_repository_dependency(repository=base_repository,
filepath=dependency_path,
repository_tuples=[repository_tuple],
strings_displayed=strings_displayed,
complex=True,
package='bwa',
version='0.5.9')
[docs] def test_0035_generate_valid_complex_repository_dependency(self):
'''Generate and upload a valid tool_dependencies.xml file that specifies package_bwa_0_5_9_0100.'''
global running_standalone
if running_standalone:
base_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
tool_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name)
dependency_path = self.generate_temp_path('test_0100', additional_paths=['complex'])
url = self.url
name = tool_repository.name
owner = tool_repository.user.username
changeset_revision = self.get_repository_tip(tool_repository)
repository_tuple = (url, name, owner, changeset_revision)
self.create_repository_dependency(repository=base_repository,
filepath=dependency_path,
repository_tuples=[repository_tuple],
complex=True,
package='bwa',
version='0.5.9')
self.check_repository_dependency(base_repository, tool_repository)
self.display_manage_repository_page(base_repository, strings_displayed=['bwa', '0.5.9', 'package'])
[docs] def test_0040_update_tool_repository(self):
'''Upload a new tool_dependencies.xml to the tool repository, and verify that the base repository displays the new changeset.'''
global running_standalone
if running_standalone:
base_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
tool_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name)
previous_changeset = self.get_repository_tip(tool_repository)
old_tool_dependency = self.get_filename(os.path.join('bwa', 'complex', 'readme', 'tool_dependencies.xml'))
new_tool_dependency_path = self.generate_temp_path('test_1100', additional_paths=['tool_dependency'])
xml_filename = os.path.abspath(os.path.join(new_tool_dependency_path, 'tool_dependencies.xml'))
open(xml_filename, 'w').write(open(old_tool_dependency)
.read().replace('__PATH__', self.get_filename('bwa/complex')))
self.upload_file(tool_repository,
filename=xml_filename,
filepath=new_tool_dependency_path,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded new tool_dependencies.xml.',
strings_displayed=[],
strings_not_displayed=[])
# Verify that the dependency display has been updated as a result of the new tool_dependencies.xml file.
self.display_manage_repository_page(base_repository,
strings_displayed=[self.get_repository_tip(tool_repository), 'bwa', '0.5.9', 'package'],
strings_not_displayed=[previous_changeset])
[docs] def test_0045_install_base_repository(self):
'''Verify installation of the repository with complex repository dependencies.'''
self.galaxy_login(email=common.admin_email, username=common.admin_username)
base_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_base_repository_name, common.test_user_1_name)
tool_repository = self.test_db_util.get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name)
preview_strings_displayed = [tool_repository.name, self.get_repository_tip(tool_repository)]
self.install_repository(bwa_base_repository_name,
common.test_user_1_name,
category_name,
install_tool_dependencies=True,
preview_strings_displayed=preview_strings_displayed,
post_submit_strings_displayed=[base_repository.name, tool_repository.name, 'New'],
includes_tools_for_display_in_tool_panel=True)
[docs] def test_0050_verify_installed_repositories(self):
'''Verify that the installed repositories are displayed properly.'''
base_repository = self.test_db_util.get_installed_repository_by_name_owner(bwa_base_repository_name, common.test_user_1_name)
tool_repository = self.test_db_util.get_installed_repository_by_name_owner(bwa_package_repository_name, common.test_user_1_name)
strings_displayed = ['bwa_base_repository_0100', 'user1', base_repository.installed_changeset_revision]
strings_displayed.extend(['package_bwa_0_5_9_0100', 'user1', tool_repository.installed_changeset_revision])
strings_displayed.append(self.url.replace('http://', ''))
self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed, strings_not_displayed=[])
strings_displayed = ['package_bwa_0_5_9_0100', 'user1', tool_repository.installed_changeset_revision]
strings_not_displayed = ['Missing tool dependencies']
self.display_installed_repository_manage_page(tool_repository,
strings_displayed=strings_displayed,
strings_not_displayed=strings_not_displayed)
strings_displayed = ['bwa_base_repository_0100',
'user1',
'package_bwa_0_5_9_0100',
base_repository.installed_changeset_revision,
tool_repository.installed_changeset_revision]
strings_not_displayed = ['Missing tool dependencies']
self.display_installed_repository_manage_page(base_repository,
strings_displayed=strings_displayed,
strings_not_displayed=strings_not_displayed)
[docs] def test_0055_verify_complex_tool_dependency(self):
'''Verify that the generated env.sh contains the right data.'''
base_repository = self.test_db_util.get_installed_repository_by_name_owner(bwa_base_repository_name, common.test_user_1_name)
tool_repository = self.test_db_util.get_installed_repository_by_name_owner(bwa_package_repository_name, common.test_user_1_name)
env_sh_path = self.get_env_sh_path(tool_dependency_name='bwa',
tool_dependency_version='0.5.9',
repository=base_repository)
assert os.path.exists(env_sh_path), 'env.sh was not generated in %s for this dependency.' % env_sh_path
contents = open(env_sh_path).read()
if tool_repository.installed_changeset_revision not in contents:
raise AssertionError('Installed changeset revision %s not found in env.sh.\nContents of env.sh: %s' %
(tool_repository.installed_changeset_revision, contents))
if 'package_bwa_0_5_9_0100' not in contents:
raise AssertionError('Repository name package_bwa_0_5_9_0100 not found in env.sh.\nContents of env.sh: %s' % contents)
[docs] def test_0060_verify_tool_dependency_uninstallation(self):
'''Uninstall the package_bwa_0_5_9_0100 repository.'''
'''
Uninstall the repository that defines a tool dependency relationship on BWA 0.5.9, and verify
that this results in the compiled binary package also being removed.
'''
tool_repository = self.test_db_util.get_installed_repository_by_name_owner(bwa_package_repository_name, common.test_user_1_name)
self.deactivate_repository(tool_repository)
env_sh_path = os.path.join(self.galaxy_tool_dependency_dir,
'bwa',
'0.5.9',
tool_repository.owner,
tool_repository.name,
tool_repository.installed_changeset_revision,
'env.sh')
assert os.path.exists(env_sh_path), 'Path %s does not exist after deactivating the repository that generated it.' % env_sh_path