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Source code for tool_shed.test.functional.test_1420_tool_dependency_environment_inheritance
import logging
from ..base.twilltestcase import common, ShedTwillTestCase
log = logging.getLogger(__name__)
category_name = 'Test 1420 Tool dependency environment variable inheritance'
category_description = 'Test script 1420 for interpolation of inherited environment variables.'
package_atlas_repository_name = 'package_atlas_3_10_1420'
package_bzlib_repository_name = 'package_bzlib_1_0_1420'
package_boost_repository_name = 'package_boost_1_53_1420'
package_numpy_repository_name = 'package_numpy_1_7_1420'
package_rdkit_repository_name = 'package_rdkit_2012_12_1420'
package_lapack_repository_name = 'package_lapack_3_4_1420'
package_atlas_repository_description = 'Automatically Tuned Linear Algebra Software'
package_bzlib_repository_description = 'Contains a tool dependency definition that downloads and compiles version 1.0 of the bzlib library.'
package_boost_repository_description = 'Contains a tool dependency definition that downloads and compiles version 1.53 of the boost C++ libraries'
package_numpy_repository_description = 'Contains a tool dependency definition that downloads and compiles version 1.7 of the the python numpy package'
package_rdkit_repository_description = 'Contains a tool dependency definition that downloads and compiles version 2012-12 of the RDKit cheminformatics and machine-learning package.'
package_lapack_repository_description = 'Linear Algebra PACKage'
package_atlas_repository_long_description = f'{package_atlas_repository_name}: {package_atlas_repository_description}'
package_bzlib_repository_long_description = f'{package_bzlib_repository_name}: {package_bzlib_repository_description}'
package_boost_repository_long_description = f'{package_boost_repository_name}: {package_boost_repository_description}'
package_numpy_repository_long_description = f'{package_numpy_repository_name}: {package_numpy_repository_description}'
package_rdkit_repository_long_description = f'{package_rdkit_repository_name}: {package_rdkit_repository_description}'
package_lapack_repository_long_description = f'{package_lapack_repository_name}: {package_lapack_repository_description}'
'''
1. Create repository package_lapack_3_4_1420
2. Create repository package_atlas_3_10_1420
3. Create repository package_bzlib_1_0_1420
4. Create repository package_boost_1_53_1420
5. Create repository package_numpy_1_7_1420
6. Create repository package_rdkit_2012_12_1420
Repository dependency structure should be as follows:
Repository package_rdkit_2012_12_1420
Repository package_boost_1_53_1420 (prior install required)
Repository package_bzlib_1_0_1420 (prior install required)
Repository package_numpy_1_7_1420 (prior install required)
Repository package_lapack_3_4_1420 (prior install required)
Repository package_atlas_3_10_1420 (prior install required)
8. Install package_rdkit_2012_12 into Galaxy.
9. Verify that the env.sh file for package_rdkit_2012_12_1420 also defines the variables inherited from package_numpy_1_7_1420 and package_boost_1_53_1420.
'''
[docs]class TestEnvironmentInheritance(ShedTwillTestCase):
'''Test referencing environment variables that were defined in a separate tool dependency.'''
[docs] def test_0000_initiate_users_and_category(self):
"""Create necessary user accounts and login as an admin user."""
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)
self.create_category(name=category_name, description=category_description)
self.login(email=common.test_user_2_email, username=common.test_user_2_name)
test_user_2 = self.test_db_util.get_user(common.test_user_2_email)
assert test_user_2 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_2_email
self.test_db_util.get_private_role(test_user_2)
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)
[docs] def test_0005_create_lapack_repository(self):
'''Create and populate package_lapack_3_4_1420.'''
'''
This is step 1 - Create repository package_lapack_3_4_1420.
All tool dependency definitions should download and extract a tarball containing precompiled binaries from the local
filesystem and install them into the path specified by $INSTALL_DIR.
'''
category = self.test_db_util.get_category_by_name(category_name)
repository = self.get_or_create_repository(name=package_lapack_repository_name,
description=package_lapack_repository_description,
long_description=package_lapack_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
strings_displayed=[])
# Load the original tool dependency definition into memory, then fill in the __PATH__ placeholder with the
# actual system path where the binary tarball is found.
tool_dependency_path = self.generate_temp_path('1420_tool_dependency', additional_paths=['package_lapack_3_4_1420'])
precompiled_binary_tarball = self.get_filename('1420_files/binary_tarballs/lapack.tar')
edited_tool_dependency_filename = self.get_filename(filepath=tool_dependency_path, filename='tool_dependencies.xml')
original_tool_dependency = self.get_filename('1420_files/package_lapack_3_4_1420/tool_dependencies.xml')
tool_dependency_definition = open(original_tool_dependency).read().replace('__PATH__', precompiled_binary_tarball)
open(edited_tool_dependency_filename, 'w').write(tool_dependency_definition)
# Upload the edited tool dependency definition to the package_lapack_3_4_1420 repository.
self.upload_file(repository,
filename='tool_dependencies.xml',
filepath=tool_dependency_path,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message='Populate package_lapack_3_4_1420 with tool dependency definitions.',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0010_create_atlas_repository(self):
'''Create and populate package_atlas_3_10_1420.'''
'''
This is step 1 - Create repository package_atlas_3_10_1420.
All tool dependency definitions should download and extract a tarball containing precompiled binaries from the local
filesystem and install them into the path specified by $INSTALL_DIR.
'''
category = self.test_db_util.get_category_by_name(category_name)
repository = self.get_or_create_repository(name=package_atlas_repository_name,
description=package_atlas_repository_description,
long_description=package_atlas_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
strings_displayed=[])
# Load the original tool dependency definition into memory, then fill in the __PATH__ placeholder with the
# actual system path where the binary tarball is found.
tool_dependency_path = self.generate_temp_path('1420_tool_dependency', additional_paths=['package_atlas_3_10_1420'])
precompiled_binary_tarball = self.get_filename('1420_files/binary_tarballs/atlas.tar')
edited_tool_dependency_filename = self.get_filename(filepath=tool_dependency_path, filename='tool_dependencies.xml')
original_tool_dependency = self.get_filename('1420_files/package_atlas_3_10_1420/tool_dependencies.xml')
tool_dependency_definition = open(original_tool_dependency).read().replace('__PATH__', precompiled_binary_tarball)
open(edited_tool_dependency_filename, 'w').write(tool_dependency_definition)
# Upload the edited tool dependency definition to the package_atlas_3_10_1420 repository.
self.upload_file(repository,
filename='tool_dependencies.xml',
filepath=tool_dependency_path,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message='Populate package_atlas_3_10_1420 with tool dependency definitions.',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0015_create_bzlib_repository(self):
'''Create and populate package_bzlib_1_0_1420.'''
'''
This is step 1 - Create repository package_bzlib_1_0_1420.
All tool dependency definitions should download and extract a tarball containing precompiled binaries from the local
filesystem and install them into the path specified by $INSTALL_DIR.
'''
category = self.test_db_util.get_category_by_name(category_name)
repository = self.get_or_create_repository(name=package_bzlib_repository_name,
description=package_bzlib_repository_description,
long_description=package_bzlib_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
strings_displayed=[])
# Load the original tool dependency definition into memory, then fill in the __PATH__ placeholder with the
# actual system path where the binary tarball is found.
tool_dependency_path = self.generate_temp_path('1420_tool_dependency', additional_paths=['package_bzlib_1_0_1420'])
precompiled_binary_tarball = self.get_filename('1420_files/binary_tarballs/bzlib.tar')
edited_tool_dependency_filename = self.get_filename(filepath=tool_dependency_path, filename='tool_dependencies.xml')
original_tool_dependency = self.get_filename('1420_files/package_bzlib_1_0_1420/tool_dependencies.xml')
tool_dependency_definition = open(original_tool_dependency).read().replace('__PATH__', precompiled_binary_tarball)
open(edited_tool_dependency_filename, 'w').write(tool_dependency_definition)
# Upload the edited tool dependency definition to the package_bzlib_1_0_1420 repository.
self.upload_file(repository,
filename='tool_dependencies.xml',
filepath=tool_dependency_path,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message='Populate package_bzlib_1_0_1420 with tool dependency definitions.',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0020_create_boost_repository(self):
'''Create and populate package_boost_1_53_1420.'''
'''
This is step 1 - Create repository package_boost_1_53_1420.
All tool dependency definitions should download and extract a tarball containing precompiled binaries from the local
filesystem and install them into the path specified by $INSTALL_DIR.
'''
category = self.test_db_util.get_category_by_name(category_name)
repository = self.get_or_create_repository(name=package_boost_repository_name,
description=package_boost_repository_description,
long_description=package_boost_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
strings_displayed=[])
# Load the original tool dependency definition into memory, then fill in the __PATH__ placeholder with the
# actual system path where the binary tarball is found.
tool_dependency_path = self.generate_temp_path('1420_tool_dependency', additional_paths=['package_boost_1_53_1420'])
precompiled_binary_tarball = self.get_filename('1420_files/binary_tarballs/boost.tar')
edited_tool_dependency_filename = self.get_filename(filepath=tool_dependency_path, filename='tool_dependencies.xml')
original_tool_dependency = self.get_filename('1420_files/package_boost_1_53_1420/tool_dependencies.xml')
tool_dependency_definition = open(original_tool_dependency).read().replace('__PATH__', precompiled_binary_tarball)
open(edited_tool_dependency_filename, 'w').write(tool_dependency_definition)
# Upload the edited tool dependency definition to the package_boost_1_53_1420 repository.
self.upload_file(repository,
filename='tool_dependencies.xml',
filepath=tool_dependency_path,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message='Populate package_boost_1_53_1420 with tool dependency definitions.',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0025_create_numpy_repository(self):
'''Create and populate package_numpy_1_7_1420.'''
'''
This is step 1 - Create repository package_numpy_1_7_1420.
All tool dependency definitions should download and extract a tarball containing precompiled binaries from the local
filesystem and install them into the path specified by $INSTALL_DIR.
'''
category = self.test_db_util.get_category_by_name(category_name)
repository = self.get_or_create_repository(name=package_numpy_repository_name,
description=package_numpy_repository_description,
long_description=package_numpy_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
strings_displayed=[])
# Load the original tool dependency definition into memory, then fill in the __PATH__ placeholder with the
# actual system path where the binary tarball is found.
tool_dependency_path = self.generate_temp_path('1420_tool_dependency', additional_paths=['package_numpy_1_7_1420'])
precompiled_binary_tarball = self.get_filename('1420_files/binary_tarballs/numpy.tar')
edited_tool_dependency_filename = self.get_filename(filepath=tool_dependency_path, filename='tool_dependencies.xml')
original_tool_dependency = self.get_filename('1420_files/package_numpy_1_7_1420/tool_dependencies.xml')
tool_dependency_definition = open(original_tool_dependency).read().replace('__PATH__', precompiled_binary_tarball)
open(edited_tool_dependency_filename, 'w').write(tool_dependency_definition)
# Upload the edited tool dependency definition to the package_numpy_1_7_1420 repository.
self.upload_file(repository,
filename='tool_dependencies.xml',
filepath=tool_dependency_path,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message='Populate package_numpy_1_7_1420 with tool dependency definitions.',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0030_create_rdkit_repository(self):
'''Create and populate package_rdkit_2012_12_1420.'''
'''
This is step 1 - Create repository package_rdkit_2012_12_1420.
All tool dependency definitions should download and extract a tarball containing precompiled binaries from the local
filesystem and install them into the path specified by $INSTALL_DIR.
'''
category = self.test_db_util.get_category_by_name(category_name)
repository = self.get_or_create_repository(name=package_rdkit_repository_name,
description=package_rdkit_repository_description,
long_description=package_rdkit_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
strings_displayed=[])
# Load the original tool dependency definition into memory, then fill in the __PATH__ placeholder with the
# actual system path where the binary tarball is found.
tool_dependency_path = self.generate_temp_path('1420_tool_dependency', additional_paths=['package_rdkit_2012_12_1420'])
precompiled_binary_tarball = self.get_filename('1420_files/binary_tarballs/rdkit.tar')
edited_tool_dependency_filename = self.get_filename(filepath=tool_dependency_path, filename='tool_dependencies.xml')
original_tool_dependency = self.get_filename('1420_files/package_rdkit_2012_12_1420/tool_dependencies.xml')
tool_dependency_definition = open(original_tool_dependency).read().replace('__PATH__', precompiled_binary_tarball)
open(edited_tool_dependency_filename, 'w').write(tool_dependency_definition)
# Upload the edited tool dependency definition to the package_rdkit_2012_12_1420 repository.
self.upload_file(repository,
filename='tool_dependencies.xml',
filepath=tool_dependency_path,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message='Populate package_rdkit_2012_12_1420 with tool dependency definitions.',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0035_install_rdkit_2012_12_repository(self):
'''Install the package_rdkit_2012_12_1420 repository into Galaxy.'''
'''
This is step 4 - Install package_rdkit_2012_12_1420 into Galaxy.
Install package_rdkit_2012_12_1420 with tool dependencies selected to be installed. The result of this should be
package_atlas_3_10_1420, package_bzlib_1_0_1420, package_boost_1_53_1420, package_numpy_1_7_1420, package_rdkit_2012_12_1420,
and package_lapack_3_4_1420 being installed, and an env.sh generated for package_rdkit_2012_12_1420 that
contains environment variables defined in package_boost_1_53_1420 and package_numpy_1_7_1420.
'''
self.galaxy_login(email=common.admin_email, username=common.admin_username)
post_submit_strings_displayed = ['package_rdkit_2012_12_1420', 'package_atlas_3_10_1420', 'package_bzlib_1_0_1420',
'package_numpy_1_7_1420', 'package_lapack_3_4_1420', 'package_boost_1_53_1420']
self.install_repository('package_rdkit_2012_12_1420',
common.test_user_1_name,
category_name,
install_tool_dependencies=True,
post_submit_strings_displayed=post_submit_strings_displayed)
[docs] def test_0040_verify_env_sh_contents(self):
'''Check the env.sh file for the appropriate contents.'''
'''
This is step 5 - Verify that the env.sh file for package_rdkit_2012_12_1420 also defines the variables inherited from package_numpy_1_7_1420
and package_boost_1_53_1420. Test for the numpy and boost tool dependency paths.
'''
package_rdkit_repository = self.test_db_util.get_installed_repository_by_name_owner('package_rdkit_2012_12_1420', common.test_user_1_name)
package_numpy_repository = self.test_db_util.get_installed_repository_by_name_owner('package_numpy_1_7_1420', common.test_user_1_name)
package_boost_repository = self.test_db_util.get_installed_repository_by_name_owner('package_boost_1_53_1420', common.test_user_1_name)
rdkit_env_sh = self.get_env_sh_path(tool_dependency_name='rdkit',
tool_dependency_version='2012_12_1',
repository=package_rdkit_repository)
numpy_tool_dependency_path = self.get_tool_dependency_path(tool_dependency_name='numpy',
tool_dependency_version='1.7.1',
repository=package_numpy_repository)
boost_tool_dependency_path = self.get_tool_dependency_path(tool_dependency_name='boost',
tool_dependency_version='1.53.0',
repository=package_boost_repository)
rdkit_env_file_contents = open(rdkit_env_sh).read()
if numpy_tool_dependency_path not in rdkit_env_file_contents or boost_tool_dependency_path not in rdkit_env_file_contents:
message = 'Environment file for package_rdkit_2012_12_1420 does not contain expected path.'
message += f'\nExpected:\n{numpy_tool_dependency_path}\n{boost_tool_dependency_path}\nContents:\n{rdkit_env_file_contents}'
raise AssertionError(message)