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Source code for tool_shed.galaxy_install.utility_containers
import logging
import threading
from tool_shed.utility_containers import utility_container_manager
log = logging.getLogger(__name__)
[docs]class GalaxyUtilityContainerManager(utility_container_manager.UtilityContainerManager):
[docs] def build_repository_containers(self, repository, datatypes, invalid_tools, missing_repository_dependencies,
missing_tool_dependencies, readme_files_dict, repository_dependencies,
tool_dependencies, valid_tools, workflows, valid_data_managers,
invalid_data_managers, data_managers_errors, new_install=False,
reinstalling=False):
"""
Return a dictionary of containers for the received repository's dependencies and readme files for
display during installation to Galaxy.
"""
containers_dict = dict(datatypes=None,
invalid_tools=None,
missing_tool_dependencies=None,
readme_files=None,
repository_dependencies=None,
missing_repository_dependencies=None,
tool_dependencies=None,
valid_tools=None,
workflows=None,
valid_data_managers=None,
invalid_data_managers=None)
# Some of the tool dependency folders will include links to display tool dependency information, and
# some of these links require the repository id. However we need to be careful because sometimes the
# repository object is None.
if repository:
repository_id = repository.id
changeset_revision = repository.changeset_revision
else:
repository_id = None
changeset_revision = None
lock = threading.Lock()
lock.acquire(True)
try:
folder_id = 0
# Datatypes container.
if datatypes:
folder_id, datatypes_root_folder = self.build_datatypes_folder(folder_id, datatypes)
containers_dict['datatypes'] = datatypes_root_folder
# Invalid tools container.
if invalid_tools:
folder_id, invalid_tools_root_folder = \
self.build_invalid_tools_folder(folder_id,
invalid_tools,
changeset_revision,
repository=repository,
label='Invalid tools')
containers_dict['invalid_tools'] = invalid_tools_root_folder
# Readme files container.
if readme_files_dict:
folder_id, readme_files_root_folder = self.build_readme_files_folder(folder_id, readme_files_dict)
containers_dict['readme_files'] = readme_files_root_folder
# Installed repository dependencies container.
if repository_dependencies:
if new_install:
label = 'Repository dependencies'
else:
label = 'Installed repository dependencies'
folder_id, repository_dependencies_root_folder = \
self.build_repository_dependencies_folder(folder_id=folder_id,
repository_dependencies=repository_dependencies,
label=label,
installed=True)
containers_dict['repository_dependencies'] = repository_dependencies_root_folder
# Missing repository dependencies container.
if missing_repository_dependencies:
folder_id, missing_repository_dependencies_root_folder = \
self.build_repository_dependencies_folder(folder_id=folder_id,
repository_dependencies=missing_repository_dependencies,
label='Missing repository dependencies',
installed=False)
containers_dict['missing_repository_dependencies'] = missing_repository_dependencies_root_folder
# Installed tool dependencies container.
if tool_dependencies:
if new_install:
label = 'Tool dependencies'
else:
label = 'Installed tool dependencies'
# We only want to display the Status column if the tool_dependency is missing.
folder_id, tool_dependencies_root_folder = \
self.build_tool_dependencies_folder(folder_id,
tool_dependencies,
label=label,
missing=False,
new_install=new_install,
reinstalling=reinstalling)
containers_dict['tool_dependencies'] = tool_dependencies_root_folder
# Missing tool dependencies container.
if missing_tool_dependencies:
# We only want to display the Status column if the tool_dependency is missing.
folder_id, missing_tool_dependencies_root_folder = \
self.build_tool_dependencies_folder(folder_id,
missing_tool_dependencies,
label='Missing tool dependencies',
missing=True,
new_install=new_install,
reinstalling=reinstalling)
containers_dict['missing_tool_dependencies'] = missing_tool_dependencies_root_folder
# Valid tools container.
if valid_tools:
folder_id, valid_tools_root_folder = self.build_tools_folder(folder_id,
valid_tools,
repository,
changeset_revision,
label='Valid tools')
containers_dict['valid_tools'] = valid_tools_root_folder
# Workflows container.
if workflows:
folder_id, workflows_root_folder = \
self.build_workflows_folder(folder_id=folder_id,
workflows=workflows,
repository_metadata_id=None,
repository_id=repository_id,
label='Workflows')
containers_dict['workflows'] = workflows_root_folder
if valid_data_managers:
folder_id, valid_data_managers_root_folder = \
self.build_data_managers_folder(folder_id=folder_id,
data_managers=valid_data_managers,
label='Valid Data Managers')
containers_dict['valid_data_managers'] = valid_data_managers_root_folder
if invalid_data_managers or data_managers_errors:
folder_id, invalid_data_managers_root_folder = \
self.build_invalid_data_managers_folder(folder_id=folder_id,
data_managers=invalid_data_managers,
error_messages=data_managers_errors,
label='Invalid Data Managers')
containers_dict['invalid_data_managers'] = invalid_data_managers_root_folder
except Exception as e:
log.debug("Exception in build_repository_containers: %s" % str(e))
finally:
lock.release()
return containers_dict