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Source code for tool_shed.utility_containers

import logging
import threading

from galaxy import util
from tool_shed.util import common_util
from tool_shed.util import container_util
from tool_shed.util import readme_util

from . import utility_container_manager

log = logging.getLogger(__name__)


[docs]class FailedTest(object): """Failed tool tests object"""
[docs] def __init__(self, id=None, stderr=None, test_id=None, tool_id=None, tool_version=None, traceback=None): self.id = id self.stderr = stderr self.test_id = test_id self.tool_id = tool_id self.tool_version = tool_version self.traceback = traceback
[docs]class InvalidRepositoryDependency(object): """Invalid repository dependency definition object"""
[docs] def __init__(self, id=None, toolshed=None, repository_name=None, repository_owner=None, changeset_revision=None, prior_installation_required=False, only_if_compiling_contained_td=False, error=None): self.id = id self.toolshed = toolshed self.repository_name = repository_name self.repository_owner = repository_owner self.changeset_revision = changeset_revision self.prior_installation_required = prior_installation_required self.only_if_compiling_contained_td = only_if_compiling_contained_td self.error = error
[docs]class InvalidToolDependency(object): """Invalid tool dependency definition object"""
[docs] def __init__(self, id=None, name=None, version=None, type=None, error=None): self.id = id self.name = name self.version = version self.type = type self.error = error
[docs]class MissingTestComponent(object): """Missing tool test components object"""
[docs] def __init__(self, id=None, missing_components=None, tool_guid=None, tool_id=None, tool_version=None): self.id = id self.missing_components = missing_components self.tool_guid = tool_guid self.tool_id = tool_id self.tool_version = tool_version
[docs]class NotTested(object): """NotTested object"""
[docs] def __init__(self, id=None, reason=None): self.id = id self.reason = reason
[docs]class PassedTest(object): """Passed tool tests object"""
[docs] def __init__(self, id=None, test_id=None, tool_id=None, tool_version=None): self.id = id self.test_id = test_id self.tool_id = tool_id self.tool_version = tool_version
[docs]class RepositoryInstallationError(object): """Repository installation error object"""
[docs] def __init__(self, id=None, tool_shed=None, name=None, owner=None, changeset_revision=None, error_message=None): self.id = id self.tool_shed = tool_shed self.name = name self.owner = owner self.changeset_revision = changeset_revision self.error_message = error_message
[docs]class RepositorySuccessfulInstallation(object): """Repository installation object"""
[docs] def __init__(self, id=None, tool_shed=None, name=None, owner=None, changeset_revision=None): self.id = id self.tool_shed = tool_shed self.name = name self.owner = owner self.changeset_revision = changeset_revision
[docs]class ToolDependencyInstallationError(object): """Tool dependency installation error object"""
[docs] def __init__(self, id=None, type=None, name=None, version=None, error_message=None): self.id = id self.type = type self.name = name self.version = version self.error_message = error_message
[docs]class ToolDependencySuccessfulInstallation(object): """Tool dependency installation object"""
[docs] def __init__(self, id=None, type=None, name=None, version=None, installation_directory=None): self.id = id self.type = type self.name = name self.version = version self.installation_directory = installation_directory
[docs]class ToolShedUtilityContainerManager(utility_container_manager.UtilityContainerManager):
[docs] def __init__(self, app): self.app = app
[docs] def build_invalid_repository_dependencies_root_folder(self, folder_id, invalid_repository_dependencies_dict): """Return a folder hierarchy containing invalid repository dependencies.""" label = 'Invalid repository dependencies' if invalid_repository_dependencies_dict: invalid_repository_dependency_id = 0 folder_id += 1 invalid_repository_dependencies_root_folder = \ utility_container_manager.Folder(id=folder_id, key='root', label='root', parent=None) folder_id += 1 invalid_repository_dependencies_folder = \ utility_container_manager.Folder(id=folder_id, key='invalid_repository_dependencies', label=label, parent=invalid_repository_dependencies_root_folder) invalid_repository_dependencies_root_folder.folders.append(invalid_repository_dependencies_folder) invalid_repository_dependencies = invalid_repository_dependencies_dict['repository_dependencies'] for invalid_repository_dependency in invalid_repository_dependencies: folder_id += 1 invalid_repository_dependency_id += 1 toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td, error = \ common_util.parse_repository_dependency_tuple(invalid_repository_dependency, contains_error=True) key = container_util.generate_repository_dependencies_key_for_repository(toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td) label = "Repository <b>%s</b> revision <b>%s</b> owned by <b>%s</b>" % (name, changeset_revision, owner) folder = utility_container_manager.Folder(id=folder_id, key=key, label=label, parent=invalid_repository_dependencies_folder) ird = InvalidRepositoryDependency(id=invalid_repository_dependency_id, toolshed=toolshed, repository_name=name, repository_owner=owner, changeset_revision=changeset_revision, prior_installation_required=util.asbool(prior_installation_required), only_if_compiling_contained_td=util.asbool(only_if_compiling_contained_td), error=error) folder.invalid_repository_dependencies.append(ird) invalid_repository_dependencies_folder.folders.append(folder) else: invalid_repository_dependencies_root_folder = None return folder_id, invalid_repository_dependencies_root_folder
[docs] def build_invalid_tool_dependencies_root_folder(self, folder_id, invalid_tool_dependencies_dict): """Return a folder hierarchy containing invalid tool dependencies.""" # # INvalid tool dependencies are always packages like: # {"R/2.15.1": {"name": "R", "readme": "some string", "type": "package", "version": "2.15.1" "error" : "some sting" } label = 'Invalid tool dependencies' if invalid_tool_dependencies_dict: invalid_tool_dependency_id = 0 folder_id += 1 invalid_tool_dependencies_root_folder = \ utility_container_manager.Folder(id=folder_id, key='root', label='root', parent=None) folder_id += 1 invalid_tool_dependencies_folder = \ utility_container_manager.Folder(id=folder_id, key='invalid_tool_dependencies', label=label, parent=invalid_tool_dependencies_root_folder) invalid_tool_dependencies_root_folder.folders.append(invalid_tool_dependencies_folder) for td_key, requirements_dict in invalid_tool_dependencies_dict.items(): folder_id += 1 invalid_tool_dependency_id += 1 try: name = requirements_dict['name'] type = requirements_dict['type'] version = requirements_dict['version'] error = requirements_dict['error'] except Exception as e: name = 'unknown' type = 'unknown' version = 'unknown' error = str(e) key = self.generate_tool_dependencies_key(name, version, type) label = "Version <b>%s</b> of the <b>%s</b> <b>%s</b>" % (version, name, type) folder = utility_container_manager.Folder(id=folder_id, key=key, label=label, parent=invalid_tool_dependencies_folder) itd = InvalidToolDependency(id=invalid_tool_dependency_id, name=name, version=version, type=type, error=error) folder.invalid_tool_dependencies.append(itd) invalid_tool_dependencies_folder.folders.append(folder) else: invalid_tool_dependencies_root_folder = None return folder_id, invalid_tool_dependencies_root_folder
[docs] def build_repository_containers(self, repository, changeset_revision, repository_dependencies, repository_metadata, exclude=None): """ Return a dictionary of containers for the received repository's dependencies and contents for display in the Tool Shed. """ if exclude is None: exclude = [] containers_dict = dict(datatypes=None, invalid_tools=None, readme_files=None, repository_dependencies=None, tool_dependencies=None, valid_tools=None, workflows=None, valid_data_managers=None) if repository_metadata: metadata = repository_metadata.metadata lock = threading.Lock() lock.acquire(True) try: folder_id = 0 # Datatypes container. if metadata: if 'datatypes' not in exclude and 'datatypes' in metadata: datatypes = metadata['datatypes'] folder_id, datatypes_root_folder = self.build_datatypes_folder(folder_id, datatypes) containers_dict['datatypes'] = datatypes_root_folder # Invalid repository dependencies container. if metadata: if 'invalid_repository_dependencies' not in exclude and 'invalid_repository_dependencies' in metadata: invalid_repository_dependencies = metadata['invalid_repository_dependencies'] folder_id, invalid_repository_dependencies_root_folder = \ self.build_invalid_repository_dependencies_root_folder(folder_id, invalid_repository_dependencies) containers_dict['invalid_repository_dependencies'] = invalid_repository_dependencies_root_folder # Invalid tool dependencies container. if metadata: if 'invalid_tool_dependencies' not in exclude and 'invalid_tool_dependencies' in metadata: invalid_tool_dependencies = metadata['invalid_tool_dependencies'] folder_id, invalid_tool_dependencies_root_folder = \ self.build_invalid_tool_dependencies_root_folder(folder_id, invalid_tool_dependencies) containers_dict['invalid_tool_dependencies'] = invalid_tool_dependencies_root_folder # Invalid tools container. if metadata: if 'invalid_tools' not in exclude and 'invalid_tools' in metadata: invalid_tool_configs = metadata['invalid_tools'] folder_id, invalid_tools_root_folder = \ self.build_invalid_tools_folder(folder_id, invalid_tool_configs, changeset_revision, repository=repository, label='Invalid tools') containers_dict['invalid_tools'] = invalid_tools_root_folder # Readme files container. if metadata: if 'readme_files' not in exclude and 'readme_files' in metadata: readme_files_dict = readme_util.build_readme_files_dict(self.app, repository, changeset_revision, metadata) folder_id, readme_files_root_folder = self.build_readme_files_folder(folder_id, readme_files_dict) containers_dict['readme_files'] = readme_files_root_folder if 'repository_dependencies' not in exclude: # Repository dependencies container. folder_id, repository_dependencies_root_folder = \ self.build_repository_dependencies_folder(folder_id=folder_id, repository_dependencies=repository_dependencies, label='Repository dependencies', installed=False) if repository_dependencies_root_folder: containers_dict['repository_dependencies'] = repository_dependencies_root_folder # Tool dependencies container. if metadata: if 'tool_dependencies' not in exclude and 'tool_dependencies' in metadata: tool_dependencies = metadata['tool_dependencies'] if 'orphan_tool_dependencies' in metadata: # The use of the orphan_tool_dependencies category in metadata has been deprecated, # but we still need to check in case the metadata is out of date. orphan_tool_dependencies = metadata['orphan_tool_dependencies'] tool_dependencies.update(orphan_tool_dependencies) # Tool dependencies can be categorized as orphans only if the repository contains tools. if 'tools' not in exclude: tools = metadata.get('tools', []) tools.extend(metadata.get('invalid_tools', [])) folder_id, tool_dependencies_root_folder = \ self.build_tool_dependencies_folder(folder_id, tool_dependencies, missing=False, new_install=False) containers_dict['tool_dependencies'] = tool_dependencies_root_folder # Valid tools container. if metadata: if 'tools' not in exclude and 'tools' in metadata: valid_tools = metadata['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 metadata: if 'workflows' not in exclude and 'workflows' in metadata: workflows = metadata['workflows'] folder_id, workflows_root_folder = \ self.build_workflows_folder(folder_id=folder_id, workflows=workflows, repository_metadata_id=repository_metadata.id, repository_id=None, label='Workflows') containers_dict['workflows'] = workflows_root_folder # Valid Data Managers container if metadata: if 'data_manager' not in exclude and 'data_manager' in metadata: data_managers = metadata['data_manager'].get('data_managers', None) folder_id, data_managers_root_folder = \ self.build_data_managers_folder(folder_id, data_managers, label="Data Managers") containers_dict['valid_data_managers'] = data_managers_root_folder error_messages = metadata['data_manager'].get('error_messages', None) data_managers = metadata['data_manager'].get('invalid_data_managers', None) folder_id, data_managers_root_folder = \ self.build_invalid_data_managers_folder(folder_id, data_managers, error_messages, label="Invalid Data Managers") containers_dict['invalid_data_managers'] = data_managers_root_folder except Exception: log.exception("Exception in build_repository_containers") finally: lock.release() return containers_dict
[docs] def generate_tool_dependencies_key(self, name, version, type): return '%s%s%s%s%s' % (str(name), container_util.STRSEP, str(version), container_util.STRSEP, str(type))