import abc import json import bioblend import six @six.add_metaclass(abc.ABCMeta) class ImporterGalaxyInterface(object): """ An abstract interface describing the interaction between Galaxy and the workflow import code. """ @abc.abstractmethod def import_workflow(self, workflow, **kwds): """ Import a workflow via POST /api/workflows or comparable interface into Galaxy. """ pass class BioBlendImporterGalaxyInterface(object): def __init__(self, **kwds): """ """ url = None admin_key = None admin_gi = None if "admin_gi" in kwds: admin_gi = kwds["admin_gi"] elif "gi" in kwds: admin_gi = kwds["gi"] elif "url" in kwds and "admin_key" in kwds: url = kwds["url"] admin_key = kwds["admin_key"] if admin_gi is None: assert url is not None assert admin_key is not None admin_gi = bioblend.GalaxyInstance(url=url, key=admin_key) user_key = None user_gi = None if "user_gi" in kwds: user_gi = kwds["user_gi"] elif "gi" in kwds: user_gi = kwds["gi"] elif "url" in kwds and "user_key" in kwds: url = kwds["url"] user_key = kwds["user_key"] if user_gi is None: assert url is not None assert user_key is not None user_gi = bioblend.GalaxyInstance(url=url, key=user_key) self._admin_gi = admin_gi self._user_gi = user_gi def import_workflow(self, workflow, **kwds): workflow_str = json.dumps(workflow, indent=4) return self._user_gi.workflows.import_workflow_json( workflow_str, **kwds ) def import_tool(self, tool_representation): pass