Mercurial > repos > shellac > guppy_basecaller
view env/lib/python3.7/site-packages/gxformat2/interface.py @ 3:758bc20232e8 draft
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author | shellac |
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date | Thu, 14 May 2020 16:20:52 -0400 |
parents | 26e78fe6e8c4 |
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"""This module contains an interface and implementation describing Galaxy interactions used by gxformat2. The interface is :class:`ImporterGalaxyInterface` and the default implementation based on `BioBlend <https://bioblend.readthedocs.io/>`__ is :class:`BioBlendImporterGalaxyInterface`. """ import abc import bioblend import six @six.add_metaclass(abc.ABCMeta) class ImporterGalaxyInterface(object): """An abstract interface describing Galaxy operations used by gxformat2. Specifically containing definitions of operations required to load workflows into Galaxy. """ @abc.abstractmethod def import_workflow(self, workflow, **kwds): """Import a workflow via POST /api/workflows or comparable interface into Galaxy.""" def import_tool(self, tool): """Import a new dynamically defined tool. Not yet implemented in vanilla Galaxy - used only in the cwl branch of Galaxy. """ raise NotImplementedError() class BioBlendImporterGalaxyInterface(object): """Implementation of :class:`ImporterGalaxyInterface` using bioblend.""" def __init__(self, **kwds): """Build a :class:`bioblend.GalaxyInstance` from supplied arguments.""" 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): """Import Galaxy workflow using instance :class:`bioblend.GalaxyInstance` object.""" return self._user_gi.workflows.import_workflow_json( workflow, **kwds ) def import_tool(self, tool_representation): """Import Galaxy tool using instance :class:`bioblend.GalaxyInstance` object.""" raise NotImplementedError()