mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
John Chilton
af7d7de596
- Fixes a bug in lib/galaxy/tools/linters/general.py found through galaxy-lib. - Brings in docstring and import order linting fixes from the gxformat2 project (https://github.com/jmchilton/gxformat2).
76 lines
2.4 KiB
Python
76 lines
2.4 KiB
Python
"""This module contains an interface and implementation describing Galaxy interactions used by gxformat2.
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The interface is :class:`ImporterGalaxyInterface` and the default
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implementation based on `bioblend <http://bioblend.readthedocs.io/>`__
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is :class:`BioBlendImporterGalaxyInterface`.
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"""
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import abc
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import bioblend
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import six
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@six.add_metaclass(abc.ABCMeta)
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class ImporterGalaxyInterface(object):
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"""An abstract interface describing Galaxy operations used by gxformat2.
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Specifically containing definitions of operations required to load
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workflows into Galaxy.
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"""
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@abc.abstractmethod
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def import_workflow(self, workflow, **kwds):
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"""Import a workflow via POST /api/workflows or comparable interface into Galaxy."""
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class BioBlendImporterGalaxyInterface(object):
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"""Implementation of :class:`ImporterGalaxyInterface` using bioblend."""
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def __init__(self, **kwds):
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"""Build a :class:`bioblend.GalaxyInstance` from supplied arguments."""
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url = None
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admin_key = None
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admin_gi = None
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if "admin_gi" in kwds:
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admin_gi = kwds["admin_gi"]
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elif "gi" in kwds:
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admin_gi = kwds["gi"]
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elif "url" in kwds and "admin_key" in kwds:
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url = kwds["url"]
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admin_key = kwds["admin_key"]
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if admin_gi is None:
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assert url is not None
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assert admin_key is not None
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admin_gi = bioblend.GalaxyInstance(url=url, key=admin_key)
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user_key = None
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user_gi = None
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if "user_gi" in kwds:
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user_gi = kwds["user_gi"]
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elif "gi" in kwds:
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user_gi = kwds["gi"]
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elif "url" in kwds and "user_key" in kwds:
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url = kwds["url"]
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user_key = kwds["user_key"]
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if user_gi is None:
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assert url is not None
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assert user_key is not None
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user_gi = bioblend.GalaxyInstance(url=url, key=user_key)
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self._admin_gi = admin_gi
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self._user_gi = user_gi
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def import_workflow(self, workflow, **kwds):
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"""Import Galaxy workflow using instance :class:`bioblend.GalaxyInstance` object."""
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return self._user_gi.workflows.import_workflow_json(
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workflow,
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**kwds
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)
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def import_tool(self, tool_representation):
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"""Import Galaxy tool using instance :class:`bioblend.GalaxyInstance` object."""
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pass
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