diff env/lib/python3.7/site-packages/gxformat2/interface.py @ 5:9b1c78e6ba9c draft default tip

"planemo upload commit 6c0a8142489327ece472c84e558c47da711a9142"
author shellac
date Mon, 01 Jun 2020 08:59:25 -0400
parents 79f47841a781
children
line wrap: on
line diff
--- a/env/lib/python3.7/site-packages/gxformat2/interface.py	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,82 +0,0 @@
-"""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()