Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/gxformat2/interface.py @ 2:6af9afd405e9 draft

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"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author shellac
date Thu, 14 May 2020 14:56:58 -0400
parents 26e78fe6e8c4
children
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1 """This module contains an interface and implementation describing Galaxy interactions used by gxformat2.
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2
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3 The interface is :class:`ImporterGalaxyInterface` and the default
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4 implementation based on `BioBlend <https://bioblend.readthedocs.io/>`__
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5 is :class:`BioBlendImporterGalaxyInterface`.
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6 """
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7 import abc
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8
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9 import bioblend
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10 import six
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11
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12
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13 @six.add_metaclass(abc.ABCMeta)
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14 class ImporterGalaxyInterface(object):
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15 """An abstract interface describing Galaxy operations used by gxformat2.
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16
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17 Specifically containing definitions of operations required to load
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18 workflows into Galaxy.
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19 """
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20
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21 @abc.abstractmethod
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22 def import_workflow(self, workflow, **kwds):
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23 """Import a workflow via POST /api/workflows or comparable interface into Galaxy."""
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24
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25 def import_tool(self, tool):
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26 """Import a new dynamically defined tool.
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27
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28 Not yet implemented in vanilla Galaxy - used only in the cwl branch of Galaxy.
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29 """
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30 raise NotImplementedError()
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31
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32
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33 class BioBlendImporterGalaxyInterface(object):
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34 """Implementation of :class:`ImporterGalaxyInterface` using bioblend."""
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35
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36 def __init__(self, **kwds):
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37 """Build a :class:`bioblend.GalaxyInstance` from supplied arguments."""
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38 url = None
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39
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40 admin_key = None
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41 admin_gi = None
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42 if "admin_gi" in kwds:
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43 admin_gi = kwds["admin_gi"]
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44 elif "gi" in kwds:
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45 admin_gi = kwds["gi"]
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46 elif "url" in kwds and "admin_key" in kwds:
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47 url = kwds["url"]
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48 admin_key = kwds["admin_key"]
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49
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50 if admin_gi is None:
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51 assert url is not None
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52 assert admin_key is not None
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53 admin_gi = bioblend.GalaxyInstance(url=url, key=admin_key)
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54
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55 user_key = None
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56 user_gi = None
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57 if "user_gi" in kwds:
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58 user_gi = kwds["user_gi"]
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59 elif "gi" in kwds:
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60 user_gi = kwds["gi"]
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61 elif "url" in kwds and "user_key" in kwds:
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62 url = kwds["url"]
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63 user_key = kwds["user_key"]
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64
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65 if user_gi is None:
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66 assert url is not None
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67 assert user_key is not None
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68 user_gi = bioblend.GalaxyInstance(url=url, key=user_key)
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69
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70 self._admin_gi = admin_gi
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71 self._user_gi = user_gi
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72
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73 def import_workflow(self, workflow, **kwds):
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74 """Import Galaxy workflow using instance :class:`bioblend.GalaxyInstance` object."""
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75 return self._user_gi.workflows.import_workflow_json(
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76 workflow,
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77 **kwds
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78 )
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79
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80 def import_tool(self, tool_representation):
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81 """Import Galaxy tool using instance :class:`bioblend.GalaxyInstance` object."""
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82 raise NotImplementedError()