Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/gxformat2/main.py @ 4:79f47841a781 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:47:39 -0400
parents 26e78fe6e8c4
children
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1 """Module containing :func:`convert_and_import_workflow`."""
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2 import os
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3
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4 from ._yaml import ordered_load
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5 from .converter import python_to_workflow, yaml_to_workflow
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6 from .interface import BioBlendImporterGalaxyInterface
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7
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8
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9 def convert_and_import_workflow(has_workflow, **kwds):
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10 """Conversion and import Format 2 workflows into a target Galaxy instance."""
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11 galaxy_interface = kwds.get("galaxy_interface", None)
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12 if galaxy_interface is None:
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13 galaxy_interface = BioBlendImporterGalaxyInterface(**kwds)
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14
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15 source_type = kwds.get("source_type", None)
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16 workflow_directory = kwds.get("workflow_directory", None)
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17 if source_type == "path":
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18 workflow_path = has_workflow
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19 if workflow_directory is None:
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20 workflow_directory = os.path.dirname(has_workflow)
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21 with open(workflow_path, "r") as f:
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22 has_workflow = ordered_load(f)
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23
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24 if workflow_directory is not None:
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25 workflow_directory = os.path.abspath(workflow_directory)
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26
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27 convert = kwds.get("convert", True)
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28 raw_yaml = kwds.get("raw_yaml", False)
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29 if raw_yaml and convert:
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30 raise Exception("Incompatible options selected.")
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31 if convert:
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32 if isinstance(has_workflow, dict):
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33 workflow = python_to_workflow(has_workflow, galaxy_interface, workflow_directory)
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34 else:
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35 workflow = yaml_to_workflow(has_workflow, galaxy_interface, workflow_directory)
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36 else:
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37 workflow = has_workflow
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38 if not isinstance(workflow, dict) and not raw_yaml:
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39 workflow = ordered_load(workflow)
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40 else:
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41 workflow = {"yaml_content": workflow}
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42
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43 name = kwds.get("name", None)
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44 if name is not None:
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45 workflow["name"] = name
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46 publish = kwds.get("publish", False)
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47 exact_tools = kwds.get("exact_tools", False)
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48 fill_defaults = kwds.get("fill_defaults", True)
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49 import_kwds = {
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50 "fill_defaults": fill_defaults
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51 }
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52 if publish:
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53 import_kwds["publish"] = True
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54 if exact_tools:
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55 import_kwds["exact_tools"] = True
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56 return galaxy_interface.import_workflow(workflow, **import_kwds)
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57
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58
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59 __all__ = (
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60 'convert_and_import_workflow',
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61 )