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annotate planemo/lib/python3.7/site-packages/cwltool/tests/test_subgraph.py @ 0:d30785e31577 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:18:57 -0400
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1 import os
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2
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3 from six.moves import urllib
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4
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5 import pytest
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6 import json
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7
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8 from cwltool.context import LoadingContext
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9 from cwltool.load_tool import load_tool
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10 from cwltool.workflow import default_make_tool
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11 from cwltool.subgraph import get_subgraph
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12 from schema_salad.utils import convert_to_dict
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13 from cwltool.resolver import Path, resolve_local
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14 from .util import get_data, working_directory
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15 from six import string_types
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16 from .test_fetch import norm
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17
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18 def test_get_subgraph():
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19 loadingContext = LoadingContext({"construct_tool_object": default_make_tool})
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20 wf = norm(Path(get_data("tests/subgraph/count-lines1-wf.cwl")).as_uri())
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21 loadingContext.do_update = False
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22 tool = load_tool(wf, loadingContext)
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23
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24 sg = norm(Path(get_data("tests/subgraph")).as_uri())
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25
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26 def clean(val):
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27 if isinstance(val, string_types):
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28 if val.startswith(sg):
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29 return val[len(sg)+1:]
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30 if isinstance(val, dict):
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31 return {k: clean(v) for k,v in val.items()}
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32 if isinstance(val, list):
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33 return [clean(v) for v in val]
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34 return val
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35
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36 for a in ("file1", "file2", "file3", "count_output",
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37 "output3", "output4", "output5",
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38 "step1", "step2", "step3", "step4", "step5"):
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39 extracted = get_subgraph([wf+"#"+a], tool)
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40 with open(get_data("tests/subgraph/extract_"+a+".json")) as f:
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41 assert json.load(f) == clean(convert_to_dict(extracted))