Mercurial > repos > guerler > springsuite
comparison planemo/lib/python3.7/site-packages/cwltool/tests/test_subgraph.py @ 0:d30785e31577 draft
"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
| author | guerler |
|---|---|
| date | Fri, 31 Jul 2020 00:18:57 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:d30785e31577 |
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| 1 import os | |
| 2 | |
| 3 from six.moves import urllib | |
| 4 | |
| 5 import pytest | |
| 6 import json | |
| 7 | |
| 8 from cwltool.context import LoadingContext | |
| 9 from cwltool.load_tool import load_tool | |
| 10 from cwltool.workflow import default_make_tool | |
| 11 from cwltool.subgraph import get_subgraph | |
| 12 from schema_salad.utils import convert_to_dict | |
| 13 from cwltool.resolver import Path, resolve_local | |
| 14 from .util import get_data, working_directory | |
| 15 from six import string_types | |
| 16 from .test_fetch import norm | |
| 17 | |
| 18 def test_get_subgraph(): | |
| 19 loadingContext = LoadingContext({"construct_tool_object": default_make_tool}) | |
| 20 wf = norm(Path(get_data("tests/subgraph/count-lines1-wf.cwl")).as_uri()) | |
| 21 loadingContext.do_update = False | |
| 22 tool = load_tool(wf, loadingContext) | |
| 23 | |
| 24 sg = norm(Path(get_data("tests/subgraph")).as_uri()) | |
| 25 | |
| 26 def clean(val): | |
| 27 if isinstance(val, string_types): | |
| 28 if val.startswith(sg): | |
| 29 return val[len(sg)+1:] | |
| 30 if isinstance(val, dict): | |
| 31 return {k: clean(v) for k,v in val.items()} | |
| 32 if isinstance(val, list): | |
| 33 return [clean(v) for v in val] | |
| 34 return val | |
| 35 | |
| 36 for a in ("file1", "file2", "file3", "count_output", | |
| 37 "output3", "output4", "output5", | |
| 38 "step1", "step2", "step3", "step4", "step5"): | |
| 39 extracted = get_subgraph([wf+"#"+a], tool) | |
| 40 with open(get_data("tests/subgraph/extract_"+a+".json")) as f: | |
| 41 assert json.load(f) == clean(convert_to_dict(extracted)) |