Mercurial > repos > shellac > guppy_basecaller

comparison env/lib/python3.7/site-packages/planemo/cwl/toil.py @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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-1:000000000000 0:26e78fe6e8c4
1 from __future__ import absolute_import
2
3 import json
4 import tempfile
5
6 try:
7 from toil.cwl import cwltoil
8 except ImportError:
9 cwltoil = None
10
11 from planemo.deps import ensure_dependency_resolvers_conf_configured
12 from planemo.io import error, real_io
13 from planemo.runnable import (
14 ErrorRunResponse,
15 )
16 from .run import (
17 CwlToolRunResponse,
18 JSON_PARSE_ERROR_MESSAGE
19 )
20
21
22 TOIL_REQUIRED_MESSAGE = "This functionality requires Toil, please install with 'pip install toil'"
23
24
25 def run_toil(ctx, path, job_path, **kwds):
26 """Translate planemo kwds to cwltool kwds and run cwltool main function."""
27 _ensure_toil_available()
28
29 args = []
30 if not ctx.verbose:
31 args.append("--quiet")
32 output_directory = kwds.get("output_directory", None)
33 if output_directory:
34 args.append("--outdir")
35 args.append(output_directory)
36 if kwds.get("no_container", False):
37 args.append("--no-container")
38 ensure_dependency_resolvers_conf_configured(ctx, kwds)
39 args.append("--beta-dependency-resolvers-configuration")
40 args.append(kwds["dependency_resolvers_config_file"])
41 if kwds.get("mulled_containers"):
42 args.append("--beta-use-biocontainers")
43
44 if kwds.get("non_strict_cwl", False):
45 args.append("--non-strict")
46
47 args.extend([path, job_path])
48 ctx.vlog("Calling cwltoil with arguments %s" % args)
49 with tempfile.NamedTemporaryFile("w") as tmp_stdout:
50 # cwltool passes sys.stderr to subprocess.Popen - ensure it has
51 # and actual fileno.
52 with real_io():
53 ret_code = cwltoil.main(
54 args,
55 stdout=tmp_stdout
56 )
57 tmp_stdout.flush()
58 with open(tmp_stdout.name, "r") as stdout_f:
59 try:
60 result = json.load(stdout_f)
61 except ValueError:
62 message = JSON_PARSE_ERROR_MESSAGE % (
63 open(tmp_stdout.name, "r").read(),
64 tmp_stdout.name,
65 )
66 error(message)
67 raise Exception(message)
68
69 if ret_code != 0:
70 return ErrorRunResponse("Error running Toil")
71 outputs = result
72 return CwlToolRunResponse(
73 "",
74 outputs=outputs,
75 )
76
77
78 def _ensure_toil_available():
79 if cwltoil is None:
80 raise Exception(TOIL_REQUIRED_MESSAGE)