Mercurial > repos > shellac > sam_consensus_v3

annotate env/lib/python3.9/site-packages/planemo/cwl/toil.py @ 0:4f3585e2f14b draft default tip

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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
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1 from __future__ import absolute_import
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2
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3 import json
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4 import tempfile
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5
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6 try:
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7 from toil.cwl import cwltoil
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8 except ImportError:
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9 cwltoil = None
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10
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11 from planemo.deps import ensure_dependency_resolvers_conf_configured
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12 from planemo.io import error, real_io
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13 from planemo.runnable import (
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14 ErrorRunResponse,
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15 )
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16 from .run import (
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17 CwlToolRunResponse,
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18 JSON_PARSE_ERROR_MESSAGE
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19 )
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20
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21
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22 TOIL_REQUIRED_MESSAGE = "This functionality requires Toil, please install with 'pip install toil'"
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23
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24
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25 def run_toil(ctx, path, job_path, **kwds):
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26 """Translate planemo kwds to cwltool kwds and run cwltool main function."""
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27 _ensure_toil_available()
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28
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29 args = []
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30 if not ctx.verbose:
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31 args.append("--quiet")
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32 output_directory = kwds.get("output_directory", None)
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33 if output_directory:
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34 args.append("--outdir")
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35 args.append(output_directory)
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36 if kwds.get("no_container", False):
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37 args.append("--no-container")
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38 ensure_dependency_resolvers_conf_configured(ctx, kwds)
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39 args.append("--beta-dependency-resolvers-configuration")
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40 args.append(kwds["dependency_resolvers_config_file"])
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41 if kwds.get("mulled_containers"):
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42 args.append("--beta-use-biocontainers")
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43
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44 if kwds.get("non_strict_cwl", False):
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45 args.append("--non-strict")
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46
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47 args.extend([path, job_path])
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48 ctx.vlog("Calling cwltoil with arguments %s" % args)
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49 with tempfile.NamedTemporaryFile("w") as tmp_stdout:
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50 # cwltool passes sys.stderr to subprocess.Popen - ensure it has
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51 # and actual fileno.
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52 with real_io():
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53 ret_code = cwltoil.main(
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54 args,
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55 stdout=tmp_stdout
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56 )
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57 tmp_stdout.flush()
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58 with open(tmp_stdout.name, "r") as stdout_f:
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59 try:
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60 result = json.load(stdout_f)
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61 except ValueError:
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62 message = JSON_PARSE_ERROR_MESSAGE % (
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63 open(tmp_stdout.name, "r").read(),
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64 tmp_stdout.name,
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65 )
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66 error(message)
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67 raise Exception(message)
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68
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69 if ret_code != 0:
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70 return ErrorRunResponse("Error running Toil")
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71 outputs = result
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72 return CwlToolRunResponse(
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73 "",
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74 outputs=outputs,
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75 )
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76
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77
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78 def _ensure_toil_available():
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79 if cwltoil is None:
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80 raise Exception(TOIL_REQUIRED_MESSAGE)