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annotate env/lib/python3.9/site-packages/planemo/cwl/run.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 """Module defines a planemo abstraction around running cwltool.
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2
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3 cwltool is an executable Python script and library mostly maintained by
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4 Peter Amstutz and serves the reference implementation for the CWL.
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5 It can be found at https://github.com/common-workflow-language/cwltool,
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6 """
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7 import json
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8 import tempfile
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9
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10 from galaxy.tool_util.cwl.cwltool_deps import (
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11 ensure_cwltool_available,
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12 main,
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13 )
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14
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15 from planemo.deps import ensure_dependency_resolvers_conf_configured
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16 from planemo.io import error, real_io
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17 from planemo.runnable import (
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18 ErrorRunResponse,
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19 SuccessfulRunResponse,
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20 )
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21
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22 JSON_PARSE_ERROR_MESSAGE = ("Failed to parse JSON from cwltool output [%s] "
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23 "in file [%s]. cwltool logs [%s].")
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24
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25
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26 class CwlToolRunResponse(SuccessfulRunResponse):
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27 """Describe the resut of a cwltool invocation."""
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28
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29 def __init__(self, log, outputs=None):
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30 self._log = log
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31 self._outputs = outputs
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32
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33 @property
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34 def log(self):
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35 return self._log
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36
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37 @property
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38 def job_info(self):
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39 return None
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40
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41 @property
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42 def invocation_details(self):
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43 return None
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44
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45 @property
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46 def outputs_dict(self):
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47 return self._outputs
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48
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49
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50 def run_cwltool(ctx, path, job_path, **kwds):
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51 """Translate planemo kwds to cwltool kwds and run cwltool main function."""
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52 ensure_cwltool_available()
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53
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54 args = []
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55 if ctx.verbose:
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56 args.append("--verbose")
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57 output_directory = kwds.get("output_directory", None)
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58 if output_directory:
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59 args.append("--outdir")
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60 args.append(output_directory)
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61 if kwds.get("no_container", False):
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62 args.append("--no-container")
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63 ensure_dependency_resolvers_conf_configured(ctx, kwds)
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64 args.append("--beta-dependency-resolvers-configuration")
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65 args.append(kwds["dependency_resolvers_config_file"])
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66 if kwds.get("mulled_containers"):
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67 args.append("--beta-use-biocontainers")
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68
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69 if kwds.get("non_strict_cwl", False):
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70 args.append("--non-strict")
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71
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72 args.extend([path, job_path])
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73 ctx.vlog("Calling cwltool with arguments %s" % args)
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74 with tempfile.NamedTemporaryFile("w") as tmp_stdout, \
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75 tempfile.NamedTemporaryFile("w") as tmp_stderr:
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76 # cwltool passes sys.stderr to subprocess.Popen - ensure it has
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77 # and actual fileno.
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78 with real_io():
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79 ret_code = main.main(
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80 args,
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81 stdout=tmp_stdout,
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82 stderr=tmp_stderr,
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83 )
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84 tmp_stdout.flush()
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85 tmp_stderr.flush()
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86 with open(tmp_stderr.name, "r") as stderr_f:
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87 log = stderr_f.read()
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88 ctx.vlog("cwltool log output [%s]" % log)
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89 with open(tmp_stdout.name, "r") as stdout_f:
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90 try:
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91 result = json.load(stdout_f)
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92 except ValueError:
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93 message = JSON_PARSE_ERROR_MESSAGE % (
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94 open(tmp_stdout.name, "r").read(),
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95 tmp_stdout.name,
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96 log
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97 )
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98 error(message)
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99 raise Exception(message)
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100
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101 if ret_code != 0:
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102 return ErrorRunResponse("Error running cwltool", log=log)
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103 outputs = result
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104 return CwlToolRunResponse(
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105 log,
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106 outputs=outputs,
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107 )
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108
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109
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110 __all__ = (
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111 "run_cwltool",
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112 )