Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/planemo/cwl/cwl2script/cwl2script.py @ 4:79f47841a781 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:47:39 -0400
parents 26e78fe6e8c4
children
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1 import argparse
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2 import cwltool.main
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3 import sys
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4 import os
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5 import schema_salad
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6 import logging
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7 from cwltool.process import checkRequirements, shortname, adjustFiles
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8 import shellescape
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9 import re
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10 import copy
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11 import json
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12
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13 needs_shell_quoting = re.compile(r"""(^$|[\s|&;()<>\'"$@])""").search
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14 glob_metacharacters = re.compile(r"""[\[\]\*?]""").search
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15
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16 def maybe_quote(arg):
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17 return shellescape.quote(arg) if needs_shell_quoting(arg) else arg
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18
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19 def generateScriptForTool(tool, job, outdir):
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20 for j in tool.job(job, "", None, outdir=outdir):
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21 return ("""mkdir -p %s # output directory
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22 mkdir -p %s # temporary directory
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23 %s%s%s
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24 rm -r %s # clean up temporary directory
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25 """ % (maybe_quote(j.outdir), maybe_quote(j.tmpdir),
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26 " ".join([maybe_quote(arg) for arg in (j.command_line)]),
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27 ' < %s' % maybe_quote(j.stdin) if j.stdin else '',
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28 ' > %s' % maybe_quote(os.path.join(j.outdir, j.stdout)) if j.stdout else '',
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29 maybe_quote(j.tmpdir)),
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30 j.outdir, j.tmpdir)
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31
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32
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33 def generateScriptForWorkflow(cwlwf, cwljob, outdir):
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34 promises = {}
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35 jobs = {}
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36 script = ["#!/bin/sh",
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37 "",
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38 "# Workflow generated from %s using cwl2script" % (cwlwf.tool["id"]),
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39 ""
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40 "set -x",
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41 ""
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42 ]
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43
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44 outdirs = []
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45
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46 for inp in cwlwf.tool["inputs"]:
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47 promises[inp["id"]] = (cwlwf, cwljob[shortname(inp["id"])])
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48
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49 alloutputs_fufilled = False
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50 while not alloutputs_fufilled:
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51 # Iteratively go over the workflow steps, adding jobs to the script as their
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52 # dependencies are fufilled by upstream workflow inputs or
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53 # step outputs. Loop exits when the workflow outputs
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54 # are satisfied.
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55
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56 alloutputs_fufilled = True
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57
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58 progress = False
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59 for step in cwlwf.steps:
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60 if step.tool["id"] not in jobs:
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61 stepinputs_fufilled = True
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62 for inp in step.tool["inputs"]:
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63 if "source" in inp and inp["source"] not in promises:
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64 stepinputs_fufilled = False
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65 if stepinputs_fufilled:
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66 jobobj = {}
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67
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68 # TODO: Handle multiple inbound links
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69 # TODO: Handle scatter/gather
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70 # (both are discussed in section 5.1.2 in CWL spec draft-2)
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71
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72 script.append("# Run step %s" % step.tool["id"])
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73
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74 for inp in step.tool["inputs"]:
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75 if "source" in inp:
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76 jobobj[shortname(inp["id"])] = promises[inp["source"]][1]
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77 script.append("# depends on step %s" % promises[inp["source"]][0].tool["id"])
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78 elif "default" in inp:
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79 d = copy.copy(inp["default"])
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80 jobobj[shortname(inp["id"])] = d
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81
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82 (wfjob, joboutdir, jobtmpdir) = generateScriptForTool(step.embedded_tool, jobobj, None)
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83 outdirs.append(joboutdir)
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84
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85 jobs[step.tool["id"]] = True
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86
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87 script.append(wfjob)
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88
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89 for out in step.tool["outputs"]:
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90 for toolout in step.embedded_tool.tool["outputs"]:
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91 if shortname(toolout["id"]) == shortname(out["id"]):
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92 if toolout["type"] != "File":
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93 raise Exception("Only supports file outputs")
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94 if glob_metacharacters(toolout["outputBinding"]["glob"]):
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95 raise Exception("Only support glob with concrete filename.")
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96 promises[out["id"]] = (step, {"class":"File", "path": os.path.join(joboutdir, toolout["outputBinding"]["glob"])})
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97 progress = True
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98
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99 for out in cwlwf.tool["outputs"]:
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100 if "source" in out:
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101 if out["source"] not in promises:
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102 alloutputs_fufilled = False
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103
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104 if not alloutputs_fufilled and not progress:
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105 raise Exception("Not making progress")
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106
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107 outobj = {}
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108 script.append("# Move output files to the current directory")
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109
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110 for out in cwlwf.tool["outputs"]:
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111 f = promises[out["source"]][1]
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112 script.append("mv %s ." % (maybe_quote(f["path"])))
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113 f["path"] = os.path.basename(f["path"])
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114
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115 if f.get("secondaryFiles"):
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116 script.append("mv %s ." % (' '.join([maybe_quote(sf["path"]) for sf in f["secondaryFiles"]])))
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117 for sf in f["secondaryFiles"]:
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118 sf["path"] = os.path.basename(sf["path"])
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119
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120 outobj[shortname(out["id"])] = f
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121
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122 script.append("")
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123 script.append("# Clean up staging output directories")
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124 script.append("rm -r %s" % (' '.join([maybe_quote(od) for od in outdirs])))
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125 script.append("")
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126
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127 script.append("# Generate final output object")
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128 script.append("echo '%s'" % json.dumps(outobj, indent=4))
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129
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130 return "\n".join(script)
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131
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132
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133
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134 supportedProcessRequirements = ["SchemaDefRequirement"]
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135
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136 def main(args=None):
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137 parser = argparse.ArgumentParser()
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138 parser.add_argument("cwltool", type=str)
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139 parser.add_argument("cwljob", type=str)
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140
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141 parser.add_argument("--conformance-test", action="store_true")
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142 parser.add_argument("--no-container", action="store_true")
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143 parser.add_argument("--basedir", type=str)
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144 parser.add_argument("--outdir", type=str, default=os.getcwd())
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145
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146 options = parser.parse_args(args)
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147
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148 uri = "file://" + os.path.abspath(options.cwljob)
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149
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150 if options.conformance_test:
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151 loader = schema_salad.ref_resolver.Loader({})
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152 else:
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153 loader = schema_salad.ref_resolver.Loader({
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154 "@base": uri,
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155 "path": {
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156 "@type": "@id"
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157 }
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158 })
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159
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160 job, _ = loader.resolve_ref(uri)
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161
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162 t = cwltool.main.load_tool(options.cwltool, False, False, cwltool.workflow.defaultMakeTool, True)
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163
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164 if type(t) == int:
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165 return t
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166
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167 try:
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168 checkRequirements(t.tool, supportedProcessRequirements)
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169 except Exception as e:
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170 logging.error(e)
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171 return 33
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172
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173 for inp in t.tool["inputs"]:
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174 if shortname(inp["id"]) in job:
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175 pass
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176 elif shortname(inp["id"]) not in job and "default" in inp:
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177 job[shortname(inp["id"])] = copy.copy(inp["default"])
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178 elif shortname(inp["id"]) not in job and inp["type"][0] == "null":
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179 pass
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180 else:
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181 raise Exception("Missing inputs `%s`" % shortname(inp["id"]))
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182
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183 if options.conformance_test:
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184 sys.stdout.write(json.dumps(cwltool.main.single_job_executor(t, job, options.basedir, options, conformance_test=True), indent=4))
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185 return 0
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186
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187 if not options.basedir:
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188 options.basedir = os.path.dirname(os.path.abspath(options.cwljob))
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189
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190 outdir = options.outdir
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191
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192 if t.tool["class"] == "Workflow":
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193 print generateScriptForWorkflow(t, job, outdir)
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194 elif t.tool["class"] == "CommandLineTool":
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195 print generateScriptForTool(t, job, outdir)
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196
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197 return 0
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198
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199 if __name__=="__main__":
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200 sys.exit(main(sys.argv[1:]))