Mercurial > repos > shellac > sam_consensus_v3

annotate env/lib/python3.9/site-packages/cwltool/main.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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0
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1 #!/usr/bin/env python3
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2 # PYTHON_ARGCOMPLETE_OK
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3 """Entry point for cwltool."""
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4
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5 import argparse
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6 import functools
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7 import io
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8 import logging
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9 import os
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10 import signal
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11 import subprocess # nosec
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12 import sys
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13 import time
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14 import urllib
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15 from codecs import StreamWriter, getwriter
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16 from collections.abc import MutableMapping, MutableSequence
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17 from typing import (
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18 IO,
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19 Any,
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20 Callable,
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21 Dict,
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22 List,
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23 Mapping,
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24 MutableMapping,
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25 MutableSequence,
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26 Optional,
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27 Sized,
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28 TextIO,
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29 Tuple,
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30 Union,
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31 cast,
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32 )
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33
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34 import argcomplete
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35 import coloredlogs
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36 import pkg_resources # part of setuptools
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37 from ruamel import yaml
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38 from ruamel.yaml.comments import CommentedMap, CommentedSeq
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39 from schema_salad.exceptions import ValidationException
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40 from schema_salad.ref_resolver import Loader, file_uri, uri_file_path
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41 from schema_salad.sourceline import strip_dup_lineno
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42 from schema_salad.utils import ContextType, FetcherCallableType, json_dumps
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43
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44 from . import CWL_CONTENT_TYPES, workflow
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45 from .argparser import arg_parser, generate_parser, get_default_args
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46 from .builder import HasReqsHints
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47 from .context import LoadingContext, RuntimeContext, getdefault
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48 from .cwlrdf import printdot, printrdf
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49 from .errors import UnsupportedRequirement, WorkflowException
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50 from .executors import JobExecutor, MultithreadedJobExecutor, SingleJobExecutor
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51 from .load_tool import (
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52 default_loader,
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53 fetch_document,
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54 jobloaderctx,
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55 load_overrides,
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56 make_tool,
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57 resolve_and_validate_document,
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58 resolve_overrides,
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59 resolve_tool_uri,
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60 )
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61 from .loghandler import _logger, defaultStreamHandler
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62 from .mpi import MpiConfig
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63 from .mutation import MutationManager
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64 from .pack import pack
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65 from .process import (
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66 CWL_IANA,
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67 Process,
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68 add_sizes,
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69 scandeps,
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70 shortname,
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71 use_custom_schema,
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72 use_standard_schema,
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73 )
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74 from .procgenerator import ProcessGenerator
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75 from .provenance import ResearchObject
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76 from .resolver import ga4gh_tool_registries, tool_resolver
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77 from .secrets import SecretStore
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78 from .software_requirements import (
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79 DependenciesConfiguration,
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80 get_container_from_software_requirements,
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81 )
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82 from .stdfsaccess import StdFsAccess
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83 from .subgraph import get_step, get_subgraph
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84 from .update import ALLUPDATES, UPDATES
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85 from .utils import (
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86 DEFAULT_TMP_PREFIX,
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87 CWLObjectType,
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88 CWLOutputAtomType,
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89 CWLOutputType,
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90 adjustDirObjs,
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91 normalizeFilesDirs,
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92 onWindows,
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93 processes_to_kill,
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94 trim_listing,
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95 versionstring,
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96 visit_class,
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97 windows_default_container_id,
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98 )
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99 from .workflow import Workflow
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100
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101
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102 def _terminate_processes() -> None:
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103 """Kill all spawned processes.
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104
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105 Processes to be killed must be appended to `utils.processes_to_kill`
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106 as they are spawned.
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107
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108 An important caveat: since there's no supported way to kill another
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109 thread in Python, this function cannot stop other threads from
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110 continuing to execute while it kills the processes that they've
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111 spawned. This may occasionally lead to unexpected behaviour.
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112 """
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113 # It's possible that another thread will spawn a new task while
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114 # we're executing, so it's not safe to use a for loop here.
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115 while processes_to_kill:
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116 process = processes_to_kill.popleft()
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117 cidfile = [
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118 str(arg).split("=")[1] for arg in process.args if "--cidfile" in str(arg)
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119 ]
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120 if cidfile:
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121 try:
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122 with open(cidfile[0]) as inp_stream:
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123 p = subprocess.Popen( # nosec
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124 ["docker", "kill", inp_stream.read()], shell=False # nosec
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125 )
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126 try:
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127 p.wait(timeout=10)
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128 except subprocess.TimeoutExpired:
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129 p.kill()
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130 except FileNotFoundError:
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131 pass
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132
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133
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134 def _signal_handler(signum: int, _: Any) -> None:
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135 """Kill all spawned processes and exit.
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136
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137 Note that it's possible for another thread to spawn a process after
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138 all processes have been killed, but before Python exits.
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139
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140 Refer to the docstring for _terminate_processes() for other caveats.
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141 """
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142 _terminate_processes()
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143 sys.exit(signum)
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144
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145
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146 def generate_example_input(
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147 inptype: Optional[CWLOutputType],
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148 default: Optional[CWLOutputType],
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149 ) -> Tuple[Any, str]:
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150 """Convert a single input schema into an example."""
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151 example = None
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152 comment = ""
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153 defaults = {
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154 "null": "null",
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155 "Any": "null",
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156 "boolean": False,
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157 "int": 0,
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158 "long": 0,
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159 "float": 0.1,
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160 "double": 0.1,
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161 "string": "a_string",
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162 "File": yaml.comments.CommentedMap(
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163 [("class", "File"), ("path", "a/file/path")]
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164 ),
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165 "Directory": yaml.comments.CommentedMap(
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166 [("class", "Directory"), ("path", "a/directory/path")]
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167 ),
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168 } # type: CWLObjectType
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169 if isinstance(inptype, MutableSequence):
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170 optional = False
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171 if "null" in inptype:
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172 inptype.remove("null")
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173 optional = True
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174 if len(inptype) == 1:
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175 example, comment = generate_example_input(inptype[0], default)
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176 if optional:
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177 if comment:
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178 comment = f"{comment} (optional)"
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179 else:
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180 comment = "optional"
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181 else:
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182 example = CommentedSeq()
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183 for index, entry in enumerate(inptype):
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184 value, e_comment = generate_example_input(entry, default)
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185 example.append(value)
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186 example.yaml_add_eol_comment(e_comment, index)
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187 if optional:
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188 comment = "optional"
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189 elif isinstance(inptype, Mapping) and "type" in inptype:
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190 if inptype["type"] == "array":
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191 first_item = cast(MutableSequence[CWLObjectType], inptype["items"])[0]
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192 items_len = len(cast(Sized, inptype["items"]))
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193 if items_len == 1 and "type" in first_item and first_item["type"] == "enum":
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194 # array of just an enum then list all the options
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195 example = first_item["symbols"]
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196 if "name" in first_item:
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197 comment = 'array of type "{}".'.format(first_item["name"])
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198 else:
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199 value, comment = generate_example_input(inptype["items"], None)
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200 comment = "array of " + comment
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201 if items_len == 1:
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202 example = [value]
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203 else:
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204 example = value
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205 if default is not None:
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206 example = default
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207 elif inptype["type"] == "enum":
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208 symbols = cast(List[str], inptype["symbols"])
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209 if default is not None:
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210 example = default
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211 elif "default" in inptype:
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212 example = inptype["default"]
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213 elif len(cast(Sized, inptype["symbols"])) == 1:
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214 example = symbols[0]
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215 else:
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216 example = "{}_enum_value".format(inptype.get("name", "valid"))
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217 comment = 'enum; valid values: "{}"'.format('", "'.join(symbols))
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218 elif inptype["type"] == "record":
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219 example = yaml.comments.CommentedMap()
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220 if "name" in inptype:
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221 comment = '"{}" record type.'.format(inptype["name"])
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222 for field in cast(List[CWLObjectType], inptype["fields"]):
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223 value, f_comment = generate_example_input(field["type"], None)
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224 example.insert(0, shortname(cast(str, field["name"])), value, f_comment)
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225 elif "default" in inptype:
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226 example = inptype["default"]
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227 comment = 'default value of type "{}".'.format(inptype["type"])
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228 else:
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229 example = defaults.get(cast(str, inptype["type"]), str(inptype))
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230 comment = 'type "{}".'.format(inptype["type"])
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231 else:
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232 if not default:
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233 example = defaults.get(str(inptype), str(inptype))
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234 comment = f'type "{inptype}"'
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235 else:
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236 example = default
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237 comment = f'default value of type "{inptype}".'
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238 return example, comment
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239
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240
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241 def realize_input_schema(
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242 input_types: MutableSequence[CWLObjectType],
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243 schema_defs: MutableMapping[str, CWLObjectType],
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244 ) -> MutableSequence[CWLObjectType]:
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245 """Replace references to named typed with the actual types."""
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246 for index, entry in enumerate(input_types):
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247 if isinstance(entry, str):
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248 if "#" in entry:
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249 _, input_type_name = entry.split("#")
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250 else:
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251 input_type_name = entry
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252 if input_type_name in schema_defs:
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253 entry = input_types[index] = schema_defs[input_type_name]
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254 if isinstance(entry, Mapping):
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255 if isinstance(entry["type"], str) and "#" in entry["type"]:
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256 _, input_type_name = entry["type"].split("#")
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257 if input_type_name in schema_defs:
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258 input_types[index]["type"] = cast(
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259 CWLOutputAtomType,
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260 realize_input_schema(
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261 cast(
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262 MutableSequence[CWLObjectType],
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263 schema_defs[input_type_name],
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264 ),
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265 schema_defs,
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266 ),
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267 )
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268 if isinstance(entry["type"], MutableSequence):
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269 input_types[index]["type"] = cast(
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270 CWLOutputAtomType,
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271 realize_input_schema(
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272 cast(MutableSequence[CWLObjectType], entry["type"]), schema_defs
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273 ),
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274 )
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275 if isinstance(entry["type"], Mapping):
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276 input_types[index]["type"] = cast(
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277 CWLOutputAtomType,
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278 realize_input_schema(
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279 [cast(CWLObjectType, input_types[index]["type"])], schema_defs
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280 ),
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281 )
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282 if entry["type"] == "array":
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283 items = (
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284 entry["items"]
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285 if not isinstance(entry["items"], str)
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286 else [entry["items"]]
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287 )
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288 input_types[index]["items"] = cast(
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289 CWLOutputAtomType,
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290 realize_input_schema(
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291 cast(MutableSequence[CWLObjectType], items), schema_defs
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292 ),
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293 )
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294 if entry["type"] == "record":
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295 input_types[index]["fields"] = cast(
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296 CWLOutputAtomType,
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297 realize_input_schema(
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298 cast(MutableSequence[CWLObjectType], entry["fields"]),
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299 schema_defs,
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300 ),
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301 )
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302 return input_types
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303
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304
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305 def generate_input_template(tool: Process) -> CWLObjectType:
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306 """Generate an example input object for the given CWL process."""
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307 template = yaml.comments.CommentedMap()
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308 for inp in realize_input_schema(tool.tool["inputs"], tool.schemaDefs):
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309 name = shortname(cast(str, inp["id"]))
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310 value, comment = generate_example_input(inp["type"], inp.get("default", None))
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311 template.insert(0, name, value, comment)
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312 return template
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313
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314
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315 def load_job_order(
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316 args: argparse.Namespace,
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317 stdin: IO[Any],
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318 fetcher_constructor: Optional[FetcherCallableType],
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319 overrides_list: List[CWLObjectType],
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320 tool_file_uri: str,
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321 ) -> Tuple[Optional[CWLObjectType], str, Loader]:
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322
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323 job_order_object = None
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324 job_order_file = None
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325
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326 _jobloaderctx = jobloaderctx.copy()
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327 loader = Loader(_jobloaderctx, fetcher_constructor=fetcher_constructor)
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328
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329 if len(args.job_order) == 1 and args.job_order[0][0] != "-":
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330 job_order_file = args.job_order[0]
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331 elif len(args.job_order) == 1 and args.job_order[0] == "-":
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332 job_order_object = yaml.main.round_trip_load(stdin)
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333 job_order_object, _ = loader.resolve_all(
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334 job_order_object, file_uri(os.getcwd()) + "/"
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335 )
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336 else:
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337 job_order_file = None
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338
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339 if job_order_object is not None:
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340 input_basedir = args.basedir if args.basedir else os.getcwd()
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341 elif job_order_file is not None:
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342 input_basedir = (
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343 args.basedir
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344 if args.basedir
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345 else os.path.abspath(os.path.dirname(job_order_file))
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346 )
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347 job_order_object, _ = loader.resolve_ref(
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348 job_order_file,
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349 checklinks=False,
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350 content_types=CWL_CONTENT_TYPES,
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351 )
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352
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353 if (
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354 job_order_object is not None
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355 and "http://commonwl.org/cwltool#overrides" in job_order_object
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356 ):
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357 ov_uri = file_uri(job_order_file or input_basedir)
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358 overrides_list.extend(
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359 resolve_overrides(job_order_object, ov_uri, tool_file_uri)
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360 )
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361 del job_order_object["http://commonwl.org/cwltool#overrides"]
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362
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363 if job_order_object is None:
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364 input_basedir = args.basedir if args.basedir else os.getcwd()
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365
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366 if job_order_object is not None and not isinstance(
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367 job_order_object, MutableMapping
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368 ):
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369 _logger.error(
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370 "CWL input object at %s is not formatted correctly, it should be a "
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371 "JSON/YAML dictionay, not %s.\n"
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372 "Raw input object:\n%s",
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373 job_order_file or "stdin",
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374 type(job_order_object),
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375 job_order_object,
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376 )
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377 sys.exit(1)
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378 return (job_order_object, input_basedir, loader)
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379
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380
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diff changeset
381 def init_job_order(
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382 job_order_object: Optional[CWLObjectType],
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383 args: argparse.Namespace,
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384 process: Process,
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385 loader: Loader,
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386 stdout: Union[TextIO, StreamWriter],
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387 print_input_deps: bool = False,
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388 relative_deps: str = "primary",
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389 make_fs_access: Callable[[str], StdFsAccess] = StdFsAccess,
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390 input_basedir: str = "",
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391 secret_store: Optional[SecretStore] = None,
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392 input_required: bool = True,
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393 ) -> CWLObjectType:
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394 secrets_req, _ = process.get_requirement("http://commonwl.org/cwltool#Secrets")
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395 if job_order_object is None:
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396 namemap = {} # type: Dict[str, str]
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397 records = [] # type: List[str]
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398 toolparser = generate_parser(
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diff changeset
399 argparse.ArgumentParser(prog=args.workflow),
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400 process,
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401 namemap,
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402 records,
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403 input_required,
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404 )
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405 if args.tool_help:
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406 toolparser.print_help()
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407 exit(0)
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408 cmd_line = vars(toolparser.parse_args(args.job_order))
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409 for record_name in records:
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410 record = {}
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411 record_items = {
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412 k: v for k, v in cmd_line.items() if k.startswith(record_name)
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413 }
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414 for key, value in record_items.items():
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415 record[key[len(record_name) + 1 :]] = value
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416 del cmd_line[key]
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417 cmd_line[str(record_name)] = record
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418 if "job_order" in cmd_line and cmd_line["job_order"]:
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419 try:
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420 job_order_object = cast(
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421 CWLObjectType,
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422 loader.resolve_ref(cmd_line["job_order"])[0],
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423 )
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424 except Exception:
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425 _logger.exception(
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426 "Failed to resolv job_order: %s", cmd_line["job_order"]
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427 )
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428 exit(1)
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429 else:
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430 job_order_object = {"id": args.workflow}
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431
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432 del cmd_line["job_order"]
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433
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434 job_order_object.update({namemap[k]: v for k, v in cmd_line.items()})
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435
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436 if secret_store and secrets_req:
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437 secret_store.store(
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438 [shortname(sc) for sc in cast(List[str], secrets_req["secrets"])],
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439 job_order_object,
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440 )
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441
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442 if _logger.isEnabledFor(logging.DEBUG):
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443 _logger.debug(
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444 "Parsed job order from command line: %s",
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445 json_dumps(job_order_object, indent=4),
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446 )
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447
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448 for inp in process.tool["inputs"]:
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449 if "default" in inp and (
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450 not job_order_object or shortname(inp["id"]) not in job_order_object
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451 ):
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diff changeset
452 if not job_order_object:
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453 job_order_object = {}
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454 job_order_object[shortname(inp["id"])] = inp["default"]
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455
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456 if job_order_object is None:
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diff changeset
457 if process.tool["inputs"]:
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diff changeset
458 if toolparser is not None:
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459 print(f"\nOptions for {args.workflow} ")
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diff changeset
460 toolparser.print_help()
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diff changeset
461 _logger.error("")
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462 _logger.error("Input object required, use --help for details")
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463 exit(1)
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diff changeset
464 else:
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465 job_order_object = {}
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diff changeset
466
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467 if print_input_deps:
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diff changeset
468 basedir = None # type: Optional[str]
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diff changeset
469 uri = cast(str, job_order_object["id"])
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parents:
diff changeset
470 if uri == args.workflow:
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diff changeset
471 basedir = os.path.dirname(uri)
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472 uri = ""
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473 printdeps(
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diff changeset
474 job_order_object,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
475 loader,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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diff changeset
476 stdout,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
477 relative_deps,
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diff changeset
478 uri,
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diff changeset
479 basedir=basedir,
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diff changeset
480 nestdirs=False,
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diff changeset
481 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
482 exit(0)
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diff changeset
483
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484 def path_to_loc(p: CWLObjectType) -> None:
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parents:
diff changeset
485 if "location" not in p and "path" in p:
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diff changeset
486 p["location"] = p["path"]
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parents:
diff changeset
487 del p["path"]
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488
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489 ns = {} # type: ContextType
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490 ns.update(cast(ContextType, job_order_object.get("$namespaces", {})))
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491 ns.update(cast(ContextType, process.metadata.get("$namespaces", {})))
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parents:
diff changeset
492 ld = Loader(ns)
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493
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494 def expand_formats(p: CWLObjectType) -> None:
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495 if "format" in p:
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496 p["format"] = ld.expand_url(cast(str, p["format"]), "")
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497
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498 visit_class(job_order_object, ("File", "Directory"), path_to_loc)
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499 visit_class(
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500 job_order_object,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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501 ("File",),
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diff changeset
502 functools.partial(add_sizes, make_fs_access(input_basedir)),
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503 )
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diff changeset
504 visit_class(job_order_object, ("File",), expand_formats)
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505 adjustDirObjs(job_order_object, trim_listing)
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parents:
diff changeset
506 normalizeFilesDirs(job_order_object)
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parents:
diff changeset
507
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508 if secret_store and secrets_req:
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parents:
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509 secret_store.store(
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diff changeset
510 [shortname(sc) for sc in cast(List[str], secrets_req["secrets"])],
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diff changeset
511 job_order_object,
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512 )
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513
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514 if "cwl:tool" in job_order_object:
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parents:
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515 del job_order_object["cwl:tool"]
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parents:
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516 if "id" in job_order_object:
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parents:
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517 del job_order_object["id"]
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518 return job_order_object
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519
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520
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521 def make_relative(base: str, obj: CWLObjectType) -> None:
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522 """Relativize the location URI of a File or Directory object."""
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523 uri = cast(str, obj.get("location", obj.get("path")))
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parents:
diff changeset
524 if ":" in uri.split("/")[0] and not uri.startswith("file://"):
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parents:
diff changeset
525 pass
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parents:
diff changeset
526 else:
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parents:
diff changeset
527 if uri.startswith("file://"):
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parents:
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528 uri = uri_file_path(uri)
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diff changeset
529 obj["location"] = os.path.relpath(uri, base)
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530
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531
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532 def printdeps(
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parents:
diff changeset
533 obj: CWLObjectType,
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534 document_loader: Loader,
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535 stdout: Union[TextIO, StreamWriter],
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536 relative_deps: str,
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parents:
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537 uri: str,
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538 basedir: Optional[str] = None,
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parents:
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539 nestdirs: bool = True,
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parents:
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540 ) -> None:
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parents:
diff changeset
541 """Print a JSON representation of the dependencies of the CWL document."""
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parents:
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542 deps = find_deps(obj, document_loader, uri, basedir=basedir, nestdirs=nestdirs)
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parents:
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543 if relative_deps == "primary":
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parents:
diff changeset
544 base = basedir if basedir else os.path.dirname(uri_file_path(str(uri)))
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parents:
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545 elif relative_deps == "cwd":
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parents:
diff changeset
546 base = os.getcwd()
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parents:
diff changeset
547 visit_class(deps, ("File", "Directory"), functools.partial(make_relative, base))
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parents:
diff changeset
548 stdout.write(json_dumps(deps, indent=4))
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parents:
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549
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550
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parents:
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551 def prov_deps(
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parents:
diff changeset
552 obj: CWLObjectType,
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parents:
diff changeset
553 document_loader: Loader,
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554 uri: str,
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diff changeset
555 basedir: Optional[str] = None,
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parents:
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556 ) -> CWLObjectType:
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parents:
diff changeset
557 deps = find_deps(obj, document_loader, uri, basedir=basedir)
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parents:
diff changeset
558
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parents:
diff changeset
559 def remove_non_cwl(deps: CWLObjectType) -> None:
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parents:
diff changeset
560 if "secondaryFiles" in deps:
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561 sec_files = cast(List[CWLObjectType], deps["secondaryFiles"])
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parents:
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562 for index, entry in enumerate(sec_files):
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parents:
diff changeset
563 if not ("format" in entry and entry["format"] == CWL_IANA):
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parents:
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564 del sec_files[index]
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parents:
diff changeset
565 else:
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parents:
diff changeset
566 remove_non_cwl(entry)
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parents:
diff changeset
567
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diff changeset
568 remove_non_cwl(deps)
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parents:
diff changeset
569 return deps
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570
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571
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parents:
diff changeset
572 def find_deps(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
573 obj: CWLObjectType,
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parents:
diff changeset
574 document_loader: Loader,
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parents:
diff changeset
575 uri: str,
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diff changeset
576 basedir: Optional[str] = None,
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parents:
diff changeset
577 nestdirs: bool = True,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
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578 ) -> CWLObjectType:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
579 """Find the dependencies of the CWL document."""
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parents:
diff changeset
580 deps = {
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parents:
diff changeset
581 "class": "File",
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parents:
diff changeset
582 "location": uri,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
583 "format": CWL_IANA,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
584 } # type: CWLObjectType
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parents:
diff changeset
585
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parents:
diff changeset
586 def loadref(base: str, uri: str) -> Union[CommentedMap, CommentedSeq, str, None]:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
587 return document_loader.fetch(document_loader.fetcher.urljoin(base, uri))
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parents:
diff changeset
588
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parents:
diff changeset
589 sfs = scandeps(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
590 basedir if basedir else uri,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
591 obj,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
592 {"$import", "run"},
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
593 {"$include", "$schemas", "location"},
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parents:
diff changeset
594 loadref,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
595 nestdirs=nestdirs,
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parents:
diff changeset
596 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
597 if sfs is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
598 deps["secondaryFiles"] = cast(MutableSequence[CWLOutputAtomType], sfs)
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parents:
diff changeset
599
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parents:
diff changeset
600 return deps
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parents:
diff changeset
601
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parents:
diff changeset
602
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parents:
diff changeset
603 def print_pack(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
604 loadingContext: LoadingContext,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
605 uri: str,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
606 ) -> str:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
607 """Return a CWL serialization of the CWL document in JSON."""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
608 packed = pack(loadingContext, uri)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
609 if len(cast(Sized, packed["$graph"])) > 1:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
610 return json_dumps(packed, indent=4)
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parents:
diff changeset
611 return json_dumps(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
612 cast(MutableSequence[CWLObjectType], packed["$graph"])[0], indent=4
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parents:
diff changeset
613 )
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shellac
parents:
diff changeset
614
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parents:
diff changeset
615
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parents:
diff changeset
616 def supported_cwl_versions(enable_dev: bool) -> List[str]:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
617 # ALLUPDATES and UPDATES are dicts
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parents:
diff changeset
618 if enable_dev:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
619 versions = list(ALLUPDATES)
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parents:
diff changeset
620 else:
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parents:
diff changeset
621 versions = list(UPDATES)
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parents:
diff changeset
622 versions.sort()
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parents:
diff changeset
623 return versions
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parents:
diff changeset
624
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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diff changeset
625
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parents:
diff changeset
626 def configure_logging(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
627 args: argparse.Namespace,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
628 stderr_handler: logging.Handler,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
629 runtimeContext: RuntimeContext,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
630 ) -> None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
631 rdflib_logger = logging.getLogger("rdflib.term")
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parents:
diff changeset
632 rdflib_logger.addHandler(stderr_handler)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
633 rdflib_logger.setLevel(logging.ERROR)
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shellac
parents:
diff changeset
634 if args.quiet:
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parents:
diff changeset
635 # Silence STDERR, not an eventual provenance log file
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parents:
diff changeset
636 stderr_handler.setLevel(logging.WARN)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
637 if runtimeContext.debug:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
638 # Increase to debug for both stderr and provenance log file
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
639 _logger.setLevel(logging.DEBUG)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
640 stderr_handler.setLevel(logging.DEBUG)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
641 rdflib_logger.setLevel(logging.DEBUG)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
642 fmtclass = coloredlogs.ColoredFormatter if args.enable_color else logging.Formatter
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
643 formatter = fmtclass("%(levelname)s %(message)s")
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parents:
diff changeset
644 if args.timestamps:
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parents:
diff changeset
645 formatter = fmtclass(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
646 "[%(asctime)s] %(levelname)s %(message)s", "%Y-%m-%d %H:%M:%S"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
647 )
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parents:
diff changeset
648 stderr_handler.setFormatter(formatter)
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parents:
diff changeset
649
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parents:
diff changeset
650
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parents:
diff changeset
651 def setup_schema(
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parents:
diff changeset
652 args: argparse.Namespace, custom_schema_callback: Optional[Callable[[], None]]
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parents:
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653 ) -> None:
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parents:
diff changeset
654 if custom_schema_callback is not None:
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parents:
diff changeset
655 custom_schema_callback()
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parents:
diff changeset
656 elif args.enable_ext:
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parents:
diff changeset
657 with pkg_resources.resource_stream(__name__, "extensions.yml") as res:
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parents:
diff changeset
658 ext10 = res.read().decode("utf-8")
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parents:
diff changeset
659 with pkg_resources.resource_stream(__name__, "extensions-v1.1.yml") as res:
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parents:
diff changeset
660 ext11 = res.read().decode("utf-8")
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parents:
diff changeset
661 use_custom_schema("v1.0", "http://commonwl.org/cwltool", ext10)
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parents:
diff changeset
662 use_custom_schema("v1.1", "http://commonwl.org/cwltool", ext11)
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parents:
diff changeset
663 use_custom_schema("v1.2.0-dev1", "http://commonwl.org/cwltool", ext11)
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parents:
diff changeset
664 use_custom_schema("v1.2.0-dev2", "http://commonwl.org/cwltool", ext11)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
665 use_custom_schema("v1.2.0-dev3", "http://commonwl.org/cwltool", ext11)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
666 else:
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parents:
diff changeset
667 use_standard_schema("v1.0")
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shellac
parents:
diff changeset
668 use_standard_schema("v1.1")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
669 use_standard_schema("v1.2.0-dev1")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
670 use_standard_schema("v1.2.0-dev2")
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parents:
diff changeset
671 use_standard_schema("v1.2.0-dev3")
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shellac
parents:
diff changeset
672
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parents:
diff changeset
673
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
674 class ProvLogFormatter(logging.Formatter):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
675 """Enforce ISO8601 with both T and Z."""
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shellac
parents:
diff changeset
676
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parents:
diff changeset
677 def __init__(self) -> None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
678 """Use the default formatter with our custom formatstring."""
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shellac
parents:
diff changeset
679 super().__init__("[%(asctime)sZ] %(message)s")
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shellac
parents:
diff changeset
680
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parents:
diff changeset
681 def formatTime(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
682 self, record: logging.LogRecord, datefmt: Optional[str] = None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
683 ) -> str:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
684 formatted_time = time.strftime(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
685 "%Y-%m-%dT%H:%M:%S", time.gmtime(float(record.created))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
686 )
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shellac
parents:
diff changeset
687 with_msecs = f"{formatted_time},{record.msecs:03f}"
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shellac
parents:
diff changeset
688 return with_msecs
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shellac
parents:
diff changeset
689
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parents:
diff changeset
690
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shellac
parents:
diff changeset
691 def setup_provenance(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
692 args: argparse.Namespace,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
693 argsl: List[str],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
694 runtimeContext: RuntimeContext,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
695 ) -> Optional[int]:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
696 if not args.compute_checksum:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
697 _logger.error("--provenance incompatible with --no-compute-checksum")
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shellac
parents:
diff changeset
698 return 1
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
699 ro = ResearchObject(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
700 getdefault(runtimeContext.make_fs_access, StdFsAccess)(""),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
701 temp_prefix_ro=args.tmpdir_prefix,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
702 orcid=args.orcid,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
703 full_name=args.cwl_full_name,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
704 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
705 runtimeContext.research_obj = ro
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
706 log_file_io = ro.open_log_file_for_activity(ro.engine_uuid)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
707 prov_log_handler = logging.StreamHandler(cast(IO[str], log_file_io))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
708
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
709 prov_log_handler.setFormatter(ProvLogFormatter())
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
710 _logger.addHandler(prov_log_handler)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
711 _logger.debug("[provenance] Logging to %s", log_file_io)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
712 if argsl is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
713 # Log cwltool command line options to provenance file
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
714 _logger.info("[cwltool] %s %s", sys.argv[0], " ".join(argsl))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
715 _logger.debug("[cwltool] Arguments: %s", args)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
716 return None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
717
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
718
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
719 def setup_loadingContext(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
720 loadingContext: Optional[LoadingContext],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
721 runtimeContext: RuntimeContext,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
722 args: argparse.Namespace,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
723 ) -> LoadingContext:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
724 if loadingContext is None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
725 loadingContext = LoadingContext(vars(args))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
726 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
727 loadingContext = loadingContext.copy()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
728 loadingContext.loader = default_loader(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
729 loadingContext.fetcher_constructor,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
730 enable_dev=args.enable_dev,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
731 doc_cache=args.doc_cache,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
732 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
733 loadingContext.research_obj = runtimeContext.research_obj
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
734 loadingContext.disable_js_validation = args.disable_js_validation or (
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
735 not args.do_validate
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
736 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
737 loadingContext.construct_tool_object = getdefault(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
738 loadingContext.construct_tool_object, workflow.default_make_tool
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
739 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
740 loadingContext.resolver = getdefault(loadingContext.resolver, tool_resolver)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
741 if loadingContext.do_update is None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
742 loadingContext.do_update = not (args.pack or args.print_subgraph)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
743
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
744 return loadingContext
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
745
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
746
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
747 def make_template(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
748 tool: Process,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
749 ) -> None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
750 """Make a template CWL input object for the give Process."""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
751
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
752 def my_represent_none(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
753 self: Any, data: Any
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
754 ) -> Any: # pylint: disable=unused-argument
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
755 """Force clean representation of 'null'."""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
756 return self.represent_scalar("tag:yaml.org,2002:null", "null")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
757
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
758 yaml.representer.RoundTripRepresenter.add_representer(type(None), my_represent_none)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
759 yaml.main.round_trip_dump(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
760 generate_input_template(tool),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
761 sys.stdout,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
762 default_flow_style=False,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
763 indent=4,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
764 block_seq_indent=2,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
765 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
766
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
767
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
768 def choose_target(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
769 args: argparse.Namespace,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
770 tool: Process,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
771 loadingContext: LoadingContext,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
772 ) -> Optional[Process]:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
773 """Walk the Workflow, extract the subset matches all the args.targets."""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
774 if loadingContext.loader is None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
775 raise Exception("loadingContext.loader cannot be None")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
776
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
777 if isinstance(tool, Workflow):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
778 url = urllib.parse.urlparse(tool.tool["id"])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
779 if url.fragment:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
780 extracted = get_subgraph(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
781 [tool.tool["id"] + "/" + r for r in args.target], tool
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
782 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
783 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
784 extracted = get_subgraph(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
785 [
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
786 loadingContext.loader.fetcher.urljoin(tool.tool["id"], "#" + r)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
787 for r in args.target
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
788 ],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
789 tool,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
790 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
791 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
792 _logger.error("Can only use --target on Workflows")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
793 return None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
794 if isinstance(loadingContext.loader.idx, MutableMapping):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
795 loadingContext.loader.idx[extracted["id"]] = extracted
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
796 tool = make_tool(extracted["id"], loadingContext)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
797 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
798 raise Exception("Missing loadingContext.loader.idx!")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
799
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
800 return tool
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
801
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
802
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
803 def choose_step(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
804 args: argparse.Namespace,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
805 tool: Process,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
806 loadingContext: LoadingContext,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
807 ) -> Optional[Process]:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
808 """Walk the given Workflow and extract just args.single_step."""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
809 if loadingContext.loader is None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
810 raise Exception("loadingContext.loader cannot be None")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
811
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
812 if isinstance(tool, Workflow):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
813 url = urllib.parse.urlparse(tool.tool["id"])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
814 if url.fragment:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
815 extracted = get_step(tool, tool.tool["id"] + "/" + args.singe_step)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
816 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
817 extracted = get_step(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
818 tool,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
819 loadingContext.loader.fetcher.urljoin(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
820 tool.tool["id"], "#" + args.single_step
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
821 ),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
822 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
823 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
824 _logger.error("Can only use --single-step on Workflows")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
825 return None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
826 if isinstance(loadingContext.loader.idx, MutableMapping):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
827 loadingContext.loader.idx[extracted["id"]] = extracted
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
828 tool = make_tool(extracted["id"], loadingContext)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
829 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
830 raise Exception("Missing loadingContext.loader.idx!")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
831
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
832 return tool
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
833
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
834
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
835 def check_working_directories(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
836 runtimeContext: RuntimeContext,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
837 ) -> Optional[int]:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
838 """Make any needed working directories."""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
839 for dirprefix in ("tmpdir_prefix", "tmp_outdir_prefix", "cachedir"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
840 if (
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
841 getattr(runtimeContext, dirprefix)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
842 and getattr(runtimeContext, dirprefix) != DEFAULT_TMP_PREFIX
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
843 ):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
844 sl = (
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
845 "/"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
846 if getattr(runtimeContext, dirprefix).endswith("/")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
847 or dirprefix == "cachedir"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
848 else ""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
849 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
850 setattr(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
851 runtimeContext,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
852 dirprefix,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
853 os.path.abspath(getattr(runtimeContext, dirprefix)) + sl,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
854 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
855 if not os.path.exists(os.path.dirname(getattr(runtimeContext, dirprefix))):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
856 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
857 os.makedirs(os.path.dirname(getattr(runtimeContext, dirprefix)))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
858 except Exception:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
859 _logger.exception("Failed to create directory.")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
860 return 1
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
861 return None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
862
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
863
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
864 def main(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
865 argsl: Optional[List[str]] = None,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
866 args: Optional[argparse.Namespace] = None,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
867 job_order_object: Optional[CWLObjectType] = None,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
868 stdin: IO[Any] = sys.stdin,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
869 stdout: Optional[Union[TextIO, StreamWriter]] = None,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
870 stderr: IO[Any] = sys.stderr,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
871 versionfunc: Callable[[], str] = versionstring,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
872 logger_handler: Optional[logging.Handler] = None,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
873 custom_schema_callback: Optional[Callable[[], None]] = None,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
874 executor: Optional[JobExecutor] = None,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
875 loadingContext: Optional[LoadingContext] = None,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
876 runtimeContext: Optional[RuntimeContext] = None,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
877 input_required: bool = True,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
878 ) -> int:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
879 if not stdout: # force UTF-8 even if the console is configured differently
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
880 if hasattr(sys.stdout, "encoding") and sys.stdout.encoding.upper() not in (
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
881 "UTF-8",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
882 "UTF8",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
883 ):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
884 if hasattr(sys.stdout, "detach"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
885 stdout = io.TextIOWrapper(sys.stdout.buffer, encoding="utf-8")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
886 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
887 stdout = getwriter("utf-8")(sys.stdout) # type: ignore
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
888 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
889 stdout = sys.stdout
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
890
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
891 _logger.removeHandler(defaultStreamHandler)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
892 stderr_handler = logger_handler
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
893 if stderr_handler is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
894 _logger.addHandler(stderr_handler)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
895 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
896 coloredlogs.install(logger=_logger, stream=stderr)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
897 stderr_handler = _logger.handlers[-1]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
898 workflowobj = None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
899 prov_log_handler = None # type: Optional[logging.StreamHandler]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
900 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
901 if args is None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
902 if argsl is None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
903 argsl = sys.argv[1:]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
904 addl = [] # type: List[str]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
905 if "CWLTOOL_OPTIONS" in os.environ:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
906 addl = os.environ["CWLTOOL_OPTIONS"].split(" ")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
907 parser = arg_parser()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
908 argcomplete.autocomplete(parser)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
909 args = parser.parse_args(addl + argsl)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
910 if args.record_container_id:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
911 if not args.cidfile_dir:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
912 args.cidfile_dir = os.getcwd()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
913 del args.record_container_id
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
914
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
915 if runtimeContext is None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
916 runtimeContext = RuntimeContext(vars(args))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
917 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
918 runtimeContext = runtimeContext.copy()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
919
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
920 # If on Windows platform, a default Docker Container is used if not
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
921 # explicitely provided by user
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
922 if onWindows() and not runtimeContext.default_container:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
923 # This docker image is a minimal alpine image with bash installed
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
924 # (size 6 mb). source: https://github.com/frol/docker-alpine-bash
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
925 runtimeContext.default_container = windows_default_container_id
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
926
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
927 # If caller parsed its own arguments, it may not include every
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
928 # cwltool option, so fill in defaults to avoid crashing when
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
929 # dereferencing them in args.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
930 for key, val in get_default_args().items():
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
931 if not hasattr(args, key):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
932 setattr(args, key, val)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
933
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
934 configure_logging(args, stderr_handler, runtimeContext)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
935
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
936 if args.version:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
937 print(versionfunc())
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
938 return 0
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
939 _logger.info(versionfunc())
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
940
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
941 if args.print_supported_versions:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
942 print("\n".join(supported_cwl_versions(args.enable_dev)))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
943 return 0
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
944
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
945 if not args.workflow:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
946 if os.path.isfile("CWLFile"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
947 args.workflow = "CWLFile"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
948 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
949 _logger.error("CWL document required, no input file was provided")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
950 parser.print_help()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
951 return 1
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
952
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
953 if args.ga4gh_tool_registries:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
954 ga4gh_tool_registries[:] = args.ga4gh_tool_registries
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
955 if not args.enable_ga4gh_tool_registry:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
956 del ga4gh_tool_registries[:]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
957
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
958 if args.mpi_config_file is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
959 runtimeContext.mpi_config = MpiConfig.load(args.mpi_config_file)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
960
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
961 setup_schema(args, custom_schema_callback)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
962
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
963 if args.provenance:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
964 if argsl is None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
965 raise Exception("argsl cannot be None")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
966 if setup_provenance(args, argsl, runtimeContext) is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
967 return 1
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
968
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
969 loadingContext = setup_loadingContext(loadingContext, runtimeContext, args)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
970
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
971 uri, tool_file_uri = resolve_tool_uri(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
972 args.workflow,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
973 resolver=loadingContext.resolver,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
974 fetcher_constructor=loadingContext.fetcher_constructor,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
975 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
976
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
977 try_again_msg = (
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
978 "" if args.debug else ", try again with --debug for more information"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
979 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
980
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
981 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
982 job_order_object, input_basedir, jobloader = load_job_order(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
983 args,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
984 stdin,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
985 loadingContext.fetcher_constructor,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
986 loadingContext.overrides_list,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
987 tool_file_uri,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
988 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
989
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
990 if args.overrides:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
991 loadingContext.overrides_list.extend(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
992 load_overrides(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
993 file_uri(os.path.abspath(args.overrides)), tool_file_uri
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
994 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
995 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
996
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
997 loadingContext, workflowobj, uri = fetch_document(uri, loadingContext)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
998
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
999 if args.print_deps and loadingContext.loader:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1000 printdeps(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1001 workflowobj, loadingContext.loader, stdout, args.relative_deps, uri
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1002 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1003 return 0
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1004
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1005 loadingContext, uri = resolve_and_validate_document(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1006 loadingContext,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1007 workflowobj,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1008 uri,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1009 preprocess_only=(args.print_pre or args.pack),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1010 skip_schemas=args.skip_schemas,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1011 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1012
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1013 if loadingContext.loader is None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1014 raise Exception("Impossible code path.")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1015 processobj, metadata = loadingContext.loader.resolve_ref(uri)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1016 processobj = cast(CommentedMap, processobj)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1017 if args.pack:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1018 stdout.write(print_pack(loadingContext, uri))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1019 return 0
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1020
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shellac
parents:
diff changeset
1021 if args.provenance and runtimeContext.research_obj:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1022 # Can't really be combined with args.pack at same time
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1023 runtimeContext.research_obj.packed_workflow(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1024 print_pack(loadingContext, uri)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1025 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1026
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1027 if args.print_pre:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1028 stdout.write(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1029 json_dumps(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1030 processobj, indent=4, sort_keys=True, separators=(",", ": ")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1031 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1032 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1033 return 0
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1034
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1035 tool = make_tool(uri, loadingContext)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1036 if args.make_template:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1037 make_template(tool)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1038 return 0
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1039
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shellac
parents:
diff changeset
1040 if args.validate:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1041 print(f"{args.workflow} is valid CWL.")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1042 return 0
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shellac
parents:
diff changeset
1043
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shellac
parents:
diff changeset
1044 if args.print_rdf:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1045 stdout.write(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1046 printrdf(tool, loadingContext.loader.ctx, args.rdf_serializer)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1047 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1048 return 0
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1049
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1050 if args.print_dot:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1051 printdot(tool, loadingContext.loader.ctx, stdout)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1052 return 0
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1053
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1054 if args.print_targets:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1055 for f in ("outputs", "steps", "inputs"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1056 if tool.tool[f]:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1057 _logger.info("%s%s targets:", f[0].upper(), f[1:-1])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1058 stdout.write(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1059 " "
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1060 + "\n ".join([shortname(t["id"]) for t in tool.tool[f]])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1061 + "\n"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1062 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1063 return 0
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1064
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1065 if args.target:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1066 ctool = choose_target(args, tool, loadingContext)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1067 if ctool is None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1068 return 1
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1069 else:
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shellac
parents:
diff changeset
1070 tool = ctool
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1071
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shellac
parents:
diff changeset
1072 elif args.single_step:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1073 ctool = choose_step(args, tool, loadingContext)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1074 if ctool is None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1075 return 1
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1076 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1077 tool = ctool
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1078
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shellac
parents:
diff changeset
1079 if args.print_subgraph:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1080 if "name" in tool.tool:
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shellac
parents:
diff changeset
1081 del tool.tool["name"]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1082 stdout.write(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1083 json_dumps(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1084 tool.tool, indent=4, sort_keys=True, separators=(",", ": ")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1085 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1086 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1087 return 0
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1088
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shellac
parents:
diff changeset
1089 except (ValidationException) as exc:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1090 _logger.error(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1091 "Tool definition failed validation:\n%s", str(exc), exc_info=args.debug
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1092 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1093 return 1
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1094 except (RuntimeError, WorkflowException) as exc:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1095 _logger.error(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1096 "Tool definition failed initialization:\n%s",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1097 str(exc),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1098 exc_info=args.debug,
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shellac
parents:
diff changeset
1099 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1100 return 1
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1101 except Exception as exc:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1102 _logger.error(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1103 "I'm sorry, I couldn't load this CWL file%s.\nThe error was: %s",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1104 try_again_msg,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1105 str(exc) if not args.debug else "",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1106 exc_info=args.debug,
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shellac
parents:
diff changeset
1107 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1108 return 1
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1109
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shellac
parents:
diff changeset
1110 if isinstance(tool, int):
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shellac
parents:
diff changeset
1111 return tool
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1112
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1113 # If on MacOS platform, TMPDIR must be set to be under one of the
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1114 # shared volumes in Docker for Mac
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1115 # More info: https://dockstore.org/docs/faq
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1116 if sys.platform == "darwin":
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1117 default_mac_path = "/private/tmp/docker_tmp"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1118 if runtimeContext.tmp_outdir_prefix == DEFAULT_TMP_PREFIX:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1119 runtimeContext.tmp_outdir_prefix = default_mac_path
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1120 if runtimeContext.tmpdir_prefix == DEFAULT_TMP_PREFIX:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1121 runtimeContext.tmpdir_prefix = default_mac_path
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1122
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1123 if check_working_directories(runtimeContext) is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1124 return 1
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1125
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1126 if args.cachedir:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1127 if args.move_outputs == "move":
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1128 runtimeContext.move_outputs = "copy"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1129 runtimeContext.tmp_outdir_prefix = args.cachedir
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1130
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1131 runtimeContext.secret_store = getdefault(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1132 runtimeContext.secret_store, SecretStore()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1133 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1134 runtimeContext.make_fs_access = getdefault(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1135 runtimeContext.make_fs_access, StdFsAccess
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1136 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1137
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1138 if not executor:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1139 if args.parallel:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1140 temp_executor = MultithreadedJobExecutor()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1141 runtimeContext.select_resources = temp_executor.select_resources
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1142 real_executor = temp_executor # type: JobExecutor
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1143 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1144 real_executor = SingleJobExecutor()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1145 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1146 real_executor = executor
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1147
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1148 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1149 runtimeContext.basedir = input_basedir
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1150
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1151 if isinstance(tool, ProcessGenerator):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1152 tfjob_order = {} # type: CWLObjectType
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1153 if loadingContext.jobdefaults:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1154 tfjob_order.update(loadingContext.jobdefaults)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1155 if job_order_object:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1156 tfjob_order.update(job_order_object)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1157 tfout, tfstatus = real_executor(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1158 tool.embedded_tool, tfjob_order, runtimeContext
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1159 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1160 if not tfout or tfstatus != "success":
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1161 raise WorkflowException(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1162 "ProcessGenerator failed to generate workflow"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1163 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1164 tool, job_order_object = tool.result(tfjob_order, tfout, runtimeContext)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1165 if not job_order_object:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1166 job_order_object = None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1167
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1168 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1169 initialized_job_order_object = init_job_order(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1170 job_order_object,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1171 args,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1172 tool,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1173 jobloader,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1174 stdout,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1175 print_input_deps=args.print_input_deps,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1176 relative_deps=args.relative_deps,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1177 make_fs_access=runtimeContext.make_fs_access,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1178 input_basedir=input_basedir,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1179 secret_store=runtimeContext.secret_store,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1180 input_required=input_required,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1181 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1182 except SystemExit as err:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1183 return err.code
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1184
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1185 del args.workflow
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1186 del args.job_order
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1187
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1188 conf_file = getattr(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1189 args, "beta_dependency_resolvers_configuration", None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1190 ) # str
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1191 use_conda_dependencies = getattr(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1192 args, "beta_conda_dependencies", None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1193 ) # str
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1194
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1195 if conf_file or use_conda_dependencies:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1196 runtimeContext.job_script_provider = DependenciesConfiguration(args)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1197 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1198 runtimeContext.find_default_container = functools.partial(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1199 find_default_container,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1200 default_container=runtimeContext.default_container,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1201 use_biocontainers=args.beta_use_biocontainers,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1202 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1203
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1204 (out, status) = real_executor(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1205 tool, initialized_job_order_object, runtimeContext, logger=_logger
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1206 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1207
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1208 if out is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1209 if runtimeContext.research_obj is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1210 runtimeContext.research_obj.create_job(out, True)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1211
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1212 def remove_at_id(doc: CWLObjectType) -> None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1213 for key in list(doc.keys()):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1214 if key == "@id":
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1215 del doc[key]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1216 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1217 value = doc[key]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1218 if isinstance(value, MutableMapping):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1219 remove_at_id(value)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1220 elif isinstance(value, MutableSequence):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1221 for entry in value:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1222 if isinstance(entry, MutableMapping):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1223 remove_at_id(entry)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1224
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1225 remove_at_id(out)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1226 visit_class(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1227 out,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1228 ("File",),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1229 functools.partial(add_sizes, runtimeContext.make_fs_access("")),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1230 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1231
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1232 def loc_to_path(obj: CWLObjectType) -> None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1233 for field in ("path", "nameext", "nameroot", "dirname"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1234 if field in obj:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1235 del obj[field]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1236 if cast(str, obj["location"]).startswith("file://"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1237 obj["path"] = uri_file_path(cast(str, obj["location"]))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1238
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1239 visit_class(out, ("File", "Directory"), loc_to_path)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1240
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1241 # Unsetting the Generation from final output object
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1242 visit_class(out, ("File",), MutationManager().unset_generation)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1243
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1244 if isinstance(out, str):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1245 stdout.write(out)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1246 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1247 stdout.write(json_dumps(out, indent=4, ensure_ascii=False))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1248 stdout.write("\n")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1249 if hasattr(stdout, "flush"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1250 stdout.flush()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1251
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1252 if status != "success":
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1253 _logger.warning("Final process status is %s", status)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1254 return 1
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1255 _logger.info("Final process status is %s", status)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1256 return 0
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1257
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1258 except (ValidationException) as exc:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1259 _logger.error(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1260 "Input object failed validation:\n%s", str(exc), exc_info=args.debug
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1261 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1262 return 1
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1263 except UnsupportedRequirement as exc:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1264 _logger.error(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1265 "Workflow or tool uses unsupported feature:\n%s",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1266 str(exc),
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shellac
parents:
diff changeset
1267 exc_info=args.debug,
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shellac
parents:
diff changeset
1268 )
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shellac
parents:
diff changeset
1269 return 33
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shellac
parents:
diff changeset
1270 except WorkflowException as exc:
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shellac
parents:
diff changeset
1271 _logger.error(
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shellac
parents:
diff changeset
1272 "Workflow error%s:\n%s",
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shellac
parents:
diff changeset
1273 try_again_msg,
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shellac
parents:
diff changeset
1274 strip_dup_lineno(str(exc)),
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shellac
parents:
diff changeset
1275 exc_info=args.debug,
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shellac
parents:
diff changeset
1276 )
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parents:
diff changeset
1277 return 1
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parents:
diff changeset
1278 except Exception as exc: # pylint: disable=broad-except
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shellac
parents:
diff changeset
1279 _logger.error(
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shellac
parents:
diff changeset
1280 "Unhandled error%s:\n %s",
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shellac
parents:
diff changeset
1281 try_again_msg,
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shellac
parents:
diff changeset
1282 str(exc),
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shellac
parents:
diff changeset
1283 exc_info=args.debug,
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parents:
diff changeset
1284 )
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shellac
parents:
diff changeset
1285 return 1
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shellac
parents:
diff changeset
1286
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shellac
parents:
diff changeset
1287 finally:
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shellac
parents:
diff changeset
1288 if (
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shellac
parents:
diff changeset
1289 args
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shellac
parents:
diff changeset
1290 and runtimeContext
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shellac
parents:
diff changeset
1291 and runtimeContext.research_obj
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shellac
parents:
diff changeset
1292 and workflowobj
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shellac
parents:
diff changeset
1293 and loadingContext
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shellac
parents:
diff changeset
1294 ):
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shellac
parents:
diff changeset
1295 research_obj = runtimeContext.research_obj
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shellac
parents:
diff changeset
1296 if loadingContext.loader is not None:
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shellac
parents:
diff changeset
1297 research_obj.generate_snapshot(
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shellac
parents:
diff changeset
1298 prov_deps(workflowobj, loadingContext.loader, uri)
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shellac
parents:
diff changeset
1299 )
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shellac
parents:
diff changeset
1300 else:
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shellac
parents:
diff changeset
1301 _logger.warning(
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shellac
parents:
diff changeset
1302 "Unable to generate provenance snapshot "
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shellac
parents:
diff changeset
1303 " due to missing loadingContext.loader."
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parents:
diff changeset
1304 )
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shellac
parents:
diff changeset
1305 if prov_log_handler is not None:
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shellac
parents:
diff changeset
1306 # Stop logging so we won't half-log adding ourself to RO
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shellac
parents:
diff changeset
1307 _logger.debug(
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shellac
parents:
diff changeset
1308 "[provenance] Closing provenance log file %s", prov_log_handler
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shellac
parents:
diff changeset
1309 )
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shellac
parents:
diff changeset
1310 _logger.removeHandler(prov_log_handler)
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shellac
parents:
diff changeset
1311 # Ensure last log lines are written out
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shellac
parents:
diff changeset
1312 prov_log_handler.flush()
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shellac
parents:
diff changeset
1313 # Underlying WritableBagFile will add the tagfile to the manifest
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shellac
parents:
diff changeset
1314 prov_log_handler.stream.close()
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shellac
parents:
diff changeset
1315 prov_log_handler.close()
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parents:
diff changeset
1316 research_obj.close(args.provenance)
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shellac
parents:
diff changeset
1317
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parents:
diff changeset
1318 _logger.removeHandler(stderr_handler)
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shellac
parents:
diff changeset
1319 _logger.addHandler(defaultStreamHandler)
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shellac
parents:
diff changeset
1320
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shellac
parents:
diff changeset
1321
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shellac
parents:
diff changeset
1322 def find_default_container(
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parents:
diff changeset
1323 builder: HasReqsHints,
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parents:
diff changeset
1324 default_container: Optional[str] = None,
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shellac
parents:
diff changeset
1325 use_biocontainers: Optional[bool] = None,
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parents:
diff changeset
1326 ) -> Optional[str]:
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parents:
diff changeset
1327 """Find a container."""
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parents:
diff changeset
1328 if not default_container and use_biocontainers:
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shellac
parents:
diff changeset
1329 default_container = get_container_from_software_requirements(
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shellac
parents:
diff changeset
1330 use_biocontainers, builder
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parents:
diff changeset
1331 )
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shellac
parents:
diff changeset
1332 return default_container
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shellac
parents:
diff changeset
1333
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shellac
parents:
diff changeset
1334
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parents:
diff changeset
1335 def run(*args, **kwargs):
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shellac
parents:
diff changeset
1336 # type: (*Any, **Any) -> None
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shellac
parents:
diff changeset
1337 """Run cwltool."""
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parents:
diff changeset
1338 signal.signal(signal.SIGTERM, _signal_handler)
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parents:
diff changeset
1339 try:
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diff changeset
1340 sys.exit(main(*args, **kwargs))
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parents:
diff changeset
1341 finally:
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shellac
parents:
diff changeset
1342 _terminate_processes()
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shellac
parents:
diff changeset
1343
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diff changeset
1344
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diff changeset
1345 if __name__ == "__main__":
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shellac
parents:
diff changeset
1346 run(sys.argv[1:])