Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/cwltool/main.py @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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1 #!/usr/bin/env python
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2 """Entry point for cwltool."""
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3 from __future__ import absolute_import, print_function
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4
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5 import argparse
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6 import copy
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7 import functools
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8 import io
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9 import logging
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10 import os
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11 import signal
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12 import sys
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13 import time
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14 from codecs import StreamWriter, getwriter # pylint: disable=unused-import
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15 from six.moves import urllib
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16 from typing import (IO, Any, Callable, Dict, Iterable, List, Mapping,
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17 MutableMapping, MutableSequence, Optional, TextIO, Tuple,
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18 Union, cast)
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19
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20 import pkg_resources # part of setuptools
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21 from ruamel import yaml
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22 from ruamel.yaml.comments import CommentedMap, CommentedSeq
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23 from schema_salad import validate
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24 from schema_salad.ref_resolver import Fetcher, Loader, file_uri, uri_file_path
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25 from schema_salad.sourceline import strip_dup_lineno, cmap
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26 from six import string_types, iteritems, PY3
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27 from typing_extensions import Text
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28 # move to a regular typing import when Python 3.3-3.6 is no longer supported
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29
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30 if PY3:
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31 from collections.abc import Iterable, Sequence, MutableSequence
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32 else: # Needed for Py3.8
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33 from collections import Iterable, Sequence, MutableSequence
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34
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35 from . import command_line_tool, workflow
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36 from .argparser import arg_parser, generate_parser, get_default_args
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37 from .builder import HasReqsHints # pylint: disable=unused-import
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38 from .context import LoadingContext, RuntimeContext, getdefault
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39 from .cwlrdf import printdot, printrdf
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40 from .errors import UnsupportedRequirement, WorkflowException
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41 from .executors import MultithreadedJobExecutor, SingleJobExecutor, JobExecutor
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42 from .load_tool import (FetcherConstructorType, # pylint: disable=unused-import
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43 fetch_document, jobloaderctx, load_overrides,
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44 make_tool, resolve_overrides, resolve_tool_uri,
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45 resolve_and_validate_document, default_loader)
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46 from .loghandler import _logger, defaultStreamHandler
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47 from .mutation import MutationManager
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48 from .pack import pack
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49 from .pathmapper import adjustDirObjs, normalizeFilesDirs, trim_listing
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50 from .process import (Process, add_sizes, # pylint: disable=unused-import
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51 scandeps, shortname, use_custom_schema,
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52 use_standard_schema, CWL_IANA)
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53 from .workflow import Workflow
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54 from .procgenerator import ProcessGenerator
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55 from .provenance import ResearchObject
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56 from .resolver import ga4gh_tool_registries, tool_resolver
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57 from .secrets import SecretStore
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58 from .software_requirements import (DependenciesConfiguration,
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59 get_container_from_software_requirements)
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60 from .stdfsaccess import StdFsAccess
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61 from .update import ALLUPDATES, UPDATES
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62 from .utils import (DEFAULT_TMP_PREFIX, json_dumps, onWindows,
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63 processes_to_kill, versionstring, visit_class,
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64 windows_default_container_id)
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65 from .subgraph import get_subgraph
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66
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67 import coloredlogs
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68
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69 def _terminate_processes():
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70 # type: () -> None
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71 """Kill all spawned processes.
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72
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73 Processes to be killed must be appended to `utils.processes_to_kill`
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74 as they are spawned.
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75
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76 An important caveat: since there's no supported way to kill another
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77 thread in Python, this function cannot stop other threads from
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78 continuing to execute while it kills the processes that they've
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79 spawned. This may occasionally lead to unexpected behaviour.
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80 """
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81 # It's possible that another thread will spawn a new task while
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82 # we're executing, so it's not safe to use a for loop here.
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83 while processes_to_kill:
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84 processes_to_kill.popleft().kill()
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85
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86
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87 def _signal_handler(signum, _):
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88 # type: (int, Any) -> None
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89 """Kill all spawned processes and exit.
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90
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91 Note that it's possible for another thread to spawn a process after
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92 all processes have been killed, but before Python exits.
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93
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94 Refer to the docstring for _terminate_processes() for other caveats.
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95 """
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96 _terminate_processes()
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97 sys.exit(signum)
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98
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99
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100 def generate_example_input(inptype, # type: Any
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101 default # type: Optional[Any]
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102 ): # type: (...) -> Tuple[Any, Text]
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103 """Convert a single input schema into an example."""
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104 example = None
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105 comment = u""
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106 defaults = {u'null': 'null',
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107 u'Any': 'null',
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108 u'boolean': False,
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109 u'int': 0,
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110 u'long': 0,
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111 u'float': 0.1,
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112 u'double': 0.1,
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113 u'string': 'a_string',
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114 u'File': yaml.comments.CommentedMap([
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115 ('class', 'File'), ('path', 'a/file/path')]),
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116 u'Directory': yaml.comments.CommentedMap([
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117 ('class', 'Directory'), ('path', 'a/directory/path')])
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118 } # type: Dict[Text, Any]
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119 if isinstance(inptype, MutableSequence):
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120 optional = False
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121 if 'null' in inptype:
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122 inptype.remove('null')
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123 optional = True
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124 if len(inptype) == 1:
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125 example, comment = generate_example_input(inptype[0], default)
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126 if optional:
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127 if comment:
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128 comment = u"{} (optional)".format(comment)
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129 else:
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130 comment = u"optional"
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131 else:
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132 example = yaml.comments.CommentedSeq()
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133 for index, entry in enumerate(inptype):
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134 value, e_comment = generate_example_input(entry, default)
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135 example.append(value)
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136 example.yaml_add_eol_comment(e_comment, index)
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137 if optional:
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138 comment = u"optional"
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139 elif isinstance(inptype, Mapping) and 'type' in inptype:
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140 if inptype['type'] == 'array':
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141 if len(inptype['items']) == 1 and 'type' in inptype['items'][0] \
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142 and inptype['items'][0]['type'] == 'enum':
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143 # array of just an enum then list all the options
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144 example = inptype['items'][0]['symbols']
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145 if 'name' in inptype['items'][0]:
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146 comment = u'array of type "{}".'.format(inptype['items'][0]['name'])
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147 else:
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148 value, comment = generate_example_input(inptype['items'], None)
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149 comment = u"array of " + comment
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150 if len(inptype['items']) == 1:
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151 example = [value]
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152 else:
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153 example = value
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154 if default is not None:
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155 example = default
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156 elif inptype['type'] == 'enum':
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157 if default is not None:
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158 example = default
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159 elif 'default' in inptype:
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160 example = inptype['default']
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161 elif len(inptype['symbols']) == 1:
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162 example = inptype['symbols'][0]
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163 else:
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164 example = '{}_enum_value'.format(inptype.get('name', 'valid'))
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165 comment = u'enum; valid values: "{}"'.format(
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166 '", "'.join(inptype['symbols']))
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167 elif inptype['type'] == 'record':
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168 example = yaml.comments.CommentedMap()
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169 if 'name' in inptype:
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170 comment = u'"{}" record type.'.format(inptype['name'])
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171 for field in inptype['fields']:
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172 value, f_comment = generate_example_input(field['type'], None)
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173 example.insert(0, shortname(field['name']), value, f_comment)
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174 elif 'default' in inptype:
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175 example = inptype['default']
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176 comment = u'default value of type "{}".'.format(inptype['type'])
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177 else:
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178 example = defaults.get(inptype['type'], Text(inptype))
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179 comment = u'type "{}".'.format(inptype['type'])
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180 else:
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181 if not default:
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182 example = defaults.get(Text(inptype), Text(inptype))
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183 comment = u'type "{}"'.format(inptype)
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184 else:
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185 example = default
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186 comment = u'default value of type "{}".'.format(inptype)
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187 return example, comment
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188
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189 def realize_input_schema(input_types, # type: MutableSequence[Dict[Text, Any]]
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190 schema_defs # type: Dict[Text, Any]
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191 ): # type: (...) -> MutableSequence[Dict[Text, Any]]
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192 """Replace references to named typed with the actual types."""
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193 for index, entry in enumerate(input_types):
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194 if isinstance(entry, string_types):
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195 if '#' in entry:
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196 _, input_type_name = entry.split('#')
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197 else:
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198 input_type_name = entry
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199 if input_type_name in schema_defs:
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200 entry = input_types[index] = schema_defs[input_type_name]
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201 if isinstance(entry, Mapping):
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202 if isinstance(entry['type'], string_types) and '#' in entry['type']:
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203 _, input_type_name = entry['type'].split('#')
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204 if input_type_name in schema_defs:
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205 input_types[index]['type'] = realize_input_schema(
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206 schema_defs[input_type_name], schema_defs)
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207 if isinstance(entry['type'], MutableSequence):
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208 input_types[index]['type'] = realize_input_schema(
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209 entry['type'], schema_defs)
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210 if isinstance(entry['type'], Mapping):
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211 input_types[index]['type'] = realize_input_schema(
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212 [input_types[index]['type']], schema_defs)
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213 if entry['type'] == 'array':
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214 items = entry['items'] if \
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215 not isinstance(entry['items'], string_types) else [entry['items']]
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216 input_types[index]['items'] = realize_input_schema(items, schema_defs)
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217 if entry['type'] == 'record':
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218 input_types[index]['fields'] = realize_input_schema(
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219 entry['fields'], schema_defs)
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220 return input_types
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221
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222 def generate_input_template(tool):
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223 # type: (Process) -> Dict[Text, Any]
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224 """Generate an example input object for the given CWL process."""
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225 template = yaml.comments.CommentedMap()
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226 for inp in realize_input_schema(tool.tool["inputs"], tool.schemaDefs):
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227 name = shortname(inp["id"])
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228 value, comment = generate_example_input(
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229 inp['type'], inp.get('default', None))
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230 template.insert(0, name, value, comment)
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231 return template
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232
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233 def load_job_order(args, # type: argparse.Namespace
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234 stdin, # type: IO[Any]
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235 fetcher_constructor, # type: Optional[Fetcher]
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236 overrides_list, # type: List[Dict[Text, Any]]
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237 tool_file_uri # type: Text
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238 ): # type: (...) -> Tuple[Optional[MutableMapping[Text, Any]], Text, Loader]
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239
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240 job_order_object = None
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241 job_order_file = None
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242
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243 _jobloaderctx = jobloaderctx.copy()
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244 loader = Loader(_jobloaderctx, fetcher_constructor=fetcher_constructor) # type: ignore
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245
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246 if len(args.job_order) == 1 and args.job_order[0][0] != "-":
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247 job_order_file = args.job_order[0]
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248 elif len(args.job_order) == 1 and args.job_order[0] == "-":
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249 job_order_object = yaml.round_trip_load(stdin)
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diff changeset
250 job_order_object, _ = loader.resolve_all(job_order_object, file_uri(os.getcwd()) + "/")
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diff changeset
251 else:
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252 job_order_file = None
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253
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diff changeset
254 if job_order_object is not None:
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diff changeset
255 input_basedir = args.basedir if args.basedir else os.getcwd()
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256 elif job_order_file is not None:
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257 input_basedir = args.basedir if args.basedir \
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diff changeset
258 else os.path.abspath(os.path.dirname(job_order_file))
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259 job_order_object, _ = loader.resolve_ref(job_order_file, checklinks=False)
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260
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261 if job_order_object is not None and "http://commonwl.org/cwltool#overrides" in job_order_object:
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262 ov_uri = file_uri(job_order_file or input_basedir)
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parents:
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263 overrides_list.extend(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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264 resolve_overrides(job_order_object, ov_uri, tool_file_uri))
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parents:
diff changeset
265 del job_order_object["http://commonwl.org/cwltool#overrides"]
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266
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parents:
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267 if job_order_object is None:
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268 input_basedir = args.basedir if args.basedir else os.getcwd()
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269
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270 if job_order_object is not None and not isinstance(job_order_object, MutableMapping):
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271 _logger.error(
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272 'CWL input object at %s is not formatted correctly, it should be a '
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273 'JSON/YAML dictionay, not %s.\n'
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274 'Raw input object:\n%s', job_order_file or "stdin",
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275 type(job_order_object), job_order_object)
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276 sys.exit(1)
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277 return (job_order_object, input_basedir, loader)
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278
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279 def init_job_order(job_order_object, # type: Optional[MutableMapping[Text, Any]]
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280 args, # type: argparse.Namespace
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281 process, # type: Process
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282 loader, # type: Loader
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283 stdout, # type: Union[TextIO, StreamWriter]
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284 print_input_deps=False, # type: bool
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285 relative_deps=False, # type: bool
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286 make_fs_access=StdFsAccess, # type: Callable[[Text], StdFsAccess]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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287 input_basedir="", # type: Text
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288 secret_store=None, # type: Optional[SecretStore]
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289 input_required=True # type: bool
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290 ): # type: (...) -> MutableMapping[Text, Any]
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291 secrets_req, _ = process.get_requirement("http://commonwl.org/cwltool#Secrets")
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parents:
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292 if job_order_object is None:
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293 namemap = {} # type: Dict[Text, Text]
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294 records = [] # type: List[Text]
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295 toolparser = generate_parser(
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diff changeset
296 argparse.ArgumentParser(prog=args.workflow), process, namemap, records, input_required)
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parents:
diff changeset
297 if args.tool_help:
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298 toolparser.print_help()
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299 exit(0)
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300 cmd_line = vars(toolparser.parse_args(args.job_order))
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parents:
diff changeset
301 for record_name in records:
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302 record = {}
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303 record_items = {
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diff changeset
304 k: v for k, v in iteritems(cmd_line)
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parents:
diff changeset
305 if k.startswith(record_name)}
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parents:
diff changeset
306 for key, value in iteritems(record_items):
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307 record[key[len(record_name) + 1:]] = value
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
308 del cmd_line[key]
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diff changeset
309 cmd_line[str(record_name)] = record
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parents:
diff changeset
310 if 'job_order' in cmd_line and cmd_line["job_order"]:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
311 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
312 job_order_object = cast(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
313 MutableMapping[Text, Any],
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diff changeset
314 loader.resolve_ref(cmd_line["job_order"])[0])
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diff changeset
315 except Exception as err:
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diff changeset
316 _logger.error(Text(err), exc_info=args.debug)
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diff changeset
317 exit(1)
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parents:
diff changeset
318 else:
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diff changeset
319 job_order_object = {"id": args.workflow}
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diff changeset
320
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diff changeset
321 del cmd_line["job_order"]
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diff changeset
322
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diff changeset
323 job_order_object.update({namemap[k]: v for k, v in cmd_line.items()})
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diff changeset
324
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parents:
diff changeset
325 if secret_store and secrets_req:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
326 secret_store.store(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
327 [shortname(sc) for sc in secrets_req["secrets"]], job_order_object)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
328
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
329 if _logger.isEnabledFor(logging.DEBUG):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
330 _logger.debug(u"Parsed job order from command line: %s",
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
331 json_dumps(job_order_object, indent=4))
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parents:
diff changeset
332
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parents:
diff changeset
333 for inp in process.tool["inputs"]:
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parents:
diff changeset
334 if "default" in inp and (
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
335 not job_order_object or shortname(inp["id"]) not in job_order_object):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
336 if not job_order_object:
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parents:
diff changeset
337 job_order_object = {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
338 job_order_object[shortname(inp["id"])] = inp["default"]
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diff changeset
339
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diff changeset
340 if job_order_object is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
341 if process.tool["inputs"]:
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parents:
diff changeset
342 if toolparser is not None:
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parents:
diff changeset
343 print(u"\nOptions for {} ".format(args.workflow))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
344 toolparser.print_help()
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diff changeset
345 _logger.error("")
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diff changeset
346 _logger.error("Input object required, use --help for details")
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diff changeset
347 exit(1)
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parents:
diff changeset
348 else:
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diff changeset
349 job_order_object = {}
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diff changeset
350
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parents:
diff changeset
351 if print_input_deps:
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parents:
diff changeset
352 basedir = None # type: Optional[Text]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
353 uri = job_order_object["id"]
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parents:
diff changeset
354 if uri == args.workflow:
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parents:
diff changeset
355 basedir = os.path.dirname(uri)
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parents:
diff changeset
356 uri = ""
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
357 printdeps(job_order_object, loader, stdout, relative_deps, uri,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
358 basedir=basedir, nestdirs=False)
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parents:
diff changeset
359 exit(0)
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parents:
diff changeset
360
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parents:
diff changeset
361 def path_to_loc(p): # type: (Dict[Text, Any]) -> None
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parents:
diff changeset
362 if "location" not in p and "path" in p:
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parents:
diff changeset
363 p["location"] = p["path"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
364 del p["path"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
365
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parents:
diff changeset
366 ns = {} # type: Dict[Text, Union[Dict[Any, Any], Text, Iterable[Text]]]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
367 ns.update(job_order_object.get("$namespaces", {}))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
368 ns.update(process.metadata.get("$namespaces", {}))
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parents:
diff changeset
369 ld = Loader(ns)
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diff changeset
370
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diff changeset
371 def expand_formats(p): # type: (Dict[Text, Any]) -> None
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parents:
diff changeset
372 if "format" in p:
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373 p["format"] = ld.expand_url(p["format"], "")
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diff changeset
374
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diff changeset
375 visit_class(job_order_object, ("File", "Directory"), path_to_loc)
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diff changeset
376 visit_class(job_order_object, ("File",), functools.partial(add_sizes, make_fs_access(input_basedir)))
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diff changeset
377 visit_class(job_order_object, ("File",), expand_formats)
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diff changeset
378 adjustDirObjs(job_order_object, trim_listing)
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diff changeset
379 normalizeFilesDirs(job_order_object)
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diff changeset
380
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diff changeset
381 if secret_store and secrets_req:
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diff changeset
382 secret_store.store(
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diff changeset
383 [shortname(sc) for sc in secrets_req["secrets"]], job_order_object)
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diff changeset
384
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diff changeset
385 if "cwl:tool" in job_order_object:
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diff changeset
386 del job_order_object["cwl:tool"]
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diff changeset
387 if "id" in job_order_object:
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388 del job_order_object["id"]
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diff changeset
389 return job_order_object
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diff changeset
390
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diff changeset
391
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392 def make_relative(base, obj): # type: (Text, Dict[Text, Any]) -> None
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diff changeset
393 """Relativize the location URI of a File or Directory object."""
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394 uri = obj.get("location", obj.get("path"))
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395 if ":" in uri.split("/")[0] and not uri.startswith("file://"):
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396 pass
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diff changeset
397 else:
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diff changeset
398 if uri.startswith("file://"):
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diff changeset
399 uri = uri_file_path(uri)
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400 obj["location"] = os.path.relpath(uri, base)
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401
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diff changeset
402 def printdeps(obj, # type: Mapping[Text, Any]
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403 document_loader, # type: Loader
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404 stdout, # type: Union[TextIO, StreamWriter]
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405 relative_deps, # type: bool
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diff changeset
406 uri, # type: Text
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diff changeset
407 basedir=None, # type: Optional[Text]
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diff changeset
408 nestdirs=True # type: bool
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diff changeset
409 ): # type: (...) -> None
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diff changeset
410 """Print a JSON representation of the dependencies of the CWL document."""
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diff changeset
411 deps = find_deps(obj, document_loader, uri, basedir=basedir,
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412 nestdirs=nestdirs)
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diff changeset
413 if relative_deps == "primary":
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diff changeset
414 base = basedir if basedir else os.path.dirname(uri_file_path(str(uri)))
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diff changeset
415 elif relative_deps == "cwd":
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diff changeset
416 base = os.getcwd()
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diff changeset
417 visit_class(deps, ("File", "Directory"), functools.partial(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
418 make_relative, base))
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diff changeset
419 stdout.write(json_dumps(deps, indent=4))
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420
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diff changeset
421 def prov_deps(obj, # type: Mapping[Text, Any]
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diff changeset
422 document_loader, # type: Loader
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diff changeset
423 uri, # type: Text
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diff changeset
424 basedir=None # type: Optional[Text]
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diff changeset
425 ): # type: (...) -> MutableMapping[Text, Any]
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426 deps = find_deps(obj, document_loader, uri, basedir=basedir)
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diff changeset
427
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428 def remove_non_cwl(deps): # type: (MutableMapping[Text, Any]) -> None
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diff changeset
429 if 'secondaryFiles' in deps:
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diff changeset
430 sec_files = deps['secondaryFiles']
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diff changeset
431 for index, entry in enumerate(sec_files):
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diff changeset
432 if not ('format' in entry and entry['format'] == CWL_IANA):
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diff changeset
433 del sec_files[index]
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diff changeset
434 else:
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diff changeset
435 remove_non_cwl(entry)
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diff changeset
436
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diff changeset
437 remove_non_cwl(deps)
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parents:
diff changeset
438 return deps
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diff changeset
439
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diff changeset
440
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diff changeset
441 def find_deps(obj, # type: Mapping[Text, Any]
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diff changeset
442 document_loader, # type: Loader
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parents:
diff changeset
443 uri, # type: Text
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diff changeset
444 basedir=None, # type: Optional[Text]
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diff changeset
445 nestdirs=True # type: bool
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diff changeset
446 ): # type: (...) -> Dict[Text, Any]
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parents:
diff changeset
447 """Find the dependencies of the CWL document."""
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parents:
diff changeset
448 deps = {"class": "File", "location": uri, "format": CWL_IANA} # type: Dict[Text, Any]
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diff changeset
449
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diff changeset
450 def loadref(base, uri): # type: (Text, Text) -> Any
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parents:
diff changeset
451 return document_loader.fetch(document_loader.fetcher.urljoin(base, uri))
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diff changeset
452
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parents:
diff changeset
453 sfs = scandeps(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
454 basedir if basedir else uri, obj, {"$import", "run"},
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
455 {"$include", "$schemas", "location"}, loadref, nestdirs=nestdirs)
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diff changeset
456 if sfs is not None:
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parents:
diff changeset
457 deps["secondaryFiles"] = sfs
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parents:
diff changeset
458
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parents:
diff changeset
459 return deps
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parents:
diff changeset
460
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parents:
diff changeset
461 def print_pack(document_loader, # type: Loader
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parents:
diff changeset
462 processobj, # type: CommentedMap
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parents:
diff changeset
463 uri, # type: Text
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
464 metadata # type: Dict[Text, Any]
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parents:
diff changeset
465 ): # type: (...) -> Text
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parents:
diff changeset
466 """Return a CWL serialization of the CWL document in JSON."""
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
467 packed = pack(document_loader, processobj, uri, metadata)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
468 if len(packed["$graph"]) > 1:
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parents:
diff changeset
469 return json_dumps(packed, indent=4)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
470 return json_dumps(packed["$graph"][0], indent=4)
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parents:
diff changeset
471
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
472
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parents:
diff changeset
473 def supported_cwl_versions(enable_dev): # type: (bool) -> List[Text]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
474 # ALLUPDATES and UPDATES are dicts
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
475 if enable_dev:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
476 versions = list(ALLUPDATES)
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parents:
diff changeset
477 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
478 versions = list(UPDATES)
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parents:
diff changeset
479 versions.sort()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
480 return versions
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
481
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
482 def configure_logging(args, # type: argparse.Namespace
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
483 stderr_handler, # type: logging.Handler
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
484 runtimeContext # type: RuntimeContext
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
485 ): # type: (...) -> None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
486 # Configure logging
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
487 rdflib_logger = logging.getLogger("rdflib.term")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
488 rdflib_logger.addHandler(stderr_handler)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
489 rdflib_logger.setLevel(logging.ERROR)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
490 if args.quiet:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
491 # Silence STDERR, not an eventual provenance log file
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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diff changeset
492 stderr_handler.setLevel(logging.WARN)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
493 if runtimeContext.debug:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
494 # Increase to debug for both stderr and provenance log file
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
495 _logger.setLevel(logging.DEBUG)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
496 stderr_handler.setLevel(logging.DEBUG)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
497 rdflib_logger.setLevel(logging.DEBUG)
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parents:
diff changeset
498 fmtclass = coloredlogs.ColoredFormatter if args.enable_color else logging.Formatter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
499 formatter = fmtclass("%(levelname)s %(message)s")
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parents:
diff changeset
500 if args.timestamps:
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parents:
diff changeset
501 formatter = fmtclass(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
502 "[%(asctime)s] %(levelname)s %(message)s",
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
503 "%Y-%m-%d %H:%M:%S")
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parents:
diff changeset
504 stderr_handler.setFormatter(formatter)
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parents:
diff changeset
505
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parents:
diff changeset
506 def setup_schema(args, # type: argparse.Namespace
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
507 custom_schema_callback # type: Optional[Callable[[], None]]
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parents:
diff changeset
508 ): # type: (...) -> None
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parents:
diff changeset
509 if custom_schema_callback is not None:
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parents:
diff changeset
510 custom_schema_callback()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
511 elif args.enable_ext:
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parents:
diff changeset
512 res = pkg_resources.resource_stream(__name__, 'extensions.yml')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
513 use_custom_schema("v1.0", "http://commonwl.org/cwltool", res.read())
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parents:
diff changeset
514 res.close()
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parents:
diff changeset
515 else:
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parents:
diff changeset
516 use_standard_schema("v1.0")
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parents:
diff changeset
517
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parents:
diff changeset
518 def setup_provenance(args, # type: argparse.Namespace
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
519 argsl, # type: List[str]
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parents:
diff changeset
520 runtimeContext # type: RuntimeContext
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parents:
diff changeset
521 ): # type: (...) -> Optional[int]
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parents:
diff changeset
522 if not args.compute_checksum:
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parents:
diff changeset
523 _logger.error("--provenance incompatible with --no-compute-checksum")
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parents:
diff changeset
524 return 1
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parents:
diff changeset
525 ro = ResearchObject(
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parents:
diff changeset
526 getdefault(runtimeContext.make_fs_access, StdFsAccess),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
527 temp_prefix_ro=args.tmpdir_prefix, orcid=args.orcid,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
528 full_name=args.cwl_full_name)
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parents:
diff changeset
529 runtimeContext.research_obj = ro
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parents:
diff changeset
530 log_file_io = ro.open_log_file_for_activity(ro.engine_uuid)
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parents:
diff changeset
531 prov_log_handler = logging.StreamHandler(cast(IO[str], log_file_io))
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parents:
diff changeset
532
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parents:
diff changeset
533 class ProvLogFormatter(logging.Formatter):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
534 """Enforce ISO8601 with both T and Z."""
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parents:
diff changeset
535
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parents:
diff changeset
536 def __init__(self): # type: () -> None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
537 super(ProvLogFormatter, self).__init__(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
538 "[%(asctime)sZ] %(message)s")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
539
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
540 def formatTime(self, record, datefmt=None):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
541 # type: (logging.LogRecord, Optional[str]) -> str
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
542 record_time = time.gmtime(record.created)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
543 formatted_time = time.strftime("%Y-%m-%dT%H:%M:%S", record_time)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
544 with_msecs = "%s,%03d" % (formatted_time, record.msecs)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
545 return with_msecs
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
546 prov_log_handler.setFormatter(ProvLogFormatter())
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
547 _logger.addHandler(prov_log_handler)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
548 _logger.debug(u"[provenance] Logging to %s", log_file_io)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
549 if argsl is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
550 # Log cwltool command line options to provenance file
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
551 _logger.info("[cwltool] %s %s", sys.argv[0], u" ".join(argsl))
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parents:
diff changeset
552 _logger.debug(u"[cwltool] Arguments: %s", args)
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parents:
diff changeset
553 return None
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parents:
diff changeset
554
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parents:
diff changeset
555 def setup_loadingContext(loadingContext, # type: Optional[LoadingContext]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
556 runtimeContext, # type: RuntimeContext
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
557 args # type: argparse.Namespace
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parents:
diff changeset
558 ): # type: (...) -> LoadingContext
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parents:
diff changeset
559 if loadingContext is None:
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parents:
diff changeset
560 loadingContext = LoadingContext(vars(args))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
561 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
562 loadingContext = loadingContext.copy()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
563 loadingContext.loader = default_loader(loadingContext.fetcher_constructor,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
564 enable_dev=args.enable_dev)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
565 loadingContext.research_obj = runtimeContext.research_obj
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
566 loadingContext.disable_js_validation = \
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
567 args.disable_js_validation or (not args.do_validate)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
568 loadingContext.construct_tool_object = getdefault(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
569 loadingContext.construct_tool_object, workflow.default_make_tool)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
570 loadingContext.resolver = getdefault(loadingContext.resolver, tool_resolver)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
571 if loadingContext.do_update is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
572 loadingContext.do_update = not (args.pack or args.print_subgraph)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
573
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
574 return loadingContext
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
575
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
576 def make_template(tool # type: Process
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
577 ): # type: (...) -> None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
578 def my_represent_none(self, data): # pylint: disable=unused-argument
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
579 # type: (Any, Any) -> Any
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
580 """Force clean representation of 'null'."""
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
581 return self.represent_scalar(u'tag:yaml.org,2002:null', u'null')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
582 yaml.RoundTripRepresenter.add_representer(type(None), my_represent_none)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
583 yaml.round_trip_dump(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
584 generate_input_template(tool), sys.stdout,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
585 default_flow_style=False, indent=4, block_seq_indent=2)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
586
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
587
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
588 def choose_target(args, # type: argparse.Namespace
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
589 tool, # type: Process
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
590 loadingContext # type: LoadingContext
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
591 ): # type: (...) -> Optional[Process]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
592
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
593 if loadingContext.loader is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
594 raise Exception("loadingContext.loader cannot be None")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
595
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
596 if isinstance(tool, Workflow):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
597 url = urllib.parse.urlparse(tool.tool["id"])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
598 if url.fragment:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
599 extracted = get_subgraph([tool.tool["id"] + "/" + r for r in args.target], tool)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
600 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
601 extracted = get_subgraph([loadingContext.loader.fetcher.urljoin(tool.tool["id"], "#" + r)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
602 for r in args.target],
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
603 tool)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
604 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
605 _logger.error("Can only use --target on Workflows")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
606 return None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
607 if isinstance(loadingContext.loader.idx, CommentedMap):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
608 loadingContext.loader.idx[extracted["id"]] = extracted
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
609 tool = make_tool(extracted["id"],
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
610 loadingContext)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
611 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
612 raise Exception("Missing loadingContext.loader.idx!")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
613
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
614 return tool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
615
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
616 def check_working_directories(runtimeContext # type: RuntimeContext
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
617 ): # type: (...) -> Optional[int]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
618 for dirprefix in ("tmpdir_prefix", "tmp_outdir_prefix", "cachedir"):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
619 if getattr(runtimeContext, dirprefix) and getattr(runtimeContext, dirprefix) != DEFAULT_TMP_PREFIX:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
620 sl = "/" if getattr(runtimeContext, dirprefix).endswith("/") or dirprefix == "cachedir" \
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
621 else ""
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
622 setattr(runtimeContext, dirprefix,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
623 os.path.abspath(getattr(runtimeContext, dirprefix)) + sl)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
624 if not os.path.exists(os.path.dirname(getattr(runtimeContext, dirprefix))):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
625 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
626 os.makedirs(os.path.dirname(getattr(runtimeContext, dirprefix)))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
627 except Exception as e:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
628 _logger.error("Failed to create directory: %s", Text(e))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
629 return 1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
630 return None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
631
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
632
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
633 def main(argsl=None, # type: Optional[List[str]]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
634 args=None, # type: Optional[argparse.Namespace]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
635 job_order_object=None, # type: Optional[MutableMapping[Text, Any]]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
636 stdin=sys.stdin, # type: IO[Any]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
637 stdout=None, # type: Optional[Union[TextIO, StreamWriter]]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
638 stderr=sys.stderr, # type: IO[Any]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
639 versionfunc=versionstring, # type: Callable[[], Text]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
640 logger_handler=None, # type: Optional[logging.Handler]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
641 custom_schema_callback=None, # type: Optional[Callable[[], None]]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
642 executor=None, # type: Optional[JobExecutor]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
643 loadingContext=None, # type: Optional[LoadingContext]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
644 runtimeContext=None, # type: Optional[RuntimeContext]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
645 input_required=True # type: bool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
646 ): # type: (...) -> int
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
647 if not stdout: # force UTF-8 even if the console is configured differently
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
648 if (hasattr(sys.stdout, "encoding")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
649 and sys.stdout.encoding != 'UTF-8'): # type: ignore
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
650 if PY3 and hasattr(sys.stdout, "detach"):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
651 stdout = io.TextIOWrapper(sys.stdout.buffer, encoding='utf-8')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
652 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
653 stdout = getwriter('utf-8')(sys.stdout) # type: ignore
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
654 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
655 stdout = cast(TextIO, sys.stdout) # type: ignore
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
656
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
657 _logger.removeHandler(defaultStreamHandler)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
658 stderr_handler = logger_handler
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
659 if stderr_handler is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
660 _logger.addHandler(stderr_handler)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
661 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
662 coloredlogs.install(logger=_logger, stream=stderr)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
663 stderr_handler = _logger.handlers[-1]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
664 workflowobj = None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
665 prov_log_handler = None # type: Optional[logging.StreamHandler]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
666 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
667 if args is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
668 if argsl is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
669 argsl = sys.argv[1:]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
670 addl = [] # type: List[str]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
671 if "CWLTOOL_OPTIONS" in os.environ:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
672 addl = os.environ["CWLTOOL_OPTIONS"].split(" ")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
673 args = arg_parser().parse_args(addl+argsl)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
674 if args.record_container_id:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
675 if not args.cidfile_dir:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
676 args.cidfile_dir = os.getcwd()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
677 del args.record_container_id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
678
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
679 if runtimeContext is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
680 runtimeContext = RuntimeContext(vars(args))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
681 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
682 runtimeContext = runtimeContext.copy()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
683
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
684 # If on Windows platform, a default Docker Container is used if not
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
685 # explicitely provided by user
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
686 if onWindows() and not runtimeContext.default_container:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
687 # This docker image is a minimal alpine image with bash installed
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
688 # (size 6 mb). source: https://github.com/frol/docker-alpine-bash
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
689 runtimeContext.default_container = windows_default_container_id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
690
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
691 # If caller parsed its own arguments, it may not include every
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
692 # cwltool option, so fill in defaults to avoid crashing when
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
693 # dereferencing them in args.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
694 for key, val in iteritems(get_default_args()):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
695 if not hasattr(args, key):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
696 setattr(args, key, val)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
697
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
698 configure_logging(args, stderr_handler, runtimeContext)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
699
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
700 if args.version:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
701 print(versionfunc())
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
702 return 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
703 _logger.info(versionfunc())
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
704
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
705 if args.print_supported_versions:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
706 print("\n".join(supported_cwl_versions(args.enable_dev)))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
707 return 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
708
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
709 if not args.workflow:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
710 if os.path.isfile("CWLFile"):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
711 setattr(args, "workflow", "CWLFile")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
712 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
713 _logger.error("CWL document required, no input file was provided")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
714 arg_parser().print_help()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
715 return 1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
716 if args.relax_path_checks:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
717 command_line_tool.ACCEPTLIST_RE = command_line_tool.ACCEPTLIST_EN_RELAXED_RE
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
718
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
719 if args.ga4gh_tool_registries:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
720 ga4gh_tool_registries[:] = args.ga4gh_tool_registries
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
721 if not args.enable_ga4gh_tool_registry:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
722 del ga4gh_tool_registries[:]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
723
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
724 setup_schema(args, custom_schema_callback)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
725
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
726 if args.provenance:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
727 if argsl is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
728 raise Exception("argsl cannot be None")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
729 if setup_provenance(args, argsl, runtimeContext) is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
730 return 1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
731
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
732 loadingContext = setup_loadingContext(loadingContext, runtimeContext, args)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
733
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
734 uri, tool_file_uri = resolve_tool_uri(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
735 args.workflow, resolver=loadingContext.resolver,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
736 fetcher_constructor=loadingContext.fetcher_constructor)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
737
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
738 try_again_msg = "" if args.debug else ", try again with --debug for more information"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
739
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
740 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
741 job_order_object, input_basedir, jobloader = load_job_order(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
742 args, stdin, loadingContext.fetcher_constructor,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
743 loadingContext.overrides_list, tool_file_uri)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
744
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
745 if args.overrides:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
746 loadingContext.overrides_list.extend(load_overrides(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
747 file_uri(os.path.abspath(args.overrides)), tool_file_uri))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
748
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
749 loadingContext, workflowobj, uri = fetch_document(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
750 uri, loadingContext)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
751
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
752 if args.print_deps and loadingContext.loader:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
753 printdeps(workflowobj, loadingContext.loader, stdout,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
754 args.relative_deps, uri)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
755 return 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
756
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
757 loadingContext, uri \
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
758 = resolve_and_validate_document(loadingContext, workflowobj, uri,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
759 preprocess_only=(args.print_pre or args.pack),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
760 skip_schemas=args.skip_schemas)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
761
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
762 if loadingContext.loader is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
763 raise Exception("Impossible code path.")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
764 processobj, metadata = loadingContext.loader.resolve_ref(uri)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
765 processobj = cast(CommentedMap, processobj)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
766 if args.pack:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
767 stdout.write(print_pack(loadingContext.loader, processobj, uri, metadata))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
768 return 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
769
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
770 if args.provenance and runtimeContext.research_obj:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
771 # Can't really be combined with args.pack at same time
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
772 runtimeContext.research_obj.packed_workflow(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
773 print_pack(loadingContext.loader, processobj, uri, metadata))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
774
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
775 if args.print_pre:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
776 stdout.write(json_dumps(processobj, indent=4, sort_keys=True, separators=(',', ': ')))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
777 return 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
778
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
779 tool = make_tool(uri, loadingContext)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
780 if args.make_template:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
781 make_template(tool)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
782 return 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
783
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
784 if args.validate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
785 print("{} is valid CWL.".format(args.workflow))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
786 return 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
787
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
788 if args.print_rdf:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
789 stdout.write(printrdf(tool, loadingContext.loader.ctx, args.rdf_serializer))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
790 return 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
791
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
792 if args.print_dot:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
793 printdot(tool, loadingContext.loader.ctx, stdout)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
794 return 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
795
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
796 if args.print_targets:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
797 for f in ("outputs", "steps", "inputs"):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
798 if tool.tool[f]:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
799 _logger.info("%s%s targets:", f[0].upper(), f[1:-1])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
800 stdout.write(" "+"\n ".join([shortname(t["id"]) for t in tool.tool[f]])+"\n")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
801 return 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
802
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
803 if args.target:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
804 ctool = choose_target(args, tool, loadingContext)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
805 if ctool is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
806 return 1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
807 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
808 tool = ctool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
809
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
810 if args.print_subgraph:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
811 if "name" in tool.tool:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
812 del tool.tool["name"]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
813 stdout.write(json_dumps(tool.tool, indent=4, sort_keys=True, separators=(',', ': ')))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
814 return 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
815
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
816 except (validate.ValidationException) as exc:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
817 _logger.error(u"Tool definition failed validation:\n%s", Text(exc),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
818 exc_info=args.debug)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
819 return 1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
820 except (RuntimeError, WorkflowException) as exc:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
821 _logger.error(u"Tool definition failed initialization:\n%s", Text(exc),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
822 exc_info=args.debug)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
823 return 1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
824 except Exception as exc:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
825 _logger.error(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
826 u"I'm sorry, I couldn't load this CWL file%s.\nThe error was: %s",
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
827 try_again_msg,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
828 Text(exc) if not args.debug else "",
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
829 exc_info=args.debug)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
830 return 1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
831
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
832 if isinstance(tool, int):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
833 return tool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
834
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
835 # If on MacOS platform, TMPDIR must be set to be under one of the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
836 # shared volumes in Docker for Mac
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
837 # More info: https://dockstore.org/docs/faq
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
838 if sys.platform == "darwin":
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
839 default_mac_path = "/private/tmp/docker_tmp"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
840 if runtimeContext.tmp_outdir_prefix == DEFAULT_TMP_PREFIX:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
841 runtimeContext.tmp_outdir_prefix = default_mac_path
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
842 if runtimeContext.tmpdir_prefix == DEFAULT_TMP_PREFIX:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
843 runtimeContext.tmpdir_prefix = default_mac_path
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
844
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
845 if check_working_directories(runtimeContext) is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
846 return 1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
847
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
848 if args.cachedir:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
849 if args.move_outputs == "move":
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
850 runtimeContext.move_outputs = "copy"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
851 runtimeContext.tmp_outdir_prefix = args.cachedir
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
852
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
853 runtimeContext.secret_store = getdefault(runtimeContext.secret_store, SecretStore())
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
854 runtimeContext.make_fs_access = getdefault(runtimeContext.make_fs_access, StdFsAccess)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
855
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
856 if not executor:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
857 if args.parallel:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
858 temp_executor = MultithreadedJobExecutor()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
859 runtimeContext.select_resources = temp_executor.select_resources
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
860 real_executor = temp_executor # type: JobExecutor
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
861 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
862 real_executor = SingleJobExecutor()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
863 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
864 real_executor = executor
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
865
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
866 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
867 runtimeContext.basedir = input_basedir
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
868
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
869 if isinstance(tool, ProcessGenerator):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
870 tfjob_order = {} # type: MutableMapping[Text, Any]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
871 if loadingContext.jobdefaults:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
872 tfjob_order.update(loadingContext.jobdefaults)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
873 if job_order_object:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
874 tfjob_order.update(job_order_object)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
875 tfout, tfstatus = real_executor(tool.embedded_tool, tfjob_order, runtimeContext)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
876 if tfstatus != "success":
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
877 raise WorkflowException("ProcessGenerator failed to generate workflow")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
878 tool, job_order_object = tool.result(tfjob_order, tfout, runtimeContext)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
879 if not job_order_object:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
880 job_order_object = None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
881
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
882 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
883 initialized_job_order_object = init_job_order(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
884 job_order_object, args, tool, jobloader, stdout,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
885 print_input_deps=args.print_input_deps,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
886 relative_deps=args.relative_deps,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
887 make_fs_access=runtimeContext.make_fs_access,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
888 input_basedir=input_basedir,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
889 secret_store=runtimeContext.secret_store,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
890 input_required=input_required)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
891 except SystemExit as err:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
892 return err.code
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
893
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
894 del args.workflow
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
895 del args.job_order
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
896
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
897 conf_file = getattr(args, "beta_dependency_resolvers_configuration", None) # Text
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
898 use_conda_dependencies = getattr(args, "beta_conda_dependencies", None) # Text
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
899
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
900 if conf_file or use_conda_dependencies:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
901 runtimeContext.job_script_provider = DependenciesConfiguration(args)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
902 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
903 runtimeContext.find_default_container = functools.partial(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
904 find_default_container,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
905 default_container=runtimeContext.default_container,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
906 use_biocontainers=args.beta_use_biocontainers)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
907
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
908 (out, status) = real_executor(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
909 tool, initialized_job_order_object, runtimeContext,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
910 logger=_logger)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
911
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
912 if out is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
913 if runtimeContext.research_obj is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
914 runtimeContext.research_obj.create_job(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
915 out, None, True)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
916 def remove_at_id(doc): # type: (MutableMapping[Text, Any]) -> None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
917 for key in list(doc.keys()):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
918 if key == '@id':
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
919 del doc[key]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
920 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
921 value = doc[key]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
922 if isinstance(value, MutableMapping):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
923 remove_at_id(value)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
924 elif isinstance(value, MutableSequence):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
925 for entry in value:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
926 if isinstance(entry, MutableMapping):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
927 remove_at_id(entry)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
928 remove_at_id(out)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
929 visit_class(out, ("File",), functools.partial(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
930 add_sizes, runtimeContext.make_fs_access('')))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
931
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
932 def loc_to_path(obj): # type: (Dict[Text, Any]) -> None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
933 for field in ("path", "nameext", "nameroot", "dirname"):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
934 if field in obj:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
935 del obj[field]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
936 if obj["location"].startswith("file://"):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
937 obj["path"] = uri_file_path(obj["location"])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
938
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
939 visit_class(out, ("File", "Directory"), loc_to_path)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
940
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
941 # Unsetting the Generation from final output object
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
942 visit_class(out, ("File", ), MutationManager().unset_generation)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
943
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
944 if isinstance(out, string_types):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
945 stdout.write(out)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
946 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
947 stdout.write(json_dumps(out, indent=4, ensure_ascii=False))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
948 stdout.write("\n")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
949 if hasattr(stdout, "flush"):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
950 stdout.flush()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
951
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
952 if status != "success":
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
953 _logger.warning(u"Final process status is %s", status)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
954 return 1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
955 _logger.info(u"Final process status is %s", status)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
956 return 0
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
957
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
958 except (validate.ValidationException) as exc:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
959 _logger.error(u"Input object failed validation:\n%s", Text(exc),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
960 exc_info=args.debug)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
961 return 1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
962 except UnsupportedRequirement as exc:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
963 _logger.error(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
964 u"Workflow or tool uses unsupported feature:\n%s", Text(exc),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
965 exc_info=args.debug)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
966 return 33
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
967 except WorkflowException as exc:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
968 _logger.error(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
969 u"Workflow error%s:\n%s", try_again_msg, strip_dup_lineno(Text(exc)),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
970 exc_info=args.debug)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
971 return 1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
972 except Exception as exc: # pylint: disable=broad-except
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
973 _logger.error(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
974 u"Unhandled error%s:\n %s", try_again_msg, Text(exc), exc_info=args.debug)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
975 return 1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
976
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
977 finally:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
978 if args and runtimeContext and runtimeContext.research_obj \
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
979 and workflowobj and loadingContext:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
980 research_obj = runtimeContext.research_obj
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
981 if loadingContext.loader is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
982 research_obj.generate_snapshot(prov_deps(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
983 workflowobj, loadingContext.loader, uri))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
984 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
985 _logger.warning("Unable to generate provenance snapshot "
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
986 " due to missing loadingContext.loader.")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
987 if prov_log_handler is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
988 # Stop logging so we won't half-log adding ourself to RO
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
989 _logger.debug(u"[provenance] Closing provenance log file %s",
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
990 prov_log_handler)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
991 _logger.removeHandler(prov_log_handler)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
992 # Ensure last log lines are written out
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
993 prov_log_handler.flush()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
994 # Underlying WritableBagFile will add the tagfile to the manifest
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
995 prov_log_handler.stream.close()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
996 prov_log_handler.close()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
997 research_obj.close(args.provenance)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
998
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999 _logger.removeHandler(stderr_handler)
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1000 _logger.addHandler(defaultStreamHandler)
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1001
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1002
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1003 def find_default_container(builder, # type: HasReqsHints
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1004 default_container=None, # type: Optional[Text]
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1005 use_biocontainers=None, # type: Optional[bool]
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1006 ): # type: (...) -> Optional[Text]
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1007 """Find a container."""
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1008 if not default_container and use_biocontainers:
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1009 default_container = get_container_from_software_requirements(
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1010 use_biocontainers, builder)
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1011 return default_container
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1012
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1013
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1014 def run(*args, **kwargs):
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1015 # type: (*Any, **Any) -> None
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1016 """Run cwltool."""
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1017 signal.signal(signal.SIGTERM, _signal_handler)
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1018 try:
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1019 sys.exit(main(*args, **kwargs))
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1020 finally:
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1021 _terminate_processes()
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1022
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1023
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1024 if __name__ == "__main__":
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1025 run(sys.argv[1:])