Mercurial > repos > shellac > sam_consensus_v3

annotate env/lib/python3.9/site-packages/cwltool/process.py @ 0:4f3585e2f14b draft default tip

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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
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1 """Classes and methods relevant for all CWL Proccess types."""
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2 import abc
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3 import copy
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4 import functools
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5 import hashlib
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6 import json
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7 import logging
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8 import math
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9 import os
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10 import shutil
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11 import stat
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12 import textwrap
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13 import urllib
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14 import uuid
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15 from os import scandir
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16 from typing import (
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17 Any,
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18 Callable,
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19 Dict,
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20 Iterable,
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21 Iterator,
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22 List,
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23 MutableMapping,
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24 MutableSequence,
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25 Optional,
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26 Set,
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27 Sized,
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28 Tuple,
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29 Type,
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30 Union,
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31 cast,
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32 )
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33
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34 from pkg_resources import resource_stream
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35 from rdflib import Graph
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36 from ruamel.yaml.comments import CommentedMap, CommentedSeq
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37 from schema_salad.avro.schema import (
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38 Names,
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39 Schema,
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40 SchemaParseException,
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41 make_avsc_object,
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42 )
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43 from schema_salad.exceptions import ValidationException
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44 from schema_salad.ref_resolver import Loader, file_uri, uri_file_path
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45 from schema_salad.schema import load_schema, make_avro_schema, make_valid_avro
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46 from schema_salad.sourceline import SourceLine, strip_dup_lineno
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47 from schema_salad.utils import convert_to_dict
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48 from schema_salad.validate import validate_ex
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49 from typing_extensions import TYPE_CHECKING
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50
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51 from . import expression
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52 from .builder import Builder, HasReqsHints
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53 from .context import LoadingContext, RuntimeContext, getdefault
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54 from .errors import UnsupportedRequirement, WorkflowException
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55 from .loghandler import _logger
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56 from .mpi import MPIRequirementName
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57 from .pathmapper import MapperEnt, PathMapper
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58 from .secrets import SecretStore
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59 from .stdfsaccess import StdFsAccess
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60 from .update import INTERNAL_VERSION
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61 from .utils import (
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62 CWLObjectType,
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63 CWLOutputAtomType,
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64 CWLOutputType,
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65 JobsGeneratorType,
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66 OutputCallbackType,
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67 adjustDirObjs,
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68 aslist,
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69 cmp_like_py2,
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70 copytree_with_merge,
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71 ensure_writable,
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72 get_listing,
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73 normalizeFilesDirs,
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74 onWindows,
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75 random_outdir,
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76 visit_class,
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77 )
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78 from .validate_js import validate_js_expressions
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79
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80 if TYPE_CHECKING:
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81 from .provenance_profile import ProvenanceProfile # pylint: disable=unused-import
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82
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83
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84 class LogAsDebugFilter(logging.Filter):
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85 def __init__(self, name: str, parent: logging.Logger) -> None:
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86 """Initialize."""
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87 name = str(name)
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88 super().__init__(name)
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89 self.parent = parent
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90
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91 def filter(self, record: logging.LogRecord) -> bool:
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92 return self.parent.isEnabledFor(logging.DEBUG)
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93
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94
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95 _logger_validation_warnings = logging.getLogger("cwltool.validation_warnings")
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96 _logger_validation_warnings.setLevel(_logger.getEffectiveLevel())
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97 _logger_validation_warnings.addFilter(
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98 LogAsDebugFilter("cwltool.validation_warnings", _logger)
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99 )
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100
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101 supportedProcessRequirements = [
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102 "DockerRequirement",
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103 "SchemaDefRequirement",
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104 "EnvVarRequirement",
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105 "ScatterFeatureRequirement",
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106 "SubworkflowFeatureRequirement",
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107 "MultipleInputFeatureRequirement",
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108 "InlineJavascriptRequirement",
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109 "ShellCommandRequirement",
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110 "StepInputExpressionRequirement",
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111 "ResourceRequirement",
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112 "InitialWorkDirRequirement",
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113 "ToolTimeLimit",
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114 "WorkReuse",
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115 "NetworkAccess",
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116 "InplaceUpdateRequirement",
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117 "LoadListingRequirement",
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118 MPIRequirementName,
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119 "http://commonwl.org/cwltool#TimeLimit",
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120 "http://commonwl.org/cwltool#WorkReuse",
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121 "http://commonwl.org/cwltool#NetworkAccess",
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122 "http://commonwl.org/cwltool#LoadListingRequirement",
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123 "http://commonwl.org/cwltool#InplaceUpdateRequirement",
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124 ]
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125
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126 cwl_files = (
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127 "Workflow.yml",
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128 "CommandLineTool.yml",
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129 "CommonWorkflowLanguage.yml",
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130 "Process.yml",
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131 "Operation.yml",
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132 "concepts.md",
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133 "contrib.md",
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134 "intro.md",
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diff changeset
135 "invocation.md",
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136 )
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137
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138 salad_files = (
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diff changeset
139 "metaschema.yml",
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140 "metaschema_base.yml",
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141 "salad.md",
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142 "field_name.yml",
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143 "import_include.md",
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144 "link_res.yml",
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diff changeset
145 "ident_res.yml",
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146 "vocab_res.yml",
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147 "vocab_res.yml",
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148 "field_name_schema.yml",
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149 "field_name_src.yml",
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150 "field_name_proc.yml",
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151 "ident_res_schema.yml",
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152 "ident_res_src.yml",
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153 "ident_res_proc.yml",
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154 "link_res_schema.yml",
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155 "link_res_src.yml",
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156 "link_res_proc.yml",
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157 "vocab_res_schema.yml",
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158 "vocab_res_src.yml",
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159 "vocab_res_proc.yml",
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160 )
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161
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162 SCHEMA_CACHE = (
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163 {}
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164 ) # type: Dict[str, Tuple[Loader, Union[Names, SchemaParseException], CWLObjectType, Loader]]
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165 SCHEMA_FILE = None # type: Optional[CWLObjectType]
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166 SCHEMA_DIR = None # type: Optional[CWLObjectType]
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167 SCHEMA_ANY = None # type: Optional[CWLObjectType]
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168
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169 custom_schemas = {} # type: Dict[str, Tuple[str, str]]
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170
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171
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172 def use_standard_schema(version: str) -> None:
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173 if version in custom_schemas:
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174 del custom_schemas[version]
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175 if version in SCHEMA_CACHE:
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176 del SCHEMA_CACHE[version]
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177
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178
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179 def use_custom_schema(version: str, name: str, text: str) -> None:
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180 custom_schemas[version] = (name, text)
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181 if version in SCHEMA_CACHE:
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182 del SCHEMA_CACHE[version]
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183
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184
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185 def get_schema(
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186 version: str,
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187 ) -> Tuple[Loader, Union[Names, SchemaParseException], CWLObjectType, Loader]:
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188
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189 if version in SCHEMA_CACHE:
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190 return SCHEMA_CACHE[version]
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191
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192 cache = {} # type: Dict[str, Union[str, Graph, bool]]
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193 version = version.split("#")[-1]
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194 if ".dev" in version:
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195 version = ".".join(version.split(".")[:-1])
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196 for f in cwl_files:
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197 try:
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198 res = resource_stream(__name__, f"schemas/{version}/{f}")
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199 cache["https://w3id.org/cwl/" + f] = res.read().decode("UTF-8")
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200 res.close()
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201 except OSError:
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202 pass
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203
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204 for f in salad_files:
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205 try:
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206 res = resource_stream(
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207 __name__,
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208 f"schemas/{version}/salad/schema_salad/metaschema/{f}",
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209 )
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diff changeset
210 cache[
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211 "https://w3id.org/cwl/salad/schema_salad/metaschema/" + f
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212 ] = res.read().decode("UTF-8")
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213 res.close()
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214 except OSError:
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215 pass
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216
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217 if version in custom_schemas:
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218 cache[custom_schemas[version][0]] = custom_schemas[version][1]
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219 SCHEMA_CACHE[version] = load_schema(custom_schemas[version][0], cache=cache)
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220 else:
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221 SCHEMA_CACHE[version] = load_schema(
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222 "https://w3id.org/cwl/CommonWorkflowLanguage.yml", cache=cache
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223 )
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224
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225 return SCHEMA_CACHE[version]
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226
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227
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228 def shortname(inputid: str) -> str:
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229 d = urllib.parse.urlparse(inputid)
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230 if d.fragment:
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231 return d.fragment.split("/")[-1]
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232 return d.path.split("/")[-1]
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233
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234
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235 def checkRequirements(
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236 rec: Union[MutableSequence[CWLObjectType], CWLObjectType, CWLOutputType, None],
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237 supported_process_requirements: Iterable[str],
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238 ) -> None:
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diff changeset
239 if isinstance(rec, MutableMapping):
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diff changeset
240 if "requirements" in rec:
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241 for i, entry in enumerate(
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242 cast(MutableSequence[CWLObjectType], rec["requirements"])
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243 ):
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244 with SourceLine(rec["requirements"], i, UnsupportedRequirement):
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245 if cast(str, entry["class"]) not in supported_process_requirements:
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246 raise UnsupportedRequirement(
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247 "Unsupported requirement {}".format(entry["class"])
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248 )
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parents:
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249 for key in rec:
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250 checkRequirements(rec[key], supported_process_requirements)
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251 if isinstance(rec, MutableSequence):
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252 for entry2 in rec:
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253 checkRequirements(entry2, supported_process_requirements)
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parents:
diff changeset
254
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255
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256 def stage_files(
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257 pathmapper: PathMapper,
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258 stage_func: Optional[Callable[[str, str], None]] = None,
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259 ignore_writable: bool = False,
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260 symlink: bool = True,
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261 secret_store: Optional[SecretStore] = None,
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262 fix_conflicts: bool = False,
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263 ) -> None:
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264 """Link or copy files to their targets. Create them as needed."""
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265 targets = {} # type: Dict[str, MapperEnt]
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266 for key, entry in pathmapper.items():
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267 if "File" not in entry.type:
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268 continue
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269 if entry.target not in targets:
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270 targets[entry.target] = entry
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271 elif targets[entry.target].resolved != entry.resolved:
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272 if fix_conflicts:
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273 # find first key that does not clash with an existing entry in targets
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274 # start with entry.target + '_' + 2 and then keep incrementing the number till there is no clash
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275 i = 2
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276 tgt = f"{entry.target}_{i}"
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277 while tgt in targets:
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278 i += 1
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279 tgt = f"{entry.target}_{i}"
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280 targets[tgt] = pathmapper.update(
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281 key, entry.resolved, tgt, entry.type, entry.staged
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282 )
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283 else:
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284 raise WorkflowException(
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285 "File staging conflict, trying to stage both %s and %s to the same target %s"
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286 % (targets[entry.target].resolved, entry.resolved, entry.target)
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287 )
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288
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289 for key, entry in pathmapper.items():
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290 if not entry.staged:
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291 continue
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292 if not os.path.exists(os.path.dirname(entry.target)):
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293 os.makedirs(os.path.dirname(entry.target))
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294 if entry.type in ("File", "Directory") and os.path.exists(entry.resolved):
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295 if symlink: # Use symlink func if allowed
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296 if onWindows():
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297 if entry.type == "File":
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298 shutil.copy(entry.resolved, entry.target)
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299 elif entry.type == "Directory":
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300 if os.path.exists(entry.target) and os.path.isdir(entry.target):
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301 shutil.rmtree(entry.target)
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302 copytree_with_merge(entry.resolved, entry.target)
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303 else:
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304 os.symlink(entry.resolved, entry.target)
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305 elif stage_func is not None:
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306 stage_func(entry.resolved, entry.target)
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307 elif (
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308 entry.type == "Directory"
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309 and not os.path.exists(entry.target)
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310 and entry.resolved.startswith("_:")
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311 ):
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312 os.makedirs(entry.target)
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313 elif entry.type == "WritableFile" and not ignore_writable:
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314 shutil.copy(entry.resolved, entry.target)
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315 ensure_writable(entry.target)
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316 elif entry.type == "WritableDirectory" and not ignore_writable:
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317 if entry.resolved.startswith("_:"):
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318 os.makedirs(entry.target)
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319 else:
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320 shutil.copytree(entry.resolved, entry.target)
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321 ensure_writable(entry.target)
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322 elif entry.type == "CreateFile" or entry.type == "CreateWritableFile":
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323 with open(entry.target, "wb") as new:
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324 if secret_store is not None:
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325 new.write(
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326 cast(str, secret_store.retrieve(entry.resolved)).encode("utf-8")
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327 )
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328 else:
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329 new.write(entry.resolved.encode("utf-8"))
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330 if entry.type == "CreateFile":
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331 os.chmod(entry.target, stat.S_IRUSR) # Read only
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332 else: # it is a "CreateWritableFile"
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333 ensure_writable(entry.target)
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334 pathmapper.update(key, entry.target, entry.target, entry.type, entry.staged)
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335
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336
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337 def relocateOutputs(
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338 outputObj: CWLObjectType,
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339 destination_path: str,
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340 source_directories: Set[str],
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341 action: str,
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342 fs_access: StdFsAccess,
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343 compute_checksum: bool = True,
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344 path_mapper: Type[PathMapper] = PathMapper,
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345 ) -> CWLObjectType:
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346 adjustDirObjs(outputObj, functools.partial(get_listing, fs_access, recursive=True))
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347
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348 if action not in ("move", "copy"):
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349 return outputObj
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350
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351 def _collectDirEntries(
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352 obj: Union[CWLObjectType, MutableSequence[CWLObjectType], None]
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353 ) -> Iterator[CWLObjectType]:
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354 if isinstance(obj, dict):
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355 if obj.get("class") in ("File", "Directory"):
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356 yield obj
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357 else:
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358 for sub_obj in obj.values():
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359 yield from _collectDirEntries(sub_obj)
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360 elif isinstance(obj, MutableSequence):
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361 for sub_obj in obj:
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362 yield from _collectDirEntries(sub_obj)
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363
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364 def _relocate(src: str, dst: str) -> None:
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365 if src == dst:
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366 return
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367
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368 # If the source is not contained in source_directories we're not allowed to delete it
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369 src = fs_access.realpath(src)
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370 src_can_deleted = any(
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371 os.path.commonprefix([p, src]) == p for p in source_directories
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372 )
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373
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374 _action = "move" if action == "move" and src_can_deleted else "copy"
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375
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376 if _action == "move":
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377 _logger.debug("Moving %s to %s", src, dst)
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378 if fs_access.isdir(src) and fs_access.isdir(dst):
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379 # merge directories
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parents:
diff changeset
380 for dir_entry in scandir(src):
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shellac
parents:
diff changeset
381 _relocate(dir_entry.path, fs_access.join(dst, dir_entry.name))
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shellac
parents:
diff changeset
382 else:
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parents:
diff changeset
383 shutil.move(src, dst)
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parents:
diff changeset
384
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parents:
diff changeset
385 elif _action == "copy":
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parents:
diff changeset
386 _logger.debug("Copying %s to %s", src, dst)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
387 if fs_access.isdir(src):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
388 if os.path.isdir(dst):
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parents:
diff changeset
389 shutil.rmtree(dst)
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parents:
diff changeset
390 elif os.path.isfile(dst):
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parents:
diff changeset
391 os.unlink(dst)
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parents:
diff changeset
392 shutil.copytree(src, dst)
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parents:
diff changeset
393 else:
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parents:
diff changeset
394 shutil.copy2(src, dst)
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parents:
diff changeset
395
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parents:
diff changeset
396 def _realpath(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
397 ob: CWLObjectType,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
398 ) -> None: # should be type Union[CWLFile, CWLDirectory]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
399 location = cast(str, ob["location"])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
400 if location.startswith("file:"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
401 ob["location"] = file_uri(os.path.realpath(uri_file_path(location)))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
402 elif location.startswith("/"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
403 ob["location"] = os.path.realpath(location)
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shellac
parents:
diff changeset
404 elif not location.startswith("_:") and ":" in location:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
405 ob["location"] = file_uri(fs_access.realpath(location))
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shellac
parents:
diff changeset
406
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shellac
parents:
diff changeset
407 outfiles = list(_collectDirEntries(outputObj))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
408 visit_class(outfiles, ("File", "Directory"), _realpath)
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shellac
parents:
diff changeset
409 pm = path_mapper(outfiles, "", destination_path, separateDirs=False)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
410 stage_files(pm, stage_func=_relocate, symlink=False, fix_conflicts=True)
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parents:
diff changeset
411
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parents:
diff changeset
412 def _check_adjust(a_file: CWLObjectType) -> CWLObjectType:
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shellac
parents:
diff changeset
413 a_file["location"] = file_uri(pm.mapper(cast(str, a_file["location"]))[1])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
414 if "contents" in a_file:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
415 del a_file["contents"]
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shellac
parents:
diff changeset
416 return a_file
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shellac
parents:
diff changeset
417
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parents:
diff changeset
418 visit_class(outputObj, ("File", "Directory"), _check_adjust)
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shellac
parents:
diff changeset
419
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
420 if compute_checksum:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
421 visit_class(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
422 outputObj, ("File",), functools.partial(compute_checksums, fs_access)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
423 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
424 return outputObj
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
425
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
426
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
427 def cleanIntermediate(output_dirs: Iterable[str]) -> None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
428 for a in output_dirs:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
429 if os.path.exists(a):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
430 _logger.debug("Removing intermediate output directory %s", a)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
431 shutil.rmtree(a, True)
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shellac
parents:
diff changeset
432
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shellac
parents:
diff changeset
433
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parents:
diff changeset
434 def add_sizes(fsaccess: StdFsAccess, obj: CWLObjectType) -> None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
435 if "location" in obj:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
436 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
437 if "size" not in obj:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
438 obj["size"] = fsaccess.size(cast(str, obj["location"]))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
439 except OSError:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
440 pass
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
441 elif "contents" in obj:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
442 obj["size"] = len(cast(Sized, obj["contents"]))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
443 return # best effort
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shellac
parents:
diff changeset
444
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shellac
parents:
diff changeset
445
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parents:
diff changeset
446 def fill_in_defaults(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
447 inputs: List[CWLObjectType],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
448 job: CWLObjectType,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
449 fsaccess: StdFsAccess,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
450 ) -> None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
451 for e, inp in enumerate(inputs):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
452 with SourceLine(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
453 inputs, e, WorkflowException, _logger.isEnabledFor(logging.DEBUG)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
454 ):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
455 fieldname = shortname(cast(str, inp["id"]))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
456 if job.get(fieldname) is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
457 pass
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
458 elif job.get(fieldname) is None and "default" in inp:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
459 job[fieldname] = copy.deepcopy(inp["default"])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
460 elif job.get(fieldname) is None and "null" in aslist(inp["type"]):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
461 job[fieldname] = None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
462 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
463 raise WorkflowException(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
464 "Missing required input parameter '%s'"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
465 % shortname(cast(str, inp["id"]))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
466 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
467
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
468
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
469 def avroize_type(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
470 field_type: Union[
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
471 CWLObjectType, MutableSequence[CWLOutputType], CWLOutputType, None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
472 ],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
473 name_prefix: str = "",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
474 ) -> None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
475 """Add missing information to a type so that CWL types are valid."""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
476 if isinstance(field_type, MutableSequence):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
477 for field in field_type:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
478 avroize_type(field, name_prefix)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
479 elif isinstance(field_type, MutableMapping):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
480 if field_type["type"] in ("enum", "record"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
481 if "name" not in field_type:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
482 field_type["name"] = name_prefix + str(uuid.uuid4())
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
483 if field_type["type"] == "record":
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
484 avroize_type(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
485 cast(MutableSequence[CWLOutputType], field_type["fields"]), name_prefix
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
486 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
487 if field_type["type"] == "array":
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
488 avroize_type(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
489 cast(MutableSequence[CWLOutputType], field_type["items"]), name_prefix
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
490 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
491 if isinstance(field_type["type"], MutableSequence):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
492 for ctype in field_type["type"]:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
493 avroize_type(cast(CWLOutputType, ctype), name_prefix)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
494
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
495
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shellac
parents:
diff changeset
496 def get_overrides(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
497 overrides: MutableSequence[CWLObjectType], toolid: str
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
498 ) -> CWLObjectType:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
499 req = {} # type: CWLObjectType
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
500 if not isinstance(overrides, MutableSequence):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
501 raise ValidationException(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
502 "Expected overrides to be a list, but was %s" % type(overrides)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
503 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
504 for ov in overrides:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
505 if ov["overrideTarget"] == toolid:
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506 req.update(ov)
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507 return req
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508
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509
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510 _VAR_SPOOL_ERROR = textwrap.dedent(
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511 """
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512 Non-portable reference to /var/spool/cwl detected: '{}'.
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513 To fix, replace /var/spool/cwl with $(runtime.outdir) or add
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514 DockerRequirement to the 'requirements' section and declare
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515 'dockerOutputDirectory: /var/spool/cwl'.
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516 """
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517 )
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518
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519
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520 def var_spool_cwl_detector(
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521 obj: CWLOutputType,
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522 item: Optional[Any] = None,
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523 obj_key: Optional[Any] = None,
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524 ) -> bool:
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525 """Detect any textual reference to /var/spool/cwl."""
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526 r = False
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527 if isinstance(obj, str):
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528 if "var/spool/cwl" in obj and obj_key != "dockerOutputDirectory":
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529 _logger.warning(
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530 SourceLine(item=item, key=obj_key, raise_type=str).makeError(
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531 _VAR_SPOOL_ERROR.format(obj)
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532 )
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533 )
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534 r = True
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535 elif isinstance(obj, MutableMapping):
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536 for mkey, mvalue in obj.items():
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537 r = var_spool_cwl_detector(cast(CWLOutputType, mvalue), obj, mkey) or r
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538 elif isinstance(obj, MutableSequence):
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539 for lkey, lvalue in enumerate(obj):
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540 r = var_spool_cwl_detector(cast(CWLOutputType, lvalue), obj, lkey) or r
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541 return r
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542
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543
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544 def eval_resource(
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545 builder: Builder, resource_req: Union[str, int, float]
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546 ) -> Optional[Union[str, int, float]]:
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547 if isinstance(resource_req, str) and expression.needs_parsing(resource_req):
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548 result = builder.do_eval(resource_req)
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549 if isinstance(result, (str, int)) or result is None:
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550 return result
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551 raise WorkflowException(
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552 "Got incorrect return type {} from resource expression evaluation of {}.".format(
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553 type(result), resource_req
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554 )
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555 )
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556 return resource_req
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557
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558
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559 # Threshold where the "too many files" warning kicks in
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560 FILE_COUNT_WARNING = 5000
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561
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562
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563 class Process(HasReqsHints, metaclass=abc.ABCMeta):
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564 def __init__(
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565 self, toolpath_object: CommentedMap, loadingContext: LoadingContext
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566 ) -> None:
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567 """Build a Process object from the provided dictionary."""
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568 super().__init__()
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569 self.metadata = getdefault(loadingContext.metadata, {}) # type: CWLObjectType
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570 self.provenance_object = None # type: Optional[ProvenanceProfile]
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571 self.parent_wf = None # type: Optional[ProvenanceProfile]
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572 global SCHEMA_FILE, SCHEMA_DIR, SCHEMA_ANY # pylint: disable=global-statement
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573 if SCHEMA_FILE is None or SCHEMA_ANY is None or SCHEMA_DIR is None:
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574 get_schema("v1.0")
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575 SCHEMA_ANY = cast(
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diff changeset
576 CWLObjectType,
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577 SCHEMA_CACHE["v1.0"][3].idx["https://w3id.org/cwl/salad#Any"],
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578 )
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579 SCHEMA_FILE = cast(
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580 CWLObjectType,
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581 SCHEMA_CACHE["v1.0"][3].idx["https://w3id.org/cwl/cwl#File"],
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582 )
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583 SCHEMA_DIR = cast(
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diff changeset
584 CWLObjectType,
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585 SCHEMA_CACHE["v1.0"][3].idx["https://w3id.org/cwl/cwl#Directory"],
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586 )
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587
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588 self.names = make_avro_schema([SCHEMA_FILE, SCHEMA_DIR, SCHEMA_ANY], Loader({}))
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589 self.tool = toolpath_object
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590 self.requirements = copy.deepcopy(getdefault(loadingContext.requirements, []))
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591 self.requirements.extend(self.tool.get("requirements", []))
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592 if "id" not in self.tool:
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593 self.tool["id"] = "_:" + str(uuid.uuid4())
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594 self.requirements.extend(
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595 cast(
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596 List[CWLObjectType],
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597 get_overrides(
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598 getdefault(loadingContext.overrides_list, []), self.tool["id"]
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599 ).get("requirements", []),
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600 )
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601 )
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602 self.hints = copy.deepcopy(getdefault(loadingContext.hints, []))
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603 self.hints.extend(self.tool.get("hints", []))
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604 # Versions of requirements and hints which aren't mutated.
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605 self.original_requirements = copy.deepcopy(self.requirements)
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606 self.original_hints = copy.deepcopy(self.hints)
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607 self.doc_loader = loadingContext.loader
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608 self.doc_schema = loadingContext.avsc_names
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609
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610 self.formatgraph = None # type: Optional[Graph]
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611 if self.doc_loader is not None:
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612 self.formatgraph = self.doc_loader.graph
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613
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614 checkRequirements(self.tool, supportedProcessRequirements)
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615 self.validate_hints(
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616 cast(Names, loadingContext.avsc_names),
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617 self.tool.get("hints", []),
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618 strict=getdefault(loadingContext.strict, False),
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619 )
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620
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621 self.schemaDefs = {} # type: MutableMapping[str, CWLObjectType]
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622
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623 sd, _ = self.get_requirement("SchemaDefRequirement")
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624
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625 if sd is not None:
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626 sdtypes = cast(MutableSequence[CWLObjectType], sd["types"])
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627 avroize_type(cast(MutableSequence[CWLOutputType], sdtypes))
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628 av = make_valid_avro(
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shellac
parents:
diff changeset
629 sdtypes,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
630 {cast(str, t["name"]): cast(Dict[str, Any], t) for t in sdtypes},
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
631 set(),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
632 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
633 for i in av:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
634 self.schemaDefs[i["name"]] = i # type: ignore
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
635 make_avsc_object(convert_to_dict(av), self.names)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
636
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
637 # Build record schema from inputs
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
638 self.inputs_record_schema = {
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
639 "name": "input_record_schema",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
640 "type": "record",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
641 "fields": [],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
642 } # type: CWLObjectType
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
643 self.outputs_record_schema = {
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
644 "name": "outputs_record_schema",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
645 "type": "record",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
646 "fields": [],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
647 } # type: CWLObjectType
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
648
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
649 for key in ("inputs", "outputs"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
650 for i in self.tool[key]:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
651 c = copy.deepcopy(i)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
652 c["name"] = shortname(c["id"])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
653 del c["id"]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
654
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
655 if "type" not in c:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
656 raise ValidationException(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
657 "Missing 'type' in parameter '{}'".format(c["name"])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
658 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
659
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
660 if "default" in c and "null" not in aslist(c["type"]):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
661 nullable = ["null"]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
662 nullable.extend(aslist(c["type"]))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
663 c["type"] = nullable
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
664 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
665 c["type"] = c["type"]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
666 avroize_type(c["type"], c["name"])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
667 if key == "inputs":
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
668 cast(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
669 List[CWLObjectType], self.inputs_record_schema["fields"]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
670 ).append(c)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
671 elif key == "outputs":
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
672 cast(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
673 List[CWLObjectType], self.outputs_record_schema["fields"]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
674 ).append(c)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
675
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
676 with SourceLine(toolpath_object, "inputs", ValidationException):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
677 self.inputs_record_schema = cast(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
678 CWLObjectType,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
679 make_valid_avro(self.inputs_record_schema, {}, set()),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
680 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
681 make_avsc_object(convert_to_dict(self.inputs_record_schema), self.names)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
682 with SourceLine(toolpath_object, "outputs", ValidationException):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
683 self.outputs_record_schema = cast(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
684 CWLObjectType,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
685 make_valid_avro(self.outputs_record_schema, {}, set()),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
686 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
687 make_avsc_object(convert_to_dict(self.outputs_record_schema), self.names)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
688
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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parents:
diff changeset
689 if toolpath_object.get("class") is not None and not getdefault(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
690 loadingContext.disable_js_validation, False
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
691 ):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
692 validate_js_options = (
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
693 None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
694 ) # type: Optional[Dict[str, Union[List[str], str, int]]]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
695 if loadingContext.js_hint_options_file is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
696 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
697 with open(loadingContext.js_hint_options_file) as options_file:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
698 validate_js_options = json.load(options_file)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
699 except (OSError, ValueError):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
700 _logger.error(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
701 "Failed to read options file %s",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
702 loadingContext.js_hint_options_file,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
703 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
704 raise
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
705 if self.doc_schema is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
706 validate_js_expressions(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
707 toolpath_object,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
708 self.doc_schema.names[toolpath_object["class"]],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
709 validate_js_options,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
710 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
711
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
712 dockerReq, is_req = self.get_requirement("DockerRequirement")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
713
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
714 if (
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
715 dockerReq is not None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
716 and "dockerOutputDirectory" in dockerReq
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
717 and is_req is not None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
718 and not is_req
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
719 ):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
720 _logger.warning(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
721 SourceLine(item=dockerReq, raise_type=str).makeError(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
722 "When 'dockerOutputDirectory' is declared, DockerRequirement "
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
723 "should go in the 'requirements' section, not 'hints'."
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
724 ""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
725 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
726 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
727
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
728 if (
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
729 dockerReq is not None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
730 and is_req is not None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
731 and dockerReq.get("dockerOutputDirectory") == "/var/spool/cwl"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
732 ):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
733 if is_req:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
734 # In this specific case, it is legal to have /var/spool/cwl, so skip the check.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
735 pass
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
736 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
737 # Must be a requirement
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
738 var_spool_cwl_detector(self.tool)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
739 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
740 var_spool_cwl_detector(self.tool)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
741
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
742 def _init_job(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
743 self, joborder: CWLObjectType, runtime_context: RuntimeContext
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
744 ) -> Builder:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
745
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
746 if self.metadata.get("cwlVersion") != INTERNAL_VERSION:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
747 raise WorkflowException(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
748 "Process object loaded with version '%s', must update to '%s' in order to execute."
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
749 % (self.metadata.get("cwlVersion"), INTERNAL_VERSION)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
750 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
751
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
752 job = copy.deepcopy(joborder)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
753
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
754 make_fs_access = getdefault(runtime_context.make_fs_access, StdFsAccess)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
755 fs_access = make_fs_access(runtime_context.basedir)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
756
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
757 load_listing_req, _ = self.get_requirement("LoadListingRequirement")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
758
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
759 load_listing = (
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
760 cast(str, load_listing_req.get("loadListing"))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
761 if load_listing_req is not None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
762 else "no_listing"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
763 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
764
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
765 # Validate job order
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
766 try:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
767 fill_in_defaults(self.tool["inputs"], job, fs_access)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
768
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
769 normalizeFilesDirs(job)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
770 schema = self.names.get_name("input_record_schema", None)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
771 if schema is None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
772 raise WorkflowException(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
773 "Missing input record schema: " "{}".format(self.names)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
774 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
775 validate_ex(schema, job, strict=False, logger=_logger_validation_warnings)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
776
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
777 if load_listing and load_listing != "no_listing":
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
778 get_listing(fs_access, job, recursive=(load_listing == "deep_listing"))
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shellac
parents:
diff changeset
779
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shellac
parents:
diff changeset
780 visit_class(job, ("File",), functools.partial(add_sizes, fs_access))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
781
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
782 if load_listing == "deep_listing":
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
783 for i, inparm in enumerate(self.tool["inputs"]):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
784 k = shortname(inparm["id"])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
785 if k not in job:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
786 continue
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shellac
parents:
diff changeset
787 v = job[k]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
788 dircount = [0]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
789
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
790 def inc(d): # type: (List[int]) -> None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
791 d[0] += 1
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
792
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
793 visit_class(v, ("Directory",), lambda x: inc(dircount))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
794 if dircount[0] == 0:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
795 continue
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
796 filecount = [0]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
797 visit_class(v, ("File",), lambda x: inc(filecount))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
798 if filecount[0] > FILE_COUNT_WARNING:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
799 # Long lines in this message are okay, will be reflowed based on terminal columns.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
800 _logger.warning(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
801 strip_dup_lineno(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
802 SourceLine(self.tool["inputs"], i, str).makeError(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
803 """Recursive directory listing has resulted in a large number of File objects (%s) passed to the input parameter '%s'. This may negatively affect workflow performance and memory use.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
804
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
805 If this is a problem, use the hint 'cwltool:LoadListingRequirement' with "shallow_listing" or "no_listing" to change the directory listing behavior:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
806
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
807 $namespaces:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
808 cwltool: "http://commonwl.org/cwltool#"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
809 hints:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
810 cwltool:LoadListingRequirement:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
811 loadListing: shallow_listing
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
812
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
813 """
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
814 % (filecount[0], k)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
815 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
816 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
817 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
818
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
819 except (ValidationException, WorkflowException) as err:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
820 raise WorkflowException("Invalid job input record:\n" + str(err)) from err
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
821
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
822 files = [] # type: List[CWLObjectType]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
823 bindings = CommentedSeq()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
824 outdir = ""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
825 tmpdir = ""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
826 stagedir = ""
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
827
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
828 docker_req, _ = self.get_requirement("DockerRequirement")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
829 default_docker = None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
830
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
831 if docker_req is None and runtime_context.default_container:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
832 default_docker = runtime_context.default_container
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
833
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
834 if (docker_req or default_docker) and runtime_context.use_container:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
835 if docker_req is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
836 # Check if docker output directory is absolute
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
837 if docker_req.get("dockerOutputDirectory") and cast(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
838 str, docker_req.get("dockerOutputDirectory")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
839 ).startswith("/"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
840 outdir = cast(str, docker_req.get("dockerOutputDirectory"))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
841 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
842 outdir = cast(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
843 str,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
844 docker_req.get("dockerOutputDirectory")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
845 or runtime_context.docker_outdir
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
846 or random_outdir(),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
847 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
848 elif default_docker is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
849 outdir = runtime_context.docker_outdir or random_outdir()
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
850 tmpdir = runtime_context.docker_tmpdir or "/tmp" # nosec
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
851 stagedir = runtime_context.docker_stagedir or "/var/lib/cwl"
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
852 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
853 if self.tool["class"] == "CommandLineTool":
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
854 outdir = fs_access.realpath(runtime_context.get_outdir())
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
855 tmpdir = fs_access.realpath(runtime_context.get_tmpdir())
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
856 stagedir = fs_access.realpath(runtime_context.get_stagedir())
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
857
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
858 cwl_version = cast(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
859 str,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
860 self.metadata.get("http://commonwl.org/cwltool#original_cwlVersion", None),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
861 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
862 builder = Builder(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
863 job,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
864 files,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
865 bindings,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
866 self.schemaDefs,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
867 self.names,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
868 self.requirements,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
869 self.hints,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
870 {},
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
871 runtime_context.mutation_manager,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
872 self.formatgraph,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
873 make_fs_access,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
874 fs_access,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
875 runtime_context.job_script_provider,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
876 runtime_context.eval_timeout,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
877 runtime_context.debug,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
878 runtime_context.js_console,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
879 runtime_context.force_docker_pull,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
880 load_listing,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
881 outdir,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
882 tmpdir,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
883 stagedir,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
884 cwl_version,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
885 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
886
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
887 bindings.extend(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
888 builder.bind_input(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
889 self.inputs_record_schema,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
890 job,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
891 discover_secondaryFiles=getdefault(runtime_context.toplevel, False),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
892 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
893 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
894
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
895 if self.tool.get("baseCommand"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
896 for index, command in enumerate(aslist(self.tool["baseCommand"])):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
897 bindings.append({"position": [-1000000, index], "datum": command})
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
898
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
899 if self.tool.get("arguments"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
900 for i, arg in enumerate(self.tool["arguments"]):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
901 lc = self.tool["arguments"].lc.data[i]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
902 filename = self.tool["arguments"].lc.filename
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
903 bindings.lc.add_kv_line_col(len(bindings), lc)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
904 if isinstance(arg, MutableMapping):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
905 arg = copy.deepcopy(arg)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
906 if arg.get("position"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
907 position = arg.get("position")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
908 if isinstance(position, str): # no need to test the
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
909 # CWLVersion as the v1.0
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shellac
parents:
diff changeset
910 # schema only allows ints
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
911 position = builder.do_eval(position)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
912 if position is None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
913 position = 0
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
914 arg["position"] = [position, i]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
915 else:
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shellac
parents:
diff changeset
916 arg["position"] = [0, i]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
917 bindings.append(arg)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
918 elif ("$(" in arg) or ("${" in arg):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
919 cm = CommentedMap((("position", [0, i]), ("valueFrom", arg)))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
920 cm.lc.add_kv_line_col("valueFrom", lc)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
921 cm.lc.filename = filename
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
922 bindings.append(cm)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
923 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
924 cm = CommentedMap((("position", [0, i]), ("datum", arg)))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
925 cm.lc.add_kv_line_col("datum", lc)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
926 cm.lc.filename = filename
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
927 bindings.append(cm)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
928
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
929 # use python2 like sorting of heterogeneous lists
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
930 # (containing str and int types),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
931 key = functools.cmp_to_key(cmp_like_py2)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
932
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
933 # This awkward construction replaces the contents of
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
934 # "bindings" in place (because Builder expects it to be
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
935 # mutated in place, sigh, I'm sorry) with its contents sorted,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
936 # supporting different versions of Python and ruamel.yaml with
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
937 # different behaviors/bugs in CommentedSeq.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
938 bindings_copy = copy.deepcopy(bindings)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
939 del bindings[:]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
940 bindings.extend(sorted(bindings_copy, key=key))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
941
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
942 if self.tool["class"] != "Workflow":
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
943 builder.resources = self.evalResources(builder, runtime_context)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
944 return builder
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
945
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
946 def evalResources(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
947 self, builder: Builder, runtimeContext: RuntimeContext
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
948 ) -> Dict[str, Union[int, float, str]]:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
949 resourceReq, _ = self.get_requirement("ResourceRequirement")
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
950 if resourceReq is None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
951 resourceReq = {}
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
952 cwl_version = self.metadata.get(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
953 "http://commonwl.org/cwltool#original_cwlVersion", None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
954 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
955 if cwl_version == "v1.0":
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
956 ram = 1024
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
957 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
958 ram = 256
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
959 request: Dict[str, Union[int, float, str]] = {
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
960 "coresMin": 1,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
961 "coresMax": 1,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
962 "ramMin": ram,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
963 "ramMax": ram,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
964 "tmpdirMin": 1024,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
965 "tmpdirMax": 1024,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
966 "outdirMin": 1024,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
967 "outdirMax": 1024,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
968 }
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
969 for a in ("cores", "ram", "tmpdir", "outdir"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
970 mn = mx = None # type: Optional[Union[int, float]]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
971 if resourceReq.get(a + "Min"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
972 mn = cast(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
973 Union[int, float],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
974 eval_resource(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
975 builder, cast(Union[str, int, float], resourceReq[a + "Min"])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
976 ),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
977 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
978 if resourceReq.get(a + "Max"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
979 mx = cast(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
980 Union[int, float],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
981 eval_resource(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
982 builder, cast(Union[str, int, float], resourceReq[a + "Max"])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
983 ),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
984 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
985 if mn is None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
986 mn = mx
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
987 elif mx is None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
988 mx = mn
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
989
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
990 if mn is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
991 request[a + "Min"] = mn
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
992 request[a + "Max"] = cast(Union[int, float], mx)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
993
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
994 if runtimeContext.select_resources is not None:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
995 return runtimeContext.select_resources(request, runtimeContext)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
996 return {
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
997 "cores": request["coresMin"],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
998 "ram": math.ceil(request["ramMin"])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
999 if not isinstance(request["ramMin"], str)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1000 else request["ramMin"],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1001 "tmpdirSize": math.ceil(request["tmpdirMin"])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1002 if not isinstance(request["tmpdirMin"], str)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1003 else request["tmpdirMin"],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1004 "outdirSize": math.ceil(request["outdirMin"])
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1005 if not isinstance(request["outdirMin"], str)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1006 else request["outdirMin"],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1007 }
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parents:
diff changeset
1008
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shellac
parents:
diff changeset
1009 def validate_hints(
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parents:
diff changeset
1010 self, avsc_names: Names, hints: List[CWLObjectType], strict: bool
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shellac
parents:
diff changeset
1011 ) -> None:
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parents:
diff changeset
1012 for i, r in enumerate(hints):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1013 sl = SourceLine(hints, i, ValidationException)
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parents:
diff changeset
1014 with sl:
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shellac
parents:
diff changeset
1015 if (
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parents:
diff changeset
1016 avsc_names.get_name(cast(str, r["class"]), None) is not None
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1017 and self.doc_loader is not None
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shellac
parents:
diff changeset
1018 ):
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shellac
parents:
diff changeset
1019 plain_hint = {
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shellac
parents:
diff changeset
1020 key: r[key]
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parents:
diff changeset
1021 for key in r
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parents:
diff changeset
1022 if key not in self.doc_loader.identifiers
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shellac
parents:
diff changeset
1023 } # strip identifiers
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shellac
parents:
diff changeset
1024 validate_ex(
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shellac
parents:
diff changeset
1025 cast(
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parents:
diff changeset
1026 Schema,
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parents:
diff changeset
1027 avsc_names.get_name(cast(str, plain_hint["class"]), None),
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parents:
diff changeset
1028 ),
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shellac
parents:
diff changeset
1029 plain_hint,
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parents:
diff changeset
1030 strict=strict,
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parents:
diff changeset
1031 )
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parents:
diff changeset
1032 elif r["class"] in ("NetworkAccess", "LoadListingRequirement"):
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shellac
parents:
diff changeset
1033 pass
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parents:
diff changeset
1034 else:
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parents:
diff changeset
1035 _logger.info(str(sl.makeError("Unknown hint %s" % (r["class"]))))
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parents:
diff changeset
1036
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parents:
diff changeset
1037 def visit(self, op: Callable[[CommentedMap], None]) -> None:
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parents:
diff changeset
1038 op(self.tool)
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parents:
diff changeset
1039
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parents:
diff changeset
1040 @abc.abstractmethod
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parents:
diff changeset
1041 def job(
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parents:
diff changeset
1042 self,
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parents:
diff changeset
1043 job_order: CWLObjectType,
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parents:
diff changeset
1044 output_callbacks: Optional[OutputCallbackType],
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parents:
diff changeset
1045 runtimeContext: RuntimeContext,
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parents:
diff changeset
1046 ) -> JobsGeneratorType:
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parents:
diff changeset
1047 pass
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parents:
diff changeset
1048
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parents:
diff changeset
1049
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parents:
diff changeset
1050 _names = set() # type: Set[str]
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parents:
diff changeset
1051
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parents:
diff changeset
1052
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parents:
diff changeset
1053 def uniquename(stem: str, names: Optional[Set[str]] = None) -> str:
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shellac
parents:
diff changeset
1054 global _names
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parents:
diff changeset
1055 if names is None:
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parents:
diff changeset
1056 names = _names
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parents:
diff changeset
1057 c = 1
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parents:
diff changeset
1058 u = stem
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parents:
diff changeset
1059 while u in names:
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parents:
diff changeset
1060 c += 1
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parents:
diff changeset
1061 u = f"{stem}_{c}"
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parents:
diff changeset
1062 names.add(u)
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parents:
diff changeset
1063 return u
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parents:
diff changeset
1064
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parents:
diff changeset
1065
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parents:
diff changeset
1066 def nestdir(base: str, deps: CWLObjectType) -> CWLObjectType:
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parents:
diff changeset
1067 dirname = os.path.dirname(base) + "/"
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parents:
diff changeset
1068 subid = cast(str, deps["location"])
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parents:
diff changeset
1069 if subid.startswith(dirname):
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parents:
diff changeset
1070 s2 = subid[len(dirname) :]
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parents:
diff changeset
1071 sp = s2.split("/")
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shellac
parents:
diff changeset
1072 sp.pop()
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parents:
diff changeset
1073 while sp:
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shellac
parents:
diff changeset
1074 nx = sp.pop()
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parents:
diff changeset
1075 deps = {"class": "Directory", "basename": nx, "listing": [deps]}
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shellac
parents:
diff changeset
1076 return deps
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shellac
parents:
diff changeset
1077
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shellac
parents:
diff changeset
1078
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parents:
diff changeset
1079 def mergedirs(listing: List[CWLObjectType]) -> List[CWLObjectType]:
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shellac
parents:
diff changeset
1080 r = [] # type: List[CWLObjectType]
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shellac
parents:
diff changeset
1081 ents = {} # type: Dict[str, CWLObjectType]
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shellac
parents:
diff changeset
1082 collided = set() # type: Set[str]
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shellac
parents:
diff changeset
1083 for e in listing:
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shellac
parents:
diff changeset
1084 basename = cast(str, e["basename"])
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shellac
parents:
diff changeset
1085 if basename not in ents:
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shellac
parents:
diff changeset
1086 ents[basename] = e
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shellac
parents:
diff changeset
1087 elif e["class"] == "Directory":
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shellac
parents:
diff changeset
1088 if e.get("listing"):
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shellac
parents:
diff changeset
1089 cast(
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parents:
diff changeset
1090 List[CWLObjectType], ents[basename].setdefault("listing", [])
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shellac
parents:
diff changeset
1091 ).extend(cast(List[CWLObjectType], e["listing"]))
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shellac
parents:
diff changeset
1092 if cast(str, ents[basename]["location"]).startswith("_:"):
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shellac
parents:
diff changeset
1093 ents[basename]["location"] = e["location"]
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shellac
parents:
diff changeset
1094 elif e["location"] != ents[basename]["location"]:
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shellac
parents:
diff changeset
1095 # same basename, different location, collision,
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shellac
parents:
diff changeset
1096 # rename both.
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parents:
diff changeset
1097 collided.add(basename)
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shellac
parents:
diff changeset
1098 e2 = ents[basename]
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parents:
diff changeset
1099
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parents:
diff changeset
1100 e["basename"] = urllib.parse.quote(cast(str, e["location"]), safe="")
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shellac
parents:
diff changeset
1101 e2["basename"] = urllib.parse.quote(cast(str, e2["location"]), safe="")
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parents:
diff changeset
1102
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parents:
diff changeset
1103 e["nameroot"], e["nameext"] = os.path.splitext(cast(str, e["basename"]))
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shellac
parents:
diff changeset
1104 e2["nameroot"], e2["nameext"] = os.path.splitext(cast(str, e2["basename"]))
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parents:
diff changeset
1105
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parents:
diff changeset
1106 ents[cast(str, e["basename"])] = e
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shellac
parents:
diff changeset
1107 ents[cast(str, e2["basename"])] = e2
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shellac
parents:
diff changeset
1108 for c in collided:
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shellac
parents:
diff changeset
1109 del ents[c]
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parents:
diff changeset
1110 for e in ents.values():
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parents:
diff changeset
1111 if e["class"] == "Directory" and "listing" in e:
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shellac
parents:
diff changeset
1112 e["listing"] = cast(
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parents:
diff changeset
1113 MutableSequence[CWLOutputAtomType],
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shellac
parents:
diff changeset
1114 mergedirs(cast(List[CWLObjectType], e["listing"])),
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parents:
diff changeset
1115 )
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parents:
diff changeset
1116 r.extend(ents.values())
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parents:
diff changeset
1117 return r
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parents:
diff changeset
1118
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parents:
diff changeset
1119
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parents:
diff changeset
1120 CWL_IANA = "https://www.iana.org/assignments/media-types/application/cwl"
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parents:
diff changeset
1121
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parents:
diff changeset
1122
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parents:
diff changeset
1123 def scandeps(
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parents:
diff changeset
1124 base: str,
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parents:
diff changeset
1125 doc: Union[CWLObjectType, MutableSequence[CWLObjectType]],
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shellac
parents:
diff changeset
1126 reffields: Set[str],
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parents:
diff changeset
1127 urlfields: Set[str],
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parents:
diff changeset
1128 loadref: Callable[[str, str], Union[CommentedMap, CommentedSeq, str, None]],
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shellac
parents:
diff changeset
1129 urljoin: Callable[[str, str], str] = urllib.parse.urljoin,
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shellac
parents:
diff changeset
1130 nestdirs: bool = True,
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shellac
parents:
diff changeset
1131 ) -> MutableSequence[CWLObjectType]:
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shellac
parents:
diff changeset
1132 r = [] # type: MutableSequence[CWLObjectType]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1133 if isinstance(doc, MutableMapping):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1134 if "id" in doc:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1135 if cast(str, doc["id"]).startswith("file://"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1136 df, _ = urllib.parse.urldefrag(cast(str, doc["id"]))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1137 if base != df:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1138 r.append({"class": "File", "location": df, "format": CWL_IANA})
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1139 base = df
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1140
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1141 if doc.get("class") in ("File", "Directory") and "location" in urlfields:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1142 u = cast(Optional[str], doc.get("location", doc.get("path")))
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1143 if u and not u.startswith("_:"):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1144 deps = {
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1145 "class": doc["class"],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1146 "location": urljoin(base, u),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1147 } # type: CWLObjectType
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1148 if "basename" in doc:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1149 deps["basename"] = doc["basename"]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1150 if doc["class"] == "Directory" and "listing" in doc:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1151 deps["listing"] = doc["listing"]
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1152 if doc["class"] == "File" and "secondaryFiles" in doc:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1153 deps["secondaryFiles"] = cast(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1154 CWLOutputAtomType,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1155 scandeps(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1156 base,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1157 cast(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1158 Union[CWLObjectType, MutableSequence[CWLObjectType]],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1159 doc["secondaryFiles"],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1160 ),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1161 reffields,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1162 urlfields,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1163 loadref,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1164 urljoin=urljoin,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1165 nestdirs=nestdirs,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1166 ),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1167 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1168 if nestdirs:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1169 deps = nestdir(base, deps)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1170 r.append(deps)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1171 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1172 if doc["class"] == "Directory" and "listing" in doc:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1173 r.extend(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1174 scandeps(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1175 base,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1176 cast(MutableSequence[CWLObjectType], doc["listing"]),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1177 reffields,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1178 urlfields,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1179 loadref,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1180 urljoin=urljoin,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1181 nestdirs=nestdirs,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1182 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1183 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1184 elif doc["class"] == "File" and "secondaryFiles" in doc:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1185 r.extend(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1186 scandeps(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1187 base,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1188 cast(MutableSequence[CWLObjectType], doc["secondaryFiles"]),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1189 reffields,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1190 urlfields,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1191 loadref,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1192 urljoin=urljoin,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1193 nestdirs=nestdirs,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1194 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1195 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1196
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1197 for k, v in doc.items():
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1198 if k in reffields:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1199 for u2 in aslist(v):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1200 if isinstance(u2, MutableMapping):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1201 r.extend(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1202 scandeps(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1203 base,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1204 u2,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1205 reffields,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1206 urlfields,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1207 loadref,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1208 urljoin=urljoin,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1209 nestdirs=nestdirs,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1210 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1211 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1212 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1213 subid = urljoin(base, u2)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1214 basedf, _ = urllib.parse.urldefrag(base)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1215 subiddf, _ = urllib.parse.urldefrag(subid)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1216 if basedf == subiddf:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1217 continue
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1218 sub = cast(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1219 Union[MutableSequence[CWLObjectType], CWLObjectType],
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1220 loadref(base, u2),
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1221 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1222 deps2 = {
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1223 "class": "File",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1224 "location": subid,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1225 "format": CWL_IANA,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1226 } # type: CWLObjectType
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1227 sf = scandeps(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1228 subid,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1229 sub,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1230 reffields,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1231 urlfields,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1232 loadref,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1233 urljoin=urljoin,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1234 nestdirs=nestdirs,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1235 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1236 if sf:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1237 deps2["secondaryFiles"] = cast(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1238 MutableSequence[CWLOutputAtomType], sf
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1239 )
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1240 if nestdirs:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1241 deps2 = nestdir(base, deps2)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1242 r.append(deps2)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1243 elif k in urlfields and k != "location":
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1244 for u3 in aslist(v):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1245 deps = {"class": "File", "location": urljoin(base, u3)}
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1246 if nestdirs:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1247 deps = nestdir(base, deps)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1248 r.append(deps)
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1249 elif doc.get("class") in ("File", "Directory") and k in (
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1250 "listing",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1251 "secondaryFiles",
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1252 ):
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1253 # should be handled earlier.
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1254 pass
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1255 else:
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1256 r.extend(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1257 scandeps(
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1258 base,
4f3585e2f14b "planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff changeset
1259 cast(Union[MutableSequence[CWLObjectType], CWLObjectType], v),
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1260 reffields,
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1261 urlfields,
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1262 loadref,
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1263 urljoin=urljoin,
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1264 nestdirs=nestdirs,
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1265 )
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1266 )
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1267 elif isinstance(doc, MutableSequence):
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1268 for d in doc:
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1269 r.extend(
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1270 scandeps(
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1271 base,
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1272 d,
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1273 reffields,
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1274 urlfields,
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1275 loadref,
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1276 urljoin=urljoin,
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1277 nestdirs=nestdirs,
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1278 )
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1279 )
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1280
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1281 if r:
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1282 normalizeFilesDirs(r)
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1283 r = mergedirs(cast(List[CWLObjectType], r))
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1284
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1285 return r
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1286
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1287
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1288 def compute_checksums(fs_access: StdFsAccess, fileobj: CWLObjectType) -> None:
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1289 if "checksum" not in fileobj:
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1290 checksum = hashlib.sha1() # nosec
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1291 location = cast(str, fileobj["location"])
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1292 with fs_access.open(location, "rb") as f:
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1293 contents = f.read(1024 * 1024)
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1294 while contents != b"":
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1295 checksum.update(contents)
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1296 contents = f.read(1024 * 1024)
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1297 fileobj["checksum"] = "sha1$%s" % checksum.hexdigest()
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1298 fileobj["size"] = fs_access.size(location)