Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/cwltool/schemas/v1.2.0-dev4/concepts.md @ 0:4f3585e2f14b draft default tip
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author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 ## References to other specifications |
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2 |
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3 **Javascript Object Notation (JSON)**: http://json.org |
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4 |
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5 **JSON Linked Data (JSON-LD)**: http://json-ld.org |
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6 |
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7 **YAML**: http://yaml.org |
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8 |
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9 **Avro**: https://avro.apache.org/docs/1.8.1/spec.html |
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10 |
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11 **Uniform Resource Identifier (URI) Generic Syntax**: https://tools.ietf.org/html/rfc3986) |
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12 |
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13 **Internationalized Resource Identifiers (IRIs)**: |
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14 https://tools.ietf.org/html/rfc3987 |
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15 |
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16 **Portable Operating System Interface (POSIX.1-2008)**: http://pubs.opengroup.org/onlinepubs/9699919799/ |
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17 |
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18 **Resource Description Framework (RDF)**: http://www.w3.org/RDF/ |
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19 |
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20 **XDG Base Directory Specification**: https://specifications.freedesktop.org/basedir-spec/basedir-spec-0.6.html |
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21 |
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22 |
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23 ## Scope |
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24 |
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25 This document describes CWL syntax, execution, and object model. It |
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26 is not intended to document a CWL specific implementation, however it may |
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27 serve as a reference for the behavior of conforming implementations. |
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28 |
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29 ## Terminology |
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30 |
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31 The terminology used to describe CWL documents is defined in the |
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32 Concepts section of the specification. The terms defined in the |
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33 following list are used in building those definitions and in describing the |
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34 actions of a CWL implementation: |
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35 |
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36 **may**: Conforming CWL documents and CWL implementations are permitted but |
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37 not required to behave as described. |
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38 |
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39 **must**: Conforming CWL documents and CWL implementations are required to behave |
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40 as described; otherwise they are in error. |
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41 |
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42 **error**: A violation of the rules of this specification; results are |
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43 undefined. Conforming implementations may detect and report an error and may |
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44 recover from it. |
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45 |
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46 **fatal error**: A violation of the rules of this specification; results are |
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47 undefined. Conforming implementations must not continue to execute the current |
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48 process and may report an error. |
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49 |
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50 **at user option**: Conforming software may or must (depending on the modal verb in |
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51 the sentence) behave as described; if it does, it must provide users a means to |
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52 enable or disable the behavior described. |
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53 |
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54 **deprecated**: Conforming software may implement a behavior for backwards |
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55 compatibility. Portable CWL documents should not rely on deprecated behavior. |
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56 Behavior marked as deprecated may be removed entirely from future revisions of |
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57 the CWL specification. |
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58 |
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59 # Data model |
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60 |
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61 ## Data concepts |
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62 |
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63 An **object** is a data structure equivalent to the "object" type in JSON, |
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64 consisting of a unordered set of name/value pairs (referred to here as |
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65 **fields**) and where the name is a string and the value is a string, number, |
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66 boolean, array, or object. |
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67 |
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68 A **document** is a file containing a serialized object, or an array of objects. |
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69 |
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70 A **process** is a basic unit of computation which accepts input data, |
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71 performs some computation, and produces output data. Examples include |
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72 CommandLineTools, Workflows, and ExpressionTools. |
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73 |
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74 An **input object** is an object describing the inputs to an invocation of |
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75 a process. |
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76 |
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77 An **output object** is an object describing the output resulting from an |
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78 invocation of a process. |
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79 |
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80 An **input schema** describes the valid format (required fields, data types) |
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81 for an input object. |
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82 |
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83 An **output schema** describes the valid format for an output object. |
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84 |
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85 **Metadata** is information about workflows, tools, or input items. |
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86 |
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87 ## Syntax |
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88 |
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89 CWL documents must consist of an object or array of objects represented using |
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90 JSON or YAML syntax. Upon loading, a CWL implementation must apply the |
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91 preprocessing steps described in the |
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92 [Semantic Annotations for Linked Avro Data (SALAD) Specification](SchemaSalad.html). |
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93 An implementation may formally validate the structure of a CWL document using |
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94 SALAD schemas located at https://github.com/common-workflow-language/cwl-v1.1/ |
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95 |
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96 ### map |
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97 |
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98 Note: This section is non-normative. |
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99 > type: array<ComplexType> | |
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100 > map<`key_field`, ComplexType> |
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101 |
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102 The above syntax in the CWL specifications means there are two or more ways to write the given value. |
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103 |
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104 Option one is a array and is the most verbose option. |
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105 |
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106 Option one generic example: |
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107 ``` |
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108 some_cwl_field: |
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109 - key_field: a_complex_type1 |
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110 field2: foo |
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111 field3: bar |
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112 - key_field: a_complex_type2 |
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113 field2: foo2 |
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114 field3: bar2 |
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115 - key_field: a_complex_type3 |
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116 ``` |
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117 |
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118 Option one specific example using [Workflow](Workflow.html#Workflow).[inputs](Workflow.html#WorkflowInputParameter): |
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119 > array<InputParameter> | |
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120 > map<`id`, `type` | InputParameter> |
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121 |
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122 |
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123 ``` |
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124 inputs: |
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125 - id: workflow_input01 |
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126 type: string |
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127 - id: workflow_input02 |
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128 type: File |
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129 format: http://edamontology.org/format_2572 |
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130 ``` |
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131 |
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132 Option two is enabled by the `map<…>` syntax. Instead of an array of entries we |
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133 use a mapping, where one field of the `ComplexType` (here named `key_field`) |
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134 becomes the key in the map, and its value is the rest of the `ComplexType` |
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135 without the key field. If all of the other fields of the `ComplexType` are |
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136 optional and unneeded, then we can indicate this with an empty mapping as the |
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137 value: `a_complex_type3: {}` |
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138 |
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139 Option two generic example: |
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140 ``` |
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141 some_cwl_field: |
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142 a_complex_type1: # this was the "key_field" from above |
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143 field2: foo |
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144 field3: bar |
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145 a_complex_type2: |
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146 field2: foo2 |
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147 field3: bar2 |
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148 a_complex_type3: {} # we accept the defualt values for "field2" and "field3" |
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149 ``` |
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150 |
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151 Option two specific example using [Workflow](Workflow.html#Workflow).[inputs](Workflow.html#WorkflowInputParameter): |
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152 > array<InputParameter> | |
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153 > map<`id`, `type` | InputParameter> |
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154 |
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155 |
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156 ``` |
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157 inputs: |
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158 workflow_input01: |
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159 type: string |
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160 workflow_input02: |
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161 type: File |
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162 format: http://edamontology.org/format_2572 |
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163 ``` |
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164 |
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165 Option two specific example using [SoftwareRequirement](#SoftwareRequirement).[packages](#SoftwarePackage): |
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166 > array<SoftwarePackage> | |
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167 > map<`package`, `specs` | SoftwarePackage> |
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168 |
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169 |
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170 ``` |
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171 hints: |
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172 SoftwareRequirement: |
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173 packages: |
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174 sourmash: |
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175 specs: [ https://doi.org/10.21105/joss.00027 ] |
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176 screed: |
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177 version: [ "1.0" ] |
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178 python: {} |
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179 ``` |
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180 ` |
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181 Sometimes we have a third and even more compact option denoted like this: |
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182 > type: array<ComplexType> | |
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183 > map<`key_field`, `field2` | ComplexType> |
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184 |
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185 For this example, if we only need the `key_field` and `field2` when specifying |
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186 our `ComplexType`s (because the other fields are optional and we are fine with |
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187 their default values) then we can abbreviate. |
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188 |
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189 Option three generic example: |
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190 ``` |
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191 some_cwl_field: |
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192 a_complex_type1: foo # we accept the default value for field3 |
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193 a_complex_type2: foo2 # we accept the default value for field3 |
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194 a_complex_type3: {} # we accept the default values for "field2" and "field3" |
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195 ``` |
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196 |
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197 Option three specific example using [Workflow](Workflow.html#Workflow).[inputs](Workflow.html#WorkflowInputParameter): |
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198 > array<InputParameter> | |
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199 > map<`id`, `type` | InputParameter> |
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200 |
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201 |
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202 ``` |
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203 inputs: |
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204 workflow_input01: string |
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205 workflow_input02: File # we accept the default of no File format |
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206 ``` |
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207 |
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208 Option three specific example using [SoftwareRequirement](#SoftwareRequirement).[packages](#SoftwarePackage): |
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209 > array<SoftwarePackage> | |
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210 > map<`package`, `specs` | SoftwarePackage> |
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211 |
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212 |
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213 ``` |
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214 hints: |
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215 SoftwareRequirement: |
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216 packages: |
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217 sourmash: [ https://doi.org/10.21105/joss.00027 ] |
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218 python: {} |
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219 ``` |
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220 |
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221 |
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222 What if some entries we want to mix the option 2 and 3? You can! |
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223 |
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224 Mixed option 2 and 3 generic example: |
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225 ``` |
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226 some_cwl_field: |
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227 my_complex_type1: foo # we accept the default value for field3 |
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228 my_complex_type2: |
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229 field2: foo2 |
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230 field3: bar2 # we did not accept the default value for field3 |
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231 # so we had to use the slightly expanded syntax |
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232 my_complex_type3: {} # as before, we accept the default values for both |
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233 # "field2" and "field3" |
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234 ``` |
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235 |
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236 Mixed option 2 and 3 specific example using [Workflow](Workflow.html#Workflow).[inputs](Workflow.html#WorkflowInputParameter): |
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237 > array<InputParameter> | |
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238 > map<`id`, `type` | InputParameter> |
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239 |
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240 |
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241 ``` |
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242 inputs: |
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243 workflow_input01: string |
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244 workflow_input02: # we use the longer way |
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245 type: File # because we want to specify the "format" too |
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246 format: http://edamontology.org/format_2572 |
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247 ``` |
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248 |
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249 Mixed option 2 and 3 specific example using [SoftwareRequirement](#SoftwareRequirement).[packages](#SoftwarePackage): |
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250 > array<SoftwarePackage> | |
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251 > map<`package`, `specs` | SoftwarePackage> |
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252 |
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253 |
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254 ``` |
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255 hints: |
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256 SoftwareRequirement: |
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257 packages: |
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258 sourmash: [ https://doi.org/10.21105/joss.00027 ] |
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259 screed: |
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260 specs: [ https://github.com/dib-lab/screed ] |
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261 version: [ "1.0" ] |
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262 python: {} |
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263 ``` |
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264 |
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265 Note: The `map<…>` (compact) versions are optional for users, the verbose option #1 is |
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266 always allowed, but for presentation reasons option 3 and 2 may be preferred |
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267 by human readers. Consumers of CWL must support all three options. |
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268 |
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269 The normative explanation for these variations, aimed at implementors, is in the |
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270 [Schema Salad specification](SchemaSalad.html#Identifier_maps). |
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271 |
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272 ## Identifiers |
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273 |
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274 If an object contains an `id` field, that is used to uniquely identify the |
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275 object in that document. The value of the `id` field must be unique over the |
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276 entire document. Identifiers may be resolved relative to either the document |
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277 base and/or other identifiers following the rules are described in the |
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278 [Schema Salad specification](SchemaSalad.html#Identifier_resolution). |
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279 |
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280 An implementation may choose to only honor references to object types for |
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281 which the `id` field is explicitly listed in this specification. |
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282 |
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283 ## Document preprocessing |
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284 |
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285 An implementation must resolve [$import](SchemaSalad.html#Import) and |
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286 [$include](SchemaSalad.html#Import) directives as described in the |
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287 [Schema Salad specification](SchemaSalad.html). |
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288 |
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289 Another transformation defined in Schema salad is simplification of data type definitions. |
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290 Type `<T>` ending with `?` should be transformed to `[<T>, "null"]`. |
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291 Type `<T>` ending with `[]` should be transformed to `{"type": "array", "items": <T>}` |
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292 |
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293 ## Extensions and metadata |
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294 |
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295 Input metadata (for example, a sample identifier) may be represented within |
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296 a tool or workflow using input parameters which are explicitly propagated to |
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297 output. Future versions of this specification may define additional facilities |
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298 for working with input/output metadata. |
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299 |
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300 Implementation extensions not required for correct execution (for example, |
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301 fields related to GUI presentation) and metadata about the tool or workflow |
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302 itself (for example, authorship for use in citations) may be provided as |
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303 additional fields on any object. Such extensions fields must use a namespace |
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304 prefix listed in the `$namespaces` section of the document as described in the |
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305 [Schema Salad specification](SchemaSalad.html#Explicit_context). |
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306 |
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307 It is recommended that concepts from schema.org are used whenever possible. |
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308 For the `$schema` field we recommend their RDF encoding: http://schema.org/version/latest/schema.rdf |
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309 |
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310 Implementation extensions which modify execution semantics must be [listed in |
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311 the `requirements` field](#Requirements_and_hints). |
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312 |
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313 # Execution model |
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314 |
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315 ## Execution concepts |
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316 |
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317 A **parameter** is a named symbolic input or output of process, with an |
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318 associated datatype or schema. During execution, values are assigned to |
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319 parameters to make the input object or output object used for concrete |
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320 process invocation. |
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321 |
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322 A **CommandLineTool** is a process characterized by the execution of a |
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323 standalone, non-interactive program which is invoked on some input, |
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324 produces output, and then terminates. |
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325 |
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326 A **workflow** is a process characterized by multiple subprocess steps, |
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327 where step outputs are connected to the inputs of downstream steps to |
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328 form a directed acylic graph, and independent steps may run concurrently. |
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329 |
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330 A **runtime environment** is the actual hardware and software environment when |
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331 executing a command line tool. It includes, but is not limited to, the |
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332 hardware architecture, hardware resources, operating system, software runtime |
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333 (if applicable, such as the specific Python interpreter or the specific Java |
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334 virtual machine), libraries, modules, packages, utilities, and data files |
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335 required to run the tool. |
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336 |
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337 A **workflow platform** is a specific hardware and software implementation |
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338 capable of interpreting CWL documents and executing the processes specified by |
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339 the document. The responsibilities of the workflow platform may include |
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340 scheduling process invocation, setting up the necessary runtime environment, |
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341 making input data available, invoking the tool process, and collecting output. |
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342 |
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343 A workflow platform may choose to only implement the Command Line Tool |
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344 Description part of the CWL specification. |
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345 |
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346 It is intended that the workflow platform has broad leeway outside of this |
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347 specification to optimize use of computing resources and enforce policies |
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348 not covered by this specification. Some areas that are currently out of |
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349 scope for CWL specification but may be handled by a specific workflow |
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350 platform include: |
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351 |
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352 * Data security and permissions |
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353 * Scheduling tool invocations on remote cluster or cloud compute nodes. |
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354 * Using virtual machines or operating system containers to manage the runtime |
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355 (except as described in [DockerRequirement](CommandLineTool.html#DockerRequirement)). |
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356 * Using remote or distributed file systems to manage input and output files. |
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357 * Transforming file paths. |
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358 * Pausing, resuming or checkpointing processes or workflows. |
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359 |
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360 Conforming CWL processes must not assume anything about the runtime |
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361 environment or workflow platform unless explicitly declared though the use |
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362 of [process requirements](#Requirements_and_hints). |
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363 |
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364 ## Generic execution process |
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365 |
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366 The generic execution sequence of a CWL process (including workflows and |
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367 command line line tools) is as follows. |
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368 |
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369 1. Load input object. |
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370 1. Load, process and validate a CWL document, yielding one or more process objects. |
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371 The [`$namespaces`](SchemaSalad.html#Explicit_context) present in the CWL document |
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372 are also used when validating and processing the input object. |
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373 1. If there are multiple process objects (due to [`$graph`](SchemaSalad.html#Document_graph)) |
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374 and which process object to start with is not specified in the input object (via |
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375 a [`cwl:tool`](#Executing_CWL_documents_as_scripts) entry) or by any other means |
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376 (like a URL fragment) then choose the process with the `id` of "#main" or "main". |
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377 1. Validate the input object against the `inputs` schema for the process. |
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378 1. Validate process requirements are met. |
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379 1. Perform any further setup required by the specific process type. |
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380 1. Execute the process. |
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381 1. Capture results of process execution into the output object. |
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382 1. Validate the output object against the `outputs` schema for the process. |
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383 1. Report the output object to the process caller. |
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384 |
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385 ## Requirements and hints |
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386 |
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387 A **process requirement** modifies the semantics or runtime |
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388 environment of a process. If an implementation cannot satisfy all |
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389 requirements, or a requirement is listed which is not recognized by the |
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390 implementation, it is a fatal error and the implementation must not attempt |
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391 to run the process, unless overridden at user option. |
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392 |
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393 A **hint** is similar to a requirement; however, it is not an error if an |
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394 implementation cannot satisfy all hints. The implementation may report a |
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395 warning if a hint cannot be satisfied. |
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396 |
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397 Optionally, implementations may allow requirements to be specified in the input |
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398 object document as an array of requirements under the field name |
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399 `cwl:requirements`. If implementations allow this, then such requirements |
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400 should be combined with any requirements present in the corresponding Process |
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401 as if they were specified there. |
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402 |
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403 Requirements specified in a parent Workflow are inherited by step processes |
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404 if they are valid for that step. If the substep is a CommandLineTool |
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405 only the `InlineJavascriptRequirement`, `SchemaDefRequirement`, `DockerRequirement`, |
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406 `SoftwareRequirement`, `InitialWorkDirRequirement`, `EnvVarRequirement`, |
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407 `ShellCommandRequirement`, `ResourceRequirement` are valid. |
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408 |
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409 *As good practice, it is best to have process requirements be self-contained, |
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410 such that each process can run successfully by itself.* |
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411 |
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412 If the same process requirement appears at different levels of the |
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413 workflow, the most specific instance of the requirement is used, that is, |
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414 an entry in `requirements` on a process implementation such as |
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415 CommandLineTool will take precedence over an entry in `requirements` |
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416 specified in a workflow step, and an entry in `requirements` on a workflow |
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417 step takes precedence over the workflow. Entries in `hints` are resolved |
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418 the same way. |
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419 |
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420 Requirements override hints. If a process implementation provides a |
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421 process requirement in `hints` which is also provided in `requirements` by |
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422 an enclosing workflow or workflow step, the enclosing `requirements` takes |
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423 precedence. |
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424 |
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425 ## Parameter references |
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426 |
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427 Parameter references are denoted by the syntax `$(...)` and may be used in any |
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428 field permitting the pseudo-type `Expression`, as specified by this document. |
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429 Conforming implementations must support parameter references. Parameter |
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430 references use the following subset of |
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431 [Javascript/ECMAScript 5.1](http://www.ecma-international.org/ecma-262/5.1/) |
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432 syntax, but they are designed to not require a Javascript engine for evaluation. |
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433 |
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434 In the following [BNF grammar](https://en.wikipedia.org/wiki/Backus%E2%80%93Naur_Form), |
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435 character classes and grammar rules are denoted in '{}', '-' denotes |
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436 exclusion from a character class, '(())' denotes grouping, '|' denotes |
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437 alternates, trailing '*' denotes zero or more repeats, '+' denote one |
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438 or more repeats, and all other characters are literal values. |
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439 |
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440 <p> |
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441 <table class="table"> |
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442 <tr><td>symbol:: </td><td>{Unicode alphanumeric}+</td></tr> |
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443 <tr><td>singleq:: </td><td>[' (( {character - { | \ ' \} } ))* ']</td></tr> |
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444 <tr><td>doubleq:: </td><td>[" (( {character - { | \ " \} } ))* "]</td></tr> |
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445 <tr><td>index:: </td><td>[ {decimal digit}+ ]</td></tr> |
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446 <tr><td>segment:: </td><td>. {symbol} | {singleq} | {doubleq} | {index}</td></tr> |
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447 <tr><td>parameter reference::</td><td>$( {symbol} {segment}*)</td></tr> |
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448 </table> |
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449 </p> |
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450 |
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451 Use the following algorithm to resolve a parameter reference: |
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452 |
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453 1. Match the leading symbol as the key |
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454 2. Look up the key in the parameter context (described below) to get the current value. |
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455 It is an error if the key is not found in the parameter context. |
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456 3. If there are no subsequent segments, terminate and return current value |
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457 4. Else, match the next segment |
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458 5. Extract the symbol, string, or index from the segment as the key |
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459 6. Look up the key in current value and assign as new current value. If |
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460 the key is a symbol or string, the current value must be an object. |
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461 If the key is an index, the current value must be an array or string. |
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462 It is an error if the key does not match the required type, or the key is not found or out |
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463 of range. |
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464 7. Repeat steps 3-6 |
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465 |
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466 The root namespace is the parameter context. The following parameters must |
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467 be provided: |
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468 |
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469 * `inputs`: The input object to the current Process. |
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470 * `self`: A context-specific value. The contextual values for 'self' are |
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471 documented for specific fields elsewhere in this specification. If |
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472 a contextual value of 'self' is not documented for a field, it |
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473 must be 'null'. |
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474 * `runtime`: An object containing configuration details. Specific to the |
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475 process type. An implementation may provide |
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476 opaque strings for any or all fields of `runtime`. These must be |
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477 filled in by the platform after processing the Tool but before actual |
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478 execution. Parameter references and expressions may only use the |
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479 literal string value of the field and must not perform computation on |
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480 the contents, except where noted otherwise. |
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481 |
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482 If the value of a field has no leading or trailing non-whitespace |
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483 characters around a parameter reference, the effective value of the field |
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484 becomes the value of the referenced parameter, preserving the return type. |
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485 |
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486 ### String interpolation |
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487 |
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488 If the value of a field has non-whitespace leading or trailing characters |
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489 around a parameter reference, it is subject to string interpolation. The |
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490 effective value of the field is a string containing the leading characters, |
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491 followed by the string value of the parameter reference, followed by the |
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492 trailing characters. The string value of the parameter reference is its |
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493 textual JSON representation with the following rules: |
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494 |
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495 * Strings are replaced the literal text of the string, any escaped |
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496 characters replaced by the literal characters they represent, and |
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497 there are no leading or trailing quotes. |
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498 * Objects entries are sorted by key |
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499 |
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500 Multiple parameter references may appear in a single field. This case |
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501 must be treated as a string interpolation. After interpolating the first |
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502 parameter reference, interpolation must be recursively applied to the |
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503 trailing characters to yield the final string value. |
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504 |
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505 When text embedded in a CWL file represents code for another |
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506 programming language, the use of `$(...)` (and `${...}` in the case of |
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507 expressions) may conflict with the syntax of that language. For |
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508 example, when writing shell scripts, `$(...)` is used to execute a |
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509 command in a subshell and replace a portion of the command line with |
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510 the standard output of that command. |
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511 |
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512 The following escaping rules apply. The scanner makes a single pass |
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513 from start to end with 3-character lookahead. After performing a |
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514 replacement scanning resumes at the next character following the |
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515 replaced substring. |
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516 |
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517 1. The substrings `\$(` and `\${` are replaced by `$(` and `${` |
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518 respectively. No parameter or expression evaluation |
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519 interpolation occurs. |
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520 2. A double backslash `\\` is replaced by a single backslash `\`. |
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521 3. A substring starting with a backslash that does not match one of |
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522 the previous rules is left unchanged. |
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523 |
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524 ## Expressions (Optional) |
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525 |
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526 An expression is a fragment of [Javascript/ECMAScript |
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527 5.1](http://www.ecma-international.org/ecma-262/5.1/) code evaluated by the |
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528 workflow platform to affect the inputs, outputs, or |
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529 behavior of a process. In the generic execution sequence, expressions may |
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530 be evaluated during step 5 (process setup), step 6 (execute process), |
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531 and/or step 7 (capture output). Expressions are distinct from regular |
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532 processes in that they are intended to modify the behavior of the workflow |
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533 itself rather than perform the primary work of the workflow. |
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534 |
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535 Expressions in CWL are an optional feature and are not required to be |
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536 implemented by all consumers of CWL documents. They should be used sparingly, |
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537 when there is no other way to achieve the desired outcome. Excessive use of |
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538 expressions may be a signal that other refactoring of the tools or workflows |
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539 would benefit the author, runtime, and users of the CWL document in question. |
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540 |
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541 To declare the use of expressions, the document must include the process |
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542 requirement `InlineJavascriptRequirement`. Expressions may be used in any |
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543 field permitting the pseudo-type `Expression`, as specified by this |
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544 document. |
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545 |
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546 Expressions are denoted by the syntax `$(...)` or `${...}`. A code |
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547 fragment wrapped in the `$(...)` syntax must be evaluated as a |
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548 [ECMAScript expression](http://www.ecma-international.org/ecma-262/5.1/#sec-11). A |
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549 code fragment wrapped in the `${...}` syntax must be evaluated as a |
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550 [ECMAScript function body](http://www.ecma-international.org/ecma-262/5.1/#sec-13) |
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551 for an anonymous, zero-argument function. Expressions must return a valid JSON |
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552 data type: one of null, string, number, boolean, array, object. Other return |
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553 values must result in a `permanentFailure`. Implementations must permit any |
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554 syntactically valid Javascript and account for nesting of parenthesis or braces |
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555 and that strings that may contain parenthesis or braces when scanning for |
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556 expressions. |
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557 |
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558 The runtime must include any code defined in the ["expressionLib" field of |
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559 InlineJavascriptRequirement](#InlineJavascriptRequirement) prior to |
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560 executing the actual expression. |
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561 |
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562 Before executing the expression, the runtime must initialize as global |
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563 variables the fields of the parameter context described above. |
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564 |
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565 The effective value of the field after expression evaluation follows the |
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566 same rules as parameter references discussed above. Multiple expressions |
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567 may appear in a single field. |
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568 |
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569 Expressions must be evaluated in an isolated context (a "sandbox") which |
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570 permits no side effects to leak outside the context. Expressions also must |
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571 be evaluated in [Javascript strict mode](http://www.ecma-international.org/ecma-262/5.1/#sec-4.2.2). |
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572 |
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573 The order in which expressions are evaluated is undefined except where |
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574 otherwise noted in this document. |
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575 |
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576 An implementation may choose to implement parameter references by |
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577 evaluating as a Javascript expression. The results of evaluating |
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578 parameter references must be identical whether implemented by Javascript |
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579 evaluation or some other means. |
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580 |
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581 Implementations may apply other limits, such as process isolation, timeouts, |
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582 and operating system containers/jails to minimize the security risks associated |
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583 with running untrusted code embedded in a CWL document. |
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584 |
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585 Javascript exceptions thrown from a CWL expression must result in a |
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586 `permanentFailure` of the CWL process. |
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587 |
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588 ## Executing CWL documents as scripts |
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589 |
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590 By convention, a CWL document may begin with `#!/usr/bin/env cwl-runner` |
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591 and be marked as executable (the POSIX "+x" permission bits) to enable it |
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592 to be executed directly. A workflow platform may support this mode of |
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593 operation; if so, it must provide `cwl-runner` as an alias for the |
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594 platform's CWL implementation. |
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595 |
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596 A CWL input object document may similarly begin with `#!/usr/bin/env |
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597 cwl-runner` and be marked as executable. In this case, the input object |
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598 must include the field `cwl:tool` supplying an IRI to the default CWL |
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599 document that should be executed using the fields of the input object as |
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600 input parameters. |
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601 |
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602 The `cwl-runner` interface is required for conformance testing and is |
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603 documented in [cwl-runner.cwl](cwl-runner.cwl). |
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604 |
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605 ## Discovering CWL documents on a local filesystem |
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606 |
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607 To discover CWL documents look in the following locations: |
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608 |
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609 For each value in the `XDG_DATA_DIRS` environment variable (which is a `:` colon |
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610 separated list), check the `./commonwl` subdirectory. If `XDG_DATA_DIRS` is |
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611 unset or empty, then check using the default value for `XDG_DATA_DIRS`: |
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612 `/usr/local/share/:/usr/share/` (That is to say, check `/usr/share/commonwl/` |
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613 and `/usr/local/share/commonwl/`) |
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614 |
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615 Then check `$XDG_DATA_HOME/commonwl/`. |
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616 |
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617 If the `XDG_DATA_HOME` environment variable is unset, its default value is |
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618 `$HOME/.local/share` (That is to say, check `$HOME/.local/share/commonwl`) |
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619 |
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620 `$XDG_DATA_HOME` and `$XDG_DATA_DIRS` are from the [XDG Base Directory |
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621 Specification](http://standards.freedesktop.org/basedir-spec/basedir-spec-0.6.html) |