Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/cwltool/schemas/v1.2.0-dev3/invocation.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 # Running a Command |
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2 |
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3 To accommodate the enormous variety in syntax and semantics for input, runtime |
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4 environment, invocation, and output of arbitrary programs, a CommandLineTool |
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5 defines an "input binding" that describes how to translate abstract input |
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6 parameters to an concrete program invocation, and an "output binding" that |
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7 describes how to generate output parameters from program output. |
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8 |
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9 ## Input binding |
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10 |
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11 The tool command line is built by applying command line bindings to the |
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12 input object. Bindings are listed either as part of an [input |
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13 parameter](#CommandInputParameter) using the `inputBinding` field, or |
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14 separately using the `arguments` field of the CommandLineTool. |
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15 |
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16 The algorithm to build the command line is as follows. In this algorithm, |
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17 the sort key is a list consisting of one or more numeric or string |
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18 elements. Strings are sorted lexicographically based on UTF-8 encoding. |
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19 |
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20 1. Collect `CommandLineBinding` objects from `arguments`. Assign a sorting |
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21 key `[position, i]` where `position` is |
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22 [`CommandLineBinding.position`](#CommandLineBinding) and `i` |
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23 is the index in the `arguments` list. |
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24 |
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25 2. Collect `CommandLineBinding` objects from the `inputs` schema and |
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26 associate them with values from the input object. Where the input type |
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27 is a record, array, or map, recursively walk the schema and input object, |
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28 collecting nested `CommandLineBinding` objects and associating them with |
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29 values from the input object. |
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30 |
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31 3. Create a sorting key by taking the value of the `position` field at |
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32 each level leading to each leaf binding object. If `position` is not |
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33 specified, it is not added to the sorting key. For bindings on arrays |
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34 and maps, the sorting key must include the array index or map key |
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35 following the position. If and only if two bindings have the same sort |
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36 key, the tie must be broken using the ordering of the field or parameter |
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37 name immediately containing the leaf binding. |
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38 |
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39 4. Sort elements using the assigned sorting keys. Numeric entries sort |
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40 before strings. |
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41 |
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42 5. In the sorted order, apply the rules defined in |
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43 [`CommandLineBinding`](#CommandLineBinding) to convert bindings to actual |
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44 command line elements. |
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45 |
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46 6. Insert elements from `baseCommand` at the beginning of the command |
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47 line. |
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48 |
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49 ## Runtime environment |
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50 |
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51 All files listed in the input object must be made available in the runtime |
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52 environment. The implementation may use a shared or distributed file |
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53 system or transfer files via explicit download to the host. Implementations |
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54 may choose not to provide access to files not explicitly specified in the input |
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55 object or process requirements. |
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56 |
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57 Output files produced by tool execution must be written to the |
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58 **designated output directory**. The initial current working |
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59 directory when executing the tool must be the designated output |
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60 directory. The designated output directory should be empty, except |
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61 for files or directories specified using |
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62 [InitialWorkDirRequirement](InitialWorkDirRequirement). |
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63 |
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64 Files may also be written to the **designated temporary directory**. This |
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65 directory must be isolated and not shared with other processes. Any files |
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66 written to the designated temporary directory may be automatically deleted by |
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67 the workflow platform immediately after the tool terminates. |
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68 |
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69 For compatibility, files may be written to the **system temporary directory** |
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70 which must be located at `/tmp`. Because the system temporary directory may be |
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71 shared with other processes on the system, files placed in the system temporary |
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72 directory are not guaranteed to be deleted automatically. A tool |
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73 must not use the system temporary directory as a backchannel communication with |
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74 other tools. It is valid for the system temporary directory to be the same as |
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75 the designated temporary directory. |
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76 |
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77 When executing the tool, the tool must execute in a new, empty environment |
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78 with only the environment variables described below; the child process must |
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79 not inherit environment variables from the parent process except as |
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80 specified or at user option. |
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81 |
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82 * `HOME` must be set to the designated output directory. |
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83 * `TMPDIR` must be set to the designated temporary directory. |
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84 * `PATH` may be inherited from the parent process, except when run in a |
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85 container that provides its own `PATH`. |
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86 * Variables defined by [EnvVarRequirement](#EnvVarRequirement) |
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87 * The default environment of the container, such as when using |
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88 [DockerRequirement](#DockerRequirement) |
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89 |
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90 An implementation may forbid the tool from writing to any location in the |
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91 runtime environment file system other than the designated temporary directory, |
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92 system temporary directory, and designated output directory. An implementation |
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93 may provide read-only input files, and disallow in-place update of input files. |
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94 The designated temporary directory, system temporary directory and designated |
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95 output directory may each reside on different mount points on different file |
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96 systems. |
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97 |
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98 An implementation may forbid the tool from directly accessing network |
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99 resources. Correct tools must not assume any network access unless they have |
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100 the 'networkAccess' field of a ['NetworkAccess'](#NetworkAccess) requirement set |
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101 to `true` but even then this does not imply a publically routable IP address or |
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102 the ability to accept inbound connections. |
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103 |
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104 The `runtime` section available in [parameter references](#Parameter_references) |
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105 and [expressions](#Expressions) contains the following fields. As noted |
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106 earlier, an implementation may perform deferred resolution of runtime fields by providing |
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107 opaque strings for any or all of the following fields; parameter references |
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108 and expressions may only use the literal string value of the field and must |
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109 not perform computation on the contents. |
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110 |
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111 * `runtime.outdir`: an absolute path to the designated output directory |
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112 * `runtime.tmpdir`: an absolute path to the designated temporary directory |
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113 * `runtime.cores`: number of CPU cores reserved for the tool process |
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114 * `runtime.ram`: amount of RAM in mebibytes (2\*\*20) reserved for the tool process |
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115 * `runtime.outdirSize`: reserved storage space available in the designated output directory |
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116 * `runtime.tmpdirSize`: reserved storage space available in the designated temporary directory |
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117 |
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118 For `cores`, `ram`, `outdirSize` and `tmpdirSize`, if an implementation can't |
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119 provide the actual number of reserved resources during the expression evaluation time, |
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120 it should report back the minimal requested amount. |
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121 |
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122 See [ResourceRequirement](#ResourceRequirement) for details on how to |
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123 describe the hardware resources required by a tool. |
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124 |
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125 The standard input stream, the standard output stream, and/or the standard error |
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126 stream may be redirected as described in the [`stdin`](#stdin), |
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127 [`stdout`](#stdout), and [`stderr`](#stderr) fields. |
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128 |
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129 ## Execution |
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130 |
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131 Once the command line is built and the runtime environment is created, the |
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132 actual tool is executed. |
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133 |
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134 The standard error stream and standard output stream may be captured by |
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135 platform logging facilities for storage and reporting. |
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136 |
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137 Tools may be multithreaded or spawn child processes; however, when the |
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138 parent process exits, the tool is considered finished regardless of whether |
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139 any detached child processes are still running. Tools must not require any |
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140 kind of console, GUI, or web based user interaction in order to start and |
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141 run to completion. |
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142 |
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143 The exit code of the process indicates if the process completed |
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144 successfully. By convention, an exit code of zero is treated as success |
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145 and non-zero exit codes are treated as failure. This may be customized by |
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146 providing the fields `successCodes`, `temporaryFailCodes`, and |
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147 `permanentFailCodes`. An implementation may choose to default unspecified |
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148 non-zero exit codes to either `temporaryFailure` or `permanentFailure`. |
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149 |
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150 The exit code of the process is available to expressions in |
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151 `outputEval` as `runtime.exitCode`. |
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152 |
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153 ## Output binding |
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154 |
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155 If the output directory contains a file named "cwl.output.json", that file |
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156 must be loaded and used as the output object. Otherwise, the output object |
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157 must be generated by walking the parameters listed in `outputs` and |
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158 applying output bindings to the tool output. Output bindings are |
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159 associated with output parameters using the `outputBinding` field. See |
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160 [`CommandOutputBinding`](#CommandOutputBinding) for details. |