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annotate planemo/lib/python3.7/site-packages/galaxy/tool_util/cwl/parser.py @ 1:56ad4e20f292 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:32:28 -0400
parents d30785e31577
children
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1 """ This module provides proxy objects around objects from the common
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2 workflow language reference implementation library cwltool. These proxies
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3 adapt cwltool to Galaxy features and abstract the library away from the rest
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4 of the framework.
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5 """
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6 from __future__ import absolute_import
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7
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8 import base64
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9 import copy
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10 import json
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11 import logging
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12 import os
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13 import pickle
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14 from abc import ABCMeta, abstractmethod
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15 from collections import OrderedDict
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16 from uuid import uuid4
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17
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18 import six
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19
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20 from galaxy.exceptions import MessageException
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21 from galaxy.util import (
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22 listify,
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23 safe_makedirs,
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24 unicodify,
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25 )
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26 from galaxy.util.bunch import Bunch
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27 from .cwltool_deps import (
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28 beta_relaxed_fmt_check,
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29 ensure_cwltool_available,
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30 getdefault,
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31 pathmapper,
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32 process,
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33 ref_resolver,
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34 relink_initialworkdir,
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35 RuntimeContext,
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36 sourceline,
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37 StdFsAccess,
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38 )
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39 from .representation import (
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40 field_to_field_type,
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41 FIELD_TYPE_REPRESENTATION,
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42 INPUT_TYPE,
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43 type_descriptions_for_field_types,
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44 USE_FIELD_TYPES,
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45 USE_STEP_PARAMETERS,
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46 )
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47 from .schema import (
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48 non_strict_non_validating_schema_loader,
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49 schema_loader,
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50 )
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51 from .util import SECONDARY_FILES_EXTRA_PREFIX
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52
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53 log = logging.getLogger(__name__)
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54
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55 JOB_JSON_FILE = ".cwl_job.json"
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56
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57 DOCKER_REQUIREMENT = "DockerRequirement"
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58 SUPPORTED_TOOL_REQUIREMENTS = [
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59 "CreateFileRequirement",
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60 "DockerRequirement",
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61 "EnvVarRequirement",
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62 "InitialWorkDirRequirement",
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63 "InlineJavascriptRequirement",
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64 "ResourceRequirement",
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65 "ShellCommandRequirement",
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66 "ScatterFeatureRequirement",
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67 "SchemaDefRequirement",
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68 "SubworkflowFeatureRequirement",
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69 "StepInputExpressionRequirement",
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70 "MultipleInputFeatureRequirement",
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71 ]
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72
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73
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74 SUPPORTED_WORKFLOW_REQUIREMENTS = SUPPORTED_TOOL_REQUIREMENTS + [
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75 ]
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76
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77 PERSISTED_REPRESENTATION = "cwl_tool_object"
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78
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79
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80 def tool_proxy(tool_path=None, tool_object=None, strict_cwl_validation=True, tool_directory=None, uuid=None):
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81 """ Provide a proxy object to cwltool data structures to just
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82 grab relevant data.
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83 """
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84 ensure_cwltool_available()
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85 # if uuid is None:
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86 # raise Exception("tool_proxy must be called with non-None uuid")
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87 tool = _to_cwl_tool_object(
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88 tool_path=tool_path,
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89 tool_object=tool_object,
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90 strict_cwl_validation=strict_cwl_validation,
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91 tool_directory=tool_directory,
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92 uuid=uuid
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93 )
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94 return tool
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95
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96
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97 def tool_proxy_from_persistent_representation(persisted_tool, strict_cwl_validation=True, tool_directory=None):
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98 """Load a ToolProxy from a previously persisted representation."""
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99 ensure_cwltool_available()
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100 if PERSISTED_REPRESENTATION == "cwl_tool_object":
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101 kwds = {"cwl_tool_object": ToolProxy.from_persistent_representation(persisted_tool)}
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102 else:
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103 raw_process_reference = persisted_tool # ???
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104 kwds = {"raw_process_reference": ToolProxy.from_persistent_representation(raw_process_reference)}
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105 uuid = persisted_tool["uuid"]
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106 tool = _to_cwl_tool_object(uuid=uuid, strict_cwl_validation=strict_cwl_validation, tool_directory=tool_directory, **kwds)
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107 return tool
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108
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109
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110 def workflow_proxy(workflow_path, strict_cwl_validation=True):
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111 ensure_cwltool_available()
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112 workflow = _to_cwl_workflow_object(workflow_path, strict_cwl_validation=strict_cwl_validation)
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113 return workflow
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114
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115
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116 def load_job_proxy(job_directory, strict_cwl_validation=True):
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117 ensure_cwltool_available()
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118 job_objects_path = os.path.join(job_directory, JOB_JSON_FILE)
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119 job_objects = json.load(open(job_objects_path, "r"))
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120 job_inputs = job_objects["job_inputs"]
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121 output_dict = job_objects["output_dict"]
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122 # Any reason to retain older tool_path variant of this? Probably not?
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123 if "tool_path" in job_objects:
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124 tool_path = job_objects["tool_path"]
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125 cwl_tool = tool_proxy(tool_path, strict_cwl_validation=strict_cwl_validation)
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126 else:
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127 persisted_tool = job_objects["tool_representation"]
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128 cwl_tool = tool_proxy_from_persistent_representation(persisted_tool=persisted_tool, strict_cwl_validation=strict_cwl_validation)
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129 cwl_job = cwl_tool.job_proxy(job_inputs, output_dict, job_directory=job_directory)
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130 return cwl_job
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131
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132
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133 def _to_cwl_tool_object(tool_path=None, tool_object=None, cwl_tool_object=None, raw_process_reference=None, strict_cwl_validation=False, tool_directory=None, uuid=None):
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134 if uuid is None:
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135 uuid = str(uuid4())
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136 schema_loader = _schema_loader(strict_cwl_validation)
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137 if raw_process_reference is None and tool_path is not None:
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138 assert cwl_tool_object is None
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139 assert tool_object is None
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140
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141 raw_process_reference = schema_loader.raw_process_reference(tool_path)
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142 cwl_tool = schema_loader.tool(
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143 raw_process_reference=raw_process_reference,
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144 )
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145 elif tool_object is not None:
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146 assert raw_process_reference is None
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147 assert cwl_tool_object is None
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148
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149 # Allow loading tools from YAML...
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150 from ruamel import yaml as ryaml
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151 as_str = json.dumps(tool_object)
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152 tool_object = ryaml.round_trip_load(as_str)
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153 path = tool_directory
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154 if path is None:
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155 path = os.getcwd()
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156 uri = ref_resolver.file_uri(path) + "/"
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157 sourceline.add_lc_filename(tool_object, uri)
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158 raw_process_reference = schema_loader.raw_process_reference_for_object(
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159 tool_object,
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160 uri=uri
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161 )
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162 cwl_tool = schema_loader.tool(
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163 raw_process_reference=raw_process_reference,
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164 )
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165 else:
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166 cwl_tool = cwl_tool_object
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167
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168 if isinstance(cwl_tool, int):
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169 raise Exception("Failed to load tool.")
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170
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171 raw_tool = cwl_tool.tool
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172 # Apply Galaxy hacks to CWL tool representation to bridge semantic differences
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173 # between Galaxy and cwltool.
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174 _hack_cwl_requirements(cwl_tool)
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175 check_requirements(raw_tool)
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176 return _cwl_tool_object_to_proxy(cwl_tool, uuid, raw_process_reference=raw_process_reference, tool_path=tool_path)
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177
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178
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179 def _cwl_tool_object_to_proxy(cwl_tool, uuid, raw_process_reference=None, tool_path=None):
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180 raw_tool = cwl_tool.tool
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181 if "class" not in raw_tool:
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182 raise Exception("File does not declare a class, not a valid Draft 3+ CWL tool.")
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183
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184 process_class = raw_tool["class"]
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185 if process_class == "CommandLineTool":
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186 proxy_class = CommandLineToolProxy
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187 elif process_class == "ExpressionTool":
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188 proxy_class = ExpressionToolProxy
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189 else:
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190 raise Exception("File not a CWL CommandLineTool.")
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191 top_level_object = tool_path is not None
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192 if top_level_object and ("cwlVersion" not in raw_tool):
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193 raise Exception("File does not declare a CWL version, pre-draft 3 CWL tools are not supported.")
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194
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195 proxy = proxy_class(cwl_tool, uuid, raw_process_reference, tool_path)
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196 return proxy
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197
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198
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199 def _to_cwl_workflow_object(workflow_path, strict_cwl_validation=None):
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200 proxy_class = WorkflowProxy
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201 cwl_workflow = _schema_loader(strict_cwl_validation).tool(path=workflow_path)
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202 raw_workflow = cwl_workflow.tool
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203 check_requirements(raw_workflow, tool=False)
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204
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205 proxy = proxy_class(cwl_workflow, workflow_path)
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206 return proxy
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207
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208
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209 def _schema_loader(strict_cwl_validation):
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210 target_schema_loader = schema_loader if strict_cwl_validation else non_strict_non_validating_schema_loader
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211 return target_schema_loader
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212
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213
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214 def _hack_cwl_requirements(cwl_tool):
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215 move_to_hints = []
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216 for i, requirement in enumerate(cwl_tool.requirements):
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217 if requirement["class"] == DOCKER_REQUIREMENT:
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218 move_to_hints.insert(0, i)
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219
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220 for i in move_to_hints:
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221 del cwl_tool.requirements[i]
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222 cwl_tool.hints.append(requirement)
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223
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224
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225 def check_requirements(rec, tool=True):
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226 if isinstance(rec, dict):
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227 if "requirements" in rec:
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228 for r in rec["requirements"]:
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229 if tool:
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230 possible = SUPPORTED_TOOL_REQUIREMENTS
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231 else:
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232 possible = SUPPORTED_WORKFLOW_REQUIREMENTS
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233 if r["class"] not in possible:
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234 raise Exception("Unsupported requirement %s" % r["class"])
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235 for d in rec:
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236 check_requirements(rec[d], tool=tool)
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237 if isinstance(rec, list):
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238 for d in rec:
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239 check_requirements(d, tool=tool)
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240
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241
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242 @six.add_metaclass(ABCMeta)
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243 class ToolProxy(object):
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244
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245 def __init__(self, tool, uuid, raw_process_reference=None, tool_path=None):
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246 self._tool = tool
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247 self._uuid = uuid
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248 self._tool_path = tool_path
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249 self._raw_process_reference = raw_process_reference
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250
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251 def job_proxy(self, input_dict, output_dict, job_directory="."):
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252 """ Build a cwltool.job.Job describing computation using a input_json
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253 Galaxy will generate mapping the Galaxy description of the inputs into
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254 a cwltool compatible variant.
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255 """
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256 return JobProxy(self, input_dict, output_dict, job_directory=job_directory)
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257
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258 @property
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259 def id(self):
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260 raw_id = self._tool.tool.get("id", None)
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261 return raw_id
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262
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263 def galaxy_id(self):
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264 raw_id = self.id
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265 tool_id = None
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266 # don't reduce "search.cwl#index" to search
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267 if raw_id:
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268 tool_id = os.path.basename(raw_id)
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269 # tool_id = os.path.splitext(os.path.basename(raw_id))[0]
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270 if not tool_id:
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271 return self._uuid
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272 assert tool_id
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273 if tool_id.startswith("#"):
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274 tool_id = tool_id[1:]
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275 return tool_id
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276
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277 @abstractmethod
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278 def input_instances(self):
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279 """ Return InputInstance objects describing mapping to Galaxy inputs. """
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280
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281 @abstractmethod
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282 def output_instances(self):
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283 """ Return OutputInstance objects describing mapping to Galaxy inputs. """
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284
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285 @abstractmethod
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286 def docker_identifier(self):
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287 """ Return docker identifier for embedding in tool description. """
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288
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289 @abstractmethod
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290 def description(self):
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291 """ Return description to tool. """
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292
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293 @abstractmethod
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294 def label(self):
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295 """ Return label for tool. """
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296
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297 def to_persistent_representation(self):
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298 """Return a JSON representation of this tool. Not for serialization
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299 over the wire, but serialization in a database."""
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300 # TODO: Replace this with some more readable serialization,
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301 # I really don't like using pickle here.
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302 if PERSISTED_REPRESENTATION == "cwl_tool_object":
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303 persisted_obj = remove_pickle_problems(self._tool)
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304 else:
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305 persisted_obj = self._raw_process_reference
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306 return {
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307 "class": self._class,
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308 "pickle": unicodify(base64.b64encode(pickle.dumps(persisted_obj, pickle.HIGHEST_PROTOCOL))),
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309 "uuid": self._uuid,
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310 }
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311
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312 @staticmethod
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313 def from_persistent_representation(as_object):
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314 """Recover an object serialized with to_persistent_representation."""
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315 if "class" not in as_object:
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316 raise Exception("Failed to deserialize tool proxy from JSON object - no class found.")
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317 if "pickle" not in as_object:
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318 raise Exception("Failed to deserialize tool proxy from JSON object - no pickle representation found.")
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319 if "uuid" not in as_object:
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320 raise Exception("Failed to deserialize tool proxy from JSON object - no uuid found.")
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321 to_unpickle = base64.b64decode(as_object["pickle"])
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322 loaded_object = pickle.loads(to_unpickle)
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323 return loaded_object
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324
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325
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326 class CommandLineToolProxy(ToolProxy):
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327 _class = "CommandLineTool"
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328
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329 def description(self):
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330 # Don't use description - typically too verbose.
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331 return ''
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332
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333 def doc(self):
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334 # TODO: parse multiple lines and merge - valid in cwl-1.1
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335 doc = self._tool.tool.get('doc')
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336 return doc
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337
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338 def label(self):
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339 label = self._tool.tool.get('label')
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340
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341 if label is not None:
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342 return label.partition(":")[0] # return substring before ':'
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343 else:
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344 return ''
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345
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346 def input_fields(self):
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347 input_records_schema = self._eval_schema(self._tool.inputs_record_schema)
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348 if input_records_schema["type"] != "record":
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349 raise Exception("Unhandled CWL tool input structure")
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350
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351 # TODO: handle this somewhere else?
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352 # schemadef_req_tool_param
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353 rval = []
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354 for input in input_records_schema["fields"]:
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355 input_copy = copy.deepcopy(input)
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356 input_type = input.get("type")
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357 if isinstance(input_type, list) or isinstance(input_type, dict):
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358 rval.append(input_copy)
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359 continue
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360
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361 if input_type in self._tool.schemaDefs:
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362 input_copy["type"] = self._tool.schemaDefs[input_type]
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363
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364 rval.append(input_copy)
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365 return rval
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366
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367 def _eval_schema(self, io_schema):
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368 schema_type = io_schema.get("type")
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369 if schema_type in self._tool.schemaDefs:
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370 io_schema = self._tool.schemaDefs[schema_type]
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371 return io_schema
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372
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373 def input_instances(self):
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374 return [_outer_field_to_input_instance(_) for _ in self.input_fields()]
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375
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376 def output_instances(self):
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377 outputs_schema = self._eval_schema(self._tool.outputs_record_schema)
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378 if outputs_schema["type"] != "record":
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379 raise Exception("Unhandled CWL tool output structure")
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380
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381 rval = []
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382 for output in outputs_schema["fields"]:
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383 rval.append(_simple_field_to_output(output))
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384
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385 return rval
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386
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387 def docker_identifier(self):
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diff changeset
388 for hint in self.hints_or_requirements_of_class("DockerRequirement"):
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diff changeset
389 if "dockerImageId" in hint:
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390 return hint["dockerImageId"]
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diff changeset
391 else:
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392 return hint["dockerPull"]
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393
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394 return None
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395
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396 def hints_or_requirements_of_class(self, class_name):
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397 tool = self._tool.tool
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398 reqs_and_hints = tool.get("requirements", []) + tool.get("hints", [])
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diff changeset
399 for hint in reqs_and_hints:
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parents:
diff changeset
400 if hint["class"] == class_name:
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401 yield hint
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402
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403 def software_requirements(self):
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404 # Roughest imaginable pass at parsing requirements, really need to take in specs, handle
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405 # multiple versions, etc...
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406 tool = self._tool.tool
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407 reqs_and_hints = tool.get("requirements", []) + tool.get("hints", [])
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408 requirements = []
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409 for hint in reqs_and_hints:
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410 if hint["class"] == "SoftwareRequirement":
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411 packages = hint.get("packages", [])
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412 for package in packages:
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413 versions = package.get("version", [])
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414 first_version = None if not versions else versions[0]
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415 requirements.append((package["package"], first_version))
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416 return requirements
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417
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418 @property
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419 def requirements(self):
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420 return getattr(self._tool, "requirements", [])
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421
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422
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423 class ExpressionToolProxy(CommandLineToolProxy):
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424 _class = "ExpressionTool"
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425
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426
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427 class JobProxy(object):
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428
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429 def __init__(self, tool_proxy, input_dict, output_dict, job_directory):
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430 self._tool_proxy = tool_proxy
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431 self._input_dict = input_dict
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432 self._output_dict = output_dict
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433 self._job_directory = job_directory
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434
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435 self._final_output = None
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436 self._ok = True
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437 self._cwl_job = None
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438 self._is_command_line_job = None
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439
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440 self._normalize_job()
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441
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442 def cwl_job(self):
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443 self._ensure_cwl_job_initialized()
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444 return self._cwl_job
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445
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446 @property
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447 def is_command_line_job(self):
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448 self._ensure_cwl_job_initialized()
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449 assert self._is_command_line_job is not None
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450 return self._is_command_line_job
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451
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452 def _ensure_cwl_job_initialized(self):
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453 if self._cwl_job is None:
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454 job_args = dict(
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455 basedir=self._job_directory,
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456 select_resources=self._select_resources,
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457 outdir=os.path.join(self._job_directory, "working"),
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458 tmpdir=os.path.join(self._job_directory, "cwltmp"),
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459 stagedir=os.path.join(self._job_directory, "cwlstagedir"),
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460 use_container=False,
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461 beta_relaxed_fmt_check=beta_relaxed_fmt_check,
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diff changeset
462 )
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463
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464 args = []
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465 kwargs = {}
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466 if RuntimeContext is not None:
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467 args.append(RuntimeContext(job_args))
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468 else:
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469 kwargs = job_args
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470 self._cwl_job = next(self._tool_proxy._tool.job(
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471 self._input_dict,
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472 self._output_callback,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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473 *args, **kwargs
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
474 ))
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475 self._is_command_line_job = hasattr(self._cwl_job, "command_line")
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476
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477 def _normalize_job(self):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
478 # Somehow reuse whatever causes validate in cwltool... maybe?
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479 def pathToLoc(p):
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480 if "location" not in p and "path" in p:
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481 p["location"] = p["path"]
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482 del p["path"]
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483
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484 runtime_context = RuntimeContext({})
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485 make_fs_access = getdefault(runtime_context.make_fs_access, StdFsAccess)
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486 fs_access = make_fs_access(runtime_context.basedir)
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diff changeset
487 process.fill_in_defaults(self._tool_proxy._tool.tool["inputs"], self._input_dict, fs_access)
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diff changeset
488 process.visit_class(self._input_dict, ("File", "Directory"), pathToLoc)
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diff changeset
489 # TODO: Why doesn't fillInDefault fill in locations instead of paths?
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diff changeset
490 process.normalizeFilesDirs(self._input_dict)
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diff changeset
491 # TODO: validate like cwltool process _init_job.
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diff changeset
492 # validate.validate_ex(self.names.get_name("input_record_schema", ""), builder.job,
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diff changeset
493 # strict=False, logger=_logger_validation_warnings)
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494
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495 def rewrite_inputs_for_staging(self):
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diff changeset
496 if hasattr(self._cwl_job, "pathmapper"):
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diff changeset
497 pass
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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498 # DO SOMETHING LIKE THE FOLLOWING?
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499 # path_rewrites = {}
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500 # for f, p in self._cwl_job.pathmapper.items():
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diff changeset
501 # if not p.staged:
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diff changeset
502 # continue
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503 # if p.type in ("File", "Directory"):
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504 # path_rewrites[p.resolved] = p.target
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505 # for key, value in self._input_dict.items():
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506 # if key in path_rewrites:
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507 # self._input_dict[key]["location"] = path_rewrites[value]
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508 else:
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509 stagedir = os.path.join(self._job_directory, "cwlstagedir")
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510 safe_makedirs(stagedir)
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511
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512 def stage_recursive(value):
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513 is_list = isinstance(value, list)
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514 is_dict = isinstance(value, dict)
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515 log.info("handling value %s, is_list %s, is_dict %s" % (value, is_list, is_dict))
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516 if is_list:
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parents:
diff changeset
517 for val in value:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
518 stage_recursive(val)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
519 elif is_dict:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
520 if "location" in value and "basename" in value:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
521 location = value["location"]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
522 basename = value["basename"]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
523 if not location.endswith(basename): # TODO: sep()[-1]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
524 staged_loc = os.path.join(stagedir, basename)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
525 if not os.path.exists(staged_loc):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
526 os.symlink(location, staged_loc)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
527 value["location"] = staged_loc
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
528 for key, dict_value in value.items():
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
529 stage_recursive(dict_value)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
530 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
531 log.info("skipping simple value...")
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
532 stage_recursive(self._input_dict)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
533
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
534 def _select_resources(self, request, runtime_context=None):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
535 new_request = request.copy()
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
536 new_request["cores"] = "$GALAXY_SLOTS"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
537 return new_request
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
538
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
539 @property
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
540 def command_line(self):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
541 if self.is_command_line_job:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
542 return self.cwl_job().command_line
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
543 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
544 return ["true"]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
545
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
546 @property
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
547 def stdin(self):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
548 if self.is_command_line_job:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
549 return self.cwl_job().stdin
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
550 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
551 return None
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
552
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
553 @property
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
554 def stdout(self):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
555 if self.is_command_line_job:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
556 return self.cwl_job().stdout
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
557 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
558 return None
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
559
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
560 @property
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
561 def stderr(self):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
562 if self.is_command_line_job:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
563 return self.cwl_job().stderr
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
564 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
565 return None
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
566
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
567 @property
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
568 def environment(self):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
569 if self.is_command_line_job:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
570 return self.cwl_job().environment
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
571 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
572 return {}
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
573
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
574 @property
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
575 def generate_files(self):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
576 if self.is_command_line_job:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
577 return self.cwl_job().generatefiles
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
578 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
579 return {}
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
580
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
581 def _output_callback(self, out, process_status):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
582 self._process_status = process_status
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
583 if process_status == "success":
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
584 self._final_output = out
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
585 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
586 self._ok = False
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
587
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
588 log.info("Output are %s, status is %s" % (out, process_status))
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
589
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
590 def collect_outputs(self, tool_working_directory, rcode):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
591 if not self.is_command_line_job:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
592 cwl_job = self.cwl_job()
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
593 if RuntimeContext is not None:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
594 cwl_job.run(
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
595 RuntimeContext({})
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
596 )
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
597 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
598 cwl_job.run()
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
599 if not self._ok:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
600 raise Exception("Final process state not ok, [%s]" % self._process_status)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
601 return self._final_output
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
602 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
603 return self.cwl_job().collect_outputs(tool_working_directory, rcode)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
604
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
605 def save_job(self):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
606 job_file = JobProxy._job_file(self._job_directory)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
607 job_objects = {
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
608 # "tool_path": os.path.abspath(self._tool_proxy._tool_path),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
609 "tool_representation": self._tool_proxy.to_persistent_representation(),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
610 "job_inputs": self._input_dict,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
611 "output_dict": self._output_dict,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
612 }
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
613 json.dump(job_objects, open(job_file, "w"))
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
614
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
615 def _output_extra_files_dir(self, output_name):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
616 output_id = self.output_id(output_name)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
617 return os.path.join(self._job_directory, "dataset_%s_files" % output_id)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
618
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
619 def output_id(self, output_name):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
620 output_id = self._output_dict[output_name]["id"]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
621 return output_id
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
622
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
623 def output_path(self, output_name):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
624 output_id = self._output_dict[output_name]["path"]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
625 return output_id
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
626
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
627 def output_directory_contents_dir(self, output_name, create=False):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
628 extra_files_dir = self._output_extra_files_dir(output_name)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
629 return extra_files_dir
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
630
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
631 def output_secondary_files_dir(self, output_name, create=False):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
632 extra_files_dir = self._output_extra_files_dir(output_name)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
633 secondary_files_dir = os.path.join(extra_files_dir, SECONDARY_FILES_EXTRA_PREFIX)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
634 if create and not os.path.exists(secondary_files_dir):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
635 safe_makedirs(secondary_files_dir)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
636 return secondary_files_dir
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
637
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
638 def stage_files(self):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
639 cwl_job = self.cwl_job()
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
640
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
641 def stageFunc(resolved_path, target_path):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
642 log.info("resolving %s to %s" % (resolved_path, target_path))
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
643 try:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
644 os.symlink(resolved_path, target_path)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
645 except OSError:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
646 pass
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
647
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
648 if hasattr(cwl_job, "pathmapper"):
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649 process.stage_files(cwl_job.pathmapper, stageFunc, ignore_writable=True, symlink=False)
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650
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651 if hasattr(cwl_job, "generatefiles"):
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652 outdir = os.path.join(self._job_directory, "working")
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diff changeset
653 # TODO: Why doesn't cwl_job.generatemapper work?
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diff changeset
654 generate_mapper = pathmapper.PathMapper(cwl_job.generatefiles["listing"],
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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655 outdir, outdir, separateDirs=False)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
656 # TODO: figure out what inplace_update should be.
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diff changeset
657 inplace_update = getattr(cwl_job, "inplace_update")
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diff changeset
658 process.stage_files(generate_mapper, stageFunc, ignore_writable=inplace_update, symlink=False)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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659 relink_initialworkdir(generate_mapper, outdir, outdir, inplace_update=inplace_update)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
660 # else: expression tools do not have a path mapper.
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661
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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662 @staticmethod
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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663 def _job_file(job_directory):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
664 return os.path.join(job_directory, JOB_JSON_FILE)
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665
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666
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667 class WorkflowProxy(object):
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668
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669 def __init__(self, workflow, workflow_path=None):
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670 self._workflow = workflow
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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671 self._workflow_path = workflow_path
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672 self._step_proxies = None
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673
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674 @property
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675 def cwl_id(self):
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676 return self._workflow.tool["id"]
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677
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678 def get_outputs_for_label(self, label):
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679 outputs = []
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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680 for output in self._workflow.tool['outputs']:
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diff changeset
681 step, output_name = split_step_references(
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682 output["outputSource"],
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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683 multiple=False,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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684 workflow_id=self.cwl_id,
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diff changeset
685 )
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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686 if step == label:
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687 output_id = output["id"]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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688 if "#" not in self.cwl_id:
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diff changeset
689 _, output_label = output_id.rsplit("#", 1)
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diff changeset
690 else:
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691 _, output_label = output_id.rsplit("/", 1)
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692
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diff changeset
693 outputs.append({
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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694 "output_name": output_name,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
695 "label": output_label,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
696 })
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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697 return outputs
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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698
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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699 def tool_reference_proxies(self):
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diff changeset
700 """Fetch tool source definitions for all referenced tools."""
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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701 references = []
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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702 for step in self.step_proxies():
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
703 references.extend(step.tool_reference_proxies())
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704 return references
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705
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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706 def step_proxies(self):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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707 if self._step_proxies is None:
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708 proxies = []
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diff changeset
709 num_input_steps = len(self._workflow.tool['inputs'])
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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710 for i, step in enumerate(self._workflow.steps):
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711 proxies.append(build_step_proxy(self, step, i + num_input_steps))
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712 self._step_proxies = proxies
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713 return self._step_proxies
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714
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715 @property
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716 def runnables(self):
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diff changeset
717 runnables = []
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
718 for step in self._workflow.steps:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
719 if "run" in step.tool:
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diff changeset
720 runnables.append(step.tool["run"])
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guerler
parents:
diff changeset
721 return runnables
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diff changeset
722
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723 def cwl_ids_to_index(self, step_proxies):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
724 index = 0
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
725 cwl_ids_to_index = {}
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
726 for i, input_dict in enumerate(self._workflow.tool['inputs']):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
727 cwl_ids_to_index[input_dict["id"]] = index
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
728 index += 1
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
729
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
730 for step_proxy in step_proxies:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
731 cwl_ids_to_index[step_proxy.cwl_id] = index
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guerler
parents:
diff changeset
732 index += 1
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
733
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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734 return cwl_ids_to_index
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
735
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
736 @property
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
737 def output_labels(self):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
738 return [self.jsonld_id_to_label(o['id']) for o in self._workflow.tool['outputs']]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
739
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
740 def input_connections_by_step(self, step_proxies):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
741 cwl_ids_to_index = self.cwl_ids_to_index(step_proxies)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
742 input_connections_by_step = []
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
743 for step_proxy in step_proxies:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
744 input_connections_step = {}
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
745 for input_proxy in step_proxy.input_proxies:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
746 cwl_source_id = input_proxy.cwl_source_id
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
747 input_name = input_proxy.input_name
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
748 # Consider only allow multiple if MultipleInputFeatureRequirement is enabled
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
749 for (output_step_name, output_name) in split_step_references(cwl_source_id, workflow_id=self.cwl_id):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
750 if "#" in self.cwl_id:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
751 sep_on = "/"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
752 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
753 sep_on = "#"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
754 output_step_id = self.cwl_id + sep_on + output_step_name
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guerler
parents:
diff changeset
755
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
756 if output_step_id not in cwl_ids_to_index:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
757 template = "Output [%s] does not appear in ID-to-index map [%s]."
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parents:
diff changeset
758 msg = template % (output_step_id, cwl_ids_to_index.keys())
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
759 raise AssertionError(msg)
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guerler
parents:
diff changeset
760
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
761 if input_name not in input_connections_step:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
762 input_connections_step[input_name] = []
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
763
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
764 input_connections_step[input_name].append({
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
765 "id": cwl_ids_to_index[output_step_id],
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
766 "output_name": output_name,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
767 "input_type": "dataset"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
768 })
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
769
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
770 input_connections_by_step.append(input_connections_step)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
771
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
772 return input_connections_by_step
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
773
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
774 def to_dict(self):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
775 name = os.path.basename(self._workflow.tool.get('label') or self._workflow_path or 'TODO - derive a name from ID')
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
776 steps = {}
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
777
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
778 step_proxies = self.step_proxies()
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
779 input_connections_by_step = self.input_connections_by_step(step_proxies)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
780 index = 0
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
781 for i, input_dict in enumerate(self._workflow.tool['inputs']):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
782 steps[index] = self.cwl_input_to_galaxy_step(input_dict, i)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
783 index += 1
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
784
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
785 for i, step_proxy in enumerate(step_proxies):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
786 input_connections = input_connections_by_step[i]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
787 steps[index] = step_proxy.to_dict(input_connections)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
788 index += 1
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
789
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
790 return {
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
791 'name': name,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
792 'steps': steps,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
793 'annotation': self.cwl_object_to_annotation(self._workflow.tool),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
794 }
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
795
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
796 def find_inputs_step_index(self, label):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
797 for i, input in enumerate(self._workflow.tool['inputs']):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
798 if self.jsonld_id_to_label(input["id"]) == label:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
799 return i
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
800
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
801 raise Exception("Failed to find index for label %s" % label)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
802
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
803 def jsonld_id_to_label(self, id):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
804 if "#" in self.cwl_id:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
805 return id.rsplit("/", 1)[-1]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
806 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
807 return id.rsplit("#", 1)[-1]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
808
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
809 def cwl_input_to_galaxy_step(self, input, i):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
810 input_type = input["type"]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
811 label = self.jsonld_id_to_label(input["id"])
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
812 input_as_dict = {
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
813 "id": i,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
814 "label": label,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
815 "position": {"left": 0, "top": 0},
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
816 "annotation": self.cwl_object_to_annotation(input),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
817 "input_connections": {}, # Should the Galaxy API really require this? - Seems to.
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
818 "workflow_outputs": self.get_outputs_for_label(label),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
819 }
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
820
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
821 if input_type == "File" and "default" not in input:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
822 input_as_dict["type"] = "data_input"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
823 elif isinstance(input_type, dict) and input_type.get("type") == "array":
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
824 input_as_dict["type"] = "data_collection_input"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
825 input_as_dict["collection_type"] = "list"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
826 elif isinstance(input_type, dict) and input_type.get("type") == "record":
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
827 input_as_dict["type"] = "data_collection_input"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
828 input_as_dict["collection_type"] = "record"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
829 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
830 if USE_STEP_PARAMETERS:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
831 input_as_dict["type"] = "parameter_input"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
832 # TODO: dispatch on actual type so this doesn't always need
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
833 # to be field - simpler types could be simpler inputs.
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
834 tool_state = {}
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
835 tool_state["parameter_type"] = "field"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
836 default_value = input.get("default")
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
837 optional = False
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
838 if isinstance(input_type, list) and "null" in input_type:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
839 optional = True
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
840 if not optional and isinstance(input_type, dict) and "type" in input_type:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
841 assert False
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
842 tool_state["default_value"] = {"src": "json", "value": default_value}
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
843 tool_state["optional"] = optional
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
844 input_as_dict["tool_state"] = tool_state
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
845 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
846 input_as_dict["type"] = "data_input"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
847 # TODO: format = expression.json
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
848
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
849 return input_as_dict
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
850
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
851 def cwl_object_to_annotation(self, cwl_obj):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
852 return cwl_obj.get("doc", None)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
853
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
854
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
855 def split_step_references(step_references, workflow_id=None, multiple=True):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
856 """Split a CWL step input or output reference into step id and name."""
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
857 # Trim off the workflow id part of the reference.
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
858 step_references = listify(step_references)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
859 split_references = []
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
860
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
861 for step_reference in step_references:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
862 if workflow_id is None:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
863 # This path works fine for some simple workflows - but not so much
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
864 # for subworkflows (maybe same for $graph workflows?)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
865 assert "#" in step_reference
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
866 _, step_reference = step_reference.split("#", 1)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
867 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
868 if "#" in workflow_id:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
869 sep_on = "/"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
870 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
871 sep_on = "#"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
872 expected_prefix = workflow_id + sep_on
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
873 if not step_reference.startswith(expected_prefix):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
874 raise AssertionError("step_reference [%s] doesn't start with %s" % (step_reference, expected_prefix))
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
875 step_reference = step_reference[len(expected_prefix):]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
876
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
877 # Now just grab the step name and input/output name.
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
878 assert "#" not in step_reference
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
879 if "/" in step_reference:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
880 step_name, io_name = step_reference.split("/", 1)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
881 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
882 # Referencing an input, not a step.
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
883 # In Galaxy workflows input steps have an implicit output named
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
884 # "output" for consistency with tools - in cwl land
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
885 # just the input name is referenced.
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
886 step_name = step_reference
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
887 io_name = "output"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
888 split_references.append((step_name, io_name))
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
889
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
890 if multiple:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
891 return split_references
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
892 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
893 assert len(split_references) == 1
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
894 return split_references[0]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
895
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
896
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
897 def build_step_proxy(workflow_proxy, step, index):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
898 step_type = step.embedded_tool.tool["class"]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
899 if step_type == "Workflow":
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
900 return SubworkflowStepProxy(workflow_proxy, step, index)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
901 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
902 return ToolStepProxy(workflow_proxy, step, index)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
903
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
904
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905 class BaseStepProxy(object):
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906
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907 def __init__(self, workflow_proxy, step, index):
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diff changeset
908 self._workflow_proxy = workflow_proxy
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diff changeset
909 self._step = step
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diff changeset
910 self._index = index
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diff changeset
911 self._uuid = str(uuid4())
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912 self._input_proxies = None
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diff changeset
913
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914 @property
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915 def step_class(self):
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diff changeset
916 return self.cwl_tool_object.tool["class"]
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diff changeset
917
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918 @property
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919 def cwl_id(self):
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920 return self._step.id
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921
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922 @property
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923 def cwl_workflow_id(self):
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diff changeset
924 return self._workflow_proxy.cwl_id
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925
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926 @property
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927 def requirements(self):
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928 return self._step.requirements
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929
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930 @property
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931 def hints(self):
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932 return self._step.hints
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933
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934 @property
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935 def label(self):
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936 label = self._workflow_proxy.jsonld_id_to_label(self._step.id)
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937 return label
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938
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939 def galaxy_workflow_outputs_list(self):
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940 return self._workflow_proxy.get_outputs_for_label(self.label)
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941
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942 @property
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943 def cwl_tool_object(self):
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944 return self._step.embedded_tool
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945
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946 @property
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947 def input_proxies(self):
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948 if self._input_proxies is None:
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949 input_proxies = []
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950 cwl_inputs = self._step.tool["inputs"]
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951 for cwl_input in cwl_inputs:
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952 input_proxies.append(InputProxy(self, cwl_input))
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953 self._input_proxies = input_proxies
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954 return self._input_proxies
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955
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956 def inputs_to_dicts(self):
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957 inputs_as_dicts = []
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958 for input_proxy in self.input_proxies:
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959 inputs_as_dicts.append(input_proxy.to_dict())
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960 return inputs_as_dicts
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961
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962
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963 class InputProxy(object):
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964
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965 def __init__(self, step_proxy, cwl_input):
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966 self._cwl_input = cwl_input
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967 self.step_proxy = step_proxy
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968 self.workflow_proxy = step_proxy._workflow_proxy
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969
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970 cwl_input_id = cwl_input["id"]
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971 cwl_source_id = cwl_input.get("source", None)
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972 if cwl_source_id is None:
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973 if "valueFrom" not in cwl_input and "default" not in cwl_input:
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974 msg = "Workflow step input must define a source, a valueFrom, or a default value. Obtained [%s]." % cwl_input
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975 raise MessageException(msg)
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976
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977 assert cwl_input_id
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978 step_name, input_name = split_step_references(
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979 cwl_input_id,
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980 multiple=False,
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981 workflow_id=step_proxy.cwl_workflow_id
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diff changeset
982 )
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983 self.step_name = step_name
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984 self.input_name = input_name
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diff changeset
985
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986 self.cwl_input_id = cwl_input_id
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diff changeset
987 self.cwl_source_id = cwl_source_id
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988
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989 scatter_inputs = [split_step_references(
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990 i, multiple=False, workflow_id=step_proxy.cwl_workflow_id
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991 )[1] for i in listify(step_proxy._step.tool.get("scatter", []))]
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992 scatter = self.input_name in scatter_inputs
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993 self.scatter = scatter
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994
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995 def to_dict(self):
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996 as_dict = {
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997 "name": self.input_name,
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998 }
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999 if "linkMerge" in self._cwl_input:
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1000 as_dict["merge_type"] = self._cwl_input["linkMerge"]
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1001 if "scatterMethod" in self.step_proxy._step.tool:
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1002 as_dict["scatter_type"] = self.step_proxy._step.tool.get("scatterMethod", "dotproduct")
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1003 else:
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1004 as_dict["scatter_type"] = "dotproduct" if self.scatter else "disabled"
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1005 if "valueFrom" in self._cwl_input:
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diff changeset
1006 # TODO: Add a table for expressions - mark the type as CWL 1.0 JavaScript.
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1007 as_dict["value_from"] = self._cwl_input["valueFrom"]
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1008 if "default" in self._cwl_input:
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diff changeset
1009 as_dict["default"] = self._cwl_input["default"]
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1010 return as_dict
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1011
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1012
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1013 class ToolStepProxy(BaseStepProxy):
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1014
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1015 def __init__(self, workflow_proxy, step, index):
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1016 super(ToolStepProxy, self).__init__(workflow_proxy, step, index)
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1017 self._tool_proxy = None
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1018
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1019 @property
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1020 def tool_proxy(self):
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1021 # Neeeds to be cached so UUID that is loaded matches UUID generated with to_dict.
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1022 if self._tool_proxy is None:
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1023 self._tool_proxy = _cwl_tool_object_to_proxy(self.cwl_tool_object, uuid=str(uuid4()))
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1024 return self._tool_proxy
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1025
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1026 def tool_reference_proxies(self):
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parents:
diff changeset
1027 # Return a list so we can handle subworkflows recursively.
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1028 return [self.tool_proxy]
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1029
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1030 def to_dict(self, input_connections):
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diff changeset
1031 # We need to stub out null entries for things getting replaced by
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1032 # connections. This doesn't seem ideal - consider just making Galaxy
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diff changeset
1033 # handle this.
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1034 tool_state = {}
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1035 for input_name in input_connections.keys():
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1036 tool_state[input_name] = None
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diff changeset
1037
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1038 outputs = self.galaxy_workflow_outputs_list()
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1039 return {
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1040 "id": self._index,
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1041 "tool_uuid": self.tool_proxy._uuid, # TODO: make sure this is respected...
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1042 "label": self.label,
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diff changeset
1043 "position": {"left": 0, "top": 0},
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1044 "type": "tool",
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1045 "annotation": self._workflow_proxy.cwl_object_to_annotation(self._step.tool),
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1046 "input_connections": input_connections,
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1047 "inputs": self.inputs_to_dicts(),
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1048 "workflow_outputs": outputs,
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1049 }
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diff changeset
1050
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1051
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1052 class SubworkflowStepProxy(BaseStepProxy):
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1053
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1054 def __init__(self, workflow_proxy, step, index):
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1055 super(SubworkflowStepProxy, self).__init__(workflow_proxy, step, index)
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1056 self._subworkflow_proxy = None
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1057
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1058 def to_dict(self, input_connections):
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1059 outputs = self.galaxy_workflow_outputs_list()
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1060 for key, input_connection_list in input_connections.items():
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1061 input_subworkflow_step_id = self.subworkflow_proxy.find_inputs_step_index(
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1062 key
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1063 )
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1064 for input_connection in input_connection_list:
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1065 input_connection["input_subworkflow_step_id"] = input_subworkflow_step_id
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1066
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1067 return {
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1068 "id": self._index,
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1069 "label": self.label,
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diff changeset
1070 "position": {"left": 0, "top": 0},
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1071 "type": "subworkflow",
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1072 "subworkflow": self.subworkflow_proxy.to_dict(),
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1073 "annotation": self.subworkflow_proxy.cwl_object_to_annotation(self._step.tool),
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1074 "input_connections": input_connections,
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1075 "inputs": self.inputs_to_dicts(),
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1076 "workflow_outputs": outputs,
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1077 }
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1078
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1079 def tool_reference_proxies(self):
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1080 return self.subworkflow_proxy.tool_reference_proxies()
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1081
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1082 @property
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1083 def subworkflow_proxy(self):
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1084 if self._subworkflow_proxy is None:
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1085 self._subworkflow_proxy = WorkflowProxy(self.cwl_tool_object)
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1086 return self._subworkflow_proxy
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1087
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1088
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1089 def remove_pickle_problems(obj):
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1090 """doc_loader does not pickle correctly"""
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1091 if hasattr(obj, "doc_loader"):
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1092 obj.doc_loader = None
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1093 if hasattr(obj, "embedded_tool"):
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1094 obj.embedded_tool = remove_pickle_problems(obj.embedded_tool)
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1095 if hasattr(obj, "steps"):
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1096 obj.steps = [remove_pickle_problems(s) for s in obj.steps]
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1097 return obj
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1098
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1099
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1100 @six.add_metaclass(ABCMeta)
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1101 class WorkflowToolReference(object):
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1102 pass
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diff changeset
1103
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1104
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1105 class EmbeddedWorkflowToolReference(WorkflowToolReference):
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1106 pass
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1107
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1108
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1109 class ExternalWorkflowToolReference(WorkflowToolReference):
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1110 pass
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1111
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1112
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1113 def _outer_field_to_input_instance(field):
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1114 field_type = field_to_field_type(field) # Must be a list if in here?
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1115 if not isinstance(field_type, list):
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1116 field_type = [field_type]
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diff changeset
1117
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1118 name, label, description = _field_metadata(field)
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diff changeset
1119
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1120 case_name = "_cwl__type_"
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1121 case_label = "Specify Parameter %s As" % label
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1122
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1123 def value_input(type_description):
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1124 value_name = "_cwl__value_"
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diff changeset
1125 value_label = label
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1126 value_description = description
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1127 return InputInstance(
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1128 value_name,
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1129 value_label,
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diff changeset
1130 value_description,
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1131 input_type=type_description.galaxy_param_type,
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diff changeset
1132 collection_type=type_description.collection_type,
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diff changeset
1133 )
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1134
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1135 select_options = []
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1136 case_options = []
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diff changeset
1137 type_descriptions = type_descriptions_for_field_types(field_type)
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diff changeset
1138 for type_description in type_descriptions:
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diff changeset
1139 select_options.append({"value": type_description.name, "label": type_description.label})
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1140 input_instances = []
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1141 if type_description.uses_param():
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diff changeset
1142 input_instances.append(value_input(type_description))
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parents:
diff changeset
1143 case_options.append((type_description.name, input_instances))
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diff changeset
1144
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1145 # If there is more than one way to represent this parameter - produce a conditional
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diff changeset
1146 # requesting user to ask for what form they want to submit the data in, else just map
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diff changeset
1147 # a simple Galaxy parameter.
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1148 if len(case_options) > 1 and not USE_FIELD_TYPES:
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1149 case_input = SelectInputInstance(
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1150 name=case_name,
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1151 label=case_label,
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1152 description=False,
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1153 options=select_options,
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diff changeset
1154 )
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1155
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1156 return ConditionalInstance(name, case_input, case_options)
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diff changeset
1157 else:
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1158 if len(case_options) > 1:
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diff changeset
1159 only_type_description = FIELD_TYPE_REPRESENTATION
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1160 else:
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diff changeset
1161 only_type_description = type_descriptions[0]
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diff changeset
1162
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guerler
parents:
diff changeset
1163 return InputInstance(
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1164 name, label, description, input_type=only_type_description.galaxy_param_type, collection_type=only_type_description.collection_type
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1165 )
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1166
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1167 # Older array to repeat handling, now we are just representing arrays as
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1168 # dataset collections - we should offer a blended approach in the future.
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1169 # if field_type in simple_map_type_map.keys():
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1170 # input_type = simple_map_type_map[field_type]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1171 # return {"input_type": input_type, "array": False}
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1172 # elif field_type == "array":
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1173 # if isinstance(field["type"], dict):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1174 # array_type = field["type"]["items"]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1175 # else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1176 # array_type = field["items"]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1177 # if array_type in simple_map_type_map.keys():
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1178 # input_type = simple_map_type_map[array_type]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1179 # return {"input_type": input_type, "array": True}
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1180 # else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1181 # raise Exception("Unhandled simple field type encountered - [%s]." % field_type)
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guerler
parents:
diff changeset
1182
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1183
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1184 def _field_metadata(field):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1185 name = field["name"]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1186 label = field.get("label", None)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1187 description = field.get("doc", None)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1188 return name, label, description
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1189
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1190
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1191 def _simple_field_to_output(field):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1192 name = field["name"]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1193 output_data_class = field["type"]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1194 output_instance = OutputInstance(
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1195 name,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1196 output_data_type=output_data_class,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1197 output_type=OUTPUT_TYPE.GLOB
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1198 )
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1199 return output_instance
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1200
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guerler
parents:
diff changeset
1201
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1202 class ConditionalInstance(object):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1203
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1204 def __init__(self, name, case, whens):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1205 self.input_type = INPUT_TYPE.CONDITIONAL
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1206 self.name = name
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1207 self.case = case
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1208 self.whens = whens
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1209
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1210 def to_dict(self):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1211
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1212 as_dict = dict(
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1213 name=self.name,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1214 type=INPUT_TYPE.CONDITIONAL,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1215 test=self.case.to_dict(),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1216 when=OrderedDict(),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1217 )
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1218 for value, block in self.whens:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1219 as_dict["when"][value] = [i.to_dict() for i in block]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1220
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1221 return as_dict
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1222
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1223
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1224 class SelectInputInstance(object):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1225
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1226 def __init__(self, name, label, description, options):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1227 self.input_type = INPUT_TYPE.SELECT
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1228 self.name = name
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1229 self.label = label
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1230 self.description = description
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1231 self.options = options
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1232
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
1233 def to_dict(self):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1234 # TODO: serialize options...
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1235 as_dict = dict(
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1236 name=self.name,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1237 label=self.label or self.name,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1238 help=self.description,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1239 type=self.input_type,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1240 options=self.options,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1241 )
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1242 return as_dict
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1243
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1244
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1245 class InputInstance(object):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1246
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1247 def __init__(self, name, label, description, input_type, array=False, area=False, collection_type=None):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1248 self.input_type = input_type
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1249 self.collection_type = collection_type
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1250 self.name = name
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1251 self.label = label
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1252 self.description = description
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1253 self.required = True
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1254 self.array = array
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1255 self.area = area
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1256
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1257 def to_dict(self, itemwise=True):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1258 if itemwise and self.array:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1259 as_dict = dict(
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1260 type="repeat",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1261 name="%s_repeat" % self.name,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1262 title="%s" % self.name,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1263 blocks=[
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1264 self.to_dict(itemwise=False)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1265 ]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1266 )
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1267 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1268 as_dict = dict(
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1269 name=self.name,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1270 label=self.label or self.name,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1271 help=self.description,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1272 type=self.input_type,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1273 optional=not self.required,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1274 )
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1275 if self.area:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1276 as_dict["area"] = True
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1277
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1278 if self.input_type == INPUT_TYPE.INTEGER:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1279 as_dict["value"] = "0"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1280 if self.input_type == INPUT_TYPE.FLOAT:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1281 as_dict["value"] = "0.0"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1282 elif self.input_type == INPUT_TYPE.DATA_COLLECTON:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1283 as_dict["collection_type"] = self.collection_type
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1284
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1285 return as_dict
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1286
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1287
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1288 OUTPUT_TYPE = Bunch(
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1289 GLOB="glob",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1290 STDOUT="stdout",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1291 )
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1292
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
1293
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
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1294 # TODO: Different subclasses - this is representing different types of things.
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1295 class OutputInstance(object):
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1296
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1297 def __init__(self, name, output_data_type, output_type, path=None, fields=None):
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1298 self.name = name
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1299 self.output_data_type = output_data_type
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1300 self.output_type = output_type
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1301 self.path = path
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1302 self.fields = fields
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1303
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1304
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1305 __all__ = (
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1306 'tool_proxy',
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1307 'load_job_proxy',
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1308 )