Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/tool_util/cwl/parser.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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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 |
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7 import base64 |
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8 import copy |
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9 import json |
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10 import logging |
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11 import os |
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12 import pickle |
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13 from abc import ABCMeta, abstractmethod |
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14 from uuid import uuid4 |
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15 |
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16 |
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17 from galaxy.exceptions import MessageException |
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18 from galaxy.util import ( |
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19 listify, |
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20 safe_makedirs, |
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21 unicodify, |
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22 ) |
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23 from galaxy.util.bunch import Bunch |
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24 from .cwltool_deps import ( |
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25 beta_relaxed_fmt_check, |
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26 ensure_cwltool_available, |
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27 getdefault, |
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28 pathmapper, |
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29 process, |
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30 ref_resolver, |
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31 relink_initialworkdir, |
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32 RuntimeContext, |
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33 sourceline, |
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34 StdFsAccess, |
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35 ) |
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36 from .representation import ( |
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37 field_to_field_type, |
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38 FIELD_TYPE_REPRESENTATION, |
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39 INPUT_TYPE, |
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40 type_descriptions_for_field_types, |
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41 USE_FIELD_TYPES, |
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42 USE_STEP_PARAMETERS, |
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43 ) |
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44 from .schema import ( |
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45 non_strict_non_validating_schema_loader, |
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46 schema_loader, |
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47 ) |
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48 from .util import SECONDARY_FILES_EXTRA_PREFIX |
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49 |
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50 log = logging.getLogger(__name__) |
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51 |
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52 JOB_JSON_FILE = ".cwl_job.json" |
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53 |
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54 DOCKER_REQUIREMENT = "DockerRequirement" |
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55 SUPPORTED_TOOL_REQUIREMENTS = [ |
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56 "CreateFileRequirement", |
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57 "DockerRequirement", |
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58 "EnvVarRequirement", |
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59 "InitialWorkDirRequirement", |
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60 "InlineJavascriptRequirement", |
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61 "ResourceRequirement", |
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62 "ShellCommandRequirement", |
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63 "ScatterFeatureRequirement", |
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64 "SchemaDefRequirement", |
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65 "SubworkflowFeatureRequirement", |
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66 "StepInputExpressionRequirement", |
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67 "MultipleInputFeatureRequirement", |
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68 ] |
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69 |
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70 |
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71 SUPPORTED_WORKFLOW_REQUIREMENTS = SUPPORTED_TOOL_REQUIREMENTS + [ |
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72 ] |
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73 |
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74 PERSISTED_REPRESENTATION = "cwl_tool_object" |
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75 |
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76 |
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77 def tool_proxy(tool_path=None, tool_object=None, strict_cwl_validation=True, tool_directory=None, uuid=None): |
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78 """ Provide a proxy object to cwltool data structures to just |
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79 grab relevant data. |
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80 """ |
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81 ensure_cwltool_available() |
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82 tool = _to_cwl_tool_object( |
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83 tool_path=tool_path, |
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84 tool_object=tool_object, |
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85 strict_cwl_validation=strict_cwl_validation, |
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86 tool_directory=tool_directory, |
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87 uuid=uuid |
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88 ) |
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89 return tool |
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90 |
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91 |
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92 def tool_proxy_from_persistent_representation(persisted_tool, strict_cwl_validation=True, tool_directory=None): |
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93 """Load a ToolProxy from a previously persisted representation.""" |
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94 ensure_cwltool_available() |
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95 if PERSISTED_REPRESENTATION == "cwl_tool_object": |
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96 kwds = {"cwl_tool_object": ToolProxy.from_persistent_representation(persisted_tool)} |
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97 else: |
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98 raw_process_reference = persisted_tool # ??? |
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99 kwds = {"raw_process_reference": ToolProxy.from_persistent_representation(raw_process_reference)} |
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100 uuid = persisted_tool["uuid"] |
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101 tool = _to_cwl_tool_object(uuid=uuid, strict_cwl_validation=strict_cwl_validation, tool_directory=tool_directory, **kwds) |
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102 return tool |
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103 |
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104 |
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105 def workflow_proxy(workflow_path, strict_cwl_validation=True): |
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106 ensure_cwltool_available() |
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107 workflow = _to_cwl_workflow_object(workflow_path, strict_cwl_validation=strict_cwl_validation) |
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108 return workflow |
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109 |
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110 |
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111 def load_job_proxy(job_directory, strict_cwl_validation=True): |
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112 ensure_cwltool_available() |
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113 job_objects_path = os.path.join(job_directory, JOB_JSON_FILE) |
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114 job_objects = json.load(open(job_objects_path)) |
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115 job_inputs = job_objects["job_inputs"] |
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116 output_dict = job_objects["output_dict"] |
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117 # Any reason to retain older tool_path variant of this? Probably not? |
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118 if "tool_path" in job_objects: |
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119 tool_path = job_objects["tool_path"] |
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120 cwl_tool = tool_proxy(tool_path, strict_cwl_validation=strict_cwl_validation) |
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121 else: |
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122 persisted_tool = job_objects["tool_representation"] |
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123 cwl_tool = tool_proxy_from_persistent_representation(persisted_tool=persisted_tool, strict_cwl_validation=strict_cwl_validation) |
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124 cwl_job = cwl_tool.job_proxy(job_inputs, output_dict, job_directory=job_directory) |
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125 return cwl_job |
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126 |
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127 |
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128 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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129 if uuid is None: |
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130 uuid = str(uuid4()) |
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131 schema_loader = _schema_loader(strict_cwl_validation) |
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132 if raw_process_reference is None and tool_path is not None: |
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133 assert cwl_tool_object is None |
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134 assert tool_object is None |
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135 |
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136 raw_process_reference = schema_loader.raw_process_reference(tool_path) |
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137 cwl_tool = schema_loader.tool( |
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138 raw_process_reference=raw_process_reference, |
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139 ) |
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140 elif tool_object is not None: |
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141 assert raw_process_reference is None |
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142 assert cwl_tool_object is None |
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143 |
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144 # Allow loading tools from YAML... |
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145 from ruamel import yaml as ryaml |
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146 as_str = json.dumps(tool_object) |
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147 tool_object = ryaml.round_trip_load(as_str) |
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148 path = tool_directory |
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149 if path is None: |
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150 path = os.getcwd() |
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151 uri = ref_resolver.file_uri(path) + "/" |
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152 sourceline.add_lc_filename(tool_object, uri) |
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153 raw_process_reference = schema_loader.raw_process_reference_for_object( |
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154 tool_object, |
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155 uri=uri |
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156 ) |
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157 cwl_tool = schema_loader.tool( |
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158 raw_process_reference=raw_process_reference, |
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159 ) |
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160 else: |
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161 cwl_tool = cwl_tool_object |
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162 |
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163 if isinstance(cwl_tool, int): |
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164 raise Exception("Failed to load tool.") |
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165 |
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166 raw_tool = cwl_tool.tool |
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167 # Apply Galaxy hacks to CWL tool representation to bridge semantic differences |
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168 # between Galaxy and cwltool. |
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169 _hack_cwl_requirements(cwl_tool) |
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170 check_requirements(raw_tool) |
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171 return _cwl_tool_object_to_proxy(cwl_tool, uuid, raw_process_reference=raw_process_reference, tool_path=tool_path) |
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172 |
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173 |
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174 def _cwl_tool_object_to_proxy(cwl_tool, uuid, raw_process_reference=None, tool_path=None): |
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175 raw_tool = cwl_tool.tool |
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176 if "class" not in raw_tool: |
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177 raise Exception("File does not declare a class, not a valid Draft 3+ CWL tool.") |
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178 |
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179 process_class = raw_tool["class"] |
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180 if process_class == "CommandLineTool": |
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181 proxy_class = CommandLineToolProxy |
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182 elif process_class == "ExpressionTool": |
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183 proxy_class = ExpressionToolProxy |
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184 else: |
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185 raise Exception("File not a CWL CommandLineTool.") |
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186 top_level_object = tool_path is not None |
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187 if top_level_object and ("cwlVersion" not in raw_tool): |
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188 raise Exception("File does not declare a CWL version, pre-draft 3 CWL tools are not supported.") |
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189 |
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190 proxy = proxy_class(cwl_tool, uuid, raw_process_reference, tool_path) |
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191 return proxy |
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192 |
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193 |
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194 def _to_cwl_workflow_object(workflow_path, strict_cwl_validation=None): |
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195 proxy_class = WorkflowProxy |
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196 cwl_workflow = _schema_loader(strict_cwl_validation).tool(path=workflow_path) |
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197 raw_workflow = cwl_workflow.tool |
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198 check_requirements(raw_workflow, tool=False) |
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199 |
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200 proxy = proxy_class(cwl_workflow, workflow_path) |
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201 return proxy |
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202 |
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203 |
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204 def _schema_loader(strict_cwl_validation): |
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205 target_schema_loader = schema_loader if strict_cwl_validation else non_strict_non_validating_schema_loader |
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206 return target_schema_loader |
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207 |
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208 |
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209 def _hack_cwl_requirements(cwl_tool): |
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210 move_to_hints = [] |
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211 for i, requirement in enumerate(cwl_tool.requirements): |
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212 if requirement["class"] == DOCKER_REQUIREMENT: |
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213 move_to_hints.insert(0, i) |
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214 |
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215 for i in move_to_hints: |
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216 del cwl_tool.requirements[i] |
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217 cwl_tool.hints.append(requirement) |
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218 |
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219 |
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220 def check_requirements(rec, tool=True): |
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221 if isinstance(rec, dict): |
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222 if "requirements" in rec: |
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223 for r in rec["requirements"]: |
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224 if tool: |
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225 possible = SUPPORTED_TOOL_REQUIREMENTS |
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226 else: |
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227 possible = SUPPORTED_WORKFLOW_REQUIREMENTS |
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228 if r["class"] not in possible: |
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229 raise Exception("Unsupported requirement %s" % r["class"]) |
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230 for d in rec: |
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231 check_requirements(rec[d], tool=tool) |
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232 if isinstance(rec, list): |
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233 for d in rec: |
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234 check_requirements(d, tool=tool) |
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235 |
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236 |
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237 class ToolProxy(metaclass=ABCMeta): |
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238 |
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239 def __init__(self, tool, uuid, raw_process_reference=None, tool_path=None): |
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240 self._tool = tool |
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241 self._uuid = uuid |
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242 self._tool_path = tool_path |
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243 self._raw_process_reference = raw_process_reference |
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244 # remove input parameter formats from CWL files so that cwltool |
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245 # does not complain they are missing in the input data |
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246 for input_field in self._tool.inputs_record_schema["fields"]: |
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247 if 'format' in input_field: |
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248 del input_field['format'] |
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249 |
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250 def job_proxy(self, input_dict, output_dict, job_directory="."): |
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251 """ Build a cwltool.job.Job describing computation using a input_json |
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252 Galaxy will generate mapping the Galaxy description of the inputs into |
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253 a cwltool compatible variant. |
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254 """ |
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255 return JobProxy(self, input_dict, output_dict, job_directory=job_directory) |
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256 |
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257 @property |
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258 def id(self): |
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259 raw_id = self._tool.tool.get("id", None) |
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260 return raw_id |
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261 |
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262 def galaxy_id(self): |
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263 raw_id = self.id |
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264 tool_id = None |
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265 # don't reduce "search.cwl#index" to search |
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266 if raw_id: |
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267 tool_id = os.path.basename(raw_id) |
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268 # tool_id = os.path.splitext(os.path.basename(raw_id))[0] |
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269 if not tool_id: |
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270 return self._uuid |
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271 assert tool_id |
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272 if tool_id.startswith("#"): |
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273 tool_id = tool_id[1:] |
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274 return tool_id |
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275 |
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276 @abstractmethod |
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277 def input_instances(self): |
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278 """ Return InputInstance objects describing mapping to Galaxy inputs. """ |
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279 |
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280 @abstractmethod |
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281 def output_instances(self): |
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282 """ Return OutputInstance objects describing mapping to Galaxy inputs. """ |
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283 |
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284 @abstractmethod |
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285 def docker_identifier(self): |
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286 """ Return docker identifier for embedding in tool description. """ |
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287 |
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288 @abstractmethod |
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289 def description(self): |
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290 """ Return description to tool. """ |
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291 |
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292 @abstractmethod |
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293 def label(self): |
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294 """ Return label for tool. """ |
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295 |
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296 def to_persistent_representation(self): |
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297 """Return a JSON representation of this tool. Not for serialization |
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298 over the wire, but serialization in a database.""" |
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299 # TODO: Replace this with some more readable serialization, |
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300 # I really don't like using pickle here. |
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301 if PERSISTED_REPRESENTATION == "cwl_tool_object": |
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302 persisted_obj = remove_pickle_problems(self._tool) |
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303 else: |
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304 persisted_obj = self._raw_process_reference |
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305 return { |
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306 "class": self._class, |
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307 "pickle": unicodify(base64.b64encode(pickle.dumps(persisted_obj, pickle.HIGHEST_PROTOCOL))), |
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308 "uuid": self._uuid, |
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309 } |
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310 |
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311 @staticmethod |
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312 def from_persistent_representation(as_object): |
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313 """Recover an object serialized with to_persistent_representation.""" |
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314 if "class" not in as_object: |
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315 raise Exception("Failed to deserialize tool proxy from JSON object - no class found.") |
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316 if "pickle" not in as_object: |
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317 raise Exception("Failed to deserialize tool proxy from JSON object - no pickle representation found.") |
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318 if "uuid" not in as_object: |
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319 raise Exception("Failed to deserialize tool proxy from JSON object - no uuid found.") |
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320 to_unpickle = base64.b64decode(as_object["pickle"]) |
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321 loaded_object = pickle.loads(to_unpickle) |
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322 return loaded_object |
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323 |
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324 |
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325 class CommandLineToolProxy(ToolProxy): |
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326 _class = "CommandLineTool" |
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327 |
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328 def description(self): |
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329 # Don't use description - typically too verbose. |
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330 return '' |
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331 |
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332 def doc(self): |
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333 # TODO: parse multiple lines and merge - valid in cwl-1.1 |
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334 doc = self._tool.tool.get('doc') |
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335 return doc |
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336 |
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337 def label(self): |
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338 label = self._tool.tool.get('label') |
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339 |
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340 if label is not None: |
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341 return label.partition(":")[0] # return substring before ':' |
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342 else: |
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343 return '' |
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344 |
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345 def input_fields(self): |
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346 input_records_schema = self._eval_schema(self._tool.inputs_record_schema) |
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347 if input_records_schema["type"] != "record": |
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348 raise Exception("Unhandled CWL tool input structure") |
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349 |
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350 # TODO: handle this somewhere else? |
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351 # schemadef_req_tool_param |
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352 rval = [] |
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353 for input in input_records_schema["fields"]: |
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354 input_copy = copy.deepcopy(input) |
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355 input_type = input.get("type") |
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356 if isinstance(input_type, list) or isinstance(input_type, dict): |
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357 rval.append(input_copy) |
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358 continue |
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359 |
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360 if input_type in self._tool.schemaDefs: |
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361 input_copy["type"] = self._tool.schemaDefs[input_type] |
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362 |
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363 rval.append(input_copy) |
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364 return rval |
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365 |
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366 def _eval_schema(self, io_schema): |
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367 schema_type = io_schema.get("type") |
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368 if schema_type in self._tool.schemaDefs: |
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369 io_schema = self._tool.schemaDefs[schema_type] |
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370 return io_schema |
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371 |
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372 def input_instances(self): |
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373 return [_outer_field_to_input_instance(_) for _ in self.input_fields()] |
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374 |
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375 def output_instances(self): |
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376 outputs_schema = self._eval_schema(self._tool.outputs_record_schema) |
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377 if outputs_schema["type"] != "record": |
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378 raise Exception("Unhandled CWL tool output structure") |
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379 |
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380 rval = [] |
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381 for output in outputs_schema["fields"]: |
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382 rval.append(_simple_field_to_output(output)) |
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383 |
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384 return rval |
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385 |
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386 def docker_identifier(self): |
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387 for hint in self.hints_or_requirements_of_class("DockerRequirement"): |
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388 if "dockerImageId" in hint: |
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389 return hint["dockerImageId"] |
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390 else: |
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391 return hint["dockerPull"] |
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392 |
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393 return None |
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394 |
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395 def hints_or_requirements_of_class(self, class_name): |
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396 tool = self._tool.tool |
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397 reqs_and_hints = tool.get("requirements", []) + tool.get("hints", []) |
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398 for hint in reqs_and_hints: |
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399 if hint["class"] == class_name: |
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400 yield hint |
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401 |
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402 def software_requirements(self): |
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403 # Roughest imaginable pass at parsing requirements, really need to take in specs, handle |
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404 # multiple versions, etc... |
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405 tool = self._tool.tool |
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406 reqs_and_hints = tool.get("requirements", []) + tool.get("hints", []) |
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407 requirements = [] |
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408 for hint in reqs_and_hints: |
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409 if hint["class"] == "SoftwareRequirement": |
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410 packages = hint.get("packages", []) |
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411 for package in packages: |
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412 versions = package.get("version", []) |
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413 first_version = None if not versions else versions[0] |
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414 requirements.append((package["package"], first_version)) |
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415 return requirements |
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416 |
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417 @property |
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418 def requirements(self): |
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419 return getattr(self._tool, "requirements", []) |
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420 |
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421 |
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422 class ExpressionToolProxy(CommandLineToolProxy): |
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423 _class = "ExpressionTool" |
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424 |
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425 |
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426 class JobProxy: |
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427 |
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428 def __init__(self, tool_proxy, input_dict, output_dict, job_directory): |
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429 self._tool_proxy = tool_proxy |
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430 self._input_dict = input_dict |
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431 self._output_dict = output_dict |
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432 self._job_directory = job_directory |
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433 |
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434 self._final_output = None |
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435 self._ok = True |
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436 self._cwl_job = None |
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437 self._is_command_line_job = None |
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438 |
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439 self._normalize_job() |
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440 |
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441 def cwl_job(self): |
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442 self._ensure_cwl_job_initialized() |
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443 return self._cwl_job |
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444 |
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445 @property |
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446 def is_command_line_job(self): |
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447 self._ensure_cwl_job_initialized() |
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448 assert self._is_command_line_job is not None |
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449 return self._is_command_line_job |
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450 |
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451 def _ensure_cwl_job_initialized(self): |
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452 if self._cwl_job is None: |
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453 job_args = dict( |
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454 basedir=self._job_directory, |
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455 select_resources=self._select_resources, |
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456 outdir=os.path.join(self._job_directory, "working"), |
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457 tmpdir=os.path.join(self._job_directory, "cwltmp"), |
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458 stagedir=os.path.join(self._job_directory, "cwlstagedir"), |
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459 use_container=False, |
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460 beta_relaxed_fmt_check=beta_relaxed_fmt_check, |
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461 ) |
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462 |
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463 args = [] |
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464 kwargs = {} |
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465 if RuntimeContext is not None: |
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466 args.append(RuntimeContext(job_args)) |
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467 else: |
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468 kwargs = job_args |
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469 self._cwl_job = next(self._tool_proxy._tool.job( |
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470 self._input_dict, |
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471 self._output_callback, |
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472 *args, **kwargs |
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473 )) |
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474 self._is_command_line_job = hasattr(self._cwl_job, "command_line") |
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475 |
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476 def _normalize_job(self): |
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477 # Somehow reuse whatever causes validate in cwltool... maybe? |
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478 def pathToLoc(p): |
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479 if "location" not in p and "path" in p: |
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480 p["location"] = p["path"] |
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481 del p["path"] |
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482 |
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483 runtime_context = RuntimeContext({}) |
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484 make_fs_access = getdefault(runtime_context.make_fs_access, StdFsAccess) |
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485 fs_access = make_fs_access(runtime_context.basedir) |
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486 process.fill_in_defaults(self._tool_proxy._tool.tool["inputs"], self._input_dict, fs_access) |
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487 process.visit_class(self._input_dict, ("File", "Directory"), pathToLoc) |
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488 # TODO: Why doesn't fillInDefault fill in locations instead of paths? |
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489 process.normalizeFilesDirs(self._input_dict) |
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490 # TODO: validate like cwltool process _init_job. |
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491 # validate.validate_ex(self.names.get_name("input_record_schema", ""), builder.job, |
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492 # strict=False, logger=_logger_validation_warnings) |
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493 |
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494 def rewrite_inputs_for_staging(self): |
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495 if hasattr(self._cwl_job, "pathmapper"): |
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496 pass |
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497 # DO SOMETHING LIKE THE FOLLOWING? |
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498 # path_rewrites = {} |
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499 # for f, p in self._cwl_job.pathmapper.items(): |
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500 # if not p.staged: |
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501 # continue |
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502 # if p.type in ("File", "Directory"): |
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503 # path_rewrites[p.resolved] = p.target |
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504 # for key, value in self._input_dict.items(): |
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505 # if key in path_rewrites: |
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506 # self._input_dict[key]["location"] = path_rewrites[value] |
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507 else: |
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508 stagedir = os.path.join(self._job_directory, "cwlstagedir") |
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509 safe_makedirs(stagedir) |
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510 |
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511 def stage_recursive(value): |
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512 is_list = isinstance(value, list) |
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513 is_dict = isinstance(value, dict) |
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514 log.info(f"handling value {value}, is_list {is_list}, is_dict {is_dict}") |
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515 if is_list: |
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516 for val in value: |
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517 stage_recursive(val) |
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518 elif is_dict: |
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519 if "location" in value and "basename" in value: |
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520 location = value["location"] |
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521 basename = value["basename"] |
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522 if not location.endswith(basename): # TODO: sep()[-1] |
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523 staged_loc = os.path.join(stagedir, basename) |
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524 if not os.path.exists(staged_loc): |
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525 os.symlink(location, staged_loc) |
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526 value["location"] = staged_loc |
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527 for dict_value in value.values(): |
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528 stage_recursive(dict_value) |
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529 else: |
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530 log.info("skipping simple value...") |
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531 stage_recursive(self._input_dict) |
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532 |
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533 def _select_resources(self, request, runtime_context=None): |
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534 new_request = request.copy() |
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535 new_request["cores"] = "$GALAXY_SLOTS" |
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536 return new_request |
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537 |
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538 @property |
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539 def command_line(self): |
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540 if self.is_command_line_job: |
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541 return self.cwl_job().command_line |
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542 else: |
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543 return ["true"] |
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544 |
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545 @property |
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546 def stdin(self): |
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547 if self.is_command_line_job: |
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548 return self.cwl_job().stdin |
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549 else: |
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550 return None |
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551 |
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552 @property |
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553 def stdout(self): |
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554 if self.is_command_line_job: |
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555 return self.cwl_job().stdout |
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556 else: |
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557 return None |
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558 |
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559 @property |
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560 def stderr(self): |
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561 if self.is_command_line_job: |
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562 return self.cwl_job().stderr |
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563 else: |
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564 return None |
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565 |
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566 @property |
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567 def environment(self): |
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568 if self.is_command_line_job: |
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569 return self.cwl_job().environment |
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570 else: |
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571 return {} |
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572 |
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573 @property |
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574 def generate_files(self): |
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575 if self.is_command_line_job: |
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576 return self.cwl_job().generatefiles |
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577 else: |
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578 return {} |
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579 |
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580 def _output_callback(self, out, process_status): |
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581 self._process_status = process_status |
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582 if process_status == "success": |
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583 self._final_output = out |
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584 else: |
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585 self._ok = False |
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586 |
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587 log.info(f"Output are {out}, status is {process_status}") |
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588 |
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589 def collect_outputs(self, tool_working_directory, rcode): |
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590 if not self.is_command_line_job: |
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591 cwl_job = self.cwl_job() |
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592 if RuntimeContext is not None: |
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593 cwl_job.run( |
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594 RuntimeContext({}) |
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595 ) |
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596 else: |
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597 cwl_job.run() |
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598 if not self._ok: |
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599 raise Exception("Final process state not ok, [%s]" % self._process_status) |
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600 return self._final_output |
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601 else: |
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602 return self.cwl_job().collect_outputs(tool_working_directory, rcode) |
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603 |
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604 def save_job(self): |
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605 job_file = JobProxy._job_file(self._job_directory) |
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606 job_objects = { |
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607 # "tool_path": os.path.abspath(self._tool_proxy._tool_path), |
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608 "tool_representation": self._tool_proxy.to_persistent_representation(), |
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609 "job_inputs": self._input_dict, |
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610 "output_dict": self._output_dict, |
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611 } |
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612 json.dump(job_objects, open(job_file, "w")) |
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613 |
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614 def _output_extra_files_dir(self, output_name): |
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615 output_id = self.output_id(output_name) |
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616 return os.path.join(self._job_directory, "outputs", "dataset_%s_files" % output_id) |
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617 |
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618 def output_id(self, output_name): |
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619 output_id = self._output_dict[output_name]["id"] |
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620 return output_id |
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621 |
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622 def output_path(self, output_name): |
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623 output_id = self._output_dict[output_name]["path"] |
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624 return output_id |
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625 |
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626 def output_directory_contents_dir(self, output_name, create=False): |
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627 extra_files_dir = self._output_extra_files_dir(output_name) |
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628 return extra_files_dir |
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629 |
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630 def output_secondary_files_dir(self, output_name, create=False): |
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631 extra_files_dir = self._output_extra_files_dir(output_name) |
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632 secondary_files_dir = os.path.join(extra_files_dir, SECONDARY_FILES_EXTRA_PREFIX) |
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633 if create and not os.path.exists(secondary_files_dir): |
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634 safe_makedirs(secondary_files_dir) |
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635 return secondary_files_dir |
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636 |
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637 def stage_files(self): |
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638 cwl_job = self.cwl_job() |
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639 |
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640 def stageFunc(resolved_path, target_path): |
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641 log.info(f"resolving {resolved_path} to {target_path}") |
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642 try: |
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643 os.symlink(resolved_path, target_path) |
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644 except OSError: |
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645 pass |
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646 |
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647 if hasattr(cwl_job, "pathmapper"): |
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648 process.stage_files(cwl_job.pathmapper, stageFunc, ignore_writable=True, symlink=False) |
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649 |
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650 if hasattr(cwl_job, "generatefiles"): |
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651 outdir = os.path.join(self._job_directory, "working") |
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652 # TODO: Why doesn't cwl_job.generatemapper work? |
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653 generate_mapper = pathmapper.PathMapper(cwl_job.generatefiles["listing"], |
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654 outdir, outdir, separateDirs=False) |
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655 # TODO: figure out what inplace_update should be. |
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656 inplace_update = cwl_job.inplace_update |
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657 process.stage_files(generate_mapper, stageFunc, ignore_writable=inplace_update, symlink=False) |
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658 relink_initialworkdir(generate_mapper, outdir, outdir, inplace_update=inplace_update) |
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659 # else: expression tools do not have a path mapper. |
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660 |
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661 @staticmethod |
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662 def _job_file(job_directory): |
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663 return os.path.join(job_directory, JOB_JSON_FILE) |
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664 |
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665 |
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666 class WorkflowProxy: |
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667 |
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668 def __init__(self, workflow, workflow_path=None): |
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669 self._workflow = workflow |
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670 self._workflow_path = workflow_path |
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671 self._step_proxies = None |
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672 |
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673 @property |
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674 def cwl_id(self): |
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675 return self._workflow.tool["id"] |
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676 |
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677 def get_outputs_for_label(self, label): |
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678 outputs = [] |
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679 for output in self._workflow.tool['outputs']: |
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680 step, output_name = split_step_references( |
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681 output["outputSource"], |
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682 multiple=False, |
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683 workflow_id=self.cwl_id, |
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684 ) |
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685 if step == label: |
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686 output_id = output["id"] |
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687 if "#" not in self.cwl_id: |
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688 _, output_label = output_id.rsplit("#", 1) |
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689 else: |
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690 _, output_label = output_id.rsplit("/", 1) |
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691 |
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692 outputs.append({ |
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693 "output_name": output_name, |
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694 "label": output_label, |
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695 }) |
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696 return outputs |
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697 |
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698 def tool_reference_proxies(self): |
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699 """Fetch tool source definitions for all referenced tools.""" |
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700 references = [] |
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701 for step in self.step_proxies(): |
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702 references.extend(step.tool_reference_proxies()) |
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703 return references |
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704 |
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705 def step_proxies(self): |
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706 if self._step_proxies is None: |
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707 proxies = [] |
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708 num_input_steps = len(self._workflow.tool['inputs']) |
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709 for i, step in enumerate(self._workflow.steps): |
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710 proxies.append(build_step_proxy(self, step, i + num_input_steps)) |
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711 self._step_proxies = proxies |
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712 return self._step_proxies |
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713 |
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714 @property |
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715 def runnables(self): |
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716 runnables = [] |
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717 for step in self._workflow.steps: |
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718 if "run" in step.tool: |
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719 runnables.append(step.tool["run"]) |
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720 return runnables |
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721 |
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722 def cwl_ids_to_index(self, step_proxies): |
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723 index = 0 |
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724 cwl_ids_to_index = {} |
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725 for input_dict in self._workflow.tool['inputs']: |
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726 cwl_ids_to_index[input_dict["id"]] = index |
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727 index += 1 |
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728 |
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729 for step_proxy in step_proxies: |
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730 cwl_ids_to_index[step_proxy.cwl_id] = index |
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731 index += 1 |
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732 |
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733 return cwl_ids_to_index |
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734 |
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735 @property |
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736 def output_labels(self): |
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737 return [self.jsonld_id_to_label(o['id']) for o in self._workflow.tool['outputs']] |
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738 |
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739 def input_connections_by_step(self, step_proxies): |
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740 cwl_ids_to_index = self.cwl_ids_to_index(step_proxies) |
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741 input_connections_by_step = [] |
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742 for step_proxy in step_proxies: |
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743 input_connections_step = {} |
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744 for input_proxy in step_proxy.input_proxies: |
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745 cwl_source_id = input_proxy.cwl_source_id |
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746 input_name = input_proxy.input_name |
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747 # Consider only allow multiple if MultipleInputFeatureRequirement is enabled |
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748 for (output_step_name, output_name) in split_step_references(cwl_source_id, workflow_id=self.cwl_id): |
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749 if "#" in self.cwl_id: |
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750 sep_on = "/" |
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751 else: |
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752 sep_on = "#" |
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753 output_step_id = self.cwl_id + sep_on + output_step_name |
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754 |
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755 if output_step_id not in cwl_ids_to_index: |
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756 template = "Output [%s] does not appear in ID-to-index map [%s]." |
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757 msg = template % (output_step_id, cwl_ids_to_index.keys()) |
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758 raise AssertionError(msg) |
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759 |
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760 if input_name not in input_connections_step: |
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761 input_connections_step[input_name] = [] |
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762 |
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763 input_connections_step[input_name].append({ |
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764 "id": cwl_ids_to_index[output_step_id], |
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765 "output_name": output_name, |
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766 "input_type": "dataset" |
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767 }) |
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768 |
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769 input_connections_by_step.append(input_connections_step) |
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770 |
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771 return input_connections_by_step |
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772 |
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773 def to_dict(self): |
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774 name = os.path.basename(self._workflow.tool.get('label') or self._workflow_path or 'TODO - derive a name from ID') |
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775 steps = {} |
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776 |
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777 step_proxies = self.step_proxies() |
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778 input_connections_by_step = self.input_connections_by_step(step_proxies) |
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779 index = 0 |
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780 for i, input_dict in enumerate(self._workflow.tool['inputs']): |
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781 steps[index] = self.cwl_input_to_galaxy_step(input_dict, i) |
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782 index += 1 |
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783 |
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784 for i, step_proxy in enumerate(step_proxies): |
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785 input_connections = input_connections_by_step[i] |
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786 steps[index] = step_proxy.to_dict(input_connections) |
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787 index += 1 |
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788 |
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789 return { |
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790 'name': name, |
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791 'steps': steps, |
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792 'annotation': self.cwl_object_to_annotation(self._workflow.tool), |
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793 } |
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794 |
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795 def find_inputs_step_index(self, label): |
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796 for i, input in enumerate(self._workflow.tool['inputs']): |
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797 if self.jsonld_id_to_label(input["id"]) == label: |
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798 return i |
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799 |
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800 raise Exception("Failed to find index for label %s" % label) |
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801 |
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802 def jsonld_id_to_label(self, id): |
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803 if "#" in self.cwl_id: |
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804 return id.rsplit("/", 1)[-1] |
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805 else: |
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806 return id.rsplit("#", 1)[-1] |
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807 |
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808 def cwl_input_to_galaxy_step(self, input, i): |
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809 input_type = input["type"] |
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810 label = self.jsonld_id_to_label(input["id"]) |
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811 input_as_dict = { |
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812 "id": i, |
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813 "label": label, |
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814 "position": {"left": 0, "top": 0}, |
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815 "annotation": self.cwl_object_to_annotation(input), |
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816 "input_connections": {}, # Should the Galaxy API really require this? - Seems to. |
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817 "workflow_outputs": self.get_outputs_for_label(label), |
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818 } |
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819 |
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820 if input_type == "File" and "default" not in input: |
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821 input_as_dict["type"] = "data_input" |
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822 elif isinstance(input_type, dict) and input_type.get("type") == "array": |
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823 input_as_dict["type"] = "data_collection_input" |
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824 input_as_dict["collection_type"] = "list" |
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825 elif isinstance(input_type, dict) and input_type.get("type") == "record": |
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826 input_as_dict["type"] = "data_collection_input" |
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827 input_as_dict["collection_type"] = "record" |
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828 else: |
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829 if USE_STEP_PARAMETERS: |
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830 input_as_dict["type"] = "parameter_input" |
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831 # TODO: dispatch on actual type so this doesn't always need |
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832 # to be field - simpler types could be simpler inputs. |
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833 tool_state = {} |
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834 tool_state["parameter_type"] = "field" |
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835 default_set = "default" in input |
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836 default_value = input.get("default") |
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837 optional = default_set |
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838 if isinstance(input_type, list) and "null" in input_type: |
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839 optional = True |
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840 if not optional and isinstance(input_type, dict) and "type" in input_type: |
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841 raise ValueError("'type' detected in non-optional input dictionary.") |
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842 if default_set: |
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843 tool_state["default"] = {"src": "json", "value": default_value} |
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844 tool_state["optional"] = optional |
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845 input_as_dict["tool_state"] = tool_state |
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846 else: |
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847 input_as_dict["type"] = "data_input" |
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848 # TODO: format = expression.json |
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849 |
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850 return input_as_dict |
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851 |
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852 def cwl_object_to_annotation(self, cwl_obj): |
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853 return cwl_obj.get("doc", None) |
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854 |
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855 |
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856 def split_step_references(step_references, workflow_id=None, multiple=True): |
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857 """Split a CWL step input or output reference into step id and name.""" |
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858 # Trim off the workflow id part of the reference. |
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859 step_references = listify(step_references) |
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860 split_references = [] |
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861 |
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862 for step_reference in step_references: |
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863 if workflow_id is None: |
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864 # This path works fine for some simple workflows - but not so much |
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865 # for subworkflows (maybe same for $graph workflows?) |
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866 assert "#" in step_reference |
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867 _, step_reference = step_reference.split("#", 1) |
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868 else: |
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869 if "#" in workflow_id: |
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870 sep_on = "/" |
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871 else: |
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872 sep_on = "#" |
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873 expected_prefix = workflow_id + sep_on |
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874 if not step_reference.startswith(expected_prefix): |
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875 raise AssertionError(f"step_reference [{step_reference}] doesn't start with {expected_prefix}") |
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876 step_reference = step_reference[len(expected_prefix):] |
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877 |
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878 # Now just grab the step name and input/output name. |
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879 assert "#" not in step_reference |
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880 if "/" in step_reference: |
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881 step_name, io_name = step_reference.split("/", 1) |
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882 else: |
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883 # Referencing an input, not a step. |
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884 # In Galaxy workflows input steps have an implicit output named |
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885 # "output" for consistency with tools - in cwl land |
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886 # just the input name is referenced. |
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887 step_name = step_reference |
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888 io_name = "output" |
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889 split_references.append((step_name, io_name)) |
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890 |
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891 if multiple: |
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|
892 return split_references |
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|
893 else: |
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|
894 assert len(split_references) == 1 |
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|
895 return split_references[0] |
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|
896 |
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|
897 |
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|
898 def build_step_proxy(workflow_proxy, step, index): |
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|
899 step_type = step.embedded_tool.tool["class"] |
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|
900 if step_type == "Workflow": |
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|
901 return SubworkflowStepProxy(workflow_proxy, step, index) |
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|
902 else: |
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parents:
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|
903 return ToolStepProxy(workflow_proxy, step, index) |
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|
904 |
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|
905 |
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|
906 class BaseStepProxy: |
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|
907 |
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|
908 def __init__(self, workflow_proxy, step, index): |
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|
909 self._workflow_proxy = workflow_proxy |
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|
910 self._step = step |
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|
911 self._index = index |
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912 self._uuid = str(uuid4()) |
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|
913 self._input_proxies = None |
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|
914 |
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|
915 @property |
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|
916 def step_class(self): |
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917 return self.cwl_tool_object.tool["class"] |
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918 |
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|
919 @property |
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|
920 def cwl_id(self): |
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921 return self._step.id |
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922 |
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|
923 @property |
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|
924 def cwl_workflow_id(self): |
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925 return self._workflow_proxy.cwl_id |
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|
926 |
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|
927 @property |
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|
928 def requirements(self): |
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|
929 return self._step.requirements |
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|
930 |
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|
931 @property |
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|
932 def hints(self): |
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933 return self._step.hints |
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|
934 |
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|
935 @property |
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|
936 def label(self): |
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|
937 label = self._workflow_proxy.jsonld_id_to_label(self._step.id) |
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|
938 return label |
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|
939 |
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|
940 def galaxy_workflow_outputs_list(self): |
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|
941 return self._workflow_proxy.get_outputs_for_label(self.label) |
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|
942 |
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|
943 @property |
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|
944 def cwl_tool_object(self): |
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945 return self._step.embedded_tool |
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946 |
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|
947 @property |
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|
948 def input_proxies(self): |
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949 if self._input_proxies is None: |
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950 input_proxies = [] |
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951 cwl_inputs = self._step.tool["inputs"] |
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|
952 for cwl_input in cwl_inputs: |
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|
953 input_proxies.append(InputProxy(self, cwl_input)) |
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954 self._input_proxies = input_proxies |
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955 return self._input_proxies |
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|
956 |
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|
957 def inputs_to_dicts(self): |
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parents:
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958 inputs_as_dicts = [] |
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parents:
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|
959 for input_proxy in self.input_proxies: |
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parents:
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|
960 inputs_as_dicts.append(input_proxy.to_dict()) |
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parents:
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|
961 return inputs_as_dicts |
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parents:
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|
962 |
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parents:
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|
963 |
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parents:
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|
964 class InputProxy: |
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parents:
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|
965 |
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parents:
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|
966 def __init__(self, step_proxy, cwl_input): |
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|
967 self._cwl_input = cwl_input |
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parents:
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|
968 self.step_proxy = step_proxy |
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parents:
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|
969 self.workflow_proxy = step_proxy._workflow_proxy |
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parents:
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|
970 |
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parents:
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|
971 cwl_input_id = cwl_input["id"] |
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parents:
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|
972 cwl_source_id = cwl_input.get("source", None) |
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parents:
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changeset
|
973 if cwl_source_id is None: |
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parents:
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|
974 if "valueFrom" not in cwl_input and "default" not in cwl_input: |
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shellac
parents:
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|
975 msg = "Workflow step input must define a source, a valueFrom, or a default value. Obtained [%s]." % cwl_input |
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parents:
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|
976 raise MessageException(msg) |
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parents:
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|
977 |
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parents:
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|
978 assert cwl_input_id |
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parents:
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|
979 step_name, input_name = split_step_references( |
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parents:
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changeset
|
980 cwl_input_id, |
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parents:
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|
981 multiple=False, |
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parents:
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|
982 workflow_id=step_proxy.cwl_workflow_id |
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parents:
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|
983 ) |
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|
984 self.step_name = step_name |
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parents:
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|
985 self.input_name = input_name |
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parents:
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|
986 |
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parents:
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|
987 self.cwl_input_id = cwl_input_id |
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parents:
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988 self.cwl_source_id = cwl_source_id |
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|
989 |
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parents:
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|
990 scatter_inputs = [split_step_references( |
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parents:
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|
991 i, multiple=False, workflow_id=step_proxy.cwl_workflow_id |
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parents:
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|
992 )[1] for i in listify(step_proxy._step.tool.get("scatter", []))] |
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|
993 scatter = self.input_name in scatter_inputs |
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|
994 self.scatter = scatter |
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|
995 |
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parents:
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|
996 def to_dict(self): |
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parents:
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997 as_dict = { |
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|
998 "name": self.input_name, |
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|
999 } |
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parents:
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1000 if "linkMerge" in self._cwl_input: |
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shellac
parents:
diff
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|
1001 as_dict["merge_type"] = self._cwl_input["linkMerge"] |
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shellac
parents:
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|
1002 if "scatterMethod" in self.step_proxy._step.tool: |
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shellac
parents:
diff
changeset
|
1003 as_dict["scatter_type"] = self.step_proxy._step.tool.get("scatterMethod", "dotproduct") |
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1004 else: |
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1005 as_dict["scatter_type"] = "dotproduct" if self.scatter else "disabled" |
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1006 if "valueFrom" in self._cwl_input: |
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1007 # TODO: Add a table for expressions - mark the type as CWL 1.0 JavaScript. |
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1008 as_dict["value_from"] = self._cwl_input["valueFrom"] |
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1009 if "default" in self._cwl_input: |
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1010 as_dict["default"] = self._cwl_input["default"] |
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1011 return as_dict |
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1012 |
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1013 |
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1014 class ToolStepProxy(BaseStepProxy): |
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1015 |
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1016 def __init__(self, workflow_proxy, step, index): |
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1017 super().__init__(workflow_proxy, step, index) |
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1018 self._tool_proxy = None |
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1019 |
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1020 @property |
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1021 def tool_proxy(self): |
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1022 # Neeeds to be cached so UUID that is loaded matches UUID generated with to_dict. |
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1023 if self._tool_proxy is None: |
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1024 self._tool_proxy = _cwl_tool_object_to_proxy(self.cwl_tool_object, uuid=str(uuid4())) |
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1025 return self._tool_proxy |
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1026 |
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1027 def tool_reference_proxies(self): |
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1028 # Return a list so we can handle subworkflows recursively. |
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1029 return [self.tool_proxy] |
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1030 |
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1031 def to_dict(self, input_connections): |
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1032 # We need to stub out null entries for things getting replaced by |
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1033 # connections. This doesn't seem ideal - consider just making Galaxy |
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1034 # handle this. |
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1035 tool_state = {} |
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1036 for input_name in input_connections.keys(): |
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1037 tool_state[input_name] = None |
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1038 |
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1039 outputs = self.galaxy_workflow_outputs_list() |
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1040 return { |
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1041 "id": self._index, |
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1042 "tool_uuid": self.tool_proxy._uuid, # TODO: make sure this is respected... |
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1043 "label": self.label, |
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1044 "position": {"left": 0, "top": 0}, |
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1045 "type": "tool", |
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1046 "annotation": self._workflow_proxy.cwl_object_to_annotation(self._step.tool), |
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1047 "input_connections": input_connections, |
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1048 "inputs": self.inputs_to_dicts(), |
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1049 "workflow_outputs": outputs, |
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1050 } |
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1051 |
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1052 |
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1053 class SubworkflowStepProxy(BaseStepProxy): |
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1054 |
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1055 def __init__(self, workflow_proxy, step, index): |
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1056 super().__init__(workflow_proxy, step, index) |
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1057 self._subworkflow_proxy = None |
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1058 |
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1059 def to_dict(self, input_connections): |
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1060 outputs = self.galaxy_workflow_outputs_list() |
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1061 for key, input_connection_list in input_connections.items(): |
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1062 input_subworkflow_step_id = self.subworkflow_proxy.find_inputs_step_index( |
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1063 key |
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1064 ) |
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1065 for input_connection in input_connection_list: |
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1066 input_connection["input_subworkflow_step_id"] = input_subworkflow_step_id |
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1067 |
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1068 return { |
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1069 "id": self._index, |
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1070 "label": self.label, |
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1071 "position": {"left": 0, "top": 0}, |
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1072 "type": "subworkflow", |
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1073 "subworkflow": self.subworkflow_proxy.to_dict(), |
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1074 "annotation": self.subworkflow_proxy.cwl_object_to_annotation(self._step.tool), |
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1075 "input_connections": input_connections, |
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1076 "inputs": self.inputs_to_dicts(), |
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1077 "workflow_outputs": outputs, |
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1078 } |
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1079 |
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1080 def tool_reference_proxies(self): |
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1081 return self.subworkflow_proxy.tool_reference_proxies() |
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1082 |
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1083 @property |
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1084 def subworkflow_proxy(self): |
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1085 if self._subworkflow_proxy is None: |
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1086 self._subworkflow_proxy = WorkflowProxy(self.cwl_tool_object) |
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1087 return self._subworkflow_proxy |
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1088 |
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1089 |
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1090 def remove_pickle_problems(obj): |
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1091 """doc_loader does not pickle correctly""" |
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1092 if hasattr(obj, "doc_loader"): |
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1093 obj.doc_loader = None |
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1094 if hasattr(obj, "embedded_tool"): |
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1095 obj.embedded_tool = remove_pickle_problems(obj.embedded_tool) |
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1096 if hasattr(obj, "steps"): |
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1097 obj.steps = [remove_pickle_problems(s) for s in obj.steps] |
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1098 return obj |
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1099 |
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1100 |
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1101 class WorkflowToolReference(metaclass=ABCMeta): |
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1102 pass |
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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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1117 |
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1118 name, label, description = _field_metadata(field) |
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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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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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1130 value_description, |
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1131 input_type=type_description.galaxy_param_type, |
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1132 collection_type=type_description.collection_type, |
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1133 ) |
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1134 |
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1135 select_options = [] |
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1136 case_options = [] |
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1137 type_descriptions = type_descriptions_for_field_types(field_type) |
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1138 for type_description in type_descriptions: |
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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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1142 input_instances.append(value_input(type_description)) |
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1143 case_options.append((type_description.name, input_instances)) |
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1144 |
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1145 # If there is more than one way to represent this parameter - produce a conditional |
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1146 # requesting user to ask for what form they want to submit the data in, else just map |
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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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1154 ) |
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1155 |
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1156 return ConditionalInstance(name, case_input, case_options) |
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1157 else: |
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1158 if len(case_options) > 1: |
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1159 only_type_description = FIELD_TYPE_REPRESENTATION |
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1160 else: |
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1161 only_type_description = type_descriptions[0] |
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1162 |
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1163 return InputInstance( |
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1164 name, label, description, input_type=only_type_description.galaxy_param_type, collection_type=only_type_description.collection_type |
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1165 ) |
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1166 |
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1167 # Older array to repeat handling, now we are just representing arrays as |
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1168 # dataset collections - we should offer a blended approach in the future. |
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1169 # if field_type in simple_map_type_map.keys(): |
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1170 # input_type = simple_map_type_map[field_type] |
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1171 # return {"input_type": input_type, "array": False} |
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1172 # elif field_type == "array": |
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1173 # if isinstance(field["type"], dict): |
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1174 # array_type = field["type"]["items"] |
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1175 # else: |
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1176 # array_type = field["items"] |
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1177 # if array_type in simple_map_type_map.keys(): |
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1178 # input_type = simple_map_type_map[array_type] |
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1179 # return {"input_type": input_type, "array": True} |
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1180 # else: |
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1181 # raise Exception("Unhandled simple field type encountered - [%s]." % field_type) |
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1182 |
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1183 |
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1184 def _field_metadata(field): |
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1185 name = field["name"] |
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1186 label = field.get("label", None) |
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1187 description = field.get("doc", None) |
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1188 return name, label, description |
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1189 |
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1190 |
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1191 def _simple_field_to_output(field): |
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1192 name = field["name"] |
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1193 output_data_class = field["type"] |
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1194 output_instance = OutputInstance( |
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1195 name, |
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1196 output_data_type=output_data_class, |
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1197 output_type=OUTPUT_TYPE.GLOB |
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1198 ) |
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1199 return output_instance |
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1200 |
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1201 |
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1202 class ConditionalInstance: |
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1203 |
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1204 def __init__(self, name, case, whens): |
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1205 self.input_type = INPUT_TYPE.CONDITIONAL |
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1206 self.name = name |
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1207 self.case = case |
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1208 self.whens = whens |
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1209 |
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1210 def to_dict(self): |
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1211 |
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1212 as_dict = dict( |
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1213 name=self.name, |
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1214 type=INPUT_TYPE.CONDITIONAL, |
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1215 test=self.case.to_dict(), |
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1216 when={}, |
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1217 ) |
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1218 for value, block in self.whens: |
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1219 as_dict["when"][value] = [i.to_dict() for i in block] |
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1220 |
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1221 return as_dict |
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1222 |
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1223 |
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1224 class SelectInputInstance: |
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1225 |
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1226 def __init__(self, name, label, description, options): |
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1227 self.input_type = INPUT_TYPE.SELECT |
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1228 self.name = name |
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1229 self.label = label |
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1230 self.description = description |
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1231 self.options = options |
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1232 |
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1233 def to_dict(self): |
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1234 # TODO: serialize options... |
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1235 as_dict = dict( |
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1236 name=self.name, |
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1237 label=self.label or self.name, |
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1238 help=self.description, |
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1239 type=self.input_type, |
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1240 options=self.options, |
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1241 ) |
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1242 return as_dict |
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1243 |
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1244 |
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1245 class InputInstance: |
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1246 |
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1247 def __init__(self, name, label, description, input_type, array=False, area=False, collection_type=None): |
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1248 self.input_type = input_type |
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1249 self.collection_type = collection_type |
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1250 self.name = name |
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1251 self.label = label |
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1252 self.description = description |
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1253 self.required = True |
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1254 self.array = array |
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1255 self.area = area |
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1256 |
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1257 def to_dict(self, itemwise=True): |
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1258 if itemwise and self.array: |
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1259 as_dict = dict( |
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1260 type="repeat", |
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1261 name="%s_repeat" % self.name, |
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1262 title="%s" % self.name, |
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1263 blocks=[ |
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1264 self.to_dict(itemwise=False) |
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1265 ] |
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1266 ) |
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1267 else: |
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1268 as_dict = dict( |
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1269 name=self.name, |
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1270 label=self.label or self.name, |
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1271 help=self.description, |
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1272 type=self.input_type, |
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1273 optional=not self.required, |
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1274 ) |
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1275 if self.area: |
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1276 as_dict["area"] = True |
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1277 |
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1278 if self.input_type == INPUT_TYPE.INTEGER: |
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1279 as_dict["value"] = "0" |
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1280 if self.input_type == INPUT_TYPE.FLOAT: |
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1281 as_dict["value"] = "0.0" |
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1282 elif self.input_type == INPUT_TYPE.DATA_COLLECTON: |
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1283 as_dict["collection_type"] = self.collection_type |
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1284 |
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1285 return as_dict |
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1286 |
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1287 |
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1288 OUTPUT_TYPE = Bunch( |
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1289 GLOB="glob", |
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1290 STDOUT="stdout", |
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1291 ) |
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1292 |
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1293 |
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1294 # TODO: Different subclasses - this is representing different types of things. |
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1295 class OutputInstance: |
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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 ) |