Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/planemo/runnable.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 """Describe artifacts that can be run, tested, and linted.""" |
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2 |
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3 from __future__ import absolute_import |
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4 |
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5 import abc |
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6 import os |
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7 from distutils.dir_util import copy_tree |
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8 from enum import auto, Enum |
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9 from pathlib import Path |
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10 from typing import NamedTuple |
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11 from urllib.parse import urlparse |
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12 |
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13 import yaml |
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14 from galaxy.tool_util.cwl.parser import workflow_proxy |
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15 from galaxy.tool_util.loader_directory import ( |
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16 is_a_yaml_with_class, |
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17 looks_like_a_cwl_artifact, |
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18 looks_like_a_data_manager_xml, |
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19 looks_like_a_tool_cwl, |
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20 looks_like_a_tool_xml, |
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21 ) |
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22 from galaxy.tool_util.parser import get_tool_source |
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23 from six import ( |
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24 add_metaclass, |
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25 python_2_unicode_compatible, |
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26 ) |
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27 |
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28 from planemo.exit_codes import EXIT_CODE_UNKNOWN_FILE_TYPE, ExitCodeException |
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29 from planemo.galaxy.workflows import describe_outputs, GALAXY_WORKFLOWS_PREFIX |
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30 from planemo.io import error |
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31 from planemo.shed import DOCKSTORE_REGISTRY_CONF |
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32 from planemo.test import check_output, for_collections |
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33 |
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34 TEST_SUFFIXES = [ |
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35 "-tests", "_tests", "-test", "_test" |
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36 ] |
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37 TEST_EXTENSIONS = [".yml", ".yaml", ".json"] |
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38 |
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39 TEST_FILE_NOT_LIST_MESSAGE = ("Invalid test definition file [%s] - file must " |
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40 "contain a list of tests") |
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41 TEST_FIELD_MISSING_MESSAGE = ("Invalid test definition [test #%d in %s] -" |
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42 "defintion must field [%s].") |
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43 |
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44 |
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45 class RunnableType(Enum): |
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46 galaxy_tool = auto() |
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47 galaxy_datamanager = auto() |
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48 galaxy_workflow = auto() |
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49 cwl_tool = auto() |
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50 cwl_workflow = auto() |
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51 directory = auto() |
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52 |
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53 @property |
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54 def has_tools(runnable_type): |
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55 return runnable_type.name in ["galaxy_tool", "galaxy_datamanager", "cwl_tool", "directory"] |
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56 |
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57 @property |
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58 def is_single_artifact(runnable_type): |
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59 return runnable_type.name not in ["directory"] |
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60 |
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61 @property |
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62 def test_data_in_parent_dir(runnable_type): |
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63 return runnable_type.name in ["galaxy_datamanager"] |
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64 |
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65 @property |
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66 def is_galaxy_artifact(runnable_type): |
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67 return "galaxy" in runnable_type.name |
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68 |
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69 @property |
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70 def is_cwl_artifact(runnable_type): |
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71 return "cwl" in runnable_type.name |
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72 |
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73 |
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74 class Runnable(NamedTuple): |
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75 """Abstraction describing tools and workflows.""" |
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76 uri: str |
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77 type: RunnableType |
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78 |
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79 @property |
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80 def path(self): |
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81 uri = self.uri |
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82 if self.is_remote_workflow_uri: |
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83 parse_result = urlparse(uri) |
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84 query = parse_result.query |
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85 if query: |
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86 assert query.startswith("runnable_path=") |
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87 return query[len("runnable_path="):] |
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88 else: |
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89 raise ValueError(f"Runnable with URI {uri} is remote resource without local path") |
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90 else: |
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91 return uri |
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92 |
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93 @property |
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94 def has_path(self): |
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95 try: |
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96 self.path |
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97 return True |
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98 except ValueError: |
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99 return False |
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100 |
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101 @property |
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102 def is_remote_workflow_uri(self): |
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103 return self.uri.startswith(GALAXY_WORKFLOWS_PREFIX) |
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104 |
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105 @property |
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106 def test_data_search_path(self): |
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107 """During testing, path to search for test data files.""" |
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108 if self.type.name in ['galaxy_datamanager']: |
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109 return os.path.join(os.path.dirname(self.path), os.path.pardir) |
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110 else: |
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111 return self.path |
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112 |
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113 @property |
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114 def tool_data_search_path(self): |
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115 """During testing, path to search for Galaxy tool data tables.""" |
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116 return self.test_data_search_path |
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117 |
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118 @property |
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119 def data_manager_conf_path(self): |
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120 """Path of a Galaxy data manager configuration for runnable or None.""" |
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121 if self.type.name in ['galaxy_datamanager']: |
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122 return os.path.join(os.path.dirname(self.path), os.pardir, 'data_manager_conf.xml') |
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123 |
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124 @property |
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125 def has_tools(self): |
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126 """Boolean indicating if this runnable corresponds to one or more tools.""" |
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127 return _runnable_delegate_attribute('has_tools') |
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128 |
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129 @property |
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130 def is_single_artifact(self): |
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131 """Boolean indicating if this runnable is a single artifact. |
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132 |
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133 Currently only directories are considered not a single artifact. |
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134 """ |
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135 return _runnable_delegate_attribute('is_single_artifact') |
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136 |
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137 |
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138 def _runnable_delegate_attribute(attribute): |
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139 |
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140 @property |
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141 def getter(runnable): |
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142 return getattr(runnable.type, attribute) |
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143 |
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144 return getter |
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145 |
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146 |
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147 def _copy_runnable_tree(path, runnable_type, temp_path): |
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148 dir_to_copy = None |
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149 if runnable_type in {RunnableType.galaxy_tool, RunnableType.cwl_tool}: |
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150 dir_to_copy = os.path.dirname(path) |
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151 path = os.path.join(temp_path, os.path.basename(path)) |
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152 elif runnable_type == RunnableType.directory: |
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153 dir_to_copy = path |
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154 path = temp_path |
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155 elif runnable_type == RunnableType.galaxy_datamanager: |
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156 dir_to_copy = os.path.join(os.path.dirname(path), os.pardir) |
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157 path_to_data_manager_tool = os.path.relpath(path, dir_to_copy) |
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158 path = os.path.join(temp_path, path_to_data_manager_tool) |
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159 if dir_to_copy: |
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160 copy_tree(dir_to_copy, temp_path, update=True) |
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161 return path |
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162 |
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163 |
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164 def workflows_from_dockstore_yaml(path): |
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165 workflows = [] |
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166 parent_dir = Path(path).absolute().parent |
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167 with open(path) as y: |
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168 for workflow in yaml.safe_load(y).get('workflows', []): |
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169 workflow_path = workflow.get('primaryDescriptorPath') |
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170 if workflow_path: |
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171 if workflow_path.startswith('/'): |
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172 workflow_path = workflow_path[1:] |
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173 workflows.append(parent_dir.joinpath(workflow_path)) |
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174 return workflows |
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175 |
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176 |
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177 def workfow_dir_runnables(path, return_all=False): |
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178 dockstore_path = os.path.join(path, DOCKSTORE_REGISTRY_CONF) |
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179 if os.path.exists(dockstore_path): |
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180 runnables = [Runnable(str(path), RunnableType.galaxy_workflow) for path in workflows_from_dockstore_yaml(dockstore_path)] |
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181 if return_all: |
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182 return runnables |
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183 else: |
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184 return runnables[0] |
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185 |
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186 |
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187 def for_path(path, temp_path=None, return_all=False): |
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188 """Produce a class:`Runnable` for supplied path.""" |
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189 runnable_type = None |
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190 if os.path.isdir(path): |
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191 runnable = workfow_dir_runnables(path, return_all=return_all) |
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192 if runnable: |
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193 return runnable |
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194 runnable_type = RunnableType.directory |
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195 elif looks_like_a_tool_cwl(path): |
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196 runnable_type = RunnableType.cwl_tool |
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197 elif looks_like_a_data_manager_xml(path): |
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198 runnable_type = RunnableType.galaxy_datamanager |
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199 elif looks_like_a_tool_xml(path): |
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200 runnable_type = RunnableType.galaxy_tool |
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201 elif is_a_yaml_with_class(path, ["GalaxyWorkflow"]): |
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202 runnable_type = RunnableType.galaxy_workflow |
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203 elif path.endswith(".ga"): |
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204 runnable_type = RunnableType.galaxy_workflow |
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205 elif looks_like_a_cwl_artifact(path, ["Workflow"]): |
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206 runnable_type = RunnableType.cwl_workflow |
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207 else: |
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208 # Check to see if it is a Galaxy workflow with a different extension |
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209 try: |
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210 with open(path, "r") as f: |
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211 as_dict = yaml.safe_load(f) |
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212 if as_dict.get("a_galaxy_workflow", False): |
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213 runnable_type = RunnableType.galaxy_workflow |
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214 except Exception: |
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215 pass |
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216 |
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217 if runnable_type is None: |
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218 error("Unable to determine runnable type for path [%s]" % path) |
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219 raise ExitCodeException(EXIT_CODE_UNKNOWN_FILE_TYPE) |
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220 |
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221 if temp_path: |
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222 path = _copy_runnable_tree(path, runnable_type, temp_path) |
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223 |
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224 return Runnable(path, runnable_type) |
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225 |
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226 |
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227 def for_paths(paths, temp_path=None): |
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228 """Return a specialized list of Runnable objects for paths.""" |
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229 return [for_path(path, temp_path=temp_path) for path in paths] |
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230 |
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231 |
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232 def for_uri(uri): |
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233 """Produce a class:`Runnable` for supplied Galaxy workflow ID.""" |
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234 # TODO: allow galaxy_tool also, this trick would work fine for running tools |
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235 runnable = Runnable(uri, RunnableType.galaxy_workflow) |
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236 return runnable |
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237 |
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238 |
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239 def cases(runnable): |
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240 """Build a `list` of :class:`TestCase` objects for specified runnable.""" |
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241 cases = [] |
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242 |
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243 tests_path = _tests_path(runnable) |
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244 if tests_path is None: |
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245 if runnable.type == RunnableType.galaxy_tool: |
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246 tool_source = get_tool_source(runnable.path) |
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247 test_dicts = tool_source.parse_tests_to_dict() |
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248 tool_id = tool_source.parse_id() |
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249 tool_version = tool_source.parse_version() |
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250 for i, test_dict in enumerate(test_dicts.get("tests", [])): |
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251 cases.append(ExternalGalaxyToolTestCase(runnable, tool_id, tool_version, i, test_dict)) |
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252 return cases |
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253 |
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254 tests_directory = os.path.abspath(os.path.dirname(tests_path)) |
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255 |
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256 def normalize_to_tests_path(path): |
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257 if not os.path.isabs(path): |
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258 absolute_path = os.path.join(tests_directory, path) |
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259 else: |
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260 absolute_path = path |
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261 return os.path.normpath(absolute_path) |
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262 |
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263 with open(tests_path, "r") as f: |
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264 tests_def = yaml.safe_load(f) |
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265 |
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266 if not isinstance(tests_def, list): |
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267 message = TEST_FILE_NOT_LIST_MESSAGE % tests_path |
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268 raise Exception(message) |
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269 |
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270 for i, test_def in enumerate(tests_def): |
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271 if "job" not in test_def: |
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272 message = TEST_FIELD_MISSING_MESSAGE % ( |
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273 i + 1, tests_path, "job" |
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274 ) |
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275 raise Exception(message) |
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276 job_def = test_def["job"] |
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277 if isinstance(job_def, dict): |
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278 job_path = None |
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279 job = job_def |
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280 else: |
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281 job_path = normalize_to_tests_path(job_def) |
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282 job = None |
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283 |
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284 doc = test_def.get("doc", None) |
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285 output_expectations = test_def.get("outputs", {}) |
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286 case = TestCase( |
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287 runnable=runnable, |
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288 tests_directory=tests_directory, |
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289 output_expectations=output_expectations, |
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290 index=i, |
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291 job_path=job_path, |
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292 job=job, |
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293 doc=doc, |
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294 ) |
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295 cases.append(case) |
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296 |
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297 return cases |
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298 |
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299 |
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300 @add_metaclass(abc.ABCMeta) |
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301 class AbstractTestCase(object): |
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302 """Description of a test case for a runnable.""" |
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303 |
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304 def structured_test_data(self, run_response): |
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305 """Result of executing this test case - a "structured_data" dict. |
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306 |
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307 :rtype: dict |
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308 :return: |
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309 For example:: |
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310 |
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311 { |
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312 "id": "", |
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313 "has_data": true, |
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314 "data": { |
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315 "status": "success", // error, skip, |
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316 "job": { |
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317 "command_line": "cat moo", |
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318 "stdout": "", |
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319 "stderr": "" |
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320 }, |
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321 "output_problems": [], |
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322 "execution_problem": "", |
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323 "inputs" = {}, |
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324 "problem_log": "" |
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325 } |
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326 } |
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327 """ |
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328 |
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329 |
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330 class TestCase(AbstractTestCase): |
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331 """Describe an abstract test case for a specified runnable.""" |
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332 |
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333 def __init__(self, runnable, tests_directory, output_expectations, job_path, job, index, doc): |
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334 """Construct TestCase object from required attributes.""" |
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335 self.runnable = runnable |
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336 self.job_path = job_path |
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337 self.job = job |
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338 self.output_expectations = output_expectations |
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339 self.tests_directory = tests_directory |
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340 self.index = index |
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341 self.doc = doc |
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342 |
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343 def __repr__(self): |
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344 return 'TestCase (%s) for runnable (%s) with job (%s) and expected outputs (%s) in directory (%s) with id (%s)' % \ |
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345 (self.doc, self.runnable, self.job, self.output_expectations, self.tests_directory, self.index) |
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346 |
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347 def structured_test_data(self, run_response): |
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348 """Check a test case against outputs dictionary.""" |
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349 output_problems = [] |
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350 if run_response.was_successful: |
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351 outputs_dict = run_response.outputs_dict |
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352 execution_problem = None |
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353 for output_id, output_test in self.output_expectations.items(): |
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354 if output_id not in outputs_dict: |
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355 message = "Expected output [%s] not found in results." % output_id |
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356 output_problems.append(message) |
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357 continue |
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358 |
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359 output_value = outputs_dict[output_id] |
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360 output_problems.extend( |
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361 self._check_output(output_id, output_value, output_test) |
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362 ) |
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363 if output_problems: |
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364 status = "failure" |
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365 else: |
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366 status = "success" |
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367 else: |
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368 execution_problem = run_response.error_message |
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369 status = "error" |
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370 data_dict = dict( |
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371 status=status |
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372 ) |
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373 if status != "success": |
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374 data_dict["output_problems"] = output_problems |
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375 data_dict["execution_problem"] = execution_problem |
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376 log = run_response.log |
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377 if log is not None: |
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378 data_dict["problem_log"] = log |
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379 job_info = run_response.job_info |
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380 if job_info is not None: |
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381 data_dict["job"] = job_info |
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382 invocation_details = run_response.invocation_details |
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383 if invocation_details is not None: |
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384 data_dict["invocation_details"] = invocation_details |
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385 data_dict["inputs"] = self._job |
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386 return dict( |
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387 id=("%s_%s" % (self._test_id, self.index)), |
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388 has_data=True, |
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389 data=data_dict, |
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390 doc=self.doc, |
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391 test_type=self.runnable.type.name, |
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392 ) |
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393 |
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394 @property |
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395 def _job(self): |
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396 if self.job_path is not None: |
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397 with open(self.job_path, "r") as f: |
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398 return f.read() |
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399 else: |
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400 return self.job |
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401 |
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402 @property |
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403 def input_ids(self): |
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404 """Labels of inputs specified in test description.""" |
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405 return list(self._job.keys()) |
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406 |
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407 @property |
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408 def tested_output_ids(self): |
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409 """Labels of outputs checked in test description.""" |
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410 return list(self.output_expectations.keys()) |
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411 |
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412 def _check_output(self, output_id, output_value, output_test): |
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413 output_problems = [] |
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414 if not isinstance(output_test, dict): |
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415 if output_test != output_value: |
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416 template = "Output [%s] value [%s] does not match expected value [%s]." |
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417 message = template % (output_id, output_value, output_test) |
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418 output_problems.append(message) |
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419 else: |
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420 if not for_collections(output_test): |
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421 if not isinstance(output_value, dict): |
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422 message = "Expected file properties for output [%s]" % output_id |
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423 print(message) |
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424 print(output_value) |
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425 output_problems.append(message) |
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426 return output_problems |
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427 if "path" not in output_value and "location" in output_value: |
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428 assert output_value["location"].startswith("file://") |
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429 output_value["path"] = output_value["location"][len("file://"):] |
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430 if "path" not in output_value: |
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431 message = "No path specified for expected output file [%s]" % output_id |
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432 output_problems.append(message) |
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433 print(message) |
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434 return output_problems |
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435 else: |
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436 output_test["name"] = output_id |
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437 |
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438 output_problems.extend( |
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439 check_output( |
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440 self.runnable, |
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441 output_value, |
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442 output_test, |
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443 # TODO: needs kwds in here... |
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444 ) |
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445 ) |
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446 |
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447 return output_problems |
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448 |
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449 @property |
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450 def _test_id(self): |
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451 if self.runnable.type in [ |
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452 RunnableType.cwl_tool, |
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453 RunnableType.galaxy_tool, |
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454 ]: |
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455 return get_tool_source(self.runnable.path).parse_id() |
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456 else: |
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457 return os.path.basename(self.runnable.path) |
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458 |
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459 |
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460 class ExternalGalaxyToolTestCase(AbstractTestCase): |
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461 """Special class of AbstractCase that doesn't use job_path but uses test data from a Galaxy server.""" |
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462 |
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463 def __init__(self, runnable, tool_id, tool_version, test_index, test_dict): |
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464 """Construct TestCase object from required attributes.""" |
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465 self.runnable = runnable |
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466 self.tool_id = tool_id |
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467 self.tool_version = tool_version |
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468 self.test_index = test_index |
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469 self.test_dict = test_dict |
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470 |
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471 def structured_test_data(self, run_response): |
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472 """Just return the structured_test_data generated from galaxy-tool-util for this test variant.""" |
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473 return run_response |
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474 |
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475 |
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476 def _tests_path(runnable): |
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477 if not runnable.is_single_artifact: |
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478 raise NotImplementedError("Tests for directories are not yet implemented.") |
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479 |
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480 runnable_path = runnable.path |
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481 base, _ = os.path.splitext(runnable_path) |
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482 |
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483 for test_suffix in TEST_SUFFIXES: |
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484 for test_extension in TEST_EXTENSIONS: |
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485 test_path = base + test_suffix + test_extension |
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486 if os.path.exists(test_path): |
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487 return test_path |
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488 |
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489 return None |
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490 |
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491 |
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492 def get_outputs(runnable, gi=None): |
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493 """Return a list of :class:`RunnableOutput` objects for this runnable. |
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494 |
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495 Supply bioblend user Galaxy instance object (as gi) if additional context |
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496 needed to resolve workflow details. |
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497 """ |
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498 if not runnable.is_single_artifact: |
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499 raise NotImplementedError("Cannot generate outputs for a directory.") |
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500 if runnable.type in [RunnableType.galaxy_tool, RunnableType.cwl_tool]: |
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501 tool_source = get_tool_source(runnable.path) |
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502 # TODO: do something with collections at some point |
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503 output_datasets, _ = tool_source.parse_outputs(None) |
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504 outputs = [ToolOutput(o) for o in output_datasets.values()] |
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505 return outputs |
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506 elif runnable.type == RunnableType.galaxy_workflow: |
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507 workflow_outputs = describe_outputs(runnable, gi=gi) |
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508 return [GalaxyWorkflowOutput(o) for o in workflow_outputs] |
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509 elif runnable.type == RunnableType.cwl_workflow: |
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510 workflow = workflow_proxy(runnable.path, strict_cwl_validation=False) |
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511 return [CwlWorkflowOutput(label) for label in workflow.output_labels] |
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512 else: |
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513 raise NotImplementedError("Getting outputs for this artifact type is not yet supported.") |
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514 |
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515 |
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516 @add_metaclass(abc.ABCMeta) |
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517 class RunnableOutput(object): |
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518 """Description of a single output of an execution of a Runnable.""" |
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519 |
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520 @abc.abstractproperty |
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521 def get_id(self): |
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522 """An identifier that describes this output.""" |
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523 |
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524 |
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525 class ToolOutput(RunnableOutput): |
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526 """Implementation of RunnableOutput corresponding to Galaxy tool outputs.""" |
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527 |
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528 def __init__(self, tool_output): |
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529 self._tool_output = tool_output |
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530 |
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531 def get_id(self): |
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532 return self._tool_output.name |
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533 |
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534 |
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535 class GalaxyWorkflowOutput(RunnableOutput): |
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536 """Implementation of RunnableOutput corresponding to Galaxy workflow outputs.""" |
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537 |
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538 def __init__(self, workflow_output): |
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539 self._workflow_output = workflow_output |
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540 |
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541 def get_id(self): |
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542 return self._workflow_output.label |
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543 |
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544 @property |
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545 def workflow_output(self): |
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546 return self._workflow_output |
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547 |
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548 |
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549 class CwlWorkflowOutput(RunnableOutput): |
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550 """Implementation of RunnableOutput corresponding to CWL outputs.""" |
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551 |
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552 def __init__(self, label): |
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553 self._label = label |
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554 |
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555 def get_id(self): |
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556 return self._label |
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557 |
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558 |
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559 @add_metaclass(abc.ABCMeta) |
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560 class RunResponse(object): |
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561 """Description of an attempt for an engine to execute a Runnable.""" |
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562 |
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563 @abc.abstractproperty |
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564 def was_successful(self): |
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565 """Indicate whether an error was encountered while executing this runnable. |
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566 |
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567 If successful, response should conform to the SuccessfulRunResponse interface, |
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568 otherwise it will conform to the ErrorRunResponse interface. |
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569 """ |
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570 |
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571 @abc.abstractproperty |
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572 def job_info(self): |
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573 """If job information is available, return as dictionary.""" |
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574 |
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575 @abc.abstractproperty |
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576 def invocation_details(self): |
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577 """If workflow invocation details are available, return as dictionary.""" |
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578 |
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579 @abc.abstractproperty |
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580 def log(self): |
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581 """If engine related log is available, return as text data.""" |
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582 |
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583 |
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584 @add_metaclass(abc.ABCMeta) |
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585 class SuccessfulRunResponse(RunResponse): |
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586 """Description of the results of an engine executing a Runnable.""" |
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587 |
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588 def was_successful(self): |
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589 """Return `True` to indicate this run was successful.""" |
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590 return True |
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591 |
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592 @abc.abstractproperty |
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593 def outputs_dict(self): |
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594 """Return a dict of output descriptions.""" |
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595 |
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596 |
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597 @python_2_unicode_compatible |
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598 class ErrorRunResponse(RunResponse): |
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599 """Description of an error while attempting to execute a Runnable.""" |
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600 |
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601 def __init__(self, error_message, job_info=None, invocation_details=None, log=None): |
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602 """Create an ErrorRunResponse with specified error message.""" |
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603 self._error_message = error_message |
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604 self._job_info = job_info |
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605 self._invocation_details = invocation_details |
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606 self._log = log |
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607 |
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608 @property |
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609 def error_message(self): |
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610 """Error message describing the problem with execution of the runnable.""" |
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611 return self._error_message |
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612 |
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613 @property |
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614 def was_successful(self): |
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615 """Return `False` to indicate this run was successful.""" |
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616 return False |
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617 |
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618 @property |
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619 def job_info(self): |
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620 """Return potentially null stored `job_info` dict.""" |
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621 return self._job_info |
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622 |
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623 @property |
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624 def invocation_details(self): |
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625 return self._invocation_details |
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626 |
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627 @property |
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628 def log(self): |
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629 """Return potentially null stored `log` text.""" |
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630 return self._log |
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631 |
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632 def __str__(self): |
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633 """Print a helpful error description of run.""" |
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634 message = "Run failed with message [%s]" % self.error_message |
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635 log = self.log |
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636 if log: |
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637 message += " and log [%s]" % log |
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638 return message |
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639 |
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640 |
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641 __all__ = ( |
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642 "cases", |
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643 "ErrorRunResponse", |
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644 "for_path", |
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645 "for_paths", |
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646 "get_outputs", |
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647 "Runnable", |
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648 "RunnableType", |
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649 "RunResponse", |
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650 "RunnableOutput", |
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651 "SuccessfulRunResponse", |
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652 "TestCase", |
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653 ) |