Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/planemo/runnable.py @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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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 collections
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7 import os
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8 from distutils.dir_util import copy_tree
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9
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10 import aenum
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11 import six
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12 import yaml
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13 from galaxy.tool_util.cwl.parser import workflow_proxy
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14 from galaxy.tool_util.loader_directory import (
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15 is_a_yaml_with_class,
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16 looks_like_a_cwl_artifact,
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17 looks_like_a_data_manager_xml,
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18 looks_like_a_tool_cwl,
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19 looks_like_a_tool_xml,
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20 )
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21 from galaxy.tool_util.parser import get_tool_source
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22
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23 from planemo.exit_codes import EXIT_CODE_UNKNOWN_FILE_TYPE, ExitCodeException
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24 from planemo.galaxy.workflows import describe_outputs
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25 from planemo.io import error
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26 from planemo.test import check_output
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27
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28 TEST_SUFFIXES = [
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29 "-tests", "_tests", "-test", "_test"
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30 ]
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31 TEST_EXTENSIONS = [".yml", ".yaml", ".json"]
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32
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33 TEST_FILE_NOT_LIST_MESSAGE = ("Invalid test definition file [%s] - file must "
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34 "contain a list of tests")
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35 TEST_FIELD_MISSING_MESSAGE = ("Invalid test definition [test #%d in %s] -"
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36 "defintion must field [%s].")
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37
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38
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39 RunnableType = aenum.Enum(
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40 "RunnableType", 'galaxy_tool galaxy_datamanager galaxy_workflow cwl_tool cwl_workflow directory'
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41 )
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42
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43
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44 @property
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45 def _runnable_type_has_tools(runnable_type):
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46 return runnable_type.name in ["galaxy_tool", "galaxy_datamanager", "cwl_tool", "directory"]
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47
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48
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49 @property
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50 def _runnable_type_is_single_artifact(runnable_type):
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51 return runnable_type.name not in ["directory"]
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52
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53
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54 @property
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55 def _runnable_type_test_data_in_parent_dir(runnable_type):
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56 return runnable_type.name in ["galaxy_datamanager"]
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57
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58
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59 RunnableType.has_tools = _runnable_type_has_tools
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60 RunnableType.is_single_artifact = _runnable_type_is_single_artifact
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61 RunnableType.test_data_in_parent_dir = _runnable_type_test_data_in_parent_dir
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62
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63 _Runnable = collections.namedtuple("Runnable", ["path", "type"])
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64
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65
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66 class Runnable(_Runnable):
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67
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68 @property
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69 def test_data_search_path(self):
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70 if self.type.name in ['galaxy_datamanager']:
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71 return os.path.join(os.path.dirname(self.path), os.path.pardir)
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72 else:
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73 return self.path
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74
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75 @property
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76 def tool_data_search_path(self):
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77 return self.test_data_search_path
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78
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79 @property
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80 def data_manager_conf_path(self):
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81 if self.type.name in ['galaxy_datamanager']:
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82 return os.path.join(os.path.dirname(self.path), os.pardir, 'data_manager_conf.xml')
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83
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84 @property
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85 def has_tools(self):
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86 return _runnable_delegate_attribute('has_tools')
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87
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88 @property
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89 def is_single_artifact(self):
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90 return _runnable_delegate_attribute('is_single_artifact')
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91
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92
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93 def _runnable_delegate_attribute(attribute):
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94
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95 @property
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96 def getter(runnable):
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97 return getattr(runnable.type, attribute)
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98
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99 return getter
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100
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101
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102 def _copy_runnable_tree(path, runnable_type, temp_path):
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103 dir_to_copy = None
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104 if runnable_type in {RunnableType.galaxy_tool, RunnableType.cwl_tool}:
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105 dir_to_copy = os.path.dirname(path)
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106 path = os.path.join(temp_path, os.path.basename(path))
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107 elif runnable_type == RunnableType.directory:
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108 dir_to_copy = path
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109 path = temp_path
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110 elif runnable_type == RunnableType.galaxy_datamanager:
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111 dir_to_copy = os.path.join(os.path.dirname(path), os.pardir)
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112 path_to_data_manager_tool = os.path.relpath(path, dir_to_copy)
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113 path = os.path.join(temp_path, path_to_data_manager_tool)
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114 if dir_to_copy:
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115 copy_tree(dir_to_copy, temp_path)
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116 return path
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117
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118
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119 def for_path(path, temp_path=None):
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120 """Produce a class:`Runnable` for supplied path."""
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121 runnable_type = None
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122 if os.path.isdir(path):
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123 runnable_type = RunnableType.directory
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124 elif looks_like_a_tool_cwl(path):
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125 runnable_type = RunnableType.cwl_tool
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126 elif looks_like_a_data_manager_xml(path):
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127 runnable_type = RunnableType.galaxy_datamanager
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128 elif looks_like_a_tool_xml(path):
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129 runnable_type = RunnableType.galaxy_tool
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130 elif is_a_yaml_with_class(path, ["GalaxyWorkflow"]):
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131 runnable_type = RunnableType.galaxy_workflow
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132 elif path.endswith(".ga"):
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133 runnable_type = RunnableType.galaxy_workflow
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134 elif looks_like_a_cwl_artifact(path, ["Workflow"]):
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135 runnable_type = RunnableType.cwl_workflow
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136
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137 if runnable_type is None:
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138 error("Unable to determine runnable type for path [%s]" % path)
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139 raise ExitCodeException(EXIT_CODE_UNKNOWN_FILE_TYPE)
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140
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141 if temp_path:
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142 path = _copy_runnable_tree(path, runnable_type, temp_path)
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143
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144 return Runnable(path, runnable_type)
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145
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146
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147 def for_paths(paths, temp_path=None):
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148 """Return a specialized list of Runnable objects for paths."""
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149 return [for_path(path, temp_path=temp_path) for path in paths]
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150
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151
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152 def cases(runnable):
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153 """Build a `list` of :class:`TestCase` objects for specified runnable."""
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154 cases = []
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155
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156 tests_path = _tests_path(runnable)
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157 if tests_path is None:
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158 if runnable.type == RunnableType.galaxy_tool:
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159 tool_source = get_tool_source(runnable.path)
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160 test_dicts = tool_source.parse_tests_to_dict()
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161 tool_id = tool_source.parse_id()
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162 tool_version = tool_source.parse_version()
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163 for i, test_dict in enumerate(test_dicts.get("tests", [])):
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164 cases.append(ExternalGalaxyToolTestCase(runnable, tool_id, tool_version, i, test_dict))
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165 return cases
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166
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167 tests_directory = os.path.abspath(os.path.dirname(tests_path))
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168
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169 def normalize_to_tests_path(path):
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170 if not os.path.isabs(path):
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171 absolute_path = os.path.join(tests_directory, path)
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172 else:
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173 absolute_path = path
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174 return os.path.normpath(absolute_path)
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175
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176 with open(tests_path, "r") as f:
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177 tests_def = yaml.safe_load(f)
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178
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179 if not isinstance(tests_def, list):
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180 message = TEST_FILE_NOT_LIST_MESSAGE % tests_path
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181 raise Exception(message)
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182
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183 for i, test_def in enumerate(tests_def):
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184 if "job" not in test_def:
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185 message = TEST_FIELD_MISSING_MESSAGE % (
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186 i + 1, tests_path, "job"
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187 )
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188 raise Exception(message)
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189 job_def = test_def["job"]
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190 if isinstance(job_def, dict):
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191 job_path = None
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192 job = job_def
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193 else:
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194 job_path = normalize_to_tests_path(job_def)
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195 job = None
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196
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197 doc = test_def.get("doc", None)
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198 output_expectations = test_def.get("outputs", {})
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199 case = TestCase(
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200 runnable=runnable,
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201 tests_directory=tests_directory,
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202 output_expectations=output_expectations,
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203 index=i,
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204 job_path=job_path,
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205 job=job,
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206 doc=doc,
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207 )
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208 cases.append(case)
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209
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210 return cases
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211
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212
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213 class AbstractTestCase(object):
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214 """Description of a test case for a runnable.
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215 """
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216
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217 __metaclass__ = abc.ABCMeta
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218
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219 def structured_test_data(self, run_response):
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220 """Result of executing this test case - a "structured_data" dict.
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221
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222 :rtype: dict
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223 :return:
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224 For example::
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225
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226 {
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227 "id": "",
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228 "has_data": true,
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229 "data": {
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230 "status": "success", // error, skip,
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231 "job": {
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232 "command_line": "cat moo",
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233 "stdout": "",
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234 "stderr": ""
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235 },
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236 "output_problems": [],
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237 "execution_problem": "",
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238 "inputs" = {},
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239 "problem_log": ""
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240 }
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241 }
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242 """
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243
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244
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245 class TestCase(AbstractTestCase):
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246 """Describe an abstract test case for a specified runnable."""
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247
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248 def __init__(self, runnable, tests_directory, output_expectations, job_path, job, index, doc):
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249 """Construct TestCase object from required attributes."""
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250 self.runnable = runnable
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251 self.job_path = job_path
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252 self.job = job
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253 self.output_expectations = output_expectations
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254 self.tests_directory = tests_directory
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255 self.index = index
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256 self.doc = doc
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257
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258 def __repr__(self):
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259 return 'TestCase (%s) for runnable (%s) with job (%s) and expected outputs (%s) in directory (%s) with id (%s)' % \
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260 (self.doc, self.runnable, self.job, self.output_expectations, self.tests_directory, self.index)
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261
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262 def structured_test_data(self, run_response):
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263 """Check a test case against outputs dictionary.
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264 """
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265 output_problems = []
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266 if run_response.was_successful:
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267 outputs_dict = run_response.outputs_dict
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268 execution_problem = None
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269 for output_id, output_test in self.output_expectations.items():
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270 if output_id not in outputs_dict:
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271 message = "Expected output [%s] not found in results." % output_id
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272 output_problems.append(message)
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273 continue
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274
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275 output_value = outputs_dict[output_id]
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276 output_problems.extend(
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277 self._check_output(output_id, output_value, output_test)
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278 )
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279 if output_problems:
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280 status = "failure"
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281 else:
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282 status = "success"
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283 else:
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284 execution_problem = run_response.error_message
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285 status = "error"
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286 data_dict = dict(
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287 status=status
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288 )
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289 if status != "success":
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290 data_dict["output_problems"] = output_problems
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291 data_dict["execution_problem"] = execution_problem
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292 log = run_response.log
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293 if log is not None:
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294 data_dict["problem_log"] = log
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295 job_info = run_response.job_info
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296 if job_info is not None:
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297 data_dict["job"] = job_info
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298 data_dict["inputs"] = self._job
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299 return dict(
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300 id=("%s_%s" % (self._test_id, self.index)),
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301 has_data=True,
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302 data=data_dict,
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303 )
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304
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305 @property
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306 def _job(self):
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307 if self.job_path is not None:
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308 with open(self.job_path, "r") as f:
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309 return f.read()
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310 else:
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311 return self.job
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312
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313 def _check_output(self, output_id, output_value, output_test):
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314 output_problems = []
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315 if not isinstance(output_test, dict):
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316 if output_test != output_value:
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317 template = "Output [%s] value [%s] does not match expected value [%s]."
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318 message = template % (output_id, output_value, output_test)
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319 output_problems.append(message)
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320 else:
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321 if not isinstance(output_value, dict):
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322 output_problems.append("Expected file properties for output [%s]" % output_id)
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323 return
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324 if "path" not in output_value and "location" in output_value:
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325 assert output_value["location"].startswith("file://")
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326 output_value["path"] = output_value["location"][len("file://"):]
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327 if "path" not in output_value:
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328 output_problems.append("No path specified for expected output file [%s]" % output_id)
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329 return
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330
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331 output_problems.extend(
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332 check_output(
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333 self.runnable,
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334 output_value,
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335 output_test,
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336 # TODO: needs kwds in here...
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337 )
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338 )
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339
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340 return output_problems
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341
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342 @property
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343 def _test_id(self):
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344 if self.runnable.type in [
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345 RunnableType.cwl_tool,
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346 RunnableType.galaxy_tool,
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347 ]:
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348 return get_tool_source(self.runnable.path).parse_id()
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349 else:
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350 return os.path.basename(self.runnable.path)
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351
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352
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353 class ExternalGalaxyToolTestCase(AbstractTestCase):
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354 """Special class of AbstractCase that doesn't use job_path but uses test data from a Galaxy server.
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355 """
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356
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357 def __init__(self, runnable, tool_id, tool_version, test_index, test_dict):
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358 """Construct TestCase object from required attributes."""
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359 self.runnable = runnable
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360 self.tool_id = tool_id
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361 self.tool_version = tool_version
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362 self.test_index = test_index
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363 self.test_dict = test_dict
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364
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365 def structured_test_data(self, run_response):
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366 """Just return the structured_test_data generated from galaxy-tool-util for this test variant.
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367 """
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368 return run_response
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369
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370
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371 def _tests_path(runnable):
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372 if not runnable.is_single_artifact:
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373 raise NotImplementedError("Tests for directories are not yet implemented.")
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374
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375 runnable_path = runnable.path
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376 base, _ = os.path.splitext(runnable_path)
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377
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378 for test_suffix in TEST_SUFFIXES:
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379 for test_extension in TEST_EXTENSIONS:
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380 test_path = base + test_suffix + test_extension
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381 if os.path.exists(test_path):
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382 return test_path
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383
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384 return None
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385
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386
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387 def get_outputs(runnable):
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388 """Return a list of :class:`RunnableOutput` objects for this runnable."""
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389 if not runnable.is_single_artifact:
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390 raise NotImplementedError("Cannot generate outputs for a directory.")
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391 if runnable.type in [RunnableType.galaxy_tool, RunnableType.cwl_tool]:
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392 tool_source = get_tool_source(runnable.path)
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393 # TODO: do something with collections at some point
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394 output_datasets, _ = tool_source.parse_outputs(None)
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395 outputs = [ToolOutput(o) for o in output_datasets.values()]
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396 return outputs
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397 elif runnable.type == RunnableType.galaxy_workflow:
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398 workflow_outputs = describe_outputs(runnable.path)
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399 return [GalaxyWorkflowOutput(o) for o in workflow_outputs]
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400 elif runnable.type == RunnableType.cwl_workflow:
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401 workflow = workflow_proxy(runnable.path, strict_cwl_validation=False)
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402 return [CwlWorkflowOutput(label) for label in workflow.output_labels]
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403 else:
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404 raise NotImplementedError("Getting outputs for this artifact type is not yet supported.")
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405
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406
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407 class RunnableOutput(object):
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408 """Description of a single output of an execution of a Runnable."""
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409
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410 __metaclass__ = abc.ABCMeta
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411
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412 @abc.abstractproperty
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413 def get_id(self):
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414 """An identifier that describes this output."""
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415
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416
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417 class ToolOutput(RunnableOutput):
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418
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419 def __init__(self, tool_output):
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420 self._tool_output = tool_output
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421
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422 def get_id(self):
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423 return self._tool_output.name
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424
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425
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426 class GalaxyWorkflowOutput(RunnableOutput):
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427
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428 def __init__(self, workflow_output):
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429 self._workflow_output = workflow_output
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430
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431 def get_id(self):
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432 return self._workflow_output.label
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433
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434 @property
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435 def workflow_output(self):
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436 return self._workflow_output
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437
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438
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439 class CwlWorkflowOutput(RunnableOutput):
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440
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441 def __init__(self, label):
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442 self._label = label
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443
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444 def get_id(self):
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445 return self._label
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446
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447
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448 class RunResponse(object):
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449 """Description of an attempt for an engine to execute a Runnable."""
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450
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451 __metaclass__ = abc.ABCMeta
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452
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453 @abc.abstractproperty
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454 def was_successful(self):
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455 """Indicate whether an error was encountered while executing this runnble.
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456
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457 If successful, response should conform to the SuccessfulRunResponse interface,
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458 otherwise it will conform to the ErrorRunResponse interface.
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459 """
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460
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461 @abc.abstractproperty
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462 def job_info(self):
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463 """If job information is available, return as dictionary."""
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464
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465 @abc.abstractproperty
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466 def log(self):
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467 """If engine related log is available, return as text data."""
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468
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469
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470 class SuccessfulRunResponse(RunResponse):
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471 """Description of the results of an engine executing a Runnable."""
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472
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473 __metaclass__ = abc.ABCMeta
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474
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475 def was_successful(self):
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476 """Return `True` to indicate this run was successful."""
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477 return True
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478
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479 @abc.abstractproperty
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480 def outputs_dict(self):
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481 """Return a dict of output descriptions."""
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482
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483
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484 @six.python_2_unicode_compatible
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485 class ErrorRunResponse(RunResponse):
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486 """Description of an error while attempting to execute a Runnable."""
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487
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488 def __init__(self, error_message, job_info=None, log=None):
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489 """Create an ErrorRunResponse with specified error message."""
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490 self._error_message = error_message
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491 self._job_info = job_info
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492 self._log = log
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493
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494 @property
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495 def error_message(self):
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496 """Error message describing the problem with execution of the runnable."""
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497 return self._error_message
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498
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499 @property
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500 def was_successful(self):
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501 """Return `False` to indicate this run was successful."""
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502 return False
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503
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504 @property
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505 def job_info(self):
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506 """Return potentially null stored `job_info` dict."""
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507 return self._job_info
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508
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509 @property
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510 def log(self):
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511 """Return potentially null stored `log` text."""
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512 return self._log
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513
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514 def __str__(self):
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515 """Print a helpful error description of run."""
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516 message = "Run failed with message [%s]" % self.error_message
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517 log = self.log
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
518 if log:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
519 message += " and log [%s]" % log
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
520 return message
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
521
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
522
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
523 __all__ = (
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
524 "cases",
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
525 "ErrorRunResponse",
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
526 "for_path",
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
527 "for_paths",
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
528 "get_outputs",
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
529 "Runnable",
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
530 "RunnableType",
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
531 "RunResponse",
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
532 "RunnableOutput",
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
533 "SuccessfulRunResponse",
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
534 "TestCase",
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
535 )