Mercurial > repos > guerler > springsuite

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

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:32:28 -0400
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1
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1 import logging
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2 import os
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3 from collections import OrderedDict
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4
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5 from galaxy.tool_util.cwl.parser import tool_proxy
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6 from galaxy.tool_util.deps import requirements
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7 from .interface import (
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8 PageSource,
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9 PagesSource,
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10 ToolSource,
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11 )
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12 from .output_actions import ToolOutputActionGroup
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13 from .output_objects import ToolOutput
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14 from .stdio import (
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15 StdioErrorLevel,
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16 ToolStdioExitCode,
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17 )
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18 from .yaml import YamlInputSource
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19
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20 log = logging.getLogger(__name__)
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21
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22
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23 class CwlToolSource(ToolSource):
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24
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25 def __init__(self, tool_file, strict_cwl_validation=True):
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26 self._cwl_tool_file = tool_file
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27 self._id, _ = os.path.splitext(os.path.basename(tool_file))
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28 self._tool_proxy = None
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29 self._source_path = tool_file
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30 self._strict_cwl_validation = strict_cwl_validation
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31
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32 @property
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33 def source_path(self):
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34 return self._source_path
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35
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36 @property
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37 def tool_proxy(self):
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38 if self._tool_proxy is None:
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39 self._tool_proxy = tool_proxy(self._source_path, strict_cwl_validation=self._strict_cwl_validation)
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40 return self._tool_proxy
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41
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42 def parse_tool_type(self):
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43 return 'cwl'
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44
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45 def parse_id(self):
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46 return self._id
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47
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48 def parse_name(self):
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49 return self.tool_proxy.label() or self.parse_id()
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50
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51 def parse_command(self):
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52 return "$__cwl_command"
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53
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54 def parse_environment_variables(self):
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55 environment_variables = []
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56 # TODO: Is this even possible from here, should instead this be moved
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57 # into the job.
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58
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59 # for environment_variable_el in environment_variables_el.findall("environment_variable"):
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60 # definition = {
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61 # "name": environment_variable_el.get("name"),
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62 # "template": environment_variable_el.text,
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63 # }
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64 # environment_variables.append(
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65 # definition
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66 # )
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67
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68 return environment_variables
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69
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70 def parse_edam_operations(self):
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71 return []
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72
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73 def parse_edam_topics(self):
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74 return []
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75
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76 def parse_help(self):
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77 return self.tool_proxy.doc()
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78
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79 def parse_sanitize(self):
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80 return False
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81
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82 def parse_strict_shell(self):
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83 return True
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84
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85 def parse_stdio(self):
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86 # TODO: remove duplication with YAML
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87 # New format - starting out just using exit code.
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88 exit_code_lower = ToolStdioExitCode()
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89 exit_code_lower.range_start = float("-inf")
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90 exit_code_lower.range_end = -1
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91 exit_code_lower.error_level = StdioErrorLevel.FATAL
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92 exit_code_high = ToolStdioExitCode()
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93 exit_code_high.range_start = 1
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94 exit_code_high.range_end = float("inf")
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95 exit_code_lower.error_level = StdioErrorLevel.FATAL
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96 return [exit_code_lower, exit_code_high], []
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97
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98 def parse_interpreter(self):
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99 return None
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100
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101 def parse_version(self):
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102 return "0.0.1"
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103
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104 def parse_description(self):
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105 return self.tool_proxy.description()
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106
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107 def parse_interactivetool(self):
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108 return []
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109
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110 def parse_input_pages(self):
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111 page_source = CwlPageSource(self.tool_proxy)
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112 return PagesSource([page_source])
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113
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114 def parse_outputs(self, tool):
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115 output_instances = self.tool_proxy.output_instances()
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116 outputs = OrderedDict()
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117 output_defs = []
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118 for output_instance in output_instances:
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119 output_defs.append(self._parse_output(tool, output_instance))
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120 # TODO: parse outputs collections
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121 for output_def in output_defs:
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122 outputs[output_def.name] = output_def
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123 return outputs, OrderedDict()
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124
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125 def _parse_output(self, tool, output_instance):
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126 name = output_instance.name
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127 # TODO: handle filters, actions, change_format
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128 output = ToolOutput(name)
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129 if "File" in output_instance.output_data_type:
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130 output.format = "_sniff_"
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131 else:
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132 output.format = "expression.json"
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133 output.change_format = []
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134 output.format_source = None
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135 output.metadata_source = ""
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136 output.parent = None
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137 output.label = None
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138 output.count = None
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139 output.filters = []
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140 output.tool = tool
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141 output.hidden = ""
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142 output.dataset_collector_descriptions = []
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143 output.actions = ToolOutputActionGroup(output, None)
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144 return output
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145
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146 def parse_requirements_and_containers(self):
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147 containers = []
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148 docker_identifier = self.tool_proxy.docker_identifier()
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149 if docker_identifier:
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150 containers.append({"type": "docker",
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151 "identifier": docker_identifier})
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152
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153 software_requirements = self.tool_proxy.software_requirements()
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154 return requirements.parse_requirements_from_dict(dict(
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155 requirements=list(map(lambda r: {"name": r[0], "version": r[1], "type": "package"}, software_requirements)),
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156 containers=containers,
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157 ))
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158
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159 def parse_profile(self):
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160 return "16.04"
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161
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162 def parse_python_template_version(self):
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163 return '3.5'
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164
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165
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166 class CwlPageSource(PageSource):
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167
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168 def __init__(self, tool_proxy):
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169 cwl_instances = tool_proxy.input_instances()
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170 self._input_list = list(map(self._to_input_source, cwl_instances))
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171
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172 def _to_input_source(self, input_instance):
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173 as_dict = input_instance.to_dict()
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174 return YamlInputSource(as_dict)
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175
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176 def parse_input_sources(self):
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177 return self._input_list