Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/tool_util/parser/cwl.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 import logging |
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2 import os |
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3 |
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4 from galaxy.tool_util.cwl.parser import tool_proxy |
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5 from galaxy.tool_util.deps import requirements |
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6 from .interface import ( |
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7 PageSource, |
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8 PagesSource, |
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9 ToolSource, |
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10 ) |
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11 from .output_actions import ToolOutputActionGroup |
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12 from .output_objects import ToolOutput |
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13 from .stdio import ( |
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14 StdioErrorLevel, |
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15 ToolStdioExitCode, |
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16 ) |
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17 from .yaml import YamlInputSource |
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18 |
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19 log = logging.getLogger(__name__) |
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20 |
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21 |
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22 class CwlToolSource(ToolSource): |
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23 |
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24 def __init__(self, tool_file, strict_cwl_validation=True): |
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25 self._cwl_tool_file = tool_file |
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26 self._id, _ = os.path.splitext(os.path.basename(tool_file)) |
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27 self._tool_proxy = None |
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28 self._source_path = tool_file |
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29 self._strict_cwl_validation = strict_cwl_validation |
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30 |
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31 @property |
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32 def source_path(self): |
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33 return self._source_path |
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34 |
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35 @property |
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36 def tool_proxy(self): |
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37 if self._tool_proxy is None: |
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38 self._tool_proxy = tool_proxy(self._source_path, strict_cwl_validation=self._strict_cwl_validation) |
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39 return self._tool_proxy |
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40 |
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41 def parse_tool_type(self): |
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42 return 'cwl' |
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43 |
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44 def parse_id(self): |
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45 return self._id |
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46 |
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47 def parse_name(self): |
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48 return self.tool_proxy.label() or self.parse_id() |
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49 |
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50 def parse_command(self): |
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51 return "$__cwl_command" |
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52 |
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53 def parse_environment_variables(self): |
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54 environment_variables = [] |
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55 # TODO: Is this even possible from here, should instead this be moved |
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56 # into the job. |
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57 |
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58 # for environment_variable_el in environment_variables_el.findall("environment_variable"): |
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59 # definition = { |
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60 # "name": environment_variable_el.get("name"), |
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61 # "template": environment_variable_el.text, |
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62 # } |
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63 # environment_variables.append( |
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64 # definition |
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65 # ) |
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66 |
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67 return environment_variables |
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68 |
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69 def parse_edam_operations(self): |
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70 return [] |
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71 |
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72 def parse_edam_topics(self): |
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73 return [] |
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74 |
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75 def parse_help(self): |
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76 return self.tool_proxy.doc() |
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77 |
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78 def parse_sanitize(self): |
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79 return False |
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80 |
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81 def parse_strict_shell(self): |
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82 return True |
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83 |
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84 def parse_stdio(self): |
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85 # TODO: remove duplication with YAML |
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86 # New format - starting out just using exit code. |
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87 exit_code_lower = ToolStdioExitCode() |
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88 exit_code_lower.range_start = float("-inf") |
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89 exit_code_lower.range_end = -1 |
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90 exit_code_lower.error_level = StdioErrorLevel.FATAL |
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91 exit_code_high = ToolStdioExitCode() |
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92 exit_code_high.range_start = 1 |
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93 exit_code_high.range_end = float("inf") |
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94 exit_code_lower.error_level = StdioErrorLevel.FATAL |
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95 return [exit_code_lower, exit_code_high], [] |
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96 |
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97 def parse_interpreter(self): |
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98 return None |
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99 |
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100 def parse_version(self): |
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101 return "0.0.1" |
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102 |
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103 def parse_description(self): |
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104 return self.tool_proxy.description() |
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105 |
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106 def parse_interactivetool(self): |
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107 return [] |
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108 |
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109 def parse_input_pages(self): |
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110 page_source = CwlPageSource(self.tool_proxy) |
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111 return PagesSource([page_source]) |
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112 |
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113 def parse_outputs(self, tool): |
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114 output_instances = self.tool_proxy.output_instances() |
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115 outputs = {} |
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116 output_defs = [] |
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117 for output_instance in output_instances: |
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118 output_defs.append(self._parse_output(tool, output_instance)) |
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119 # TODO: parse outputs collections |
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120 for output_def in output_defs: |
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121 outputs[output_def.name] = output_def |
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122 return outputs, {} |
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123 |
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124 def _parse_output(self, tool, output_instance): |
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125 name = output_instance.name |
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126 # TODO: handle filters, actions, change_format |
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127 output = ToolOutput(name) |
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128 if "File" in output_instance.output_data_type: |
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129 output.format = "_sniff_" |
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130 else: |
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131 output.format = "expression.json" |
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132 output.change_format = [] |
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133 output.format_source = None |
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134 output.metadata_source = "" |
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135 output.parent = None |
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136 output.label = None |
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137 output.count = None |
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138 output.filters = [] |
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139 output.tool = tool |
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140 output.hidden = "" |
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141 output.dataset_collector_descriptions = [] |
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142 output.actions = ToolOutputActionGroup(output, None) |
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143 return output |
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144 |
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145 def parse_requirements_and_containers(self): |
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146 containers = [] |
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147 docker_identifier = self.tool_proxy.docker_identifier() |
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148 if docker_identifier: |
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149 containers.append({"type": "docker", |
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150 "identifier": docker_identifier}) |
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151 |
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152 software_requirements = self.tool_proxy.software_requirements() |
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153 return requirements.parse_requirements_from_dict(dict( |
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154 requirements=list(map(lambda r: {"name": r[0], "version": r[1], "type": "package"}, software_requirements)), |
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155 containers=containers, |
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156 )) |
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157 |
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158 def parse_profile(self): |
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159 return "16.04" |
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160 |
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161 def parse_license(self): |
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162 return None |
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163 |
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164 def parse_python_template_version(self): |
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165 return '3.5' |
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166 |
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167 |
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168 class CwlPageSource(PageSource): |
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169 |
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170 def __init__(self, tool_proxy): |
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171 cwl_instances = tool_proxy.input_instances() |
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172 self._input_list = list(map(self._to_input_source, cwl_instances)) |
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173 |
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174 def _to_input_source(self, input_instance): |
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175 as_dict = input_instance.to_dict() |
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176 return YamlInputSource(as_dict) |
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177 |
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178 def parse_input_sources(self): |
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179 return self._input_list |