Mercurial > repos > lain > ms_to_peakforest_it

annotate server.py @ 0:b58b229c4cbf draft

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planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty
author lain
date Fri, 03 Mar 2023 14:10:24 +0000
parents
children 7e3085fc60c1
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0
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1 #!/usr/bin/env python3
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2
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3 import atexit
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4 import csv
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5 import http.server
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6 import json
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7 import logging
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8 import os
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9 import re
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10 import shutil
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11 import socketserver
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12 import sys
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13 import tempfile
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14 import yaml
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15
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16 TAB_LIST_PLACEHOLDER = "TAB_LIST_PLACEHOLDER"
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17 MS_PEAK_VALUES_PLACEHOLDER = "MS_PEAK_VALUES_PLACEHOLDER"
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18 COMPOUND_NAME_PLACEHOLDER = "COMPOUND_NAME_PLACEHOLDER"
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19 TAB_INDEX_PLACEHOLDER = "TAB_INDEX_PLACEHOLDER"
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20 EMBED_JS_PLACEHOLDER = "EMBED_JS"
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21 ACTIVE_TAB_PLACEHOLDER = "ACTIVE_TAB_PLACEHOLDER"
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22 ADD_SPECTRUM_FORM = "ADD_SPECTRUM_FORM"
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23 PRODUCE_JSON_PLACEHOLDER = "PRODUCE_JSON_PLACEHOLDER"
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24
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25 COMPOUND_REF = "compound-ref"
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26 COMPOUND_MIX = "compound-mix"
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27
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28 END_MS_PEAK_VALUES_PLACEHOLDER = " ]"
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29 MS_DATA_COLUMN_NUMBER = 9
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30 DEFAULT_MS_PEAK_VALUES = (
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31 "[\n"
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32 + (" [" + ','.join([' ""'] * MS_DATA_COLUMN_NUMBER) + "],\n") * 17
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33 + END_MS_PEAK_VALUES_PLACEHOLDER
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34 )
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35
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36 FRAGNOT_HEADER = {
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37 "m/z": "fragment_mz",
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38 "absolute_intensity": "abs_intensity",
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39 "relative_intensity": "rel_intensity",
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40 "theo_mass": "",
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41 "delta_ppm": "ppm",
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42 "rdbequiv": "",
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43 "composition": "",
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44 "attribution": "fragment",
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45 }
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46
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47 MS_2_SNOOP_HEADER = {
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48 "name": str,
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49 "inchikey": str,
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50 "composition": str,
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51 "fragment": str,
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52 "fragment_mz": str,
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53 "ppm": str,
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54 "fileid": str,
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55 "correlation": str,
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56 "abs_intensity": lambda x:float(x) * 100,
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57 "rel_intensity": lambda x:float(x) * 100,
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58 "valid_corelation": str
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59 }
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60
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61
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62 class ConfigException(ValueError):
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63 """
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64 An exception raised when something went wrong in the config and we
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65 cannot continue - i.e: when there's no token for peakforest
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66 """
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67
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68 class YAMLConfig(dict):
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69
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70 """
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71 Dictionary that handles key with dot in them:
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72 test["truc.chose"]
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73 is equivalant to
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74 test["truc"]["chose"]
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75 Assignation works too.
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76 Add the possibility to use placeholders:
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77 --- yaml
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78 test: {{ truc.chose }}
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79 truc:
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80 chose: bidule
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81 ---
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82 here, test's value is "bidule"
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83 """
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84
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85 def __init__(self, *args, **kwargs):
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86 meta_conf = kwargs.pop("__meta_config__", {})
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87 self._debug = meta_conf.get("__debug__", False)
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88 self._stream_name = meta_conf.get("__debug_stream__", "stdout")
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89 self._debug_stream = getattr(sys, self._stream_name)
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90 self._only_root_debug = meta_conf.get("__only_root_debug__", False)
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91 if "__root__" in kwargs:
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92 if self._only_root_debug:
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93 self._debug = False
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94 self._name = kwargs.pop("__name__")
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95 self._debugger("Is not root config.")
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96 self._root = kwargs.pop("__root__")
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97 else:
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98 self._name = "root"
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99 self._debugger("Is root config.")
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100 self._root = self
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101 super().__init__(*args, **kwargs)
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102 for key, value in self.copy().items():
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103 if isinstance(value, dict) and not isinstance(value, YAMLConfig):
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104 self._debugger(f"Parsing sub-config for {key}")
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105 self[key] = self._propagate(value, key)
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106 self._replace_placeholders(self)
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107 self._extract_defaults()
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108
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109 def _propagate(self, sub_dict, name):
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110 if isinstance(sub_dict, dict) and not isinstance(sub_dict, self.__class__):
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111 return YAMLConfig(
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112 **sub_dict,
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113 __name__=name,
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114 __root__=self._root,
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115 __meta_config__={
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116 "__debug__": self._debug,
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117 "__debug_stream__": self._stream_name,
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118 "__only_root_debug__": self._only_root_debug,
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119 }
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120 )
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121 return sub_dict
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122
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123 def _debugger(self, message):
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124 if self._debug:
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125 self._debug_stream.write(f"[{self._name}]: {message}\n")
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126 self._debug_stream.flush()
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127
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128 def __getattr__(self, attr):
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129 if attr in self:
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130 return self[attr]
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131 if '.' in attr:
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132 attr, sub = attr.split('.', 1)
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133 return getattr(getattr(self, attr), sub)
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134 return super().__getattribute__(attr)
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135
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136 def _replace_placeholders(self, subpart):
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137 self._debugger("Replacing placeholders...")
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138 for sub_key, sub_item in subpart.copy().items():
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139 if isinstance(sub_item, str):
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140 for placeholder in re.findall("{{ (?P<placeholder>.*?) }}", sub_item):
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141 if placeholder not in self._root:
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142 self._debugger(f"Could not fine replacement for {placeholder}")
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143 continue
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144 replacement = self._root[placeholder]
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145 if isinstance(replacement, str):
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146 self._debugger(f"Found placeholder: {placeholder} -> {replacement}")
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147 sub_item = sub_item.replace(
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148 "{{ " + placeholder + " }}",
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149 replacement
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150 )
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151 else:
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152 self._debugger(f"Found placeholder: {placeholder} -> {replacement.__class__.__name__}")
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153 sub_item = self._propagate(replacement, placeholder)
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154 dict.__setitem__(subpart, sub_key, sub_item)
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155 elif isinstance(sub_item, dict):
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156 super().__setitem__(sub_key, self._propagate(sub_item, sub_key))
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157
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158 def _extract_defaults(self):
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159 if self._root is not self:
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160 return
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161 if "defaults" not in self:
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162 self._debugger("No defaults here.")
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163 return
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164 if "arguments" not in self:
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165 self._debugger("Arguments creation...")
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166 self["arguments"] = self._propagate({}, "arguments")
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167 self._debugger("Populating arguments with defaults values")
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168 for key, value in self.defaults.items():
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169 if key not in self:
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170 if isinstance(value, dict):
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171 value = self._propagate(value, key)
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172 self.arguments[key] = value
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173 self._debugger(f"Default {key} = {value}")
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174
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175 def __setitem__(self, key, value):
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176 if isinstance(value, dict):
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177 value = self._propagate(value, key)
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178 if "." not in key:
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179 return super().__setitem__(key, value)
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180 curent = self
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181 key, subkey = key.rsplit(".", 1)
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182 self[key][subkey] = value
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183
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184 def __getitem__(self, key):
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185 if super().__contains__(key):
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186 return super().__getitem__(key)
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187 if "." not in key:
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188 return super().__getitem__(key)
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189 curent = self
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190 while "." in key:
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191 key, subkey = key.split(".", 1)
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192 curent = curent[key]
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193 key = subkey
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194 if subkey not in curent:
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195 curent[subkey] = self._propagate({}, subkey)
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196 result = curent[subkey]
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197 return result
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198
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199 def __contains__(self, key):
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200 if "." not in key:
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201 return super().__contains__(key)
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202 key, subkey = key.split(".", 1)
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203 if not super().__contains__(key):
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204 return False
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205 return subkey in self[key]
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206
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207 def copy(self):
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208 return {
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209 key: (
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210 value if not isinstance(value, dict)
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211 else value.copy()
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212 ) for key, value in self.items()
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213 }
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214
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215 class YAMLParameters(YAMLConfig):
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216
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217 """
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218 Parses parameters from the command line and put them
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219 in the config.
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220 Uses the config to know which parameter is recognized, or not,
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221 to know the metadata (author, version),
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222 which command is a flag, is optional, the help strings, etc...
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223 Assigns default small parameter if not defined in the "shortcut"
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224 section of the config file.
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225 CLI config must be in the root section "parameters":
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226 ---
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227 parameters:
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228 mandatory:
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229 input: input file path
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230 flags:
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231 help: Show this help
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232 optional:
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233 method: "default is {{ defaults.method }}"
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234 meta:
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235 author: Lain Pavot
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236 version: 1.1.0
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237 shortcuts:
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238 help: h
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239 ## will autogenerate -i for input and -m for method
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240 ---
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241 default parameters are searched in the "default" root section.
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242 """
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243
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244 def __init__(self, *args, **kwargs):
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245 super().__init__(*args, **kwargs)
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246 self._errors = list()
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247 if not self.parameters.shortcuts:
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248 self.parameters["shortcuts"] = YAMLConfig()
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249 self._mandatory = self.parameters.mandatory
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250 self._optional = self.parameters.optional
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251 self._flags = {
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252 flag: False
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253 for flag in self.parameters.flags
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254 }
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255 self._all_params = self._optional.copy()
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256 self._all_params.update(self._mandatory)
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257 self._all_params.update(self._flags)
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258 self._small_params = dict()
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259 self._determine_small_params()
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260
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261 @property
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262 def in_error(self):
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263 return bool(self._errors)
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264
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265 @property
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266 def sorted_keys(self):
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267 return sorted(self._all_params.keys())
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268
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269 @property
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270 def sorted_items(self):
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271 return sorted(self._all_params.items())
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272
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273 def _determine_small_params(self, verbose=False):
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274 self._small_params = (self.parameters.shortcuts or {}).copy()
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275 chars = list(map(chr, range(97, 123))) + list(map(chr, range(65, 91)))
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276 all_params = self._all_params.copy()
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277 for long, short in self._small_params.items():
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278 chars.remove(short)
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279 del all_params[long]
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280 for param in all_params.copy().keys():
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281 for operation in (
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282 lambda x:x[0], ## select first char
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283 lambda x:x.split('-', 1)[-1][0], ## first char after -
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284 lambda x:x.split('_', 1)[-1][0], ## first char after _
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285 lambda x:x.split('.', 1)[-1][0], ## first char after .
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286 lambda x:x[0].upper(), ## select first char
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287 lambda x:x.split('-', 1)[-1][0].upper(), ## first char after -
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288 lambda x:x.split('_', 1)[-1][0].upper(), ## first char after _
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289 lambda x:x.split('.', 1)[-1][0].upper(), ## first char after .
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290 lambda x: chars[0], ## first letter in the alphabet
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291 ):
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292 char = operation(param)
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293 if char not in self._small_params.values():
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294 self._small_params[param] = char
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295 chars.remove(char)
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296 del all_params[param]
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297 break
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298
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299 def _get_parameter_index(self, parameter, original):
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300 if f"--{parameter}" in sys.argv:
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301 return sys.argv.index(f"--{parameter}")
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302 parameter = self._small_params[original]
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303 if f"-{parameter}" in sys.argv:
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304 return sys.argv.index(f"-{parameter}")
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305 return None
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306
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307 def as_parameter(self, string):
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308 return (
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309 string
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310 .replace('.', '-')
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311 .replace('_', '-')
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312 )
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313
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314 def show_version(self):
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315 print(self.parameters.meta.version)
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316
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317 def show_help(self):
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318 parameters = [
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319 f"-{self._small_params[arg]}|--{self.as_parameter(arg)} {arg}"
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320 for arg in self._mandatory
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321 ] + [
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322 f"[-{self._small_params[arg]}|--{self.as_parameter(arg)} {arg}]"
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323 for arg in self._optional
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324 ] + [
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325 f"[-{self._small_params[arg]}|--{self.as_parameter(arg)}]"
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326 for arg in self._flags
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327 ]
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328 print(
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329 f"Usage: {__file__} " + ' '.join(parameters)
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330 + "\n\n"
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331 + '\n'.join(
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332 f" -{self._small_params[args]}|--{self.as_parameter(args)}: {help_str}"
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333 for args, help_str in self.sorted_items
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334 )
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335 + "\n\n"
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336 + '\n'.join(
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337 f"{key}: {value}"
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338 for key, value in self.parameters.meta.items()
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339 )
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340 )
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341 sys.exit(0)
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342
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343 def parse_args(self):
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344 errors = list()
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345 for kind in ("mandatory", "optional", "flags"):
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346 keys = list(sorted(getattr(self, f"_{kind}").keys()))
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347 for original_param, actual_param in zip(
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348 keys,
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349 map(self.as_parameter, keys),
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350 ):
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351 if original_param in self.defaults:
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352 self.arguments[original_param] = self.defaults[original_param]
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353 elif kind == "flags":
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354 self.arguments[original_param] = False
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355 parser = getattr(self, f"parse_{kind}")
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356 if (error := parser(original_param, actual_param)):
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357 errors.append(error)
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358 self._errors = errors
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359 return self
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360
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361 def parse_mandatory(self, original, actual):
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362 if (index := self._get_parameter_index(actual, original)) is None:
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363 return f"The parameter --{actual} is mandatory."
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364 if index == len(sys.argv) - 1:
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365 return f"The parameter --{actual} needs a value."
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366 self.arguments[original] = sys.argv[index + 1]
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367
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368 def parse_optional(self, original, actual):
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369 if (index := self._get_parameter_index(actual, original)) is None:
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370 return
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371 if index == len(sys.argv) - 1:
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372 return f"The parameter --{actual} needs a value."
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373 self.arguments[original] = sys.argv[index + 1]
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374
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375 def parse_flags(self, original, actual):
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376 if (index := self._get_parameter_index(actual, original)) is None:
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377 return
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378 self.arguments[original] = True
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379
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380 def parse_config(**kwargs):
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381 """
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382 opens the config file, extract it using pyyaml's safe loader
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383 and tries to extract and apply a maximum of informations/directives
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384 from the config:
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385 - token retrieval
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386 - workdir management
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387 - tempfile management
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388 """
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389 root_dir = os.path.dirname(os.path.abspath(__file__))
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390 with open(os.path.join(root_dir, "config.yml")) as config_file:
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391 config = YAMLConfig(
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392 **yaml.load(config_file.read(), Loader=yaml.SafeLoader),
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393 **kwargs
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394 )
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395
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396 if not config.token.value:
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397 if config.token.use_file:
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398 if (not os.path.exists(path := config.token.file_path)):
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399 raise ConfigException("Missing token value or token file.")
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400 with open(path) as token_file:
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401 config.token["value"] = token_file.read()
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402 elif config.defaults.peakforest.token:
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403 config.token["value"] = config.defaults.peakforest.token
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404
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405 if config.workdir.create_tmp:
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406 tmp_dir = tempfile.mkdtemp()
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407 atexit.register(lambda:shutil.rmtree(tmp_dir))
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408 else:
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409 tmp_dir = tempfile.gettempdir()
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410 config.workdir["tmp_dir"] = tmp_dir
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411
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412 config["root_dir"] = root_dir
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413 config["tab_list"] = []
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414 config["form_template"] = os.path.join(root_dir, config.templates.form)
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415 config["meta_template"] = os.path.join(root_dir, config.templates.main)
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416 config["js_template"] = os.path.join(root_dir, config.templates.js)
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417 config["tab_list_template"] = os.path.join(root_dir, config.templates.tab_list)
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418 config["placeholders"] = dict()
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419 config.placeholders[MS_PEAK_VALUES_PLACEHOLDER] = DEFAULT_MS_PEAK_VALUES
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420 config.placeholders[TAB_INDEX_PLACEHOLDER] = "1"
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421 config.placeholders[ACTIVE_TAB_PLACEHOLDER] = "active"
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422 config.placeholders[ADD_SPECTRUM_FORM] = ""
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423 config.placeholders[EMBED_JS_PLACEHOLDER] = ""
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424 config.placeholders[TAB_LIST_PLACEHOLDER] = ""
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425 config.placeholders["DEFAULT_MIN_MZ"] = "50"
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426 config.placeholders["DEFAULT_MAX_MZ"] = "500"
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427 config.placeholders["DEFAULT_RESOLUTION_LOW"] = ""
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428 config.placeholders["DEFAULT_RESOLUTION_HIGH"] = "selected=\"selected\""
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429 config.placeholders["DEFAULT_RESOLUTION_UNSET"] = ""
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430 config.placeholders["DEFAULT_MIN_RT"] = "0.9"
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431 config.placeholders["DEFAULT_MAX_RT"] = "1.4"
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432 return config
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433
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434 def parse_parameters(config):
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435 """
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436 parses command line and checks provided values are acceptable/usable.
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437 Raises some error if not.
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438 """
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439 parameters = YAMLParameters(**config)
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440 parameters.parse_args()
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441
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442 parameters["json_result"] = []
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443
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444 get_logger(parameters)
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445
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446 arguments = parameters.arguments
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447 if arguments.help:
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448 parameters.show_help()
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449 sys.exit(0)
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450
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451 if arguments.version:
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452 parameters.show_version()
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453 sys.exit(0)
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454
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455 if parameters.in_error:
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456 raise ValueError(
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457 "Some errors occured during parameters extraction: \n"
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458 + '\n'.join(parameters.errors)
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459 )
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460
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461 if arguments.sample_type == COMPOUND_MIX:
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462 parameters["form_template"] = os.path.join(
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463 parameters["root_dir"],
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464 parameters.templates.form_mix
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465 )
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466 parameters["meta_template"] = os.path.join(
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467 parameters["root_dir"],
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468 parameters.templates.main_mix
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469 )
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470 elif arguments.sample_type == COMPOUND_REF:
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471 parameters["form_template"] = os.path.join(
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472 parameters["root_dir"],
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473 parameters.templates.form_ref
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474 )
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475 parameters["meta_template"] = os.path.join(
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476 parameters["root_dir"],
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477 parameters.templates.main_ref
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478 )
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479
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480 arguments["produce_json"] = (
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481 "output_json" in arguments
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482 and arguments["output_json"] != ""
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483 )
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484 if arguments.produce_json:
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485 parameters.placeholders[PRODUCE_JSON_PLACEHOLDER] = "true"
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486 parameters.json_result = []
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487 arguments["output_json"] = os.path.abspath(arguments["output_json"])
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488 atexit.register(save_json, parameters)
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489 else:
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490 parameters.placeholders[PRODUCE_JSON_PLACEHOLDER] = "false"
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491
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492 if arguments.run_dry_html:
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493 arguments["do_run_dry"] = True
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494 parameters.generated["html"] = os.path.abspath(arguments.run_dry_html)
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495
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496 if arguments.run_dry_js:
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497 arguments["do_run_dry"] = True
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498 parameters.generated["js"] = os.path.abspath(arguments.run_dry_js)
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499
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500 if arguments.do_run_dry:
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501 parameters.logger.info("Dry run. Server will ne be run.")
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502 if arguments.run_dry_html:
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503 parameters.logger.info(f"HTML file will be put in {arguments.run_dry_html}")
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504 if arguments.run_dry_js:
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505 parameters.logger.info(f"JS file will be put in {arguments.run_dry_js}")
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506
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507 if arguments.peakforest.token:
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508 config.token["value"] = arguments.peakforest.token
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509 if not config.token.value:
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510 raise ConfigException(
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511 "No token provided. We will not be able to connect to peakforest."
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512 )
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513
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514 if os.path.exists(arguments.input):
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515 single_file = True
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516 file_paths = [arguments.input]
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517 else:
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518 path_list = arguments.input.split(',')
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519 if all(map(os.path.exists, path_list)):
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520 single_file = False
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521 file_paths = path_list
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522 else:
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diff changeset
523 raise ValueError(
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parents:
diff changeset
524 f"Some files cannot be found: "
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parents:
diff changeset
525 + ', '.join(
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parents:
diff changeset
526 path for path in path_list
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diff changeset
527 if not os.path.exists(path)
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parents:
diff changeset
528 )
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parents:
diff changeset
529 )
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diff changeset
530 arguments["input"] = list(map(os.path.abspath, file_paths))
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parents:
diff changeset
531
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diff changeset
532 if single_file:
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parents:
diff changeset
533 arguments["name"] = [arguments.name]
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parents:
diff changeset
534 arguments["raw_metadata"] = [arguments.raw_metadata]
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parents:
diff changeset
535 parameters.logger.info(f"Single file processing: {arguments.input}")
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parents:
diff changeset
536 else:
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parents:
diff changeset
537 parameters.logger.info(f"Multiple file processing:")
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parents:
diff changeset
538 arguments["raw_metadata"] = arguments.raw_metadata.split(
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parents:
diff changeset
539 arguments.raw_metadata_sep
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parents:
diff changeset
540 )
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parents:
diff changeset
541 if not arguments.name:
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diff changeset
542 arguments["name"] = arguments["raw_metadata"]
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diff changeset
543 else:
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parents:
diff changeset
544 arguments["name"] = arguments.name.split(',')
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diff changeset
545 for i in range(len(arguments.name)):
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parents:
diff changeset
546 parameters.logger.info(f" - file: {arguments.input[i]}")
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parents:
diff changeset
547 parameters.logger.info(f" - name: {arguments.name[i]}")
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parents:
diff changeset
548 parameters.logger.info(f" - metadata: {arguments.raw_metadata[i]}")
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parents:
diff changeset
549 parameters.logger.info(f" ")
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parents:
diff changeset
550 if (
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551 len(arguments.name) != len(arguments.raw_metadata)
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parents:
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552 or len(arguments.name) != len(arguments.input)
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parents:
diff changeset
553 ):
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parents:
diff changeset
554 raise ValueError(
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parents:
diff changeset
555 "name, raw_metadata and input parameters have different lengths: \n"
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parents:
diff changeset
556 f"input is {len(arguments.input)} elements long, "
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parents:
diff changeset
557 f"raw_metadata is {len(arguments.raw_metadata)} elements long "
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parents:
diff changeset
558 f"and name is {len(arguments.name)} elements long."
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parents:
diff changeset
559 )
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parents:
diff changeset
560 if arguments.spectrum_type == "LC_MS":
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parents:
diff changeset
561 arguments["scan_type"] = "ms"
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parents:
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562 elif arguments.spectrum_type == "LC_MSMS":
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parents:
diff changeset
563 arguments["scan_type"] = "ms2"
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parents:
diff changeset
564 if arguments.method == "test":
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parents:
diff changeset
565 if arguments.spectrum_type == "LC_MS":
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parents:
diff changeset
566 arguments["method"] = "cf_pfem_urine_qtof"
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parents:
diff changeset
567 else:
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parents:
diff changeset
568 arguments["method"] = "cf_pfem_urine_method1_qtof-msms"
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parents:
diff changeset
569 if arguments["sample_type"] == COMPOUND_MIX:
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parents:
diff changeset
570 check_mix_compound_files(parameters)
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parents:
diff changeset
571 more_info_in_logs(parameters)
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parents:
diff changeset
572 return parameters
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parents:
diff changeset
573
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parents:
diff changeset
574 def check_mix_compound_files(parameters):
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parents:
diff changeset
575 arguments = parameters.arguments
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parents:
diff changeset
576 try:
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parents:
diff changeset
577 numbarz = [
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diff changeset
578 list(map(int, os.path.basename(metadata).split("_", 1)[0].split("-")))
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parents:
diff changeset
579 for metadata in arguments.raw_metadata
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parents:
diff changeset
580 ]
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parents:
diff changeset
581 except ValueError:
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parents:
diff changeset
582 parameters.logger.error(
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parents:
diff changeset
583 "Metadata/file names does not start with `[0-9]+-[0-9]+_.*` . "
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parents:
diff changeset
584 "This is necessary in the case of compounds mix."
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parents:
diff changeset
585 )
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parents:
diff changeset
586 sys.exit(-1)
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parents:
diff changeset
587 runs, samples = zip(*numbarz)
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diff changeset
588 if not all(runs[0] == i for i in runs[1:]):
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parents:
diff changeset
589 parameters.logger.error(
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parents:
diff changeset
590 "Run numbers in metadata/file names are not identical. "
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty
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parents:
diff changeset
591 "You mixed some files."
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parents:
diff changeset
592 )
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parents:
diff changeset
593 sys.exit(-1)
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parents:
diff changeset
594 length = len(samples)
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diff changeset
595 if list(sorted(samples)) != list(range(1, length+1)):
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parents:
diff changeset
596 if not all(samples.count(i) == 1 for i in samples):
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parents:
diff changeset
597 parameters.logger.error("Some samples are duplicated. ")
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parents:
diff changeset
598 else:
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diff changeset
599 parameters.logger.error("Some samples files are missing. ")
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parents:
diff changeset
600 sys.exit(-1)
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parents:
diff changeset
601
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parents:
diff changeset
602 def more_info_in_logs(config):
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diff changeset
603 arguments = config.arguments
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diff changeset
604 if arguments.embed_js:
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parents:
diff changeset
605 config.logger.info(f"JS will be embed in HTML page to form a HTML bundle.")
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parents:
diff changeset
606 else:
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diff changeset
607 config.logger.info(f"JS are separated files, needed to be served.")
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parents:
diff changeset
608 config.logger.info(f"Choosen parameters:")
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parents:
diff changeset
609 config.logger.info(f" - method: {arguments.method}")
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parents:
diff changeset
610 config.logger.info(f" - peakforest instance: {arguments.peakforest.url}")
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parents:
diff changeset
611 config.logger.info(f" - polarity instance: {arguments.polarity}")
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diff changeset
612 config.logger.info(f" - spectrum type: {arguments.spectrum_type}")
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parents:
diff changeset
613 config.logger.info(f" - scan type: {arguments.scan_type}")
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parents:
diff changeset
614 config.logger.info(f" - produce JSON: {arguments.produce_json}")
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parents:
diff changeset
615 config.logger.info(f" - sample type: {arguments.sample_type}")
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parents:
diff changeset
616
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617 def process_all_files(config):
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618 """
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diff changeset
619 for each file and its metadata, read and process them,
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diff changeset
620 then fills the meta html template file with the whole result.
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parents:
diff changeset
621 """
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diff changeset
622 arguments = config.arguments
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diff changeset
623 extra_defaults = [
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diff changeset
624 process_fragnot_metadata(metadata, config)
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parents:
diff changeset
625 for metadata in arguments.raw_metadata
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parents:
diff changeset
626 ]
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parents:
diff changeset
627 for i, name in enumerate(arguments.name):
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parents:
diff changeset
628 extra_defaults[i]["name"] = name
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diff changeset
629
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diff changeset
630 if not extra_defaults:
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diff changeset
631 extra_defaults = [{}] * len(arguments.input)
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parents:
diff changeset
632
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diff changeset
633 index = 0
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diff changeset
634 for input_path, extra_default in zip(arguments.input, extra_defaults):
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635 config.logger.info(f"Processing file at {input_path}...")
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parents:
diff changeset
636 curent_defaults = arguments.copy()
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diff changeset
637 curent_defaults.update(extra_default)
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diff changeset
638 if config.arguments.verbose:
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parents:
diff changeset
639 config.logger.info(
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parents:
diff changeset
640 "[VERBOSE] Defaults for curent file: "
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parents:
diff changeset
641 + ';'.join(f"{key}={value}" for key, value in curent_defaults.items())
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parents:
diff changeset
642 )
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parents:
diff changeset
643 tsv_content, tsv_data_extractor = read_input(input_path, config)
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parents:
diff changeset
644 index = process_tsv(
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parents:
diff changeset
645 tsv_content,
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646 tsv_data_extractor,
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diff changeset
647 config,
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diff changeset
648 defaults_data = curent_defaults,
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diff changeset
649 index = index+1,
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diff changeset
650 )
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651 if arguments.embed_js:
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diff changeset
652 config.logger.info(f"Embeding JS in HTML file... ")
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diff changeset
653 for index in range(len(config.tab_list)):
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diff changeset
654 config.placeholders[EMBED_JS_PLACEHOLDER] += "<script type='text/javascript'>"
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diff changeset
655 with open(f"add-one-spectrum-{index+1}.js") as js_file:
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diff changeset
656 config.placeholders[EMBED_JS_PLACEHOLDER] += js_file.read()
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diff changeset
657 config.placeholders[EMBED_JS_PLACEHOLDER] += "</script>"
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diff changeset
658 config.placeholders[EMBED_JS_PLACEHOLDER] += "\n"
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diff changeset
659 config.logger.info(f" - add-one-spectrum-{index+1}.js embed.")
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diff changeset
660 config.placeholders[TAB_LIST_PLACEHOLDER] = "\n".join(config.tab_list)
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diff changeset
661 else:
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diff changeset
662 config.placeholders[EMBED_JS_PLACEHOLDER] += "<script type='text/javascript'>"
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diff changeset
663 config.placeholders[EMBED_JS_PLACEHOLDER] += "</script>"
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diff changeset
664 config.placeholders[EMBED_JS_PLACEHOLDER] += "\n".join(
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diff changeset
665 [""] + [
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diff changeset
666 " "*12 + f"<script src=\"./add-one-spectrum-{index+1}.js\"></script>"
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diff changeset
667 for index in range(len(config.tab_list))
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diff changeset
668 ]
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diff changeset
669 )
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diff changeset
670 config.placeholders[EMBED_JS_PLACEHOLDER] += "\n"
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diff changeset
671 config.placeholders[TAB_LIST_PLACEHOLDER] = "\n".join(config.tab_list)
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diff changeset
672
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673 fill_template("meta_template", "pf_path", config)
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diff changeset
674
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diff changeset
675 def fill_template(
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676 template_name,
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diff changeset
677 output_name,
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diff changeset
678 config,
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diff changeset
679 additional_placeholders=dict()
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680 ):
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681 """
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parents:
diff changeset
682 Fills a template, replaces the placeholders.
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diff changeset
683 Either outputs the result in a given file, or returns it if path is none.
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diff changeset
684 """
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diff changeset
685 template_path = config[template_name]
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diff changeset
686 config.logger.debug(f"Filling template {template_name} at {template_path}...")
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687 with open(template_path) as template_file:
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diff changeset
688 template_content = template_file.read()
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diff changeset
689 placeholders = config.placeholders.copy()
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diff changeset
690 placeholders.update(additional_placeholders)
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diff changeset
691 for placeholder, replacement in placeholders.items():
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diff changeset
692 if not placeholder.startswith(config.templates.placeholders.start):
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diff changeset
693 placeholder = placeholder.join((
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diff changeset
694 config.templates.placeholders.start,
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diff changeset
695 config.templates.placeholders.stop
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diff changeset
696 ))
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diff changeset
697 template_content = template_content.replace(placeholder, replacement)
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diff changeset
698 if output_name is None:
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diff changeset
699 config.logger.debug(f"Returning template content")
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700 return template_content
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701 output_path = config[output_name]
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diff changeset
702 if "{{ index }}" in output_path:
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diff changeset
703 index_value = additional_placeholders["{{ index }}"]
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diff changeset
704 config.logger.debug(f"Changing index value for {index_value}")
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diff changeset
705 output_path = output_path.replace("{{ index }}", index_value)
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diff changeset
706 config.logger.debug(f"Full output path {output_path}")
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diff changeset
707 with open(output_path, "w") as output_file:
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diff changeset
708 output_file.write(template_content)
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parents:
diff changeset
709
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diff changeset
710 def read_input(input_path, config):
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711 """
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diff changeset
712 reads a tsv file and determin its processor, based on its header.
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diff changeset
713 """
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diff changeset
714 with open(input_path) as input_file:
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diff changeset
715 config.logger.info(f"Reading {input_path}...")
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diff changeset
716 tsv_file = csv.reader(input_file, delimiter='\t')
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diff changeset
717 header = next(tsv_file)
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diff changeset
718 tsv_file = list(tsv_file)
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diff changeset
719 config.logger.info(f"Header is: {', '.join(header)}")
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parents:
diff changeset
720 if header == list(FRAGNOT_HEADER):
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parents:
diff changeset
721 config.logger.info(f"Fragnot recognized.")
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diff changeset
722 processor = fragnot_extractor
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diff changeset
723 return uniformize_fragnot(tsv_file, header), processor
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diff changeset
724 else:
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diff changeset
725 config.logger.info(f"MS2Snoop recognized.")
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diff changeset
726 processor = ms2snoop_extractor
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diff changeset
727 return uniformize_ms2snoop(tsv_file, header), processor
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parents:
diff changeset
728
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diff changeset
729 def uniformize_fragnot(content, header):
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parents:
diff changeset
730 """
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parents:
diff changeset
731 sorts fragnot data so they appear always in the same order
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diff changeset
732 """
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diff changeset
733 return sorted(content, key=lambda x:(float(x[0]), float(x[4])))
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parents:
diff changeset
734
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diff changeset
735 def uniformize_ms2snoop(content, header):
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parents:
diff changeset
736 """
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parents:
diff changeset
737 sorts ms2snoop data so they appear always in the same order
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parents:
diff changeset
738 """
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diff changeset
739 return sorted(content, key=lambda x:(x[0], float(x[4])))
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parents:
diff changeset
740
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diff changeset
741 def process_fragnot_metadata(raw_metadata, config):
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parents:
diff changeset
742 """
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parents:
diff changeset
743 Tries to extract informations from the metadata provided by fragnot
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diff changeset
744 files names.
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diff changeset
745 Heavily based on regex defined in conf file.
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parents:
diff changeset
746 """
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diff changeset
747 regex = config.regex.copy()
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diff changeset
748 del regex["values"]
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diff changeset
749 result = {}
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diff changeset
750 config.logger.info(f"Extracting info from {raw_metadata}...")
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diff changeset
751 count = 0
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parents:
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752 for name, expression in regex.items():
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parents:
diff changeset
753 if (match := re.search(expression, raw_metadata)):
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parents:
diff changeset
754 result[name] = match[name]
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parents:
diff changeset
755 count += 1
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parents:
diff changeset
756 did = "+ did"
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diff changeset
757 else:
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parents:
diff changeset
758 did = "- did not"
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parents:
diff changeset
759 if config.arguments.verbose:
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parents:
diff changeset
760 config.logger.info(f" {did} match {expression}")
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parents:
diff changeset
761 config.logger.info(f"{count} useful informations extracted.")
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parents:
diff changeset
762 return result
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parents:
diff changeset
763
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parents:
diff changeset
764 def process_tsv(
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parents:
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765 tsv_content,
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parents:
diff changeset
766 tsv_data_extractor,
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parents:
diff changeset
767 config,
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parents:
diff changeset
768 defaults_data={},
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parents:
diff changeset
769 index=1
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parents:
diff changeset
770 ):
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parents:
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771 """
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parents:
diff changeset
772 processes one tsv file, containing one or multiple compounds.
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parents:
diff changeset
773 Creation of the peak table for each compound
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parents:
diff changeset
774 """
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parents:
diff changeset
775 tsv_content = list(tsv_content)
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parents:
diff changeset
776 curent_name, ms_data = get_ms_data(
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parents:
diff changeset
777 tsv_content[0],
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parents:
diff changeset
778 tsv_data_extractor,
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parents:
diff changeset
779 defaults_data,
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parents:
diff changeset
780 config
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parents:
diff changeset
781 )
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parents:
diff changeset
782 _, second_ms_data = get_ms_data(
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parents:
diff changeset
783 tsv_content[1],
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parents:
diff changeset
784 tsv_data_extractor,
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parents:
diff changeset
785 defaults_data,
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parents:
diff changeset
786 config
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diff changeset
787 )
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diff changeset
788 ms_peak_table = []
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parents:
diff changeset
789 config.logger.info(f"Processing compound {curent_name}...")
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parents:
diff changeset
790
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791 for line in tsv_content:
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diff changeset
792 name, new_ms_data = get_ms_data(line, tsv_data_extractor, defaults_data, config)
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793 if name != curent_name:
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parents:
diff changeset
794 new_compound(curent_name, index, ms_data, config, ms_peak_table)
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parents:
diff changeset
795 curent_name = name
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diff changeset
796 index += 1
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diff changeset
797 config.logger.info(f"Processing compound {curent_name}...")
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diff changeset
798 ms_peak_table = []
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diff changeset
799 ms_data = new_ms_data
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diff changeset
800 ms_peak_table.append(
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diff changeset
801 ", ".join(
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parents:
diff changeset
802 f'"{value}"' if value not in ("na", "NA")
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parents:
diff changeset
803 else '""'
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diff changeset
804 for value in (
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diff changeset
805 ms_data["fragment_mz"],
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parents:
diff changeset
806 ms_data["abs_intensity"],
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parents:
diff changeset
807 ms_data["rel_intensity"],
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parents:
diff changeset
808 ms_data["ppm"],
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parents:
diff changeset
809 ms_data["composition"],
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parents:
diff changeset
810 ms_data["fragment"],
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parents:
diff changeset
811 str(ms_data["valid_corelation"] == "TRUE").lower(),
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parents:
diff changeset
812 "true" if ms_data.get("correlation") == "1" else "false"
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parents:
diff changeset
813 )
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parents:
diff changeset
814 )
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parents:
diff changeset
815 )
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diff changeset
816 new_compound(curent_name, index, ms_data, config, ms_peak_table)
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817 return index
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diff changeset
818
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819 def get_ms_data(line, extractor, defaults, config):
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parents:
diff changeset
820 ms_data = defaults.copy()
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diff changeset
821 ms_data.update(extractor(config, *line))
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822 return ms_data["name"], ms_data
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diff changeset
823
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824 def new_compound(name, index, ms_data, config, ms_peak_table):
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825 """
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parents:
diff changeset
826 aggregates informations to form the peak table,
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parents:
diff changeset
827 adds the compound to the tab list,
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parents:
diff changeset
828 creates the js file for this tab
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parents:
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829 """
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830 if len([x for x in ms_peak_table if x.split(", ")[7] == "\"true\""]) > 1:
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parents:
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831 for i in range(len(ms_peak_table)):
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diff changeset
832 ms_peak_table[i] = ", ".join(
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diff changeset
833 ms_peak_table[i].split(", ")[:-1] + [", \"false\""]
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parents:
diff changeset
834 )
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diff changeset
835 config.placeholders[MS_PEAK_VALUES_PLACEHOLDER] = f"""[
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parents:
diff changeset
836 {','.join('['+line+']' for line in ms_peak_table)}
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parents:
diff changeset
837 ]"""
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838 tab_list = fill_template(
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839 "tab_list_template",
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diff changeset
840 None,
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diff changeset
841 config, {
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diff changeset
842 COMPOUND_NAME_PLACEHOLDER: name,
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parents:
diff changeset
843 TAB_INDEX_PLACEHOLDER: str(index),
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parents:
diff changeset
844 })
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diff changeset
845 config.tab_list.append(tab_list)
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parents:
diff changeset
846 create_js_file(index, ms_data, config)
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parents:
diff changeset
847 config.placeholders[ADD_SPECTRUM_FORM] += fill_template(
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parents:
diff changeset
848 "form_template",
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diff changeset
849 None,
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diff changeset
850 config,
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diff changeset
851 {TAB_INDEX_PLACEHOLDER: str(index)},
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parents:
diff changeset
852 )
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parents:
diff changeset
853 if index == 1:
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parents:
diff changeset
854 config.placeholders[ACTIVE_TAB_PLACEHOLDER] = ""
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parents:
diff changeset
855
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diff changeset
856 def fragnot_extractor(config, *line):
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parents:
diff changeset
857 """
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parents:
diff changeset
858 Fragnot processor - extracts one fragnot line of content and
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty
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parents:
diff changeset
859 produces a uniformised output.
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parents:
diff changeset
860 """
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parents:
diff changeset
861 fragnot_data = {
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parents:
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862 FRAGNOT_HEADER[header]: line[i].strip()
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parents:
diff changeset
863 for i, header in enumerate(FRAGNOT_HEADER)
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parents:
diff changeset
864 }
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parents:
diff changeset
865 fragnot_data["composition"] = "unknown"
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parents:
diff changeset
866 fragnot_data["valid_corelation"] = config.arguments.validation
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parents:
diff changeset
867 return fragnot_data
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parents:
diff changeset
868
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parents:
diff changeset
869 def ms2snoop_extractor(config, *line):
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parents:
diff changeset
870 """
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parents:
diff changeset
871 Fragnot processor - extracts one ms2snoop line of content and
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parents:
diff changeset
872 produces a uniformised output.
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parents:
diff changeset
873 """
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parents:
diff changeset
874 ms2snoop_data = {
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parents:
diff changeset
875 header: MS_2_SNOOP_HEADER[header](line[i])
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parents:
diff changeset
876 for i, header in enumerate(MS_2_SNOOP_HEADER)
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parents:
diff changeset
877 }
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parents:
diff changeset
878 return ms2snoop_data
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parents:
diff changeset
879
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parents:
diff changeset
880 def create_js_file(index, ms_data, config):
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parents:
diff changeset
881 """
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parents:
diff changeset
882 fills the js template file for one tab (compound)
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parents:
diff changeset
883 """
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diff changeset
884 if (method := ms_data["method"]):
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parents:
diff changeset
885 method = f'"{method}"'
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parents:
diff changeset
886 else:
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parents:
diff changeset
887 method = "null"
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parents:
diff changeset
888 if config.arguments.verbose:
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parents:
diff changeset
889 config.logger.info(
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parents:
diff changeset
890 "[VERBOSE] "
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parents:
diff changeset
891 + ';'.join(f"{key}={value}" for key, value in ms_data.items())
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parents:
diff changeset
892 )
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parents:
diff changeset
893 fill_template(
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parents:
diff changeset
894 "js_template",
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parents:
diff changeset
895 "js_file",
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parents:
diff changeset
896 config,
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parents:
diff changeset
897 {
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diff changeset
898 TAB_INDEX_PLACEHOLDER: str(index),
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parents:
diff changeset
899 "INCHIKEY_PLACEHOLDER": ms_data["inchikey"],
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parents:
diff changeset
900 "DEFAULT_DATA": f"""{{
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parents:
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901 name: "{ms_data["name"]}",
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parents:
diff changeset
902 inchikey: "{ms_data["inchikey"]}",
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parents:
diff changeset
903 method: {method},
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parents:
diff changeset
904 spectrum_type: "{ms_data["spectrum_type"]}",
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parents:
diff changeset
905 scan_type: "{ms_data["scan_type"]}",
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parents:
diff changeset
906 polarity: "{ms_data["polarity"]}",
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parents:
diff changeset
907 resolution: "{ms_data["resolution"]}",
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parents:
diff changeset
908 sample_type: "{ms_data["sample_type"]}",
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parents:
diff changeset
909 }}""",
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diff changeset
910 "{{ index }}": str(index)
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diff changeset
911 },
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parents:
diff changeset
912 )
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parents:
diff changeset
913
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diff changeset
914 def prepare_workplace(config):
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diff changeset
915 """
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parents:
diff changeset
916 prepares the directory we will work in.
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parents:
diff changeset
917 """
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diff changeset
918 if config.workdir.work_in_tmp:
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parents:
diff changeset
919 os.chdir(config.workdir.tmp_dir)
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parents:
diff changeset
920 config.logger.info(f"Moving to {os.getcwd()}")
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parents:
diff changeset
921 if config.workdir.generate_in_tmp:
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parents:
diff changeset
922 gen_dir = config.workdir.tmp_dir
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parents:
diff changeset
923 else:
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diff changeset
924 gen_dir = tempfile.gettempdir()
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parents:
diff changeset
925 config.workdir.tmp_dir = gen_dir
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parents:
diff changeset
926 shutil.copy(os.path.join(config["root_dir"], "common.js"), gen_dir)
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parents:
diff changeset
927 config.logger.info(f"Outputs will be generated in {config.workdir.tmp_dir}")
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parents:
diff changeset
928 return gen_dir
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diff changeset
929
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diff changeset
930 def get_hander_for(directory, config):
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parents:
diff changeset
931 """
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diff changeset
932 generates the handler class for the directory we provide.
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parents:
diff changeset
933 """
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diff changeset
934 config["json_result"] = [{}] * len(config.tab_list)
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parents:
diff changeset
935
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936 class HTTPHandler(http.server.SimpleHTTPRequestHandler):
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parents:
diff changeset
937
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diff changeset
938 def __init__(self, *args, **kwargs):
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parents:
diff changeset
939 super().__init__(*args, **kwargs, directory=directory)
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parents:
diff changeset
940
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diff changeset
941 def do_POST(self):
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parents:
diff changeset
942 content_length = int(self.headers.get("Content-Length"))
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parents:
diff changeset
943 json_bytes = self.rfile.read(content_length).decode("utf-8")
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parents:
diff changeset
944 json_list = json.loads(json_bytes)
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parents:
diff changeset
945 for i, obj in enumerate(json_list):
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parents:
diff changeset
946 print(obj)
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diff changeset
947 if obj:
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diff changeset
948 config["json_result"][i] = obj
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parents:
diff changeset
949 save_json(config)
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diff changeset
950 self.send_head()
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diff changeset
951 self.wfile.write(json_bytes.encode("utf-8"))
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parents:
diff changeset
952 return
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diff changeset
953
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954 def do_GET(self):
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955 if self.path == "/quit":
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diff changeset
956 self.path = "/"
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diff changeset
957 super().do_GET()
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diff changeset
958 exit(0)
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959 self.path = os.path.join(directory, self.path)
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960 if self.path == "/":
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961 self.path = config.generated.html
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diff changeset
962 return super().do_GET()
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diff changeset
963
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964 return HTTPHandler
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diff changeset
965
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diff changeset
966
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967 def save_json(config):
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968 json_string = json.dumps(config["json_result"])
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diff changeset
969 print(json_string)
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970 with open(config.arguments.output_json, "w") as json_file:
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diff changeset
971 json_file.write(json_string)
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diff changeset
972
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973 def run_server(config):
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974 """
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diff changeset
975 prepare and runs the server, with the handler for the given directory
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976 """
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977 ip, port = config.network.ip, config.network.port
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diff changeset
978 config.logger.debug(f"IP and port: {ip}:{port}")
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diff changeset
979 socketserver.TCPServer.allow_reuse_address = True
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diff changeset
980 config.logger.debug(f"Allow reuse adress.")
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parents:
diff changeset
981 handler = get_hander_for(config.workdir.tmp_dir, config)
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diff changeset
982 config.logger.debug(f"Created server handler for {config.workdir.tmp_dir}")
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diff changeset
983 config.logger.debug(
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diff changeset
984 f"Content of directory {config.workdir.tmp_dir}: "
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parents:
diff changeset
985 + "\n"
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parents:
diff changeset
986 + '\n'.join(sorted(
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parents:
diff changeset
987 f" - {path}"for path in os.listdir(config.workdir.tmp_dir)
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parents:
diff changeset
988 ))
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diff changeset
989 )
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diff changeset
990 config.logger.debug(f"Creating TCP server...")
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parents:
diff changeset
991 server = socketserver.TCPServer((ip, port), handler)
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diff changeset
992 if ip == "0.0.0.0":
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diff changeset
993 displayed_ip = "localhost"
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diff changeset
994 else:
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diff changeset
995 displayed_ip = ip
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diff changeset
996 config.logger.debug(f"Serving...")
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diff changeset
997 print()
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diff changeset
998 print(f"http://{displayed_ip}:{port}")
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parents:
diff changeset
999 server.serve_forever()
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diff changeset
1000
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diff changeset
1001 def get_logger(config, dummy=False):
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parents:
diff changeset
1002 dummy_log = lambda msg:dummy and config.logger.info(msg)
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parents:
diff changeset
1003 arguments = config.arguments
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diff changeset
1004 if not dummy:
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diff changeset
1005 logger = logging.getLogger(__file__)
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1006 if arguments.debug:
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diff changeset
1007 dummy_log(f"Output debug info.")
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parents:
diff changeset
1008 level = logging.DEBUG
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diff changeset
1009 else:
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diff changeset
1010 level = logging.INFO
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diff changeset
1011 if not dummy:
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1012 logger.setLevel(level)
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diff changeset
1013 formatter = logging.Formatter(
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diff changeset
1014 "%(asctime)s - %(levelname)s - %(message)s"
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diff changeset
1015 )
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1016 if arguments.logging.std == "err":
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diff changeset
1017 dummy_log(f"Handler added to output logs in stderr.")
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diff changeset
1018 if not dummy:
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diff changeset
1019 handler = logging.StreamHandler(sys.stderr)
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diff changeset
1020 handler.setLevel(level)
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diff changeset
1021 handler.setFormatter(formatter)
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1022 logger.addHandler(handler)
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diff changeset
1023 elif arguments.logging.std == "out":
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diff changeset
1024 dummy_log(f"Handler added to output logs in stdout.")
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parents:
diff changeset
1025 if not dummy:
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diff changeset
1026 handler = logging.StreamHandler(sys.stdout)
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parents:
diff changeset
1027 handler.setLevel(level)
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diff changeset
1028 handler.setFormatter(formatter)
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diff changeset
1029 logger.addHandler(handler)
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diff changeset
1030 else:
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diff changeset
1031 dummy_log(f"Logs will not be output in stderr not stdout.")
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1032 if (path := arguments.logging.file.path):
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diff changeset
1033 dummy_log(f"Add log file: {arguments.logging.file.path}.")
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1034 if not arguments.logging.file.append:
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1035 dummy_log(f"Log file content cleaned.")
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1036 with open(path, "w"):pass
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1037 else:
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1038 dummy_log(f"Logs appended to log file.")
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1039 if not dummy:
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1040 file_handler = logging.FileHandler(filename=path)
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1041 file_handler.setLevel(level)
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1042 file_handler.setFormatter(formatter)
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1043 logger.addHandler(file_handler)
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1044 if not dummy:
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1045 config["logger"] = logger
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1046 starting_sequence(logger)
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1047 get_logger(config, dummy=True)
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1048 return logger
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1049
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1050 def starting_sequence(logger):
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1051 logger.info("*bip* *bop*")
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1052 logger.info("starting...")
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1053 logger.info("program...")
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1054 logger.info("MS2PF is running...")
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1055 logger.info("*bip* *bop* am a robot")
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1056 atexit.register(stoping_sequence, logger)
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1057
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1058 def stoping_sequence(logger):
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1059 logger.info("*bip* *bop*")
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1060 logger.info("ending...")
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1061 logger.info("program...")
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1062 logger.info("MS2PF is shuting down...")
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1063 logger.info("...robot")
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1064 logger.info("*bip* *bop*")
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1065 logger.info("shutdown")
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1066 logger.info("...")
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1067
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1068 if __name__ == "__main__":
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1069
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1070 base_config = parse_config()
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1071 config = parse_parameters(base_config)
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1072
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1073 """
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1074 The config contains result of the parsed config file.
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1075 """
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1076 arguments = config.arguments
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1077
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1078 config.logger.info(f"Starting MS2PF from {os.getcwd()}")
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1079
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1080 gen_dir = prepare_workplace(config)
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1081
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1082 config["pf_path"] = os.path.join(gen_dir, config.generated.html)
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1083 config.logger.info(f"HTML output file will be {config.pf_path}")
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1084 config["js_file"] = os.path.join(gen_dir, config.generated.js)
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1085 config.logger.info(f"JS output files will like {config.js_file}")
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1086 config.placeholders["PF_URL_PLACEHOLDER"] = arguments.peakforest.url
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1087 config.placeholders["PF_TOKEN_PLACEHOLDER"] = (
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1088 arguments.peakforest.token
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1089 or config.token.value
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1090 )
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1091 if (token := config.placeholders.PF_TOKEN_PLACEHOLDER):
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1092 config.logger.info(f"Using a token for authentification - length: {len(token)}")
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1093 else:
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1094 config.logger.info(f"No token provided for peakforest authentification.")
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1095
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1096 process_all_files(config)
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1097
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1098 if not arguments.do_run_dry:
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1099 config.logger.debug(f"Running the server.")
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1100 if arguments.firefox or arguments.chromium:
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1101 config.logger.debug(f"Running the server.")
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1102 import threading
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1103 import time
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1104 if arguments.firefox:
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1105 browser = "firefox"
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1106 else:
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1107 browser = "chromium"
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1108 if (ip := config.network.ip) == "0.0.0.0":
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1109 ip = "localhost"
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1110 adress = f"http://{ip}:{config.network.port}"
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1111 threading.Thread(
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1112 target=lambda:(
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1113 time.sleep(1),
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1114 os.system(f"{browser} {adress}")
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1115 ),
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1116 daemon=True
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1117 ).start()
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1118 run_server(config)
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1119 else:
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1120 config.logger.debug(f"Server not run.")