Mercurial > repos > lain > ms_to_peakforest_it

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master branch Updating
author lain
date Wed, 30 Aug 2023 14:21:18 +0000
parents b58b229c4cbf
children
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1 ##
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2 ## when you see {{ something }} in a string, this means the string is
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3 ## a template, and the "{{ something }}" will be replaced by its value
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4 ## at runtime.
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5 ## This is usefull to build strings from other strings.
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6 ## to reference an item in a tree, you can use dots as branches:
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7 ## {{ parameters.flags.help }}
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8 ## will be extrapolated to "Show this help"
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9 ##
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10 ## But beware:
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11 ## {{ parameters.mandatory }}
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12 ## will be extrapolated to
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13 ## "{'input': 'input file path'}"
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14 ##
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15
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16 ## this config is used for debug.
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17 ## it allows to define debug options before everything else is parsed
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18 __meta_config__:
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19 __debug__: False
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20 __debug_stream__: stderr
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21 __only_root_debug__: False
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22
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23
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24 ## the cli parameters
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25 parameters:
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26 mandatory:
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27 ## input is mandatory
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28 input: input file path
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29 flags:
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30 ## help, verbose and version can be provided with no parameter.
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31 help: Show this help
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32 verbose: More verbose outputs
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33 version: Show this tool's version
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34 debug: show debug outputs
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35 do_run_dry: Runs the whole process, without the server. Usefull for tests.
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36 embed_js: Embed js in html file instead of using a separated js file.
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37 firefox: Open firefox on the web page.
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38 chromium: Open chromium or chrome on the web page.
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39 optional:
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40 ## these optional parameters need a value "--opt value --opt2 value2"
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41 method: "default is {{ defaults.method }}"
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42 spectrum_type: "default is {{ defaults.spectrum_type }}"
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43 sample_type: "default is {{ defaults.sample_type }}"
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44 resolution: "default is {{ defaults.resolution }}"
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45 name: The precursor name
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46 peakforest.url: "default={{ defaults.peakforest.url }}"
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47 peakforest.token: The token to comunicate with peakforest api
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48 polarity: positive|negative
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49 raw_metadata: example - 1-1__INCHIKEY__=QNAYBMKLOCPYGJ-REOHCLBHSA-N_L-Alanine_MS_POS_plasma_RT__=0.84_filtree.csv
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50 scan_type: ms|msms|rmn
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51 rt_min: Min retention time
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52 rt_max: Max retention time
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53 run_dry_html: when "--run-dry", provides the output directory for {{ generated.html }}
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54 run_dry_js: when "--run-dry", provides the output directory for {{ generated.js }}
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55 raw_metadata_sep: "raw metadata separator"
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56 logging.std: "Either out, err, or anything else to not output"
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57 logging.file.path: "The file path to output logs to"
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58 validation: "Set the default validation to the provided value, TRUE or FALSE."
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59 output_json: "Provide a path to output a JSON file."
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60 pid: "Path to the pid file"
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61 ip: "the net intf to link to"
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62 port: "the net port to bind on"
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63 meta:
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64 ## meta info about the tool itself
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65 author: Lain Pavot
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66 version: 1.2.1
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67 shortcuts:
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68 ## to define things like: "we can use -p instead of --polarity"
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69 peakforest.token: t
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70 polarity: p
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71 help: h
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72 version: v
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73 verbose: V
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74 debug: d
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75 logging.std: l
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76
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77 ## some default parameters
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78 ## logging defines two elements: std and file.
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79 ## std should be either empty, err or out.
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80 ## it tells where to outputs logs:
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81 ## - nowhere (empty value)
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82 ## - in sterr (err)
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83 ## - in stdout (out)
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84 ## and file. Id a path is provided, add outputs to this file.
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85 ## if append is true, outputs are appended to the file.
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86 ## otherwise, the file is emptied each time the app runs.
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87 defaults:
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88 ip: 0.0.0.0
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89 port: 8000
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90 peakforest:
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91 url: https://nightly.peakforest.org
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92 token: ''
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93 spectrum_type: LC_MSMS
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94 method: cf_pfem_urine_method1_qtof-msms
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95 # api-msms-fia__idf-cea
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96 # cf_pfem_plasma_method1_qtof-msms
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97 # cf_pfem_urine_method1_qtof-msms
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98 # lc-msms__test
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99 scan_type: ms2
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100 resolution: high
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101 sample_type: compound-ref
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102 # sample_type: compound-mix
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103 polarity: positive
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104 raw_metadata: ''
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105 name: ''
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106 run_dry_html:
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107 run_dry_js:
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108 raw_metadata_sep: ','
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109 validation: "TRUE"
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110 verbose: false
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111 debug: true
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112 logging:
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113 std: out ## out || err
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114 file:
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115 path:
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116 append: False
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117 output_json: ''
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118 rt_min: 0.9
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119 rt_max: 1.9
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120 pid:
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121
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122 ## token related info
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123 token:
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124 ## do you use a file to store your token?
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125 use_file: false
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126 ## if so, what path the file is located at?
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127 file_path: .token
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128 ## if not, you can provide you token here
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129 value:
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130
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131 workdir:
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132 ## create a tmp directory
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133 create_tmp: true
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134 ## works in the created tmp directory, or if not created, in /tmp
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135 work_in_tmp: true
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136 ## generate outputs in the created tmp directory, or if not created, in /tmp
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137 generate_in_tmp: true
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138
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139 ## the templates paths
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140 templates:
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141 ## meta is what wrapps the whole page.
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142 main: src/meta.html
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143 main_mix: src/meta-compound-mix.html
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144 main_ref: src/meta-compound-ref.html
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145 ## form is one instance of a pf form
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146 # form: src/form.html
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147 # form: src/compound-ref.html
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148 form: src/form.html
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149 form_mix: src/compound-mix.html
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150 form_ref: src/compound-ref.html
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151 ## one item of the tab list
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152 tab_list: src/tab_list.html
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153 ## the js for one form
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154 js: src/add-one-spectrum-index.js
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155 ## placeholders for the html templates.
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156 ## this will not change the placeholders syntax for this file.
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157 placeholders:
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158 start: "{{ "
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159 stop: " }}"
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160
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161 generated:
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162 ## what filename to give to the whole html file
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163 html: pf.html
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164 ## what filename to give to js files
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165 js: add-one-spectrum-{{ index }}.js
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166
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167 regex:
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168 values:
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169 ## reuse these smol regex in bigger regex!
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170 spectrum_type: "NMR|LC_MS|LC_MSMS|MRM(_\\d+)?"
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171 matrix: "[Uu]rine|[Pp]lasma|[Pp]las"
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172 mode: "POS|NEG"
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173 energy: "\\d+ev"
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174 pool: "[Pp]ool\\d+"
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175 rt: "\\d+\\.\\d+"
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176 runs: "\\d+-\\d+"
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177 inchikey: "[A-Z]{14}-[A-Z]{10}-[A-Z]"
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178
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179 ## the "INCHIKEY" word
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180 ## one or more underscores
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181 ## may be followed by a equal sign
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182 ## captures in the "inchikey" variable:
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183 ## 14, 10 and 1 letters
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184 ## in caps
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185 ## separated by a hyphen
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186 inchikey: "INCHIKEY_+=?(?P<inchikey>{{ regex.values.inchikey }})"
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187
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188 ## method is one of values defined bellow, between underscores
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189 spectrum_type: "_(?P<method>{{ regex.values.method }})_"
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190
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191 ## matrix is one of values defined bellow, between underscores
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192 matrix: "_(?P<matrix>{{ regex.values.matrix }})_"
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193
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194 ## pool is one of values defined bellow, between underscores
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195 pool: "_(?P<pool>{{ regex.values.pool }})_"
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196
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197 ## molecule everything between inchikey and method.
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198 molecule: "{{ regex.inchikey }}_(?P<molecule>.*?){{ regex.method }}"
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199
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200 ## mode is one of values defined bellow, between underscores
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201 mode: "_(?P<mode>{{ regex.values.mode }})_"
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202
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203 ## energy is one of values defined bellow, between underscores
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204 energy: "_(?P<energy>{{ regex.values.energy }})_"
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205
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206 ## - A underscore,
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207 ## - the "RT" word,
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208 ## - some underscore(s),
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209 ## - an optional interrogation mark,
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210 ## - the actual RT value is captured here,
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211 ## - there is a underscore at the end
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212 rt: "_RT_+=?(?P<rt>{{ regex.values.rt }})_"
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213
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214 ## "runs" is at the beginning, and ends with an underscore.
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215 runs: "^(?P<runs>{{ regex.values.runs }})_"
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216
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217
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218 ## BEGIN
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219 ## anything
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220 ## the inchikey
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221 ## anything else can follow
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222 ## END
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223 # fragnot: ^.*{{ regex.inchikey }}.*$
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224
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225
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226 ## This is the most exhaustive regex I came with to extract info from
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227 ## fragnot files name.
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228 # fragnot:
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229 # ^
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230 # .* (?# there may be anything at the begining)
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231 # (?P<runs>\d+-\d+) (?# the run numbers)
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232 # _+ (?# followed by anything - underscores usualy)
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233 # INCHIKEY_+=?(?P<inchikey>{{ regex.inchikey }}) (?# we insert inchikey regex here - see above)
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234 # _+ (?# there is one or more underscores)
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235 # (?P<molecule>.*?) (?# the molecule name follows the inchikey)
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236 # _+ (?# there is one or more underscores)
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237 # (?P<method>{{ regex.method }}) (?# then, there is the method - nmr, ms or mrm???)
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238 # _+ (?# there may be some underscores to separate)
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239 # (?P<matrix>{{ regex.matrix }})? (?# the matrix - urine or plasma)
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240 # _* (?# there may be some underscores to separate)
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241 # (?P<mode>POS|NEG) (?# the acq mode - pos or neg)
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242 # _+ (?# there may be some underscores to separate)
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243 # (?P<pool>{{ regex.pool }})? (?# the pool - "Pool"+numbers, optional)
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244 # _* (?# there may be some underscores to separate)
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245 # (?P<energy>\d+ev)? (?# the energy - only for nmr, so it's optional)
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246 # _* (?# there may be some underscores to separate)
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247 # (?P<pool2>{{ regex.pool }})? (?# the pool - sometimes the pool if *after* the energy...)
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248 # _* (?# there may be some underscores to separate)
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249 # (?P<matrix2>{{ regex.matrix }})? (?# the matrix is here, sometimes)
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250 # _* (?# there may be anything here)
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251 # RT_+=?(?P<rt>\d+\.\d+) (?# the retension time is a decimal number)
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252 # _* (?# there may be anything at the end)
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253 # (?P<filtered>[fF]iltree)? (?# sometimes, "Filtree" appears, lets capture it)
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254 # \.[ct]sv (?# the extension)
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255 # $