annotate data/models.R @ 17:d8112d636210 draft

" master branch Updating"
author lain
date Mon, 31 Jan 2022 15:54:14 +0000
parents 00079fadc240
children 2937e72e5891
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1
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2 tryCatch({
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3 DBModelR::ModelDefinition(table="yui", fields=list(yui="INTEGER"))
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4 }, error=function(e) {
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5 stop("Please, install DBModelR before you source this file.")
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6 })
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7
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8 list(
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9 adduct=DBModelR::ModelDefinition(
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10 table="adduct",
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11 fields=list(
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12 name="TEXT",
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13 mass="FLOAT",
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14 charge="INTEGER",
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15 multi="INTEGER",
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16 formula_add="TEXT",
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17 formula_ded="TEXT",
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18 sign="TEXT",
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19 oidscore="INTEGER",
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20 quasi="INTEGER",
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21 ips="FLOAT"
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22 )
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23 ),
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24 cluster=DBModelR::ModelDefinition(
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25 table="cluster",
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26 fields=list(
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27 clusterID="INTEGER",
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28 formula="TEXT",
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29 annotation="TEXT",
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30 coeff="FLOAT",
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31 r_squared="FLOAT",
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32 charge="INTEGER",
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33 mean_rt="FLOAT",
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34 score="FLOAT",
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35 deviation="FLOAT",
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36 status="TEXT",
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37 # adduct="TEXT",
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38 curent_group="INTEGER",
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39 pc_group="INTEGER",
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40 align_group="INTEGER",
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41 xcms_group="INTEGER"
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42 ),
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43 one=list("compound", "adduct"),
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44 many=list("sample")
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45 ),
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46 compound=DBModelR::ModelDefinition(
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47 table="compound",
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48 fields=list(
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49 name="TEXT",
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50 common_name="TEXT",
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51 formula="TEXT",
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52 charge="INTEGER",
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53 date="TEXT",
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54 mz="FLOAT"
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55 )
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56 ),
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57 feature=DBModelR::ModelDefinition(
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58 table="feature",
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59 fields=list(
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60 featureID="INTEGER",
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61 mz="FLOAT",
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62 mz_min="FLOAT",
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63 mz_max="FLOAT",
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64 rt="FLOAT",
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65 rt_min="FLOAT",
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66 rt_max="FLOAT",
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67 int_o="FLOAT",
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68 int_b="FLOAT",
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69 max_o="FLOAT",
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70 iso="TEXT",
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71 abundance="FLOAT"
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72 ),
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73 one=list("cluster"),
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74 many=list("sample")
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75 ),
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76 instrument=DBModelR::ModelDefinition(
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77 table="instrument",
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78 fields=list(
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79 model="TEXT",
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80 manufacturer="TEXT",
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81 analyzer="TEXT",
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82 detector_type="TEXT",
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83 ion_source="TEXT"
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84 )
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85 ),
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86 instrument_config=DBModelR::ModelDefinition(
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87 table="instrument_config",
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88 fields=list(
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89 resolution="TEXT",
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90 agc_target="TEXT",
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91 maximum_IT="TEXT",
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92 number_of_scan_range="TEXT",
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93 scan_range="TEXT",
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94 version="TEXT"
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95 )
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96 ),
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97 project=DBModelR::ModelDefinition(
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98 table="project",
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99 fields=list(
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100 name="TEXT",
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101 comment="TEXT"
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102 ),
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103 one=list("sample")
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104 ),
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105 sample=DBModelR::ModelDefinition(
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106 table="sample",
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107 fields=list(
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108 name="TEXT",
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109 path="TEXT",
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110 polarity="TEXT",
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111 kind="TEXT", ## rdata or mxml or enriched_rdata
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112 raw="BLOB"
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113 ),
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114 one=list(
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115 "peak_picking_parameters",
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116 "pairing_parameters",
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117 "alignmenmt_parameters",
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118 "camera_parameters",
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119 "instrument",
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120 "instrument_config",
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121 "software",
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122 "smol_xcms_set"
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123 )
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124 ),
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125 smol_xcms_set=DBModelR::ModelDefinition(
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126 table="smol_xcms_set",
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127 fields=list(
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128 raw="BLOB"
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129 )
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130 ),
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131 software=DBModelR::ModelDefinition(
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132 table="software",
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133 fields=list(
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134 name="TEXT",
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135 version="TEXT"
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136 )
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137 ),
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138 # camera_parameters=DBModelR::ModelDefinition(
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139 # table="camera_parameters",
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140 # fields=list()
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141 # ),
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142 # pairing_parameters=DBModelR::ModelDefinition(
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143 # table="pairing_parameters",
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144 # fields=list()
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145 # ),
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146 peak_picking_parameters=DBModelR::ModelDefinition(
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147 table="peak_picking_parameters",
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148 fields=list(
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149 ppm="FLOAT",
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150 peakwidth="TEXT",
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151 snthresh="TEXT",
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152 prefilterStep="TEXT",
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153 prefilterLevel="TEXT",
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154 mzdiff="TEXT",
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155 fitgauss="TEXT",
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156 noise="TEXT",
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157 mzCenterFun="TEXT",
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158 integrate="INTEGER",
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159 firstBaselineCheck="TEXT",
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160 snthreshIsoROIs="TEXT",
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161 maxCharge="INTEGER",
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162 maxIso="INTEGER",
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163 mzIntervalExtension="TEXT"
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164 )
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165 ),
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166 alignmenmt_parameters=DBModelR::ModelDefinition(
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167 table="alignmenmt_parameters",
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168 fields=list(
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169 binSize="TEXT",
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170 centerSample="TEXT",
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171 response="TEXT",
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172 distFun="TEXT",
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173 gapInit="TEXT",
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174 gapExtend="TEXT",
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175 factorDiag="TEXT",
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176 factorGap="TEXT",
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177 localAlignment="INTEGER",
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178 initPenalty="TEXT",
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179 bw="TEXT",
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180 minFraction="TEXT",
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181 minSamples="TEXT",
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182 maxFeatures="TEXT"
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183 )
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184 )
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185 )