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1
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2 this.ctx = () => context;
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3 var all_contexts = [] ;
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4 var inchidata = {} ;
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5 var all_mix_data = {} ;
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6 var already_sent_data = {} ;
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7
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8 function no_success(tab_index, inchi, data) {
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9 console.log(`inchikey ${inchi} not found...`) ;
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10 console.log(`disabling ${data} ...`)
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11 disable_tab(
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12 tab_index,
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13 "red",
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14 "This compound has not been found on peakforest"
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15 ) ;
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16 }
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17
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18 function disable_tab(tab_index, color, title) {
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19 var element = $(`#open_tab_${tab_index}`) ;
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20 element.attr("disabled", "disabled").off("click");
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21 element.attr("onclick", null) ;
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22 element.attr("title", title) ;
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23 element.attr("data-toggle", null) ;
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24 element.attr("href", null) ;
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25 element.css("color", color) ;
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26 element.css("cursor", "not-allowed") ;
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27 }
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28
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29 function successfull_send_to_pf(bundle, json, index) {
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30 for (var i = 0 ; i < all_contexts.length ; i += 1) {
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31 if (all_contexts[i] === null || all_contexts[i] === undefined) {
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32 continue ;
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33 }
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34 if (all_contexts[i].inchikey == bundle["sample"]["inchikey"]) {
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35 disable_tab(
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36 all_contexts[i].tab_index,
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37 "green",
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38 "This compound has already been sent to peakforest"
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39 )
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40 }
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41 }
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42 if (already_sent_data[index] == null) {
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43 already_sent_data[index] = [] ;
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44 }
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45 json.forEach((id) => {
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46 already_sent_data[index].push(id)
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47 $("#send_buttons_div").prepend(`
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48 <div class="row">
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49 <div class="col-lg-3">
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50 <div class="alert alert-success alert-dismissible" role="alert">
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51 <button type="button" class="close" data-dismiss="alert">
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52 <span aria-hidden="true">×</span>
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53 <span class="sr-only">
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54 <spring:message code="alert.close" text="Close"></spring:message>
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55 </span>
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56 </button>
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57 <strong>
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58 <spring:message code="alert.strong.info" text="Success!"></spring:message>
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59 </strong> Spectrum has been sent:
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60 <a
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61 href="${ctx().peakforest_url}/webapp/home?PFs=${id.slice(3)}"
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62 target="_blank"
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63 >${id}</a>
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64 </div>
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65 </div>
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66 </div>`)
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67 })
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68 }
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69
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70 function failed_send_to_pf(err, bundle) {
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71 console.log(err) ;
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72 $("#send_buttons_div").prepend(`
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73 <div class="row">
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74 <div class="col-lg-3">
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75 <div class="alert alert-error alert-dismissible" role="alert">
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76 <button type="button" class="close" data-dismiss="alert">
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77 <span aria-hidden="true">×</span>
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78 <span class="sr-only">
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79 <spring:message code="alert.close" text="Close"></spring:message>
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80 </span>
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81 </button>
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82 <strong>
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83 <spring:message code="alert.strong.info" text="Error!"></spring:message>
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84 </strong> Spectrum has not been sent!
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85 </div>
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86 </div>
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87 </div>`)
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88 }
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89
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90 function already_sent(bundle, index) {
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91 return already_sent_data[index] != null ;
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92 }
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93
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94 function failed_already_sent(bundle, index) {
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95 already_sent_data[index].forEach((id) => {
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96 $("#send_buttons_div").prepend(`
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97 <div class="row">
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98 <div class="col-lg-3">
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99 <div class="alert alert-warning alert-dismissible" role="alert">
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100 <button type="button" class="close" data-dismiss="alert">
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101 <span aria-hidden="true">×</span>
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102 <span class="sr-only">
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103 <spring:message code="alert.close" text="Close"></spring:message>
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104 </span>
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105 </button>
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106 <strong>
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107 <spring:message code="alert.strong.info" text="warning!"></spring:message>
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108 </strong> Spectrum has already been sent:
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109 <a
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110 href="${ctx().peakforest_url}/webapp/home?PFs=${id.slice(3)}"
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111 target="_blank"
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112 >${id}</a>
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113 </div>
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114 </div>
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115 </div>`)
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116 }) ;
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117 }
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118
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119 function send_everything_to_peakforest(url, token) {
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120 var bundles ;
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121 if (context.is_mix()) {
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122 bundles = [all_mix_data] ;
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123 } else {
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124 bundles = create_dataset_bundles() ;
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125 }
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126 bundles.forEach((bundle, index) => {
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127 if (already_sent(bundle, index)) {
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128 return failed_already_sent(bundle, index) ;
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129 }
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130 console.log(bundle)
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131 $.ajax({
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132 type: "post",
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133 url: `${url}/rest/v2/spectrum?token=${token}`,
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134 data: JSON.stringify(bundle),
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135 contentType: "application/json",
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136 success: function(json) {
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137 successfull_send_to_pf(bundle, json, index)
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138 }, error: function(err) {
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139 failed_send_to_pf(err, bundle)
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140 }
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141 })
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142 $.ajax({
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143 type: "post",
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144 url: "/",
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145 data: `{"index": ${index}, "object": ${JSON.stringify(bundle)}}`,
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146 contentType: "application/json",
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147 error: function(err) {
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148 console.log(`Error: JSON will not be produced by the application.`)
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149 }
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150 })
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151 })
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152 // console.log(bundles)
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153 }
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154
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155 function create_dataset_bundles() {
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156 var bundles = [] ;
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157 var data ;
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158 all_contexts.forEach((context, index) => {
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159 if ((data = context.sent_json) === null) {
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160 return ;
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161 }
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162 if (bundles.length === 0) {
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163 // console.log("First metadata!")
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164 return bundles.push(data) ;
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165 }
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166 if (merge_in_bundle(bundles, data)) {
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167 // console.log("Merged!")
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168 } else {
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169 // console.log("New metadata!")
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170 }
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171 }) ;
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172 return bundles ;
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173 }
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174
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175 function merge_in_bundle(bundles, data) {
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176 for(var i = 0 ; i < bundles.length ; i += 1) {
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177 if (
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178 identical(bundles[i]["sample"], data["sample"])
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179 && identical(bundles[i]["chromatography"], data["chromatography"])
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180 && identical(bundles[i]["analyzer"], data["analyzer"])
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181 && identical(bundles[i]["ionization_mode_positive"], data["ionization_mode_positive"])
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182 && identical(bundles[i]["ionization_mode_negative"], data["ionization_mode_negative"])
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183 && identical(bundles[i]["other_metadata"], data["other_metadata"])
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184 ) {
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185 bundles[i]["peaklists"].push(data["peaklists"][0]) ;
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186 return true ;
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187 } else {
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188 continue ;
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189 console.log(
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190 "sample: "
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191 + identical(bundles[i]["sample"], data["sample"])
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192 )
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193 console.log(
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194 "chromatography: "
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195 + identical(bundles[i]["chromatography"], data["chromatography"])
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196 )
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197 console.log(
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198 "analyzer: "
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199 + identical(bundles[i]["analyzer"], data["analyzer"])
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200 )
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201 console.log(
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202 "ionization_mode_positive: "
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203 + identical(bundles[i]["ionization_mode_positive"], data["ionization_mode_positive"])
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204 )
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205 console.log(
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206 "ionization_mode_negative: "
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207 + identical(bundles[i]["ionization_mode_negative"], data["ionization_mode_negative"])
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208 )
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209 console.log(
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210 "other_metadata: "
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211 + identical(bundles[i]["other_metadata"], data["other_metadata"])
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212 )
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213 }
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214 }
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215 bundles.push(data) ;
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216 return false ;
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217 }
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218
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219 function identical(left, right) {
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220 if (typeof left !== typeof right) {
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221 return false ;
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222 }
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223 if (left === null) {
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224 return right === null ;
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225 }
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226 if (right === null) {
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227 return left === null ;
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228 }
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229 switch (typeof left) {
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230 case "array":
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231 return identical_array(left, right) ;
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232 break ;
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233 case "object":
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234 return identical_object(left, right) ;
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235 break ;
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236 default:
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237 break ;
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238 }
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239 return (left === right)
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240 }
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241
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242 function identical_array(left, right) {
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243 if (right.length !== left.length) {
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244 return false ;
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245 }
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246 for(var i = 0 ; i < left.length ; i += 1) {
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247 if (!identical(left[i], right[i])) {
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248 return false ;
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249 }
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250 }
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251 return true ;
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252 }
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253
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254 function identical_object(left, right) {
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255 var left_keys ;
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256
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257 if (!(
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258 share_keys(left, right)
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259 && share_keys(right, left)
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260 )) {
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261 return true ;
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262 }
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263 left_keys = Object.keys(left) ;
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264 for (var i = 0 ; i < left_keys.length ; i += 1){
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265 if (!identical(left[left_keys[i]], right[left_keys[i]])) {
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266 return false ;
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267 }
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268 }
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269 return true ;
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270 }
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271
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272 function share_keys(left, right) {
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273 var left_keys ;
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274 var right_keys ;
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275
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276 left_keys = Object.keys(left) ;
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277 right_keys = Object.keys(right) ;
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278 for(var i = 0 ; i < left_keys.length ; i += 1) {
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279 if (!right_keys.includes(left_keys[i])) {
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280 return false ;
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281 }
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282 }
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283 return true ;
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284 }
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285
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286 var set_inchi_data = function(data, tab_index) {
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287 inchidata[data.inchikey] = data ;
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288 $(`#add1spectrum-sample-inchi-${tab_index}`).val(data.inchi);
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289 $(`#add1spectrum-sample-inchi-${tab_index}`).change();
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290 $(`#add1spectrum-sample-commonName-${tab_index}`).val(data.name);
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291 $(`#add1spectrum-sample-commonName-${tab_index}`).change();
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292 $(`#sample-bonus-display-${tab_index}`).html(
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293 `<img
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294 class=""
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295 src="{{ PF_URL_PLACEHOLDER }}/webapp/image/${data.type}/${data.inchikey}"
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296 alt="${data.name}"
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297 >`
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298 );
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299 }
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300
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301 var lightgrayRenderer = function(instance, td, row, col, prop, value, cellProperties) {
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302 Handsontable.renderers.TextRenderer.apply(this, arguments);
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303 td.style.backgroundColor = "#EEE";
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304 }
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