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1
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1
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2 var token = "{{ PF_TOKEN_PLACEHOLDER }}" ;
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3 if ({{ TAB_INDEX_PLACEHOLDER }} == 1) {
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4 }
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5
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6 context_{{ TAB_INDEX_PLACEHOLDER }} = {
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7 prefix: "#accordion-{{ TAB_INDEX_PLACEHOLDER }} ",
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8 name: "Context[{{ TAB_INDEX_PLACEHOLDER }}]",
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9 produce_json: {{ PRODUCE_JSON_PLACEHOLDER }},
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10 DEFAULT_MS_PEAK_VALUES: {{ MS_PEAK_VALUES_PLACEHOLDER }},
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11 DEFAULT_DATA: {{ DEFAULT_DATA }},
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12 peakforest_url: "{{ PF_URL_PLACEHOLDER }}",
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13 tab_index: "{{ TAB_INDEX_PLACEHOLDER }}",
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14 modeEditSpectrum: false,
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15 isSeparationFlowRateInit: false,
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16 isMSpeaksInit: false,
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17 isLC: false,
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18 isGC: false,
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19 isIC: false,
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20 hot_LC_SFG: null ,
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21 hot_MS_Peaks: null,
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22 hot_RCC_ADDED: null,
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23 jsonSpectrumType: null,
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24 isJsonSpectrumTypeComplete: false,
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25 jsonSample: null,
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26 isJsonSampleComplete: false,
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27 isJsonRCCaddedComplete: false,
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28 jsonChromato: null,
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29 isJsonChromatoComplete: false,
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30 jsonAnalyzer: null,
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31 isJsonAnalyzerComplete: false,
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32 jsonPeaksList: [],
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33 isJsonPeaksListComplete: false,
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34 jsonOtherMetadata: null,
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35 isJsonOtherMetadataComplete: false,
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36 jsonMolIonization: null,
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37 jsonMolIonBeam: null,
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38 cptPeakListTab: 0,
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39 jsonAnalyzerAcquisition: [],
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40 idMetadataMap: {},
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41 listOfViewableSpectra: [],
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42 singlePick: true,
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43 multiPickLine: -1,
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44 subjects: [],
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45 fitlerSearchLoadlCpd: 5,
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46 inchikey: null,
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47 initialized: false,
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48 selected_ion_index: null,
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49 lock: {
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50 precursor_ion: false
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51 },
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52
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53 sent_json: null,
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54
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55 init: function() {
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56
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57 var self = this ;
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58
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59 $(document).ready(() => self.on_ready());
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60 $(document).ready(function() {
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61 console.log("adding click on open_tab_{{ TAB_INDEX_PLACEHOLDER }}.") ;
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62 var activate_tab = function() {
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63 if (self.initialized) {
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64 return ;
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65 }
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66 self.auto_set_spec_type() ;
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67 }
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68 if (self.is_ref()) {
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69 $("#open_tab_{{ TAB_INDEX_PLACEHOLDER }}").click(activate_tab) ;
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70 }
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71 if ({{ TAB_INDEX_PLACEHOLDER }} == 1) {
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72 activate_tab() ;
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73 }
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74 }) ;
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75
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76 return (self) ;
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77
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78 },
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79
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80 on_ready: function() {
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81 var self = this ;
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82
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83 $(self.prefix+".pickChemicalCompound").click(self.pickChemicalCompound);
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84 $(self.prefix+".add1spectrum").change(
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85 function(){self.add1spectrum_change_handler(this)}
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86 )
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87 self.attach_search() ;
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88 self.add_date_check() ;
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89 self.populate_selects() ;
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90 self.add_change_handlers() ;
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91 self.show_hide_ms_ms2_fields() ;
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92 },
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93
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94 populate_selects: function() {
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95 var self = this ;
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96 var choose_in_list ;
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97
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98 choose_in_list = `
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99 <option value="" selected="selected" disabled="disabled">
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100 choose in list…
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101 </option>
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102 ` ;
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103 $("#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}").append(choose_in_list) ;
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104 $("#add1spectrum-chromatoLC-colConstructor-{{ TAB_INDEX_PLACEHOLDER }}").append(choose_in_list) ;
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105 $("#add1spectrum-chromatoLC-separationSolvA-{{ TAB_INDEX_PLACEHOLDER }}").append(choose_in_list) ;
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106 $("#add1spectrum-chromatoLC-separationSolvB-{{ TAB_INDEX_PLACEHOLDER }}").append(choose_in_list) ;
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107 $("#add1spectrum-sample-lcmsSolvent-{{ TAB_INDEX_PLACEHOLDER }}").append(choose_in_list) ;
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108 $.getJSON("{{ PF_URL_PLACEHOLDER }}/webapp/resources/json/list-lc-methods.json", self.populate_lc_methods) ;
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109 $.getJSON("{{ PF_URL_PLACEHOLDER }}/webapp/resources/json/list-lc-columns.json", self.populate_lc_columns) ;
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110 $.getJSON("{{ PF_URL_PLACEHOLDER }}/webapp/resources/json/list-lc-solvents.json", self.populate_lc_solvents) ;
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111 $.getJSON("{{ PF_URL_PLACEHOLDER }}/webapp/resources/json/list-ms-ionization-methods.json", self.populate_ms_ionization) ;
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112 $.getJSON("{{ PF_URL_PLACEHOLDER }}/webapp/resources/json/list-lcms-solvents.json", self.populate_lcms_solvents) ;
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113 self.resetFromColors();
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114 },
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115
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116 attach_search: function() {
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117 var self = this ;
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118
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119 $("#add-one-cc-s1-value-{{ TAB_INDEX_PLACEHOLDER }}").bind("keypress", function(e) {
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120 var code = e.keyCode || e.which;
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121 if (code == 13) {
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122 self.searchLocalCompound();
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123 }
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124 });
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125 $("#add-one-cc-s1-value-{{ TAB_INDEX_PLACEHOLDER }}").typeahead({
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126 source: function(query, process) {
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127 return self.searchAjax();
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128 }
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129 });
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130 },
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131
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132 add_date_check: function() {
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133 var self = this ;
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134
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135 $("#add1spectrum-other-date-{{ TAB_INDEX_PLACEHOLDER }}").focusout(function() {
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136 var element = $(this) ;
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137 self.rm_warning(element);
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138 self.rm_success(element) ;
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139 if (element.val() == "") {
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140 element.parent().addClass("has-warning");
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141 } else {
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142 element.parent().addClass("has-success");
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143 }
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144 });
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145 },
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146
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147 populate_lc_methods: function(data) {
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148 // load data from json
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149 $.each(data.methods,function() {
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150 if (this.name !== undefined) {
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151 if (this.value !== undefined) {
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152 $("#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}").append(
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153 `<option value="${this.value}">${this.name}</option>`
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154 );
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155 } else {
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156 $("#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}").append(
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157 `<option disabled>${this.name}</option>`
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158 );
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159 }
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160 }
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161 });
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162 },
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163
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164 populate_lc_columns: function(data) {
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165 // load data from json
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166 $.each(data.columns, function() {
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167 $("#add1spectrum-chromatoLC-colConstructor-{{ TAB_INDEX_PLACEHOLDER }}").append(
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168 `<option value="${this.value}">${this.name}</option>`
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169 );
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170 });
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171 $("#add1spectrum-chromatoLC-colConstructor-{{ TAB_INDEX_PLACEHOLDER }}").append(
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172 '<option value="other" >Other</option>'
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173 );
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174 },
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175
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176 populate_lc_solvents: function(data) {
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177 // load data from json
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178 $.each(data.solvents, function() {
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179 $("#add1spectrum-chromatoLC-separationSolvA-{{ TAB_INDEX_PLACEHOLDER }}").append(
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180 `<option value="${this.value}">${this.name}</option>`
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181 );
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182 $("#add1spectrum-chromatoLC-separationSolvB-{{ TAB_INDEX_PLACEHOLDER }}").append(
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183 `<option value="${this.value}">${this.name}</option>`
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184 );
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185 });
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186 },
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187
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188 populate_ms_ionization: function(data) {
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189 // load data from json
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190 $.each(data.methods,function() {
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191 if (this.name !==undefined) {
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192 if (this.value !==undefined) {
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193 $("#add1spectrum-analyzserMS-ionizationMethod-pos-{{ TAB_INDEX_PLACEHOLDER }}").append(
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194 `<option value="${this.value}">${this.name}</option>`
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195 );
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196 $("#add1spectrum-analyzserMS-ionizationMethod-neg-{{ TAB_INDEX_PLACEHOLDER }}").append(
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197 `<option value="${this.value}">${this.name}</option>`
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198 );
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199 } else {
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200 $("#add1spectrum-analyzserMS-ionizationMethod-pos-{{ TAB_INDEX_PLACEHOLDER }}").append(
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201 `<option disabled>${this.name}</option>`
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202 );
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203 $("#add1spectrum-analyzserMS-ionizationMethod-neg-{{ TAB_INDEX_PLACEHOLDER }}").append(
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204 `<option disabled>${this.name}</option>`
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205 );
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206 }
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207 }
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208 });
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209 },
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210
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211 populate_lcms_solvents: function(data) {
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212 // load data from json
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213 $.each(data.solvents, function () {
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214 $("#add1spectrum-sample-lcmsSolvent-{{ TAB_INDEX_PLACEHOLDER }}").append(
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215 `<option value="${this.value}" class="${this.classD}">${this.name}</option>`
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216 );
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217 });
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218 },
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219
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220 add_change_handlers: function() {
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221 var self = this ;
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222
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223 $("#add1spectrum-ionTrapBeam-type-{{ TAB_INDEX_PLACEHOLDER }}").on("change", function() {
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224 var v = $("#add1spectrum-ionTrapBeam-type-{{ TAB_INDEX_PLACEHOLDER }}").val();
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225 $(self.prefix + ".add1spectrum-ionTrap").hide();
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226 if (v == "beam") {
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227 } else if (v == "trap") {
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228 $(self.prefix + ".add1spectrum-ionTrap").show();
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229 }
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230 }) ;
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231 },
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232
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233 show_hide_ms_ms2_fields: function() {
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234 var self = this ;
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235 $(self.prefix + " .disabled-if-ms").attr("disabled", self.is_ms())
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236 $(self.prefix + " .disabled-if-msms").attr("disabled", self.is_ms2())
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237 $(self.prefix + " .disabled-if-ms2").attr("disabled", self.is_ms2())
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238 if (self.is_ms()) {
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239 self.hide(self.prefix + " .hidden-if-ms") ;
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240 }
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241 if (self.is_ms2()) {
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242 self.hide(self.prefix + " .hidden-if-msms") ;
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243 self.hide(self.prefix + " .hidden-if-ms2") ;
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244 }
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245 },
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246
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247 is_mix: function() {
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248 return this.DEFAULT_DATA["sample_type"] == "compound-mix" ;
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249 },
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250
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251 is_ref: function() {
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252 return this.DEFAULT_DATA["sample_type"] == "compound-ref" ;
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253 },
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254
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255 is_ms: function() {
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256 return this.DEFAULT_DATA["spectrum_type"] == "LC_MS" ;
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257 },
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258
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259 is_ms2: function() {
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260 return this.DEFAULT_DATA["spectrum_type"] == "LC_MSMS" ;
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261 },
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262
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263 is_other_in_mix() {
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264 return this.is_mix() && {{ TAB_INDEX_PLACEHOLDER }} > 1 ;
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265 },
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266
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267 hide: function(id) {
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268 if (typeof id == Array) {
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269 return (id.forEach(hide)) ;
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270 }
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271 $(id).hide()
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272 },
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273
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274 rm_success: function(element) {
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275 return (this.rm_parent_class(element, "has-success"))
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276 },
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277 rm_error: function(element) {
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278 return (this.rm_parent_class(element, "has-error"))
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279 },
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280 rm_warning: function(element) {
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281 return (this.rm_parent_class(element, "has-warning"))
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282 },
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283 set_success: function(element) {
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284 return (this.set_parent_class(element, "has-success"))
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285 },
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286 set_error: function(element) {
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287 return (this.set_parent_class(element, "has-error"))
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288 },
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289 set_warning: function(element) {
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290 return (this.set_parent_class(element, "has-warning"))
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291 },
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292 rm_parent_class: function(element, cls) {
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293 var parent ;
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294
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295 if ((parent = element.parent()) == null) {
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296 return false ;
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297 }
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298 return this.rm_class(parent, cls) ;
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299 },
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300 set_parent_class: function(element, cls) {
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301 var parent ;
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302
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303 if ((parent = element.parent()) == null) {
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304 return false ;
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305 }
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306 return this.set_class(parent, cls) ;
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307 },
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308 rm_class: function(element, cls) {
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309 if (element.hasClass(cls)) {
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310 element.removeClass(cls) ;
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311 return true ;
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312 }
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313 return false ;
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314 },
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315 set_class: function(element, cls) {
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316 if (element.hasClass(cls)) {
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317 return false ;
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318 }
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319 element.addClass(cls) ;
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320 return true ;
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321 },
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322 is_success: function(element) {
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323 return (this.parent_has_class(element, "has-success"))
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324 },
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325 is_warning: function(element) {
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326 return (this.parent_has_class(element, "has-warning"))
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327 },
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328 is_error: function(element) {
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329 return (this.parent_has_class(element, "has-error"))
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330 },
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331 is_optional: function(element) {
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332 return (element.hasClass("is-optional"))
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333 },
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334 is_mandatory: function(element) {
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335 return (element.hasClass("is-mandatory"))
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336 },
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337 parent_has_class: function(element, cls) {
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338 var parent ;
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339
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340 if ((parent = element.parent()) == null) {
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341 return false ;
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342 }
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343 return (parent.hasClass(cls)) ;
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344 },
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345
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346 add1spectrum_change_handler: function(element) {
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347 var self = this ;
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348 var idElem ;
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349 var valElem ;
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350 var isSuccess ;
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351 var isWarning ;
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352 var isError ;
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353 var isOptional ;
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354 var isMandatory ;
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355
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356 element = $(element) ;
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357 idElem = element.attr("id") ;
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358 valElem = element.val();
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359 console.log(`Change handler called for [${idElem}]=${valElem}`) ;
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360 if (idElem.split("-").slice(0, -1).join("-") == "add1spectrum-peaksMS-msPrecursorIon") {
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361 var index = idElem.split("-")[3] - 1 ;
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362 if (all_contexts[index] !== null && all_contexts[index] !== undefined) {
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363 all_contexts[index].sync_precursor_ion() ;
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364 if (all_contexts[index].hot_MS_Peaks != null) {
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365 all_contexts[index].hot_MS_Peaks.render()
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366 }
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367 }
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368 }
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369 isSuccess = self.is_success(element);
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370 isWarning = self.is_warning(element);
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371 isError = self.is_error(element);
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372 isOptional = self.is_optional(element);
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373 isMandatory = self.is_mandatory(element);
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374
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375 switch(idElem) {
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376 case "add1spectrum-sample-type-{{ TAB_INDEX_PLACEHOLDER }}":
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377 if (valElem == "compound-ref") {
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378 $("#add1spectrum-sample-type-compound-ref-{{ TAB_INDEX_PLACEHOLDER }}").show();
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379 $("#add1spectrum-sample-type-compound-mix-{{ TAB_INDEX_PLACEHOLDER }}").hide();
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380 $("#add1spectrum-sample-type-rcc-added-{{ TAB_INDEX_PLACEHOLDER }}").hide();
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381 } else if (valElem == "compound-mix") {
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382 $("#add1spectrum-sample-type-compound-mix-{{ TAB_INDEX_PLACEHOLDER }}").show();
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383 $("#add1spectrum-sample-type-compound-ref-{{ TAB_INDEX_PLACEHOLDER }}").hide();
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384 $("#add1spectrum-sample-type-rcc-added-{{ TAB_INDEX_PLACEHOLDER }}").show();
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385 self.handsontableRefChemCpdAdded(null);
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386 }
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387 break;
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|
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388 case "add1spectrum-chromatoLC-colConstructor-{{ TAB_INDEX_PLACEHOLDER }}":
|
|
|
389 self.resetElemColor("add1spectrum-chromatoLC-colConstructorOther-{{ TAB_INDEX_PLACEHOLDER }}");
|
|
|
390 if (valElem == "" || valElem == null || valElem != "other" ) {
|
|
|
391 self.disableElem("add1spectrum-chromatoLC-colConstructorOther-{{ TAB_INDEX_PLACEHOLDER }}");
|
|
|
392 } else {
|
|
|
393 self.enableElem("add1spectrum-chromatoLC-colConstructorOther-{{ TAB_INDEX_PLACEHOLDER }}");
|
|
|
394 }
|
|
|
395 break;
|
|
|
396 case "add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}":
|
|
|
397 self.fulfillLCdata(valElem);
|
|
|
398 break;
|
|
|
399 case "add1spectrum-analyzserMS-ionizationMethod-pos-{{ TAB_INDEX_PLACEHOLDER }}":
|
|
|
400 if ($("#add1spectrum-analyzserMS-ionizationMethod-pos-{{ TAB_INDEX_PLACEHOLDER }}").val() != null) {
|
|
|
401 $($("#add1spectrum-peaksMS-polarity-{{ TAB_INDEX_PLACEHOLDER }} option")[1]).attr("disabled", false);
|
|
|
402 }
|
|
|
403 break;
|
|
|
404 case "add1spectrum-analyzserMS-ionizationMethod-neg-{{ TAB_INDEX_PLACEHOLDER }}":
|
|
|
405 if ($("#add1spectrum-analyzserMS-ionizationMethod-neg-{{ TAB_INDEX_PLACEHOLDER }}").val() != null) {
|
|
|
406 $($("#add1spectrum-peaksMS-polarity-{{ TAB_INDEX_PLACEHOLDER }} option")[2]).attr("disabled", false);
|
|
|
407 }
|
|
|
408 break;
|
|
|
409 }
|
|
|
410 if ((isMandatory || isOptional) && (valElem == "" || valElem == null)) {
|
|
|
411 if (isSuccess) {
|
|
|
412 self.rm_success(element) ;
|
|
|
413 } else if (isWarning) {
|
|
|
414 self.rm_warning(element) ;
|
|
|
415 } else if (isError) {
|
|
|
416 self.rm_error(element) ;
|
|
|
417 }
|
|
|
418 if (isMandatory) {
|
|
|
419 self.set_error(element) ;
|
|
|
420 } else {
|
|
|
421 self.set_warning(element) ;
|
|
|
422 }
|
|
|
423 }
|
|
|
424 if (isMandatory && (valElem != "" && valElem != null)) {
|
|
|
425 if (isError) {
|
|
|
426 self.rm_error(element) ;
|
|
|
427 }
|
|
|
428 self.set_success(element) ;
|
|
|
429 } else if (isOptional && valElem != "") {
|
|
|
430 if (isWarning) {
|
|
|
431 self.rm_warning(element) ;
|
|
|
432 }
|
|
|
433 self.set_success(element) ;
|
|
|
434 }
|
|
|
435 if (element.parent().children("input").size() == 2) {
|
|
|
436 if (isMandatory) {
|
|
|
437 if (isSuccess) {
|
|
|
438 self.rm_success(element) ;
|
|
|
439 } else if (isWarning) {
|
|
|
440 self.rm_warning(element) ;
|
|
|
441 } else if (isError) {
|
|
|
442 self.rm_error(element) ;
|
|
|
443 }
|
|
|
444 if (element.parent().children("input").toArray().some(
|
|
|
445 (el) => $(el).val() === null || $(el).val() === ""
|
|
|
446 )) {
|
|
|
447 self.set_error(element) ;
|
|
|
448 } else {
|
|
|
449 self.set_success(element) ;
|
|
|
450 }
|
|
|
451 } else if (isOptional) {
|
|
|
452 isSuccess = self.is_success(element);
|
|
|
453 isWarning = self.is_warning(element);
|
|
|
454 isError = self.is_error(element);
|
|
|
455 if (isSuccess) {
|
|
|
456 self.rm_success(element)
|
|
|
457 } else if (isWarning) {
|
|
|
458 self.rm_warning(element) ;
|
|
|
459 } else if (isError) {
|
|
|
460 self.rm_error(element) ;
|
|
|
461 }
|
|
|
462 if (element.parent().children("input").toArray().some(
|
|
|
463 (el) => ($(el).val() == null || $(el).val() == "")
|
|
|
464 )) {
|
|
|
465 self.set_warning(element) ;
|
|
|
466 } else {
|
|
|
467 self.set_success(element) ;
|
|
|
468 }
|
|
|
469 }
|
|
|
470 }
|
|
|
471 if (element.hasClass("one-or-more")) {
|
|
|
472 // get parent class
|
|
|
473 isSuccess = self.is_success(element);
|
|
|
474 isWarning = self.is_warning(element);
|
|
|
475 isError = self.is_error(element);
|
|
|
476 // reset class
|
|
|
477 if (isSuccess) {
|
|
|
478 self.rm_success(element) ;
|
|
|
479 } else if (isWarning) {
|
|
|
480 self.rm_warning(element) ;
|
|
|
481 } else if (isError) {
|
|
|
482 self.rm_error(element) ;
|
|
|
483 }
|
|
|
484 isTmpSuccess = false;
|
|
|
485 $.each(element.parent().children("input"), function(id, child){
|
|
|
486 if ($(child).val() != null && $(child).val() != "") {
|
|
|
487 isTmpSuccess = true;
|
|
|
488 }
|
|
|
489 });
|
|
|
490 $.each(element.parent().children("select"), function(id, child){
|
|
|
491 if ($(child).val() != null && $(child).val() != "") {
|
|
|
492 isTmpSuccess = true;
|
|
|
493 }
|
|
|
494 });
|
|
|
495 // end parkour
|
|
|
496 element.parent().addClass(
|
|
|
497 isTmpSuccess ? "has-success" : "has-error"
|
|
|
498 );
|
|
|
499 }
|
|
|
500 // CHECK IF OK STEP 2
|
|
|
501 if (element.hasClass("add1spectrum-sampleForm")) {
|
|
|
502 var isBtnStep2OK = true;
|
|
|
503 $.each($(self.prefix + ".add1spectrum-sampleForm"), (id, elem) => {
|
|
|
504 if (self.is_error($(elem)) && $(elem).is(":visible")) {
|
|
|
505 isBtnStep2OK = false;
|
|
|
506 }
|
|
|
507 });
|
|
|
508 if (isBtnStep2OK) {
|
|
|
509 self.rm_class($("#btnSwitch-gotoStep2-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-disabled") ;
|
|
|
510 self.set_class($("#btnSwitch-gotoStep2-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-primary") ;
|
|
|
511 $("#btnSwitch-gotoStep2-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", false);
|
|
|
512 } else {
|
|
|
513 self.set_class($("#btnSwitch-gotoStep2-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-disabled") ;
|
|
|
514 self.rm_class($("#btnSwitch-gotoStep2-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-primary") ;
|
|
|
515 $("#btnSwitch-gotoStep2-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", true);
|
|
|
516 }
|
|
|
517 }
|
|
|
518 // CHECK IF OK STEP 3 - LC
|
|
|
519 if (
|
|
|
520 element.hasClass("add1spectrum-chromatoLCForm")
|
|
|
521 && $("#btnSwitch-gotoStep3-lc-{{ TAB_INDEX_PLACEHOLDER }}").is(":visible")
|
|
|
522 ) {
|
|
|
523 var isBtnStep3OK = true;
|
|
|
524 $.each($(self.prefix+".add1spectrum-chromatoLCForm"), (id, elem) => {
|
|
|
525 if (self.is_error($(elem)) && $(elem).is(":visible"))
|
|
|
526 isBtnStep3OK = false;
|
|
|
527 });
|
|
|
528 if (isBtnStep3OK) {
|
|
|
529 self.rm_class($("#btnSwitch-gotoStep3-lc-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-disabled") ;
|
|
|
530 self.set_class($("#btnSwitch-gotoStep3-lc-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-primary") ;
|
|
|
531 $("#btnSwitch-gotoStep3-lc-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", false);
|
|
|
532 } else {
|
|
|
533 self.set_class($("#btnSwitch-gotoStep3-lc-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-disabled") ;
|
|
|
534 self.rm_class($("#btnSwitch-gotoStep3-lc-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-primary") ;
|
|
|
535 $("#btnSwitch-gotoStep3-lc-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", true);
|
|
|
536 }
|
|
|
537 }
|
|
|
538 // TODO CHECK IF OK STEP 3 - GC
|
|
|
539 // CHECK IF OK STEP 4 - MS ANALYZER
|
|
|
540 if (
|
|
|
541 element.hasClass("add1spectrum-analyzerMSForm")
|
|
|
542 && $("#btnSwitch-gotoStep4-ms-{{ TAB_INDEX_PLACEHOLDER }}").is(":visible")
|
|
|
543 ) {
|
|
|
544 var isBtnStep4OK = true;
|
|
|
545 $.each($(self.prefix+".add1spectrum-analyzerMSForm"), (id, elem) => {
|
|
|
546 if (self.is_error($(elem)) && $(elem).is(":visible"))
|
|
|
547 isBtnStep4OK = false;
|
|
|
548 });
|
|
|
549 if (isBtnStep4OK) {
|
|
|
550 self.rm_class($("#btnSwitch-gotoStep4-ms-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-disabled") ;
|
|
|
551 self.set_class($("#btnSwitch-gotoStep4-ms-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-primary") ;
|
|
|
552 $("#btnSwitch-gotoStep4-ms-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", false);
|
|
|
553 } else {
|
|
|
554 self.set_class($("#btnSwitch-gotoStep4-ms-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-disabled") ;
|
|
|
555 self.rm_class($("#btnSwitch-gotoStep4-ms-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-primary") ;
|
|
|
556 $("#btnSwitch-gotoStep4-ms-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", true);
|
|
|
557 }
|
|
|
558 }
|
|
|
559 // CHECK IF OK STEP 5 - PEAKS
|
|
|
560 if (
|
|
|
561 element.hasClass("add1spectrum-peaksMSForm-peaklist")
|
|
|
562 && $("#btnSwitch-gotoStep5-ms-{{ TAB_INDEX_PLACEHOLDER }}").is(":visible")
|
|
|
563 ) {
|
|
|
564 var isBtnStep5OK = true;
|
|
|
565 $.each($(self.prefix+".add1spectrum-peaksMSForm-peaklist"), (id, elem) => {
|
|
|
566 if (self.is_error($(elem)) && $(elem).is(":visible"))
|
|
|
567 isBtnStep5OK = false;
|
|
|
568 });
|
|
|
569 if (isBtnStep5OK && (self.is_ms() || self.a_ion_parent_is_selected())) {
|
|
|
570 self.rm_class($("#btnSwitch-gotoStep5-ms-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-disabled") ;
|
|
|
571 self.set_class($("#btnSwitch-gotoStep5-ms-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-primary") ;
|
|
|
572 $("#btnSwitch-gotoStep5-ms-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", false);
|
|
|
573 } else {
|
|
|
574 self.set_class($("#btnSwitch-gotoStep5-ms-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-disabled") ;
|
|
|
575 self.rm_class($("#btnSwitch-gotoStep5-ms-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-primary") ;
|
|
|
576 $("#btnSwitch-gotoStep5-ms-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", true);
|
|
|
577 }
|
|
|
578 }
|
|
|
579 // CHECK IF OK STEP 6 - OTHER DATA
|
|
|
580 if (
|
|
|
581 element.hasClass("add1spectrum-otherForm")
|
|
|
582 && $("#btnSwitch-gotoStep6-{{ TAB_INDEX_PLACEHOLDER }}").is(":visible")
|
|
|
583 ) {
|
|
|
584 self.checkIfEnableSubmit() ;
|
|
|
585 }
|
|
|
586 },
|
|
|
587
|
|
|
588 a_ion_parent_is_selected: function() {
|
|
|
589 return (this.get_selected_parent_ion_mz() !== null) ;
|
|
|
590 },
|
|
|
591
|
|
|
592 get_selected_parent_ion_index: function() {
|
|
|
593 var curent_mz = this.get_selected_parent_ion_mz() ;
|
|
|
594 if (curent_mz === null) {
|
|
|
595 return null;
|
|
|
596 }
|
|
|
597 if (this.hot_MS_Peaks == undefined) {
|
|
|
598 return null ;
|
|
|
599 }
|
|
|
600 var data = this.hot_MS_Peaks.getData() ;
|
|
|
601 for (var i = 0 ; i < data.length ; i += 1) {
|
|
|
602 if (Math.abs(data[i][0] - curent_mz) < 0.0001) {
|
|
|
603 return i ;
|
|
|
604 }
|
|
|
605 }
|
|
|
606 return null ;
|
|
|
607 },
|
|
|
608
|
|
|
609 get_selected_parent_ion_mz: function() {
|
|
|
610 return $(
|
|
|
611 "#add1spectrum-peaksMS-msPrecursorIon-{{ TAB_INDEX_PLACEHOLDER }}"
|
|
|
612 ).val() || null ;
|
|
|
613 },
|
|
|
614
|
|
|
615 auto_set_spec_type: function() {
|
|
|
616 console.log("auto_set_spec_type...") ;
|
|
|
617 var self = this ;
|
|
|
618 var id = `#set_${self.DEFAULT_DATA["spectrum_type"]}_spectrum_button` ;
|
|
|
619 var element = $(self.prefix + id) ;
|
|
|
620 if (element.length) {
|
|
|
621 element.click() ;
|
|
|
622 console.log(`auto_set_spec_type to ${self.DEFAULT_DATA["spectrum_type"]} ok.`)
|
|
|
623 } else {
|
|
|
624 console.log(element)
|
|
|
625 console.log("Failed!")
|
|
|
626 }
|
|
|
627 if (self.DEFAULT_DATA["sample_type"]) {
|
|
|
628 self.auto_set_sample_type(self) ;
|
|
|
629 }
|
|
|
630 },
|
|
|
631
|
|
|
632 auto_set_sample_type: function() {
|
|
|
633 console.log("auto_set_sample_type...") ;
|
|
|
634 var self = this ;
|
|
|
635 var id = "#add1spectrum-sample-type-{{ TAB_INDEX_PLACEHOLDER }}" ;
|
|
|
636 var element = $(id) ;
|
|
|
637 if (element.length) {
|
|
|
638 element.val(self.DEFAULT_DATA["sample_type"]).change() ;
|
|
|
639 console.log(`auto_set_sample_type to ${self.DEFAULT_DATA["sample_type"]} ok.`) ;
|
|
|
640 if (self.DEFAULT_DATA["sample_type"] == "compound-ref") {
|
|
|
641 $("#add1spectrum-sample-mixSolvent-{{ TAB_INDEX_PLACEHOLDER }}").val(
|
|
|
642 "H2O/ethanol (75/25)"
|
|
|
643 ).change() ;
|
|
|
644 }
|
|
|
645 } else {
|
|
|
646 console.log(element)
|
|
|
647 console.log("Failed!")
|
|
|
648 }
|
|
|
649 if (self.DEFAULT_DATA["inchikey"]) {
|
|
|
650 setTimeout(() => self.auto_set_inchikey(self), 1000) ;
|
|
|
651 }
|
|
|
652 },
|
|
|
653
|
|
|
654 auto_set_inchikey: function() {
|
|
|
655 console.log("auto_set_inchikey...") ;
|
|
|
656 var self = this ;
|
|
|
657 var id ;
|
|
|
658 var element ;
|
|
|
659 self.inchikey = self.DEFAULT_DATA["inchikey"] ;
|
|
|
660 if (self.is_ref()) {
|
|
|
661 id = "#add1spectrum-sample-inchikey-{{ TAB_INDEX_PLACEHOLDER }}:text" ;
|
|
|
662 element = $(id) ;
|
|
|
663 if (element.length) {
|
|
|
664 console.log(`auto_set_inchikey to ${self.inchikey} ok.`)
|
|
|
665 element.val(self.inchikey).change() ;
|
|
|
666 console.log(`Inchikey set!`) ;
|
|
|
667 } else {
|
|
|
668 console.log(element)
|
|
|
669 console.log("Failed!")
|
|
|
670 }
|
|
|
671 } else {
|
|
|
672 for (var index = 0 ; index < all_contexts.length ; index += 1) {
|
|
|
673 if (all_contexts[index] === null || all_contexts[index] === undefined) {
|
|
|
674 continue;
|
|
|
675 }
|
|
|
676 var inchikey = all_contexts[index].DEFAULT_DATA["inchikey"] ;
|
|
|
677 id = `#container_RCC_ADDED-1 tbody:nth(0) tr:nth(${index}) td:nth(1)` ;
|
|
|
678 element = $(id) ;
|
|
|
679 if (element.length) {
|
|
|
680 console.log(`auto_set_inchikey to ${inchikey} ok.`)
|
|
|
681 self.hot_RCC_ADDED.setDataAtCell(index, 1, inchikey) ;
|
|
|
682 element.innerHTML = inchikey ;
|
|
|
683 element.change() ;
|
|
|
684 console.log(element) ;
|
|
|
685 console.log(`Inchikey set!`) ;
|
|
|
686 } else {
|
|
|
687 console.log(element)
|
|
|
688 console.log("Failed!")
|
|
|
689 }
|
|
|
690 }
|
|
|
691 console.log(self.hot_RCC_ADDED)
|
|
|
692 self.hot_RCC_ADDED.render() ;
|
|
|
693 }
|
|
|
694 $("#btnSwitch-gotoStep2-{{ TAB_INDEX_PLACEHOLDER }}").click() ;
|
|
|
695 if (self.DEFAULT_DATA["method"]) {
|
|
|
696 setTimeout(() => self.auto_set_method(self), 1000) ;
|
|
|
697 }
|
|
|
698 },
|
|
|
699
|
|
|
700 auto_set_method: function() {
|
|
|
701 console.log("auto_set_method...") ;
|
|
|
702 var self = this ;
|
|
|
703 var id = "#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}" ;
|
|
|
704 var element = $(id) ;
|
|
|
705 element.length && element.val(self.DEFAULT_DATA["method"]).change() ;
|
|
|
706 $("#btnSwitch-gotoStep3-lc-{{ TAB_INDEX_PLACEHOLDER }}").click() ;
|
|
|
707 setTimeout(() => {
|
|
|
708 (() => {
|
|
|
709 $("#btnSwitch-gotoStep4-ms-{{ TAB_INDEX_PLACEHOLDER }}").click() ;
|
|
|
710 console.log(`auto_set_method to ${self.DEFAULT_DATA["method"]} ok.`)
|
|
|
711 if (self.DEFAULT_DATA["scan_type"]) {
|
|
|
712
|
|
|
713 // The scan type needs to be skipped, as it is already defined
|
|
|
714 // at build-time
|
|
|
715 // The code is kept for future modifications of this behavior
|
|
|
716 setTimeout(() => self.auto_set_scan_type(self, skip = true), 1000) ;
|
|
|
717 }
|
|
|
718 })(self)
|
|
|
719 }, 1000) ;
|
|
|
720 },
|
|
|
721
|
|
|
722 auto_set_scan_type: function(skip = false) {
|
|
|
723 var self = this ;
|
|
|
724 if (!skip) {
|
|
|
725 console.log("auto_set_scan_type...") ;
|
|
|
726 var id = "#add1spectrum-peaksMS-msLevel-{{ TAB_INDEX_PLACEHOLDER }}" ;
|
|
|
727 var element = $(id) ;
|
|
|
728 if (element.length) {
|
|
|
729 element.val(self.DEFAULT_DATA["scan_type"]).change() ;
|
|
|
730 console.log(`auto_set_scan_type to ${self.DEFAULT_DATA["scan_type"]} ok.`)
|
|
|
731 } else {
|
|
|
732 console.log("Failed!")
|
|
|
733 }
|
|
|
734 }
|
|
|
735 if (self.DEFAULT_DATA["polarity"]) {
|
|
|
736 self.auto_set_polarity(self) ;
|
|
|
737 }
|
|
|
738 },
|
|
|
739
|
|
|
740 auto_set_polarity: function() {
|
|
|
741 console.log("auto_set_polarity...") ;
|
|
|
742 var self = this ;
|
|
|
743 var id = "#add1spectrum-peaksMS-polarity-{{ TAB_INDEX_PLACEHOLDER }}" ;
|
|
|
744 var element = $(id) ;
|
|
|
745 if (element.length) {
|
|
|
746 element.val(self.DEFAULT_DATA["polarity"]).change() ;
|
|
|
747 console.log(`auto_set_polarity to ${self.DEFAULT_DATA["polarity"]} ok.`)
|
|
|
748 } else {
|
|
|
749 console.log("Failed!")
|
|
|
750 }
|
|
|
751 if (self.DEFAULT_DATA["resolution"]) {
|
|
|
752 self.auto_set_resolution(self) ;
|
|
|
753 }
|
|
|
754 },
|
|
|
755
|
|
|
756 auto_set_resolution: function() {
|
|
|
757 console.log("auto_set_resolution...") ;
|
|
|
758 var self = this ;
|
|
|
759 var id = "#add1spectrum-peaksMS-resolution-{{ TAB_INDEX_PLACEHOLDER }}" ;
|
|
|
760 var element = $(id) ;
|
|
|
761 if (element.length) {
|
|
|
762 element.val(self.DEFAULT_DATA["resolution"]).change() ;
|
|
|
763 console.log(`auto_set_resolution to ${self.DEFAULT_DATA["resolution"]} ok.`)
|
|
|
764 } else {
|
|
|
765 console.log("Failed!")
|
|
|
766 }
|
|
|
767 if (self.DEFAULT_DATA["next"] || true) {
|
|
|
768 setTimeout(() => self.finish_initialized(self), 1000) ;
|
|
|
769 }
|
|
|
770 },
|
|
|
771
|
|
|
772 finish_initialized: function() {
|
|
|
773 var self = this ;
|
|
|
774 if (ctx() === self) {
|
|
|
775 self.initialized = true ;
|
|
|
776 }
|
|
|
777 },
|
|
|
778
|
|
|
779 //USED IN HTML
|
|
|
780 updateLCMSspectraViewer: function() {
|
|
|
781 var self = this ;
|
|
|
782 var tab_no ;
|
|
|
783 console.log(`Updating spectral view for tab {{ TAB_INDEX_PLACEHOLDER }}`) ;
|
|
|
784 // reset current viewer
|
|
|
785 $("#containter-lcms-spectrum-preview-{{ TAB_INDEX_PLACEHOLDER }}").empty();
|
|
|
786 // reset data.
|
|
|
787
|
|
|
788 if (self.is_mix()) {
|
|
|
789 tab_no = 1 ;
|
|
|
790 } else {
|
|
|
791 tab_no = {{ TAB_INDEX_PLACEHOLDER }} ;
|
|
|
792 }
|
|
|
793 var range_from = $(`#add1spectrum-peaksMS-rangeFrom-${tab_no}`) ;
|
|
|
794 if ((spectrumMinPPM = Number(range_from.val())) == "") {
|
|
|
795 spectrumMinPPM = 10000;
|
|
|
796 }
|
|
|
797 var range_to = $(`#add1spectrum-peaksMS-rangeTo-${tab_no}`) ;
|
|
|
798 if ((spectrumMaxPPM = Number(range_to.val())) == "") {
|
|
|
799 spectrumMaxPPM = 0;
|
|
|
800 }
|
|
|
801 maxGraph = 0;
|
|
|
802 var localData = [];
|
|
|
803 var localDataAnnot = [];
|
|
|
804 // gather new data
|
|
|
805 // TODO switch tab in function of technic
|
|
|
806 $.each(self.hot_MS_Peaks.getData(), function() {
|
|
|
807 if(this[0] != undefined && this[0] != "") {
|
|
|
808 var x = (Number(this[0]));
|
|
|
809 var y = Number(this[2]);
|
|
|
810 var a = this[6];
|
|
|
811 localData.push([(x-0.000001),-150]);
|
|
|
812 localData.push([(x+0.000001),-150]);
|
|
|
813 localData.push([x,y]);
|
|
|
814 localDataAnnot[x] = a;
|
|
|
815 if (x < spectrumMinPPM) {
|
|
|
816 spectrumMinPPM = x;
|
|
|
817 }
|
|
|
818 if (x > spectrumMaxPPM) {
|
|
|
819 spectrumMaxPPM = x;
|
|
|
820 }
|
|
|
821 if (y > maxGraph) {
|
|
|
822 maxGraph = y;
|
|
|
823 }
|
|
|
824 }
|
|
|
825 });
|
|
|
826
|
|
|
827 // build new one
|
|
|
828 spectrumMinPPM = spectrumMinPPM - (0.1 * spectrumMinPPM);
|
|
|
829 spectrumMaxPPM = spectrumMaxPPM + (0.1 * spectrumMaxPPM);
|
|
|
830 maxGraph = maxGraph + (0.1 * maxGraph);
|
|
|
831 localData.sort();
|
|
|
832 console.log(localData)
|
|
|
833 // build graph
|
|
|
834 $("#containter-lcms-spectrum-preview-{{ TAB_INDEX_PLACEHOLDER }}").highcharts({
|
|
|
835 chart: {
|
|
|
836 zoomType: "x",
|
|
|
837 spacingRight: 10,
|
|
|
838 spacingLeft: 10,
|
|
|
839 type: "scatter"
|
|
|
840 },
|
|
|
841 title: {
|
|
|
842 text: "Spectrum Preview",
|
|
|
843 useHTML: true
|
|
|
844 },
|
|
|
845 subtitle: {
|
|
|
846 text: (
|
|
|
847 document.ontouchstart === undefined
|
|
|
848 ? "Select area"
|
|
|
849 : "Pinch the chart to zoom in"
|
|
|
850 )
|
|
|
851 },
|
|
|
852 xAxis: {
|
|
|
853 type: "number",
|
|
|
854 title: {text: "m/z"},
|
|
|
855 min: spectrumMinPPM,
|
|
|
856 max: spectrumMaxPPM,
|
|
|
857 labels: {
|
|
|
858 formatter: function() {
|
|
|
859 return (Math.abs(this.value) + "");
|
|
|
860 }
|
|
|
861 }
|
|
|
862 },
|
|
|
863 yAxis: {
|
|
|
864 title: {text: "Relative Intensity (%)"},
|
|
|
865 min: 0,
|
|
|
866 max: maxGraph
|
|
|
867 },
|
|
|
868 tooltip: {
|
|
|
869 crosshairs: true,
|
|
|
870 formatter: function() {
|
|
|
871 var compo = "";
|
|
|
872 return (
|
|
|
873 "<b>" + this.series.name
|
|
|
874 + "</b><br/>m/z:" + Math.abs(this.x) + ""
|
|
|
875 + ";<br/>Relative Intensity: " + this.y
|
|
|
876 + "%;<br/>Annotation: " + localDataAnnot[ this.x]
|
|
|
877 + ""
|
|
|
878 );
|
|
|
879 }
|
|
|
880 },
|
|
|
881 legend: {enabled: false},
|
|
|
882 plotOptions: {scatter: {}},
|
|
|
883 series: [{
|
|
|
884 name: "preview",
|
|
|
885 showInLegend: true,
|
|
|
886 color: "#f00",
|
|
|
887 lineColor: "#f00",
|
|
|
888 pointInterval: 10,
|
|
|
889 pointStart: 100,
|
|
|
890 lineWidth : 2,
|
|
|
891 marker: {
|
|
|
892 enabled: true,
|
|
|
893 radius: 2,
|
|
|
894 lineColor: "#f00"
|
|
|
895 },
|
|
|
896 data: localData,
|
|
|
897 zIndex: 10
|
|
|
898 }]
|
|
|
899 });
|
|
|
900 },
|
|
|
901
|
|
|
902 //USED HERE
|
|
|
903 fulfillLCdata: function(jsonFileName) {
|
|
|
904 var self = this ;
|
|
|
905 var url = `{{ PF_URL_PLACEHOLDER }}/webapp/resources/json/lc-methods/${jsonFileName}.json` ;
|
|
|
906 $.getJSON(url, function(json) {
|
|
|
907 // $.POST
|
|
|
908 console.log(json);
|
|
|
909 // lc chromato
|
|
|
910 if (json.lc_chromatography != null) {
|
|
|
911 [
|
|
|
912 ["colConstructor", "column_constructor"],
|
|
|
913 ["colConstructorOther", "column_constructor_other"],
|
|
|
914 ["colName", "column_name"],
|
|
|
915 ["colLength", "column_length"],
|
|
|
916 ["colDiameter", "column_diameter"],
|
|
|
917 ["colParticuleSize", "particule_size"],
|
|
|
918 ["colTemperature", "column_temperature"],
|
|
|
919 ["separationFlowRate", "separation_flow_rate"],
|
|
|
920 ["separationSolvA", "separation_solvent_a"],
|
|
|
921 ["separationSolvApH", "ph_solvent_a"],
|
|
|
922 ["separationSolvB", "separation_solvent_b"],
|
|
|
923 ["separationSolvBpH", "ph_solvent_b"]
|
|
|
924 ].forEach((arr) => {
|
|
|
925 var el ;
|
|
|
926 console.log(arr)
|
|
|
927 el = $(`#add1spectrum-chromatoLC-${arr[0]}-{{ TAB_INDEX_PLACEHOLDER }}`)
|
|
|
928 el.val(json.lc_chromatography[arr[1]]) ;
|
|
|
929 el.change()
|
|
|
930 })
|
|
|
931 try {
|
|
|
932 $("#add1spectrum-chromatoLC-LCMode-{{ TAB_INDEX_PLACEHOLDER }}").val(json.lc_chromatography.LC_mode);
|
|
|
933 $("#add1spectrum-chromatoLC-LCMode-{{ TAB_INDEX_PLACEHOLDER }}").change();
|
|
|
934 } catch (e) {}
|
|
|
935 var handsontableSeparationFlowRateData = [] ;
|
|
|
936 if (json.lc_chromatography.separation_flow_gradient != null) {
|
|
|
937 $.each(json.lc_chromatography.separation_flow_gradient, function() {
|
|
|
938 var e = [
|
|
|
939 "" + this.time,
|
|
|
940 "" + this.solvA,
|
|
|
941 "" + this.solvB
|
|
|
942 ];
|
|
|
943 handsontableSeparationFlowRateData.push(e);
|
|
|
944 });
|
|
|
945 } else {
|
|
|
946 handsontableSeparationFlowRateData = null;
|
|
|
947 }
|
|
|
948 self.handsontableSeparationFlowRate(handsontableSeparationFlowRateData);
|
|
|
949 }
|
|
|
950 // ms_analyzer
|
|
|
951 if (json.ms_analyzer != null) {
|
|
|
952 $("#add1spectrum-analyzer-ms-instrument-{{ TAB_INDEX_PLACEHOLDER }}").val(json.ms_analyzer.instrument);
|
|
|
953 $("#add1spectrum-analyzer-ms-instrument-{{ TAB_INDEX_PLACEHOLDER }}").change();
|
|
|
954 $("#add1spectrum-analyzer-ms-model-{{ TAB_INDEX_PLACEHOLDER }}").val(json.ms_analyzer.model);
|
|
|
955 $("#add1spectrum-analyzer-ms-model-{{ TAB_INDEX_PLACEHOLDER }}").change();
|
|
|
956 $("#add1spectrum-analyzer-ms-resolutionFWHM-{{ TAB_INDEX_PLACEHOLDER }}").val(json.ms_analyzer.resolution_FWHM);
|
|
|
957 $("#add1spectrum-analyzer-ms-resolutionFWHM-{{ TAB_INDEX_PLACEHOLDER }}").change();
|
|
|
958 $("#add1spectrum-analyzer-ms-ionAnalyzerType-{{ TAB_INDEX_PLACEHOLDER }}").val(json.ms_analyzer.ion_analyzer_type);
|
|
|
959 $("#add1spectrum-analyzer-ms-ionAnalyzerType-{{ TAB_INDEX_PLACEHOLDER }}").change();
|
|
|
960 }
|
|
|
961 if (json.molecule_ionization != null) {
|
|
|
962 ["pos", "neg"].forEach((mode) => {
|
|
|
963 if (json.molecule_ionization[`mode_${mode}`] != null) {
|
|
|
964 [
|
|
|
965 ["ionizationMethod", "ionisation_method"],
|
|
|
966 ["sprayGazFlow", "spray_gaz_flow"],
|
|
|
967 ["vaporizerGazFlow", "vaporizer_gaz_flow"],
|
|
|
968 ["vaporizerTemperature", "vaporizer_temperature"],
|
|
|
969 ["sourceGazFlow", "source_gaz_flow"],
|
|
|
970 ["ionTransferTubeTemperatureOrTransferCapillaryTemperature", "transfer_tube_or_capillary_temperature"],
|
|
|
971 ["highVoltageOrCoronaVoltage", "voltage"],
|
|
|
972 ].forEach((tuple) => {
|
|
|
973 var el ;
|
|
|
974 var id = tuple[0] ;
|
|
|
975 var key = tuple[1] ;
|
|
|
976 el = $(`#add1spectrum-analyzserMS-${id}-${mode}-{{ TAB_INDEX_PLACEHOLDER }}`) ;
|
|
|
977 console.log(el)
|
|
|
978 el.val(json.molecule_ionization[`mode_${mode}`][key]);
|
|
|
979 el.change() ;
|
|
|
980 })
|
|
|
981 }
|
|
|
982 })
|
|
|
983 }
|
|
|
984
|
|
|
985 if (json.molecule_beamOrTrap != null) {
|
|
|
986 if (json.molecule_beamOrTrap.ion_beam != null) {
|
|
|
987 $("#add1spectrum-ionTrapBeam-type-{{ TAB_INDEX_PLACEHOLDER }}").val("beam").change();
|
|
|
988 $("#add1spectrum-ionTrapBeam-ionGas-{{ TAB_INDEX_PLACEHOLDER }}").val(json.molecule_beamOrTrap.ion_beam.ion_gas).change();
|
|
|
989 $("#add1spectrum-ionTrapBeam-ionGasPressureValue-{{ TAB_INDEX_PLACEHOLDER }}").val(json.molecule_beamOrTrap.ion_beam.ion_pressure_value).change();
|
|
|
990 $("#add1spectrum-ionTrapBeam-ionGasPressureUnit-{{ TAB_INDEX_PLACEHOLDER }}").val(json.molecule_beamOrTrap.ion_beam.ion_pressure_unit).change();
|
|
|
991 }
|
|
|
992 if (json.molecule_beamOrTrap.ion_trap != null) {
|
|
|
993 $("#add1spectrum-ionTrapBeam-type-{{ TAB_INDEX_PLACEHOLDER }}").val("trap").change();
|
|
|
994 $("#add1spectrum-ionTrapBeam-ionGas-{{ TAB_INDEX_PLACEHOLDER }}").val(json.molecule_beamOrTrap.ion_trap.ion_gas).change();
|
|
|
995 $("#add1spectrum-ionTrapBeam-ionGasPressureValue-{{ TAB_INDEX_PLACEHOLDER }}").val(json.molecule_beamOrTrap.ion_trap.ion_pressure_value).change();
|
|
|
996 $("#add1spectrum-ionTrapBeam-ionGasPressureUnit-{{ TAB_INDEX_PLACEHOLDER }}").val(json.molecule_beamOrTrap.ion_trap.ion_pressure_unit).change();
|
|
|
997 $("#add1spectrum-ionTrapBeam-ionNumber-{{ TAB_INDEX_PLACEHOLDER }}").val(json.molecule_beamOrTrap.ion_trap.ion_number).change();
|
|
|
998 $("#add1spectrum-ionTrapBeam-ionFrequencyShift-{{ TAB_INDEX_PLACEHOLDER }}").val(json.molecule_beamOrTrap.ion_trap.ion_freq_shift).change();
|
|
|
999 }
|
|
|
1000 }
|
|
|
1001 // other
|
|
|
1002 if (json.other != null) {
|
|
|
1003 $("#add1spectrum-other-author-{{ TAB_INDEX_PLACEHOLDER }}").val(json.other.data_authors);
|
|
|
1004 $("#add1spectrum-other-author-{{ TAB_INDEX_PLACEHOLDER }}").change();
|
|
|
1005 $("#add1spectrum-other-validator-{{ TAB_INDEX_PLACEHOLDER }}").val(json.other.data_validator);
|
|
|
1006 $("#add1spectrum-other-validator-{{ TAB_INDEX_PLACEHOLDER }}").change();
|
|
|
1007 $("#add1spectrum-other-date-{{ TAB_INDEX_PLACEHOLDER }}").val(json.other.acquisition_date);
|
|
|
1008 $("#add1spectrum-other-date-{{ TAB_INDEX_PLACEHOLDER }}").change();
|
|
|
1009 $("#add1spectrum-other-owner-{{ TAB_INDEX_PLACEHOLDER }}").val(json.other.data_ownership);
|
|
|
1010 $("#add1spectrum-other-owner-{{ TAB_INDEX_PLACEHOLDER }}").change();
|
|
|
1011 }
|
|
|
1012 }).error(function(event, jqxhr, exception) {
|
|
|
1013 if (event.status == 404) {
|
|
|
1014 $("#alertBoxSelectTemplate-{{ TAB_INDEX_PLACEHOLDER }}").html(`
|
|
|
1015 <div class="alert alert-danger alert-dismissible" role="alert">
|
|
|
1016 <button type="button" class="close" data-dismiss="alert">
|
|
|
1017 <span aria-hidden="true">×</span>
|
|
|
1018 <span class="sr-only"><spring:message code="alert.close" text="Close" /></span>
|
|
|
1019 </button>
|
|
|
1020 <strong>
|
|
|
1021 <spring:message code="alert.strong.error" text="Error!" />
|
|
|
1022 </strong> unable to load pre-filled data!
|
|
|
1023 </div>
|
|
|
1024 `);
|
|
|
1025 }
|
|
|
1026 });
|
|
|
1027 },
|
|
|
1028
|
|
|
1029 //USED HERE
|
|
|
1030 resetFromColors: function() {
|
|
|
1031
|
|
|
1032 var self = this ;
|
|
|
1033 $.each($(self.prefix+".add1spectrum"), function(id, elem) {
|
|
|
1034 element = $(elem)
|
|
|
1035 self.rm_success(element) ;
|
|
|
1036 self.rm_warning(element) ;
|
|
|
1037 self.rm_error(element) ;
|
|
|
1038 if ($(elem).hasClass("is-mandatory") && ($(elem).val() == "" || $(elem).val() == null)) {
|
|
|
1039 self.set_error($(elem)) ;
|
|
|
1040 }
|
|
|
1041 if ($(elem).hasClass("is-optional") && ($(elem).val() == "" || $(elem).val() == null)) {
|
|
|
1042 self.set_warning($(elem)) ;
|
|
|
1043 }
|
|
|
1044 if ($(elem).val() != "" && $(elem).val() != null) {
|
|
|
1045 self.set_success($(elem)) ;
|
|
|
1046 }
|
|
|
1047 });
|
|
|
1048 $.each($(self.prefix+"button.switchStep"), function(id, elem) {
|
|
|
1049 if (!$(this).hasClass("btn-disabled")) {
|
|
|
1050 $(this).addClass("btn-disabled");
|
|
|
1051 }
|
|
|
1052 if ($(this).hasClass("btn-primary")) {
|
|
|
1053 $(this).removeClass("btn-primary");
|
|
|
1054 }
|
|
|
1055 $(this).prop("disabled", true);
|
|
|
1056 });
|
|
|
1057
|
|
|
1058 // peak list: no data to check
|
|
|
1059 $("#btnSwitch-gotoStep5-ms-{{ TAB_INDEX_PLACEHOLDER }}").removeClass("btn-disabled");
|
|
|
1060 $("#btnSwitch-gotoStep5-ms-{{ TAB_INDEX_PLACEHOLDER }}").addClass("btn-primary");
|
|
|
1061 $("#btnSwitch-gotoStep5-ms-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", false);
|
|
|
1062
|
|
|
1063 $("#add1spectrum-other-author-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", false);
|
|
|
1064 $("#add1spectrum-other-validator-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", false);
|
|
|
1065 $("#add1spectrum-other-date-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", false);
|
|
|
1066 $("#add1spectrum-other-owner-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", false);
|
|
|
1067 $("#add1spectrum-other-fileName-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", false);
|
|
|
1068 $("#add1spectrum-other-fileSize-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", false);
|
|
|
1069 },
|
|
|
1070
|
|
|
1071 //USED IN HTML
|
|
|
1072 switchToStep: function(step) {
|
|
|
1073
|
|
|
1074 var self = this ;
|
|
|
1075 switch(step) {
|
|
|
1076 case 2:
|
|
|
1077 // hide after step 2 / alt step 2
|
|
|
1078 $("#add1spectrum-chromatographyData-LC-{{ TAB_INDEX_PLACEHOLDER }}").hide();
|
|
|
1079 $("#add1spectrum-chromatographyData-GC-{{ TAB_INDEX_PLACEHOLDER }}").hide();
|
|
|
1080 $("#add1spectrum-analyserData-MS-{{ TAB_INDEX_PLACEHOLDER }}").hide();
|
|
|
1081 $("#add1spectrum-peaksData-MS-{{ TAB_INDEX_PLACEHOLDER }}").hide();
|
|
|
1082 $("#add1spectrum-otherData-{{ TAB_INDEX_PLACEHOLDER }}").hide();
|
|
|
1083 if ($("#step1sign-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("fa-question-circle")) {
|
|
|
1084 $("#step1sign-{{ TAB_INDEX_PLACEHOLDER }}").removeClass("fa-question-circle").addClass("fa-check-circle");
|
|
|
1085 }
|
|
|
1086 if (self.is_ms()) {
|
|
|
1087 $("#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}").empty();
|
|
|
1088 $("#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}").append(
|
|
|
1089 '<option value="" selected="selected" disabled="disabled">choose in list…</option>'
|
|
|
1090 );
|
|
|
1091 $.getJSON("{{ PF_URL_PLACEHOLDER }}/webapp/resources/json/list-lc-methods.json", function(data) {
|
|
|
1092 // load data from json
|
|
|
1093 $.each(data.methods,function() {
|
|
|
1094 if (this.name !== undefined) {
|
|
|
1095 if (this.value !== undefined) {
|
|
|
1096 $("#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}").append(
|
|
|
1097 `<option value="${this.value}">${this.name}</option>`
|
|
|
1098 );
|
|
|
1099 } else {
|
|
|
1100 $("#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}").append(
|
|
|
1101 `<option disabled>${this.name}</option>`
|
|
|
1102 );
|
|
|
1103 }
|
|
|
1104 }
|
|
|
1105 });
|
|
|
1106 });
|
|
|
1107 } else if (self.is_ms2()) {
|
|
|
1108 $("#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}").empty();
|
|
|
1109 $("#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}").append(
|
|
|
1110 '<option value="" selected="selected" disabled="disabled">choose in list…</option>'
|
|
|
1111 );
|
|
|
1112 $.getJSON(
|
|
|
1113 "{{ PF_URL_PLACEHOLDER }}/webapp/resources/json/list-lc-msms-methods.json",
|
|
|
1114 function(data) {
|
|
|
1115 // load data from json
|
|
|
1116 $.each(data.methods, function() {
|
|
|
1117 if (this.name !== undefined) {
|
|
|
1118 if (this.value !== undefined) {
|
|
|
1119 $("#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}").append(
|
|
|
1120 `<option value="${this.value}">${this.name}</option>`
|
|
|
1121 );
|
|
|
1122 } else {
|
|
|
1123 $("#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}").append(
|
|
|
1124 `<option disabled>${this.name}</option>`
|
|
|
1125 );
|
|
|
1126 }
|
|
|
1127 }
|
|
|
1128 });
|
|
|
1129 }
|
|
|
1130 );
|
|
|
1131 }
|
|
|
1132 // check panel to show
|
|
|
1133 if (self.isLC) {
|
|
|
1134 $("#add1spectrum-chromatographyData-LC-{{ TAB_INDEX_PLACEHOLDER }}").show();
|
|
|
1135 $("#linkActivateStep2-lc-{{ TAB_INDEX_PLACEHOLDER }}").trigger("click");
|
|
|
1136 var sign = $("#step2-lc-sign-{{ TAB_INDEX_PLACEHOLDER }}") ;
|
|
|
1137 self.rm_class(sign, "fa-check-circle") && self.set_class(sign, "fa-question-circle") ;
|
|
|
1138 if (!self.isSeparationFlowRateInit) {
|
|
|
1139 self.handsontableSeparationFlowRate(null);
|
|
|
1140 self.isSeparationFlowRateInit = true;
|
|
|
1141 }
|
|
|
1142 } else if (self.isGC) {
|
|
|
1143 $("#add1spectrum-chromatographyData-GC-{{ TAB_INDEX_PLACEHOLDER }}").show();
|
|
|
1144 $("#linkActivateStep2-gc-{{ TAB_INDEX_PLACEHOLDER }}").trigger("click");
|
|
|
1145 var sign = $("#step2-gc-sign-{{ TAB_INDEX_PLACEHOLDER }}") ;
|
|
|
1146 sign.removeClass("fa-check-circle").addClass("fa-question-circle");
|
|
|
1147 if ($("#step2-gc-sign-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("fa-check-circle")) {
|
|
|
1148 }
|
|
|
1149 } else if (self.isIC) {
|
|
|
1150 $("#add1spectrum-chromatographyData-IC-{{ TAB_INDEX_PLACEHOLDER }}").show();
|
|
|
1151 $("#linkActivateStep2-ic-{{ TAB_INDEX_PLACEHOLDER }}").trigger("click");
|
|
|
1152 if ($("#step2-ic-sign-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("fa-check-circle")) {
|
|
|
1153 $("#step2-ic-sign-{{ TAB_INDEX_PLACEHOLDER }}").removeClass("fa-check-circle").addClass("fa-question-circle");
|
|
|
1154 }
|
|
|
1155 }
|
|
|
1156 break;
|
|
|
1157 case 3:
|
|
|
1158 // hide after step 3 / alt step 3
|
|
|
1159 $("#add1spectrum-analyserData-MS-{{ TAB_INDEX_PLACEHOLDER }}").hide();
|
|
|
1160 $("#add1spectrum-peaksData-MS-{{ TAB_INDEX_PLACEHOLDER }}").hide();
|
|
|
1161 $("#add1spectrum-otherData-{{ TAB_INDEX_PLACEHOLDER }}").hide();
|
|
|
1162 // step 2 ok
|
|
|
1163 if ($("#step2-lc-sign-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("fa-question-circle")) {
|
|
|
1164 $("#step2-lc-sign-{{ TAB_INDEX_PLACEHOLDER }}").removeClass("fa-question-circle").addClass("fa-check-circle");
|
|
|
1165 }
|
|
|
1166 if ($("#step2-gc-sign-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("fa-question-circle")) {
|
|
|
1167 $("#step2-gc-sign-{{ TAB_INDEX_PLACEHOLDER }}").removeClass("fa-question-circle").addClass("fa-check-circle");
|
|
|
1168 }
|
|
|
1169 // check panel to show
|
|
|
1170 if (self.is_ms() || self.is_ms2()) {
|
|
|
1171 $("#add1spectrum-analyserData-MS-{{ TAB_INDEX_PLACEHOLDER }}").show();
|
|
|
1172 $("#linkActivateStep3-ms-{{ TAB_INDEX_PLACEHOLDER }}").trigger('click');
|
|
|
1173 // debug display
|
|
|
1174 [
|
|
|
1175 "add1spectrum-analyzserMS-sprayGazFlow-pos",
|
|
|
1176 "add1spectrum-analyzserMS-sprayGazFlow-neg",
|
|
|
1177 "add1spectrum-analyzserMS-vaporizerGazFlow-pos",
|
|
|
1178 "add1spectrum-analyzserMS-vaporizerGazFlow-neg",
|
|
|
1179 "add1spectrum-analyzserMS-vaporizerTemperature-pos",
|
|
|
1180 "add1spectrum-analyzserMS-vaporizerTemperature-neg",
|
|
|
1181 "add1spectrum-analyzserMS-sourceGazFlow-pos",
|
|
|
1182 "add1spectrum-analyzserMS-sourceGazFlow-neg",
|
|
|
1183 "add1spectrum-analyzserMS-ionTransferTubeTemperatureOrTransferCapillaryTemperature-pos",
|
|
|
1184 "add1spectrum-analyzserMS-ionTransferTubeTemperatureOrTransferCapillaryTemperature-neg",
|
|
|
1185 "add1spectrum-analyzserMS-highVoltageOrCoronaVoltage-pos",
|
|
|
1186 "add1spectrum-analyzserMS-highVoltageOrCoronaVoltage-neg"
|
|
|
1187 ].forEach((id) => {
|
|
|
1188 var element = $(`#id-{{ TAB_INDEX_PLACEHOLDER }}`)
|
|
|
1189 element.height(element.parent().children("span").height())
|
|
|
1190 })
|
|
|
1191 if ($("#step3-ms-sign-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("fa-check-circle")) {
|
|
|
1192 $("#step3-ms-sign-{{ TAB_INDEX_PLACEHOLDER }}").removeClass("fa-check-circle").addClass("fa-question-circle");
|
|
|
1193 }
|
|
|
1194 // MSMS only
|
|
|
1195 $(self.prefix+".enable-if-ms").attr("disabled", !self.is_ms());
|
|
|
1196 $(self.prefix+".enable-if-msms").attr("disabled", !self.is_ms2());
|
|
|
1197 }
|
|
|
1198 // avoid display bug
|
|
|
1199 $("#add1spectrum-analyzer-ms-instrument-{{ TAB_INDEX_PLACEHOLDER }}").change();
|
|
|
1200 break;
|
|
|
1201 case 4:
|
|
|
1202 // hide after step 4 / alt step 4
|
|
|
1203 $("#add1spectrum-peaksData-MS-{{ TAB_INDEX_PLACEHOLDER }}").hide();
|
|
|
1204 $("#add1spectrum-otherData-{{ TAB_INDEX_PLACEHOLDER }}").hide();
|
|
|
1205 // step 3 ok
|
|
|
1206 if ($("#step3-ms-sign-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("fa-question-circle")) {
|
|
|
1207 $("#step3-ms-sign-{{ TAB_INDEX_PLACEHOLDER }}").removeClass("fa-question-circle").addClass("fa-check-circle");
|
|
|
1208 }
|
|
|
1209 if (self.is_ms() || self.is_ms2()) {
|
|
|
1210 $("#add1spectrum-peaksData-MS-{{ TAB_INDEX_PLACEHOLDER }}").show();
|
|
|
1211 $("#linkActivateStep4-ms-{{ TAB_INDEX_PLACEHOLDER }}").trigger("click");
|
|
|
1212 if ($("#step4-ms-sign-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("fa-check-circle")) {
|
|
|
1213 $("#step4-ms-sign-{{ TAB_INDEX_PLACEHOLDER }}").removeClass("fa-check-circle").addClass("fa-question-circle");
|
|
|
1214 }
|
|
|
1215 // LC MS
|
|
|
1216 if (!self.isMSpeaksInit) {
|
|
|
1217 console.log(`self.is_mix(): ${self.is_mix()}`)
|
|
|
1218 if (self.is_mix()) {
|
|
|
1219 all_contexts.forEach((context, index) => {
|
|
|
1220 if (context === null) {
|
|
|
1221 return;
|
|
|
1222 }
|
|
|
1223 context.handsontableMSpeaks(null) ;
|
|
|
1224 context.updateLCMSspectraViewer() ;
|
|
|
1225 context.isMSpeaksInit = true;
|
|
|
1226 $(context.prefix+".add1spectrum-peaksMSForm-peaklist-reset").val("").change();
|
|
|
1227 })
|
|
|
1228 } else {
|
|
|
1229 self.handsontableMSpeaks(null);
|
|
|
1230 self.isMSpeaksInit = true;
|
|
|
1231 $(self.prefix+".add1spectrum-peaksMSForm-peaklist-reset").val("").change();
|
|
|
1232 }
|
|
|
1233 }
|
|
|
1234 }
|
|
|
1235 // show ms tab
|
|
|
1236 setTimeout(() => $("#container_MS_Peaks-{{ TAB_INDEX_PLACEHOLDER }}").trigger("click"), 250);
|
|
|
1237 $("#add1spectrum-peaksMS-msLevel-{{ TAB_INDEX_PLACEHOLDER }}").change();
|
|
|
1238 break;
|
|
|
1239 case 5:
|
|
|
1240 // hide after step 5 / alt step 5
|
|
|
1241 $("#add1spectrum-otherData-{{ TAB_INDEX_PLACEHOLDER }}").hide();
|
|
|
1242 // step 4 ok
|
|
|
1243 if ($("#step4-ms-sign-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("fa-question-circle")) {
|
|
|
1244 $("#step4-ms-sign-{{ TAB_INDEX_PLACEHOLDER }}").removeClass("fa-question-circle").addClass("fa-check-circle");
|
|
|
1245 }
|
|
|
1246 if ($("#step5sign-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("fa-check-circle")) {
|
|
|
1247 $("#step5sign-{{ TAB_INDEX_PLACEHOLDER }}").removeClass("fa-check-circle").addClass("fa-question-circle");
|
|
|
1248 }
|
|
|
1249 $("#add1spectrum-otherData-{{ TAB_INDEX_PLACEHOLDER }}").show();
|
|
|
1250 $("#linkActivateStep5-{{ TAB_INDEX_PLACEHOLDER }}").trigger("click");
|
|
|
1251 // reset step 6 button
|
|
|
1252 self.checkIfEnableSubmit();
|
|
|
1253 $("#import1SpectrumLoadingBare-{{ TAB_INDEX_PLACEHOLDER }}").hide();
|
|
|
1254 $("#import1SpectrumResults-{{ TAB_INDEX_PLACEHOLDER }}").hide();
|
|
|
1255 break;
|
|
|
1256 case 6:
|
|
|
1257 self.postOneSpectrumFrom();
|
|
|
1258 self.cptPeakListTab++;
|
|
|
1259 break;
|
|
|
1260 case 7:
|
|
|
1261 self.dumpOneSpectrumFrom();
|
|
|
1262 break;
|
|
|
1263 }
|
|
|
1264 },
|
|
|
1265
|
|
|
1266 //USED HERE
|
|
|
1267 resetElemColor: function(idElem) {
|
|
|
1268
|
|
|
1269 var self = this ;
|
|
|
1270 if ($(`#${idElem}`).parent().hasClass("has-success")) {
|
|
|
1271 $(`#${idElem}`).parent().removeClass("has-success") ;
|
|
|
1272 }
|
|
|
1273 if ($(`#${idElem}`).parent().hasClass("has-warning")) {
|
|
|
1274 $(`#${idElem}`).parent().removeClass("has-warning") ;
|
|
|
1275 }
|
|
|
1276 if ($(`#${idElem}`).parent().hasClass("has-error")) {
|
|
|
1277 $(`#${idElem}`).parent().removeClass("has-error") ;
|
|
|
1278 }
|
|
|
1279 },
|
|
|
1280
|
|
|
1281 //USED HERE
|
|
|
1282 disableElem: function(idElem) {
|
|
|
1283
|
|
|
1284 var self = this ;
|
|
|
1285 $(`#${idElem}`).prop("disabled", true) ;
|
|
|
1286 $(`#${idElem}`).val("") ;
|
|
|
1287 if ($(`#${idElem}`).hasClass("is-mandatory")) {
|
|
|
1288 $(`#${idElem}`).removeClass("is-mandatory") ;
|
|
|
1289 }
|
|
|
1290 },
|
|
|
1291
|
|
|
1292 //USED HERE
|
|
|
1293 enableElem: function(idElem) {
|
|
|
1294
|
|
|
1295 var self = this ;
|
|
|
1296 $(`#${idElem}`).prop("disabled", false) ;
|
|
|
1297 $(`#${idElem}`).parent().addClass("has-error") ;
|
|
|
1298 if (!$(`#${idElem}`).hasClass("is-mandatory")) {
|
|
|
1299 $(`#${idElem}`).addClass("is-mandatory") ;
|
|
|
1300 }
|
|
|
1301 },
|
|
|
1302
|
|
|
1303 //USED HERE
|
|
|
1304 checkIfEnableSubmit: function() {
|
|
|
1305
|
|
|
1306 var self = this ;
|
|
|
1307 var isBtnStep6OK = true;
|
|
|
1308 $.each($(self.prefix+".add1spectrum-otherForm"), (id, elem) => {
|
|
|
1309 if (self.is_error($(elem)) && $(elem).is(":visible")) {
|
|
|
1310 isBtnStep6OK = false;
|
|
|
1311 }
|
|
|
1312 });
|
|
|
1313 if (isBtnStep6OK) {
|
|
|
1314 self.rm_class($("#btnSwitch-gotoStep6-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-disabled") ;
|
|
|
1315 self.set_class($("#btnSwitch-gotoStep6-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-primary") ;
|
|
|
1316 $("#btnSwitch-gotoStep6-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", false);
|
|
|
1317 self.rm_class($("#btnSwitch-gotoStep7-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-disabled") ;
|
|
|
1318 self.set_class($("#btnSwitch-gotoStep7-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-primary") ;
|
|
|
1319 $("#btnSwitch-gotoStep7-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", false);
|
|
|
1320 } else {
|
|
|
1321 if (!$("#btnSwitch-gotoStep6-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("btn-disabled")) {
|
|
|
1322 $("#btnSwitch-gotoStep6-{{ TAB_INDEX_PLACEHOLDER }}").addClass("btn-disabled");
|
|
|
1323 }
|
|
|
1324 if ($("#btnSwitch-gotoStep6-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("btn-primary")) {
|
|
|
1325 $("#btnSwitch-gotoStep6-{{ TAB_INDEX_PLACEHOLDER }}").removeClass("btn-primary");
|
|
|
1326 }
|
|
|
1327 $("#btnSwitch-gotoStep6-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", true);
|
|
|
1328 if (!$("#btnSwitch-gotoStep7-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("btn-disabled")) {
|
|
|
1329 $("#btnSwitch-gotoStep7-{{ TAB_INDEX_PLACEHOLDER }}").addClass("btn-disabled");
|
|
|
1330 }
|
|
|
1331 if ($("#btnSwitch-gotoStep7-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("btn-primary")) {
|
|
|
1332 $("#btnSwitch-gotoStep7-{{ TAB_INDEX_PLACEHOLDER }}").removeClass("btn-primary");
|
|
|
1333 }
|
|
|
1334 $("#btnSwitch-gotoStep7-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", true);
|
|
|
1335 }
|
|
|
1336 },
|
|
|
1337
|
|
|
1338 //USED IN HTML
|
|
|
1339 addOneSpectrum: function(type) {
|
|
|
1340
|
|
|
1341 var self = this ;
|
|
|
1342 // unlock
|
|
|
1343 $(self.prefix+".add1spectrum-sampleForm").prop("disabled", false);
|
|
|
1344 $(self.prefix+".add1spectrum-chromatoLCForm").prop("disabled", false);
|
|
|
1345 $(self.prefix+".add1spectrum-analyzerMSForm").prop("disabled", false);
|
|
|
1346 $(self.prefix+".add1spectrum-otherForm").prop("disabled", false);
|
|
|
1347 $("#add1spectrum-chromatoLC-colConstructor-{{ TAB_INDEX_PLACEHOLDER }}").change();
|
|
|
1348 // reset
|
|
|
1349 self.isLC = false;
|
|
|
1350 self.isGC = false;
|
|
|
1351 self.isIC = false;
|
|
|
1352 $("#alertBoxSubmitSpectrum-{{ TAB_INDEX_PLACEHOLDER }}").html("");
|
|
|
1353 // hide in all steps
|
|
|
1354 $(self.prefix+".opt-ms").hide();
|
|
|
1355 $(self.prefix+".opt-msms").hide();
|
|
|
1356 // hide step 2
|
|
|
1357 $("#add1spectrum-chromatographyData-LC-{{ TAB_INDEX_PLACEHOLDER }}").hide();
|
|
|
1358 $("#add1spectrum-chromatographyData-GC-{{ TAB_INDEX_PLACEHOLDER }}").hide();
|
|
|
1359 // hide step 3
|
|
|
1360 $("#add1spectrum-analyserData-MS-{{ TAB_INDEX_PLACEHOLDER }}").hide();
|
|
|
1361 $(self.prefix+".add1spectrum-ionTrap").hide();
|
|
|
1362 // hide step 4
|
|
|
1363 $("#add1spectrum-peaksData-MS-{{ TAB_INDEX_PLACEHOLDER }}").hide();
|
|
|
1364 // hide step 5
|
|
|
1365 $("#add1spectrum-otherData-{{ TAB_INDEX_PLACEHOLDER }}").hide();
|
|
|
1366 // reset field step 1
|
|
|
1367 $("#add1spectrum-sample-type-{{ TAB_INDEX_PLACEHOLDER }}").val("");
|
|
|
1368 $(self.prefix+".add1spectrum-sample-type-panel").hide();
|
|
|
1369 $(self.prefix+".add1spectrum-sampleForm").val("");
|
|
|
1370 $("#sample-bonus-display-{{ TAB_INDEX_PLACEHOLDER }}").html("");
|
|
|
1371 // reset field step 2
|
|
|
1372 $(self.prefix+".add1spectrum-chromatoLCForm").val("");
|
|
|
1373 // reset field step 3
|
|
|
1374 $(self.prefix+".add1spectrum-analyzerMSForm").val("");
|
|
|
1375 // reset field step 4
|
|
|
1376 // reset peak lists / all tabs
|
|
|
1377 self.isSeparationFlowRateInit = false;
|
|
|
1378 self.isMSpeaksInit = false;
|
|
|
1379 $(self.prefix+".handsontable").html("");
|
|
|
1380 // reset field step 5 => NO!
|
|
|
1381 // set icon
|
|
|
1382 $("#step0sign-{{ TAB_INDEX_PLACEHOLDER }}").removeClass("fa-question-circle").addClass("fa-check-circle");
|
|
|
1383 if ($("#step1sign-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("fa-check-circle")) {
|
|
|
1384 $("#step1sign-{{ TAB_INDEX_PLACEHOLDER }}").removeClass("fa-check-circle").addClass("fa-question-circle");
|
|
|
1385 }
|
|
|
1386 // collapse step 0 / uncollaspe step 1
|
|
|
1387 $("#linkActivateStep1-{{ TAB_INDEX_PLACEHOLDER }}").trigger("click");
|
|
|
1388 // show step 1 content
|
|
|
1389 $("#add1spectrum-sampleData-{{ TAB_INDEX_PLACEHOLDER }}").show();
|
|
|
1390 switch(type) {
|
|
|
1391 case 1:
|
|
|
1392 // TODO GC-MS stuff
|
|
|
1393 self.isGC = true;
|
|
|
1394 break;
|
|
|
1395 case 2:
|
|
|
1396 // LC-MS stuff
|
|
|
1397 self.isLC = true;
|
|
|
1398 $(self.prefix+".opt-ms").show();
|
|
|
1399 break;
|
|
|
1400 case 5:
|
|
|
1401 // LC-MSMS stuff
|
|
|
1402 self.isLC = true;
|
|
|
1403 $(self.prefix+".opt-ms").show();
|
|
|
1404 $(self.prefix+".opt-msms").show();
|
|
|
1405 break;
|
|
|
1406 case 6:
|
|
|
1407 // IC-MS stuff
|
|
|
1408 self.isIC = true;
|
|
|
1409 $(self.prefix+".opt-ms").show();
|
|
|
1410 break;
|
|
|
1411 case 7:
|
|
|
1412 // IC-MSMS stuff
|
|
|
1413 self.isIC = true;
|
|
|
1414 $(self.prefix+".opt-ms").show();
|
|
|
1415 $(self.prefix+".opt-msms").show();
|
|
|
1416 break;
|
|
|
1417 }
|
|
|
1418 self.resetFromColors();
|
|
|
1419 // reset json obj to submit form
|
|
|
1420 self.jsonSpectrumType = null;
|
|
|
1421 self.isJsonSpectrumTypeComplete = false;
|
|
|
1422 self.jsonSample = null;
|
|
|
1423 self.isJsonSampleComplete = false;
|
|
|
1424 self.isJsonRCCaddedComplete = false;
|
|
|
1425 self.jsonChromato = null;
|
|
|
1426 self.isJsonChromatoComplete = false;
|
|
|
1427 self.jsonAnalyzer = null;
|
|
|
1428 self.isJsonAnalyzerComplete = false;
|
|
|
1429 self.jsonPeaksList = [];
|
|
|
1430 self.isJsonPeaksListComplete = false;
|
|
|
1431 self.jsonOtherMetadata = null;
|
|
|
1432 self.isJsonOtherMetadataComplete = false;
|
|
|
1433
|
|
|
1434 self.cptPeakListTab = 0;
|
|
|
1435 self.jsonAnalyzerAcquisition = [];
|
|
|
1436 self.idMetadataMap = {}
|
|
|
1437 self.listOfViewableSpectra = [];
|
|
|
1438
|
|
|
1439 // spec MS
|
|
|
1440 self.jsonMolIonization = null;
|
|
|
1441
|
|
|
1442 // spec MSMS
|
|
|
1443 self.jsonMolIonBeam = null;
|
|
|
1444
|
|
|
1445 // try load cpd
|
|
|
1446 if (self.inchikey !== null) {
|
|
|
1447 self.loadJSCompound(self.inchikey);
|
|
|
1448 }
|
|
|
1449 },
|
|
|
1450
|
|
|
1451 //USED HERE
|
|
|
1452 loadJSCompound: function(inchikey) {
|
|
|
1453 var self = this ;
|
|
|
1454
|
|
|
1455 $("#add1spectrum-sample-type-{{ TAB_INDEX_PLACEHOLDER }}").val("compound-ref");
|
|
|
1456 $("#add1spectrum-sample-type-{{ TAB_INDEX_PLACEHOLDER }}").change();
|
|
|
1457 $("#add1spectrum-sample-inchikey-{{ TAB_INDEX_PLACEHOLDER }}").val(inchikey);
|
|
|
1458 $("#add1spectrum-sample-inchikey-{{ TAB_INDEX_PLACEHOLDER }}").change();
|
|
|
1459 if (inchidata[inchikey] !== null) {
|
|
|
1460 return (set_inchi_data(inchidata[inchikey]), {{ TAB_INDEX_PLACEHOLDER }}) ;
|
|
|
1461 }
|
|
|
1462 $.ajax({
|
|
|
1463 type: "get",
|
|
|
1464 url: "{{ PF_URL_PLACEHOLDER }}/webapp/get-cpd-data",
|
|
|
1465 data: "inchikey="+inchikey,
|
|
|
1466 dataType: "json",
|
|
|
1467 success: function(data) {
|
|
|
1468 if (data.success) {
|
|
|
1469 set_inchi_data(data) ;
|
|
|
1470 }
|
|
|
1471 },
|
|
|
1472 error : function(data) {
|
|
|
1473 }
|
|
|
1474 }).always(function() {
|
|
|
1475 });
|
|
|
1476 },
|
|
|
1477
|
|
|
1478 //USED HERE
|
|
|
1479 handsontableSeparationFlowRate: function(data) {
|
|
|
1480 var self = this ;
|
|
|
1481
|
|
|
1482 // reset
|
|
|
1483 $("#container_LC_SFG-{{ TAB_INDEX_PLACEHOLDER }}").html("");
|
|
|
1484 // init
|
|
|
1485 var data_LC_SFG;
|
|
|
1486 if (data==null) {
|
|
|
1487 data_LC_SFG = [
|
|
|
1488 [ "", "", "" ],
|
|
|
1489 [ "", "", "" ],
|
|
|
1490 [ "", "", "" ],
|
|
|
1491 [ "", "", "" ],
|
|
|
1492 [ "", "", "" ],
|
|
|
1493 [ "", "", "" ],
|
|
|
1494 [ "", "", "" ],
|
|
|
1495 [ "", "", "" ],
|
|
|
1496 [ "", "", "" ],
|
|
|
1497 ];
|
|
|
1498 } else {
|
|
|
1499 data_LC_SFG = data;
|
|
|
1500 }
|
|
|
1501
|
|
|
1502 var container_LC_SFG = document.getElementById("container_LC_SFG-{{ TAB_INDEX_PLACEHOLDER }}");
|
|
|
1503 self.hot_LC_SFG = new Handsontable(container_LC_SFG, {
|
|
|
1504 data : data_LC_SFG,
|
|
|
1505 minSpareRows : 1,
|
|
|
1506 colHeaders : true,
|
|
|
1507 colHeaders: ["time (min)", "solv. A (%)", "solv. B (%)"],
|
|
|
1508 contextMenu : false
|
|
|
1509 });
|
|
|
1510 Handsontable.Dom.addEvent(document.body, "click", function(e) {
|
|
|
1511 var element = e.target || e.srcElement;
|
|
|
1512 if (element.nodeName == "BUTTON"&& element.name == "dump") {
|
|
|
1513 var name = element.getAttribute("data-dump");
|
|
|
1514 var instance = element.getAttribute("data-instance");
|
|
|
1515 self.hot_LC_SFG = window[instance];
|
|
|
1516 console.log("data of " + name, self.hot_LC_SFG.getData());
|
|
|
1517 }
|
|
|
1518 });
|
|
|
1519 $("#container_LC_SFG table.htCore-{{ TAB_INDEX_PLACEHOLDER }}").css("width","100%");
|
|
|
1520 },
|
|
|
1521
|
|
|
1522 //USED HERE
|
|
|
1523 handsontableMSpeaks: function(data) {
|
|
|
1524 console.log("handsontableMSpeaks")
|
|
|
1525 console.log(data)
|
|
|
1526 var self = this ;
|
|
|
1527 var data_MS_Peaks ;
|
|
|
1528 var container_MS_Peaks ;
|
|
|
1529
|
|
|
1530 if (data != null) {
|
|
|
1531 data_MS_Peaks = data;
|
|
|
1532 } else {
|
|
|
1533 data_MS_Peaks = JSON.parse(JSON.stringify(self.DEFAULT_MS_PEAK_VALUES));
|
|
|
1534 }
|
|
|
1535 $("#container_MS_Peaks-{{ TAB_INDEX_PLACEHOLDER }}").html("");
|
|
|
1536 container_MS_Peaks = document.getElementById(
|
|
|
1537 "container_MS_Peaks-{{ TAB_INDEX_PLACEHOLDER }}"
|
|
|
1538 );
|
|
|
1539 var colHeaders = [
|
|
|
1540 "m/z", "absolute intensity", "relative intensity (%)", "delta (ppm)",
|
|
|
1541 "composition", "attribution", "Validated"
|
|
|
1542 ]
|
|
|
1543 var columns = [
|
|
|
1544 {type: "numeric", format: "0.0000"},
|
|
|
1545 {type: "numeric", format: "0.00"},
|
|
|
1546 {type: "numeric", format: "0.00"},
|
|
|
1547 {type: "numeric", format: "0.0000"},
|
|
|
1548 {type: "text"},
|
|
|
1549 {type: "text"},
|
|
|
1550 {type: "checkbox"}
|
|
|
1551 ] ;
|
|
|
1552 if (self.is_ms2()) {
|
|
|
1553 colHeaders.push("Parent ion") ;
|
|
|
1554 columns.push({type: "checkbox"}) ;
|
|
|
1555 }
|
|
|
1556 self.hot_MS_Peaks = new Handsontable(container_MS_Peaks, {
|
|
|
1557 data: data_MS_Peaks,
|
|
|
1558 minSpareRows: 1,
|
|
|
1559 colHeaders: true,
|
|
|
1560 colHeaders: colHeaders,
|
|
|
1561 contextMenu: false,
|
|
|
1562 maxRows: data_MS_Peaks.length,
|
|
|
1563 minRows: data_MS_Peaks.length,
|
|
|
1564 columns: columns,
|
|
|
1565 afterChange: function(changes) {
|
|
|
1566 if (self.lock.precursor_ion) {
|
|
|
1567 return ;
|
|
|
1568 }
|
|
|
1569 self.lock.precursor_ion = true ;
|
|
|
1570 try {
|
|
|
1571 changes?.forEach(([row, prop, old, value]) => {
|
|
|
1572 var data ;
|
|
|
1573 var precursor_ion ;
|
|
|
1574
|
|
|
1575 var data = self.hot_MS_Peaks.getData() ;
|
|
|
1576 if (prop !== 7 || value !== true || data === undefined) {
|
|
|
1577 return ;
|
|
|
1578 }
|
|
|
1579 for (var i = 0; i < data.length ; i += 1) {
|
|
|
1580 data[i][7] = false ;
|
|
|
1581 }
|
|
|
1582 data[row][7] = true ;
|
|
|
1583 precursor_ion = $(`#add1spectrum-peaksMS-msPrecursorIon-{{ TAB_INDEX_PLACEHOLDER }}`) ;
|
|
|
1584 console.log(`setting preco ion to ${data[row][0]}`) ;
|
|
|
1585 precursor_ion.val(data[row][0]) ;
|
|
|
1586 precursor_ion.change() ;
|
|
|
1587 self.hot_MS_Peaks.render() ;
|
|
|
1588 })
|
|
|
1589 } finally {
|
|
|
1590 self.lock.precursor_ion = false ;
|
|
|
1591 }
|
|
|
1592 }
|
|
|
1593 });
|
|
|
1594 Handsontable.Dom.addEvent(document.body, "click", (e) => {
|
|
|
1595 var element ;
|
|
|
1596 var name ;
|
|
|
1597 var instance ;
|
|
|
1598
|
|
|
1599 element = e.target || e.srcElement ;
|
|
|
1600 if (element.nodeName == "BUTTON" && element.name == "dump") {
|
|
|
1601 name = element.getAttribute("data-dump") ;
|
|
|
1602 instance = element.getAttribute("data-instance") ;
|
|
|
1603 self.hot_MS_Peaks = window[instance] ;
|
|
|
1604 console.log("data of " + name, self.hot_MS_Peaks.getData()) ;
|
|
|
1605 }
|
|
|
1606 }) ;
|
|
|
1607
|
|
|
1608 $("#container_MS_Peaks-{{ TAB_INDEX_PLACEHOLDER }} table.htCore").css(
|
|
|
1609 "width","100%"
|
|
|
1610 ) ;
|
|
|
1611 if (self.is_ms2()) {
|
|
|
1612 setTimeout(() => self.select_precursor_ion(), 200) ;
|
|
|
1613 }
|
|
|
1614 },
|
|
|
1615
|
|
|
1616 change_tab: function() {
|
|
|
1617 var self = this ;
|
|
|
1618 setTimeout(() => self.auto_select_ion_parent(), 1000) ;
|
|
|
1619 },
|
|
|
1620
|
|
|
1621 auto_select_ion_parent: function() {
|
|
|
1622 var self = this ;
|
|
|
1623 if (!self.a_ion_parent_is_selected()) {
|
|
|
1624 setTimeout(() => self.select_precursor_ion(), 1000) ;
|
|
|
1625 }
|
|
|
1626 },
|
|
|
1627
|
|
|
1628 select_precursor_ion: function() {
|
|
|
1629 var self = this ;
|
|
|
1630 var data ;
|
|
|
1631 var precuirsor_ion ;
|
|
|
1632
|
|
|
1633 if (self.hot_MS_Peaks == null) {
|
|
|
1634 return setTimeout(() => self.select_precursor_ion(), 200) ;
|
|
|
1635 }
|
|
|
1636 console.log("Selecting ion preco for tab {{ TAB_INDEX_PLACEHOLDER }}")
|
|
|
1637 data = self.hot_MS_Peaks.getData() ;
|
|
|
1638 for (var i = 0 ; i < data.length ; i += 1) {
|
|
|
1639 if (data[i][5] === "[M+H]+" || data[i][5] === "[M+H]-" || data[i][2] == 100.0) {
|
|
|
1640 precursor_ion = $("#add1spectrum-peaksMS-msPrecursorIon-{{ TAB_INDEX_PLACEHOLDER }}") ;
|
|
|
1641 precursor_ion.val(data[i][0]) ;
|
|
|
1642 precursor_ion.change() ;
|
|
|
1643 return ;
|
|
|
1644 }
|
|
|
1645 }
|
|
|
1646 },
|
|
|
1647
|
|
|
1648 sync_precursor_ion: function() {
|
|
|
1649 var self = this ;
|
|
|
1650 var data ;
|
|
|
1651
|
|
|
1652 if (self.lock.precursor_ion || self.hot_MS_Peaks == undefined) {
|
|
|
1653 return ;
|
|
|
1654 }
|
|
|
1655 self.lock.precursor_ion = true ;
|
|
|
1656 console.log("Syncing precursor ion")
|
|
|
1657 var val = $("#add1spectrum-peaksMS-msPrecursorIon-{{ TAB_INDEX_PLACEHOLDER }}").val() ;
|
|
|
1658 var data = self.hot_MS_Peaks.getData() ;
|
|
|
1659 for (var i = 0; i < data.length ; i += 1) {
|
|
|
1660 if (Math.abs(data[i][0] - val) < 0.0001) {
|
|
|
1661 for (var j = 0; j < data.length ; j += 1) {
|
|
|
1662 data[j][7] = false ;
|
|
|
1663 }
|
|
|
1664 data[i][7] = true ;
|
|
|
1665 self.hot_MS_Peaks.render() ;
|
|
|
1666 return ;
|
|
|
1667 }
|
|
|
1668 }
|
|
|
1669 self.lock.precursor_ion = false ;
|
|
|
1670 },
|
|
|
1671
|
|
|
1672 // USED HERE
|
|
|
1673 handsontableRefChemCpdAdded: function(data) {
|
|
|
1674 var self = this ;
|
|
|
1675 // reset
|
|
|
1676 $("#container_RCC_ADDED-{{ TAB_INDEX_PLACEHOLDER }}").html("");
|
|
|
1677 $("#sample-bonus-display-{{ TAB_INDEX_PLACEHOLDER }}").html("");
|
|
|
1678 // init
|
|
|
1679 var data_RCC_ADDED, colHeaderData, container_RCC_ADDED;
|
|
|
1680
|
|
|
1681 colHeaderData = [
|
|
|
1682 {data: "common name", type: "text"},
|
|
|
1683 {data: "<b>InChIKey</b>", type: "text"},
|
|
|
1684 {data: "composition", renderer: lightgrayRenderer},
|
|
|
1685 {data: "<b>concentration (µg/ml)</b>", type: "text"},
|
|
|
1686 {data: "exact mass", renderer: lightgrayRenderer},
|
|
|
1687 {data: "(M+H)+ or (M-H)-", renderer: lightgrayRenderer}
|
|
|
1688 ] ;
|
|
|
1689
|
|
|
1690 if (data == null) {
|
|
|
1691 data_RCC_ADDED = [
|
|
|
1692 [ "", "", "","", "", "" ],
|
|
|
1693 [ "", "", "","", "", "" ],
|
|
|
1694 [ "", "", "","", "", "" ],
|
|
|
1695 [ "", "", "","", "", "" ],
|
|
|
1696 [ "", "", "","", "", "" ],
|
|
|
1697 [ "", "", "","", "", "" ],
|
|
|
1698 [ "", "", "","", "", "" ],
|
|
|
1699 [ "", "", "","", "", "" ],
|
|
|
1700 [ "", "", "","", "", "" ],
|
|
|
1701 [ "", "", "","", "", "" ],
|
|
|
1702 [ "", "", "","", "", "" ],
|
|
|
1703 [ "", "", "","", "", "" ],
|
|
|
1704 ];
|
|
|
1705 } else {
|
|
|
1706 container_RCC_ADDED = data;
|
|
|
1707 }
|
|
|
1708
|
|
|
1709 container_RCC_ADDED = document.getElementById("container_RCC_ADDED-{{ TAB_INDEX_PLACEHOLDER }}");
|
|
|
1710 self.hot_RCC_ADDED = new Handsontable(container_RCC_ADDED, {
|
|
|
1711 data: data_RCC_ADDED,
|
|
|
1712 minSpareRows : 1,
|
|
|
1713 colHeaders : true,
|
|
|
1714 colHeaders: [
|
|
|
1715 "common name",
|
|
|
1716 "<b>InChIKey</b>",
|
|
|
1717 "composition",
|
|
|
1718 "<b>concentration (µg/ml)</b>",
|
|
|
1719 "exact mass",
|
|
|
1720 "(M+H)+ or (M-H)-"
|
|
|
1721 ],
|
|
|
1722 contextMenu : false,
|
|
|
1723 columns: colHeaderData
|
|
|
1724 });
|
|
|
1725 function bindDumpButton_RCC_ADDED() {
|
|
|
1726 Handsontable.Dom.addEvent(document.body, "click", (e) => {
|
|
|
1727 var element = e.target || e.srcElement;
|
|
|
1728 if (element.nodeName == "BUTTON"&& element.name == "dump") {
|
|
|
1729 var name = element.getAttribute("data-dump");
|
|
|
1730 var instance = element.getAttribute("data-instance");
|
|
|
1731 self.hot_RCC_ADDED = window[instance];
|
|
|
1732 console.log("data of " + name, self.hot_RCC_ADDED.getData());
|
|
|
1733 }
|
|
|
1734 });
|
|
|
1735 }
|
|
|
1736 bindDumpButton_RCC_ADDED();
|
|
|
1737 $("#container_RCC_ADDED-{{ TAB_INDEX_PLACEHOLDER }} table.htCore").css("width","100%");
|
|
|
1738 // celect cell
|
|
|
1739 self.hot_RCC_ADDED.selectCell(0, 0);
|
|
|
1740 // add select listener
|
|
|
1741 self.hot_RCC_ADDED.addHook("afterSelection", (r, c) => self.hookSelection(r, c));
|
|
|
1742 },
|
|
|
1743
|
|
|
1744 //USED HERE
|
|
|
1745 hookSelection: function(r, c) {
|
|
|
1746 var self = this ;
|
|
|
1747 if (c == 0 || c == 1 || c == 2)
|
|
|
1748 self.pickChemicalCompound4Mix(r);
|
|
|
1749 },
|
|
|
1750
|
|
|
1751 //USED HERE
|
|
|
1752 postOneSpectrumFrom: function() {
|
|
|
1753 var self = this ;
|
|
|
1754 $("#import1SpectrumLoadingBare-{{ TAB_INDEX_PLACEHOLDER }}").show();
|
|
|
1755
|
|
|
1756 // II - form data -> json object
|
|
|
1757 self.loadFomDataIntoJsonObjects();
|
|
|
1758 // II.A - check if json object complete
|
|
|
1759 var alertMsg = self.getFormErrorMessage();
|
|
|
1760
|
|
|
1761 if (alertMsg != "") {
|
|
|
1762 $("#alertBoxSubmitSpectrum-{{ TAB_INDEX_PLACEHOLDER }}").html(alertMsg);
|
|
|
1763 $("#import1SpectrumLoadingBare-{{ TAB_INDEX_PLACEHOLDER }}").hide();
|
|
|
1764 return false;
|
|
|
1765 }
|
|
|
1766 // all OK: lock!
|
|
|
1767 // lock sample
|
|
|
1768 $(self.prefix+".add1spectrum-sampleForm").prop("disabled", true);
|
|
|
1769 // lock chromato
|
|
|
1770 $(self.prefix+".add1spectrum-chromatoLCForm").prop("disabled", true);
|
|
|
1771 if (!$("#container_LC_SFG-{{ TAB_INDEX_PLACEHOLDER }}").is(":empty")) {
|
|
|
1772 self.hot_LC_SFG.updateSettings({
|
|
|
1773 cells: function(row, col, prop) {
|
|
|
1774 var cellProperties = {};
|
|
|
1775 cellProperties.readOnly = true;
|
|
|
1776 return cellProperties;
|
|
|
1777 }
|
|
|
1778 });
|
|
|
1779 }
|
|
|
1780 if (!$("#container_MS_Peaks-{{ TAB_INDEX_PLACEHOLDER }}").is(":empty")) {
|
|
|
1781 self.hot_MS_Peaks.updateSettings({
|
|
|
1782 cells: function(row, col, prop) {
|
|
|
1783 var cellProperties = {};
|
|
|
1784 cellProperties.readOnly = true;
|
|
|
1785 return cellProperties;
|
|
|
1786 }
|
|
|
1787 });
|
|
|
1788 }
|
|
|
1789 if (!$("#container_RCC_ADDED-{{ TAB_INDEX_PLACEHOLDER }}").is(":empty")) {
|
|
|
1790 self.hot_RCC_ADDED.updateSettings({
|
|
|
1791 cells: function(row, col, prop) {
|
|
|
1792 var cellProperties = {};
|
|
|
1793 cellProperties.readOnly = true;
|
|
|
1794 return cellProperties;
|
|
|
1795 }
|
|
|
1796 });
|
|
|
1797 self.hot_RCC_ADDED.removeHook(
|
|
|
1798 "afterSelection",
|
|
|
1799 (r, c) => self.hookSelection(r, c)
|
|
|
1800 );
|
|
|
1801 }
|
|
|
1802
|
|
|
1803 // lock analyzer
|
|
|
1804 $(self.prefix+".add1spectrum-analyzerMSForm").prop("disabled", true);
|
|
|
1805 // lock other metadata field
|
|
|
1806 $(self.prefix+".add1spectrum-otherForm").prop("disabled", true);
|
|
|
1807 // lock switch btn
|
|
|
1808 $("#btnSwitch-gotoStep2-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", true);
|
|
|
1809 $("#btnSwitch-gotoStep3-lc-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", true);
|
|
|
1810 $("#btnSwitch-gotoStep4-ms-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", true);
|
|
|
1811 self.postSpectrumToServer() ;
|
|
|
1812 },
|
|
|
1813
|
|
|
1814 postSpectrumToServer: function(jsonData, tab_index) {
|
|
|
1815 var self = this ;
|
|
|
1816 var base_peakdata ;
|
|
|
1817 var new_peakdata ;
|
|
|
1818 var is_ms2 = self.is_ms2() ;
|
|
|
1819
|
|
|
1820 if (self.is_mix()) {
|
|
|
1821 if ({{ TAB_INDEX_PLACEHOLDER }} != 1) {
|
|
|
1822 return ;
|
|
|
1823 }
|
|
|
1824 jsonData = self.gatherJsonObjects() ;
|
|
|
1825 all_mix_data = Object.assign({}, jsonData) ;
|
|
|
1826 all_mix_data["peaklists"] = [] ;
|
|
|
1827 base_peakdata = Object.assign({}, jsonData["peaklists"][0]) ;
|
|
|
1828 all_contexts.forEach((context, index) => {
|
|
|
1829 if (context === null) {
|
|
|
1830 return;
|
|
|
1831 }
|
|
|
1832 new_peakdata = Object.assign({}, base_peakdata) ;
|
|
|
1833 context.loadFomDataIntoJsonObjects()
|
|
|
1834 if (is_ms2) {
|
|
|
1835 new_peakdata["precursor_ion"] = context.jsonPeaksList["precursor_ion"] ;
|
|
|
1836 }
|
|
|
1837 new_peakdata["peaklist"] = context.jsonPeaksList["peaklist"] ;
|
|
|
1838 all_mix_data["peaklists"].push(new_peakdata)
|
|
|
1839 })
|
|
|
1840 }
|
|
|
1841 // II.B - rebuild json full object (with all metadata or just id if already in base)
|
|
|
1842 if (jsonData == null) {
|
|
|
1843 jsonData = self.gatherJsonObjects();
|
|
|
1844 }
|
|
|
1845 // II.C - add id metadata (if exist)
|
|
|
1846 var json_array = [] ;
|
|
|
1847 if (!tab_index) {
|
|
|
1848 tab_index = {{ TAB_INDEX_PLACEHOLDER }} ;
|
|
|
1849 }
|
|
|
1850 json_array[tab_index-1] = jsonData ;
|
|
|
1851
|
|
|
1852 // III - post json object
|
|
|
1853 // III.A - success
|
|
|
1854 self.sent_json = jsonData ;
|
|
|
1855 console.warn(
|
|
|
1856 "This data has been validated without going through the internal server!"
|
|
|
1857 )
|
|
|
1858 if ($("#step5sign-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("fa-question-circle")) {
|
|
|
1859 $("#step5sign-{{ TAB_INDEX_PLACEHOLDER }}").removeClass("fa-question-circle").addClass("fa-check-circle");
|
|
|
1860 }
|
|
|
1861 if ($("#step5sign-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("fa-spinner")) {
|
|
|
1862 $("#step5sign-{{ TAB_INDEX_PLACEHOLDER }}").removeClass("fa-spinner fa-spin").addClass("fa-check-circle");
|
|
|
1863 }
|
|
|
1864 $("#import1SpectrumLoadingBare-{{ TAB_INDEX_PLACEHOLDER }}").hide();
|
|
|
1865 $("#alertBoxSubmitSpectrum-{{ TAB_INDEX_PLACEHOLDER }}").html(`
|
|
|
1866 <div class="alert alert-success alert-dismissible" role="alert">
|
|
|
1867 <button type="button" class="close" data-dismiss="alert">
|
|
|
1868 <span aria-hidden="true">×</span>
|
|
|
1869 <span class="sr-only">
|
|
|
1870 <spring:message code="alert.close" text="Close" />
|
|
|
1871 </span>
|
|
|
1872 </button>
|
|
|
1873 <strong>
|
|
|
1874 <spring:message code="alert.strong.info" text="Success!" />
|
|
|
1875 </strong> Spectrum ready to be sent!
|
|
|
1876 </div>
|
|
|
1877 `);
|
|
|
1878 return true;
|
|
|
1879 },
|
|
|
1880
|
|
|
1881 //USED HERE
|
|
|
1882 loadFomDataIntoJsonObjects: function() {
|
|
|
1883 var self = this ;
|
|
|
1884 // I - Spectrum type
|
|
|
1885 self.isJsonSpectrumTypeComplete = false ;
|
|
|
1886 if (self.isGC && self.is_ms()) {
|
|
|
1887 self.jsonSpectrumType = "gc-ms" ;
|
|
|
1888 } else if (self.isLC && self.is_ms()) {
|
|
|
1889 self.jsonSpectrumType = "lc-ms" ;
|
|
|
1890 } else if (self.isLC && self.is_ms2()) {
|
|
|
1891 self.jsonSpectrumType = "lc-msms" ;
|
|
|
1892 } else if (self.isGC && self.is_ms()) {
|
|
|
1893 self.jsonSpectrumType = "ic-ms" ;
|
|
|
1894 } else if (self.isLC && self.is_ms()) {
|
|
|
1895 self.jsonSpectrumType = "ic-msms" ;
|
|
|
1896 }
|
|
|
1897 if (self.jsonSpectrumType != null && self.jsonSpectrumType != "") {
|
|
|
1898 self.isJsonSpectrumTypeComplete = true;
|
|
|
1899 }
|
|
|
1900
|
|
|
1901 // II - Sample
|
|
|
1902 self.isJsonSampleComplete = true;
|
|
|
1903 self.isJsonRCCaddedComplete = true;
|
|
|
1904 self.jsonSample = {};
|
|
|
1905
|
|
|
1906 switch($("#add1spectrum-sample-type-{{ TAB_INDEX_PLACEHOLDER }}").val()) {
|
|
|
1907 // II.A - chemical lib. compound
|
|
|
1908 case "compound-ref":
|
|
|
1909 if ($("#add1spectrum-sample-inchikey-{{ TAB_INDEX_PLACEHOLDER }}").val() == "") {
|
|
|
1910 return false;
|
|
|
1911 }
|
|
|
1912 self.jsonSample["sample_type"] = "reference-chemical-compound";
|
|
|
1913 self.jsonSample["inchikey"] = $("#add1spectrum-sample-inchikey-{{ TAB_INDEX_PLACEHOLDER }}").val();
|
|
|
1914 self.jsonSample["concentration"] = $("#add1spectrum-sample-concentration-{{ TAB_INDEX_PLACEHOLDER }}").val();
|
|
|
1915 if (self.is_ms()) {
|
|
|
1916 self.jsonSample["solvent"] = $("#add1spectrum-sample-lcmsSolvent-{{ TAB_INDEX_PLACEHOLDER }}").val();
|
|
|
1917 }
|
|
|
1918 self.isJsonSampleComplete = true;
|
|
|
1919 break;
|
|
|
1920 // II.B - chemical lib. compound mix
|
|
|
1921 case "compound-mix":
|
|
|
1922 // solvent
|
|
|
1923 self.jsonSample["solvent"] = $("#add1spectrum-sample-mixSolvent-{{ TAB_INDEX_PLACEHOLDER }}").val();
|
|
|
1924 // cpd added
|
|
|
1925 self.jsonSample.inchikeys_list = self.getRCCADDED();
|
|
|
1926 self.jsonSample.concentrations_list = self.getRCCADDEDConcentration();
|
|
|
1927 if (self.jsonSample.inchikeys_list.length == 0 && !self.is_other_in_mix()) {
|
|
|
1928 self.isJsonRCCaddedComplete = false;
|
|
|
1929 console.log(`isJsonRCCaddedComplete: false`)
|
|
|
1930 return false;
|
|
|
1931 }
|
|
|
1932 self.isJsonSampleComplete = true;
|
|
|
1933 break;
|
|
|
1934 default:
|
|
|
1935 if (!self.is_other_in_mix()) {
|
|
|
1936 return false;
|
|
|
1937 }
|
|
|
1938 }
|
|
|
1939
|
|
|
1940 // III - Chromato
|
|
|
1941 self.isJsonChromatoComplete = true;
|
|
|
1942 self.jsonChromato = {};
|
|
|
1943
|
|
|
1944 // III.A - no chromato
|
|
|
1945 // nope?
|
|
|
1946
|
|
|
1947 // III.B - GC
|
|
|
1948 if (self.isGC) {
|
|
|
1949 self.isJsonChromatoComplete = false;
|
|
|
1950 // TODO
|
|
|
1951 }
|
|
|
1952
|
|
|
1953 // III.C - LC
|
|
|
1954 if (self.isLC) {
|
|
|
1955 self.isJsonChromatoComplete = true;
|
|
|
1956 self.jsonChromato = {};
|
|
|
1957 // check error
|
|
|
1958 $.each($(self.prefix+".add1spectrum-chromatoLCForm").parent(), function() {
|
|
|
1959 if ($(this).hasClass("has-error"))
|
|
|
1960 self.isJsonChromatoComplete = false;
|
|
|
1961 });
|
|
|
1962 if (
|
|
|
1963 !self.isJsonChromatoComplete
|
|
|
1964 && !self.is_other_in_mix()
|
|
|
1965 ) {
|
|
|
1966 console.log(`isJsonChromatoComplete: false`)
|
|
|
1967 return false;
|
|
|
1968 }
|
|
|
1969 var id = `#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}` ;
|
|
|
1970 self.jsonChromato["method"] = $(`${id} option:selected`).text();
|
|
|
1971 [
|
|
|
1972 ["column_constructor", "colConstructor"],
|
|
|
1973 ["column_constructor_other", "colConstructorOther"],
|
|
|
1974 ["column_name", "colName"],
|
|
|
1975 ["column_length", "colLength"],
|
|
|
1976 ["column_diameter", "colDiameter"],
|
|
|
1977 ["particule_size", "colParticuleSize"],
|
|
|
1978 ["column_temperature", "colTemperature"],
|
|
|
1979 ["mode", "LCMode"],
|
|
|
1980 ["separation_flow_rate", "separationFlowRate"],
|
|
|
1981 ["solvent_a", "separationSolvA"],
|
|
|
1982 ["solvent_a_ph", "separationSolvApH"],
|
|
|
1983 ["solvent_b", "separationSolvB"],
|
|
|
1984 ["solvent_b_ph", "separationSolvBApH"]
|
|
|
1985 ].forEach((field) => {
|
|
|
1986 id = `#add1spectrum-chromatoLC-${field[1]}-{{ TAB_INDEX_PLACEHOLDER }}` ;
|
|
|
1987 self.jsonChromato[field[0]] = $(id).val();
|
|
|
1988 })
|
|
|
1989 // fulfill json object
|
|
|
1990
|
|
|
1991 jsonSFG = [];
|
|
|
1992 var formatData = {
|
|
|
1993 time: [],
|
|
|
1994 solvent_a_percent: [],
|
|
|
1995 solvent_b_percent: []
|
|
|
1996 };
|
|
|
1997 var uniq_times = [] ;
|
|
|
1998 $.each(self.hot_LC_SFG.getData(), function() {
|
|
|
1999 var time = this[0] ;
|
|
|
2000 if (time != "" && time !== null) {
|
|
|
2001 if (
|
|
|
2002 !isNaN(time)
|
|
|
2003 && !isNaN(this[1])
|
|
|
2004 && !isNaN(this[2])
|
|
|
2005 && ! (time in uniq_times)
|
|
|
2006 ) {
|
|
|
2007 formatData["time"].push(Number(time));
|
|
|
2008 formatData["solvent_a_percent"].push(Number(this[1]));
|
|
|
2009 formatData["solvent_b_percent"].push(Number(this[2]));
|
|
|
2010 uniq_times.push(time) ;
|
|
|
2011 }
|
|
|
2012 }
|
|
|
2013 });
|
|
|
2014 self.jsonChromato.separation_flow_gradient = formatData;
|
|
|
2015 }
|
|
|
2016
|
|
|
2017 // III.D - IC
|
|
|
2018 if (self.isIC) {
|
|
|
2019 self.isJsonChromatoComplete = false;
|
|
|
2020 // TODO
|
|
|
2021 }
|
|
|
2022
|
|
|
2023 // IV - Analyzer
|
|
|
2024 self.isJsonAnalyzerComplete = true;
|
|
|
2025 self.isJsonAnalyzer = {};
|
|
|
2026 // IV.A - MS
|
|
|
2027 if (self.is_ms() || self.is_ms2()) {
|
|
|
2028 self.isJsonAnalyzerComplete = true;
|
|
|
2029 self.jsonAnalyzer = {};
|
|
|
2030 // check error
|
|
|
2031 $.each($(self.prefix+".add1spectrum-analyzerMSForm").parent(), function(){
|
|
|
2032 if ($(this).hasClass("has-error"))
|
|
|
2033 self.isJsonAnalyzerComplete = false;
|
|
|
2034 });
|
|
|
2035 if (
|
|
|
2036 !self.isJsonAnalyzerComplete
|
|
|
2037 && !self.is_other_in_mix()
|
|
|
2038 ) {
|
|
|
2039 console.log(`isJsonAnalyzerComplete: false`)
|
|
|
2040 return false;
|
|
|
2041 }
|
|
|
2042
|
|
|
2043 // fulfill json object
|
|
|
2044 self.jsonAnalyzer["instrument_name"] = $("#add1spectrum-analyzer-ms-instrument-{{ TAB_INDEX_PLACEHOLDER }}").val();
|
|
|
2045 self.jsonAnalyzer["instrument_model"] = $("#add1spectrum-analyzer-ms-model-{{ TAB_INDEX_PLACEHOLDER }}").val();
|
|
|
2046 self.jsonAnalyzer["instrument_brand"] = $("#add1spectrum-analyzer-ms-model-{{ TAB_INDEX_PLACEHOLDER }}").val();
|
|
|
2047 self.jsonAnalyzer["ion_analyzer_type"] = $("#add1spectrum-analyzer-ms-ionAnalyzerType-{{ TAB_INDEX_PLACEHOLDER }}").val();
|
|
|
2048
|
|
|
2049 if (self.is_ms2()) {
|
|
|
2050 // MSMS ion BEAM or TRAP
|
|
|
2051 self.jsonMolIonBeam = {}
|
|
|
2052 var jsonIonTrapBeam = {
|
|
|
2053 ion_gas: $("#add1spectrum-ionTrapBeam-ionGas-{{ TAB_INDEX_PLACEHOLDER }}").val(),
|
|
|
2054 ion_pressure_value: $("#add1spectrum-ionTrapBeam-ionGasPressureValue-{{ TAB_INDEX_PLACEHOLDER }}").val(),
|
|
|
2055 ion_pressure_unit: $("#add1spectrum-ionTrapBeam-ionGasPressureUnit-{{ TAB_INDEX_PLACEHOLDER }}").val()
|
|
|
2056 } ;
|
|
|
2057 var key = null ;
|
|
|
2058 if ($("#add1spectrum-ionTrapBeam-type-{{ TAB_INDEX_PLACEHOLDER }}").val() == "trap") {
|
|
|
2059 // sp
|
|
|
2060 jsonIonTrapBeam["ion_freq_shift"] = $("#add1spectrum-ionTrapBeam-ionFrequencyShift-{{ TAB_INDEX_PLACEHOLDER }}").val();
|
|
|
2061 jsonIonTrapBeam["ion_number"] = $("#add1spectrum-ionTrapBeam-ionNumber-{{ TAB_INDEX_PLACEHOLDER }}").val();
|
|
|
2062 key = "ion_trap" ;
|
|
|
2063 } else if ($("#add1spectrum-ionTrapBeam-type-{{ TAB_INDEX_PLACEHOLDER }}").val() == "beam") {
|
|
|
2064 key = "ion_beam_storage" ;
|
|
|
2065 }
|
|
|
2066 if (key !== null) {
|
|
|
2067 self.jsonMolIonBeam[key] = jsonIonTrapBeam;
|
|
|
2068 }
|
|
|
2069 }
|
|
|
2070
|
|
|
2071 self.jsonMolIonization = {};
|
|
|
2072 var json_mode ;
|
|
|
2073 ["pos", "neg"].forEach((kind) => {
|
|
|
2074 json_mode = {} ;
|
|
|
2075 [
|
|
|
2076 ["ionisation_method", "ionizationMethod"],
|
|
|
2077 ["spray_gas_flow", "sprayGazFlow"],
|
|
|
2078 ["vaporizer_gas_flow", "vaporizerGazFlow"],
|
|
|
2079 ["vaporizer_temperature", "vaporizerTemperature"],
|
|
|
2080 ["source_gas_flow", "sourceGazFlow"],
|
|
|
2081 ["transfer_tube_or_capillary_temperature", "ionTransferTubeTemperatureOrTransferCapillaryTemperature"],
|
|
|
2082 ["high_voltage", "highVoltageOrCoronaVoltage"]
|
|
|
2083 ].forEach((field) => {
|
|
|
2084 var id = `#add1spectrum-analyzserMS-${field[1]}-${kind}-{{ TAB_INDEX_PLACEHOLDER }}` ;
|
|
|
2085 json_mode[field[0]] = $(id).val() ;
|
|
|
2086 })
|
|
|
2087 self.jsonMolIonization[`mode_${kind}`] = json_mode ;
|
|
|
2088 })
|
|
|
2089 }
|
|
|
2090
|
|
|
2091 // IV.B - NMR
|
|
|
2092 if (self.is_ms() || self.is_ms2()) {
|
|
|
2093 self.isJsonPeaksListComplete = false;
|
|
|
2094 // init
|
|
|
2095 var peaklist = [];
|
|
|
2096 var peakdata = {};
|
|
|
2097 var spectrumData = {};
|
|
|
2098 // peaklist
|
|
|
2099 var ms_peak_data = self.hot_MS_Peaks.getData();
|
|
|
2100 $.each(ms_peak_data, function(index) {
|
|
|
2101 var data = ms_peak_data[index] ;
|
|
|
2102 var formatData = {};
|
|
|
2103 if (
|
|
|
2104 data[0] != ""
|
|
|
2105 && !isNaN(data[0])
|
|
|
2106 // && !isNaN(data[2])
|
|
|
2107 && (data[6] === "true" || data[6] === true)
|
|
|
2108 ) {
|
|
|
2109 peaklist.push({
|
|
|
2110 mz: Number(data[0]),
|
|
|
2111 ri: Number(data[2]),
|
|
|
2112 delta_ppm: Number(data[3]),
|
|
|
2113 composition: (data[4]),
|
|
|
2114 annotation: (data[5])
|
|
|
2115 });
|
|
|
2116 self.isJsonPeaksListComplete = true;
|
|
|
2117 }
|
|
|
2118 });
|
|
|
2119 // peak list data
|
|
|
2120 peakdata["scan_type"] = (
|
|
|
2121 self.is_ms2() ? "ms2" : "ms"
|
|
|
2122 );
|
|
|
2123 peakdata["polarity"] = $("#add1spectrum-peaksMS-polarity-{{ TAB_INDEX_PLACEHOLDER }}").val();
|
|
|
2124 peakdata["resolution"] = $("#add1spectrum-peaksMS-resolution-{{ TAB_INDEX_PLACEHOLDER }}").val();
|
|
|
2125 peakdata["curation"] = $("#add1spectrum-peaksMS-curation-{{ TAB_INDEX_PLACEHOLDER }}").val();
|
|
|
2126 peakdata["mz_from"] = $("#add1spectrum-peaksMS-rangeFrom-{{ TAB_INDEX_PLACEHOLDER }}").val();
|
|
|
2127 peakdata["mz_to"] = $("#add1spectrum-peaksMS-rangeTo-{{ TAB_INDEX_PLACEHOLDER }}").val();
|
|
|
2128 peakdata["retention_min_time_from"] = $("#add1spectrum-peaksMS-rtMinFrom-{{ TAB_INDEX_PLACEHOLDER }}").val();
|
|
|
2129 peakdata["retention_min_time_to"] = $("#add1spectrum-peaksMS-rtMinTo-{{ TAB_INDEX_PLACEHOLDER }}").val();
|
|
|
2130 peakdata["rt_solv_from"] = $("#add1spectrum-peaksMS-rtSolvFrom-{{ TAB_INDEX_PLACEHOLDER }}").val();
|
|
|
2131 peakdata["rt_solv_to"] = $("#add1spectrum-peaksMS-rtSolvTo-{{ TAB_INDEX_PLACEHOLDER }}").val();
|
|
|
2132 peakdata["resolution_FWHM"] = $("#add1spectrum-analyzer-ms-resolutionFWHM-{{ TAB_INDEX_PLACEHOLDER }}").val();
|
|
|
2133 if (self.is_ms2()) {
|
|
|
2134 var data = self.hot_MS_Peaks.getData() ;
|
|
|
2135 if (data.length != 0) {
|
|
|
2136 var selected_ion = self.get_selected_parent_ion_index() ;
|
|
|
2137 if (selected_ion !== null) {
|
|
|
2138 peakdata["precursor_ion"] = data[selected_ion][0] ;
|
|
|
2139 peakdata["precursor_spectrum_id"] = null ;
|
|
|
2140 } else {
|
|
|
2141 peakdata["precursor_ion"] = self.get_selected_parent_ion_mz() ;
|
|
|
2142 peakdata["precursor_spectrum_id"] = null ;
|
|
|
2143 }
|
|
|
2144 }
|
|
|
2145 }
|
|
|
2146 peakdata["peaklist"] = peaklist;
|
|
|
2147 self.jsonPeaksList = peakdata;
|
|
|
2148 }
|
|
|
2149
|
|
|
2150 self.isJsonOtherMetadataComplete = true;
|
|
|
2151 self.jsonOtherMetadata = {};
|
|
|
2152 // check error
|
|
|
2153 $.each($(self.prefix+".add1spectrum-otherForm").parent(), function(){
|
|
|
2154 if ($(this).hasClass("has-error"))
|
|
|
2155 self.isJsonOtherMetadataComplete = false;
|
|
|
2156 });
|
|
|
2157 if (!self.isJsonOtherMetadataComplete && !self.is_other_in_mix()) {
|
|
|
2158 console.log(`isJsonOtherMetadataComplete: false`)
|
|
|
2159 return false;
|
|
|
2160 }
|
|
|
2161 self.jsonOtherMetadata["data_authors"] = $("#add1spectrum-other-author-{{ TAB_INDEX_PLACEHOLDER }}").val();
|
|
|
2162 self.jsonOtherMetadata["data_validator"] = $("#add1spectrum-other-validator-{{ TAB_INDEX_PLACEHOLDER }}").val();;
|
|
|
2163 self.jsonOtherMetadata["acquisition_date"] = $("#add1spectrum-other-date-{{ TAB_INDEX_PLACEHOLDER }}").val();
|
|
|
2164 if (!self.jsonOtherMetadata["acquisition_date"]) {
|
|
|
2165 self.jsonOtherMetadata["acquisition_date"] = null ;
|
|
|
2166 }
|
|
|
2167 self.jsonOtherMetadata["data_ownership"] = $("#add1spectrum-other-owner-{{ TAB_INDEX_PLACEHOLDER }}").val();
|
|
|
2168 self.jsonOtherMetadata["raw_file_name"] = $("#add1spectrum-other-fileName-{{ TAB_INDEX_PLACEHOLDER }}").val();
|
|
|
2169 self.jsonOtherMetadata["raw_file_size"] = $("#add1spectrum-other-fileSize-{{ TAB_INDEX_PLACEHOLDER }}").val();
|
|
|
2170 return true;
|
|
|
2171 },
|
|
|
2172
|
|
|
2173 //USED HERE
|
|
|
2174 getFormErrorMessage: function() {
|
|
|
2175 var self = this ;
|
|
|
2176 var alertMsg = "";
|
|
|
2177 if (!self.isJsonSpectrumTypeComplete) {
|
|
|
2178 alertMsg = `
|
|
|
2179 <div class="alert alert-danger alert-dismissible" role="alert">
|
|
|
2180 <button type="button" class="close" data-dismiss="alert">
|
|
|
2181 <span aria-hidden="true">×</span>
|
|
|
2182 <span class="sr-only">
|
|
|
2183 <spring:message code="alert.close" text="Close" />
|
|
|
2184 </span>
|
|
|
2185 </button>
|
|
|
2186 <strong>
|
|
|
2187 <spring:message code="alert.strong.error" text="Error!" />
|
|
|
2188 </strong> Error processing spectrum type!
|
|
|
2189 </div>` ;
|
|
|
2190 } else if (!self.isJsonSampleComplete) {
|
|
|
2191 alertMsg = `
|
|
|
2192 <div class="alert alert-danger alert-dismissible" role="alert">
|
|
|
2193 <button type="button" class="close" data-dismiss="alert">
|
|
|
2194 <span aria-hidden="true">×</span>
|
|
|
2195 <span class="sr-only">
|
|
|
2196 <spring:message code="alert.close" text="Close" />
|
|
|
2197 </span>
|
|
|
2198 </button>
|
|
|
2199 <strong>
|
|
|
2200 <spring:message code="alert.strong.error" text="Error!" />
|
|
|
2201 </strong> Missing mandatory data into sample section!
|
|
|
2202 <br />
|
|
|
2203 <a
|
|
|
2204 href="#"
|
|
|
2205 onclick="$('#linkActivateStep1-{{ TAB_INDEX_PLACEHOLDER }}').trigger('click');"
|
|
|
2206 >Go to this section</a>
|
|
|
2207 </div>` ;
|
|
|
2208 } else if (!self.isJsonRCCaddedComplete) {
|
|
|
2209 alertMsg = `
|
|
|
2210 <div class="alert alert-danger alert-dismissible" role="alert">
|
|
|
2211 <button type="button" class="close" data-dismiss="alert">
|
|
|
2212 <span aria-hidden="true">×</span>
|
|
|
2213 <span class="sr-only">
|
|
|
2214 <spring:message code="alert.close" text="Close" />
|
|
|
2215 </span>
|
|
|
2216 </button>
|
|
|
2217 <strong>
|
|
|
2218 <spring:message code="alert.strong.error" text="Error!" />
|
|
|
2219 </strong> Pease enter at least ONE compound in mix into sample section!
|
|
|
2220 <br />
|
|
|
2221 <a
|
|
|
2222 href="#"
|
|
|
2223 onclick="$('#linkActivateStep1-{{ TAB_INDEX_PLACEHOLDER }}').trigger('click');"
|
|
|
2224 >Go to this section</a>
|
|
|
2225 </div>`;
|
|
|
2226 } else if (!self.isJsonChromatoComplete) {
|
|
|
2227 alertMsg = `
|
|
|
2228 <div class="alert alert-danger alert-dismissible" role="alert">
|
|
|
2229 <button type="button" class="close" data-dismiss="alert">
|
|
|
2230 <span aria-hidden="true">×</span>
|
|
|
2231 <span class="sr-only">
|
|
|
2232 <spring:message code="alert.close" text="Close" />
|
|
|
2233 </span>
|
|
|
2234 </button>
|
|
|
2235 <strong>
|
|
|
2236 <spring:message code="alert.strong.error" text="Error!" />
|
|
|
2237 </strong> Missing data in chromatography section!
|
|
|
2238 ` ;
|
|
|
2239 if (self.is_ms()) {
|
|
|
2240 alertMsg += `
|
|
|
2241 <br />
|
|
|
2242 <a
|
|
|
2243 href="#"
|
|
|
2244 onclick="$('#linkActivateStep4-ms-{{ TAB_INDEX_PLACEHOLDER }}').trigger('click');"
|
|
|
2245 >Go to this section</a>`;
|
|
|
2246 }
|
|
|
2247 alertMsg += ' </div>';
|
|
|
2248 } else if (!self.isJsonPeaksListComplete) {
|
|
|
2249 alertMsg = `
|
|
|
2250 <div class="alert alert-danger alert-dismissible" role="alert">
|
|
|
2251 <button type="button" class="close" data-dismiss="alert">
|
|
|
2252 <span aria-hidden="true">×</span>
|
|
|
2253 <span class="sr-only">
|
|
|
2254 <spring:message code="alert.close" text="Close" />
|
|
|
2255 </span>
|
|
|
2256 </button>
|
|
|
2257 <strong>
|
|
|
2258 <spring:message code="alert.strong.error" text="Error!" />
|
|
|
2259 </strong> Missing peaklist!
|
|
|
2260 ` ;
|
|
|
2261 if (self.is_ms()) {
|
|
|
2262 alertMsg += `
|
|
|
2263 <br />
|
|
|
2264 <a
|
|
|
2265 href="#"
|
|
|
2266 onclick="$('#linkActivateStep4-ms-{{ TAB_INDEX_PLACEHOLDER }}').trigger('click');"
|
|
|
2267 >Go to this section</a>`;
|
|
|
2268 }
|
|
|
2269 alertMsg += ' </div>';
|
|
|
2270 } else if (self.is_mix() && self.is_ms2()) {
|
|
|
2271 for (var i = 0 ; i < all_contexts.length ; i += 1) {
|
|
|
2272 if (all_contexts[i] === null || all_contexts[i] === undefined) {
|
|
|
2273 continue;
|
|
|
2274 }
|
|
|
2275 if (all_contexts[i].get_selected_parent_ion_index() === null) {
|
|
|
2276 return alertMsg + `
|
|
|
2277 <div class="alert alert-danger alert-dismissible" role="alert">
|
|
|
2278 <button type="button" class="close" data-dismiss="alert">
|
|
|
2279 <span aria-hidden="true">×</span>
|
|
|
2280 <span class="sr-only">
|
|
|
2281 <spring:message code="alert.close" text="Close" />
|
|
|
2282 </span>
|
|
|
2283 </button>
|
|
|
2284 <strong>
|
|
|
2285 <spring:message code="alert.strong.error" text="Error!" />
|
|
|
2286 </strong> Select precursor ion in all peak lists!
|
|
|
2287 </div>
|
|
|
2288 `
|
|
|
2289 }
|
|
|
2290 }
|
|
|
2291 }
|
|
|
2292 // TODO other
|
|
|
2293 return alertMsg;
|
|
|
2294 },
|
|
|
2295
|
|
|
2296 //USED HERE
|
|
|
2297 gatherJsonObjects: function() {
|
|
|
2298 var self = this ;
|
|
|
2299 var jsonData = {};
|
|
|
2300 if (self.is_mix()) {
|
|
|
2301 jsonData["sample_type"] = "mix_of_reference_chemical_compounds" ;
|
|
|
2302 } else {
|
|
|
2303 jsonData["sample_type"] = "reference_chemical_compound" ;
|
|
|
2304 }
|
|
|
2305 jsonData["spectrum_type"] = self.jsonSpectrumType.toUpperCase().replaceAll("-", "");
|
|
|
2306 jsonData["sample"] = self.jsonSample;
|
|
|
2307 if (self.isLC) {
|
|
|
2308 jsonData["chromatography"] = self.jsonChromato;
|
|
|
2309 } else if (self.isGC) {
|
|
|
2310 jsonData["chromatography"] = self.jsonChromato;
|
|
|
2311 } else if (self.isIC) {
|
|
|
2312 jsonData["chromatography"] = self.jsonChromato;
|
|
|
2313 }
|
|
|
2314 if (self.is_ms()) {
|
|
|
2315 jsonData["analyzer"] = self.jsonAnalyzer;
|
|
|
2316 var molecule_ionization = self.jsonMolIonization;
|
|
|
2317 jsonData["ionization_mode_positive"] = molecule_ionization["mode_pos"] ;
|
|
|
2318 jsonData["ionization_mode_negative"] = molecule_ionization["mode_neg"] ;
|
|
|
2319 jsonData["peaklists"] = [self.jsonPeaksList] ;
|
|
|
2320 } else if (self.is_ms2()) {
|
|
|
2321 jsonData["analyzer"] = self.jsonAnalyzer;
|
|
|
2322 var molecule_ionization = self.jsonMolIonization;
|
|
|
2323 jsonData["ionization_mode_positive"] = molecule_ionization["mode_pos"] ;
|
|
|
2324 jsonData["ionization_mode_negative"] = molecule_ionization["mode_neg"] ;
|
|
|
2325 if (self.jsonMolIonBeam != null) {
|
|
|
2326 jsonData["ion_beam_storage"] = self.jsonMolIonBeam["ion_beam_storage"];
|
|
|
2327 }
|
|
|
2328 jsonData["peaklists"] = [self.jsonPeaksList] ;
|
|
|
2329 }
|
|
|
2330 jsonData["other_metadata"] = self.jsonOtherMetadata;
|
|
|
2331 return jsonData;
|
|
|
2332 },
|
|
|
2333
|
|
|
2334 //USED IN HTML
|
|
|
2335 pickChemicalCompound: function() {
|
|
|
2336 var self = this ;
|
|
|
2337 self.singlePick = true;
|
|
|
2338 $("#modalPickCompound-{{ TAB_INDEX_PLACEHOLDER }}").modal("show");
|
|
|
2339 $("#add-one-cc-s1-value-{{ TAB_INDEX_PLACEHOLDER }}").focus();
|
|
|
2340 },
|
|
|
2341
|
|
|
2342 //USED HERE
|
|
|
2343 pickChemicalCompound4Mix: function(rowNumber) {
|
|
|
2344 var self = this ;
|
|
|
2345 self.singlePick = false;
|
|
|
2346 self.multiPickLine = rowNumber;
|
|
|
2347 $("#modalPickCompound-{{ TAB_INDEX_PLACEHOLDER }}").modal("show");
|
|
|
2348 $("#add-one-cc-s1-value-{{ TAB_INDEX_PLACEHOLDER }}").focus();
|
|
|
2349 },
|
|
|
2350
|
|
|
2351 //USED HERE
|
|
|
2352 searchAjax: function() {
|
|
|
2353 var self = this ;
|
|
|
2354 var results ;
|
|
|
2355 var rawQuery = $('#add-one-cc-s1-value-{{ TAB_INDEX_PLACEHOLDER }}').val();
|
|
|
2356 if (rawQuery.length > 2) {
|
|
|
2357 return [] ;
|
|
|
2358 }
|
|
|
2359 results = [] ;
|
|
|
2360 $.ajax({
|
|
|
2361 type: "post",
|
|
|
2362 url: "{{ PF_URL_PLACEHOLDER }}/webapp/search",
|
|
|
2363 dataType: "json",
|
|
|
2364 async: false,
|
|
|
2365 data: "query=" + $("#add-one-cc-s1-value-{{ TAB_INDEX_PLACEHOLDER }}").val(),
|
|
|
2366 success: function(json) {
|
|
|
2367 if (json.success) {
|
|
|
2368 $.each(json.compoundNames, function(){
|
|
|
2369 results.push(this.name) ;
|
|
|
2370 }) ;
|
|
|
2371 $.each(json.compounds, function(){
|
|
|
2372 if (this.inChIKey.indexOf(rawQuery)) {
|
|
|
2373 results.push(this.inChIKey) ;
|
|
|
2374 }
|
|
|
2375 }) ;
|
|
|
2376 }
|
|
|
2377 },
|
|
|
2378 error : function(xhr) {
|
|
|
2379 self.subjects = [] ;
|
|
|
2380 console.log(xhr) ;
|
|
|
2381 }
|
|
|
2382 }) ;
|
|
|
2383 return results ;
|
|
|
2384 },
|
|
|
2385
|
|
|
2386 //USED HERE
|
|
|
2387 searchLocalCompound: function() {
|
|
|
2388 var self = this ;
|
|
|
2389 $("#load-step-1-{{ TAB_INDEX_PLACEHOLDER }}").show();
|
|
|
2390 $.ajax({
|
|
|
2391 type: "get",
|
|
|
2392 url: "{{ PF_URL_PLACEHOLDER }}/rest/v2/compounds",
|
|
|
2393 async: true,
|
|
|
2394 data: "limit=1&query=" + $('#add-one-cc-s1-value-{{ TAB_INDEX_PLACEHOLDER }}').val() + "&query_filter=" + self.fitlerSearchLoadlCpd+"&token={{ PF_TOKEN_PLACEHOLDER }}",
|
|
|
2395 success: function(data) {
|
|
|
2396 data = data[0] ;
|
|
|
2397 var id = parseInt(data["id"]) ;
|
|
|
2398 var name = data["name"] ;
|
|
|
2399 var inchikey = data["inchikey"] ;
|
|
|
2400 var inchi = data["inchi"] ;
|
|
|
2401 data = `
|
|
|
2402 <div class="table-responsive">
|
|
|
2403 <table id="tabPickCpd-{{ TAB_INDEX_PLACEHOLDER }}" class="table table-bordered table-hover table-striped tablesorter" style="cursor: pointer;">
|
|
|
2404 <thead>
|
|
|
2405 <tr>
|
|
|
2406 <th class="header">Chemical Name <i class="fa fa-sort"></i></th>
|
|
|
2407 <th class="header">Monoisotopic Mass <i class="fa fa-sort"></i></th>
|
|
|
2408 <th class="header">Formula <i class="fa fa-sort"></i></th>
|
|
|
2409 <th class="header" style="">Structure</th>
|
|
|
2410 </tr>
|
|
|
2411 </thead>
|
|
|
2412 <tbody>
|
|
|
2413 <tr class="success" onclick="loadCompoundInForm(${id}, '${inchikey}', '${inchi}', '${data["formula"]}', '${data["exactMass"]}' , 100);">
|
|
|
2414 <td style="vertical-align: middle;">
|
|
|
2415 <span id="cpt-load-name-${id}-{{ TAB_INDEX_PLACEHOLDER }}">${name}</span>
|
|
|
2416 <br><small style="white-space: nowrap;">${inchikey}</small>
|
|
|
2417 </td>
|
|
|
2418 <td style="vertical-align: middle;" class="compoundMass">${data["exactMass"]}</td>
|
|
|
2419 <td style="vertical-align: middle;" class="compoundFormula">${data["formula"]}</sub></td>
|
|
|
2420 <td><span class="avatar">
|
|
|
2421 <img class="compoundSVG" src="{{ PF_URL_PLACEHOLDER }}/webapp/image/generic/${inchikey}" alt="${name}">
|
|
|
2422 </span>
|
|
|
2423 </td>
|
|
|
2424 </tr>
|
|
|
2425 </tbody>
|
|
|
2426 </table>
|
|
|
2427 <small><sup><b>*</b></sup>: Generic Compounds (abstract "flat" compound without (+) or (-) center).</small>
|
|
|
2428 <` + "script" + ` type="text/javascript">
|
|
|
2429 $("#tabPickCpd-{{ TAB_INDEX_PLACEHOLDER }}").tablesorter();
|
|
|
2430 $.each($(self.prefix+".compoundFormula"), function(id, elem) {
|
|
|
2431 var rawFromula = $(elem).text();
|
|
|
2432 var formatedFormula = rawFromula;
|
|
|
2433 try {
|
|
|
2434 $.each($.unique( rawFromula.match(/\d+/g)), function(keyF, valF) {
|
|
|
2435 var re = new RegExp(valF,"g");
|
|
|
2436 formatedFormula = formatedFormula.replace(re, "<sub>" + valF + "</sub>");
|
|
|
2437 });
|
|
|
2438 } catch (e){}
|
|
|
2439 formatedFormula = formatedFormula.replace("</sub><sub>", "");
|
|
|
2440 $(elem).html(formatedFormula);
|
|
|
2441 });
|
|
|
2442 $.each($(self.prefix+".compoundMass"), function(id, elem) {
|
|
|
2443 var exactMass = parseFloat( $(elem).text());
|
|
|
2444 exactMass = roundNumber(exactMass,7)
|
|
|
2445 $(elem).html(exactMass);
|
|
|
2446 });
|
|
|
2447 </` + "script" + `>
|
|
|
2448
|
|
|
2449 </div>
|
|
|
2450 <` + "script" + ` type="text/javascript">
|
|
|
2451 var listOfRefCompoundsMatch = null;
|
|
|
2452
|
|
|
2453 loadCompoundInForm = function(id, inchikey, inchi, composition, exactMass, type) {
|
|
|
2454 if (ctx().modeEditSpectrum) {
|
|
|
2455 var name = $("#cpt-load-name-" + id + "-{{ TAB_INDEX_PLACEHOLDER }}").html();
|
|
|
2456 if (ctx().multiPickLine >= 0) {
|
|
|
2457 ctx().hot_RCC_ADDED.setDataAtCell(ctx().multiPickLine, 0, name);
|
|
|
2458
|
|
|
2459 // restet form
|
|
|
2460 setTimeout(function(){
|
|
|
2461 $("#add-one-cc-s1-value-{{ TAB_INDEX_PLACEHOLDER }}").val("");
|
|
|
2462 $("#ok-step-1-{{ TAB_INDEX_PLACEHOLDER }}").html("");
|
|
|
2463 }, 200);
|
|
|
2464 // img
|
|
|
2465 var typeS = "chemical";
|
|
|
2466 if (type == 100)
|
|
|
2467 typeS = "generic";
|
|
|
2468 else if (type == 101)
|
|
|
2469 typeS = "chemical";
|
|
|
2470 // '<img class="mixRCCadd'+ctx().multiPickLine+' compoundSVGZoom" src="{{ PF_URL_PLACEHOLDER }}/webapp/image/'+typeS+'/'+inchikey+'" alt="'+name+'">'
|
|
|
2471 var currentCpt = {
|
|
|
2472 "name": name,
|
|
|
2473 "type": typeS,
|
|
|
2474 "concentration": "?",
|
|
|
2475 "inchikey": inchikey
|
|
|
2476 };
|
|
|
2477 updatedCpdMixData[name] = currentCpt;
|
|
|
2478 }
|
|
|
2479 // display
|
|
|
2480 $("#modalPickCompound-{{ TAB_INDEX_PLACEHOLDER }}").modal("hide");
|
|
|
2481 $("#modalEditSpectrum-{{ TAB_INDEX_PLACEHOLDER }} .modal-dialog").show();
|
|
|
2482 return;
|
|
|
2483 } // else: add one spectrum
|
|
|
2484 var name = $("#cpt-load-name-" + id + "-{{ TAB_INDEX_PLACEHOLDER }}").html();
|
|
|
2485 if (ctx().singlePick) {
|
|
|
2486 $("#add1spectrum-sample-inchikey-{{ TAB_INDEX_PLACEHOLDER }}").val(inchikey);
|
|
|
2487 $("#add1spectrum-sample-inchikey-{{ TAB_INDEX_PLACEHOLDER }}").change();
|
|
|
2488 $("#add1spectrum-sample-inchi-{{ TAB_INDEX_PLACEHOLDER }}").val(inchi);
|
|
|
2489 $("#add1spectrum-sample-inchi-{{ TAB_INDEX_PLACEHOLDER }}").change();
|
|
|
2490 $("#add1spectrum-sample-commonName-{{ TAB_INDEX_PLACEHOLDER }}").val(name);
|
|
|
2491 $("#add1spectrum-sample-commonName-{{ TAB_INDEX_PLACEHOLDER }}").change();
|
|
|
2492
|
|
|
2493 $("#importspectrum-sample-inchikey-{{ TAB_INDEX_PLACEHOLDER }}").val(inchikey);
|
|
|
2494 $("#importspectrum-sample-inchikey-{{ TAB_INDEX_PLACEHOLDER }}").change();
|
|
|
2495 } else if (ctx().multiPickLine >= 0) {
|
|
|
2496 ctx().hot_RCC_ADDED.setDataAtCell(ctx().multiPickLine, 0, name);
|
|
|
2497 ctx().hot_RCC_ADDED.setDataAtCell(ctx().multiPickLine, 1, inchikey);
|
|
|
2498 ctx().hot_RCC_ADDED.setDataAtCell(ctx().multiPickLine, 2, composition);
|
|
|
2499 ctx().hot_RCC_ADDED.setDataAtCell(ctx().multiPickLine, 4, exactMass);
|
|
|
2500 // restet form
|
|
|
2501 setTimeout(function(){
|
|
|
2502 $("#add-one-cc-s1-value-{{ TAB_INDEX_PLACEHOLDER }}").val("");
|
|
|
2503 $("#ok-step-1-{{ TAB_INDEX_PLACEHOLDER }}").html("");
|
|
|
2504 }, 200);
|
|
|
2505 }
|
|
|
2506 var typeS = "chemical";
|
|
|
2507 if (type == 100)
|
|
|
2508 typeS = "generic";
|
|
|
2509 else if (type == 101)
|
|
|
2510 typeS = "chemical";
|
|
|
2511 if (ctx().singlePick)
|
|
|
2512 $("#sample-bonus-display-{{ TAB_INDEX_PLACEHOLDER }}").html('<img class="" src="{{ PF_URL_PLACEHOLDER }}/webapp/image/'+typeS+'/'+inchikey+'" alt="'+name+'">');
|
|
|
2513 else {
|
|
|
2514 // delete
|
|
|
2515 $(ctx().prefix+"img.mixRCCadd"+ctx().multiPickLine).remove();
|
|
|
2516 // add
|
|
|
2517 $("#sample-bonus-display-{{ TAB_INDEX_PLACEHOLDER }}").append('<img class="mixRCCadd'+ctx().multiPickLine+' compoundSVGZoom" src="{{ PF_URL_PLACEHOLDER }}/webapp/image/'+typeS+'/'+inchikey+'" alt="'+name+'">');
|
|
|
2518 $(ctx().prefix+"img.mixRCCadd"+ctx().multiPickLine+"").mouseenter(function() {
|
|
|
2519 $(this).removeClass("compoundSVGZoom");
|
|
|
2520 }).mouseleave(function() {
|
|
|
2521 $(this).addClass("compoundSVGZoom");
|
|
|
2522 });
|
|
|
2523 }
|
|
|
2524 $("#modalPickCompound-{{ TAB_INDEX_PLACEHOLDER }}").modal("hide");
|
|
|
2525 }
|
|
|
2526 </` + "script" + `></` + "div" + `>` ;
|
|
|
2527 $("#ok-step-1-{{ TAB_INDEX_PLACEHOLDER }}").html(data);
|
|
|
2528 },
|
|
|
2529 error : function(xhr) {
|
|
|
2530 // log
|
|
|
2531 console.log(xhr);
|
|
|
2532 // error
|
|
|
2533 $("#ok-step-1-{{ TAB_INDEX_PLACEHOLDER }}").html("Error: could not process request.");
|
|
|
2534 }
|
|
|
2535 }).always(function() {
|
|
|
2536 $("#load-step-1-{{ TAB_INDEX_PLACEHOLDER }}").hide();
|
|
|
2537 });
|
|
|
2538 },
|
|
|
2539
|
|
|
2540 //USED HERE
|
|
|
2541 getRCCADDED: function() {
|
|
|
2542 var self = this ;
|
|
|
2543 jsonRCC_ADDED = [];
|
|
|
2544 $.each(self.hot_RCC_ADDED.getData(), function(){
|
|
|
2545 var formatData = {};
|
|
|
2546 if ("<b>InChIKey</b>" in this && this["<b>InChIKey</b>"]!= undefined && this["<b>InChIKey</b>"] != "") {
|
|
|
2547 jsonRCC_ADDED.push(this["<b>InChIKey</b>"]);
|
|
|
2548 }
|
|
|
2549 });
|
|
|
2550 return jsonRCC_ADDED;
|
|
|
2551 },
|
|
|
2552
|
|
|
2553 //USED HERE
|
|
|
2554 getRCCADDEDConcentration: function() {
|
|
|
2555 var self = this ;
|
|
|
2556 jsonRCC_ADDED = [];
|
|
|
2557 $.each(self.hot_RCC_ADDED.getData(), function(){
|
|
|
2558 var formatData = {};
|
|
|
2559 if ("<b>InChIKey</b>" in this && this["<b>InChIKey</b>"]!= undefined && this["<b>InChIKey</b>"] != "") {
|
|
|
2560 jsonRCC_ADDED.push(this["<b>concentration (µg/ml)</b>"]);
|
|
|
2561 }
|
|
|
2562 });
|
|
|
2563 return jsonRCC_ADDED;
|
|
|
2564 },
|
|
|
2565
|
|
|
2566 //USED IN HTML
|
|
|
2567 clearLine: function() {
|
|
|
2568 var self = this ;
|
|
|
2569 // restet form
|
|
|
2570 setTimeout(function(){
|
|
|
2571 $("#add-one-cc-s1-value-{{ TAB_INDEX_PLACEHOLDER }}").val("");
|
|
|
2572 $("#ok-step-1-{{ TAB_INDEX_PLACEHOLDER }}").html("");
|
|
|
2573 }, 200);
|
|
|
2574 $(self.prefix+"img.mixRCCadd"+self.multiPickLine).remove();
|
|
|
2575 if (self.singlePick) {
|
|
|
2576 $("#add1spectrum-sample-inchikey-{{ TAB_INDEX_PLACEHOLDER }}").val("");
|
|
|
2577 $("#add1spectrum-sample-inchikey-{{ TAB_INDEX_PLACEHOLDER }}").change();
|
|
|
2578 $("#add1spectrum-sample-inchi-{{ TAB_INDEX_PLACEHOLDER }}").val("");
|
|
|
2579 $("#add1spectrum-sample-inchi-{{ TAB_INDEX_PLACEHOLDER }}").change();
|
|
|
2580 $("#add1spectrum-sample-commonName-{{ TAB_INDEX_PLACEHOLDER }}").val("");
|
|
|
2581 $("#add1spectrum-sample-commonName-{{ TAB_INDEX_PLACEHOLDER }}").change();
|
|
|
2582 $("#sample-bonus-display-{{ TAB_INDEX_PLACEHOLDER }}").html("");
|
|
|
2583 } else if (self.multiPickLine >= 0) {
|
|
|
2584 for(var i = 0 ; i < 6 ; i += 1) {
|
|
|
2585 self.hot_RCC_ADDED.setDataAtCell(self.multiPickLine, i, "");
|
|
|
2586 }
|
|
|
2587 }
|
|
|
2588 },
|
|
|
2589
|
|
|
2590 exit: function() {
|
|
|
2591 $.ajax({type: "get", url: "/quit", async: true, success: ()=>window.close()});
|
|
|
2592 },
|
|
|
2593
|
|
|
2594 } ;
|
|
|
2595
|
|
|
2596 $.ajax({
|
|
|
2597 type: "get",
|
|
|
2598 url: "{{ PF_URL_PLACEHOLDER }}/webapp/get-cpd-data?token={{ PF_TOKEN_PLACEHOLDER }}",
|
|
|
2599 data: "inchikey=" + "{{ INCHIKEY_PLACEHOLDER }}",
|
|
|
2600 dataType: "json",
|
|
|
2601 success: function(data) {
|
|
|
2602 if (data.success) {
|
|
|
2603 var self = context_{{ TAB_INDEX_PLACEHOLDER }} ;
|
|
|
2604 console.log(`inchikey {{ INCHIKEY_PLACEHOLDER }} found!!`)
|
|
|
2605 inchidata["{{ INCHIKEY_PLACEHOLDER }}"] = data ;
|
|
|
2606 self.init() ;
|
|
|
2607 self.fitlerSearchLoadlCpd = 5;
|
|
|
2608 self.inchikey = null;
|
|
|
2609 all_contexts[{{ TAB_INDEX_PLACEHOLDER }}] = self ;
|
|
|
2610 } else {
|
|
|
2611 no_success(
|
|
|
2612 {{ TAB_INDEX_PLACEHOLDER }},
|
|
|
2613 "{{ INCHIKEY_PLACEHOLDER }}",
|
|
|
2614 {{ DEFAULT_DATA }}["name"]
|
|
|
2615 ) ;
|
|
|
2616 all_contexts[{{ TAB_INDEX_PLACEHOLDER }}] = null ;
|
|
|
2617 }
|
|
|
2618 },
|
|
|
2619 error : function(data) {
|
|
|
2620 no_success(
|
|
|
2621 {{ TAB_INDEX_PLACEHOLDER }},
|
|
|
2622 "{{ INCHIKEY_PLACEHOLDER }}",
|
|
|
2623 {{ DEFAULT_DATA }}["name"]
|
|
|
2624 ) ;
|
|
|
2625 all_contexts[{{ TAB_INDEX_PLACEHOLDER }}] = null ;
|
|
|
2626 }
|
|
|
2627 }).always(() => null);
|
