Mercurial > repos > lain > ms_to_peakforest_it
diff src/add-one-spectrum-index.js @ 1:7e3085fc60c1 draft default tip
master branch Updating
| author | lain |
|---|---|
| date | Wed, 30 Aug 2023 14:21:18 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/src/add-one-spectrum-index.js Wed Aug 30 14:21:18 2023 +0000 @@ -0,0 +1,2627 @@ + +var token = "{{ PF_TOKEN_PLACEHOLDER }}" ; +if ({{ TAB_INDEX_PLACEHOLDER }} == 1) { +} + +context_{{ TAB_INDEX_PLACEHOLDER }} = { + prefix: "#accordion-{{ TAB_INDEX_PLACEHOLDER }} ", + name: "Context[{{ TAB_INDEX_PLACEHOLDER }}]", + produce_json: {{ PRODUCE_JSON_PLACEHOLDER }}, + DEFAULT_MS_PEAK_VALUES: {{ MS_PEAK_VALUES_PLACEHOLDER }}, + DEFAULT_DATA: {{ DEFAULT_DATA }}, + peakforest_url: "{{ PF_URL_PLACEHOLDER }}", + tab_index: "{{ TAB_INDEX_PLACEHOLDER }}", + modeEditSpectrum: false, + isSeparationFlowRateInit: false, + isMSpeaksInit: false, + isLC: false, + isGC: false, + isIC: false, + hot_LC_SFG: null , + hot_MS_Peaks: null, + hot_RCC_ADDED: null, + jsonSpectrumType: null, + isJsonSpectrumTypeComplete: false, + jsonSample: null, + isJsonSampleComplete: false, + isJsonRCCaddedComplete: false, + jsonChromato: null, + isJsonChromatoComplete: false, + jsonAnalyzer: null, + isJsonAnalyzerComplete: false, + jsonPeaksList: [], + isJsonPeaksListComplete: false, + jsonOtherMetadata: null, + isJsonOtherMetadataComplete: false, + jsonMolIonization: null, + jsonMolIonBeam: null, + cptPeakListTab: 0, + jsonAnalyzerAcquisition: [], + idMetadataMap: {}, + listOfViewableSpectra: [], + singlePick: true, + multiPickLine: -1, + subjects: [], + fitlerSearchLoadlCpd: 5, + inchikey: null, + initialized: false, + selected_ion_index: null, + lock: { + precursor_ion: false + }, + + sent_json: null, + + init: function() { + + var self = this ; + + $(document).ready(() => self.on_ready()); + $(document).ready(function() { + console.log("adding click on open_tab_{{ TAB_INDEX_PLACEHOLDER }}.") ; + var activate_tab = function() { + if (self.initialized) { + return ; + } + self.auto_set_spec_type() ; + } + if (self.is_ref()) { + $("#open_tab_{{ TAB_INDEX_PLACEHOLDER }}").click(activate_tab) ; + } + if ({{ TAB_INDEX_PLACEHOLDER }} == 1) { + activate_tab() ; + } + }) ; + + return (self) ; + + }, + + on_ready: function() { + var self = this ; + + $(self.prefix+".pickChemicalCompound").click(self.pickChemicalCompound); + $(self.prefix+".add1spectrum").change( + function(){self.add1spectrum_change_handler(this)} + ) + self.attach_search() ; + self.add_date_check() ; + self.populate_selects() ; + self.add_change_handlers() ; + self.show_hide_ms_ms2_fields() ; + }, + + populate_selects: function() { + var self = this ; + var choose_in_list ; + + choose_in_list = ` + <option value="" selected="selected" disabled="disabled"> + choose in list… + </option> + ` ; + $("#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}").append(choose_in_list) ; + $("#add1spectrum-chromatoLC-colConstructor-{{ TAB_INDEX_PLACEHOLDER }}").append(choose_in_list) ; + $("#add1spectrum-chromatoLC-separationSolvA-{{ TAB_INDEX_PLACEHOLDER }}").append(choose_in_list) ; + $("#add1spectrum-chromatoLC-separationSolvB-{{ TAB_INDEX_PLACEHOLDER }}").append(choose_in_list) ; + $("#add1spectrum-sample-lcmsSolvent-{{ TAB_INDEX_PLACEHOLDER }}").append(choose_in_list) ; + $.getJSON("{{ PF_URL_PLACEHOLDER }}/webapp/resources/json/list-lc-methods.json", self.populate_lc_methods) ; + $.getJSON("{{ PF_URL_PLACEHOLDER }}/webapp/resources/json/list-lc-columns.json", self.populate_lc_columns) ; + $.getJSON("{{ PF_URL_PLACEHOLDER }}/webapp/resources/json/list-lc-solvents.json", self.populate_lc_solvents) ; + $.getJSON("{{ PF_URL_PLACEHOLDER }}/webapp/resources/json/list-ms-ionization-methods.json", self.populate_ms_ionization) ; + $.getJSON("{{ PF_URL_PLACEHOLDER }}/webapp/resources/json/list-lcms-solvents.json", self.populate_lcms_solvents) ; + self.resetFromColors(); + }, + + attach_search: function() { + var self = this ; + + $("#add-one-cc-s1-value-{{ TAB_INDEX_PLACEHOLDER }}").bind("keypress", function(e) { + var code = e.keyCode || e.which; + if (code == 13) { + self.searchLocalCompound(); + } + }); + $("#add-one-cc-s1-value-{{ TAB_INDEX_PLACEHOLDER }}").typeahead({ + source: function(query, process) { + return self.searchAjax(); + } + }); + }, + + add_date_check: function() { + var self = this ; + + $("#add1spectrum-other-date-{{ TAB_INDEX_PLACEHOLDER }}").focusout(function() { + var element = $(this) ; + self.rm_warning(element); + self.rm_success(element) ; + if (element.val() == "") { + element.parent().addClass("has-warning"); + } else { + element.parent().addClass("has-success"); + } + }); + }, + + populate_lc_methods: function(data) { + // load data from json + $.each(data.methods,function() { + if (this.name !== undefined) { + if (this.value !== undefined) { + $("#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}").append( + `<option value="${this.value}">${this.name}</option>` + ); + } else { + $("#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}").append( + `<option disabled>${this.name}</option>` + ); + } + } + }); + }, + + populate_lc_columns: function(data) { + // load data from json + $.each(data.columns, function() { + $("#add1spectrum-chromatoLC-colConstructor-{{ TAB_INDEX_PLACEHOLDER }}").append( + `<option value="${this.value}">${this.name}</option>` + ); + }); + $("#add1spectrum-chromatoLC-colConstructor-{{ TAB_INDEX_PLACEHOLDER }}").append( + '<option value="other" >Other</option>' + ); + }, + + populate_lc_solvents: function(data) { + // load data from json + $.each(data.solvents, function() { + $("#add1spectrum-chromatoLC-separationSolvA-{{ TAB_INDEX_PLACEHOLDER }}").append( + `<option value="${this.value}">${this.name}</option>` + ); + $("#add1spectrum-chromatoLC-separationSolvB-{{ TAB_INDEX_PLACEHOLDER }}").append( + `<option value="${this.value}">${this.name}</option>` + ); + }); + }, + + populate_ms_ionization: function(data) { + // load data from json + $.each(data.methods,function() { + if (this.name !==undefined) { + if (this.value !==undefined) { + $("#add1spectrum-analyzserMS-ionizationMethod-pos-{{ TAB_INDEX_PLACEHOLDER }}").append( + `<option value="${this.value}">${this.name}</option>` + ); + $("#add1spectrum-analyzserMS-ionizationMethod-neg-{{ TAB_INDEX_PLACEHOLDER }}").append( + `<option value="${this.value}">${this.name}</option>` + ); + } else { + $("#add1spectrum-analyzserMS-ionizationMethod-pos-{{ TAB_INDEX_PLACEHOLDER }}").append( + `<option disabled>${this.name}</option>` + ); + $("#add1spectrum-analyzserMS-ionizationMethod-neg-{{ TAB_INDEX_PLACEHOLDER }}").append( + `<option disabled>${this.name}</option>` + ); + } + } + }); + }, + + populate_lcms_solvents: function(data) { + // load data from json + $.each(data.solvents, function () { + $("#add1spectrum-sample-lcmsSolvent-{{ TAB_INDEX_PLACEHOLDER }}").append( + `<option value="${this.value}" class="${this.classD}">${this.name}</option>` + ); + }); + }, + + add_change_handlers: function() { + var self = this ; + + $("#add1spectrum-ionTrapBeam-type-{{ TAB_INDEX_PLACEHOLDER }}").on("change", function() { + var v = $("#add1spectrum-ionTrapBeam-type-{{ TAB_INDEX_PLACEHOLDER }}").val(); + $(self.prefix + ".add1spectrum-ionTrap").hide(); + if (v == "beam") { + } else if (v == "trap") { + $(self.prefix + ".add1spectrum-ionTrap").show(); + } + }) ; + }, + + show_hide_ms_ms2_fields: function() { + var self = this ; + $(self.prefix + " .disabled-if-ms").attr("disabled", self.is_ms()) + $(self.prefix + " .disabled-if-msms").attr("disabled", self.is_ms2()) + $(self.prefix + " .disabled-if-ms2").attr("disabled", self.is_ms2()) + if (self.is_ms()) { + self.hide(self.prefix + " .hidden-if-ms") ; + } + if (self.is_ms2()) { + self.hide(self.prefix + " .hidden-if-msms") ; + self.hide(self.prefix + " .hidden-if-ms2") ; + } + }, + + is_mix: function() { + return this.DEFAULT_DATA["sample_type"] == "compound-mix" ; + }, + + is_ref: function() { + return this.DEFAULT_DATA["sample_type"] == "compound-ref" ; + }, + + is_ms: function() { + return this.DEFAULT_DATA["spectrum_type"] == "LC_MS" ; + }, + + is_ms2: function() { + return this.DEFAULT_DATA["spectrum_type"] == "LC_MSMS" ; + }, + + is_other_in_mix() { + return this.is_mix() && {{ TAB_INDEX_PLACEHOLDER }} > 1 ; + }, + + hide: function(id) { + if (typeof id == Array) { + return (id.forEach(hide)) ; + } + $(id).hide() + }, + + rm_success: function(element) { + return (this.rm_parent_class(element, "has-success")) + }, + rm_error: function(element) { + return (this.rm_parent_class(element, "has-error")) + }, + rm_warning: function(element) { + return (this.rm_parent_class(element, "has-warning")) + }, + set_success: function(element) { + return (this.set_parent_class(element, "has-success")) + }, + set_error: function(element) { + return (this.set_parent_class(element, "has-error")) + }, + set_warning: function(element) { + return (this.set_parent_class(element, "has-warning")) + }, + rm_parent_class: function(element, cls) { + var parent ; + + if ((parent = element.parent()) == null) { + return false ; + } + return this.rm_class(parent, cls) ; + }, + set_parent_class: function(element, cls) { + var parent ; + + if ((parent = element.parent()) == null) { + return false ; + } + return this.set_class(parent, cls) ; + }, + rm_class: function(element, cls) { + if (element.hasClass(cls)) { + element.removeClass(cls) ; + return true ; + } + return false ; + }, + set_class: function(element, cls) { + if (element.hasClass(cls)) { + return false ; + } + element.addClass(cls) ; + return true ; + }, + is_success: function(element) { + return (this.parent_has_class(element, "has-success")) + }, + is_warning: function(element) { + return (this.parent_has_class(element, "has-warning")) + }, + is_error: function(element) { + return (this.parent_has_class(element, "has-error")) + }, + is_optional: function(element) { + return (element.hasClass("is-optional")) + }, + is_mandatory: function(element) { + return (element.hasClass("is-mandatory")) + }, + parent_has_class: function(element, cls) { + var parent ; + + if ((parent = element.parent()) == null) { + return false ; + } + return (parent.hasClass(cls)) ; + }, + + add1spectrum_change_handler: function(element) { + var self = this ; + var idElem ; + var valElem ; + var isSuccess ; + var isWarning ; + var isError ; + var isOptional ; + var isMandatory ; + + element = $(element) ; + idElem = element.attr("id") ; + valElem = element.val(); + console.log(`Change handler called for [${idElem}]=${valElem}`) ; + if (idElem.split("-").slice(0, -1).join("-") == "add1spectrum-peaksMS-msPrecursorIon") { + var index = idElem.split("-")[3] - 1 ; + if (all_contexts[index] !== null && all_contexts[index] !== undefined) { + all_contexts[index].sync_precursor_ion() ; + if (all_contexts[index].hot_MS_Peaks != null) { + all_contexts[index].hot_MS_Peaks.render() + } + } + } + isSuccess = self.is_success(element); + isWarning = self.is_warning(element); + isError = self.is_error(element); + isOptional = self.is_optional(element); + isMandatory = self.is_mandatory(element); + + switch(idElem) { + case "add1spectrum-sample-type-{{ TAB_INDEX_PLACEHOLDER }}": + if (valElem == "compound-ref") { + $("#add1spectrum-sample-type-compound-ref-{{ TAB_INDEX_PLACEHOLDER }}").show(); + $("#add1spectrum-sample-type-compound-mix-{{ TAB_INDEX_PLACEHOLDER }}").hide(); + $("#add1spectrum-sample-type-rcc-added-{{ TAB_INDEX_PLACEHOLDER }}").hide(); + } else if (valElem == "compound-mix") { + $("#add1spectrum-sample-type-compound-mix-{{ TAB_INDEX_PLACEHOLDER }}").show(); + $("#add1spectrum-sample-type-compound-ref-{{ TAB_INDEX_PLACEHOLDER }}").hide(); + $("#add1spectrum-sample-type-rcc-added-{{ TAB_INDEX_PLACEHOLDER }}").show(); + self.handsontableRefChemCpdAdded(null); + } + break; + case "add1spectrum-chromatoLC-colConstructor-{{ TAB_INDEX_PLACEHOLDER }}": + self.resetElemColor("add1spectrum-chromatoLC-colConstructorOther-{{ TAB_INDEX_PLACEHOLDER }}"); + if (valElem == "" || valElem == null || valElem != "other" ) { + self.disableElem("add1spectrum-chromatoLC-colConstructorOther-{{ TAB_INDEX_PLACEHOLDER }}"); + } else { + self.enableElem("add1spectrum-chromatoLC-colConstructorOther-{{ TAB_INDEX_PLACEHOLDER }}"); + } + break; + case "add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}": + self.fulfillLCdata(valElem); + break; + case "add1spectrum-analyzserMS-ionizationMethod-pos-{{ TAB_INDEX_PLACEHOLDER }}": + if ($("#add1spectrum-analyzserMS-ionizationMethod-pos-{{ TAB_INDEX_PLACEHOLDER }}").val() != null) { + $($("#add1spectrum-peaksMS-polarity-{{ TAB_INDEX_PLACEHOLDER }} option")[1]).attr("disabled", false); + } + break; + case "add1spectrum-analyzserMS-ionizationMethod-neg-{{ TAB_INDEX_PLACEHOLDER }}": + if ($("#add1spectrum-analyzserMS-ionizationMethod-neg-{{ TAB_INDEX_PLACEHOLDER }}").val() != null) { + $($("#add1spectrum-peaksMS-polarity-{{ TAB_INDEX_PLACEHOLDER }} option")[2]).attr("disabled", false); + } + break; + } + if ((isMandatory || isOptional) && (valElem == "" || valElem == null)) { + if (isSuccess) { + self.rm_success(element) ; + } else if (isWarning) { + self.rm_warning(element) ; + } else if (isError) { + self.rm_error(element) ; + } + if (isMandatory) { + self.set_error(element) ; + } else { + self.set_warning(element) ; + } + } + if (isMandatory && (valElem != "" && valElem != null)) { + if (isError) { + self.rm_error(element) ; + } + self.set_success(element) ; + } else if (isOptional && valElem != "") { + if (isWarning) { + self.rm_warning(element) ; + } + self.set_success(element) ; + } + if (element.parent().children("input").size() == 2) { + if (isMandatory) { + if (isSuccess) { + self.rm_success(element) ; + } else if (isWarning) { + self.rm_warning(element) ; + } else if (isError) { + self.rm_error(element) ; + } + if (element.parent().children("input").toArray().some( + (el) => $(el).val() === null || $(el).val() === "" + )) { + self.set_error(element) ; + } else { + self.set_success(element) ; + } + } else if (isOptional) { + isSuccess = self.is_success(element); + isWarning = self.is_warning(element); + isError = self.is_error(element); + if (isSuccess) { + self.rm_success(element) + } else if (isWarning) { + self.rm_warning(element) ; + } else if (isError) { + self.rm_error(element) ; + } + if (element.parent().children("input").toArray().some( + (el) => ($(el).val() == null || $(el).val() == "") + )) { + self.set_warning(element) ; + } else { + self.set_success(element) ; + } + } + } + if (element.hasClass("one-or-more")) { + // get parent class + isSuccess = self.is_success(element); + isWarning = self.is_warning(element); + isError = self.is_error(element); + // reset class + if (isSuccess) { + self.rm_success(element) ; + } else if (isWarning) { + self.rm_warning(element) ; + } else if (isError) { + self.rm_error(element) ; + } + isTmpSuccess = false; + $.each(element.parent().children("input"), function(id, child){ + if ($(child).val() != null && $(child).val() != "") { + isTmpSuccess = true; + } + }); + $.each(element.parent().children("select"), function(id, child){ + if ($(child).val() != null && $(child).val() != "") { + isTmpSuccess = true; + } + }); + // end parkour + element.parent().addClass( + isTmpSuccess ? "has-success" : "has-error" + ); + } + // CHECK IF OK STEP 2 + if (element.hasClass("add1spectrum-sampleForm")) { + var isBtnStep2OK = true; + $.each($(self.prefix + ".add1spectrum-sampleForm"), (id, elem) => { + if (self.is_error($(elem)) && $(elem).is(":visible")) { + isBtnStep2OK = false; + } + }); + if (isBtnStep2OK) { + self.rm_class($("#btnSwitch-gotoStep2-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-disabled") ; + self.set_class($("#btnSwitch-gotoStep2-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-primary") ; + $("#btnSwitch-gotoStep2-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", false); + } else { + self.set_class($("#btnSwitch-gotoStep2-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-disabled") ; + self.rm_class($("#btnSwitch-gotoStep2-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-primary") ; + $("#btnSwitch-gotoStep2-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", true); + } + } + // CHECK IF OK STEP 3 - LC + if ( + element.hasClass("add1spectrum-chromatoLCForm") + && $("#btnSwitch-gotoStep3-lc-{{ TAB_INDEX_PLACEHOLDER }}").is(":visible") + ) { + var isBtnStep3OK = true; + $.each($(self.prefix+".add1spectrum-chromatoLCForm"), (id, elem) => { + if (self.is_error($(elem)) && $(elem).is(":visible")) + isBtnStep3OK = false; + }); + if (isBtnStep3OK) { + self.rm_class($("#btnSwitch-gotoStep3-lc-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-disabled") ; + self.set_class($("#btnSwitch-gotoStep3-lc-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-primary") ; + $("#btnSwitch-gotoStep3-lc-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", false); + } else { + self.set_class($("#btnSwitch-gotoStep3-lc-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-disabled") ; + self.rm_class($("#btnSwitch-gotoStep3-lc-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-primary") ; + $("#btnSwitch-gotoStep3-lc-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", true); + } + } + // TODO CHECK IF OK STEP 3 - GC + // CHECK IF OK STEP 4 - MS ANALYZER + if ( + element.hasClass("add1spectrum-analyzerMSForm") + && $("#btnSwitch-gotoStep4-ms-{{ TAB_INDEX_PLACEHOLDER }}").is(":visible") + ) { + var isBtnStep4OK = true; + $.each($(self.prefix+".add1spectrum-analyzerMSForm"), (id, elem) => { + if (self.is_error($(elem)) && $(elem).is(":visible")) + isBtnStep4OK = false; + }); + if (isBtnStep4OK) { + self.rm_class($("#btnSwitch-gotoStep4-ms-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-disabled") ; + self.set_class($("#btnSwitch-gotoStep4-ms-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-primary") ; + $("#btnSwitch-gotoStep4-ms-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", false); + } else { + self.set_class($("#btnSwitch-gotoStep4-ms-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-disabled") ; + self.rm_class($("#btnSwitch-gotoStep4-ms-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-primary") ; + $("#btnSwitch-gotoStep4-ms-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", true); + } + } + // CHECK IF OK STEP 5 - PEAKS + if ( + element.hasClass("add1spectrum-peaksMSForm-peaklist") + && $("#btnSwitch-gotoStep5-ms-{{ TAB_INDEX_PLACEHOLDER }}").is(":visible") + ) { + var isBtnStep5OK = true; + $.each($(self.prefix+".add1spectrum-peaksMSForm-peaklist"), (id, elem) => { + if (self.is_error($(elem)) && $(elem).is(":visible")) + isBtnStep5OK = false; + }); + if (isBtnStep5OK && (self.is_ms() || self.a_ion_parent_is_selected())) { + self.rm_class($("#btnSwitch-gotoStep5-ms-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-disabled") ; + self.set_class($("#btnSwitch-gotoStep5-ms-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-primary") ; + $("#btnSwitch-gotoStep5-ms-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", false); + } else { + self.set_class($("#btnSwitch-gotoStep5-ms-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-disabled") ; + self.rm_class($("#btnSwitch-gotoStep5-ms-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-primary") ; + $("#btnSwitch-gotoStep5-ms-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", true); + } + } + // CHECK IF OK STEP 6 - OTHER DATA + if ( + element.hasClass("add1spectrum-otherForm") + && $("#btnSwitch-gotoStep6-{{ TAB_INDEX_PLACEHOLDER }}").is(":visible") + ) { + self.checkIfEnableSubmit() ; + } + }, + + a_ion_parent_is_selected: function() { + return (this.get_selected_parent_ion_mz() !== null) ; + }, + + get_selected_parent_ion_index: function() { + var curent_mz = this.get_selected_parent_ion_mz() ; + if (curent_mz === null) { + return null; + } + if (this.hot_MS_Peaks == undefined) { + return null ; + } + var data = this.hot_MS_Peaks.getData() ; + for (var i = 0 ; i < data.length ; i += 1) { + if (Math.abs(data[i][0] - curent_mz) < 0.0001) { + return i ; + } + } + return null ; + }, + + get_selected_parent_ion_mz: function() { + return $( + "#add1spectrum-peaksMS-msPrecursorIon-{{ TAB_INDEX_PLACEHOLDER }}" + ).val() || null ; + }, + + auto_set_spec_type: function() { + console.log("auto_set_spec_type...") ; + var self = this ; + var id = `#set_${self.DEFAULT_DATA["spectrum_type"]}_spectrum_button` ; + var element = $(self.prefix + id) ; + if (element.length) { + element.click() ; + console.log(`auto_set_spec_type to ${self.DEFAULT_DATA["spectrum_type"]} ok.`) + } else { + console.log(element) + console.log("Failed!") + } + if (self.DEFAULT_DATA["sample_type"]) { + self.auto_set_sample_type(self) ; + } + }, + + auto_set_sample_type: function() { + console.log("auto_set_sample_type...") ; + var self = this ; + var id = "#add1spectrum-sample-type-{{ TAB_INDEX_PLACEHOLDER }}" ; + var element = $(id) ; + if (element.length) { + element.val(self.DEFAULT_DATA["sample_type"]).change() ; + console.log(`auto_set_sample_type to ${self.DEFAULT_DATA["sample_type"]} ok.`) ; + if (self.DEFAULT_DATA["sample_type"] == "compound-ref") { + $("#add1spectrum-sample-mixSolvent-{{ TAB_INDEX_PLACEHOLDER }}").val( + "H2O/ethanol (75/25)" + ).change() ; + } + } else { + console.log(element) + console.log("Failed!") + } + if (self.DEFAULT_DATA["inchikey"]) { + setTimeout(() => self.auto_set_inchikey(self), 1000) ; + } + }, + + auto_set_inchikey: function() { + console.log("auto_set_inchikey...") ; + var self = this ; + var id ; + var element ; + self.inchikey = self.DEFAULT_DATA["inchikey"] ; + if (self.is_ref()) { + id = "#add1spectrum-sample-inchikey-{{ TAB_INDEX_PLACEHOLDER }}:text" ; + element = $(id) ; + if (element.length) { + console.log(`auto_set_inchikey to ${self.inchikey} ok.`) + element.val(self.inchikey).change() ; + console.log(`Inchikey set!`) ; + } else { + console.log(element) + console.log("Failed!") + } + } else { + for (var index = 0 ; index < all_contexts.length ; index += 1) { + if (all_contexts[index] === null || all_contexts[index] === undefined) { + continue; + } + var inchikey = all_contexts[index].DEFAULT_DATA["inchikey"] ; + id = `#container_RCC_ADDED-1 tbody:nth(0) tr:nth(${index}) td:nth(1)` ; + element = $(id) ; + if (element.length) { + console.log(`auto_set_inchikey to ${inchikey} ok.`) + self.hot_RCC_ADDED.setDataAtCell(index, 1, inchikey) ; + element.innerHTML = inchikey ; + element.change() ; + console.log(element) ; + console.log(`Inchikey set!`) ; + } else { + console.log(element) + console.log("Failed!") + } + } + console.log(self.hot_RCC_ADDED) + self.hot_RCC_ADDED.render() ; + } + $("#btnSwitch-gotoStep2-{{ TAB_INDEX_PLACEHOLDER }}").click() ; + if (self.DEFAULT_DATA["method"]) { + setTimeout(() => self.auto_set_method(self), 1000) ; + } + }, + + auto_set_method: function() { + console.log("auto_set_method...") ; + var self = this ; + var id = "#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}" ; + var element = $(id) ; + element.length && element.val(self.DEFAULT_DATA["method"]).change() ; + $("#btnSwitch-gotoStep3-lc-{{ TAB_INDEX_PLACEHOLDER }}").click() ; + setTimeout(() => { + (() => { + $("#btnSwitch-gotoStep4-ms-{{ TAB_INDEX_PLACEHOLDER }}").click() ; + console.log(`auto_set_method to ${self.DEFAULT_DATA["method"]} ok.`) + if (self.DEFAULT_DATA["scan_type"]) { + + // The scan type needs to be skipped, as it is already defined + // at build-time + // The code is kept for future modifications of this behavior + setTimeout(() => self.auto_set_scan_type(self, skip = true), 1000) ; + } + })(self) + }, 1000) ; + }, + + auto_set_scan_type: function(skip = false) { + var self = this ; + if (!skip) { + console.log("auto_set_scan_type...") ; + var id = "#add1spectrum-peaksMS-msLevel-{{ TAB_INDEX_PLACEHOLDER }}" ; + var element = $(id) ; + if (element.length) { + element.val(self.DEFAULT_DATA["scan_type"]).change() ; + console.log(`auto_set_scan_type to ${self.DEFAULT_DATA["scan_type"]} ok.`) + } else { + console.log("Failed!") + } + } + if (self.DEFAULT_DATA["polarity"]) { + self.auto_set_polarity(self) ; + } + }, + + auto_set_polarity: function() { + console.log("auto_set_polarity...") ; + var self = this ; + var id = "#add1spectrum-peaksMS-polarity-{{ TAB_INDEX_PLACEHOLDER }}" ; + var element = $(id) ; + if (element.length) { + element.val(self.DEFAULT_DATA["polarity"]).change() ; + console.log(`auto_set_polarity to ${self.DEFAULT_DATA["polarity"]} ok.`) + } else { + console.log("Failed!") + } + if (self.DEFAULT_DATA["resolution"]) { + self.auto_set_resolution(self) ; + } + }, + + auto_set_resolution: function() { + console.log("auto_set_resolution...") ; + var self = this ; + var id = "#add1spectrum-peaksMS-resolution-{{ TAB_INDEX_PLACEHOLDER }}" ; + var element = $(id) ; + if (element.length) { + element.val(self.DEFAULT_DATA["resolution"]).change() ; + console.log(`auto_set_resolution to ${self.DEFAULT_DATA["resolution"]} ok.`) + } else { + console.log("Failed!") + } + if (self.DEFAULT_DATA["next"] || true) { + setTimeout(() => self.finish_initialized(self), 1000) ; + } + }, + + finish_initialized: function() { + var self = this ; + if (ctx() === self) { + self.initialized = true ; + } + }, + + //USED IN HTML + updateLCMSspectraViewer: function() { + var self = this ; + var tab_no ; + console.log(`Updating spectral view for tab {{ TAB_INDEX_PLACEHOLDER }}`) ; + // reset current viewer + $("#containter-lcms-spectrum-preview-{{ TAB_INDEX_PLACEHOLDER }}").empty(); + // reset data. + + if (self.is_mix()) { + tab_no = 1 ; + } else { + tab_no = {{ TAB_INDEX_PLACEHOLDER }} ; + } + var range_from = $(`#add1spectrum-peaksMS-rangeFrom-${tab_no}`) ; + if ((spectrumMinPPM = Number(range_from.val())) == "") { + spectrumMinPPM = 10000; + } + var range_to = $(`#add1spectrum-peaksMS-rangeTo-${tab_no}`) ; + if ((spectrumMaxPPM = Number(range_to.val())) == "") { + spectrumMaxPPM = 0; + } + maxGraph = 0; + var localData = []; + var localDataAnnot = []; + // gather new data + // TODO switch tab in function of technic + $.each(self.hot_MS_Peaks.getData(), function() { + if(this[0] != undefined && this[0] != "") { + var x = (Number(this[0])); + var y = Number(this[2]); + var a = this[6]; + localData.push([(x-0.000001),-150]); + localData.push([(x+0.000001),-150]); + localData.push([x,y]); + localDataAnnot[x] = a; + if (x < spectrumMinPPM) { + spectrumMinPPM = x; + } + if (x > spectrumMaxPPM) { + spectrumMaxPPM = x; + } + if (y > maxGraph) { + maxGraph = y; + } + } + }); + + // build new one + spectrumMinPPM = spectrumMinPPM - (0.1 * spectrumMinPPM); + spectrumMaxPPM = spectrumMaxPPM + (0.1 * spectrumMaxPPM); + maxGraph = maxGraph + (0.1 * maxGraph); + localData.sort(); + console.log(localData) + // build graph + $("#containter-lcms-spectrum-preview-{{ TAB_INDEX_PLACEHOLDER }}").highcharts({ + chart: { + zoomType: "x", + spacingRight: 10, + spacingLeft: 10, + type: "scatter" + }, + title: { + text: "Spectrum Preview", + useHTML: true + }, + subtitle: { + text: ( + document.ontouchstart === undefined + ? "Select area" + : "Pinch the chart to zoom in" + ) + }, + xAxis: { + type: "number", + title: {text: "m/z"}, + min: spectrumMinPPM, + max: spectrumMaxPPM, + labels: { + formatter: function() { + return (Math.abs(this.value) + ""); + } + } + }, + yAxis: { + title: {text: "Relative Intensity (%)"}, + min: 0, + max: maxGraph + }, + tooltip: { + crosshairs: true, + formatter: function() { + var compo = ""; + return ( + "<b>" + this.series.name + + "</b><br/>m/z:" + Math.abs(this.x) + "" + + ";<br/>Relative Intensity: " + this.y + + "%;<br/>Annotation: " + localDataAnnot[ this.x] + + "" + ); + } + }, + legend: {enabled: false}, + plotOptions: {scatter: {}}, + series: [{ + name: "preview", + showInLegend: true, + color: "#f00", + lineColor: "#f00", + pointInterval: 10, + pointStart: 100, + lineWidth : 2, + marker: { + enabled: true, + radius: 2, + lineColor: "#f00" + }, + data: localData, + zIndex: 10 + }] + }); + }, + + //USED HERE + fulfillLCdata: function(jsonFileName) { + var self = this ; + var url = `{{ PF_URL_PLACEHOLDER }}/webapp/resources/json/lc-methods/${jsonFileName}.json` ; + $.getJSON(url, function(json) { + // $.POST + console.log(json); + // lc chromato + if (json.lc_chromatography != null) { + [ + ["colConstructor", "column_constructor"], + ["colConstructorOther", "column_constructor_other"], + ["colName", "column_name"], + ["colLength", "column_length"], + ["colDiameter", "column_diameter"], + ["colParticuleSize", "particule_size"], + ["colTemperature", "column_temperature"], + ["separationFlowRate", "separation_flow_rate"], + ["separationSolvA", "separation_solvent_a"], + ["separationSolvApH", "ph_solvent_a"], + ["separationSolvB", "separation_solvent_b"], + ["separationSolvBpH", "ph_solvent_b"] + ].forEach((arr) => { + var el ; + console.log(arr) + el = $(`#add1spectrum-chromatoLC-${arr[0]}-{{ TAB_INDEX_PLACEHOLDER }}`) + el.val(json.lc_chromatography[arr[1]]) ; + el.change() + }) + try { + $("#add1spectrum-chromatoLC-LCMode-{{ TAB_INDEX_PLACEHOLDER }}").val(json.lc_chromatography.LC_mode); + $("#add1spectrum-chromatoLC-LCMode-{{ TAB_INDEX_PLACEHOLDER }}").change(); + } catch (e) {} + var handsontableSeparationFlowRateData = [] ; + if (json.lc_chromatography.separation_flow_gradient != null) { + $.each(json.lc_chromatography.separation_flow_gradient, function() { + var e = [ + "" + this.time, + "" + this.solvA, + "" + this.solvB + ]; + handsontableSeparationFlowRateData.push(e); + }); + } else { + handsontableSeparationFlowRateData = null; + } + self.handsontableSeparationFlowRate(handsontableSeparationFlowRateData); + } + // ms_analyzer + if (json.ms_analyzer != null) { + $("#add1spectrum-analyzer-ms-instrument-{{ TAB_INDEX_PLACEHOLDER }}").val(json.ms_analyzer.instrument); + $("#add1spectrum-analyzer-ms-instrument-{{ TAB_INDEX_PLACEHOLDER }}").change(); + $("#add1spectrum-analyzer-ms-model-{{ TAB_INDEX_PLACEHOLDER }}").val(json.ms_analyzer.model); + $("#add1spectrum-analyzer-ms-model-{{ TAB_INDEX_PLACEHOLDER }}").change(); + $("#add1spectrum-analyzer-ms-resolutionFWHM-{{ TAB_INDEX_PLACEHOLDER }}").val(json.ms_analyzer.resolution_FWHM); + $("#add1spectrum-analyzer-ms-resolutionFWHM-{{ TAB_INDEX_PLACEHOLDER }}").change(); + $("#add1spectrum-analyzer-ms-ionAnalyzerType-{{ TAB_INDEX_PLACEHOLDER }}").val(json.ms_analyzer.ion_analyzer_type); + $("#add1spectrum-analyzer-ms-ionAnalyzerType-{{ TAB_INDEX_PLACEHOLDER }}").change(); + } + if (json.molecule_ionization != null) { + ["pos", "neg"].forEach((mode) => { + if (json.molecule_ionization[`mode_${mode}`] != null) { + [ + ["ionizationMethod", "ionisation_method"], + ["sprayGazFlow", "spray_gaz_flow"], + ["vaporizerGazFlow", "vaporizer_gaz_flow"], + ["vaporizerTemperature", "vaporizer_temperature"], + ["sourceGazFlow", "source_gaz_flow"], + ["ionTransferTubeTemperatureOrTransferCapillaryTemperature", "transfer_tube_or_capillary_temperature"], + ["highVoltageOrCoronaVoltage", "voltage"], + ].forEach((tuple) => { + var el ; + var id = tuple[0] ; + var key = tuple[1] ; + el = $(`#add1spectrum-analyzserMS-${id}-${mode}-{{ TAB_INDEX_PLACEHOLDER }}`) ; + console.log(el) + el.val(json.molecule_ionization[`mode_${mode}`][key]); + el.change() ; + }) + } + }) + } + + if (json.molecule_beamOrTrap != null) { + if (json.molecule_beamOrTrap.ion_beam != null) { + $("#add1spectrum-ionTrapBeam-type-{{ TAB_INDEX_PLACEHOLDER }}").val("beam").change(); + $("#add1spectrum-ionTrapBeam-ionGas-{{ TAB_INDEX_PLACEHOLDER }}").val(json.molecule_beamOrTrap.ion_beam.ion_gas).change(); + $("#add1spectrum-ionTrapBeam-ionGasPressureValue-{{ TAB_INDEX_PLACEHOLDER }}").val(json.molecule_beamOrTrap.ion_beam.ion_pressure_value).change(); + $("#add1spectrum-ionTrapBeam-ionGasPressureUnit-{{ TAB_INDEX_PLACEHOLDER }}").val(json.molecule_beamOrTrap.ion_beam.ion_pressure_unit).change(); + } + if (json.molecule_beamOrTrap.ion_trap != null) { + $("#add1spectrum-ionTrapBeam-type-{{ TAB_INDEX_PLACEHOLDER }}").val("trap").change(); + $("#add1spectrum-ionTrapBeam-ionGas-{{ TAB_INDEX_PLACEHOLDER }}").val(json.molecule_beamOrTrap.ion_trap.ion_gas).change(); + $("#add1spectrum-ionTrapBeam-ionGasPressureValue-{{ TAB_INDEX_PLACEHOLDER }}").val(json.molecule_beamOrTrap.ion_trap.ion_pressure_value).change(); + $("#add1spectrum-ionTrapBeam-ionGasPressureUnit-{{ TAB_INDEX_PLACEHOLDER }}").val(json.molecule_beamOrTrap.ion_trap.ion_pressure_unit).change(); + $("#add1spectrum-ionTrapBeam-ionNumber-{{ TAB_INDEX_PLACEHOLDER }}").val(json.molecule_beamOrTrap.ion_trap.ion_number).change(); + $("#add1spectrum-ionTrapBeam-ionFrequencyShift-{{ TAB_INDEX_PLACEHOLDER }}").val(json.molecule_beamOrTrap.ion_trap.ion_freq_shift).change(); + } + } + // other + if (json.other != null) { + $("#add1spectrum-other-author-{{ TAB_INDEX_PLACEHOLDER }}").val(json.other.data_authors); + $("#add1spectrum-other-author-{{ TAB_INDEX_PLACEHOLDER }}").change(); + $("#add1spectrum-other-validator-{{ TAB_INDEX_PLACEHOLDER }}").val(json.other.data_validator); + $("#add1spectrum-other-validator-{{ TAB_INDEX_PLACEHOLDER }}").change(); + $("#add1spectrum-other-date-{{ TAB_INDEX_PLACEHOLDER }}").val(json.other.acquisition_date); + $("#add1spectrum-other-date-{{ TAB_INDEX_PLACEHOLDER }}").change(); + $("#add1spectrum-other-owner-{{ TAB_INDEX_PLACEHOLDER }}").val(json.other.data_ownership); + $("#add1spectrum-other-owner-{{ TAB_INDEX_PLACEHOLDER }}").change(); + } + }).error(function(event, jqxhr, exception) { + if (event.status == 404) { + $("#alertBoxSelectTemplate-{{ TAB_INDEX_PLACEHOLDER }}").html(` + <div class="alert alert-danger alert-dismissible" role="alert"> + <button type="button" class="close" data-dismiss="alert"> + <span aria-hidden="true">×</span> + <span class="sr-only"><spring:message code="alert.close" text="Close" /></span> + </button> + <strong> + <spring:message code="alert.strong.error" text="Error!" /> + </strong> unable to load pre-filled data! + </div> + `); + } + }); + }, + + //USED HERE + resetFromColors: function() { + + var self = this ; + $.each($(self.prefix+".add1spectrum"), function(id, elem) { + element = $(elem) + self.rm_success(element) ; + self.rm_warning(element) ; + self.rm_error(element) ; + if ($(elem).hasClass("is-mandatory") && ($(elem).val() == "" || $(elem).val() == null)) { + self.set_error($(elem)) ; + } + if ($(elem).hasClass("is-optional") && ($(elem).val() == "" || $(elem).val() == null)) { + self.set_warning($(elem)) ; + } + if ($(elem).val() != "" && $(elem).val() != null) { + self.set_success($(elem)) ; + } + }); + $.each($(self.prefix+"button.switchStep"), function(id, elem) { + if (!$(this).hasClass("btn-disabled")) { + $(this).addClass("btn-disabled"); + } + if ($(this).hasClass("btn-primary")) { + $(this).removeClass("btn-primary"); + } + $(this).prop("disabled", true); + }); + + // peak list: no data to check + $("#btnSwitch-gotoStep5-ms-{{ TAB_INDEX_PLACEHOLDER }}").removeClass("btn-disabled"); + $("#btnSwitch-gotoStep5-ms-{{ TAB_INDEX_PLACEHOLDER }}").addClass("btn-primary"); + $("#btnSwitch-gotoStep5-ms-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", false); + + $("#add1spectrum-other-author-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", false); + $("#add1spectrum-other-validator-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", false); + $("#add1spectrum-other-date-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", false); + $("#add1spectrum-other-owner-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", false); + $("#add1spectrum-other-fileName-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", false); + $("#add1spectrum-other-fileSize-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", false); + }, + + //USED IN HTML + switchToStep: function(step) { + + var self = this ; + switch(step) { + case 2: + // hide after step 2 / alt step 2 + $("#add1spectrum-chromatographyData-LC-{{ TAB_INDEX_PLACEHOLDER }}").hide(); + $("#add1spectrum-chromatographyData-GC-{{ TAB_INDEX_PLACEHOLDER }}").hide(); + $("#add1spectrum-analyserData-MS-{{ TAB_INDEX_PLACEHOLDER }}").hide(); + $("#add1spectrum-peaksData-MS-{{ TAB_INDEX_PLACEHOLDER }}").hide(); + $("#add1spectrum-otherData-{{ TAB_INDEX_PLACEHOLDER }}").hide(); + if ($("#step1sign-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("fa-question-circle")) { + $("#step1sign-{{ TAB_INDEX_PLACEHOLDER }}").removeClass("fa-question-circle").addClass("fa-check-circle"); + } + if (self.is_ms()) { + $("#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}").empty(); + $("#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}").append( + '<option value="" selected="selected" disabled="disabled">choose in list…</option>' + ); + $.getJSON("{{ PF_URL_PLACEHOLDER }}/webapp/resources/json/list-lc-methods.json", function(data) { + // load data from json + $.each(data.methods,function() { + if (this.name !== undefined) { + if (this.value !== undefined) { + $("#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}").append( + `<option value="${this.value}">${this.name}</option>` + ); + } else { + $("#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}").append( + `<option disabled>${this.name}</option>` + ); + } + } + }); + }); + } else if (self.is_ms2()) { + $("#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}").empty(); + $("#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}").append( + '<option value="" selected="selected" disabled="disabled">choose in list…</option>' + ); + $.getJSON( + "{{ PF_URL_PLACEHOLDER }}/webapp/resources/json/list-lc-msms-methods.json", + function(data) { + // load data from json + $.each(data.methods, function() { + if (this.name !== undefined) { + if (this.value !== undefined) { + $("#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}").append( + `<option value="${this.value}">${this.name}</option>` + ); + } else { + $("#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}").append( + `<option disabled>${this.name}</option>` + ); + } + } + }); + } + ); + } + // check panel to show + if (self.isLC) { + $("#add1spectrum-chromatographyData-LC-{{ TAB_INDEX_PLACEHOLDER }}").show(); + $("#linkActivateStep2-lc-{{ TAB_INDEX_PLACEHOLDER }}").trigger("click"); + var sign = $("#step2-lc-sign-{{ TAB_INDEX_PLACEHOLDER }}") ; + self.rm_class(sign, "fa-check-circle") && self.set_class(sign, "fa-question-circle") ; + if (!self.isSeparationFlowRateInit) { + self.handsontableSeparationFlowRate(null); + self.isSeparationFlowRateInit = true; + } + } else if (self.isGC) { + $("#add1spectrum-chromatographyData-GC-{{ TAB_INDEX_PLACEHOLDER }}").show(); + $("#linkActivateStep2-gc-{{ TAB_INDEX_PLACEHOLDER }}").trigger("click"); + var sign = $("#step2-gc-sign-{{ TAB_INDEX_PLACEHOLDER }}") ; + sign.removeClass("fa-check-circle").addClass("fa-question-circle"); + if ($("#step2-gc-sign-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("fa-check-circle")) { + } + } else if (self.isIC) { + $("#add1spectrum-chromatographyData-IC-{{ TAB_INDEX_PLACEHOLDER }}").show(); + $("#linkActivateStep2-ic-{{ TAB_INDEX_PLACEHOLDER }}").trigger("click"); + if ($("#step2-ic-sign-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("fa-check-circle")) { + $("#step2-ic-sign-{{ TAB_INDEX_PLACEHOLDER }}").removeClass("fa-check-circle").addClass("fa-question-circle"); + } + } + break; + case 3: + // hide after step 3 / alt step 3 + $("#add1spectrum-analyserData-MS-{{ TAB_INDEX_PLACEHOLDER }}").hide(); + $("#add1spectrum-peaksData-MS-{{ TAB_INDEX_PLACEHOLDER }}").hide(); + $("#add1spectrum-otherData-{{ TAB_INDEX_PLACEHOLDER }}").hide(); + // step 2 ok + if ($("#step2-lc-sign-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("fa-question-circle")) { + $("#step2-lc-sign-{{ TAB_INDEX_PLACEHOLDER }}").removeClass("fa-question-circle").addClass("fa-check-circle"); + } + if ($("#step2-gc-sign-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("fa-question-circle")) { + $("#step2-gc-sign-{{ TAB_INDEX_PLACEHOLDER }}").removeClass("fa-question-circle").addClass("fa-check-circle"); + } + // check panel to show + if (self.is_ms() || self.is_ms2()) { + $("#add1spectrum-analyserData-MS-{{ TAB_INDEX_PLACEHOLDER }}").show(); + $("#linkActivateStep3-ms-{{ TAB_INDEX_PLACEHOLDER }}").trigger('click'); + // debug display + [ + "add1spectrum-analyzserMS-sprayGazFlow-pos", + "add1spectrum-analyzserMS-sprayGazFlow-neg", + "add1spectrum-analyzserMS-vaporizerGazFlow-pos", + "add1spectrum-analyzserMS-vaporizerGazFlow-neg", + "add1spectrum-analyzserMS-vaporizerTemperature-pos", + "add1spectrum-analyzserMS-vaporizerTemperature-neg", + "add1spectrum-analyzserMS-sourceGazFlow-pos", + "add1spectrum-analyzserMS-sourceGazFlow-neg", + "add1spectrum-analyzserMS-ionTransferTubeTemperatureOrTransferCapillaryTemperature-pos", + "add1spectrum-analyzserMS-ionTransferTubeTemperatureOrTransferCapillaryTemperature-neg", + "add1spectrum-analyzserMS-highVoltageOrCoronaVoltage-pos", + "add1spectrum-analyzserMS-highVoltageOrCoronaVoltage-neg" + ].forEach((id) => { + var element = $(`#id-{{ TAB_INDEX_PLACEHOLDER }}`) + element.height(element.parent().children("span").height()) + }) + if ($("#step3-ms-sign-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("fa-check-circle")) { + $("#step3-ms-sign-{{ TAB_INDEX_PLACEHOLDER }}").removeClass("fa-check-circle").addClass("fa-question-circle"); + } + // MSMS only + $(self.prefix+".enable-if-ms").attr("disabled", !self.is_ms()); + $(self.prefix+".enable-if-msms").attr("disabled", !self.is_ms2()); + } + // avoid display bug + $("#add1spectrum-analyzer-ms-instrument-{{ TAB_INDEX_PLACEHOLDER }}").change(); + break; + case 4: + // hide after step 4 / alt step 4 + $("#add1spectrum-peaksData-MS-{{ TAB_INDEX_PLACEHOLDER }}").hide(); + $("#add1spectrum-otherData-{{ TAB_INDEX_PLACEHOLDER }}").hide(); + // step 3 ok + if ($("#step3-ms-sign-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("fa-question-circle")) { + $("#step3-ms-sign-{{ TAB_INDEX_PLACEHOLDER }}").removeClass("fa-question-circle").addClass("fa-check-circle"); + } + if (self.is_ms() || self.is_ms2()) { + $("#add1spectrum-peaksData-MS-{{ TAB_INDEX_PLACEHOLDER }}").show(); + $("#linkActivateStep4-ms-{{ TAB_INDEX_PLACEHOLDER }}").trigger("click"); + if ($("#step4-ms-sign-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("fa-check-circle")) { + $("#step4-ms-sign-{{ TAB_INDEX_PLACEHOLDER }}").removeClass("fa-check-circle").addClass("fa-question-circle"); + } + // LC MS + if (!self.isMSpeaksInit) { + console.log(`self.is_mix(): ${self.is_mix()}`) + if (self.is_mix()) { + all_contexts.forEach((context, index) => { + if (context === null) { + return; + } + context.handsontableMSpeaks(null) ; + context.updateLCMSspectraViewer() ; + context.isMSpeaksInit = true; + $(context.prefix+".add1spectrum-peaksMSForm-peaklist-reset").val("").change(); + }) + } else { + self.handsontableMSpeaks(null); + self.isMSpeaksInit = true; + $(self.prefix+".add1spectrum-peaksMSForm-peaklist-reset").val("").change(); + } + } + } + // show ms tab + setTimeout(() => $("#container_MS_Peaks-{{ TAB_INDEX_PLACEHOLDER }}").trigger("click"), 250); + $("#add1spectrum-peaksMS-msLevel-{{ TAB_INDEX_PLACEHOLDER }}").change(); + break; + case 5: + // hide after step 5 / alt step 5 + $("#add1spectrum-otherData-{{ TAB_INDEX_PLACEHOLDER }}").hide(); + // step 4 ok + if ($("#step4-ms-sign-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("fa-question-circle")) { + $("#step4-ms-sign-{{ TAB_INDEX_PLACEHOLDER }}").removeClass("fa-question-circle").addClass("fa-check-circle"); + } + if ($("#step5sign-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("fa-check-circle")) { + $("#step5sign-{{ TAB_INDEX_PLACEHOLDER }}").removeClass("fa-check-circle").addClass("fa-question-circle"); + } + $("#add1spectrum-otherData-{{ TAB_INDEX_PLACEHOLDER }}").show(); + $("#linkActivateStep5-{{ TAB_INDEX_PLACEHOLDER }}").trigger("click"); + // reset step 6 button + self.checkIfEnableSubmit(); + $("#import1SpectrumLoadingBare-{{ TAB_INDEX_PLACEHOLDER }}").hide(); + $("#import1SpectrumResults-{{ TAB_INDEX_PLACEHOLDER }}").hide(); + break; + case 6: + self.postOneSpectrumFrom(); + self.cptPeakListTab++; + break; + case 7: + self.dumpOneSpectrumFrom(); + break; + } + }, + + //USED HERE + resetElemColor: function(idElem) { + + var self = this ; + if ($(`#${idElem}`).parent().hasClass("has-success")) { + $(`#${idElem}`).parent().removeClass("has-success") ; + } + if ($(`#${idElem}`).parent().hasClass("has-warning")) { + $(`#${idElem}`).parent().removeClass("has-warning") ; + } + if ($(`#${idElem}`).parent().hasClass("has-error")) { + $(`#${idElem}`).parent().removeClass("has-error") ; + } + }, + + //USED HERE + disableElem: function(idElem) { + + var self = this ; + $(`#${idElem}`).prop("disabled", true) ; + $(`#${idElem}`).val("") ; + if ($(`#${idElem}`).hasClass("is-mandatory")) { + $(`#${idElem}`).removeClass("is-mandatory") ; + } + }, + + //USED HERE + enableElem: function(idElem) { + + var self = this ; + $(`#${idElem}`).prop("disabled", false) ; + $(`#${idElem}`).parent().addClass("has-error") ; + if (!$(`#${idElem}`).hasClass("is-mandatory")) { + $(`#${idElem}`).addClass("is-mandatory") ; + } + }, + + //USED HERE + checkIfEnableSubmit: function() { + + var self = this ; + var isBtnStep6OK = true; + $.each($(self.prefix+".add1spectrum-otherForm"), (id, elem) => { + if (self.is_error($(elem)) && $(elem).is(":visible")) { + isBtnStep6OK = false; + } + }); + if (isBtnStep6OK) { + self.rm_class($("#btnSwitch-gotoStep6-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-disabled") ; + self.set_class($("#btnSwitch-gotoStep6-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-primary") ; + $("#btnSwitch-gotoStep6-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", false); + self.rm_class($("#btnSwitch-gotoStep7-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-disabled") ; + self.set_class($("#btnSwitch-gotoStep7-{{ TAB_INDEX_PLACEHOLDER }}"), "btn-primary") ; + $("#btnSwitch-gotoStep7-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", false); + } else { + if (!$("#btnSwitch-gotoStep6-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("btn-disabled")) { + $("#btnSwitch-gotoStep6-{{ TAB_INDEX_PLACEHOLDER }}").addClass("btn-disabled"); + } + if ($("#btnSwitch-gotoStep6-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("btn-primary")) { + $("#btnSwitch-gotoStep6-{{ TAB_INDEX_PLACEHOLDER }}").removeClass("btn-primary"); + } + $("#btnSwitch-gotoStep6-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", true); + if (!$("#btnSwitch-gotoStep7-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("btn-disabled")) { + $("#btnSwitch-gotoStep7-{{ TAB_INDEX_PLACEHOLDER }}").addClass("btn-disabled"); + } + if ($("#btnSwitch-gotoStep7-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("btn-primary")) { + $("#btnSwitch-gotoStep7-{{ TAB_INDEX_PLACEHOLDER }}").removeClass("btn-primary"); + } + $("#btnSwitch-gotoStep7-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", true); + } + }, + + //USED IN HTML + addOneSpectrum: function(type) { + + var self = this ; + // unlock + $(self.prefix+".add1spectrum-sampleForm").prop("disabled", false); + $(self.prefix+".add1spectrum-chromatoLCForm").prop("disabled", false); + $(self.prefix+".add1spectrum-analyzerMSForm").prop("disabled", false); + $(self.prefix+".add1spectrum-otherForm").prop("disabled", false); + $("#add1spectrum-chromatoLC-colConstructor-{{ TAB_INDEX_PLACEHOLDER }}").change(); + // reset + self.isLC = false; + self.isGC = false; + self.isIC = false; + $("#alertBoxSubmitSpectrum-{{ TAB_INDEX_PLACEHOLDER }}").html(""); + // hide in all steps + $(self.prefix+".opt-ms").hide(); + $(self.prefix+".opt-msms").hide(); + // hide step 2 + $("#add1spectrum-chromatographyData-LC-{{ TAB_INDEX_PLACEHOLDER }}").hide(); + $("#add1spectrum-chromatographyData-GC-{{ TAB_INDEX_PLACEHOLDER }}").hide(); + // hide step 3 + $("#add1spectrum-analyserData-MS-{{ TAB_INDEX_PLACEHOLDER }}").hide(); + $(self.prefix+".add1spectrum-ionTrap").hide(); + // hide step 4 + $("#add1spectrum-peaksData-MS-{{ TAB_INDEX_PLACEHOLDER }}").hide(); + // hide step 5 + $("#add1spectrum-otherData-{{ TAB_INDEX_PLACEHOLDER }}").hide(); + // reset field step 1 + $("#add1spectrum-sample-type-{{ TAB_INDEX_PLACEHOLDER }}").val(""); + $(self.prefix+".add1spectrum-sample-type-panel").hide(); + $(self.prefix+".add1spectrum-sampleForm").val(""); + $("#sample-bonus-display-{{ TAB_INDEX_PLACEHOLDER }}").html(""); + // reset field step 2 + $(self.prefix+".add1spectrum-chromatoLCForm").val(""); + // reset field step 3 + $(self.prefix+".add1spectrum-analyzerMSForm").val(""); + // reset field step 4 + // reset peak lists / all tabs + self.isSeparationFlowRateInit = false; + self.isMSpeaksInit = false; + $(self.prefix+".handsontable").html(""); + // reset field step 5 => NO! + // set icon + $("#step0sign-{{ TAB_INDEX_PLACEHOLDER }}").removeClass("fa-question-circle").addClass("fa-check-circle"); + if ($("#step1sign-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("fa-check-circle")) { + $("#step1sign-{{ TAB_INDEX_PLACEHOLDER }}").removeClass("fa-check-circle").addClass("fa-question-circle"); + } + // collapse step 0 / uncollaspe step 1 + $("#linkActivateStep1-{{ TAB_INDEX_PLACEHOLDER }}").trigger("click"); + // show step 1 content + $("#add1spectrum-sampleData-{{ TAB_INDEX_PLACEHOLDER }}").show(); + switch(type) { + case 1: + // TODO GC-MS stuff + self.isGC = true; + break; + case 2: + // LC-MS stuff + self.isLC = true; + $(self.prefix+".opt-ms").show(); + break; + case 5: + // LC-MSMS stuff + self.isLC = true; + $(self.prefix+".opt-ms").show(); + $(self.prefix+".opt-msms").show(); + break; + case 6: + // IC-MS stuff + self.isIC = true; + $(self.prefix+".opt-ms").show(); + break; + case 7: + // IC-MSMS stuff + self.isIC = true; + $(self.prefix+".opt-ms").show(); + $(self.prefix+".opt-msms").show(); + break; + } + self.resetFromColors(); + // reset json obj to submit form + self.jsonSpectrumType = null; + self.isJsonSpectrumTypeComplete = false; + self.jsonSample = null; + self.isJsonSampleComplete = false; + self.isJsonRCCaddedComplete = false; + self.jsonChromato = null; + self.isJsonChromatoComplete = false; + self.jsonAnalyzer = null; + self.isJsonAnalyzerComplete = false; + self.jsonPeaksList = []; + self.isJsonPeaksListComplete = false; + self.jsonOtherMetadata = null; + self.isJsonOtherMetadataComplete = false; + + self.cptPeakListTab = 0; + self.jsonAnalyzerAcquisition = []; + self.idMetadataMap = {} + self.listOfViewableSpectra = []; + + // spec MS + self.jsonMolIonization = null; + + // spec MSMS + self.jsonMolIonBeam = null; + + // try load cpd + if (self.inchikey !== null) { + self.loadJSCompound(self.inchikey); + } + }, + + //USED HERE + loadJSCompound: function(inchikey) { + var self = this ; + + $("#add1spectrum-sample-type-{{ TAB_INDEX_PLACEHOLDER }}").val("compound-ref"); + $("#add1spectrum-sample-type-{{ TAB_INDEX_PLACEHOLDER }}").change(); + $("#add1spectrum-sample-inchikey-{{ TAB_INDEX_PLACEHOLDER }}").val(inchikey); + $("#add1spectrum-sample-inchikey-{{ TAB_INDEX_PLACEHOLDER }}").change(); + if (inchidata[inchikey] !== null) { + return (set_inchi_data(inchidata[inchikey]), {{ TAB_INDEX_PLACEHOLDER }}) ; + } + $.ajax({ + type: "get", + url: "{{ PF_URL_PLACEHOLDER }}/webapp/get-cpd-data", + data: "inchikey="+inchikey, + dataType: "json", + success: function(data) { + if (data.success) { + set_inchi_data(data) ; + } + }, + error : function(data) { + } + }).always(function() { + }); + }, + + //USED HERE + handsontableSeparationFlowRate: function(data) { + var self = this ; + + // reset + $("#container_LC_SFG-{{ TAB_INDEX_PLACEHOLDER }}").html(""); + // init + var data_LC_SFG; + if (data==null) { + data_LC_SFG = [ + [ "", "", "" ], + [ "", "", "" ], + [ "", "", "" ], + [ "", "", "" ], + [ "", "", "" ], + [ "", "", "" ], + [ "", "", "" ], + [ "", "", "" ], + [ "", "", "" ], + ]; + } else { + data_LC_SFG = data; + } + + var container_LC_SFG = document.getElementById("container_LC_SFG-{{ TAB_INDEX_PLACEHOLDER }}"); + self.hot_LC_SFG = new Handsontable(container_LC_SFG, { + data : data_LC_SFG, + minSpareRows : 1, + colHeaders : true, + colHeaders: ["time (min)", "solv. A (%)", "solv. B (%)"], + contextMenu : false + }); + Handsontable.Dom.addEvent(document.body, "click", function(e) { + var element = e.target || e.srcElement; + if (element.nodeName == "BUTTON"&& element.name == "dump") { + var name = element.getAttribute("data-dump"); + var instance = element.getAttribute("data-instance"); + self.hot_LC_SFG = window[instance]; + console.log("data of " + name, self.hot_LC_SFG.getData()); + } + }); + $("#container_LC_SFG table.htCore-{{ TAB_INDEX_PLACEHOLDER }}").css("width","100%"); + }, + + //USED HERE + handsontableMSpeaks: function(data) { + console.log("handsontableMSpeaks") + console.log(data) + var self = this ; + var data_MS_Peaks ; + var container_MS_Peaks ; + + if (data != null) { + data_MS_Peaks = data; + } else { + data_MS_Peaks = JSON.parse(JSON.stringify(self.DEFAULT_MS_PEAK_VALUES)); + } + $("#container_MS_Peaks-{{ TAB_INDEX_PLACEHOLDER }}").html(""); + container_MS_Peaks = document.getElementById( + "container_MS_Peaks-{{ TAB_INDEX_PLACEHOLDER }}" + ); + var colHeaders = [ + "m/z", "absolute intensity", "relative intensity (%)", "delta (ppm)", + "composition", "attribution", "Validated" + ] + var columns = [ + {type: "numeric", format: "0.0000"}, + {type: "numeric", format: "0.00"}, + {type: "numeric", format: "0.00"}, + {type: "numeric", format: "0.0000"}, + {type: "text"}, + {type: "text"}, + {type: "checkbox"} + ] ; + if (self.is_ms2()) { + colHeaders.push("Parent ion") ; + columns.push({type: "checkbox"}) ; + } + self.hot_MS_Peaks = new Handsontable(container_MS_Peaks, { + data: data_MS_Peaks, + minSpareRows: 1, + colHeaders: true, + colHeaders: colHeaders, + contextMenu: false, + maxRows: data_MS_Peaks.length, + minRows: data_MS_Peaks.length, + columns: columns, + afterChange: function(changes) { + if (self.lock.precursor_ion) { + return ; + } + self.lock.precursor_ion = true ; + try { + changes?.forEach(([row, prop, old, value]) => { + var data ; + var precursor_ion ; + + var data = self.hot_MS_Peaks.getData() ; + if (prop !== 7 || value !== true || data === undefined) { + return ; + } + for (var i = 0; i < data.length ; i += 1) { + data[i][7] = false ; + } + data[row][7] = true ; + precursor_ion = $(`#add1spectrum-peaksMS-msPrecursorIon-{{ TAB_INDEX_PLACEHOLDER }}`) ; + console.log(`setting preco ion to ${data[row][0]}`) ; + precursor_ion.val(data[row][0]) ; + precursor_ion.change() ; + self.hot_MS_Peaks.render() ; + }) + } finally { + self.lock.precursor_ion = false ; + } + } + }); + Handsontable.Dom.addEvent(document.body, "click", (e) => { + var element ; + var name ; + var instance ; + + element = e.target || e.srcElement ; + if (element.nodeName == "BUTTON" && element.name == "dump") { + name = element.getAttribute("data-dump") ; + instance = element.getAttribute("data-instance") ; + self.hot_MS_Peaks = window[instance] ; + console.log("data of " + name, self.hot_MS_Peaks.getData()) ; + } + }) ; + + $("#container_MS_Peaks-{{ TAB_INDEX_PLACEHOLDER }} table.htCore").css( + "width","100%" + ) ; + if (self.is_ms2()) { + setTimeout(() => self.select_precursor_ion(), 200) ; + } + }, + + change_tab: function() { + var self = this ; + setTimeout(() => self.auto_select_ion_parent(), 1000) ; + }, + + auto_select_ion_parent: function() { + var self = this ; + if (!self.a_ion_parent_is_selected()) { + setTimeout(() => self.select_precursor_ion(), 1000) ; + } + }, + + select_precursor_ion: function() { + var self = this ; + var data ; + var precuirsor_ion ; + + if (self.hot_MS_Peaks == null) { + return setTimeout(() => self.select_precursor_ion(), 200) ; + } + console.log("Selecting ion preco for tab {{ TAB_INDEX_PLACEHOLDER }}") + data = self.hot_MS_Peaks.getData() ; + for (var i = 0 ; i < data.length ; i += 1) { + if (data[i][5] === "[M+H]+" || data[i][5] === "[M+H]-" || data[i][2] == 100.0) { + precursor_ion = $("#add1spectrum-peaksMS-msPrecursorIon-{{ TAB_INDEX_PLACEHOLDER }}") ; + precursor_ion.val(data[i][0]) ; + precursor_ion.change() ; + return ; + } + } + }, + + sync_precursor_ion: function() { + var self = this ; + var data ; + + if (self.lock.precursor_ion || self.hot_MS_Peaks == undefined) { + return ; + } + self.lock.precursor_ion = true ; + console.log("Syncing precursor ion") + var val = $("#add1spectrum-peaksMS-msPrecursorIon-{{ TAB_INDEX_PLACEHOLDER }}").val() ; + var data = self.hot_MS_Peaks.getData() ; + for (var i = 0; i < data.length ; i += 1) { + if (Math.abs(data[i][0] - val) < 0.0001) { + for (var j = 0; j < data.length ; j += 1) { + data[j][7] = false ; + } + data[i][7] = true ; + self.hot_MS_Peaks.render() ; + return ; + } + } + self.lock.precursor_ion = false ; + }, + + // USED HERE + handsontableRefChemCpdAdded: function(data) { + var self = this ; + // reset + $("#container_RCC_ADDED-{{ TAB_INDEX_PLACEHOLDER }}").html(""); + $("#sample-bonus-display-{{ TAB_INDEX_PLACEHOLDER }}").html(""); + // init + var data_RCC_ADDED, colHeaderData, container_RCC_ADDED; + + colHeaderData = [ + {data: "common name", type: "text"}, + {data: "<b>InChIKey</b>", type: "text"}, + {data: "composition", renderer: lightgrayRenderer}, + {data: "<b>concentration (µg/ml)</b>", type: "text"}, + {data: "exact mass", renderer: lightgrayRenderer}, + {data: "(M+H)+ or (M-H)-", renderer: lightgrayRenderer} + ] ; + + if (data == null) { + data_RCC_ADDED = [ + [ "", "", "","", "", "" ], + [ "", "", "","", "", "" ], + [ "", "", "","", "", "" ], + [ "", "", "","", "", "" ], + [ "", "", "","", "", "" ], + [ "", "", "","", "", "" ], + [ "", "", "","", "", "" ], + [ "", "", "","", "", "" ], + [ "", "", "","", "", "" ], + [ "", "", "","", "", "" ], + [ "", "", "","", "", "" ], + [ "", "", "","", "", "" ], + ]; + } else { + container_RCC_ADDED = data; + } + + container_RCC_ADDED = document.getElementById("container_RCC_ADDED-{{ TAB_INDEX_PLACEHOLDER }}"); + self.hot_RCC_ADDED = new Handsontable(container_RCC_ADDED, { + data: data_RCC_ADDED, + minSpareRows : 1, + colHeaders : true, + colHeaders: [ + "common name", + "<b>InChIKey</b>", + "composition", + "<b>concentration (µg/ml)</b>", + "exact mass", + "(M+H)+ or (M-H)-" + ], + contextMenu : false, + columns: colHeaderData + }); + function bindDumpButton_RCC_ADDED() { + Handsontable.Dom.addEvent(document.body, "click", (e) => { + var element = e.target || e.srcElement; + if (element.nodeName == "BUTTON"&& element.name == "dump") { + var name = element.getAttribute("data-dump"); + var instance = element.getAttribute("data-instance"); + self.hot_RCC_ADDED = window[instance]; + console.log("data of " + name, self.hot_RCC_ADDED.getData()); + } + }); + } + bindDumpButton_RCC_ADDED(); + $("#container_RCC_ADDED-{{ TAB_INDEX_PLACEHOLDER }} table.htCore").css("width","100%"); + // celect cell + self.hot_RCC_ADDED.selectCell(0, 0); + // add select listener + self.hot_RCC_ADDED.addHook("afterSelection", (r, c) => self.hookSelection(r, c)); + }, + + //USED HERE + hookSelection: function(r, c) { + var self = this ; + if (c == 0 || c == 1 || c == 2) + self.pickChemicalCompound4Mix(r); + }, + + //USED HERE + postOneSpectrumFrom: function() { + var self = this ; + $("#import1SpectrumLoadingBare-{{ TAB_INDEX_PLACEHOLDER }}").show(); + + // II - form data -> json object + self.loadFomDataIntoJsonObjects(); + // II.A - check if json object complete + var alertMsg = self.getFormErrorMessage(); + + if (alertMsg != "") { + $("#alertBoxSubmitSpectrum-{{ TAB_INDEX_PLACEHOLDER }}").html(alertMsg); + $("#import1SpectrumLoadingBare-{{ TAB_INDEX_PLACEHOLDER }}").hide(); + return false; + } + // all OK: lock! + // lock sample + $(self.prefix+".add1spectrum-sampleForm").prop("disabled", true); + // lock chromato + $(self.prefix+".add1spectrum-chromatoLCForm").prop("disabled", true); + if (!$("#container_LC_SFG-{{ TAB_INDEX_PLACEHOLDER }}").is(":empty")) { + self.hot_LC_SFG.updateSettings({ + cells: function(row, col, prop) { + var cellProperties = {}; + cellProperties.readOnly = true; + return cellProperties; + } + }); + } + if (!$("#container_MS_Peaks-{{ TAB_INDEX_PLACEHOLDER }}").is(":empty")) { + self.hot_MS_Peaks.updateSettings({ + cells: function(row, col, prop) { + var cellProperties = {}; + cellProperties.readOnly = true; + return cellProperties; + } + }); + } + if (!$("#container_RCC_ADDED-{{ TAB_INDEX_PLACEHOLDER }}").is(":empty")) { + self.hot_RCC_ADDED.updateSettings({ + cells: function(row, col, prop) { + var cellProperties = {}; + cellProperties.readOnly = true; + return cellProperties; + } + }); + self.hot_RCC_ADDED.removeHook( + "afterSelection", + (r, c) => self.hookSelection(r, c) + ); + } + + // lock analyzer + $(self.prefix+".add1spectrum-analyzerMSForm").prop("disabled", true); + // lock other metadata field + $(self.prefix+".add1spectrum-otherForm").prop("disabled", true); + // lock switch btn + $("#btnSwitch-gotoStep2-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", true); + $("#btnSwitch-gotoStep3-lc-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", true); + $("#btnSwitch-gotoStep4-ms-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", true); + self.postSpectrumToServer() ; + }, + + postSpectrumToServer: function(jsonData, tab_index) { + var self = this ; + var base_peakdata ; + var new_peakdata ; + var is_ms2 = self.is_ms2() ; + + if (self.is_mix()) { + if ({{ TAB_INDEX_PLACEHOLDER }} != 1) { + return ; + } + jsonData = self.gatherJsonObjects() ; + all_mix_data = Object.assign({}, jsonData) ; + all_mix_data["peaklists"] = [] ; + base_peakdata = Object.assign({}, jsonData["peaklists"][0]) ; + all_contexts.forEach((context, index) => { + if (context === null) { + return; + } + new_peakdata = Object.assign({}, base_peakdata) ; + context.loadFomDataIntoJsonObjects() + if (is_ms2) { + new_peakdata["precursor_ion"] = context.jsonPeaksList["precursor_ion"] ; + } + new_peakdata["peaklist"] = context.jsonPeaksList["peaklist"] ; + all_mix_data["peaklists"].push(new_peakdata) + }) + } + // II.B - rebuild json full object (with all metadata or just id if already in base) + if (jsonData == null) { + jsonData = self.gatherJsonObjects(); + } + // II.C - add id metadata (if exist) + var json_array = [] ; + if (!tab_index) { + tab_index = {{ TAB_INDEX_PLACEHOLDER }} ; + } + json_array[tab_index-1] = jsonData ; + + // III - post json object + // III.A - success + self.sent_json = jsonData ; + console.warn( + "This data has been validated without going through the internal server!" + ) + if ($("#step5sign-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("fa-question-circle")) { + $("#step5sign-{{ TAB_INDEX_PLACEHOLDER }}").removeClass("fa-question-circle").addClass("fa-check-circle"); + } + if ($("#step5sign-{{ TAB_INDEX_PLACEHOLDER }}").hasClass("fa-spinner")) { + $("#step5sign-{{ TAB_INDEX_PLACEHOLDER }}").removeClass("fa-spinner fa-spin").addClass("fa-check-circle"); + } + $("#import1SpectrumLoadingBare-{{ TAB_INDEX_PLACEHOLDER }}").hide(); + $("#alertBoxSubmitSpectrum-{{ TAB_INDEX_PLACEHOLDER }}").html(` + <div class="alert alert-success alert-dismissible" role="alert"> + <button type="button" class="close" data-dismiss="alert"> + <span aria-hidden="true">×</span> + <span class="sr-only"> + <spring:message code="alert.close" text="Close" /> + </span> + </button> + <strong> + <spring:message code="alert.strong.info" text="Success!" /> + </strong> Spectrum ready to be sent! + </div> + `); + return true; + }, + + //USED HERE + loadFomDataIntoJsonObjects: function() { + var self = this ; + // I - Spectrum type + self.isJsonSpectrumTypeComplete = false ; + if (self.isGC && self.is_ms()) { + self.jsonSpectrumType = "gc-ms" ; + } else if (self.isLC && self.is_ms()) { + self.jsonSpectrumType = "lc-ms" ; + } else if (self.isLC && self.is_ms2()) { + self.jsonSpectrumType = "lc-msms" ; + } else if (self.isGC && self.is_ms()) { + self.jsonSpectrumType = "ic-ms" ; + } else if (self.isLC && self.is_ms()) { + self.jsonSpectrumType = "ic-msms" ; + } + if (self.jsonSpectrumType != null && self.jsonSpectrumType != "") { + self.isJsonSpectrumTypeComplete = true; + } + + // II - Sample + self.isJsonSampleComplete = true; + self.isJsonRCCaddedComplete = true; + self.jsonSample = {}; + + switch($("#add1spectrum-sample-type-{{ TAB_INDEX_PLACEHOLDER }}").val()) { + // II.A - chemical lib. compound + case "compound-ref": + if ($("#add1spectrum-sample-inchikey-{{ TAB_INDEX_PLACEHOLDER }}").val() == "") { + return false; + } + self.jsonSample["sample_type"] = "reference-chemical-compound"; + self.jsonSample["inchikey"] = $("#add1spectrum-sample-inchikey-{{ TAB_INDEX_PLACEHOLDER }}").val(); + self.jsonSample["concentration"] = $("#add1spectrum-sample-concentration-{{ TAB_INDEX_PLACEHOLDER }}").val(); + if (self.is_ms()) { + self.jsonSample["solvent"] = $("#add1spectrum-sample-lcmsSolvent-{{ TAB_INDEX_PLACEHOLDER }}").val(); + } + self.isJsonSampleComplete = true; + break; + // II.B - chemical lib. compound mix + case "compound-mix": + // solvent + self.jsonSample["solvent"] = $("#add1spectrum-sample-mixSolvent-{{ TAB_INDEX_PLACEHOLDER }}").val(); + // cpd added + self.jsonSample.inchikeys_list = self.getRCCADDED(); + self.jsonSample.concentrations_list = self.getRCCADDEDConcentration(); + if (self.jsonSample.inchikeys_list.length == 0 && !self.is_other_in_mix()) { + self.isJsonRCCaddedComplete = false; + console.log(`isJsonRCCaddedComplete: false`) + return false; + } + self.isJsonSampleComplete = true; + break; + default: + if (!self.is_other_in_mix()) { + return false; + } + } + + // III - Chromato + self.isJsonChromatoComplete = true; + self.jsonChromato = {}; + + // III.A - no chromato + // nope? + + // III.B - GC + if (self.isGC) { + self.isJsonChromatoComplete = false; + // TODO + } + + // III.C - LC + if (self.isLC) { + self.isJsonChromatoComplete = true; + self.jsonChromato = {}; + // check error + $.each($(self.prefix+".add1spectrum-chromatoLCForm").parent(), function() { + if ($(this).hasClass("has-error")) + self.isJsonChromatoComplete = false; + }); + if ( + !self.isJsonChromatoComplete + && !self.is_other_in_mix() + ) { + console.log(`isJsonChromatoComplete: false`) + return false; + } + var id = `#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}` ; + self.jsonChromato["method"] = $(`${id} option:selected`).text(); + [ + ["column_constructor", "colConstructor"], + ["column_constructor_other", "colConstructorOther"], + ["column_name", "colName"], + ["column_length", "colLength"], + ["column_diameter", "colDiameter"], + ["particule_size", "colParticuleSize"], + ["column_temperature", "colTemperature"], + ["mode", "LCMode"], + ["separation_flow_rate", "separationFlowRate"], + ["solvent_a", "separationSolvA"], + ["solvent_a_ph", "separationSolvApH"], + ["solvent_b", "separationSolvB"], + ["solvent_b_ph", "separationSolvBApH"] + ].forEach((field) => { + id = `#add1spectrum-chromatoLC-${field[1]}-{{ TAB_INDEX_PLACEHOLDER }}` ; + self.jsonChromato[field[0]] = $(id).val(); + }) + // fulfill json object + + jsonSFG = []; + var formatData = { + time: [], + solvent_a_percent: [], + solvent_b_percent: [] + }; + var uniq_times = [] ; + $.each(self.hot_LC_SFG.getData(), function() { + var time = this[0] ; + if (time != "" && time !== null) { + if ( + !isNaN(time) + && !isNaN(this[1]) + && !isNaN(this[2]) + && ! (time in uniq_times) + ) { + formatData["time"].push(Number(time)); + formatData["solvent_a_percent"].push(Number(this[1])); + formatData["solvent_b_percent"].push(Number(this[2])); + uniq_times.push(time) ; + } + } + }); + self.jsonChromato.separation_flow_gradient = formatData; + } + + // III.D - IC + if (self.isIC) { + self.isJsonChromatoComplete = false; + // TODO + } + + // IV - Analyzer + self.isJsonAnalyzerComplete = true; + self.isJsonAnalyzer = {}; + // IV.A - MS + if (self.is_ms() || self.is_ms2()) { + self.isJsonAnalyzerComplete = true; + self.jsonAnalyzer = {}; + // check error + $.each($(self.prefix+".add1spectrum-analyzerMSForm").parent(), function(){ + if ($(this).hasClass("has-error")) + self.isJsonAnalyzerComplete = false; + }); + if ( + !self.isJsonAnalyzerComplete + && !self.is_other_in_mix() + ) { + console.log(`isJsonAnalyzerComplete: false`) + return false; + } + + // fulfill json object + self.jsonAnalyzer["instrument_name"] = $("#add1spectrum-analyzer-ms-instrument-{{ TAB_INDEX_PLACEHOLDER }}").val(); + self.jsonAnalyzer["instrument_model"] = $("#add1spectrum-analyzer-ms-model-{{ TAB_INDEX_PLACEHOLDER }}").val(); + self.jsonAnalyzer["instrument_brand"] = $("#add1spectrum-analyzer-ms-model-{{ TAB_INDEX_PLACEHOLDER }}").val(); + self.jsonAnalyzer["ion_analyzer_type"] = $("#add1spectrum-analyzer-ms-ionAnalyzerType-{{ TAB_INDEX_PLACEHOLDER }}").val(); + + if (self.is_ms2()) { + // MSMS ion BEAM or TRAP + self.jsonMolIonBeam = {} + var jsonIonTrapBeam = { + ion_gas: $("#add1spectrum-ionTrapBeam-ionGas-{{ TAB_INDEX_PLACEHOLDER }}").val(), + ion_pressure_value: $("#add1spectrum-ionTrapBeam-ionGasPressureValue-{{ TAB_INDEX_PLACEHOLDER }}").val(), + ion_pressure_unit: $("#add1spectrum-ionTrapBeam-ionGasPressureUnit-{{ TAB_INDEX_PLACEHOLDER }}").val() + } ; + var key = null ; + if ($("#add1spectrum-ionTrapBeam-type-{{ TAB_INDEX_PLACEHOLDER }}").val() == "trap") { + // sp + jsonIonTrapBeam["ion_freq_shift"] = $("#add1spectrum-ionTrapBeam-ionFrequencyShift-{{ TAB_INDEX_PLACEHOLDER }}").val(); + jsonIonTrapBeam["ion_number"] = $("#add1spectrum-ionTrapBeam-ionNumber-{{ TAB_INDEX_PLACEHOLDER }}").val(); + key = "ion_trap" ; + } else if ($("#add1spectrum-ionTrapBeam-type-{{ TAB_INDEX_PLACEHOLDER }}").val() == "beam") { + key = "ion_beam_storage" ; + } + if (key !== null) { + self.jsonMolIonBeam[key] = jsonIonTrapBeam; + } + } + + self.jsonMolIonization = {}; + var json_mode ; + ["pos", "neg"].forEach((kind) => { + json_mode = {} ; + [ + ["ionisation_method", "ionizationMethod"], + ["spray_gas_flow", "sprayGazFlow"], + ["vaporizer_gas_flow", "vaporizerGazFlow"], + ["vaporizer_temperature", "vaporizerTemperature"], + ["source_gas_flow", "sourceGazFlow"], + ["transfer_tube_or_capillary_temperature", "ionTransferTubeTemperatureOrTransferCapillaryTemperature"], + ["high_voltage", "highVoltageOrCoronaVoltage"] + ].forEach((field) => { + var id = `#add1spectrum-analyzserMS-${field[1]}-${kind}-{{ TAB_INDEX_PLACEHOLDER }}` ; + json_mode[field[0]] = $(id).val() ; + }) + self.jsonMolIonization[`mode_${kind}`] = json_mode ; + }) + } + + // IV.B - NMR + if (self.is_ms() || self.is_ms2()) { + self.isJsonPeaksListComplete = false; + // init + var peaklist = []; + var peakdata = {}; + var spectrumData = {}; + // peaklist + var ms_peak_data = self.hot_MS_Peaks.getData(); + $.each(ms_peak_data, function(index) { + var data = ms_peak_data[index] ; + var formatData = {}; + if ( + data[0] != "" + && !isNaN(data[0]) + // && !isNaN(data[2]) + && (data[6] === "true" || data[6] === true) + ) { + peaklist.push({ + mz: Number(data[0]), + ri: Number(data[2]), + delta_ppm: Number(data[3]), + composition: (data[4]), + annotation: (data[5]) + }); + self.isJsonPeaksListComplete = true; + } + }); + // peak list data + peakdata["scan_type"] = ( + self.is_ms2() ? "ms2" : "ms" + ); + peakdata["polarity"] = $("#add1spectrum-peaksMS-polarity-{{ TAB_INDEX_PLACEHOLDER }}").val(); + peakdata["resolution"] = $("#add1spectrum-peaksMS-resolution-{{ TAB_INDEX_PLACEHOLDER }}").val(); + peakdata["curation"] = $("#add1spectrum-peaksMS-curation-{{ TAB_INDEX_PLACEHOLDER }}").val(); + peakdata["mz_from"] = $("#add1spectrum-peaksMS-rangeFrom-{{ TAB_INDEX_PLACEHOLDER }}").val(); + peakdata["mz_to"] = $("#add1spectrum-peaksMS-rangeTo-{{ TAB_INDEX_PLACEHOLDER }}").val(); + peakdata["retention_min_time_from"] = $("#add1spectrum-peaksMS-rtMinFrom-{{ TAB_INDEX_PLACEHOLDER }}").val(); + peakdata["retention_min_time_to"] = $("#add1spectrum-peaksMS-rtMinTo-{{ TAB_INDEX_PLACEHOLDER }}").val(); + peakdata["rt_solv_from"] = $("#add1spectrum-peaksMS-rtSolvFrom-{{ TAB_INDEX_PLACEHOLDER }}").val(); + peakdata["rt_solv_to"] = $("#add1spectrum-peaksMS-rtSolvTo-{{ TAB_INDEX_PLACEHOLDER }}").val(); + peakdata["resolution_FWHM"] = $("#add1spectrum-analyzer-ms-resolutionFWHM-{{ TAB_INDEX_PLACEHOLDER }}").val(); + if (self.is_ms2()) { + var data = self.hot_MS_Peaks.getData() ; + if (data.length != 0) { + var selected_ion = self.get_selected_parent_ion_index() ; + if (selected_ion !== null) { + peakdata["precursor_ion"] = data[selected_ion][0] ; + peakdata["precursor_spectrum_id"] = null ; + } else { + peakdata["precursor_ion"] = self.get_selected_parent_ion_mz() ; + peakdata["precursor_spectrum_id"] = null ; + } + } + } + peakdata["peaklist"] = peaklist; + self.jsonPeaksList = peakdata; + } + + self.isJsonOtherMetadataComplete = true; + self.jsonOtherMetadata = {}; + // check error + $.each($(self.prefix+".add1spectrum-otherForm").parent(), function(){ + if ($(this).hasClass("has-error")) + self.isJsonOtherMetadataComplete = false; + }); + if (!self.isJsonOtherMetadataComplete && !self.is_other_in_mix()) { + console.log(`isJsonOtherMetadataComplete: false`) + return false; + } + self.jsonOtherMetadata["data_authors"] = $("#add1spectrum-other-author-{{ TAB_INDEX_PLACEHOLDER }}").val(); + self.jsonOtherMetadata["data_validator"] = $("#add1spectrum-other-validator-{{ TAB_INDEX_PLACEHOLDER }}").val();; + self.jsonOtherMetadata["acquisition_date"] = $("#add1spectrum-other-date-{{ TAB_INDEX_PLACEHOLDER }}").val(); + if (!self.jsonOtherMetadata["acquisition_date"]) { + self.jsonOtherMetadata["acquisition_date"] = null ; + } + self.jsonOtherMetadata["data_ownership"] = $("#add1spectrum-other-owner-{{ TAB_INDEX_PLACEHOLDER }}").val(); + self.jsonOtherMetadata["raw_file_name"] = $("#add1spectrum-other-fileName-{{ TAB_INDEX_PLACEHOLDER }}").val(); + self.jsonOtherMetadata["raw_file_size"] = $("#add1spectrum-other-fileSize-{{ TAB_INDEX_PLACEHOLDER }}").val(); + return true; + }, + + //USED HERE + getFormErrorMessage: function() { + var self = this ; + var alertMsg = ""; + if (!self.isJsonSpectrumTypeComplete) { + alertMsg = ` + <div class="alert alert-danger alert-dismissible" role="alert"> + <button type="button" class="close" data-dismiss="alert"> + <span aria-hidden="true">×</span> + <span class="sr-only"> + <spring:message code="alert.close" text="Close" /> + </span> + </button> + <strong> + <spring:message code="alert.strong.error" text="Error!" /> + </strong> Error processing spectrum type! + </div>` ; + } else if (!self.isJsonSampleComplete) { + alertMsg = ` + <div class="alert alert-danger alert-dismissible" role="alert"> + <button type="button" class="close" data-dismiss="alert"> + <span aria-hidden="true">×</span> + <span class="sr-only"> + <spring:message code="alert.close" text="Close" /> + </span> + </button> + <strong> + <spring:message code="alert.strong.error" text="Error!" /> + </strong> Missing mandatory data into sample section! + <br /> + <a + href="#" + onclick="$('#linkActivateStep1-{{ TAB_INDEX_PLACEHOLDER }}').trigger('click');" + >Go to this section</a> + </div>` ; + } else if (!self.isJsonRCCaddedComplete) { + alertMsg = ` + <div class="alert alert-danger alert-dismissible" role="alert"> + <button type="button" class="close" data-dismiss="alert"> + <span aria-hidden="true">×</span> + <span class="sr-only"> + <spring:message code="alert.close" text="Close" /> + </span> + </button> + <strong> + <spring:message code="alert.strong.error" text="Error!" /> + </strong> Pease enter at least ONE compound in mix into sample section! + <br /> + <a + href="#" + onclick="$('#linkActivateStep1-{{ TAB_INDEX_PLACEHOLDER }}').trigger('click');" + >Go to this section</a> + </div>`; + } else if (!self.isJsonChromatoComplete) { + alertMsg = ` + <div class="alert alert-danger alert-dismissible" role="alert"> + <button type="button" class="close" data-dismiss="alert"> + <span aria-hidden="true">×</span> + <span class="sr-only"> + <spring:message code="alert.close" text="Close" /> + </span> + </button> + <strong> + <spring:message code="alert.strong.error" text="Error!" /> + </strong> Missing data in chromatography section! + ` ; + if (self.is_ms()) { + alertMsg += ` + <br /> + <a + href="#" + onclick="$('#linkActivateStep4-ms-{{ TAB_INDEX_PLACEHOLDER }}').trigger('click');" + >Go to this section</a>`; + } + alertMsg += ' </div>'; + } else if (!self.isJsonPeaksListComplete) { + alertMsg = ` + <div class="alert alert-danger alert-dismissible" role="alert"> + <button type="button" class="close" data-dismiss="alert"> + <span aria-hidden="true">×</span> + <span class="sr-only"> + <spring:message code="alert.close" text="Close" /> + </span> + </button> + <strong> + <spring:message code="alert.strong.error" text="Error!" /> + </strong> Missing peaklist! + ` ; + if (self.is_ms()) { + alertMsg += ` + <br /> + <a + href="#" + onclick="$('#linkActivateStep4-ms-{{ TAB_INDEX_PLACEHOLDER }}').trigger('click');" + >Go to this section</a>`; + } + alertMsg += ' </div>'; + } else if (self.is_mix() && self.is_ms2()) { + for (var i = 0 ; i < all_contexts.length ; i += 1) { + if (all_contexts[i] === null || all_contexts[i] === undefined) { + continue; + } + if (all_contexts[i].get_selected_parent_ion_index() === null) { + return alertMsg + ` + <div class="alert alert-danger alert-dismissible" role="alert"> + <button type="button" class="close" data-dismiss="alert"> + <span aria-hidden="true">×</span> + <span class="sr-only"> + <spring:message code="alert.close" text="Close" /> + </span> + </button> + <strong> + <spring:message code="alert.strong.error" text="Error!" /> + </strong> Select precursor ion in all peak lists! + </div> + ` + } + } + } + // TODO other + return alertMsg; + }, + + //USED HERE + gatherJsonObjects: function() { + var self = this ; + var jsonData = {}; + if (self.is_mix()) { + jsonData["sample_type"] = "mix_of_reference_chemical_compounds" ; + } else { + jsonData["sample_type"] = "reference_chemical_compound" ; + } + jsonData["spectrum_type"] = self.jsonSpectrumType.toUpperCase().replaceAll("-", ""); + jsonData["sample"] = self.jsonSample; + if (self.isLC) { + jsonData["chromatography"] = self.jsonChromato; + } else if (self.isGC) { + jsonData["chromatography"] = self.jsonChromato; + } else if (self.isIC) { + jsonData["chromatography"] = self.jsonChromato; + } + if (self.is_ms()) { + jsonData["analyzer"] = self.jsonAnalyzer; + var molecule_ionization = self.jsonMolIonization; + jsonData["ionization_mode_positive"] = molecule_ionization["mode_pos"] ; + jsonData["ionization_mode_negative"] = molecule_ionization["mode_neg"] ; + jsonData["peaklists"] = [self.jsonPeaksList] ; + } else if (self.is_ms2()) { + jsonData["analyzer"] = self.jsonAnalyzer; + var molecule_ionization = self.jsonMolIonization; + jsonData["ionization_mode_positive"] = molecule_ionization["mode_pos"] ; + jsonData["ionization_mode_negative"] = molecule_ionization["mode_neg"] ; + if (self.jsonMolIonBeam != null) { + jsonData["ion_beam_storage"] = self.jsonMolIonBeam["ion_beam_storage"]; + } + jsonData["peaklists"] = [self.jsonPeaksList] ; + } + jsonData["other_metadata"] = self.jsonOtherMetadata; + return jsonData; + }, + + //USED IN HTML + pickChemicalCompound: function() { + var self = this ; + self.singlePick = true; + $("#modalPickCompound-{{ TAB_INDEX_PLACEHOLDER }}").modal("show"); + $("#add-one-cc-s1-value-{{ TAB_INDEX_PLACEHOLDER }}").focus(); + }, + + //USED HERE + pickChemicalCompound4Mix: function(rowNumber) { + var self = this ; + self.singlePick = false; + self.multiPickLine = rowNumber; + $("#modalPickCompound-{{ TAB_INDEX_PLACEHOLDER }}").modal("show"); + $("#add-one-cc-s1-value-{{ TAB_INDEX_PLACEHOLDER }}").focus(); + }, + + //USED HERE + searchAjax: function() { + var self = this ; + var results ; + var rawQuery = $('#add-one-cc-s1-value-{{ TAB_INDEX_PLACEHOLDER }}').val(); + if (rawQuery.length > 2) { + return [] ; + } + results = [] ; + $.ajax({ + type: "post", + url: "{{ PF_URL_PLACEHOLDER }}/webapp/search", + dataType: "json", + async: false, + data: "query=" + $("#add-one-cc-s1-value-{{ TAB_INDEX_PLACEHOLDER }}").val(), + success: function(json) { + if (json.success) { + $.each(json.compoundNames, function(){ + results.push(this.name) ; + }) ; + $.each(json.compounds, function(){ + if (this.inChIKey.indexOf(rawQuery)) { + results.push(this.inChIKey) ; + } + }) ; + } + }, + error : function(xhr) { + self.subjects = [] ; + console.log(xhr) ; + } + }) ; + return results ; + }, + + //USED HERE + searchLocalCompound: function() { + var self = this ; + $("#load-step-1-{{ TAB_INDEX_PLACEHOLDER }}").show(); + $.ajax({ + type: "get", + url: "{{ PF_URL_PLACEHOLDER }}/rest/v2/compounds", + async: true, + data: "limit=1&query=" + $('#add-one-cc-s1-value-{{ TAB_INDEX_PLACEHOLDER }}').val() + "&query_filter=" + self.fitlerSearchLoadlCpd+"&token={{ PF_TOKEN_PLACEHOLDER }}", + success: function(data) { + data = data[0] ; + var id = parseInt(data["id"]) ; + var name = data["name"] ; + var inchikey = data["inchikey"] ; + var inchi = data["inchi"] ; + data = ` + <div class="table-responsive"> + <table id="tabPickCpd-{{ TAB_INDEX_PLACEHOLDER }}" class="table table-bordered table-hover table-striped tablesorter" style="cursor: pointer;"> + <thead> + <tr> + <th class="header">Chemical Name <i class="fa fa-sort"></i></th> + <th class="header">Monoisotopic Mass <i class="fa fa-sort"></i></th> + <th class="header">Formula <i class="fa fa-sort"></i></th> + <th class="header" style="">Structure</th> + </tr> + </thead> + <tbody> + <tr class="success" onclick="loadCompoundInForm(${id}, '${inchikey}', '${inchi}', '${data["formula"]}', '${data["exactMass"]}' , 100);"> + <td style="vertical-align: middle;"> + <span id="cpt-load-name-${id}-{{ TAB_INDEX_PLACEHOLDER }}">${name}</span> + <br><small style="white-space: nowrap;">${inchikey}</small> + </td> + <td style="vertical-align: middle;" class="compoundMass">${data["exactMass"]}</td> + <td style="vertical-align: middle;" class="compoundFormula">${data["formula"]}</sub></td> + <td><span class="avatar"> + <img class="compoundSVG" src="{{ PF_URL_PLACEHOLDER }}/webapp/image/generic/${inchikey}" alt="${name}"> + </span> + </td> + </tr> + </tbody> + </table> + <small><sup><b>*</b></sup>: Generic Compounds (abstract "flat" compound without (+) or (-) center).</small> + <` + "script" + ` type="text/javascript"> + $("#tabPickCpd-{{ TAB_INDEX_PLACEHOLDER }}").tablesorter(); + $.each($(self.prefix+".compoundFormula"), function(id, elem) { + var rawFromula = $(elem).text(); + var formatedFormula = rawFromula; + try { + $.each($.unique( rawFromula.match(/\d+/g)), function(keyF, valF) { + var re = new RegExp(valF,"g"); + formatedFormula = formatedFormula.replace(re, "<sub>" + valF + "</sub>"); + }); + } catch (e){} + formatedFormula = formatedFormula.replace("</sub><sub>", ""); + $(elem).html(formatedFormula); + }); + $.each($(self.prefix+".compoundMass"), function(id, elem) { + var exactMass = parseFloat( $(elem).text()); + exactMass = roundNumber(exactMass,7) + $(elem).html(exactMass); + }); + </` + "script" + `> + + </div> + <` + "script" + ` type="text/javascript"> + var listOfRefCompoundsMatch = null; + + loadCompoundInForm = function(id, inchikey, inchi, composition, exactMass, type) { + if (ctx().modeEditSpectrum) { + var name = $("#cpt-load-name-" + id + "-{{ TAB_INDEX_PLACEHOLDER }}").html(); + if (ctx().multiPickLine >= 0) { + ctx().hot_RCC_ADDED.setDataAtCell(ctx().multiPickLine, 0, name); + + // restet form + setTimeout(function(){ + $("#add-one-cc-s1-value-{{ TAB_INDEX_PLACEHOLDER }}").val(""); + $("#ok-step-1-{{ TAB_INDEX_PLACEHOLDER }}").html(""); + }, 200); + // img + var typeS = "chemical"; + if (type == 100) + typeS = "generic"; + else if (type == 101) + typeS = "chemical"; + // '<img class="mixRCCadd'+ctx().multiPickLine+' compoundSVGZoom" src="{{ PF_URL_PLACEHOLDER }}/webapp/image/'+typeS+'/'+inchikey+'" alt="'+name+'">' + var currentCpt = { + "name": name, + "type": typeS, + "concentration": "?", + "inchikey": inchikey + }; + updatedCpdMixData[name] = currentCpt; + } + // display + $("#modalPickCompound-{{ TAB_INDEX_PLACEHOLDER }}").modal("hide"); + $("#modalEditSpectrum-{{ TAB_INDEX_PLACEHOLDER }} .modal-dialog").show(); + return; + } // else: add one spectrum + var name = $("#cpt-load-name-" + id + "-{{ TAB_INDEX_PLACEHOLDER }}").html(); + if (ctx().singlePick) { + $("#add1spectrum-sample-inchikey-{{ TAB_INDEX_PLACEHOLDER }}").val(inchikey); + $("#add1spectrum-sample-inchikey-{{ TAB_INDEX_PLACEHOLDER }}").change(); + $("#add1spectrum-sample-inchi-{{ TAB_INDEX_PLACEHOLDER }}").val(inchi); + $("#add1spectrum-sample-inchi-{{ TAB_INDEX_PLACEHOLDER }}").change(); + $("#add1spectrum-sample-commonName-{{ TAB_INDEX_PLACEHOLDER }}").val(name); + $("#add1spectrum-sample-commonName-{{ TAB_INDEX_PLACEHOLDER }}").change(); + + $("#importspectrum-sample-inchikey-{{ TAB_INDEX_PLACEHOLDER }}").val(inchikey); + $("#importspectrum-sample-inchikey-{{ TAB_INDEX_PLACEHOLDER }}").change(); + } else if (ctx().multiPickLine >= 0) { + ctx().hot_RCC_ADDED.setDataAtCell(ctx().multiPickLine, 0, name); + ctx().hot_RCC_ADDED.setDataAtCell(ctx().multiPickLine, 1, inchikey); + ctx().hot_RCC_ADDED.setDataAtCell(ctx().multiPickLine, 2, composition); + ctx().hot_RCC_ADDED.setDataAtCell(ctx().multiPickLine, 4, exactMass); + // restet form + setTimeout(function(){ + $("#add-one-cc-s1-value-{{ TAB_INDEX_PLACEHOLDER }}").val(""); + $("#ok-step-1-{{ TAB_INDEX_PLACEHOLDER }}").html(""); + }, 200); + } + var typeS = "chemical"; + if (type == 100) + typeS = "generic"; + else if (type == 101) + typeS = "chemical"; + if (ctx().singlePick) + $("#sample-bonus-display-{{ TAB_INDEX_PLACEHOLDER }}").html('<img class="" src="{{ PF_URL_PLACEHOLDER }}/webapp/image/'+typeS+'/'+inchikey+'" alt="'+name+'">'); + else { + // delete + $(ctx().prefix+"img.mixRCCadd"+ctx().multiPickLine).remove(); + // add + $("#sample-bonus-display-{{ TAB_INDEX_PLACEHOLDER }}").append('<img class="mixRCCadd'+ctx().multiPickLine+' compoundSVGZoom" src="{{ PF_URL_PLACEHOLDER }}/webapp/image/'+typeS+'/'+inchikey+'" alt="'+name+'">'); + $(ctx().prefix+"img.mixRCCadd"+ctx().multiPickLine+"").mouseenter(function() { + $(this).removeClass("compoundSVGZoom"); + }).mouseleave(function() { + $(this).addClass("compoundSVGZoom"); + }); + } + $("#modalPickCompound-{{ TAB_INDEX_PLACEHOLDER }}").modal("hide"); + } + </` + "script" + `></` + "div" + `>` ; + $("#ok-step-1-{{ TAB_INDEX_PLACEHOLDER }}").html(data); + }, + error : function(xhr) { + // log + console.log(xhr); + // error + $("#ok-step-1-{{ TAB_INDEX_PLACEHOLDER }}").html("Error: could not process request."); + } + }).always(function() { + $("#load-step-1-{{ TAB_INDEX_PLACEHOLDER }}").hide(); + }); + }, + + //USED HERE + getRCCADDED: function() { + var self = this ; + jsonRCC_ADDED = []; + $.each(self.hot_RCC_ADDED.getData(), function(){ + var formatData = {}; + if ("<b>InChIKey</b>" in this && this["<b>InChIKey</b>"]!= undefined && this["<b>InChIKey</b>"] != "") { + jsonRCC_ADDED.push(this["<b>InChIKey</b>"]); + } + }); + return jsonRCC_ADDED; + }, + + //USED HERE + getRCCADDEDConcentration: function() { + var self = this ; + jsonRCC_ADDED = []; + $.each(self.hot_RCC_ADDED.getData(), function(){ + var formatData = {}; + if ("<b>InChIKey</b>" in this && this["<b>InChIKey</b>"]!= undefined && this["<b>InChIKey</b>"] != "") { + jsonRCC_ADDED.push(this["<b>concentration (µg/ml)</b>"]); + } + }); + return jsonRCC_ADDED; + }, + + //USED IN HTML + clearLine: function() { + var self = this ; + // restet form + setTimeout(function(){ + $("#add-one-cc-s1-value-{{ TAB_INDEX_PLACEHOLDER }}").val(""); + $("#ok-step-1-{{ TAB_INDEX_PLACEHOLDER }}").html(""); + }, 200); + $(self.prefix+"img.mixRCCadd"+self.multiPickLine).remove(); + if (self.singlePick) { + $("#add1spectrum-sample-inchikey-{{ TAB_INDEX_PLACEHOLDER }}").val(""); + $("#add1spectrum-sample-inchikey-{{ TAB_INDEX_PLACEHOLDER }}").change(); + $("#add1spectrum-sample-inchi-{{ TAB_INDEX_PLACEHOLDER }}").val(""); + $("#add1spectrum-sample-inchi-{{ TAB_INDEX_PLACEHOLDER }}").change(); + $("#add1spectrum-sample-commonName-{{ TAB_INDEX_PLACEHOLDER }}").val(""); + $("#add1spectrum-sample-commonName-{{ TAB_INDEX_PLACEHOLDER }}").change(); + $("#sample-bonus-display-{{ TAB_INDEX_PLACEHOLDER }}").html(""); + } else if (self.multiPickLine >= 0) { + for(var i = 0 ; i < 6 ; i += 1) { + self.hot_RCC_ADDED.setDataAtCell(self.multiPickLine, i, ""); + } + } + }, + + exit: function() { + $.ajax({type: "get", url: "/quit", async: true, success: ()=>window.close()}); + }, + +} ; + +$.ajax({ + type: "get", + url: "{{ PF_URL_PLACEHOLDER }}/webapp/get-cpd-data?token={{ PF_TOKEN_PLACEHOLDER }}", + data: "inchikey=" + "{{ INCHIKEY_PLACEHOLDER }}", + dataType: "json", + success: function(data) { + if (data.success) { + var self = context_{{ TAB_INDEX_PLACEHOLDER }} ; + console.log(`inchikey {{ INCHIKEY_PLACEHOLDER }} found!!`) + inchidata["{{ INCHIKEY_PLACEHOLDER }}"] = data ; + self.init() ; + self.fitlerSearchLoadlCpd = 5; + self.inchikey = null; + all_contexts[{{ TAB_INDEX_PLACEHOLDER }}] = self ; + } else { + no_success( + {{ TAB_INDEX_PLACEHOLDER }}, + "{{ INCHIKEY_PLACEHOLDER }}", + {{ DEFAULT_DATA }}["name"] + ) ; + all_contexts[{{ TAB_INDEX_PLACEHOLDER }}] = null ; + } + }, + error : function(data) { + no_success( + {{ TAB_INDEX_PLACEHOLDER }}, + "{{ INCHIKEY_PLACEHOLDER }}", + {{ DEFAULT_DATA }}["name"] + ) ; + all_contexts[{{ TAB_INDEX_PLACEHOLDER }}] = null ; + } +}).always(() => null);