# HG changeset patch # User lain # Date 1693405278 0 # Node ID 7e3085fc60c110e1b3fd6879953c5472b4441896 # Parent b58b229c4cbffbe5e2bccc1557f78e52b89cc378 master branch Updating diff -r b58b229c4cbf -r 7e3085fc60c1 README.md --- a/README.md Fri Mar 03 14:10:24 2023 +0000 +++ b/README.md Wed Aug 30 14:21:18 2023 +0000 @@ -5,7 +5,7 @@ -------- * **@name**: MS2PF - * **@version**: 1.1.0 + * **@version**: 1.2.1 * **@authors**: Lain Pavot (PFEM - INRAE - MetaboHUB) * **@maintainers**: Lain Pavot (PFEM - INRAE - MetaboHUB) * **@init date**: 2022, November diff -r b58b229c4cbf -r 7e3085fc60c1 add-one-spectrum-index.js --- a/add-one-spectrum-index.js Fri Mar 03 14:10:24 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2584 +0,0 @@ - -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 }}, - 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() ; - }, - - populate_selects: function() { - var self = this ; - var choose_in_list ; - - choose_in_list = ` - - ` ; - $("#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( - `` - ); - } else { - $("#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}").append( - `` - ); - } - } - }); - }, - - populate_lc_columns: function(data) { - // load data from json - $.each(data.columns, function() { - $("#add1spectrum-chromatoLC-colConstructor-{{ TAB_INDEX_PLACEHOLDER }}").append( - `` - ); - }); - $("#add1spectrum-chromatoLC-colConstructor-{{ TAB_INDEX_PLACEHOLDER }}").append( - '' - ); - }, - - populate_lc_solvents: function(data) { - // load data from json - $.each(data.solvents, function() { - $("#add1spectrum-chromatoLC-separationSolvA-{{ TAB_INDEX_PLACEHOLDER }}").append( - `` - ); - $("#add1spectrum-chromatoLC-separationSolvB-{{ TAB_INDEX_PLACEHOLDER }}").append( - `` - ); - }); - }, - - 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( - `` - ); - $("#add1spectrum-analyzserMS-ionizationMethod-neg-{{ TAB_INDEX_PLACEHOLDER }}").append( - `` - ); - } else { - $("#add1spectrum-analyzserMS-ionizationMethod-pos-{{ TAB_INDEX_PLACEHOLDER }}").append( - `` - ); - $("#add1spectrum-analyzserMS-ionizationMethod-neg-{{ TAB_INDEX_PLACEHOLDER }}").append( - `` - ); - } - } - }); - }, - - populate_lcms_solvents: function(data) { - // load data from json - $.each(data.solvents, function () { - $("#add1spectrum-sample-lcmsSolvent-{{ TAB_INDEX_PLACEHOLDER }}").append( - `` - ); - }); - }, - - 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(); - } - }) ; - $("#add1spectrum-peaksMS-msLevel-{{ TAB_INDEX_PLACEHOLDER }}").on("change", function() { - var v = $("#add1spectrum-peaksMS-msLevel-{{ TAB_INDEX_PLACEHOLDER }}").val(); - $(self.prefix + ".disabled-if-ms-in-msms").attr( - "disabled", - (v == "ms2" || v == "ms3") - ) ; - $(self.prefix + ".enabled-if-ms-in-msms").attr( - "disabled", - !(v == "ms2" || v == "ms3") - ) ; - $(self.prefix + ".hidden-if-ms-in-msms").css( - "display", - !(v == "ms2" || v == "ms3") ? "none" : "" - ) ; - }) ; - }, - - 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 ; - 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 || $(el).val() === "" - )) { - self.set_error(element) ; - } else { - eslf.set_success(element) ; - } - } else if (isOptional) { - isSuccess = self.is_success(element); - isWarning = self.is_warning(element); - isError = self.is_error(element); - if (isSuccess) { - self.rm_success(element) - } else if (isWarning) { - self.rm_warning(element) ; - } else if (isError) { - self.rm_error(element) ; - } - if (element.parent().children("input").toArray().some( - (el) => ($(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") - && $("#btnSwitch-gotoStep6-{{ TAB_INDEX_PLACEHOLDER }}").is(":visible") - ) { - self.checkIfEnableSubmit() ; - } - }, - - a_ion_parent_is_selected: function() { - return (this.get_selected_parent_ion_index() !== null) ; - }, - - get_selected_parent_ion_index: function() { - if (this.hot_MS_Peaks == undefined) { - return null ; - } - var data = this.hot_MS_Peaks.getData() ; - for (var i = 0 ; i < data.length ; i += 1) { - if (data[i][7] === "true" || data[i][7] === true) { - return i ; - } - } - return null ; - }, - - auto_set_spec_type: function() { - console.log("auto_set_spec_type...") ; - var self = this ; - var id = `#set_${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 ; - if (self.is_ref()) { - id = "#add1spectrum-sample-inchikey-{{ TAB_INDEX_PLACEHOLDER }}:text" ; - element = $(id) ; - if (element.length) { - console.log(`auto_set_inchikey to ${self.DEFAULT_DATA["inchikey"]} ok.`) - element.val(self.DEFAULT_DATA["inchikey"]).change() ; - console.log(`Inchikey set!`) ; - } else { - console.log(element) - console.log("Failed!") - } - } else { - for (var index = 0 ; index < all_contexts.length ; index += 1) { - var inchikey = all_contexts[index].DEFAULT_DATA["inchikey"] ; - id = `#container_RCC_ADDED-1 tbody:nth(0) tr:nth(${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"]) { - setTimeout(() => self.auto_set_scan_type(self), 1000) ; - } - })(self) - }, 1000) ; - }, - - auto_set_scan_type: function() { - console.log("auto_set_scan_type...") ; - var self = this ; - 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 - $("#containter-lcms-spectrum-preview-{{ TAB_INDEX_PLACEHOLDER }}").highcharts({ - chart: { - zoomType: "x", - spacingRight: 10, - spacingLeft: 10, - type: "scatter" - }, - title: { - text: "Spectrum Preview", - useHTML: true - }, - subtitle: { - text: ( - document.ontouchstart === undefined - ? "Select area" - : "Pinch the chart to zoom in" - ) - }, - xAxis: { - type: "number", - title: {text: "m/z"}, - min: spectrumMinPPM, - max: spectrumMaxPPM, - labels: { - formatter: function() { - return (Math.abs(this.value) + ""); - } - } - }, - yAxis: { - title: {text: "Relative Intensity (%)"}, - min: 0, - max: maxGraph - }, - tooltip: { - crosshairs: true, - formatter: function() { - var compo = ""; - return ( - "" + this.series.name - + "
m/z:" + Math.abs(this.x) + "" - + ";
Relative Intensity: " + this.y - + "%;
Annotation: " + localDataAnnot[ this.x] - + "" - ); - } - }, - legend: {enabled: false}, - plotOptions: {scatter: {}}, - series: [{ - name: "preview", - showInLegend: true, - color: "#f00", - lineColor: "#f00", - pointInterval: 10, - pointStart: 100, - lineWidth : 2, - marker: { - enabled: true, - radius: 2, - lineColor: "#f00" - }, - data: localData, - zIndex: 10 - }] - }); - }, - - //USED HERE - fulfillLCdata: function(jsonFileName) { - var self = this ; - var url = `{{ PF_URL_PLACEHOLDER }}/webapp/resources/json/lc-methods/${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(` - - `); - } - }); - }, - - //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( - '' - ); - $.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( - `` - ); - } else { - $("#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}").append( - `` - ); - } - } - }); - }); - } else if (self.is_ms2()) { - $("#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}").empty(); - $("#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}").append( - '' - ); - $.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( - `` - ); - } else { - $("#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}").append( - `` - ); - } - } - }); - } - ); - } - // 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) => { - 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]-") { - precursor_ion = $("#add1spectrum-peaksMS-msPrecursorIon-{{ TAB_INDEX_PLACEHOLDER }}") ; - console.log(precursor_ion) - 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: "InChIKey", type: "text"}, - {data: "composition", renderer: lightgrayRenderer}, - {data: "concentration (µg/ml)", 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", - "InChIKey", - "composition", - "concentration (µg/ml)", - "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); - $("#btnSwitch-gotoStep4-ms-{{ TAB_INDEX_PLACEHOLDER }}").prop("disabled", true); - self.postSpectrumToServer() ; - }, - - postSpectrumToServer: function(jsonData, tab_index) { - var self = this ; - var base_peakdata ; - var new_peakdata ; - var is_ms2 = self.is_ms2() ; - - if (self.is_mix()) { - if ({{ TAB_INDEX_PLACEHOLDER }} != 1) { - return ; - } - jsonData = self.gatherJsonObjects() ; - all_mix_data = Object.assign({}, jsonData) ; - all_mix_data["peaklists"] = [] ; - base_peakdata = Object.assign({}, jsonData["peaklists"][0]) ; - base_peakdata["msms_ms_precursor_ion"] = undefined ; - all_contexts.forEach((context, index) => { - new_peakdata = Object.assign({}, base_peakdata) ; - context.loadFomDataIntoJsonObjects() - if (is_ms2) { - new_peakdata["precursor_ion"] = context.jsonPeaksList["msms_ms_precursor_ion"]["m/z"] ; - } - new_peakdata["peaklist"] = context.jsonPeaksList["peaklist"] ; - all_mix_data["peaklists"].push(new_peakdata) - }) - } - // II.B - rebuild json full object (with all metadata or just id if already in base) - if (jsonData == null) { - jsonData = self.gatherJsonObjects(); - } - // II.C - add id metadata (if exist) - var json_array = [] ; - if (!tab_index) { - tab_index = {{ TAB_INDEX_PLACEHOLDER }} ; - } - json_array[tab_index-1] = jsonData ; - - // III - post json object - // III.A - success - self.sent_json = jsonData ; - console.warn( - "This data has been validated without going through the internal server!" - ) - if ($("#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(); - $("#alertBoxSubmitSpectrum-{{ TAB_INDEX_PLACEHOLDER }}").html(` - - `); - return true; - }, - - //USED HERE - loadFomDataIntoJsonObjects: function() { - var self = this ; - // I - Spectrum type - self.isJsonSpectrumTypeComplete = false ; - if (self.isGC && self.is_ms()) { - self.jsonSpectrumType = "gc-ms" ; - } else if (self.isLC && self.is_ms()) { - self.jsonSpectrumType = "lc-ms" ; - } else if (self.isLC && self.is_ms2()) { - self.jsonSpectrumType = "lc-msms" ; - } else if (self.isGC && self.is_ms()) { - self.jsonSpectrumType = "ic-ms" ; - } else if (self.isLC && self.is_ms()) { - self.jsonSpectrumType = "ic-msms" ; - } - if (self.jsonSpectrumType != null && self.jsonSpectrumType != "") { - self.isJsonSpectrumTypeComplete = true; - } - - // II - Sample - self.isJsonSampleComplete = true; - self.isJsonRCCaddedComplete = true; - self.jsonSample = {}; - - switch($("#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: [] - }; - $.each(self.hot_LC_SFG.getData(), function(){ - if (this[0]!="") { - if (!isNaN(this[0]) && !isNaN(this[1]) && !isNaN(this[2])) { - formatData["time"].push(Number(this[0])); - formatData["solvent_a_percent"].push(Number(this[1])); - formatData["solvent_b_percent"].push(Number(this[2])); - } - } - }); - 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_gaz_flow", "sprayGazFlow"], - ["vaporizer_gaz_flow", "vaporizerGazFlow"], - ["vaporizer_temperature", "vaporizerTemperature"], - ["source_gaz_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]), - deltaPPM: Number(data[3]), - composition: (data[4]), - attribution: (data[5]) - }); - self.isJsonPeaksListComplete = true; - } - }); - // peak list data - peakdata["ms_lvl"] = $("#add1spectrum-peaksMS-msLevel-{{ TAB_INDEX_PLACEHOLDER }}").val(); - 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_range_from"] = $("#add1spectrum-peaksMS-rangeFrom-{{ TAB_INDEX_PLACEHOLDER }}").val(); - peakdata["mz_range_to"] = $("#add1spectrum-peaksMS-rangeTo-{{ TAB_INDEX_PLACEHOLDER }}").val(); - peakdata["rt_abs_from"] = $("#add1spectrum-peaksMS-rtMinFrom-{{ TAB_INDEX_PLACEHOLDER }}").val(); - peakdata["rt_abs_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() ; - peakdata["msms_ms_precursor_ion"] = { - "m/z": data[selected_ion][0], - "abs_intensity": data[selected_ion][1], - "rel_intensity": data[selected_ion][2], - "attribution": data[selected_ion][5] - } ; - } - } - 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 = ` - ` ; - } else if (!self.isJsonSampleComplete) { - alertMsg = ` - ` ; - } else if (!self.isJsonRCCaddedComplete) { - alertMsg = ` - `; - } else if (!self.isJsonChromatoComplete) { - alertMsg = ` - '; - } else if (!self.isJsonPeaksListComplete) { - alertMsg = ` - '; - } else if (self.is_mix() && self.is_ms2()) { - for (var i = 0 ; i < all_contexts.length ; i += 1) { - if (all_contexts[i].get_selected_parent_ion_index() === null) { - return alertMsg + ` - - ` - } - } - } - // 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 = ` -
- - - - - - - - - - - - - - - - - -
Chemical Name Monoisotopic Mass Formula Structure
- ${name} -
${inchikey} - 		${data["exactMass"]}${data["formula"]} - ${name} - -
- *: Generic Compounds (abstract "flat" compound without (+) or (-) center). - <` + "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, "" + valF + ""); - }); - } catch (e){} - formatedFormula = formatedFormula.replace("", ""); - $(elem).html(formatedFormula); - }); - $.each($(self.prefix+".compoundMass"), function(id, elem) { - var exactMass = parseFloat( $(elem).text()); - exactMass = roundNumber(exactMass,7) - $(elem).html(exactMass); - }); - - -
- <` + "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); - // ctx().hot_RCC_ADDED.setDataAtCell(ctx().multiPickLine, 1, inchikey); - - // 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"; - // ''+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(''+name+''); - else { - // delete - $(ctx().prefix+"img.mixRCCadd"+ctx().multiPickLine).remove(); - // add - $("#sample-bonus-display-{{ TAB_INDEX_PLACEHOLDER }}").append(''+name+''); - $(ctx().prefix+"img.mixRCCadd"+ctx().multiPickLine+"").mouseenter(function() { - $(this).removeClass("compoundSVGZoom"); - }).mouseleave(function() { - $(this).addClass("compoundSVGZoom"); - }); - } - $("#modalPickCompound-{{ TAB_INDEX_PLACEHOLDER }}").modal("hide"); - } - ` ; - $("#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 ("InChIKey" in this && this["InChIKey"]!= undefined && this["InChIKey"] != "") { - jsonRCC_ADDED.push(this["InChIKey"]); - } - }); - return jsonRCC_ADDED; - }, - - //USED HERE - getRCCADDEDConcentration: function() { - var self = this ; - jsonRCC_ADDED = []; - $.each(self.hot_RCC_ADDED.getData(), function(){ - var formatData = {}; - if ("InChIKey" in this && this["InChIKey"]!= undefined && this["InChIKey"] != "") { - jsonRCC_ADDED.push(this["concentration (µg/ml)"]); - } - }); - 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.push(self) ; - } else { - no_success( - {{ TAB_INDEX_PLACEHOLDER }}, - "{{ INCHIKEY_PLACEHOLDER }}", - {{ DEFAULT_DATA }}["name"] - ) ; - } - }, - error : function(data) { - no_success( - {{ TAB_INDEX_PLACEHOLDER }}, - "{{ INCHIKEY_PLACEHOLDER }}", - {{ DEFAULT_DATA }}["name"] - ) ; - } -}).always(() => null); diff -r b58b229c4cbf -r 7e3085fc60c1 common.js --- a/common.js Fri Mar 03 14:10:24 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,195 +0,0 @@ - -this.ctx = () => context; -var all_contexts = [] ; -var inchidata = {} ; -var all_mix_data = {} ; -function no_success(tab_index, inchi, data) { - console.log(`inchikey ${inchi} not found...`) ; - console.log(`disabling ${data} ...`) - disable_tab( - tab_index, - "red", - "This compound has not been found on peakforest" - ) ; -} - -function disable_tab(tab_index, color, title) { - var element = $(`#open_tab_${tab_index}`) ; - element.attr("disabled", "disabled").off("click"); - element.attr("onclick", null) ; - element.attr("title", title) ; - element.attr("data-toggle", null) ; - element.attr("href", null) ; - element.css("color", color) ; - element.css("cursor", "not-allowed") ; -} - -function send_everything_to_peakforest(url, token) { - var bundles ; - if (context.is_mix()) { - bundles = [all_mix_data] ; - } else { - bundles = create_dataset_bundles() ; - } - bundles.forEach((bundle, index) => { - console.log(bundle) - $.ajax({ - type: "post", - url: `${url}/rest/v2/spectrum?token=${token}`, - data: JSON.stringify(bundle), - contentType: "application/json" - }) - }) - // console.log(bundles) -} - -function create_dataset_bundles() { - var bundles = [] ; - var data ; - all_contexts.forEach((context, index) => { - if ((data = context.sent_json) === null) { - return ; - } - if (bundles.length === 0) { - // console.log("First metadata!") - return bundles.push(data) ; - } - if (merge_in_bundle(bundles, data)) { - // console.log("Merged!") - } else { - // console.log("New metadata!") - } - }) ; - return bundles ; -} - -function merge_in_bundle(bundles, data) { - for(var i = 0 ; i < bundles.length ; i += 1) { - if ( - identical(bundles[i]["sample"], data["sample"]) - && identical(bundles[i]["chromatography"], data["chromatography"]) - && identical(bundles[i]["analyzer"], data["analyzer"]) - && identical(bundles[i]["ionization_mode_positive"], data["ionization_mode_positive"]) - && identical(bundles[i]["ionization_mode_negative"], data["ionization_mode_negative"]) - && identical(bundles[i]["other_metadata"], data["other_metadata"]) - ) { - bundles[i]["peaklists"].push(data["peaklists"][0]) ; - return true ; - } else { - continue ; - console.log( - "sample: " - + identical(bundles[i]["sample"], data["sample"]) - ) - console.log( - "chromatography: " - + identical(bundles[i]["chromatography"], data["chromatography"]) - ) - console.log( - "analyzer: " - + identical(bundles[i]["analyzer"], data["analyzer"]) - ) - console.log( - "ionization_mode_positive: " - + identical(bundles[i]["ionization_mode_positive"], data["ionization_mode_positive"]) - ) - console.log( - "ionization_mode_negative: " - + identical(bundles[i]["ionization_mode_negative"], data["ionization_mode_negative"]) - ) - console.log( - "other_metadata: " - + identical(bundles[i]["other_metadata"], data["other_metadata"]) - ) - } - } - bundles.push(data) ; - return false ; -} - -function identical(left, right) { - if (typeof left !== typeof right) { - return false ; - } - if (left === null) { - return right === null ; - } - if (right === null) { - return left === null ; - } - switch (typeof left) { - case "array": - return identical_array(left, right) ; - break ; - case "object": - return identical_object(left, right) ; - break ; - default: - break ; - } - return (left === right) -} - -function identical_array(left, right) { - if (right.length !== left.length) { - return false ; - } - for(var i = 0 ; i < left.length ; i += 1) { - if (!identical(left[i], right[i])) { - return false ; - } - } - return true ; -} - -function identical_object(left, right) { - var left_keys ; - - if (!( - share_keys(left, right) - && share_keys(right, left) - )) { - return true ; - } - left_keys = Object.keys(left) ; - for (var i = 0 ; i < left_keys.length ; i += 1){ - if (!identical(left[left_keys[i]], right[left_keys[i]])) { - return false ; - } - } - return true ; -} - -function share_keys(left, right) { - var left_keys ; - var right_keys ; - - left_keys = Object.keys(left) ; - right_keys = Object.keys(right) ; - for(var i = 0 ; i < left_keys.length ; i += 1) { - if (!right_keys.includes(left_keys[i])) { - return false ; - } - } - return true ; -} - -var set_inchi_data = function(data, tab_index) { - inchidata[data.inchikey] = data ; - $(`#add1spectrum-sample-inchi-${tab_index}`).val(data.inchi); - $(`#add1spectrum-sample-inchi-${tab_index}`).change(); - $(`#add1spectrum-sample-commonName-${tab_index}`).val(data.name); - $(`#add1spectrum-sample-commonName-${tab_index}`).change(); - $(`#sample-bonus-display-${tab_index}`).html( - `${data.name}` - ); -} - -var lightgrayRenderer = function(instance, td, row, col, prop, value, cellProperties) { - Handsontable.renderers.TextRenderer.apply(this, arguments); - td.style.backgroundColor = "#EEE"; -} diff -r b58b229c4cbf -r 7e3085fc60c1 compound-mix.html --- a/compound-mix.html Fri Mar 03 14:10:24 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,36 +0,0 @@ -
-
-
-
-
- -
-
-
- - Precursor ion (M/Z) - - - -
-
-
-
-
-
\ No newline at end of file diff -r b58b229c4cbf -r 7e3085fc60c1 compound-ref.html --- a/compound-ref.html Fri Mar 03 14:10:24 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,660 +0,0 @@ -
-
-
-
-

- - Spectrum Type - -

-
-
-
- - - -
-
-
- - - - - - -
- - - -
- - diff -r b58b229c4cbf -r 7e3085fc60c1 config.yml --- a/config.yml Fri Mar 03 14:10:24 2023 +0000 +++ b/config.yml Wed Aug 30 14:21:18 2023 +0000 @@ -42,13 +42,14 @@ spectrum_type: "default is {{ defaults.spectrum_type }}" sample_type: "default is {{ defaults.sample_type }}" resolution: "default is {{ defaults.resolution }}" - resolution: "default is {{ defaults.resolution }}" name: The precursor name peakforest.url: "default={{ defaults.peakforest.url }}" peakforest.token: The token to comunicate with peakforest api polarity: positive|negative raw_metadata: example - 1-1__INCHIKEY__=QNAYBMKLOCPYGJ-REOHCLBHSA-N_L-Alanine_MS_POS_plasma_RT__=0.84_filtree.csv scan_type: ms|msms|rmn + rt_min: Min retention time + rt_max: Max retention time run_dry_html: when "--run-dry", provides the output directory for {{ generated.html }} run_dry_js: when "--run-dry", provides the output directory for {{ generated.js }} raw_metadata_sep: "raw metadata separator" @@ -56,10 +57,13 @@ logging.file.path: "The file path to output logs to" validation: "Set the default validation to the provided value, TRUE or FALSE." output_json: "Provide a path to output a JSON file." + pid: "Path to the pid file" + ip: "the net intf to link to" + port: "the net port to bind on" meta: ## meta info about the tool itself author: Lain Pavot - version: 1.1.0 + version: 1.2.1 shortcuts: ## to define things like: "we can use -p instead of --polarity" peakforest.token: t @@ -81,6 +85,8 @@ ## if append is true, outputs are appended to the file. ## otherwise, the file is emptied each time the app runs. defaults: + ip: 0.0.0.0 + port: 8000 peakforest: url: https://nightly.peakforest.org token: '' @@ -109,6 +115,9 @@ path: append: False output_json: '' + rt_min: 0.9 + rt_max: 1.9 + pid: ## token related info token: @@ -119,10 +128,6 @@ ## if not, you can provide you token here value: -network: - ip: 0.0.0.0 - port: 8000 - workdir: ## create a tmp directory create_tmp: true @@ -134,19 +139,19 @@ ## the templates paths templates: ## meta is what wrapps the whole page. - main: meta.html - main_mix: meta-compound-mix.html - main_ref: meta-compound-ref.html + main: src/meta.html + main_mix: src/meta-compound-mix.html + main_ref: src/meta-compound-ref.html ## form is one instance of a pf form - # form: form.html - # form: compound-ref.html - form: form.html - form_mix: compound-mix.html - form_ref: compound-ref.html + # form: src/form.html + # form: src/compound-ref.html + form: src/form.html + form_mix: src/compound-mix.html + form_ref: src/compound-ref.html ## one item of the tab list - tab_list: tab_list.html + tab_list: src/tab_list.html ## the js for one form - js: add-one-spectrum-index.js + js: src/add-one-spectrum-index.js ## placeholders for the html templates. ## this will not change the placeholders syntax for this file. placeholders: diff -r b58b229c4cbf -r 7e3085fc60c1 macros.xml --- a/macros.xml Fri Mar 03 14:10:24 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,202 +0,0 @@ - - 1.1.0 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - -
- - - - - - \ No newline at end of file diff -r b58b229c4cbf -r 7e3085fc60c1 meta-compound-mix.html --- a/meta-compound-mix.html Fri Mar 03 14:10:24 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1272 +0,0 @@ - - - - - - - - PeakForest MetaboHub - - - - - - - - - - - - - - - - - - - - - - - - - - -
-
- -
-
-
-
-
-
-

- - Spectrum Type - - -

-
-
-
- - - -
-
-
- - - - - - - - - - - - - -
-
-
-
- - -
- - -
- - - - {{ EMBED_JS }} - - - \ No newline at end of file diff -r b58b229c4cbf -r 7e3085fc60c1 meta-compound-ref.html --- a/meta-compound-ref.html Fri Mar 03 14:10:24 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,112 +0,0 @@ - - - - - - - - PeakForest MetaboHub - - - - - - - - - - - - - - - - - - - - - - - - - - -
-
- -
-
- -
- {{ ADD_SPECTRUM_FORM }} -
-
-
- - -
- - -
- - - - - {{ EMBED_JS }} - - - \ No newline at end of file diff -r b58b229c4cbf -r 7e3085fc60c1 ms2pf_it.xml --- a/ms2pf_it.xml Fri Mar 03 14:10:24 2023 +0000 +++ b/ms2pf_it.xml Wed Aug 30 14:21:18 2023 +0000 @@ -1,44 +1,148 @@ - - adds you MS spectrum to peakforest. - - - 0 - macros.xml - - - python - pyyaml - - - - 8000 - / - - - + + adds you MS spectrum to peakforest. + + + 1.2.1 + 0 + + + quay.io/pfem/ms2peakforest:@TOOL_VERSION@ + + + + 8000 + / + + + - - -@MS2PF_COMMON_CMD@ - - - - - - - - do_output_json - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + +
+ + + + + do_output_json + + + + - + diff -r b58b229c4cbf -r 7e3085fc60c1 server.py --- a/server.py Fri Mar 03 14:10:24 2023 +0000 +++ b/server.py Wed Aug 30 14:21:18 2023 +0000 @@ -40,21 +40,22 @@ "theo_mass": "", "delta_ppm": "ppm", "rdbequiv": "", - "composition": "", - "attribution": "fragment", + "composition": "fragment", + "attribution": "composition", } MS_2_SNOOP_HEADER = { "name": str, "inchikey": str, - "composition": str, + # "composition": str, + "composition": lambda *args:"", "fragment": str, "fragment_mz": str, "ppm": str, "fileid": str, "correlation": str, - "abs_intensity": lambda x:float(x) * 100, - "rel_intensity": lambda x:float(x) * 100, + "abs_intensity": lambda x:float(x), # * 100, + "rel_intensity": lambda x:float(x) * 100 if x != "" else "", "valid_corelation": str } @@ -233,7 +234,7 @@ method: "default is {{ defaults.method }}" meta: author: Lain Pavot - version: 1.1.0 + version: 1.2.0 shortcuts: help: h ## will autogenerate -i for input and -m for method @@ -422,13 +423,11 @@ config.placeholders[ADD_SPECTRUM_FORM] = "" config.placeholders[EMBED_JS_PLACEHOLDER] = "" config.placeholders[TAB_LIST_PLACEHOLDER] = "" - config.placeholders["DEFAULT_MIN_MZ"] = "50" - config.placeholders["DEFAULT_MAX_MZ"] = "500" + # config.placeholders["DEFAULT_MIN_MZ"] = "50" + # config.placeholders["DEFAULT_MAX_MZ"] = "500" config.placeholders["DEFAULT_RESOLUTION_LOW"] = "" config.placeholders["DEFAULT_RESOLUTION_HIGH"] = "selected=\"selected\"" config.placeholders["DEFAULT_RESOLUTION_UNSET"] = "" - config.placeholders["DEFAULT_MIN_RT"] = "0.9" - config.placeholders["DEFAULT_MAX_RT"] = "1.4" return config def parse_parameters(config): @@ -458,6 +457,9 @@ + '\n'.join(parameters.errors) ) + parameters.placeholders["DEFAULT_MIN_RT"] = str(arguments.rt_min) + parameters.placeholders["DEFAULT_MAX_RT"] = str(arguments.rt_max) + if arguments.sample_type == COMPOUND_MIX: parameters["form_template"] = os.path.join( parameters["root_dir"], @@ -467,7 +469,7 @@ parameters["root_dir"], parameters.templates.main_mix ) - elif arguments.sample_type == COMPOUND_REF: + else: # elif arguments.sample_type == COMPOUND_REF: parameters["form_template"] = os.path.join( parameters["root_dir"], parameters.templates.form_ref @@ -566,6 +568,7 @@ arguments["method"] = "cf_pfem_urine_qtof" else: arguments["method"] = "cf_pfem_urine_method1_qtof-msms" + arguments["method"] = "toulouse-metatoul-agromix__ft-esi__msms" if arguments["sample_type"] == COMPOUND_MIX: check_mix_compound_files(parameters) more_info_in_logs(parameters) @@ -579,11 +582,14 @@ for metadata in arguments.raw_metadata ] except ValueError: - parameters.logger.error( - "Metadata/file names does not start with `[0-9]+-[0-9]+_.*` . " - "This is necessary in the case of compounds mix." - ) - sys.exit(-1) + ## file does not start with `[0-9]+-[0-9]+_.*`: probably + ## a ms2snoop file. + return + # parameters.logger.error( + # "Metadata/file names does not start with `[0-9]+-[0-9]+_.*` . " + # "This is necessary in the case of compounds mix." + # ) + # sys.exit(-1) runs, samples = zip(*numbarz) if not all(runs[0] == i for i in runs[1:]): parameters.logger.error( @@ -806,8 +812,8 @@ ms_data["abs_intensity"], ms_data["rel_intensity"], ms_data["ppm"], + ms_data["fragment"], ms_data["composition"], - ms_data["fragment"], str(ms_data["valid_corelation"] == "TRUE").lower(), "true" if ms_data.get("correlation") == "1" else "false" ) @@ -827,11 +833,10 @@ adds the compound to the tab list, creates the js file for this tab """ - if len([x for x in ms_peak_table if x.split(", ")[7] == "\"true\""]) > 1: - for i in range(len(ms_peak_table)): - ms_peak_table[i] = ", ".join( - ms_peak_table[i].split(", ")[:-1] + [", \"false\""] - ) + ignore_multiple_parent_ion(ms_peak_table) + determine_min_max_mz(ms_peak_table) + guess_relative_intensities(ms_peak_table) + accept_all_fragments_if_all_false(ms_peak_table) config.placeholders[MS_PEAK_VALUES_PLACEHOLDER] = f"""[ {','.join('['+line+']' for line in ms_peak_table)} ]""" @@ -853,6 +858,64 @@ if index == 1: config.placeholders[ACTIVE_TAB_PLACEHOLDER] = "" +def determine_min_max_mz(ms_peak_table): + mz_list = [ + float(ms_peak_table[i].split(", ")[0].strip("\"")) + for i in range(len(ms_peak_table)) + ] + config.placeholders["DEFAULT_MIN_MZ"] = str(min(mz_list)) + config.placeholders["DEFAULT_MAX_MZ"] = str(max(mz_list)) + +def guess_relative_intensities(ms_peak_table): + if all( + ms_peak_table[i].split(", ")[2].strip("\"") == "" + for i in range(len(ms_peak_table)) + ): + absolute_intensities = [ + float(ms_peak_table[i].split(", ")[1].strip("\"")) + for i in range(len(ms_peak_table)) + ] + greatest = float(max(absolute_intensities)) + relative_intensities = [ + intensity / greatest * 100 + for intensity in absolute_intensities + ] + replace_ms_table_value(ms_peak_table, 2, relative_intensities) + +def ignore_multiple_parent_ion(ms_peak_table): + if len([ + None for x in ms_peak_table + if x.split(", ")[7].strip("\"") == "true" + ]) > 1: + ## if more than one is the precursor, then none is the precursor + replace_ms_table_value(ms_peak_table, 7, "\"false\"") + +def accept_all_fragments_if_all_false(ms_peak_table): + if all( + ms_peak_table[i].split(", ")[6].strip("\"") == "false" + for i in range(len(ms_peak_table)) + ): + replace_ms_table_value(ms_peak_table, 6, "true") + +def replace_ms_table_value(ms_peak_table, index, value, sep=", "): + length = len(ms_peak_table) + if not isinstance(value, list): + if isinstance(value, str): + value = [value.join('""')] * length + else: + value = [str(value)] * length + if not isinstance(value[0], str): + value = [str(x) for x in value] + count = ms_peak_table[0].count(sep) + endindex = count - index + neg_endindex = -endindex + for i in range(length): + ms_peak_table[i] = sep.join(( + *ms_peak_table[i].split(sep, index)[:index], + value[i], + *ms_peak_table[i].rsplit(sep, endindex)[neg_endindex:] + )) + def fragnot_extractor(config, *line): """ Fragnot processor - extracts one fragnot line of content and @@ -862,7 +925,7 @@ FRAGNOT_HEADER[header]: line[i].strip() for i, header in enumerate(FRAGNOT_HEADER) } - fragnot_data["composition"] = "unknown" + # fragnot_data["composition"] = "unknown" fragnot_data["valid_corelation"] = config.arguments.validation return fragnot_data @@ -923,7 +986,7 @@ else: gen_dir = tempfile.gettempdir() config.workdir.tmp_dir = gen_dir - shutil.copy(os.path.join(config["root_dir"], "common.js"), gen_dir) + shutil.copy(os.path.join(config["root_dir"], "src", "common.js"), gen_dir) config.logger.info(f"Outputs will be generated in {config.workdir.tmp_dir}") return gen_dir @@ -941,11 +1004,13 @@ def do_POST(self): content_length = int(self.headers.get("Content-Length")) json_bytes = self.rfile.read(content_length).decode("utf-8") - json_list = json.loads(json_bytes) - for i, obj in enumerate(json_list): - print(obj) - if obj: - config["json_result"][i] = obj + # json_list = json.loads(json_bytes) + # for i, obj in enumerate(json_list): + # print(obj) + # if obj: + # config["json_result"][i] = obj + json_obj = json.loads(json_bytes) + config["json_result"][json_obj["index"]] = json_obj["object"] save_json(config) self.send_head() self.wfile.write(json_bytes.encode("utf-8")) @@ -974,7 +1039,7 @@ """ prepare and runs the server, with the handler for the given directory """ - ip, port = config.network.ip, config.network.port + ip, port = config.arguments.ip, int(config.arguments.port) config.logger.debug(f"IP and port: {ip}:{port}") socketserver.TCPServer.allow_reuse_address = True config.logger.debug(f"Allow reuse adress.") @@ -1066,6 +1131,10 @@ logger.info("...") if __name__ == "__main__": + print(os.listdir("test-data")) + + if not os.path.exists("config.yml"): + shutil.copy("config.default.yml", "config.yml") base_config = parse_config() config = parse_parameters(base_config) @@ -1075,6 +1144,12 @@ """ arguments = config.arguments + if arguments.pid: + print(arguments.pid) + with open(arguments.pid, "w") as pid_file: + pid_file.write(str(os.getpid())) + atexit.register(lambda:os.unlink(arguments.pid)) + config.logger.info(f"Starting MS2PF from {os.getcwd()}") gen_dir = prepare_workplace(config) diff -r b58b229c4cbf -r 7e3085fc60c1 src/add-one-spectrum-index.js --- /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 = ` + + ` ; + $("#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( + `` + ); + } else { + $("#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}").append( + `` + ); + } + } + }); + }, + + populate_lc_columns: function(data) { + // load data from json + $.each(data.columns, function() { + $("#add1spectrum-chromatoLC-colConstructor-{{ TAB_INDEX_PLACEHOLDER }}").append( + `` + ); + }); + $("#add1spectrum-chromatoLC-colConstructor-{{ TAB_INDEX_PLACEHOLDER }}").append( + '' + ); + }, + + populate_lc_solvents: function(data) { + // load data from json + $.each(data.solvents, function() { + $("#add1spectrum-chromatoLC-separationSolvA-{{ TAB_INDEX_PLACEHOLDER }}").append( + `` + ); + $("#add1spectrum-chromatoLC-separationSolvB-{{ TAB_INDEX_PLACEHOLDER }}").append( + `` + ); + }); + }, + + 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( + `` + ); + $("#add1spectrum-analyzserMS-ionizationMethod-neg-{{ TAB_INDEX_PLACEHOLDER }}").append( + `` + ); + } else { + $("#add1spectrum-analyzserMS-ionizationMethod-pos-{{ TAB_INDEX_PLACEHOLDER }}").append( + `` + ); + $("#add1spectrum-analyzserMS-ionizationMethod-neg-{{ TAB_INDEX_PLACEHOLDER }}").append( + `` + ); + } + } + }); + }, + + populate_lcms_solvents: function(data) { + // load data from json + $.each(data.solvents, function () { + $("#add1spectrum-sample-lcmsSolvent-{{ TAB_INDEX_PLACEHOLDER }}").append( + `` + ); + }); + }, + + 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 + $("#containter-lcms-spectrum-preview-{{ TAB_INDEX_PLACEHOLDER }}").highcharts({ + chart: { + zoomType: "x", + spacingRight: 10, + spacingLeft: 10, + type: "scatter" + }, + title: { + text: "Spectrum Preview", + useHTML: true + }, + subtitle: { + text: ( + document.ontouchstart === undefined + ? "Select area" + : "Pinch the chart to zoom in" + ) + }, + xAxis: { + type: "number", + title: {text: "m/z"}, + min: spectrumMinPPM, + max: spectrumMaxPPM, + labels: { + formatter: function() { + return (Math.abs(this.value) + ""); + } + } + }, + yAxis: { + title: {text: "Relative Intensity (%)"}, + min: 0, + max: maxGraph + }, + tooltip: { + crosshairs: true, + formatter: function() { + var compo = ""; + return ( + "" + this.series.name + + "
m/z:" + Math.abs(this.x) + "" + + ";
Relative Intensity: " + this.y + + "%;
Annotation: " + localDataAnnot[ this.x] + + "" + ); + } + }, + legend: {enabled: false}, + plotOptions: {scatter: {}}, + series: [{ + name: "preview", + showInLegend: true, + color: "#f00", + lineColor: "#f00", + pointInterval: 10, + pointStart: 100, + lineWidth : 2, + marker: { + enabled: true, + radius: 2, + lineColor: "#f00" + }, + data: localData, + zIndex: 10 + }] + }); + }, + + //USED HERE + fulfillLCdata: function(jsonFileName) { + var self = this ; + var url = `{{ PF_URL_PLACEHOLDER }}/webapp/resources/json/lc-methods/${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(` + + `); + } + }); + }, + + //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( + '' + ); + $.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( + `` + ); + } else { + $("#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}").append( + `` + ); + } + } + }); + }); + } else if (self.is_ms2()) { + $("#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}").empty(); + $("#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}").append( + '' + ); + $.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( + `` + ); + } else { + $("#add1spectrum-chromatoLC-method-{{ TAB_INDEX_PLACEHOLDER }}").append( + `` + ); + } + } + }); + } + ); + } + // 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: "InChIKey", type: "text"}, + {data: "composition", renderer: lightgrayRenderer}, + {data: "concentration (µg/ml)", 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", + "InChIKey", + "composition", + "concentration (µg/ml)", + "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(); + $("#alertBoxSubmitSpectrum-{{ TAB_INDEX_PLACEHOLDER }}").html(` + + `); + return true; + }, + + //USED HERE + loadFomDataIntoJsonObjects: function() { + var self = this ; + // I - Spectrum type + self.isJsonSpectrumTypeComplete = false ; + if (self.isGC && self.is_ms()) { + self.jsonSpectrumType = "gc-ms" ; + } else if (self.isLC && self.is_ms()) { + self.jsonSpectrumType = "lc-ms" ; + } else if (self.isLC && self.is_ms2()) { + self.jsonSpectrumType = "lc-msms" ; + } else if (self.isGC && self.is_ms()) { + self.jsonSpectrumType = "ic-ms" ; + } else if (self.isLC && self.is_ms()) { + self.jsonSpectrumType = "ic-msms" ; + } + if (self.jsonSpectrumType != null && self.jsonSpectrumType != "") { + self.isJsonSpectrumTypeComplete = true; + } + + // II - Sample + self.isJsonSampleComplete = true; + self.isJsonRCCaddedComplete = true; + self.jsonSample = {}; + + switch($("#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 = ` + ` ; + } else if (!self.isJsonSampleComplete) { + alertMsg = ` + ` ; + } else if (!self.isJsonRCCaddedComplete) { + alertMsg = ` + `; + } else if (!self.isJsonChromatoComplete) { + alertMsg = ` + '; + } else if (!self.isJsonPeaksListComplete) { + alertMsg = ` + '; + } 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 + ` + + ` + } + } + } + // 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 = ` +
+ + + + + + + + + + + + + + + + + +
Chemical Name Monoisotopic Mass Formula Structure
+ ${name} +
${inchikey} + 		${data["exactMass"]}${data["formula"]} + ${name} + +
+ *: Generic Compounds (abstract "flat" compound without (+) or (-) center). + <` + "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, "" + valF + ""); + }); + } catch (e){} + formatedFormula = formatedFormula.replace("", ""); + $(elem).html(formatedFormula); + }); + $.each($(self.prefix+".compoundMass"), function(id, elem) { + var exactMass = parseFloat( $(elem).text()); + exactMass = roundNumber(exactMass,7) + $(elem).html(exactMass); + }); + + +
+ <` + "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"; + // ''+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(''+name+''); + else { + // delete + $(ctx().prefix+"img.mixRCCadd"+ctx().multiPickLine).remove(); + // add + $("#sample-bonus-display-{{ TAB_INDEX_PLACEHOLDER }}").append(''+name+''); + $(ctx().prefix+"img.mixRCCadd"+ctx().multiPickLine+"").mouseenter(function() { + $(this).removeClass("compoundSVGZoom"); + }).mouseleave(function() { + $(this).addClass("compoundSVGZoom"); + }); + } + $("#modalPickCompound-{{ TAB_INDEX_PLACEHOLDER }}").modal("hide"); + } + ` ; + $("#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 ("InChIKey" in this && this["InChIKey"]!= undefined && this["InChIKey"] != "") { + jsonRCC_ADDED.push(this["InChIKey"]); + } + }); + return jsonRCC_ADDED; + }, + + //USED HERE + getRCCADDEDConcentration: function() { + var self = this ; + jsonRCC_ADDED = []; + $.each(self.hot_RCC_ADDED.getData(), function(){ + var formatData = {}; + if ("InChIKey" in this && this["InChIKey"]!= undefined && this["InChIKey"] != "") { + jsonRCC_ADDED.push(this["concentration (µg/ml)"]); + } + }); + 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); diff -r b58b229c4cbf -r 7e3085fc60c1 src/common.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/src/common.js Wed Aug 30 14:21:18 2023 +0000 @@ -0,0 +1,304 @@ + +this.ctx = () => context; +var all_contexts = [] ; +var inchidata = {} ; +var all_mix_data = {} ; +var already_sent_data = {} ; + +function no_success(tab_index, inchi, data) { + console.log(`inchikey ${inchi} not found...`) ; + console.log(`disabling ${data} ...`) + disable_tab( + tab_index, + "red", + "This compound has not been found on peakforest" + ) ; +} + +function disable_tab(tab_index, color, title) { + var element = $(`#open_tab_${tab_index}`) ; + element.attr("disabled", "disabled").off("click"); + element.attr("onclick", null) ; + element.attr("title", title) ; + element.attr("data-toggle", null) ; + element.attr("href", null) ; + element.css("color", color) ; + element.css("cursor", "not-allowed") ; +} + +function successfull_send_to_pf(bundle, json, index) { + for (var i = 0 ; i < all_contexts.length ; i += 1) { + if (all_contexts[i] === null || all_contexts[i] === undefined) { + continue ; + } + if (all_contexts[i].inchikey == bundle["sample"]["inchikey"]) { + disable_tab( + all_contexts[i].tab_index, + "green", + "This compound has already been sent to peakforest" + ) + } + } + if (already_sent_data[index] == null) { + already_sent_data[index] = [] ; + } + json.forEach((id) => { + already_sent_data[index].push(id) + $("#send_buttons_div").prepend(` +
+
+ +
+
`) + }) +} + +function failed_send_to_pf(err, bundle) { + console.log(err) ; + $("#send_buttons_div").prepend(` +
+
+ +
+
`) +} + +function already_sent(bundle, index) { + return already_sent_data[index] != null ; +} + +function failed_already_sent(bundle, index) { + already_sent_data[index].forEach((id) => { + $("#send_buttons_div").prepend(` +
+
+ +
+
`) + }) ; +} + +function send_everything_to_peakforest(url, token) { + var bundles ; + if (context.is_mix()) { + bundles = [all_mix_data] ; + } else { + bundles = create_dataset_bundles() ; + } + bundles.forEach((bundle, index) => { + if (already_sent(bundle, index)) { + return failed_already_sent(bundle, index) ; + } + console.log(bundle) + $.ajax({ + type: "post", + url: `${url}/rest/v2/spectrum?token=${token}`, + data: JSON.stringify(bundle), + contentType: "application/json", + success: function(json) { + successfull_send_to_pf(bundle, json, index) + }, error: function(err) { + failed_send_to_pf(err, bundle) + } + }) + $.ajax({ + type: "post", + url: "/", + data: `{"index": ${index}, "object": ${JSON.stringify(bundle)}}`, + contentType: "application/json", + error: function(err) { + console.log(`Error: JSON will not be produced by the application.`) + } + }) + }) + // console.log(bundles) +} + +function create_dataset_bundles() { + var bundles = [] ; + var data ; + all_contexts.forEach((context, index) => { + if ((data = context.sent_json) === null) { + return ; + } + if (bundles.length === 0) { + // console.log("First metadata!") + return bundles.push(data) ; + } + if (merge_in_bundle(bundles, data)) { + // console.log("Merged!") + } else { + // console.log("New metadata!") + } + }) ; + return bundles ; +} + +function merge_in_bundle(bundles, data) { + for(var i = 0 ; i < bundles.length ; i += 1) { + if ( + identical(bundles[i]["sample"], data["sample"]) + && identical(bundles[i]["chromatography"], data["chromatography"]) + && identical(bundles[i]["analyzer"], data["analyzer"]) + && identical(bundles[i]["ionization_mode_positive"], data["ionization_mode_positive"]) + && identical(bundles[i]["ionization_mode_negative"], data["ionization_mode_negative"]) + && identical(bundles[i]["other_metadata"], data["other_metadata"]) + ) { + bundles[i]["peaklists"].push(data["peaklists"][0]) ; + return true ; + } else { + continue ; + console.log( + "sample: " + + identical(bundles[i]["sample"], data["sample"]) + ) + console.log( + "chromatography: " + + identical(bundles[i]["chromatography"], data["chromatography"]) + ) + console.log( + "analyzer: " + + identical(bundles[i]["analyzer"], data["analyzer"]) + ) + console.log( + "ionization_mode_positive: " + + identical(bundles[i]["ionization_mode_positive"], data["ionization_mode_positive"]) + ) + console.log( + "ionization_mode_negative: " + + identical(bundles[i]["ionization_mode_negative"], data["ionization_mode_negative"]) + ) + console.log( + "other_metadata: " + + identical(bundles[i]["other_metadata"], data["other_metadata"]) + ) + } + } + bundles.push(data) ; + return false ; +} + +function identical(left, right) { + if (typeof left !== typeof right) { + return false ; + } + if (left === null) { + return right === null ; + } + if (right === null) { + return left === null ; + } + switch (typeof left) { + case "array": + return identical_array(left, right) ; + break ; + case "object": + return identical_object(left, right) ; + break ; + default: + break ; + } + return (left === right) +} + +function identical_array(left, right) { + if (right.length !== left.length) { + return false ; + } + for(var i = 0 ; i < left.length ; i += 1) { + if (!identical(left[i], right[i])) { + return false ; + } + } + return true ; +} + +function identical_object(left, right) { + var left_keys ; + + if (!( + share_keys(left, right) + && share_keys(right, left) + )) { + return true ; + } + left_keys = Object.keys(left) ; + for (var i = 0 ; i < left_keys.length ; i += 1){ + if (!identical(left[left_keys[i]], right[left_keys[i]])) { + return false ; + } + } + return true ; +} + +function share_keys(left, right) { + var left_keys ; + var right_keys ; + + left_keys = Object.keys(left) ; + right_keys = Object.keys(right) ; + for(var i = 0 ; i < left_keys.length ; i += 1) { + if (!right_keys.includes(left_keys[i])) { + return false ; + } + } + return true ; +} + +var set_inchi_data = function(data, tab_index) { + inchidata[data.inchikey] = data ; + $(`#add1spectrum-sample-inchi-${tab_index}`).val(data.inchi); + $(`#add1spectrum-sample-inchi-${tab_index}`).change(); + $(`#add1spectrum-sample-commonName-${tab_index}`).val(data.name); + $(`#add1spectrum-sample-commonName-${tab_index}`).change(); + $(`#sample-bonus-display-${tab_index}`).html( + `${data.name}` + ); +} + +var lightgrayRenderer = function(instance, td, row, col, prop, value, cellProperties) { + Handsontable.renderers.TextRenderer.apply(this, arguments); + td.style.backgroundColor = "#EEE"; +} diff -r b58b229c4cbf -r 7e3085fc60c1 src/compound-mix.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/src/compound-mix.html Wed Aug 30 14:21:18 2023 +0000 @@ -0,0 +1,36 @@ +
+
+
+
+
+ +
+
+
+ + Precursor ion (M/Z) + + + +
+
+
+
+
+
\ No newline at end of file diff -r b58b229c4cbf -r 7e3085fc60c1 src/compound-ref.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/src/compound-ref.html Wed Aug 30 14:21:18 2023 +0000 @@ -0,0 +1,661 @@ +
+
+
+
+

+ + Spectrum Type + +

+
+
+
+ + + +
+
+
+ + + + + + +
+ + + +
+ + diff -r b58b229c4cbf -r 7e3085fc60c1 src/meta-compound-mix.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/src/meta-compound-mix.html Wed Aug 30 14:21:18 2023 +0000 @@ -0,0 +1,1231 @@ + + + + + + + + PeakForest MetaboHub + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ +
+
+
+
+
+
+

+ + Spectrum Type + + +

+
+
+
+ + + +
+
+
+ + + + + + + + + + + + + +
+
+
+
+ + +
+ + +
+ + + + {{ EMBED_JS }} + + + \ No newline at end of file diff -r b58b229c4cbf -r 7e3085fc60c1 src/meta-compound-ref.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/src/meta-compound-ref.html Wed Aug 30 14:21:18 2023 +0000 @@ -0,0 +1,112 @@ + + + + + + + + PeakForest MetaboHub + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ +
+
+ +
+ {{ ADD_SPECTRUM_FORM }} +
+
+
+ + +
+ + +
+ + + + + {{ EMBED_JS }} + + + \ No newline at end of file diff -r b58b229c4cbf -r 7e3085fc60c1 src/tab_list.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/src/tab_list.html Wed Aug 30 14:21:18 2023 +0000 @@ -0,0 +1,14 @@ +
  • + + + {{ COMPOUND_NAME_PLACEHOLDER }} + +
    • diff -r b58b229c4cbf -r 7e3085fc60c1 tab_list.html --- a/tab_list.html Fri Mar 03 14:10:24 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,14 +0,0 @@ -
  • - - - {{ COMPOUND_NAME_PLACEHOLDER }} - -