| Chemical Name | +Monoisotopic Mass | +Formula | +Structure | +
|---|---|---|---|
|
+ ${name}
+ ${inchikey} + |
+ ${data["exactMass"]} | +${data["formula"]} | +
+ 
+
+ |
+
| Chemical Name | +Monoisotopic Mass | +Formula | +Structure | +
|---|---|---|---|
|
+ ${name}
+ ${inchikey} + |
+ ${data["exactMass"]} | +${data["formula"]} | +
+
+
+ |
+
'
+ 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('');
+ else {
+ // delete
+ $(ctx().prefix+"img.mixRCCadd"+ctx().multiPickLine).remove();
+ // add
+ $("#sample-bonus-display-{{ TAB_INDEX_PLACEHOLDER }}").append('');
+ $(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 000000000000 -r b58b229c4cbf common.js
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/common.js Fri Mar 03 14:10:24 2023 +0000
@@ -0,0 +1,195 @@
+
+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(
+ `
`
+ );
+}
+
+var lightgrayRenderer = function(instance, td, row, col, prop, value, cellProperties) {
+ Handsontable.renderers.TextRenderer.apply(this, arguments);
+ td.style.backgroundColor = "#EEE";
+}
diff -r 000000000000 -r b58b229c4cbf compound-mix.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/compound-mix.html Fri Mar 03 14:10:24 2023 +0000
@@ -0,0 +1,36 @@
+ 