Merge branch 'export' into 'master'

export to json and tsv

See merge request !3

src/js/index.js

@@ -112,6 +112,11 @@ function getContainerClass() {
 function initMainContainer(){
     const container = $(`<div class="${getContainerClass()}"></div>`).appendTo(pluginContainer);
     container.append(`
+    <div class="modal fade modal-container" role="dialog">
+            <div class="modal-dialog">
+                <div class="modal-content"></div>
+            </div>
+    </div>
     <div class="panel panel-default gsea-pw-loading">
         <div class="panel-body">  
             <i class="fa fa-circle-o-notch fa-spin"></i> Obtaining pathway-gene mapping from the map
@@ -301,6 +306,14 @@ function calculateGSEA() {
             });
         });
 
+        const dataForExport = {
+            overlays: globals.overlayNames,
+            mapProjectId: minervaProxy.project.data.getProjectId(),
+            mapApi: ServerConnector.getApiBaseUrl(),
+            data: []
+        };
+
+
         Object.keys(globals.ModelPathway).forEach(modelId => {
 
             let pVals = Object.keys(globals.ModelPathway[modelId])
@@ -335,6 +348,7 @@ function calculateGSEA() {
             const $table = $mapResultsPanel.find('table');
 
 
+            const exportVals = [];
 
             pVals.sort(function (a, b) {
                 return a.adjustedPVal - b.adjustedPVal;
@@ -348,6 +362,7 @@ function calculateGSEA() {
                 const pwName = p.pw.bioEntities[0].getName();
 
                 $table.append(`<tr><td class="first-column">${pValText}</td><td>${pwName}</td></tr>`);
+                exportVals.push({enrichedArea: pwName, adjustedPVal: p.adjustedPVal});
 
                 p.pw.bioEntities.forEach(e => {
                     highlightPathways.push({
@@ -365,8 +380,13 @@ function calculateGSEA() {
                 });
 
             });
+
+            dataForExport.data.push({mapName: mapName, areas: exportVals})
+
         });
 
+        addExport(pluginContainer.find('.gsea-results'), dataForExport);
+
         minervaProxy.project.map.showBioEntity(highlightPathways);
     });
 
@@ -457,4 +477,105 @@ function calculateGSEA() {
     //     gsea_html += '</table>';
     //     pluginContainer.find('.panel-events .panel-body').html(gsea_html);
     // });
+}
+
+function addExport($container, data){
+    $container.append($(`<div class="row">
+                            <div class="col-sm-12">
+                                <button type="button" class="btn-calc btn btn-success btn-default btn-block">Export</button>            
+                            </div>
+                        </div>`));
+
+    $container.find("button").on("click", () => exportData(data, $container));
+
+}
+
+const exportData = function (data, $container) {
+    openModal({
+        body:
+            '<button type="button" class="btn btn-block ceButtonExportJSON">JSON</button>' +
+            '<button type="button" class="btn btn-block ceButtonExportTSV">TSV</button>'
+    });
+
+    pluginContainer.find('.ceButtonExportJSON').on('click', () => exportToFormat('json', data, $container));
+    pluginContainer.find('.ceButtonExportTSV').on('click', () => exportToFormat('tsv', data, $container));
+};
+
+const exportToFormat = function (format, data, $container) {
+    let exportString;
+    if (format === "json") exportString = exportToJson(data);
+    if (format === "tsv") exportString = exportToTsv(data);
+
+    let fileName = 'export.' + format;
+    let blob = new Blob([exportString], { type: 'text/' + format + ';charset=utf-8;' });
+    if (navigator.msSaveBlob) { // IE 10+
+        navigator.msSaveBlob(blob, fileName);
+    } else {
+        let link = document.createElement("a");
+        if (link.download !== undefined) { // feature detection
+            // Browsers that support HTML5 download attribute
+            const url = URL.createObjectURL(blob);
+            link.setAttribute("href", url);
+            link.setAttribute("download", fileName);
+            link.style.visibility = 'hidden';
+            document.body.appendChild(link);
+            link.click();
+            document.body.removeChild(link);
+        }
+    }
+
+    closeModal();
+};
+
+function closeModal() {
+    pluginContainer.find(".modal-container").modal("hide");
+}
+
+function openModal(params) {
+
+    let modal = pluginContainer.find(".modal-container");
+    let modalContent = modal.find(".modal-content");
+    modalContent.empty();
+    let modalContentClass = "modal-content";
+    if ("modalClass" in params) modalContentClass += " " + params.modalClass;
+    modalContent.attr("class", modalContentClass);
+    if ("header" in params) {
+        let header = pluginContainer.find('<div class="modal-header panel-heading"></div>').appendTo(modalContent);
+        header.append('<button type="button" class="close">&times;</button>');
+        header.append('<h4>' + params.header + '</h4>');
+
+    }
+    if ("body" in params) {
+        let body = $('<div class="modal-body"></div>').appendTo(modalContent);
+        body.append(params.body);
+    }
+    // '           <div class="modal-footer">' +
+    // '               <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>' +
+    // '           </div>' +
+
+    modal.modal("show");
+}
+function exportToTsv(data) {
+
+    let res = `# overlays: ${data.overlays}; mainMapProjectName: ${data.mainMapProjectName}; mainMapProjectId: ${data.mainMapProjectId}; mainMapApi: ${data.mainMapApi} ,mapProjectName: ${data.mapProjectName};  mapProjectId: ${data.mapProjectId}; mapApi: ${data.mapApi}\n`;
+
+    for (let i = 0; i < data.data.length; ++i) {
+        res += `${data.data[i].mapName}\n`;
+        res += '"p-val (adj)"\t"Enriched area"\n';
+        const areas = data.data[i].areas;
+        for (let j = 0; j < areas.length; ++j) {
+            res += `"${areas[j].enrichedArea}"\t"${areas[j].adjustedPVal}"\n`
+        }
+        res += '\n'
+    }
+    return res;
+
+
+}
+
+function exportToJson(data) {
+
+    return JSON.stringify(data, null, 2);
+
+
 }
\ No newline at end of file