refresh of progress is synchronized

frontend-js/src/main/css/global.css

@@ -643,7 +643,8 @@ h1 {
 .minerva-plugin-tab .minerva-menu-row button,
 .minerva-edit-project-dialog .minerva-menu-row button,
 .minerva-users-tab .minerva-menu-row button,
-.minerva-genome-tab .minerva-menu-row button {
+.minerva-genome-tab .minerva-menu-row button,
+.minerva-edit-genome-dialog .minerva-menu-row button {
     margin: 5px;
 }
 
@@ -1104,6 +1105,7 @@ input[type=file] {
     background: #f5f5f5;
     cursor: pointer;
 }
+
 #minervaAppDiv table.dataTable.hover tbody tr:hover,
 #minervaAppDiv table.dataTable.display tbody tr:hover,
 #minervaAppDiv table.dataTable.display tbody tr:hover > .sorting_1,

frontend-js/src/main/js/gui/admin/EditGenomeDialog.js

@@ -32,6 +32,7 @@ function EditGenomeDialog(params) {
   self.setReferenceGenome(params.referenceGenome);
 
   $(self.getElement()).css({overflow: "hidden"});
+  $(self.getElement()).addClass("minerva-edit-genome-dialog");
 
   self.createGui();
   self.registerListenerType("onSave");
@@ -240,6 +241,18 @@ EditGenomeDialog.prototype.createGeneMappingTabContent = function () {
 
   menuRow.appendChild(addGeneMappingButton);
 
+  var refreshButton = Functions.createElement({
+    type: "button",
+    name: "saveGenome",
+    content: ' REFRESH',
+    onclick: function () {
+      return self.refresh();
+    },
+    xss: false
+  });
+
+  menuRow.appendChild(refreshButton);
+
   return result;
 };
 
@@ -259,7 +272,7 @@ EditGenomeDialog.prototype.onSaveClicked = function () {
     genome.setVersion(self.getSelectedVersion());
     return self.getServerConnector().addReferenceGenome(genome).then(function () {
       return self.callListeners("onSave");
-    }).catch(function(e){
+    }).catch(function (e) {
       if (e instanceof ObjectExistsError) {
         GuiConnector.alert("Reference genome already exists");
       } else {
@@ -433,7 +446,7 @@ EditGenomeDialog.prototype.geneMappingToTableRow = function (geneMapping) {
   var row = [];
   row[0] = geneMapping.getName();
   row[1] = geneMapping.getSourceUrl();
-  row[2] = geneMapping.getProgress();
+  row[2] = geneMapping.getProgressStatus();
   row[3] = "<button name='removeMapping' data='" + geneMapping.getId() + "'><i class='fa fa-trash-o' style='font-size:17px'></button>";
   return row;
 };
@@ -468,34 +481,40 @@ EditGenomeDialog.prototype.init = function () {
  */
 EditGenomeDialog.prototype.refresh = function () {
   var self = this;
-
-  var genome = self.getReferenceGenome();
-
-  var dataTable = $("[name=detailsTable]", self.getElement()).DataTable();
-  var data = [];
-
-  data.push(['Organism', Functions.createElement({type: "select", name: "genomeOrganismSelect"}).outerHTML]);
-  data.push(['Type', Functions.createElement({type: "select", name: "genomeTypeSelect"}).outerHTML]);
-  data.push(['Version', Functions.createElement({type: "select", name: "genomeVersionSelect"}).outerHTML]);
-  data.push(['Source url', Functions.createElement({type: "input", name: "genomeSourceUrl"}).outerHTML]);
-  data.push(['Local url', Functions.createElement({type: "input", name: "genomeLocalUrl"}).outerHTML]);
-  data.push(['Progress', Functions.createElement({type: "input", name: "genomeProgress"}).outerHTML]);
-
-  dataTable.clear().rows.add(data).draw();
-
-  dataTable = $("[name=geneMappingTable]", self.getElement()).DataTable();
-  data = [];
-  var page = dataTable.page();
-
-  for (var i = 0; i < genome.getGeneMappings().length; i++) {
-    var geneMapping = genome.getGeneMappings()[i];
-    var rowData = self.geneMappingToTableRow(geneMapping);
-    data.push(rowData);
+  var refreshReferenceGenomePromise = Promise.resolve();
+  if (!self.isNew()) {
+    refreshReferenceGenomePromise = self.getServerConnector().getReferenceGenome({genomeId: self.getReferenceGenome().getId()}).then(function (genome) {
+      self.setReferenceGenome(genome);
+    });
   }
-  //it should be simplified, but I couldn't make it work
-  dataTable.clear().rows.add(data).page(page).draw(false).page(page).draw(false);
+  return refreshReferenceGenomePromise.then(function () {
+    var genome = self.getReferenceGenome();
+    var dataTable = $("[name=detailsTable]", self.getElement()).DataTable();
+    var data = [];
+
+    data.push(['Organism', Functions.createElement({type: "select", name: "genomeOrganismSelect"}).outerHTML]);
+    data.push(['Type', Functions.createElement({type: "select", name: "genomeTypeSelect"}).outerHTML]);
+    data.push(['Version', Functions.createElement({type: "select", name: "genomeVersionSelect"}).outerHTML]);
+    data.push(['Source url', Functions.createElement({type: "input", name: "genomeSourceUrl"}).outerHTML]);
+    data.push(['Local url', Functions.createElement({type: "input", name: "genomeLocalUrl"}).outerHTML]);
+    data.push(['Progress', Functions.createElement({type: "input", name: "genomeProgress"}).outerHTML]);
+
+    dataTable.clear().rows.add(data).draw();
+
+    dataTable = $("[name=geneMappingTable]", self.getElement()).DataTable();
+    data = [];
+    var page = dataTable.page();
+
+    for (var i = 0; i < genome.getGeneMappings().length; i++) {
+      var geneMapping = genome.getGeneMappings()[i];
+      var rowData = self.geneMappingToTableRow(geneMapping);
+      data.push(rowData);
+    }
+    //it should be simplified, but I couldn't make it work
+    dataTable.clear().rows.add(data).page(page).draw(false).page(page).draw(false);
 
-  return self._fillOrganismSelect(genome);
+    return self._fillOrganismSelect(genome);
+  });
 };
 
 /**
@@ -522,6 +541,7 @@ EditGenomeDialog.prototype.destroy = function () {
 
 /**
  *
+ * @return {Promise}
  */
 EditGenomeDialog.prototype.open = function () {
   var self = this;
@@ -541,6 +561,8 @@ EditGenomeDialog.prototype.open = function () {
     });
   }
   $(div).dialog("open");
+
+  return self.refresh();
 };
 
 /**

frontend-js/src/main/js/gui/admin/GenomeAdminPanel.js

@@ -297,11 +297,9 @@ GenomeAdminPanel.prototype.showEditDialog = function (id) {
     }
     return self.getDialog(referenceGenome);
   }).then(function (dialog) {
-    dialog.open();
+    return dialog.open();
+  }).finally(function () {
     GuiConnector.hideProcessing();
-  }).catch(function (error) {
-    GuiConnector.hideProcessing();
-    return Promise.reject(error);
   });
 };
 
@@ -314,11 +312,9 @@ GenomeAdminPanel.prototype.onAddClicked = function () {
   GuiConnector.showProcessing();
   var referenceGenome = new ReferenceGenome();
   return self.getDialog(referenceGenome).then(function (dialog) {
-    dialog.open();
-    GuiConnector.hideProcessing();
-  }).catch(function (error) {
+    return dialog.open();
+  }).finally(function () {
     GuiConnector.hideProcessing();
-    return Promise.reject(error);
   });
 };
 

frontend-js/src/main/js/map/data/ReferenceGenomeGeneMapping.js

@@ -84,6 +84,27 @@ ReferenceGenomeGeneMapping.prototype.getSourceUrl = function () {
   return this._sourceUrl;
 };
 
+/**
+ *
+ * @returns {string}
+ */
+ReferenceGenomeGeneMapping.prototype.getProgressStatus = function () {
+  var progress = this.getProgress();
+  if (progress === 100) {
+    if (this.getLocalUrl() !== undefined) {
+      return "READY";
+    } else {
+      return "ERROR";
+    }
+  } else {
+    if (progress === undefined) {
+      return "N/A";
+    } else {
+      return progress.toFixed(2) + ' %';
+    }
+  }
+};
+
 /**
  *
  * @param {string} url