Merge branch...

Merge branch '728-gene-mapping-upload-progress-counter-freezes-at-0-until-upload-finishes' into 'master'

Resolve "Gene mapping upload progress counter freezes at 0 until upload finishes"

Closes #728

See merge request !681

annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/AbstractReferenceGenomeConnector.java

@@ -159,8 +159,9 @@ public abstract class AbstractReferenceGenomeConnector extends CachableInterface
 		 *          {@link #referenceGenome}
 		 * @param name
 		 *          {@link #name}
+		 * @throws ReferenceGenomeConnectorException 
 		 */
-		private DownloadGeneMappingGenomeVersionTask(ReferenceGenome referenceGenome, String name, String url, IProgressUpdater updater) {
+		private DownloadGeneMappingGenomeVersionTask(ReferenceGenome referenceGenome, String name, String url, IProgressUpdater updater) throws ReferenceGenomeConnectorException {
 			this.url = url;
 			this.referenceGenome = referenceGenome;
 			this.name = name;
@@ -173,36 +174,36 @@ public abstract class AbstractReferenceGenomeConnector extends CachableInterface
 					}
 				};
 			}
+
 		}
 
 		@Override
 		public Void call() throws Exception {
 			getDbUtils().createSessionForCurrentThread();
 			try {
-				ReferenceGenome referenceGenome = getReferenceGenomeDao().getById(this.referenceGenome.getId());
-				for (ReferenceGenomeGeneMapping mapping : referenceGenome.getGeneMapping()) {
-					if (mapping.getName().equals(name)) {
-						throw new ReferenceGenomeConnectorException("Gene mapping with name: \"" + name + "\" already exists.");
-					}
-				}
-				if (!url.toLowerCase().endsWith("bb")) {
-					throw new ReferenceGenomeConnectorException("Only big bed format files are supported but found: \"" + url + "\".");
-				}
+	            ReferenceGenome referenceGenome = getReferenceGenomeDao().getById(this.referenceGenome.getId());
+	            for (ReferenceGenomeGeneMapping mapping : referenceGenome.getGeneMapping()) {
+	                if (mapping.getName().equals(name)) {
+	                    throw new ReferenceGenomeConnectorException("Gene mapping with name: \"" + name + "\" already exists.");
+	                }
+	            }
+	            if (!url.toLowerCase().endsWith("bb")) {
+	                throw new ReferenceGenomeConnectorException("Only big bed format files are supported but found: \"" + url + "\".");
+	            }
 				ReferenceGenomeGeneMapping mapping = new ReferenceGenomeGeneMapping();
-				mapping.setReferenceGenome(referenceGenome);
 				mapping.setName(name);
 				mapping.setSourceUrl(url);
 				referenceGenome.addReferenceGenomeGeneMapping(mapping);
-				getReferenceGenomeGeneMappingDao().add(mapping);
-				getReferenceGenomeGeneMappingDao().flush();
+				getReferenceGenomeDao().update(referenceGenome);
 				getReferenceGenomeDao().commit();
+                getReferenceGenomeDao().flush();
 				getBigFileCache().downloadFile(url, false, new IProgressUpdater() {
 					@Override
 					public void setProgress(double progress) {
 						if (updater != null) {
 							updater.setProgress(progress);
 						}
-						// we have to get the object because it's in separate thred
+						// we have to get the object because it's in separate thread
 						ReferenceGenomeGeneMapping temp = getReferenceGenomeGeneMappingDao().getById(mapping.getId());
 						temp.setDownloadProgress(progress);
 						getReferenceGenomeGeneMappingDao().update(temp);

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/ServerConnector.js

@@ -38,6 +38,7 @@ var SbmlParameter = require('./map/data/SbmlParameter');
 var SecurityError = require('./SecurityError');
 var SessionData = require('./SessionData');
 var User = require('./map/data/User');
+var ValidationError = require('./ValidationError');
 var PrivilegeType = require('./map/data/PrivilegeType');
 
 var GuiConnector = require('./GuiConnector');
@@ -2433,7 +2434,14 @@ ServerConnector.addGeneMapping = function (params) {
     name: params.mappingName,
     url: params.mappingUrl
   };
-  return self.sendPostRequest(self.getReferenceGenomeGeneMappingsUrl(params), data);
+  return self.sendPostRequest(self.getReferenceGenomeGeneMappingsUrl(params), data).catch(function (e) {
+    if (e instanceof NetworkError && e.statusCode === HttpStatus.BAD_REQUEST) {
+      var content = JSON.parse(e.content);
+      throw new ValidationError(content.reason);
+    } else {
+      return self.processNetworkError(e);
+    }
+  });
 };
 /**
  *

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();
 };
 
 /**
@@ -621,7 +643,7 @@ EditGenomeDialog.prototype.openAddGeneMapping = function () {
           return self.refresh();
         }).then(function () {
           $(dialog).dialog('destroy').remove();
-        });
+        }).catch(GuiConnector.alert);
       },
       'Cancel': function () {
         $(this).dialog('destroy').remove();

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

rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeRestImpl.java

@@ -244,7 +244,7 @@ public class ReferenceGenomeRestImpl extends BaseRestImpl {
     try {
       referenceGenomeService.addReferenceGenome(genomeType, organism, version, url);
       return okStatus();
-    } catch(ReferenceGenomeExistsException e) {
+    } catch (ReferenceGenomeExistsException e) {
       throw new ObjectExistsException(e);
     } catch (URISyntaxException e) {
       throw new QueryException("Problem wih given uri", e);
@@ -262,6 +262,10 @@ public class ReferenceGenomeRestImpl extends BaseRestImpl {
       ReferenceGenome genome = referenceGenomeService.getReferenceGenomeById(id, token);
       String name = getFirstValue(formData.get("name"));
       String url = getFirstValue(formData.get("url"));
+      if (!url.toLowerCase().endsWith("bb")) {
+        throw new QueryException("Only big bed format files are supported but found: \"" + url + "\".");
+      }
+
       referenceGenomeService.addReferenceGenomeGeneMapping(genome, name, url);
       return okStatus();
     } catch (URISyntaxException e) {