merge 13.1.3 and master

CHANGELOG

 minerva (14.0.0~alpha.1) unstable; urgency=low
   * Feature removal: support for tomcat7 removed (#828)
   * Small improvement: debian package can be installed on debian:buster (#879)
-  * Bug fix: REST API bioEntities:search method didn't limit results to the 
+  * Bug fix: REST API bioEntities:search method didn't limit results to the
     submodel id (#860)
   * Bug fix: Empty Overlay colours were not preserved during export to
     CellDesigner (#714)
-  * Bug fix: some project couldn't be accessed due to problem with migration of 
+  * Bug fix: some project couldn't be accessed due to problem with migration of
     reaction with unknown boolean operator (#880)
   * Bug fix: problem with unloading plugin is properly handled (#884)
-  * Bug fix: upload of invalid plugin doesn't add it to plugin tab and list of 
+  * Bug fix: upload of invalid plugin doesn't add it to plugin tab and list of
     loaded plugins (#885)
   * Bug fix: link to molart was brokwn (#886)
   * Bug fix: context menu visualization fixed
@@ -17,16 +17,16 @@ minerva (14.0.0~alpha.1) unstable; urgency=low
  -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 13 Aug 2019 21:00:00 +0200
 
 minerva (14.0.0~alpha.0) unstable; urgency=low
-  * Feature: security layer redesigned - privilege types and scope changed 
+  * Feature: security layer redesigned - privilege types and scope changed
     (#636, #624)
   * Feature: log4j is replaced with log4j2 logging mechanism (#291)
   * Feature: database installed via debian package is done via dbconfig-commons
     (#469)
   * Feature: Replaced connection pool manager C3P0 with better maintained
-    Hikari - restart of postgresql database doesn't require restart of tomcat 
+    Hikari - restart of postgresql database doesn't require restart of tomcat
     (#564)
   * Feature removal: BioCompendium annotator removed (#32)
-  * Small improvement: anonymous login is no longer required - each API query 
+  * Small improvement: anonymous login is no longer required - each API query
     outside session is authorized with anonymous user privileges (#629)
   * Small improvement: bcrypt is used for password encryption (#387)
   * Small improvement: caching is active by default for new users when
@@ -34,14 +34,14 @@ minerva (14.0.0~alpha.0) unstable; urgency=low
   * Small improvement: when removing overlay in admin panel there is a
     confirmation dialog (#696)
   * Small improvement: overlay name is obligatory (#698)
-  * Small improvement: list of projects in admin panel contains creation date 
+  * Small improvement: list of projects in admin panel contains creation date
     (#447)
   * Small improvement: links in list of publications open in new tab (#447)
   * Small improvement: target gene in search panel contains also information
     about type of database that identifies the target (#66)
-  * Small improvement: redundant 'references' field in gene variants data 
+  * Small improvement: redundant 'references' field in gene variants data
     overlay is now deprecated (#850)
-  * Small improvement: information about deprecated columns in data overlay is 
+  * Small improvement: information about deprecated columns in data overlay is
     visible in overlay list (#838)
   * Small improvement: publication list is resizeable (#740)
   * Small improvement: user list on project edit dialog is sortable (#808)
@@ -60,6 +60,21 @@ minerva (14.0.0~alpha.0) unstable; urgency=low
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 09 Aug 2019 10:00:00 +0200
 
+minerva (13.1.4) stable; urgency=medium
+  * Bug fix:search by drugs didn't check synonyms in chembl database
+
+ -- Piotr Gawron <piotr.gawron@uni.lu> Wed,  21 Aug 2019 17:00:00 +0200
+
+minerva (13.1.3) stable; urgency=medium
+  * Bug fix: refreshing list of projects or list of users doesn't change active
+    page (#870)
+  * Bug fix: submap list must be selected to export from every submap (#874)
+  * Bug fix: export map as image properly uses bottom limit (#875)
+  * Bug fix: reaction info window wasn't closed on CLEAR (#876)
+  * Bug fix: name of the uploaded file is displayed when adding overlay (#849)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu> Wed,  14 Aug 2019 17:00:00 +0200
+
 minerva (13.1.2) stable; urgency=medium
   * Bug fix: Information about problematic zip file is more specific (#865)
   * Bug fix: Url didn't contain list of opened plugins and they weren't reload
@@ -77,7 +92,7 @@ minerva (13.1.1) stable; urgency=medium
   * Bug fix: user wasn't logged out in all tabs when the log out event appeard
     in only one of them (#847)
 
- -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 2 Jul 2019 19:00:00 +0200
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Tue,  2 Jul 2019 19:00:00 +0200
 
 minerva (13.1.0) stable; urgency=medium
   * Feature: annotators are more flexible - you can define set of input and

annotation/src/main/java/lcsb/mapviewer/annotation/services/ChEMBLParser.java

@@ -52,6 +52,12 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
    * Url that access data of drug identified by name.
    */
   private static final String DRUG_NAME_API_URL = "https://www.ebi.ac.uk/chembl/api/data/molecule?pref_name__exact=";
+
+  /**
+   * Url that access data of drug identified by name.
+   */
+  private static final String DRUG_SYNONYM_API_URL = "https://www.ebi.ac.uk/chembl/api/data/molecule?molecule_synonyms__molecule_synonym__iexact=";
+
   /**
    * Url that access target by identifier.
    */
@@ -324,29 +330,22 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
       String page = getWebPageContent(accessUrl);
 
       Document document = XmlParser.getXmlDocumentFromString(page);
-      Node response = XmlParser.getNode("response", document.getChildNodes());
-      Node molecules = XmlParser.getNode("molecules", response.getChildNodes());
-
-      NodeList list = molecules.getChildNodes();
-
-      for (int i = 0; i < list.getLength(); i++) {
-        Node node = list.item(i);
-        if (node.getNodeType() == Node.ELEMENT_NODE) {
-          if (node.getNodeName().equalsIgnoreCase("molecule")) {
-            if (drug == null) {
-              drug = parseDrug(node);
-            } else {
-              logger.warn("More drugs than one found for query: " + query);
-            }
-          }
-        }
+      List<Drug> drugs = extractDrugsFromDocument(document);
+      if (drugs.size()==0) {
+        accessUrl = DRUG_SYNONYM_API_URL + name;
+        page = getWebPageContent(accessUrl);
+        document = XmlParser.getXmlDocumentFromString(page);
+        drugs = extractDrugsFromDocument(document);
+      }
+      if (drugs.size()>1) {
+        logger.warn("More drugs than one found for query: " + query);
       }
 
-      if (drug == null) {
+      if (drugs.size() == 0) {
         return null;
       }
-      setCacheValue(query, getDrugSerializer().objectToString(drug));
-      return drug;
+      setCacheValue(query, getDrugSerializer().objectToString(drugs.get(0)));
+      return drugs.get(0);
     } catch (IOException e) {
       throw new DrugSearchException("Problem with accessing CHEMBL database", e);
     } catch (InvalidXmlSchemaException e) {
@@ -354,6 +353,24 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
     }
   }
 
+  private List<Drug> extractDrugsFromDocument(Document document) throws DrugSearchException {
+    List<Drug> result = new ArrayList<>();
+    Node response = XmlParser.getNode("response", document.getChildNodes());
+    Node molecules = XmlParser.getNode("molecules", response.getChildNodes());
+
+    NodeList list = molecules.getChildNodes();
+
+    for (int i = 0; i < list.getLength(); i++) {
+      Node node = list.item(i);
+      if (node.getNodeType() == Node.ELEMENT_NODE) {
+        if (node.getNodeName().equalsIgnoreCase("molecule")) {
+          result.add(parseDrug(node));
+        }
+      }
+    }
+    return result;
+  }
+
   @Override
   public List<Drug> getDrugListByTarget(MiriamData target, Collection<MiriamData> organisms)
       throws DrugSearchException {

annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java

@@ -877,4 +877,16 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
     }
   }
 
+  @Test
+  public void testFindDrugBryBrandName() throws Exception {
+    try {
+      Drug drug = chemblParser.findDrug("picato");
+      assertNotNull(drug);
+      assertEquals("CHEMBL1863513", drug.getSources().get(0).getResource());
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
 }

frontend-js/src/main/js/gui/AddOverlayDialog.js

@@ -95,9 +95,7 @@ AddOverlayDialog.prototype.createGui = function () {
     name: "overlay-file"
   });
   fileInput.addEventListener("change", function () {
-    return self.processFile(fileInput.files[0]).then(function () {
-      $(fileInput).val("");
-    }).catch(GuiConnector.alert);
+    return self.processFile(fileInput.files[0]).catch(GuiConnector.alert);
   }, false);
   content.appendChild(fileInput);
   content.appendChild(guiUtils.createNewLine());
@@ -294,9 +292,10 @@ AddOverlayDialog.prototype.open = function () {
           return self.addOverlay().then(function (result) {
             $(dialog).dialog("close");
             return result;
-          }, function (error) {
+          }).catch(function (error) {
             GuiConnector.hideProcessing();
             if (error instanceof NetworkError && error.statusCode === HttpStatus.BAD_REQUEST) {
+              $("[name='overlay-file']", self.getElement()).val("");
               var errorMessage = JSON.parse(error.content);
               GuiConnector.alert("Problematic input: <br/>" + errorMessage.reason);
             } else if (error instanceof SecurityError) {

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

@@ -346,7 +346,9 @@ MapsAdminPanel.prototype.addUpdateListener = function (project) {
         var data = row.data();
         if (data[0].indexOf(">" + project.getProjectId() + "<") >= 0) {
           self.projectToTableRow(project, data, user);
+          var page = dataTable.page();
           row.data(data).draw();
+          dataTable.page(page);
         }
       }
     });

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

@@ -303,11 +303,13 @@ UsersAdminPanel.prototype.addUpdateListener = function (user, dataTableRow) {
   var listener = function () {
     var login = Functions.escapeSelector(user.getLogin());
     self.userToTableRow(user, dataTableRow);
-    var row = $($("[name='usersTable']", self.getElement())[0]).DataTable().row("#" + login);
+    var dataTable =$("[name='usersTable']", self.getElement()).DataTable();
+    var row = dataTable.row("#" + login);
     if (row.length > 0) {
+      var page = dataTable.page();
       row.data(dataTableRow).draw();
+      dataTable.page(page);
     }
-
   };
   listener.listenerName = listenerName;
   user.addListener("onreload", listener);

frontend-js/src/main/js/gui/export/AbstractExportPanel.js

@@ -223,7 +223,7 @@ AbstractExportPanel.prototype._createSelectSubmapDiv = function (models) {
     var id = model.getId();
     var row = Functions.createElement({
       type: "li",
-      content: "<div class=\"checkbox\"><label> <input type=\"checkbox\" name=\"" + name + "\" value=\"" + id + "\" />" + name + "</label></div>",
+      content: "<div class=\"checkbox\"><label> <input type=\"checkbox\" name=\"" + name + "\" value=\"" + id + "\" checked/>" + name + "</label></div>",
       xss: false
     });
     choicesContainer.appendChild(row);

frontend-js/src/main/js/gui/export/ElementExportPanel.js

@@ -95,7 +95,7 @@ ElementExportPanel.prototype.createResponseString = function () {
     var promises = [];
     for (var i = 0; i < models.length; i++) {
       var model = models[i];
-      if (submapIds.length === 0 || $.inArray(model.getId(), submapIds) >= 0) {
+      if ($.inArray(model.getId(), submapIds) >= 0) {
         promises.push(model.getAliases({
           type: types,
           complete: true,

frontend-js/src/main/js/gui/export/NetworkExportPanel.js

@@ -147,10 +147,8 @@ function matchReaction(reaction, elementIds, reactionTypes, submapIds) {
   if ($.inArray(reaction.getType(), reactionTypes) === -1) {
     return false;
   }
-  if (submapIds.length > 0) {
-    if ($.inArray(reaction.getModelId(), submapIds) === -1) {
-      return false;
-    }
+  if ($.inArray(reaction.getModelId(), submapIds) === -1) {
+    return false;
   }
   var count = 0;
   reaction.getElements().forEach(function (element) {

frontend-js/src/main/js/map/AbstractCustomMap.js

@@ -207,7 +207,7 @@ AbstractCustomMap.prototype.registerMapClickEvents = function () {
     var y1 = Math.max(0, topLeft.y);
 
     var x2 = Math.min(self.getModel().getWidth(), rightBottom.x);
-    var y2 = Math.max(self.getModel().getHeight(), rightBottom.y);
+    var y2 = Math.min(self.getModel().getHeight(), rightBottom.y);
 
     var polygon = "";
     polygon += x1 + "," + y1 + ";";

frontend-js/src/main/js/map/canvas/OpenLayers/OpenLayerPolyline.js

@@ -12,6 +12,8 @@ function OpenLayerPolyline(options) {
 
   var self = this;
 
+  self.registerListenerType("onHide");
+
   if (options.strokeColor === undefined) {
     options.strokeColor = "#000000";
   }
@@ -74,7 +76,8 @@ OpenLayerPolyline.prototype.show = function () {
 };
 
 OpenLayerPolyline.prototype.hide = function () {
-  return this.getOpenLayersPolyline().setStyle(new ol.style.Style({}));
+  this.getOpenLayersPolyline().setStyle(new ol.style.Style({}));
+  return this.callListeners("onHide");
 };
 
 OpenLayerPolyline.prototype.isShown = function () {

frontend-js/src/main/js/map/marker/MarkerSurfaceCollection.js

@@ -228,7 +228,12 @@ MarkerSurfaceCollection.prototype.createSurfaceForDbOverlay = function (element,
         onClick: onclickFunctions
       });
       result.addListener("onClick", function () {
-        return map.getTopMap().openInfoWindowForIdentifiedElement(element);
+        return map.getTopMap().openInfoWindowForIdentifiedElement(element).then(function (infoWindow) {
+          result.getMapCanvasObjects()[0].addListener("onHide", function () {
+            return infoWindow._infoWindow.hide();
+          });
+          return infoWindow;
+        });
       });
       self.putSurface({element: element, overlay: dbOverlay}, result);
       if (self.getMap().isInitialized()) {

persist/src/main/resources/db/migration/13.1.4/V13.1.4.20190821__remove_chembl_cache.sql

+delete from cache_query_table where type in (select id from cache_type_table where class_name ='lcsb.mapviewer.annotation.services.ChEMBLParser');

service/src/main/java/lcsb/mapviewer/services/search/drug/DrugService.java

@@ -174,9 +174,15 @@ public class DrugService extends DbSearchService implements IDrugService {
     if (name.trim().equals("")) {
       return null;
     }
+    DrugAnnotation secondParser = chEMBLParser;
     Drug drug = null;
     try {
       drug = drugBankParser.findDrug(name);
+      
+      if (drug==null) {
+        drug = chEMBLParser.findDrug(name);
+        secondParser = drugBankParser;
+      }
       if (drug != null) {
         removeUnknownOrganisms(drug, searchCriteria.getOrganisms());
       }
@@ -190,13 +196,13 @@ public class DrugService extends DbSearchService implements IDrugService {
       // * search for name
       searchNames.add(name);
       if (drug != null && drug.getName() != null) {
-        // * search for name of a drug in drugbanke
+        // * search for name of a drug in drugbank
         searchNames.add(drug.getName());
         // * search for all synonyms found in drugbank
         // searchNames.addAll(drug.getSynonyms());
       }
       for (String string : searchNames) {
-        Drug drug2 = chEMBLParser.findDrug(string);
+        Drug drug2 = secondParser.findDrug(string);
         if (drug2 != null) {
           removeUnknownOrganisms(drug2, searchCriteria.getOrganisms());
           // don't add drugs that were already found

service/src/test/java/lcsb/mapviewer/services/search/drug/DrugServiceTest.java

@@ -42,6 +42,17 @@ public class DrugServiceTest extends ServiceTestFunctions {
     assertNull(drug);
   }
 
+  @Test
+  public void testGetIstodax() throws Exception {
+    try {
+      Drug drug = drugService.getByName("istodax", new DbSearchCriteria());
+      assertEquals(2, drug.getSources().size());
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
   @Test
   public void testGetTargets() throws Exception {
     long count = searchHistoryDao.getCount();