Merge remote-tracking branch 'origin/devel_13.1.x' into merge-13.1.1

CHANGELOG

@@ -27,6 +27,18 @@ minerva (14.0.0~alpha.0) unstable; urgency=low
 
  -- Sascha Herzinger <sascha.herzinger@uni.lu>  Wed, 22 May 2019 10:30:00 +0200
 
+minerva (13.1.1) stable; urgency=medium
+  * Bug fix: adding gene mapping before the genome caused an error (#835)
+  * Bug fix: "Terms of Use" change to "Terms of Service" in all places (#843)
+  * Bug fix: upgrade to 13.1.0 crashed on machines where every element was
+    inside compartment (#856)
+  * Bug fix: searching for some drugs in chembl didn't provide any results even
+    though that data exists, for instance 'DORLIMOMAB ARITOX' (#842)
+  * 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
+
 minerva (13.1.0) stable; urgency=medium
   * Feature: annotators are more flexible - you can define set of input and
     outputs used by annotator (#617)

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

@@ -256,12 +256,15 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
     MiriamData result = null;
     Node uniprotAccessionId = XmlParser.getNode("accession", targetComponent.getChildNodes());
     if (uniprotAccessionId != null) {
-      try {
-        result = uniprotAnnotator
-            .uniProtToHgnc(new MiriamData(MiriamType.UNIPROT, uniprotAccessionId.getTextContent()));
-        result.setAnnotator(null);
-      } catch (UniprotSearchException e) {
-        throw new DrugSearchException(e);
+      String uniprotId = uniprotAccessionId.getTextContent();
+      if (uniprotId != null && !uniprotId.isEmpty()) {
+        try {
+          result = uniprotAnnotator
+              .uniProtToHgnc(new MiriamData(MiriamType.UNIPROT, uniprotId));
+          result.setAnnotator(null);
+        } catch (UniprotSearchException e) {
+          throw new DrugSearchException(e);
+        }
       }
     }
     return result;

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

@@ -273,6 +273,19 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
 
   }
 
+  @Test
+  public void testGetTargetWithRnaComponent() throws Exception {
+    try {
+      Target test = chemblParser.getTargetFromId(new MiriamData(MiriamType.CHEMBL_TARGET, "CHEMBL2363135"));
+
+      assertEquals(test.getSource().getResource(), "CHEMBL2363135");
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+
+  }
+
   @Test
   public void testGetTargetFromInvalidId() throws Exception {
     try {

frontend-js/src/main/js/ServerConnector.js

@@ -99,6 +99,30 @@ ServerConnector.getMinOverlayColorInt = function () {
   });
 };
 
+ServerConnector.checkIfUserLogoutFromDifferentTab = function () {
+  var self = this;
+  var sessionLogin = self.getSessionData(null).getLogin();
+  var tabLogin = self._currentTabLogin;
+  if (tabLogin === undefined) {
+    self._currentTabLogin = ServerConnector.getSessionData(null).getLogin();
+    tabLogin = self._currentTabLogin;
+  }
+  if (tabLogin !== sessionLogin) {
+    setTimeout(function () {
+      var sessionLogin = self.getSessionData(null).getLogin();
+      var tabLogin = self._currentTabLogin;
+      if (tabLogin !== sessionLogin) {
+        logger.warn("User was log out in different tab. Reloading page");
+        window.location.reload(false);
+      }
+    }, 100);
+  }
+};
+
+setInterval(function () {
+  ServerConnector.checkIfUserLogoutFromDifferentTab();
+}, 1000);
+
 ServerConnector.returnUserOrSystemColor = function (userColor, systemPromisedColor) {
   return systemPromisedColor.then(function (systemColor) {
     var color = userColor;
@@ -1884,9 +1908,10 @@ ServerConnector.login = function (login, password) {
     if (data["login"] !== undefined) {
       params.login = data["login"];
     }
+    self._currentTabLogin = params.login;
     self.getSessionData().setLogin(params.login);
     return Promise.resolve(self.getSessionData().getToken());
-  }, function (error) {
+  }).catch(function (error) {
     if (error instanceof NetworkError && error.statusCode === HttpStatus.FORBIDDEN) {
       throw new InvalidCredentialsError("Invalid credentials");
     } else {
@@ -2822,5 +2847,4 @@ ServerConnector.submitErrorToMinervaNet = function (report, callback) {
   }, callback);
 };
 
-
 module.exports = ServerConnector;

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

@@ -175,7 +175,8 @@ EditGenomeDialog.prototype.createGeneMappingTabContent = function () {
 
   var result = Functions.createElement({
     type: "div",
-    style: "margin-top:10px;"
+    style: "margin-top:10px;",
+    className: "minerva-gene-mapping-tab"
   });
 
   var geneMappingTable = Functions.createElement({
@@ -513,6 +514,10 @@ EditGenomeDialog.prototype.refresh = function () {
     //it should be simplified, but I couldn't make it work
     dataTable.clear().rows.add(data).page(page).draw(false).page(page).draw(false);
 
+    if (self.isNew()) {
+      guiUtils.disableTab($(".minerva-gene-mapping-tab", self.getElement())[0], "First add a genome to be able to add mapping");
+    }
+
     return self._fillOrganismSelect(genome);
   });
 };

frontend-js/src/main/js/minerva.js

@@ -127,7 +127,7 @@ function requestConsent(user, termsOfUseUrl) {
   var dialogContent = document.createElement("div");
   dialogContent.appendChild(functions.createElement({
     type: "span",
-    content: "I agree to the minerva <a href='" + termsOfUseUrl + "' target='_blank'>Terms of Use</a>.",
+    content: "I agree to the minerva <a href='" + termsOfUseUrl + "' target='_blank'>Terms of Service</a>.",
     xss: false
   }));
   var checkbox = functions.createElement({type: "input", inputType: "checkbox", style: "float: left"});
@@ -167,7 +167,7 @@ function requestConsent(user, termsOfUseUrl) {
     },
     modal: true,
     closeOnEscape: false,
-    title: "Terms of Use"
+    title: "Terms of Service"
   }).siblings('.ui-dialog-titlebar').css("background", "red");
   $(".ui-dialog-titlebar-close", $(dialog).dialog().siblings('.ui-dialog-titlebar')).hide();
   $(dialog).dialog("open");

frontend-js/src/test/js/ServerConnector-mock.js

@@ -43,6 +43,10 @@ function encodeParams(params) {
   return result;
 }
 
+ServerConnectorMock.checkIfUserLogoutFromDifferentTab = function () {
+  logger.debug("checkIfUserLogoutFromDifferentTab is ignored");
+};
+
 ServerConnectorMock._sendRequest = function (params) {
   var self = this;
   var url = params.url;

persist/src/main/resources/db/migration/13.1.0~alpha.0/V13.1.0.20190503__z_index_to_elements_added.sql

@@ -2,6 +2,8 @@
 alter table element_table add column z integer;
 alter table reaction_table add column z integer;
 
+--add artificial element outside compartment, so the update queries will always return non-null values
+insert into element_table (id, element_type_db, visibility_level, width, height) values(-1, 'GENERIC_PROTEIN', 0, 1,1);
 
 with v_element_table as
 (
@@ -69,3 +71,6 @@ update element_table set z = (select max(z) from element_table) where z is null;
 
 ALTER TABLE element_table ALTER COLUMN z SET NOT NULL;
 ALTER TABLE reaction_table ALTER COLUMN z SET NOT NULL;
+
+--remove artificial element added at the beginning of the script
+delete from element_table where id = -1;

rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java

@@ -491,7 +491,7 @@ public abstract class BaseRestImpl {
     return result;
   }
 
-  protected Integer parseInteger(Object value) throws QueryException {
+  protected Integer parseInteger(Object value, String fieldName) throws QueryException {
     if (value instanceof Integer) {
       return (Integer) value;
     } else if (value instanceof Double) {
@@ -506,12 +506,16 @@ public abstract class BaseRestImpl {
         try {
           return Integer.parseInt((String) value);
         } catch (NumberFormatException e) {
-          throw new QueryException("Invalid integer value: " + value);
+          throw new QueryException("Invalid " + fieldName + " value: " + value);
         }
       }
     } else {
-      throw new QueryException("Invalid integer value: " + value);
+      throw new QueryException("Invalid " + fieldName + " value: " + value);
     }
   }
 
+  protected Integer parseInteger(Object value) throws QueryException {
+    return parseInteger(value, "integer");
+  }
+
 }

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

@@ -256,8 +256,9 @@ public class ReferenceGenomeRestImpl extends BaseRestImpl {
     if (!getUserService().userHasPrivilege(token, PrivilegeType.MANAGE_GENOMES)) {
       throw new SecurityException("Access denied");
     }
+    
 
-    int id = Integer.parseInt(genomeId);
+    int id = parseInteger(genomeId, "genomeId");
     try {
       ReferenceGenome genome = referenceGenomeService.getReferenceGenomeById(id, token);
       String name = getFirstValue(formData.get("name"));