Merge remote-tracking branch 'origin/devel_13.2.x' into merge-13.2.0

CHANGELOG

@@ -2,40 +2,40 @@ minerva (14.0.0~beta.0) unstable; urgency=low
   * Small improvement: sorting by columns that doesn't make sense in admin
     panel is disabled (#895)
   * Small improvement: version of minerva is visible in map browser panel
-  * Small improvement: small info about annotator details is available in 
+  * Small improvement: small info about annotator details is available in
     select anntoators dialog (#923)
-  * Small improvement: CellDesigner layers are always visualized as pathways 
+  * Small improvement: CellDesigner layers are always visualized as pathways
     (#813)
   * Small improvement: setting "Modify project| checkbox automatically select
     "View project" checkbox when editing privileges (#920)
   * Small improvement: notification email uses minerva name and id of affected
     project (#926)
-  * Small improvement: information about person who uploaded project is visible 
+  * Small improvement: information about person who uploaded project is visible
     in list of projects (#927)
   * Small improvement: user role introduced in edit user dialog (#924)
   * Small improvement: tab with list of glyps is available when adding project
     with glyphs (#925)
-  * Small improvement: BackgroundColor parameter should be assigned using ":" 
+  * Small improvement: BackgroundColor parameter should be assigned using ":"
     character (#929)
   * Bug fix: work on FF Private Window mode could cause logout or raise an
     error on when opening new tab with minerva (#892)
-  * Bug fix: fetching list of miRnas resulted sometimes in "Internal Server 
+  * Bug fix: fetching list of miRnas resulted sometimes in "Internal Server
     Error" (#889)
   * Bug fix: user without admin right can accept terms of service (#893)
   * Bug fix: edit project dialog verifies organism id  (#914)
-  * Bug fix: user without admin or curator privileges shouldn't be able to 
+  * Bug fix: user without admin or curator privileges shouldn't be able to
     check logs (#894)
   * Bug fix: user without admin or curator privileges had issues with accesing
     and removing data overlays (#897, #898, #899, #903)
-  * Bug fix: privilege checking on updating privileges, data overlays were not 
+  * Bug fix: privilege checking on updating privileges, data overlays were not
     sufficient and could lead to access escalation
   * Bug fix: user without privileges had edit map input options enabled
-  * Bug fix: user without privileges had edit map input options for managing 
+  * Bug fix: user without privileges had edit map input options for managing
     project users
   * Bug fix: curator couldn't update data overlay in some situations (#905)
-  * Bug fix: alignment of tabs fixed for dialogs: "Add Project", "Edit Genome", 
+  * Bug fix: alignment of tabs fixed for dialogs: "Add Project", "Edit Genome",
     "Edit Project", "Edit User" (#881)
-  * Bug fix: all colors in boolean reaction (from CellDesigner) are processed 
+  * Bug fix: all colors in boolean reaction (from CellDesigner) are processed
     properly (#907)
   * Bug fix: proper line type for boolean reaction is used on the whole
     reaction (#908)
@@ -48,7 +48,7 @@ minerva (14.0.0~beta.0) unstable; urgency=low
     case the type was not specified in the input file (#906)
   * Bug fix: list of types when copying from annotators contains only types
     that are selectable in the dialog (#911)
-  * Bug fix: remove of data overlay didn't update numbering of data overlays 
+  * Bug fix: remove of data overlay didn't update numbering of data overlays
     that are still in the system (#918)
   * Bug fix: too long name for data overlay in info window is trimmed (#919)
   * Bug fix: too long name in general overlay list is wrapped (#857)
@@ -122,10 +122,17 @@ 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
+minerva (13.2.0) stable; urgency=medium
+  * Small improvement: MolArt v1.4 is used which provide information from
+    PredictProtein (#913)
+  * Bug fix: search by drugs didn't check synonyms in chembl database
+  * Bug fix: verification of overlay type added (#917)
+  * Bug fix: opening edit project/user dialog returned list of users/projects
+    to the 1st page (#909)
+  * Bug fix: show element title option wasn't influencing title visibility
+    (#910)
 
- -- Piotr Gawron <piotr.gawron@uni.lu> Wed,  21 Aug 2019 17:00:00 +0200
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 29 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
@@ -135,7 +142,7 @@ minerva (13.1.3) stable; urgency=medium
   * 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
+ -- 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)

frontend-js/package.json

@@ -31,7 +31,7 @@
     "mkdirp": "^0.5.1",
     "mocha": "^3.5.3",
     "mock-local-storage": "^1.1.8",
-    "molart": "1.3.2",
+    "molart": "1.4.0",
     "stream-to-blob": "^1.0.1",
     "uglifyjs": "^2.4.10"
   },

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

@@ -164,6 +164,9 @@ AddOverlayDialog.prototype.processFile = function (file) {
           }
 
           if (overlay.getType() !== undefined) {
+            if ($("option[value='" + overlay.getType() + "']", typeSelect).length === 0) {
+              GuiConnector.warn("Invalid type: " + overlay.getType());
+            }
             self.setType(overlay.getType());
           } else {
             self.setType("GENERIC");

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

@@ -376,7 +376,7 @@ MapsAdminPanel.prototype.addUpdateListener = function (project) {
           self.projectToTableRow(project, data, user);
           var page = dataTable.page();
           row.data(data).draw();
-          dataTable.page(page);
+          dataTable.page(page).draw(false);
         }
       }
     });

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

@@ -311,7 +311,7 @@ UsersAdminPanel.prototype.addUpdateListener = function (user, dataTableRow) {
     if (row.length > 0) {
       var page = dataTable.page();
       row.data(dataTableRow).draw();
-      dataTable.page(page);
+      dataTable.page(page).draw(false);
     }
   };
   listener.listenerName = listenerName;

frontend-js/src/main/js/gui/leftPanel/GuiUtils.js

@@ -823,9 +823,17 @@ GuiUtils.prototype.createAliasElement = function (params) {
       }));
     }
 
-    div.appendChild(this.createParamLine({label: alias.getType() + ": ", value: alias.getName()}));
+    div.appendChild(this.createParamLine({
+      label: alias.getType() + ": ",
+      className: self._configurationOptionToClassName(ConfigurationType.SHOW_ELEMENT_TITLE),
+      value: alias.getName()
+    }));
     if (alias.getModelId() !== self.getMap().getId()) {
-      div.appendChild(self.createSubMapLink({label: "In submap: ", mapId: alias.getModelId()}));
+      div.appendChild(self.createSubMapLink({
+        label: "In submap: ",
+        className: self._configurationOptionToClassName(ConfigurationType.SHOW_ELEMENT_TITLE),
+        mapId: alias.getModelId()
+      }));
     }
   }
   div.appendChild(self.createSubMapLink({

service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java

@@ -85,7 +85,14 @@ public class ColorSchemaReader {
         return readGenericColorSchema(colorInputStream);
       }
     } else {
-      ColorSchemaType type = ColorSchemaType.valueOf(params.get(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE));
+      ColorSchemaType type = null;
+      try {
+        type = ColorSchemaType.valueOf(params.get(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE));
+      } catch (IllegalArgumentException e) {
+        String options = StringUtils.join(ColorSchemaType.values(), ", ");
+        throw new InvalidColorSchemaException("Invalid overlay type: "
+            + params.get(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE) + ". Allowed options: " + options);
+      }
       if (type == null) {
         logger.warn("Unknown type of layout file: " + params.get(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE));
         return readGenericColorSchema(colorInputStream);

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

@@ -53,6 +53,17 @@ public class DrugServiceTest extends ServiceTestFunctions {
     }
   }
 
+  @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();

service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java

@@ -367,4 +367,13 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
     overlay.setInputData(file);
     assertEquals(0, reader.getDeprecatedColumns(overlay).size());
   }
+
+  @Test(expected = InvalidColorSchemaException.class)
+  public void testReadColorSchemaWithInvalidType() throws Exception {
+    FileInputStream fis = new FileInputStream("testFiles/coloring/invalidType.txt");
+    FileInputStream fis2 = new FileInputStream("testFiles/coloring/invalidType.txt");
+    ColorSchemaReader reader = new ColorSchemaReader();
+    reader.readColorSchema(fis, TextFileUtils.getHeaderParametersFromFile(fis2));
+
+  }
 }

service/testFiles/coloring/invalidType.txt

+#TYPE=gen
+value	identifier	Chebi
+-0,943978048	HGNC:11138	
+-0,941309505		CHEBI:15377
+1		CHEBI:15376