Merge branch 'devel_11.1.x-clean'

CHANGELOG

@@ -123,6 +123,13 @@ minerva (12.0.0~alpha.0) unstable; urgency=medium
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 21 Feb 2018 12:00:00 +0200
 
+minerva (11.1.2) stable; urgency=medium
+  * Bug fix: Searching for chemicals with invalid mesh ID crashed
+  * Bug fix: opening map that was removed and re-uploaded could crash
+  * warning message due to lack of google consent improved
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 04 Jul 2018 16:00:00 +0200
+
 minerva (11.1.1) stable; urgency=medium
   * Bug fix: Updating privileges takes much less time
   * Bug fix: Concurent update on privileges shouldn't crash anymore

frontend-js/src/main/js/GuiConnector.js

@@ -298,6 +298,9 @@ GuiConnector.prototype.destroy = function () {
   if (self._infoDialog !== undefined) {
     $(self._infoDialog).dialog("destroy").remove();
   }
+  if (self._warnDialog !== undefined) {
+    $(self._warnDialog).dialog("destroy").remove();
+  }
   if (self._processingDialog !== undefined) {
     $(self._processingDialog).dialog("destroy").remove();
   }
@@ -316,3 +319,24 @@ GuiConnector.singleton = new GuiConnector();
 
 
 module.exports = GuiConnector.singleton;
+GuiConnector.warn = function (message) {
+  var self = GuiConnector;
+  logger.warn(message);
+  if (self._warnDialog === undefined) {
+    self._warnDialog = document.createElement("div");
+    self._warnDialogContent = document.createElement("div");
+    self._warnDialog.appendChild(self._warnDialogContent);
+    document.body.appendChild(self._warnDialog);
+    $(self._warnDialog).dialog({
+      classes: {
+        "ui-dialog": "ui-state-highlight"
+      },
+      modal: true,
+      title: "WARNING"
+    });
+  }
+  self._warnDialogContent.innerHTML = message;
+  $(self._warnDialog).dialog("open");
+};
+
+module.exports = GuiConnector;

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

@@ -237,7 +237,17 @@ OverlayPanel.prototype.createOverlayRow = function (overlay, checked, disabled)
     });
     checkbox.checked = checked;
     $(checkbox).prop("disabled", disabled);
-    viewTd.appendChild(checkbox);
+    if (disabled) {
+      var warningDiv = Functions.createElement({
+        type: "div",
+        content: "<i class='fa fa-exclamation-triangle' style='font-size:18px; font-weight:400; padding-right:10px;color:orange'></i>",
+        xss: false
+      });
+      warningDiv.title = "You did not consent to terms of the license of Google Maps Platform. Click the \"Edit\" button to do so.";
+      viewTd.appendChild(warningDiv)
+    } else {
+      viewTd.appendChild(checkbox);
+    }
   } else {
     var img = guiUtils.createIcon("icons/search.png");
     var link = Functions.createElement({type: "a", href: "#", name: "overlayLink", data: overlay.getId()});

frontend-js/src/main/js/map/overlay/AbstractDbOverlay.js

@@ -203,6 +203,12 @@ AbstractDbOverlay.prototype.searchByEncodedQuery = function (originalQuery, fitB
     return this.searchByTarget(new IdentifiedElement(query.target));
   } else if (query.type === AbstractDbOverlay.QueryType.SEARCH_BY_COORDINATES) {
     query.coordinates = new Point(query.coordinates.x, query.coordinates.y);
+    if (this.getMap().getSubmapById(query.modelId) === null) {
+      //this can happen when cached data comes from project that was removed and something else
+      //was uploaded with the same name
+      logger.warn("Invalid search query. Model doesn't exist: " + query.modelId);
+      return Promise.resolve();
+    }
     return this.searchByCoordinates(query);
   } else {
     throw new Error("Unknown type of query: " + query.type);

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

@@ -408,7 +408,7 @@ function create(params) {
     return ServerConnector.getLoggedUser();
   }).then(function (user) {
     if (leftPanel.isGoogleLicenseConsentRequired()) {
-      GuiConnector.alert("Some data overlays doesn't have consent to the terms of the <a href='https://cloud.google.com/maps-platform/terms/' target='_blank'>license of Google Maps Platform</a>. To be able to visualize them you must edit data overlay. ")
+      GuiConnector.warn("Visualization of data overlays (Overlays tab) requires consent to terms of the <a href='https://cloud.google.com/maps-platform/terms/' target='_blank'>license of Google Maps Platform</a>. Click the \"Edit\" button for the overlay to do so.");
     }
     if (user.getLogin() !== "anonymous" && !user.isTermsOfUseConsent()) {
       requestConsent(user, params.getConfiguration().getOption(ConfigurationType.TERMS_OF_USE).getValue());

persist/src/db/11.1.2/fix_db_20180704.sql

+-- empty file to force directory to be commited to git repo

rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java

@@ -81,13 +81,17 @@ public class ChemicalRestImpl extends BaseRestImpl {
     String description = "Mesh term not available";
     List<String> synonyms = new ArrayList<>();
 
-    try {
-      MeSH mesh = meSHParser.getMeSH(chemical.getChemicalId());
-      description = mesh.getDescription();
-      synonyms = mesh.getSynonyms();
-    } catch (AnnotatorException e) {
-      logger.error("Problem with accessing mesh database", e);
-    }
+	try {
+		MeSH mesh = meSHParser.getMeSH(chemical.getChemicalId());
+		if (mesh != null) {
+		  description = mesh.getDescription();
+		  synonyms = mesh.getSynonyms();
+		} else {
+		  logger.warn("Mesh used by chemical is invalid: " + chemical.getChemicalId());
+		}
+	} catch (AnnotatorException e) {
+		logger.error("Problem with accessing mesh database", e);
+	}
 
     for (String string : columnsSet) {
       String column = string.toLowerCase();

rest-api/src/test/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImplTest.java

@@ -21,13 +21,18 @@ import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.MiriamType;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.services.interfaces.IModelService;
+import lcsb.mapviewer.services.search.db.DbSearchCriteria;
+import lcsb.mapviewer.services.search.db.chemical.IChemicalService;
 
 public class ChemicalRestImplTest extends RestTestFunctions {
 	Logger									 logger	= Logger.getLogger(ChemicalRestImplTest.class);
 
-	@Autowired
+    @Autowired
 
-	private ChemicalRestImpl _drugRestImpl;
+    private ChemicalRestImpl _drugRestImpl;
+
+    @Autowired
+    private IChemicalService chemicalService;
 
 	@AfterClass
 	public static void tearDownAfterClass() throws Exception {
@@ -41,18 +46,30 @@ public class ChemicalRestImplTest extends RestTestFunctions {
 	public void tearDown() throws Exception {
 	}
 
-	@Test
-	public void testPrepareChemical() throws Exception {
-		try {
-			Chemical chemical = new Chemical();
-			chemical.setChemicalId(new MiriamData(MiriamType.MESH_2012, "D010300"));
-			Map<String, Object> result = _drugRestImpl.prepareChemical(chemical, _drugRestImpl.createChemicalColumnSet(""), new ArrayList<>());
-			assertNotNull(result);
-		} catch (Exception e) {
-			e.printStackTrace();
-			throw e;
-		}
-	}
+    @Test
+    public void testPrepareChemical() throws Exception {
+        try {
+            Chemical chemical = new Chemical();
+            chemical.setChemicalId(new MiriamData(MiriamType.MESH_2012, "D010300"));
+            Map<String, Object> result = _drugRestImpl.prepareChemical(chemical, _drugRestImpl.createChemicalColumnSet(""), new ArrayList<>());
+            assertNotNull(result);
+        } catch (Exception e) {
+            e.printStackTrace();
+            throw e;
+        }
+    }
+
+    @Test
+    public void testPrepareChemicalWithProblematicMesh() throws Exception {
+        try {
+            Chemical chemical = chemicalService.getByName("Tetrachlorodibenzodioxin", new DbSearchCriteria().disease(new MiriamData(MiriamType.MESH_2012, "D010300")));
+            Map<String, Object> result = _drugRestImpl.prepareChemical(chemical, _drugRestImpl.createChemicalColumnSet(""), new ArrayList<>());
+            assertNotNull(result);
+        } catch (Exception e) {
+            e.printStackTrace();
+            throw e;
+        }
+    }
 
 	protected ChemicalRestImpl createMockChemicalRest(String string) throws Exception {
 		Model model = super.getModelForFile(string, true);