diff --git a/CHANGELOG b/CHANGELOG
index 85156b159c8346f9739e2cbe3807d119352daf1e..d7970ed615c3ba461daba42295b45c2c618d41c2 100644
--- a/CHANGELOG
+++ b/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
diff --git a/frontend-js/src/main/js/GuiConnector.js b/frontend-js/src/main/js/GuiConnector.js
index af8f68cdef0985d7f1782218192b70608a7761b4..c9f44579346a898451e82003e8d823a9bf3e0ba6 100644
--- a/frontend-js/src/main/js/GuiConnector.js
+++ b/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;
diff --git a/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js b/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
index ad6006a376b58b4ed02ce95909ace8e77cbb471b..fd81dc33ffd165d20dec913a6d029f80b766000a 100644
--- a/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
+++ b/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()});
diff --git a/frontend-js/src/main/js/map/overlay/AbstractDbOverlay.js b/frontend-js/src/main/js/map/overlay/AbstractDbOverlay.js
index 8c92adff938335911b0c4ac0c2a717bd0db2b639..85906d905631f2323f1f1d6e243da80ff87f7c49 100644
--- a/frontend-js/src/main/js/map/overlay/AbstractDbOverlay.js
+++ b/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);
diff --git a/frontend-js/src/main/js/minerva.js b/frontend-js/src/main/js/minerva.js
index c9fc776c29db4036bf132dc1a3293162eb346695..f14b4795e068c5221acb7deaeba2379a13e1165d 100644
--- a/frontend-js/src/main/js/minerva.js
+++ b/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());
diff --git a/persist/src/db/11.1.2/fix_db_20180704.sql b/persist/src/db/11.1.2/fix_db_20180704.sql
new file mode 100644
index 0000000000000000000000000000000000000000..a33b6ad89d4881c84fb355b8c56d309760e66b70
--- /dev/null
+++ b/persist/src/db/11.1.2/fix_db_20180704.sql
@@ -0,0 +1 @@
+-- empty file to force directory to be commited to git repo
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java
index a282a983db27dc5f58a2c1bf127923c8f6e5f6ba..babedeb740627fcdbc1d62139d7ead2aae5b28f6 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java
+++ b/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();
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImplTest.java
index 32b1acd9ede8099f67a72ad949d864f29c081051..ba530e1803d366a1989f6c10a25e80048655e5ff 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImplTest.java
+++ b/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);