Merge branch '790-sorting-list' into 'devel_12.2.x'

Resolve "Sorting list is not working"

See merge request !751

CHANGELOG

+minerva (12.2.3) stable; urgency=medium
+  * Bug fix: sorting of entries in "Edit project->overlays" dialog fixed (#790)
+  * Bug fix: searching of chemicals stopped working due to expired SSL 
+    certificate on https://ctdbase.org/
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 24 Apr 2019 17:00:00 +0200
+
 minerva (12.2.2) stable; urgency=medium
   * Bug fix: downloading overlays didn't work from admin panel when project 
     with different id than default map was accessed

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

@@ -70,18 +70,18 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
   /**
    * Home page of ctd database.
    */
-  static final String URL = "https://ctdbase.org/";
+  static final String URL = "http://ctdbase.org/";
 
   /**
    * URL to get a list of chemicals by disease id.
    */
-  public static final String DISEASE_URL = "https://ctdbase.org/detail.go?6578706f7274=1&d-1332398-e=5&view=chem&"
+  public static final String DISEASE_URL = URL + "detail.go?6578706f7274=1&d-1332398-e=5&view=chem&"
       + "type=disease&acc=MESH%3A";
 
   /**
    * URL to get a list of chemicals by gene id.
    */
-  public static final String DISEASE_GENE_URL = "https://ctdbase.org/detail.go?slimTerm=all&6578706f7274=1&qid=3464576&"
+  public static final String DISEASE_GENE_URL = URL + "detail.go?slimTerm=all&6578706f7274=1&qid=3464576&"
       + "d-1332398-e=5&view=disease&type=gene&assnType=curated&acc=";
 
   /**
@@ -404,10 +404,10 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
       }
       if (result != null) {
         MeSH mesh = meshParser.getMeSH(result.getChemicalId());
-        if (mesh!=null) {
-        result.addSynonyms(mesh.getSynonyms());
+        if (mesh != null) {
+          result.addSynonyms(mesh.getSynonyms());
         } else {
-          logger.warn("Problematic mesh id: "+result.getChemicalId());
+          logger.warn("Problematic mesh id: " + result.getChemicalId());
         }
       }
 
@@ -486,7 +486,7 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
         if (entrez == null) {
           invalidHgnc.add(md);
         } else {
-          String query = "https://ctdbase.org/detail.go?type=gene&view=ixn&chemAcc=" + chemID.getResource() + "&acc="
+          String query = URL + "detail.go?type=gene&view=ixn&chemAcc=" + chemID.getResource() + "&acc="
               + entrez.getResource();
           String referencesPage = getWebPageContent(query);
           Matcher matcher = pattern.matcher(referencesPage);
@@ -494,7 +494,7 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
             idx.add(matcher.group(1));
           }
           for (String string : idx) {
-            String query2 = "https://ctdbase.org/detail.go?6578706f7274=1&d-1340579-e=5&type=relationship&ixnId="
+            String query2 = URL + "detail.go?6578706f7274=1&d-1340579-e=5&type=relationship&ixnId="
                 + string;
             String referencesPage2 = getWebPageContent(query2);
             String[] lines = referencesPage2.split("\n");

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

@@ -157,7 +157,6 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
       assertNotNull(drug);
       assertTrue(drug.getBrandNames().contains("PK-Merz"));
       assertTrue(drug.getBrandNames().contains("Symadine"));
-      assertTrue(drug.getBrandNames().contains("Symmetrel"));
     } catch (Exception e) {
       e.printStackTrace();
       throw e;

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

@@ -106,6 +106,13 @@ GuiConnector.prototype.init = function () {
     };
   }
   newUrl = "";
+
+  //sorting of datatable column by input value https://stackoverflow.com/a/29221907/1127920
+  $.fn.dataTable.ext.order['dom-input'] = function (settings, col) {
+    return this.api().column(col, {order: 'index'}).nodes().map(function (td, i) {
+      return $('input', td).val();
+    });
+  }
 };
 
 

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

@@ -61,7 +61,8 @@ CommentsAdminPanel.prototype._createGui = function () {
     }, {
       title: 'Content'
     }, {
-      title: 'Removed'
+      title: 'Removed',
+      orderable: false
     }, {
       title: 'Pinned'
     }]

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

@@ -325,13 +325,17 @@ EditProjectDialog.prototype._createMapsTable = function () {
     }, {
       title: 'Name'
     }, {
-      title: 'Default center x'
+      title: 'Default center x',
+      orderable: false
     }, {
-      title: 'Default center y'
+      title: 'Default center y',
+      orderable: false
     }, {
-      title: 'Default zoom level'
+      title: 'Default zoom level',
+      orderable: false
     }, {
-      title: 'Update'
+      title: 'Update',
+      orderable: false
     }]
   });
 
@@ -397,18 +401,31 @@ EditProjectDialog.prototype._createOverlayTable = function () {
     }, {
       title: 'Description'
     }, {
-      title: 'Public'
+      title: 'Public',
+      orderable: false
     }, {
-      title: 'Default'
+      title: 'Default',
+      orderable: false
     }, {
-      title: 'Owner'
+      title: 'Owner',
+      orderable: false
     }, {
-      title: 'Data'
+      title: 'Data',
+      orderable: false
     }, {
-      title: 'Update'
+      title: 'Update',
+      orderable: false
     }, {
-      title: 'Remove'
+      title: 'Remove',
+      orderable: false
     }],
+    columnDefs: [
+      {
+        orderDataType: "dom-input",
+        type: "string",
+        targets: [1, 2]
+      }
+    ],
     dom: '<"minerva-datatable-toolbar">frtip',
     initComplete: function () {
       $("div.minerva-datatable-toolbar", $(result)).html('<button name="addOverlay">Add overlay</button>');
@@ -437,7 +454,7 @@ EditProjectDialog.prototype._createOverlayTable = function () {
     var button = this;
     return self.getServerConnector().getOverlaySourceDownloadUrl({
       overlayId: $(button).attr("data"),
-      projectId:self.getProject().getProjectId()
+      projectId: self.getProject().getProjectId()
     }).then(function (url) {
       return self.downloadFile(url);
     }).then(null, GuiConnector.alert);
@@ -622,7 +639,8 @@ EditProjectDialog.prototype.initUsersTab = function () {
 
   var columns = self.createUserPrivilegeColumns();
   $(usersTable).DataTable({
-    columns: columns
+    columns: columns,
+    ordering: false
   });
   return Promise.resolve();
 };