12.1.3 into master

.gitlab-ci.yml

@@ -278,7 +278,7 @@ test_install_debian_package:
      - echo "PUT $debian_file /docker/incoming" | sftp -o StrictHostKeyChecking=no user@debian-repo
      - ssh root@debian-repo /usr/local/sbin/reprepro-import
      - apt-add-repository "deb http://ppa.launchpad.net/webupd8team/java/ubuntu trusty main"
-     - apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys EEA14886
+     - apt-key adv --no-tty --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys EEA14886
      - apt-add-repository "deb http://debian-repo/ unstable main"
      - apt-get update
 # auto accept oracle license

CHANGELOG

 minerva (12.2.0~alpha.0) stable; urgency=medium
   * Bug fix: export to CellDesigner align inhibition reaction properly
-  * Bug fix: export/import to/from SBML handles Heterodimer Association 
+  * Bug fix: export/import to/from SBML handles Heterodimer Association
     reaction properly
   * Small improvement: export to SBML includes unit factors
-  
+
+
+minerva (12.1.3) stable; urgency=medium
+  * Bug fix: add project button is disabled when user has no privileges
+  * Bug fix: projectId was missing in the edit window
+  * Bug fix: user could provide invalid mesh ID that caused errors when
+    browsing map
+  * Bug fix: user created from LDAP connection doesn't have a password
+    stored in the database
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 14 Dec 2018 14:00:00 +0200
+
+minerva (12.1.2) stable; urgency=medium
+  * Bug fix: vmh annotations should be properly matching id entered in the input
+  * Bug fix: opacity was not working when highliting objects in plugins
+  * Bug fix: integer configurtion options (like SMTP_PORT) are properly
+    validated before saving
+  * Bug fix: inside of reaction box wasn't properly aligned
+  * Bug fix: too long data overlay name disturbed size of the map div and
+    interaction with the map
+  * Bug fix: search for some drugs resulted in internal server error
+  * Bug fix: LDAP login is case insensitive
+  * Bug fix: adding user could end up with error in the frontend
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 12 Dec 2018 16:00:00 +0200
 
 minerva (12.1.1) stable; urgency=medium
   * Bug fix: lineWidth in data overlays was ignored

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

@@ -156,6 +156,9 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
       throw new InvalidArgumentException(
           "Target must be of a type: " + MiriamType.CHEMBL_TARGET + ". But found: " + md.getDataType());
     }
+    if (md.getResource().isEmpty()) {
+      throw new InvalidArgumentException("Invalid target id" + md);
+    }
     try {
       Target target = new Target();
       target.setSource(md);
@@ -264,13 +267,13 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
   }
 
   /**
-   * REturns list of targes for given drug.
+   * Returns list of targets for given drug.
    * 
    * @param drugId
    *          identifier of a drug for which targets are looked
    * @throws DrugSearchException
    *           thrown when there are problems with connection to ChEMBL database
-   * @return list of targes for given drug
+   * @return list of targets for given drug
    */
   List<Target> getTargetsByDrugId(MiriamData drugId) throws DrugSearchException {
     if (!MiriamType.CHEMBL_COMPOUND.equals(drugId.getDataType())) {
@@ -278,8 +281,8 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
     }
     List<Target> targets = new ArrayList<>();
     try {
-
-      String page = getWebPageContent(TARGET_MECHANISM_BY_DRUG_ID_API_URL + drugId.getResource());
+      String url = TARGET_MECHANISM_BY_DRUG_ID_API_URL + drugId.getResource();
+      String page = getWebPageContent(url);
       Document document = getXmlDocumentFromString(page);
 
       Node response = getNode("response", document);
@@ -290,14 +293,17 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
         if (node.getNodeType() == Node.ELEMENT_NODE) {
           if (node.getNodeName().equalsIgnoreCase("mechanism")) {
             Node chemblTargetIdNode = getNode("target_chembl_id", node);
-            MiriamData targetMiriam = new MiriamData(MiriamType.CHEMBL_TARGET, chemblTargetIdNode.getTextContent());
+            String chemblTargetId = chemblTargetIdNode.getTextContent();
+            if (chemblTargetId != null && !chemblTargetId.isEmpty()) {
+              MiriamData targetMiriam = new MiriamData(MiriamType.CHEMBL_TARGET, chemblTargetId);
 
-            Target target = getTargetFromId(targetMiriam);
-            Node referenceNode = getNode("mechanism_refs", node);
+              Target target = getTargetFromId(targetMiriam);
+              Node referenceNode = getNode("mechanism_refs", node);
 
-            Set<MiriamData> references = parseReferences(referenceNode);
-            target.addReferences(references);
-            targets.add(target);
+              Set<MiriamData> references = parseReferences(referenceNode);
+              target.addReferences(references);
+              targets.add(target);
+            }
           }
         }
       }
@@ -327,7 +333,7 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
             Node typeNode = super.getNode("ref_type", node);
             if ("PubMed".equalsIgnoreCase(typeNode.getTextContent())) {
               Node idNode = super.getNode("ref_id", node);
-              String id = idNode.getTextContent();
+              String id = idNode.getTextContent().trim();
               result.add(new MiriamData(MiriamType.PUBMED, id));
             }
           } else {

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

@@ -305,13 +305,8 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
    * @return list of drug {@link Target} parsed from input string
    */
   List<Target> getTargetsForDrug(String page) throws DrugSearchException {
-    List<Target> result = new ArrayList<>();
     try {
-      int pageStart;
-      Target target = new Target();
-      target.setType(TargetType.SINGLE_PROTEIN);
-
-      pageStart = page.indexOf("bond-list-container targets");
+      int pageStart = page.indexOf("bond-list-container targets");
 
       int end = page.indexOf("bond-list-container enzymes");
       if (end < 0) {
@@ -328,28 +323,35 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
         }
       }
 
-      while (pageStart > 0 && pageStart < end) {
-        int targetStart = page.indexOf("Details</a>", pageStart);
-        if (targetStart < 0) {
-          break;
-        }
-        int nextTargetStart = page.indexOf("Details</a>", targetStart + 1);
-        if (nextTargetStart < 0) {
-          nextTargetStart = end;
-        }
-
-        target = parseTarget(page.substring(targetStart, nextTargetStart));
-        if (target != null) {
-          result.add(target);
-        }
-        pageStart = nextTargetStart;
-
-      }
+      List<Target> result = extractTargetsFromPageContent(page, pageStart, end);
+      return result;
     } catch (TaxonomySearchException e) {
       throw new DrugSearchException("Problem with finidng information about organism", e);
     } catch (UniprotSearchException e) {
       throw new DrugSearchException("Problem with finidng information about protein", e);
     }
+  }
+
+  List<Target> extractTargetsFromPageContent(String page, int pageStart, int end)
+      throws UniprotSearchException, TaxonomySearchException {
+    List<Target> result = new ArrayList<>();
+    while (pageStart > 0 && pageStart < end) {
+      int targetStart = page.indexOf("Details</a>", pageStart);
+      if (targetStart < 0 || targetStart > end) {
+        break;
+      }
+      int nextTargetStart = page.indexOf("Details</a>", targetStart + 1);
+      if (nextTargetStart < 0) {
+        nextTargetStart = end;
+      }
+
+      Target target = parseTarget(page.substring(targetStart, nextTargetStart));
+      if (target != null) {
+        result.add(target);
+      }
+      pageStart = nextTargetStart;
+
+    }
     return result;
   }
 
@@ -743,7 +745,7 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
    * Sometimes when we search for targets drugbank returns something similar to
    * the target and we need to filter it out (here is an example for TF targets:
    * https://www.drugbank.ca/unearth/q?utf8=%E2%9C%93&searcher=targets&query=TF)
-   * 
+   *
    * @param page - target webpage content
    * @param hgncTarget - HGNC identifier that should match the target
    * @return

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

@@ -110,6 +110,9 @@ public class MeSHParser extends CachableInterface implements IExternalService {
     if (meshID == null || meshID.getResource() == null) {
       throw new InvalidArgumentException("mesh cannot be null ");
     }
+    if (meshID.getResource().indexOf(" ") >= 0) {
+      return null;
+    }
 
     MeSH mesh = null;
     // look for Mesh in the cache

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

@@ -1102,6 +1102,19 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
     }
   }
 
+  @Test
+  public void testParseReferencesWithSpecInId() throws Exception {
+    try {
+      Node node = super.getXmlDocumentFromFile("testFiles/chembl/references_with_space.xml");
+      Set<MiriamData> references = chemblParser.parseReferences(node.getFirstChild());
+      assertEquals(1, references.size());
+      assertFalse(references.iterator().next().getResource().contains(" "));
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
   @Test
   public void testGetDrugByInvalidDrugId() throws Exception {
     try {

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

@@ -780,5 +780,22 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
     }
 
   }
+  
+  @Test
+  public void testExtractTargetsFromPageContent() throws Exception {
+    try {
+      String pageContent = " Details</a>blablablablabla Details</a>";
+      List<Target> result = drugBankHTMLParser.extractTargetsFromPageContent(pageContent,2,3);
+
+      assertEquals(0, result.size());
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+
+  }
+  
+  
 
 }

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

@@ -110,6 +110,18 @@ public class MeSHParserTest extends AnnotationTestFunctions {
     }
   }
 
+  @Test
+  public void testIsValidWithSpace() throws Exception {
+    try {
+      MiriamData meshID = new MiriamData(MiriamType.MESH_2012, "some disease");
+      assertFalse(meshParser.isValidMeshId(meshID));
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
   @Test
   public void testGetInvalidMesh() throws Exception {
     try {

annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotatorTest.java

@@ -190,6 +190,21 @@ public class ReconAnnotatorTest extends AnnotationTestFunctions {
     }
   }
 
+  @Test
+  public void testAnnotatingForOxygen() throws Exception {
+    try {
+      SimpleMolecule molecule = new SimpleMolecule("id");
+      molecule.setName("o2");
+      reconAnnotator.annotateElement(molecule);
+      assertTrue(molecule.getMiriamData().size() > 0);
+      assertEquals(0, getWarnings().size());
+      assertEquals("O2", molecule.getFormula());
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
   @Test
   public void testAnnotatingWithWhitespace() throws Exception {
     try {

annotation/testFiles/chembl/references_with_space.xml

+<mechanism_refs>
+<mechanism>
+<ref_id>18540918 </ref_id>
+<ref_type>PubMed</ref_type>
+<ref_url>http://europepmc.org/abstract/MED/18540918</ref_url>
+</mechanism>
+</mechanism_refs>
\ No newline at end of file

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverter.java

@@ -161,6 +161,9 @@ public class ReactionConverter extends BioEntityConverter<Reaction> {
 			// draw rect border
 			graphics.draw(rect);
 
+	         // unrotate the graphics
+            graphics.rotate(-angle, pointX, pointY);
+
 			// draw text inside rect
 			Font tmpFont = graphics.getFont();
 			graphics.setFont(descFont);
@@ -182,8 +185,6 @@ public class ReactionConverter extends BioEntityConverter<Reaction> {
 				graphics.draw(path);
 			}
 
-			// unrotate the graphics
-			graphics.rotate(-angle, pointX, pointY);
 		}
 	}
 

converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverterTest.java

@@ -2,6 +2,9 @@ package lcsb.mapviewer.converter.graphics.bioEntity.reaction;
 
 import static org.junit.Assert.assertTrue;
 import static org.mockito.ArgumentMatchers.nullable;
+import static org.mockito.Matchers.any;
+import static org.mockito.Matchers.anyDouble;
+import static org.mockito.Matchers.anyInt;
 import static org.mockito.Mockito.times;
 import static org.mockito.Mockito.verify;
 
@@ -20,9 +23,11 @@ import org.apache.commons.io.output.ByteArrayOutputStream;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
+import org.mockito.InOrder;
 import org.mockito.Mockito;
 
 import lcsb.mapviewer.commands.ColorExtractor;
+import lcsb.mapviewer.common.geometry.PointTransformation;
 import lcsb.mapviewer.converter.graphics.ConverterParams;
 import lcsb.mapviewer.converter.graphics.GraphicsTestFunctions;
 import lcsb.mapviewer.model.graphics.PolylineData;
@@ -36,6 +41,8 @@ import lcsb.mapviewer.model.map.reaction.Product;
 import lcsb.mapviewer.model.map.reaction.Reactant;
 import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.reaction.SplitOperator;
+import lcsb.mapviewer.model.map.reaction.type.KnownTransitionOmittedReaction;
+import lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction;
 import lcsb.mapviewer.model.map.species.GenericProtein;
 
 public class ReactionConverterTest extends GraphicsTestFunctions {
@@ -391,4 +398,53 @@ public class ReactionConverterTest extends GraphicsTestFunctions {
     }
   }
 
+  private Reaction createUnknownTransitionReaction(double angle) {
+    PointTransformation pt = new PointTransformation();
+
+    Reaction result = new UnknownTransitionReaction();
+
+    Point2D center = new Point2D.Double(100, 90);
+    Point2D reactantCenter = new Point2D.Double(10, 90);
+    Point2D productCenter = new Point2D.Double(200, 90);
+
+    Point2D reactantEnd = new Point2D.Double(90, 90);
+    Point2D productEnd = new Point2D.Double(110, 90);
+
+    Reactant reactant = new Reactant(new GenericProtein("s2"));
+
+    reactant.setLine(
+        new PolylineData(pt.rotatePoint(reactantEnd, angle, center), pt.rotatePoint(reactantCenter, angle, center)));
+    reactant.getLine().setWidth(1.0);
+    Product product = new Product(new GenericProtein("s3"));
+    product.setLine(
+        new PolylineData(pt.rotatePoint(productCenter, angle, center), pt.rotatePoint(productEnd, angle, center)));
+    product.getLine().setWidth(1.0);
+    result.addProduct(product);
+    result.addReactant(reactant);
+    return result;
+  }
+
+  @Test
+  public void testDrawReactionWithRectangle() throws Exception {
+    try {
+      for (double angle = 0.0; angle <= Math.PI * 2; angle += 0.1) {
+        Graphics2D graphics = createGraphicsMock();
+        ReactionConverter rc = new ReactionConverter(colorExtractor);
+
+        Reaction reaction = createUnknownTransitionReaction(angle);
+        rc.draw(reaction, graphics, new ConverterParams().sbgnFormat(false));
+
+        InOrder inOrder = Mockito.inOrder(graphics);
+
+        inOrder.verify(graphics).rotate(anyDouble(), anyDouble(), anyDouble());
+        inOrder.verify(graphics).rotate(anyDouble(), anyDouble(), anyDouble());
+        inOrder.verify(graphics).drawString(any(String.class), anyInt(), anyInt());
+
+      }
+
+    } catch (Exception e) {
+      throw e;
+    }
+  }
+
 }

frontend-js/src/main/css/global.css

@@ -465,6 +465,7 @@ table.minerva-window-drug-table td {
 .minerva-left-panel {
     position: relative;
     flex: 0 0 357px;
+    max-width: 357px;
     border: none;
     background-color: #ffffff;
     height: 100%;

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

@@ -229,7 +229,7 @@ GuiConnector.prototype.hideProcessing = function () {
 
 /**
  *
- * @param {string} error
+ * @param {string|Error} error
  * @param {boolean} [redirectIfSecurityError]
  */
 GuiConnector.prototype.alert = function (error, redirectIfSecurityError) {

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

@@ -1796,7 +1796,12 @@ ServerConnector.login = function (login, password) {
   } else {
     params.login = "anonymous";
   }
-  return self.sendPostRequest(self.loginUrl(), params).then(function () {
+  return self.sendPostRequest(self.loginUrl(), params).then(function (content) {
+    var data = JSON.parse(content);
+    if (data["login"] !== undefined) {
+      params.login = data["login"];
+    }
+    console.log(params.login);
     self.getSessionData().setLogin(params.login);
     return Promise.resolve(self.getSessionData().getToken());
   }, function (error) {

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

@@ -254,7 +254,7 @@ AddProjectDialog.prototype.createGeneralTabContent = function () {
     inputName: "project-annotate-automatically",
     elements: [showAnnotatorsButton],
     help: 'If this checkbox is checked, elements of the uploaded map will be automatically annotated using built in ' +
-    'annotators. Behavior of the annotators can be configured by clicking the Advanced button.'
+      'annotators. Behavior of the annotators can be configured by clicking the Advanced button.'
   }));
   table.appendChild(self.createCheckboxRow({
     labelName: "Verify manual annotations:",
@@ -262,36 +262,46 @@ AddProjectDialog.prototype.createGeneralTabContent = function () {
     inputName: "project-verify-annotations",
     elements: [showValidatorsButton],
     help: 'If this checkbox is checked, elements and interactions of the uploaded map will be scanned for existing ' +
-    'annotations; if present these existing annotations will be validated against a set of rules. Verification rules ' +
-    'can be configured by clicking the Advanced button.'
+      'annotations; if present these existing annotations will be validated against a set of rules. Verification rules ' +
+      'can be configured by clicking the Advanced button.'
   }));
   table.appendChild(self.createCheckboxRow({
     labelName: "Cache data:",
     defaultValue: false,
     inputName: "project-cache-data",
     help: 'If this checkbox is checked, all hyperlinks in the project resolved by MIRIAM repository (e.g. cross-links ' +
-    'to external bioinformatics databases) are resolved and cached.'
+      'to external bioinformatics databases) are resolved and cached.'
   }));
   table.appendChild(self.createCheckboxRow({
     labelName: "Auto margin:",
     defaultValue: true,
     inputName: "project-auto-margin",
     help: 'If this checkbox is checked, upon generation of the graphics, empty spaces surrounding elements and ' +
-    'interactions will be cropped.'
+      'interactions will be cropped.'
   }));
   table.appendChild(self.createCheckboxRow({
     labelName: "Display as SBGN:",
     defaultValue: false,
     inputName: "project-sbgn-visualization",
     help: 'If this checkbox is checked, the uploaded model will be displayed in SBGN format, instead of default ' +
-    'CellDesigner format.'
+      'CellDesigner format.'
   }));
   table.appendChild(self.createCheckboxRow({
     labelName: "Custom semantic zooming contains multiple overlays:",
     defaultValue: false,
-    inputName: "project-semantic-zooming-contains-multiple-overlays"
+    inputName: "project-semantic-zooming-contains-multiple-overlays",
+    help: "Check this checkbox to display each semantic zoom level in the General Overlays"
   }));
 
+  $("[name='project-semantic-zooming']", table).change(function () {
+    var disable = !$("[name='project-semantic-zooming']", table).is(":checked");
+    $("[name='project-semantic-zooming-contains-multiple-overlays']", table).prop("disabled", disable);
+    if (disable) {
+      $("[name='project-semantic-zooming-contains-multiple-overlays']", table).prop("checked", false);
+    }
+  });
+  $("[name='project-semantic-zooming-contains-multiple-overlays']", table).prop("disabled", !$("[name='project-semantic-zooming']", table).is(":checked"));
+
   var saveProjectButton = Functions.createElement({
     type: "button",
     name: "saveProject",

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

@@ -10,6 +10,8 @@ var CommentsTab = require('./CommentsAdminPanel');
 var GuiConnector = require('../../GuiConnector');
 var PrivilegeType = require('../../map/data/PrivilegeType');
 var ValidationError = require("../../ValidationError");
+var HttpStatus = require('http-status-codes');
+var NetworkError = require('../../NetworkError');
 
 var Functions = require('../../Functions');
 // noinspection JSUnusedLocalSymbols
@@ -256,7 +258,14 @@ EditProjectDialog.prototype.createGeneralTabContent = function () {
         return self.callListeners("onSave");
       }).then(function () {
         return self.close();
-      }).catch(GuiConnector.alert);
+      }).catch(function (error) {
+
+        if ((error instanceof NetworkError && error.statusCode === HttpStatus.BAD_REQUEST)) {
+          GuiConnector.alert(error.content.reason);
+        } else {
+          GuiConnector.alert(error);
+        }
+      });
     },
     xss: false
   });
@@ -543,7 +552,7 @@ EditProjectDialog.prototype.refresh = function () {
   var element = self.getElement();
   var project = self.getProject();
   $("[name='projectName']", element).val(xss(project.getName()));
-  $("[name='projectId']", element).val(project.getProjectId());
+  $("[name='projectId']", element).html(xss(project.getProjectId()));
   $("[name='projectVersion']", element).val(xss(project.getVersion()));
 
   var disease = "";

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

@@ -693,7 +693,10 @@ EditUserDialog.prototype.getSurname = function () {
  */
 EditUserDialog.prototype.close = function () {
   var self = this;
-  $(self.getElement()).dialog("close");
+  if ($(self.getElement()).hasClass("ui-dialog-content")) {
+    //close it only if it wasn't destroyed
+    $(self.getElement()).dialog("close");
+  }
 };
 
 /**

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

@@ -187,6 +187,12 @@ MapsAdminPanel.prototype.init = function () {
   var self = this;
   return self.getServerConnector().getProjects().then(function (projects) {
     return self.setProjects(projects);
+  }).then(function () {
+    return self.getServerConnector().getLoggedUser();
+  }).then(function (user) {
+    var configuration = self.getConfiguration();
+    var canAddProject = user.hasPrivilege(configuration.getPrivilegeType(PrivilegeType.PROJECT_MANAGEMENT));
+    $("[name='addProject']", self.getElement()).attr("disabled", !canAddProject);
   });
 };
 

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

@@ -69,7 +69,7 @@ UsersAdminPanel.prototype._createMenuRow = function () {
 
   var addUserButton = Functions.createElement({
     type: "button",
-    name: "addProject",
+    name: "addUser",
     content: '<span class="ui-icon ui-icon-circle-plus"></span>&nbsp;ADD USER',
     onclick: function () {
       return self.onAddClicked().then(null, GuiConnector.alert);
@@ -78,7 +78,7 @@ UsersAdminPanel.prototype._createMenuRow = function (