Merge branch 'devel_12.0.x'

CHANGELOG

@@ -14,6 +14,15 @@ minerva (12.1.0~alpha.0) experimental; urgency=medium
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 03 Aug 2018 10:00:00 +0200
 
+minerva (12.0.3) stable; urgency=medium
+  * Bug fix: SBML model annotations caused errors on upload
+  * Bug fix: Export of some models to SBML didn't work properly
+  * Bug fix: zip files weren't processed properly
+  * Bug fix: required annotations were always required for some types
+  * Bug fix: user cannot remove default map anymore
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 27 Aug 2018 11:00:00 +0200
+
 minerva (12.0.2) stable; urgency=medium
   * Bug fix: data overlay by annotation type fixed
   * Bug fix: [plugin] getting reactions with set of id larger than 100 elements

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java

@@ -19,11 +19,11 @@ import org.sbml.jsbml.SBMLReader;
 import org.sbml.jsbml.ext.SBasePlugin;
 import org.sbml.jsbml.ext.layout.Layout;
 import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
-import org.sbml.jsbml.util.NotImplementedException;
 
 import lcsb.mapviewer.commands.CommandExecutionException;
 import lcsb.mapviewer.commands.layout.ApplySimpleLayoutModelCommand;
 import lcsb.mapviewer.common.MimeType;
+import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.converter.ConverterException;
 import lcsb.mapviewer.converter.ConverterParams;
 import lcsb.mapviewer.converter.IConverter;
@@ -103,13 +103,10 @@ public class SbmlParser implements IConverter {
         throw new NotImplementedException("ConversionFactor not implemented for model");
       }
       if (sbmlModel.getCVTermCount() > 0) {
-        throw new NotImplementedException("CVTerms not implemented for model");
+        logger.warn("Handling of CVTerms is not implemented for model");
       }
-      if (sbmlModel.getEventCount() > 0) {
-        throw new NotImplementedException("Events not implemented for model");
-      }
-      if (sbmlModel.getEventAssignmentCount() > 0) {
-        throw new NotImplementedException("EventAssignemnts not implemented for model");
+      if (sbmlModel.getEventCount() > 0 || sbmlModel.getEventAssignmentCount() > 0) {
+        logger.warn("Handling of Events is not implemented for model");
       }
       if (sbmlModel.getInitialAssignmentCount() > 0) {
         throw new NotImplementedException("InitialAssignment not implemented for model");

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java

@@ -103,8 +103,12 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
         LocalParameter parameter = new LocalParameter();
         parameter.setId(minervaParameter.getElementId());
         parameter.setName(minervaParameter.getName());
-        parameter.setValue(minervaParameter.getValue());
-        parameter.setUnits(minervaParameter.getUnits().getUnitId());
+        if (minervaParameter.getValue() != null) {
+          parameter.setValue(minervaParameter.getValue());
+        }
+        if (minervaParameter.getUnits() != null) {
+          parameter.setUnits(minervaParameter.getUnits().getUnitId());
+        }
         result.addLocalParameter(parameter);
       }
     }

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporterTest.java

@@ -13,7 +13,10 @@ import lcsb.mapviewer.converter.model.sbml.SbmlBioEntityExporter;
 import lcsb.mapviewer.converter.model.sbml.SbmlCompartmentExporter;
 import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesExporter;
 import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
+import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
 import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.reaction.type.TriggerReaction;
 import lcsb.mapviewer.model.map.species.Species;
 
@@ -28,6 +31,22 @@ public class SbmlReactionExporterTest {
     assertNotNull(result);
   }
 
+  @Test
+  public void testReactionWithKineticsWithoutUnitsToSbml() throws InconsistentModelException {
+    ModelFullIndexed model = new ModelFullIndexed(null);
+
+    SbmlReactionExporter exporter = createExporter(model);
+    Reaction reaction = new TriggerReaction();
+    SbmlKinetics kinetics = new SbmlKinetics();
+    reaction.setKinetics(kinetics);
+    kinetics.setDefinition("<lambda>" + "<bvar><ci> x </ci></bvar>" + "<bvar><ci> y </ci></bvar>"
+        + "<apply><plus/><ci> x </ci><ci> x </ci><cn type=\"integer\"> 2 </cn></apply>" + "</lambda>\n\n");
+    SbmlParameter parameter = new SbmlParameter("x");
+    kinetics.addParameter(parameter);
+    org.sbml.jsbml.Reaction result = exporter.createSbmlElement(reaction);
+    assertNotNull(result);
+  }
+
   private SbmlReactionExporter createExporter(ModelFullIndexed model) {
     SBMLDocument doc = new SBMLDocument(3, 1);
     Model result = doc.createModel(model.getIdModel());

frontend-js/src/main/js/Configuration.js

@@ -625,7 +625,11 @@ Configuration.prototype.getElementTypeTree = function () {
   var treeNodes = {
     "lcsb.mapviewer.model.map.BioEntity": {
       text: "BioEntity",
-      children: []
+      children: [],
+      data: {
+        className: "lcsb.mapviewer.model.map.BioEntity",
+        name: "BioEntity"
+      }
     }
   };
 
@@ -655,7 +659,7 @@ Configuration.prototype.getElementTypeTree = function () {
   for (var treeNodeName in treeNodes) {
     if (treeNodes.hasOwnProperty(treeNodeName)) {
       var treeNode = treeNodes[treeNodeName];
-      if (treeNode.data !== undefined) {
+      if (treeNode.data !== undefined && treeNode.data.parentClass !== undefined) {
         var parentNode = treeNodes[treeNode.data.parentClass];
         if (parentNode.data === undefined || parentNode.data.name !== "Compartment") {
           parentNode.children.push(treeNode);

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

@@ -42,6 +42,7 @@ var GuiConnector = require('./GuiConnector');
 var ObjectWithListeners = require('./ObjectWithListeners');
 
 var Point = require('./map/canvas/Point');
+var ZipEntry = require('./gui/admin/ZipEntry');
 
 /**
  * This object contains methods that will communicate with server.
@@ -309,7 +310,12 @@ ServerConnector.objectToRequestString = function (object) {
   if (object instanceof Point) {
     value = this.pointToString(object);
   } else if (Object.prototype.toString.call(object) === '[object Array]') {
-    value = this.idsToString(object);
+    var arrayObject = object[0];
+    if (arrayObject instanceof ZipEntry) {
+      value = object;
+    } else {
+      value = this.idsToString(object);
+    }
   } else if (object === null) {
     value = undefined;
   } else if (typeof object === 'string' || object instanceof String || !isNaN(object)) {

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

@@ -7,6 +7,7 @@ var AddProjectDialog = require('./AddProjectDialog');
 var EditProjectDialog = require('./EditProjectDialog');
 var LogListDialog = require('./LogListDialog');
 var PrivilegeType = require('../../map/data/PrivilegeType');
+var ConfigurationType = require('../../ConfigurationType');
 var UserPreferences = require('../../map/data/UserPreferences');
 
 // noinspection JSUnusedLocalSymbols
@@ -234,6 +235,10 @@ MapsAdminPanel.prototype.projectToTableRow = function (project, row, user) {
     disabled = "";
   }
   row[5] = "<button name='showEditDialog' data='" + project.getProjectId() + "'" + disabled + "><i class='fa fa-edit' style='font-size:17px'></i></button>";
+
+  if (self.getConfiguration().getOption(ConfigurationType.DEFAULT_MAP).getValue() === projectId) {
+    disabled = " disabled ";
+  }
   row[6] = "<button name='removeProject' data='" + project.getProjectId() + "'" + disabled + "><i class='fa fa-trash-o' style='font-size:17px'></button>";
 
   return row;

model/src/main/java/lcsb/mapviewer/model/user/ConfigurationElementType.java

@@ -167,7 +167,7 @@ public enum ConfigurationElementType {
   /**
    * Opacity of data overlay objects in the frontend.
    */
-  OVERLAY_OPACITY("Opacity used when drwaing data overlays (value between 0.0-1.0)", "0.8",
+  OVERLAY_OPACITY("Opacity used when drawing data overlays (value between 0.0-1.0)", "0.8",
       ConfigurationElementEditType.DOUBLE, false, ConfigurationElementTypeGroup.OVERLAYS),
 
   /**

model/src/main/java/lcsb/mapviewer/model/user/UserAnnotationSchema.java

@@ -337,6 +337,15 @@ public class UserAnnotationSchema implements Serializable {
     return new ArrayList<MiriamType>();
   }
 
+  public boolean requiresAtLeastOneAnnotation(Class<?> clazz) {
+    for (UserClassRequiredAnnotations cva : classRequiredAnnotators) {
+      if (cva.getClassName().equals(clazz.getCanonicalName())) {
+        return cva.getRequireAtLeastOneAnnotation();
+      }
+    }
+    return false;
+  }
+
   /**
    * @return the classRequiredAnnotators
    * @see #classRequiredAnnotators

persist/src/db/12.0.3/fix_db_20180827.sql

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

rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java

@@ -46,6 +46,7 @@ import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.services.SecurityException;
+import lcsb.mapviewer.services.interfaces.IConfigurationService;
 import lcsb.mapviewer.services.interfaces.IModelService;
 import lcsb.mapviewer.services.interfaces.IProjectService;
 import lcsb.mapviewer.services.interfaces.IUserService;
@@ -68,6 +69,9 @@ public abstract class BaseRestImpl {
   @Autowired
   private IUserService userService;
 
+  @Autowired
+  private IConfigurationService configurationService;
+
   @Autowired
   private MiriamConnector miriamConnector;
 
@@ -375,4 +379,12 @@ public abstract class BaseRestImpl {
     }
   }
 
+  public IConfigurationService getConfigurationService() {
+    return configurationService;
+  }
+
+  public void setConfigurationService(IConfigurationService configurationService) {
+    this.configurationService = configurationService;
+  }
+
 }

rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java

@@ -24,7 +24,6 @@ import java.util.TreeMap;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.log4j.Logger;
-import org.primefaces.model.map.LatLng;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.transaction.annotation.Transactional;
 import org.springframework.util.MultiValueMap;
@@ -73,6 +72,7 @@ import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.model.SubmodelType;
 import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.user.ConfigurationElementType;
 import lcsb.mapviewer.model.user.PrivilegeType;
 import lcsb.mapviewer.model.user.User;
 import lcsb.mapviewer.persist.dao.ProjectDao;
@@ -362,11 +362,11 @@ public class ProjectRestImpl extends BaseRestImpl {
 
     List<Point2D> points = new ArrayList<>();
     for (String string : stringPointArray) {
-        if (!string.trim().equals("")) {
-            double x = Double.valueOf(string.split(",")[0]);
-            double y= Double.valueOf(string.split(",")[1]);
-            points.add(new Point2D.Double(x, y));
-        }
+      if (!string.trim().equals("")) {
+        double x = Double.valueOf(string.split(",")[0]);
+        double y = Double.valueOf(string.split(",")[1]);
+        points.add(new Point2D.Double(x, y));
+      }
     }
 
     if (points.size() <= 2) {
@@ -375,13 +375,13 @@ public class ProjectRestImpl extends BaseRestImpl {
       points.add(new Point2D.Double(colorModel.getWidth(), 0));
       points.add(new Point2D.Double(colorModel.getWidth(), colorModel.getHeight()));
       points.add(new Point2D.Double(0, colorModel.getHeight()));
-  }
+    }
 
     Path2D polygon = new Path2D.Double();
     polygon.moveTo(points.get(0).getX(), points.get(0).getY());
     for (int i = 1; i < points.size(); i++) {
-        Point2D point = points.get(i);
-        polygon.lineTo(point.getX(), point.getY());
+      Point2D point = points.get(i);
+      polygon.lineTo(point.getX(), point.getY());
     }
     polygon.closePath();
     return polygon;
@@ -736,8 +736,11 @@ public class ProjectRestImpl extends BaseRestImpl {
   }
 
   public Map<String, Object> removeProject(String token, String projectId, String path)
-      throws ObjectNotFoundException, SecurityException {
+      throws SecurityException, QueryException {
     Project project = getProjectService().getProjectByProjectId(projectId, token);
+    if (getConfigurationService().getConfigurationValue(ConfigurationElementType.DEFAULT_MAP).equals(project.getProjectId())) {
+      throw new QueryException("You cannot remove default map");
+    }
     getProjectService().removeProject(project, path, true, token);
     return getProject(projectId, token);
   }

service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java

@@ -1138,6 +1138,7 @@ public class ProjectService implements IProjectService {
     ClassTreeNode top = elementUtils.getAnnotatedElementClassTree();
 
     Class<?> clazz = top.getClazz();
+    top.setData(annotationSchema.requiresAtLeastOneAnnotation(clazz));
     TreeNode root = new DefaultTreeNode(new AnnotatedObjectTreeRow(top, modelAnnotator.getAvailableAnnotators(clazz),
         modelAnnotator.getAnnotatorsFromCommonNames(annotationSchema.getAnnotatorsForClass(clazz)),
         annotationSchema.getValidAnnotations(clazz), annotationSchema.getRequiredAnnotations(clazz)), null);
@@ -1156,6 +1157,7 @@ public class ProjectService implements IProjectService {
       for (ClassTreeNode node : element.getLeft().getChildren()) {
 
         clazz = node.getClazz();
+        node.setData(annotationSchema.requiresAtLeastOneAnnotation(clazz));
         AnnotatedObjectTreeRow data = new AnnotatedObjectTreeRow(node, modelAnnotator.getAvailableAnnotators(clazz),
             modelAnnotator.getAnnotatorsFromCommonNames(annotationSchema.getAnnotatorsForClass(clazz)),
             annotationSchema.getValidAnnotations(clazz), annotationSchema.getRequiredAnnotations(clazz));