Merge branch '1596-click-on-reaction-annotations' into 'devel_16.0.x'

Resolve "Make annotations for 'clicked' elements and reactions visible by default"

See merge request !1394

CHANGELOG

+minerva (16.0.2) stable; urgency=medium
+  * Bug fix: clicking on reaction stopped working (regression 16.0.1, #1599)
+  * Bug fix: clicking on map should show expanded results in left panel (#1596)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 22 Nov 2021 12:00:00 +0200
+
 minerva (16.0.1) stable; urgency=medium
   * Bug fix: pubmed identifier is visible in link name (#1564)
   * Bug fix: auto discovery of genomics file stopped working

CellDesigner-plugin/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>16.0.1</version>
+		<version>16.0.2</version>
 	</parent>
 	<artifactId>CellDesigner-plugin</artifactId>
 	<!-- dependency from the MapViewer model -->
@@ -50,19 +50,19 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model</artifactId>
-			<version>16.0.1</version>
+			<version>16.0.2</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>commons</artifactId>
-			<version>16.0.1</version>
+			<version>16.0.2</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter-CellDesigner</artifactId>
-			<version>16.0.1</version>
+			<version>16.0.2</version>
 		</dependency>
 
 		<dependency>

annotation/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>16.0.1</version>
+		<version>16.0.2</version>
 	</parent>
 	<artifactId>annotation</artifactId>
 	<name>Annotation module</name>
@@ -18,7 +18,7 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model</artifactId>
-			<version>16.0.1</version>
+			<version>16.0.2</version>
 		</dependency>
 
 		<!-- dependency from the MapViewer dao -->
@@ -26,7 +26,7 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>persist</artifactId>
-			<version>16.0.1</version>
+			<version>16.0.2</version>
 		</dependency>
 
 		<!-- dependency from the MapViewer cell designer parser (we need access 
@@ -34,13 +34,13 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter-CellDesigner</artifactId>
-			<version>16.0.1</version>
+			<version>16.0.2</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter</artifactId>
-			<version>16.0.1</version>
+			<version>16.0.2</version>
 		</dependency>
 
 		<!-- Log4J2 -->

commons/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>16.0.1</version>
+		<version>16.0.2</version>
 	</parent>
 	<artifactId>commons</artifactId>
 	<name>Mapviewer commons</name>

converter-CellDesigner/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>16.0.1</version>
+		<version>16.0.2</version>
 	</parent>
 	<artifactId>converter-CellDesigner</artifactId>
 	<name>CellDesigner converter</name>
@@ -17,13 +17,13 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model</artifactId>
-			<version>16.0.1</version>
+			<version>16.0.2</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter</artifactId>
-			<version>16.0.1</version>
+			<version>16.0.2</version>
 		</dependency>
 
 		<!-- Log4J2 -->

converter-SBGNML/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>16.0.1</version>
+		<version>16.0.2</version>
 	</parent>
 	<artifactId>converter-SBGNML</artifactId>
 
@@ -20,26 +20,26 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model</artifactId>
-			<version>16.0.1</version>
+			<version>16.0.2</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>persist</artifactId>
-			<version>16.0.1</version>
+			<version>16.0.2</version>
 			<scope>test</scope>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter-CellDesigner</artifactId>
-			<version>16.0.1</version>
+			<version>16.0.2</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter-graphics</artifactId>
-			<version>16.0.1</version>
+			<version>16.0.2</version>
 		</dependency>
 
 		<dependency>

converter-graphics/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>16.0.1</version>
+		<version>16.0.2</version>
 	</parent>
 	<artifactId>converter-graphics</artifactId>
 	<name>MapViewer graphics converter</name>
@@ -18,13 +18,13 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model</artifactId>
-			<version>16.0.1</version>
+			<version>16.0.2</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model-command</artifactId>
-			<version>16.0.1</version>
+			<version>16.0.2</version>
 		</dependency>
 
 		<!-- Log4J2-->

converter-sbml/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>16.0.1</version>
+		<version>16.0.2</version>
 	</parent>
 	<artifactId>converter-sbml</artifactId>
 	<name>converter-sbml</name>
@@ -40,22 +40,22 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model</artifactId>
-			<version>16.0.1</version>
+			<version>16.0.2</version>
 		</dependency>
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model-command</artifactId>
-			<version>16.0.1</version>
+			<version>16.0.2</version>
 		</dependency>
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter-CellDesigner</artifactId>
-			<version>16.0.1</version>
+			<version>16.0.2</version>
 		</dependency>
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter</artifactId>
-			<version>16.0.1</version>
+			<version>16.0.2</version>
 		</dependency>
 
 		<!-- Log4J2 -->
@@ -154,7 +154,7 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter-graphics</artifactId>
-			<version>16.0.1</version>
+			<version>16.0.2</version>
 			<scope>test</scope>
 		</dependency>
 

converter/pom.xml

@@ -5,7 +5,7 @@
   <parent>
     <groupId>lcsb.mapviewer</groupId>
     <artifactId>parent</artifactId>
-    <version>16.0.1</version>
+    <version>16.0.2</version>
   </parent>
   
   <artifactId>converter</artifactId>
@@ -15,7 +15,7 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
       <artifactId>model</artifactId>
-      <version>16.0.1</version>
+      <version>16.0.2</version>
     </dependency>
 		<dependency>
 			<groupId>xerces</groupId>

frontend-js/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>16.0.1</version>
+		<version>16.0.2</version>
 	</parent>
 	<artifactId>frontend-js</artifactId>
 	<name>frontend-js</name>

frontend-js/src/main/js/SessionData.js

@@ -92,9 +92,7 @@ SessionData.prototype.setSearchQuery = function (value) {
  */
 SessionData.prototype._setStorageItem = function (key, value) {
   try {
-    logger.debug("X")
     window.localStorage.setItem(key, value);
-    logger.debug("Y")
   } catch (e) {
     window.localStorage.clear();
     logger.warn("Problem with setting value in local storage: " + key);

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

@@ -19,6 +19,7 @@ var SearchBioEntityGroup = require('../../map/data/SearchBioEntityGroup');
 var logger = require('../../logger');
 var Functions = require('../../Functions');
 var SearchMapBioEntityGroup = require("../../map/data/SearchMapBioEntityGroup");
+var QueryType = require("../../map/overlay/AbstractDbOverlay").QueryType;
 
 /**
  *
@@ -71,7 +72,6 @@ function GenericSearchPanel(params) {
       }
     });
   });
-
 }
 
 GenericSearchPanel.prototype = Object.create(AbstractDbPanel.prototype);
@@ -131,7 +131,7 @@ GenericSearchPanel.prototype.createTableElement = function (element, icon) {
         label = "Top map: ";
       }
       var headerDiv = guiUtils.createSubMapLink({
-        label: label + "("+element.getBioEntities().length + " hits): ",
+        label: label + "(" + element.getBioEntities().length + " hits): ",
         mapId: element.getModelId()
       });
       $(headerDiv).css("padding", "5px");
@@ -172,6 +172,10 @@ GenericSearchPanel.prototype.createTableElement = function (element, icon) {
 };
 
 GenericSearchPanel.prototype.addResultTab = function (query, elements) {
+  var queryObj = JSON.parse(query);
+  if (queryObj.type === QueryType.SEARCH_BY_COORDINATES) {
+    return AbstractDbPanel.prototype.addResultTab.call(this, query, elements);
+  }
   var self = this;
   var groupsByMap = {};
   var groups = [];

model-command/pom.xml

@@ -3,7 +3,7 @@
   <parent>
     <groupId>lcsb.mapviewer</groupId>
     <artifactId>parent</artifactId>
-    <version>16.0.1</version>
+    <version>16.0.2</version>
   </parent>
   <artifactId>model-command</artifactId>
   <name>Model commands</name>
@@ -16,7 +16,7 @@
 		<dependency>
     	<groupId>lcsb.mapviewer</groupId>
       <artifactId>model</artifactId>
-      <version>16.0.1</version>
+      <version>16.0.2</version>
     </dependency>
     
 
@@ -24,7 +24,7 @@
 		<dependency>
       <groupId>lcsb.mapviewer</groupId>
       <artifactId>converter-CellDesigner</artifactId>
-      <version>16.0.1</version>
+      <version>16.0.2</version>
     </dependency>
 
 		<!-- Log4J2-->

model/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>16.0.1</version>
+		<version>16.0.2</version>
 	</parent>
 	<artifactId>model</artifactId>
 	<name>model MapViewer</name>
@@ -15,7 +15,7 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>commons</artifactId>
-			<version>16.0.1</version>
+			<version>16.0.2</version>
 		</dependency>
 		
 		<!-- Java xml serialization -->

pathvisio/pom.xml

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>16.0.1</version>
+		<version>16.0.2</version>
 	</parent>
 	<artifactId>pathvisio</artifactId>
 	<name>Pathvisio plugin</name>
@@ -77,20 +77,20 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model</artifactId>
-			<version>16.0.1</version>
+			<version>16.0.2</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter-CellDesigner</artifactId>
-			<version>16.0.1</version>
+			<version>16.0.2</version>
 		</dependency>
 
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>converter-graphics</artifactId>
 			<scope>test</scope>
-			<version>16.0.1</version>
+			<version>16.0.2</version>
 		</dependency>
 
 		<!-- Log4J2 -->

persist/pom.xml

@@ -7,7 +7,7 @@
 	<parent>
 		<groupId>lcsb.mapviewer</groupId>
 		<artifactId>parent</artifactId>
-		<version>16.0.1</version>
+		<version>16.0.2</version>
 	</parent>
 
 	<artifactId>persist</artifactId>
@@ -27,7 +27,7 @@
 		<dependency>
 			<groupId>lcsb.mapviewer</groupId>
 			<artifactId>model</artifactId>
-			<version>16.0.1</version>
+			<version>16.0.2</version>
 		</dependency>
 
 		<!-- apache ftp -->

persist/src/main/java/lcsb/mapviewer/persist/dao/map/ReactionDao.java

@@ -41,7 +41,7 @@ public class ReactionDao extends BaseDao<Reaction> {
     super(Reaction.class);
   }
 
-  public Reaction getById(int id, ModelData map) {
+  public Reaction getById(final int id, final ModelData map) {
     List<?> list = getSession()
         .createQuery(
             " from " + this.getClazz().getSimpleName() + " where id=:id and model = :map" + removableAndStatemant())
@@ -56,14 +56,16 @@ public class ReactionDao extends BaseDao<Reaction> {
   }
 
   /**
-   * Fetch proxy of reaction objects together with distance from point 
+   * Fetch proxy of reaction objects together with distance from point
+   * 
    * @param map
    * @param point
    * @param numberOfElements
    * @param classes
    * @return
    */
-  public List<Pair<Reaction,Double>> getByCoordinatesWithDistance(ModelData map, Point2D point, int numberOfElements, List<Class<? extends BioEntity>> classes) {
+  public List<Pair<Reaction, Double>> getByCoordinatesWithDistance(final ModelData map, final Point2D point, final int numberOfElements,
+      final List<Class<? extends BioEntity>> classes) {
     String typeClause = getTypeClause(classes);
 
     org.hibernate.query.Query<?> query = getSession()
@@ -92,18 +94,19 @@ public class ReactionDao extends BaseDao<Reaction> {
 
     @SuppressWarnings("unchecked")
     List<Object[]> orderedList = (List<Object[]>) query.list();
-    List<Pair<Reaction,Double>> result = new ArrayList<>();
-    for (Object[] row: orderedList) {
-      Reaction reaction = getSession().load(Reaction.class, (Integer)row[0]);
-      Double dist = Math.max((Double)row[1], (Double)row[2]);
+    List<Pair<Reaction, Double>> result = new ArrayList<>();
+    for (Object[] row : orderedList) {
+      Reaction reaction = getSession().load(Reaction.class, (Integer) row[0]);
+      Double dist = Math.min((Double) row[1], (Double) row[2]);
       result.add(new Pair<>(reaction, dist));
     }
     return result;
-    
+
   }
 
-  public List<Reaction> getByCoordinates(ModelData map, Point2D point, int numberOfElements, List<Class<? extends BioEntity>> classes) {
-    List<Pair<Reaction,Double>> data = getByCoordinatesWithDistance(map, point, numberOfElements, classes);
+  public List<Reaction> getByCoordinates(final ModelData map, final Point2D point, final int numberOfElements,
+      final List<Class<? extends BioEntity>> classes) {
+    List<Pair<Reaction, Double>> data = getByCoordinatesWithDistance(map, point, numberOfElements, classes);
     List<Reaction> result = new ArrayList<>();
     for (Pair<Reaction, Double> pair : data) {
       result.add(pair.getLeft());
@@ -111,7 +114,7 @@ public class ReactionDao extends BaseDao<Reaction> {
     return result;
   }
 
-  private String getTypeClause(List<Class<? extends BioEntity>> classes) {
+  private String getTypeClause(final List<Class<? extends BioEntity>> classes) {
     String typeClause = "";
     if (classes.size() > 0) {
       typeClause = " and type(reaction) in :classes ";
@@ -119,7 +122,7 @@ public class ReactionDao extends BaseDao<Reaction> {
     return typeClause;
   }
 
-  private List<Reaction> genericListToReactionList(List<?> list) {
+  private List<Reaction> genericListToReactionList(final List<?> list) {
     List<Reaction> result = new ArrayList<>();
 
     for (Object object : list) {
@@ -128,7 +131,7 @@ public class ReactionDao extends BaseDao<Reaction> {
     return result;
   }
 
-  public List<Reaction> getByIds(Collection<Integer> ids, Collection<Integer> participantIds, List<ModelData> maps) {
+  public List<Reaction> getByIds(final Collection<Integer> ids, final Collection<Integer> participantIds, final List<ModelData> maps) {
     String idClause = "";
     if (ids.size() > 0) {
       idClause = " and reaction.id in :ids ";
@@ -158,7 +161,7 @@ public class ReactionDao extends BaseDao<Reaction> {
   }
 
   @SuppressWarnings("unchecked")
-  public List<SbmlParameter> getParametersByMaps(List<ModelData> maps) {
+  public List<SbmlParameter> getParametersByMaps(final List<ModelData> maps) {
     List<?> list = getSession()
         .createQuery("select parameter_t from " + this.getClazz().getSimpleName()
             + " reaction inner join reaction.kinetics.parameters parameter_t where "
@@ -170,7 +173,7 @@ public class ReactionDao extends BaseDao<Reaction> {
     return (List<SbmlParameter>) list;
   }
 
-  public Map<MiriamType, Integer> getAnnotationStatistics(List<ModelData> maps) {
+  public Map<MiriamType, Integer> getAnnotationStatistics(final List<ModelData> maps) {
     Map<MiriamType, Integer> result = new HashMap<>();
     List<?> list = getSession()
         .createQuery(
@@ -186,7 +189,7 @@ public class ReactionDao extends BaseDao<Reaction> {
     return result;
   }
 
-  public Page<Reaction> getByFilter(Pageable pageable, Map<ReactionProperty, List<? extends Object>> filter) {
+  public Page<Reaction> getByFilter(final Pageable pageable, final Map<ReactionProperty, List<? extends Object>> filter) {
     String queryString = "select distinct(reaction) from " + this.getClazz().getSimpleName() + " reaction "
         + getJoinsForFilter(filter)
         + getWhereByFilter(filter);
@@ -206,7 +209,7 @@ public class ReactionDao extends BaseDao<Reaction> {
     return new PageImpl<Reaction>(genericListToReactionList(query.list()), pageable, getCountByFilter(filter));
   }
 
-  public long getCountByFilter(Map<ReactionProperty, List<? extends Object>> filter) {
+  public long getCountByFilter(final Map<ReactionProperty, List<? extends Object>> filter) {
     String countQueryString = "select count(distinct reaction) from " + this.getClazz().getSimpleName() + " reaction "
         + getJoinsForFilter(filter)
         + getWhereByFilter(filter);
@@ -215,86 +218,86 @@ public class ReactionDao extends BaseDao<Reaction> {
     return (Long) countQuery.list().get(0);
   }
 
-  private void assignFilterOptions(Query<?> query, Map<ReactionProperty, List<? extends Object>> filter) {
+  private void assignFilterOptions(final Query<?> query, final Map<ReactionProperty, List<? extends Object>> filter) {
     for (ReactionProperty property : filter.keySet()) {
       List<? extends Object> list = filter.get(property);
       if (list != null && list.size() > 0) {
         switch (property) {
-        case ANNOTATION:
-          for (int i = 0; i < list.size(); i++) {
-            MiriamData annotation = (MiriamData) list.get(i);
-            query.setParameter("type" + i, annotation.getDataType());
-            query.setParameter("resource" + i, annotation.getResource().toLowerCase());
+          case ANNOTATION:
+            for (int i = 0; i < list.size(); i++) {
+              MiriamData annotation = (MiriamData) list.get(i);
+              query.setParameter("type" + i, annotation.getDataType());
+              query.setParameter("resource" + i, annotation.getResource().toLowerCase());
+            }
+            break;
+          case CLASS:
+            query.setParameter("classes", list);
+            break;
+          case MAP:
+            query.setParameter("maps", list);
+            break;
+          case PERFECT_TEXT: {
+            String text = (String) list.get(0);
+            text = text.toLowerCase().trim();
+            query.setParameter("query", text);
+            if (StringUtils.isNumeric(text)) {
+              query.setParameter("query_integer", Integer.valueOf(text));
+            }
+            break;
           }
-          break;
-        case CLASS:
-          query.setParameter("classes", list);
-          break;
-        case MAP:
-          query.setParameter("maps", list);
-          break;
-        case PERFECT_TEXT: {
-          String text = (String) list.get(0);
-          text = text.toLowerCase().trim();
-          query.setParameter("query", text);
-          if (StringUtils.isNumeric(text)) {
-            query.setParameter("query_integer", Integer.valueOf(text));
+          case TEXT: {
+            String text = (String) list.get(0);
+            text = text.toLowerCase().trim();
+            query.setParameter("query", text);
+            break;
           }
-          break;
-        }
-        case TEXT: {
-          String text = (String) list.get(0);
-          text = text.toLowerCase().trim();
-          query.setParameter("query", text);
-          break;
-        }
-        default:
-          throw new NotImplementedException("Search by " + property + " not implemented");
+          default:
+            throw new NotImplementedException("Search by " + property + " not implemented");
         }
       }
     }
   }
 
-  private String getWhereByFilter(Map<ReactionProperty, List<? extends Object>> filter) {
+  private String getWhereByFilter(final Map<ReactionProperty, List<? extends Object>> filter) {
     List<String> statements = new ArrayList<>();
 
     for (ReactionProperty property : filter.keySet()) {
       List<? extends Object> list = filter.get(property);
       if (list != null && list.size() > 0) {
         switch (property) {
-        case ANNOTATION: {
-          StringBuilder statement = new StringBuilder("(");
-          for (int i = 0; i < list.size(); i++) {
-            if (i > 0) {
-              statement.append(" or ");
+          case ANNOTATION: {
+            StringBuilder statement = new StringBuilder("(");
+            for (int i = 0; i < list.size(); i++) {
+              if (i > 0) {
+                statement.append(" or ");
+              }
+              statement.append("md.dataType = :type" + i + " and lower(md.resource) = :resource" + i + " ");