Merge branch 'devel_11.0.x'

CHANGELOG

@@ -7,8 +7,8 @@ minerva (12.0.0~alpha.0) unstable; urgency=medium
   * Feature: kinetics support
   * Feature: plugin API
   * Feature: all functionalities are provided via REST API
-  * Feature: visualization of two (or more) overlaying results (like drug 
-    target, mirna target) is highlighted with different icon 
+  * Feature: visualization of two (or more) overlaying results (like drug
+    target, mirna target) is highlighted with different icon
   * Small improvement: email for account request contain configurable text
   * Small improvement: transparency level for data overlays is configurable
   * Small improvement: CellDesigner reactions of Modifier type are acceptable
@@ -19,33 +19,39 @@ minerva (12.0.0~alpha.0) unstable; urgency=medium
   * Small improvement: Description of chemical panel refers to the disease
     connected to the map
   * Small improvement: Confirm button when removing data overlay
-  * Small improvement: Clicking on data overlayed element behaves in the same 
-    way as clicking on not overlayed element 
+  * Small improvement: Clicking on data overlayed element behaves in the same
+    way as clicking on not overlayed element
   * Small improvement: Title of list of submaps doesn't contain UNKNOWN tag
   * Small improvement: DOI is supported as miriam type
   * Small improvement: When loading data in search tab there is "LOADING" icon
-  * Small improvement: Data overlays can use source element identifiers for 
-    filtering 
+  * Small improvement: Data overlays can use source element identifiers for
+    filtering
   * Small improvement: Data overlays can submap column to differentiate between
     maps
   * Small improvement: search by chemical names is possible
-  * Small improvement: auto complete functionality for drugs, mirnas and 
+  * Small improvement: auto complete functionality for drugs, mirnas and
     chemicals
-  * Small improvement: columns value and type are not mutually exclusive in 
+  * Small improvement: columns value and type are not mutually exclusive in
     data overlays
   * Small improvement: column type is case insensitive in data overlays
   * Small improvement: every submap contains default center position and zoom
     level to customize default view when entering map for the first time
-  * Small improvement: data overlays color scale contains configurable default 
+  * Small improvement: data overlays color scale contains configurable default
     middle color (for 0 values)
   * Small improvement: opening data overlay switch to empty background
   * Bug fix: uploading of zip files created by mac doesn't crash due to
-    .DS_Store folder 
-  * Bug fix: auto complete is case insensitive 
+    .DS_Store folder
+  * Bug fix: auto complete is case insensitive
   * Bug fix: google maps API 404 errors for non existing tiles are removed
-   
+
  -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 21 Feb 2018 12:00:00 +0200
 
+minerva (11.0.9) stable; urgency=medium
+  * Bug fix: some comment couldn't be loaded
+  * Bug fix: when adding comment it didn't appear on map immediately
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 21 Feb 2018 18:00:00 +0200
+
 minerva (11.0.8) stable; urgency=medium
   * Bug fix: XSS vulnerability
   * Bug fix: "java.lang.IllegalStateException: getWriter()" exceptions

model/src/main/java/lcsb/mapviewer/model/map/species/Element.java

@@ -65,7 +65,7 @@ import lcsb.mapviewer.model.map.model.ModelData;
 public abstract class Element implements BioEntity, Serializable, SbmlArgument {
 
   /**
-   * 
+   *
    */
   private static final long serialVersionUID = 1L;
 
@@ -170,7 +170,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
 
   /**
    * From which level element should be visible.
-   * 
+   *
    * @see #transparencyLevel
    * @see lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params#level
    *      AbstractImageGenerator.Params#level
@@ -179,7 +179,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
 
   /**
    * From which level element should be transparent.
-   * 
+   *
    * @see #visibilityLevel
    * @see AbstractImageGenerator.Params#level
    */
@@ -268,7 +268,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
 
   /**
    * Constructor that creates a copy of the element given in the parameter.
-   * 
+   *
    * @param original
    *          original object that will be used for creating copy
    */
@@ -303,7 +303,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
 
   /**
    * Adds list of former symbol to the object.
-   * 
+   *
    * @param formerSymbols
    *          list of former symbols to add
    */
@@ -327,7 +327,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
 
   /**
    * Parse and set x coordinate from string.
-   * 
+   *
    * @param string
    *          text representing x coordinate
    * @see x
@@ -338,7 +338,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
 
   /**
    * Parse and set y coordinate from string.
-   * 
+   *
    * @param string
    *          text representing y coordinate
    * @see y
@@ -349,7 +349,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
 
   /**
    * Parse and set font size.
-   * 
+   *
    * @param string
    *          text representing font size
    * @see fontSize
@@ -360,7 +360,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
 
   /**
    * Returns x coordinate of the element center.
-   * 
+   *
    * @return x coordinate of the element center
    */
   public double getCenterX() {
@@ -369,7 +369,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
 
   /**
    * Returns y coordinate of the element center.
-   * 
+   *
    * @return y coordinate of the element center
    */
   public double getCenterY() {
@@ -378,7 +378,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
 
   /**
    * Returns coordinates of the element center point.
-   * 
+   *
    * @return coordinates of the element center point
    */
   public Point2D getCenter() {
@@ -388,7 +388,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
   /**
    * Methods that increase size of the element by increaseSize. It influence x, y,
    * width and height fields of the element.
-   * 
+   *
    * @param increaseSize
    *          by how many units we want to increase size of the element
    */
@@ -401,7 +401,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
 
   /**
    * Parse and set width.
-   * 
+   *
    * @param string
    *          text representing width
    * @see width
@@ -416,7 +416,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
 
   /**
    * Parse and set height.
-   * 
+   *
    * @param string
    *          text representing height
    * @see height
@@ -430,7 +430,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
   }
 
   /**
-   * 
+   *
    * @param width
    *          the width value to set
    * @see #width
@@ -440,7 +440,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
   }
 
   /**
-   * 
+   *
    * @param height
    *          the height value to set
    * @see #height
@@ -452,7 +452,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
   /**
    * This method computes the distance between point and the element. It assumes
    * that element is a rectangle.
-   * 
+   *
    * @param point
    *          point from which we are looking for a distance
    * @return distance between point and this element
@@ -475,7 +475,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
 
   /**
    * Checks if element contains a point. It assumes that element is a rectangle.
-   * 
+   *
    * @param point
    *          point to check
    * @return <i>true</i> if point belongs to the element, <i>false</i> otherwise
@@ -490,7 +490,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
 
   /**
    * Returns a rectangle that determines a rectangle border.
-   * 
+   *
    * @return rectangle border
    */
   public Rectangle2D getBorder() {
@@ -499,7 +499,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
 
   /**
    * Returns size of the element in square units.
-   * 
+   *
    * @return size of the element
    */
   public double getSize() {
@@ -510,7 +510,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
    * Checks if the element2 (given as parameter) is placed inside this element.
    * This method should be overridden by all inheriting classes - it should
    * properly handle other shapes than rectangle.
-   * 
+   *
    * @param element2
    *          object to be checked
    * @return true if element2 lies in this object, false otherwise
@@ -532,13 +532,13 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
 
   /**
    * Makes a copy of the element.
-   * 
+   *
    * @return copy of the element
    */
   public abstract Element copy();
 
   /**
-   * 
+   *
    * @param x
    *          the x value to set
    * @see x
@@ -548,7 +548,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
   }
 
   /**
-   * 
+   *
    * @param y
    *          the y value to set
    * @see y
@@ -784,7 +784,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
   }
 
   /**
-   * 
+   *
    * @param searchIndexes
    *          new {@link #searchIndexes} list
    */
@@ -835,7 +835,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
 
   /**
    * Checks if element contains a {@link LayerText}.
-   * 
+   *
    * @param lt
    *          text to check
    * @return <i>true</i> if {@link LayerText} belongs to the element, <i>false</i>
@@ -848,7 +848,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
 
   /**
    * Adds {@link SearchIndex} to the element.
-   * 
+   *
    * @param searchIndex
    *          search index to add
    * @see #searchIndexes
@@ -995,7 +995,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
 
   /**
    * Adds synonyms to the element.
-   * 
+   *
    * @param synonyms
    *          list of synonyms to be added
    */
@@ -1045,7 +1045,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
 
   /**
    * Adds former symbol to the object.
-   * 
+   *
    * @param formerSymbol
    *          former symbol to add
    */
@@ -1055,7 +1055,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
 
   /**
    * Adds synonym to object.
-   * 
+   *
    * @param synonym
    *          synonym to be added
    */
@@ -1082,7 +1082,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
 
   /**
    * Adds data mining suggestion.
-   * 
+   *
    * @param dataMining
    *          data mining to add
    */

persist/src/db/11.0.9/fix_db_20180221.sql

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

rest-api/src/main/java/lcsb/mapviewer/api/projects/comments/CommentRestImpl.java

@@ -235,8 +235,8 @@ public class CommentRestImpl extends BaseRestImpl {
       columnsSet.add("modelId");
       columnsSet.add("elementId");
       columnsSet.add("id");
+      columnsSet.add("pinned");
       if (admin) {
-        columnsSet.add("pinned");
         columnsSet.add("author");
         columnsSet.add("email");
         columnsSet.add("removeReason");