Commit 462a4f08 authored by Piotr Gawron's avatar Piotr Gawron
Browse files

Merge branch 'devel_11.0.x'

parents fde6ec63 f5545817
Pipeline #4026 passed with stage
in 1 minute and 6 seconds
......@@ -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
......
......@@ -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
*/
......
-- empty file to force directory to be commited to git repo
......@@ -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");
......
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