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Devrim Gunyel
core
Commits
462a4f08
Commit
462a4f08
authored
Mar 13, 2018
by
Piotr Gawron
Browse files
Merge branch 'devel_11.0.x'
parents
fde6ec63
f5545817
Changes
4
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CHANGELOG
View file @
462a4f08
...
...
@@ -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
View file @
462a4f08
...
...
@@ -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
0 → 100644
View file @
462a4f08
-- empty file to force directory to be commited to git repo
rest-api/src/main/java/lcsb/mapviewer/api/projects/comments/CommentRestImpl.java
View file @
462a4f08
...
...
@@ -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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