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minerva
core
Commits
223d7bc7
Commit
223d7bc7
authored
Apr 26, 2019
by
Piotr Gawron
Browse files
TransparencyZoomLevelVisibility changed to SemanticZoomLevelTransparency
parent
da0a20af
Pipeline
#10027
failed with stage
in 9 minutes and 43 seconds
Changes
6
Pipelines
1
Hide whitespace changes
Inline
Side-by-side
CHANGELOG
View file @
223d7bc7
...
...
@@ -46,6 +46,8 @@ minerva (12.3.0~alpha.0) unstable; urgency=low
* Small improvement: when adding new project columns "Root map", "Mapping
file" and "Map type" are merged (#700)
* Small improvement: allow admin to disable CORS check (#802)
* Small improvement: TransparencyZoomLevelVisibility parameter renamed to
SemanticZoomLevelTransparency (#801)
* Bug fix: progress bar of gene genome mapping upload is refreshing properly
(#728)
* Bug fix: when editing project Disease and Organism could not be removed
...
...
converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java
View file @
223d7bc7
...
...
@@ -128,7 +128,13 @@ public enum NoteField {
/**
* {@link Element#getSemanticZoomLevelVisibility()}.
*/
TRANSPARENCY_ZOOM_LEVEL_VISIBILITY
(
"TransparencyZoomLevelVisibility"
,
Element
.
class
,
null
),
TRANSPARENCY_ZOOM_LEVEL_VISIBILITY
(
"SemanticZoomLevelTransparency"
,
Element
.
class
,
null
),
/**
* {@link Element#getSemanticZoomLevelVisibility()}.
*/
@Deprecated
TRANSPARENCY_ZOOM_LEVEL_VISIBILITY_OLD
(
"TransparencyZoomLevelVisibility"
,
Element
.
class
,
null
),
;
/**
...
...
converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
View file @
223d7bc7
...
...
@@ -160,7 +160,7 @@ public class RestAnnotationParser {
return
""
;
}
}
else
if
(
value
instanceof
String
)
{
String
string
=(
String
)
value
;
String
string
=
(
String
)
value
;
if
(!(
string
.
trim
().
isEmpty
())
||
forceFullInfo
)
{
return
type
.
getCommonName
()
+
": "
+
XmlParser
.
escapeXml
(
string
)
+
"\n"
;
}
else
{
...
...
@@ -684,7 +684,14 @@ public class RestAnnotationParser {
String
transparencyZoomLevelVisibility
=
getParamByPrefix
(
annotationString
,
NoteField
.
TRANSPARENCY_ZOOM_LEVEL_VISIBILITY
.
getCommonName
()
+
":"
);
if
(
transparencyZoomLevelVisibility
==
null
)
{
return
;
transparencyZoomLevelVisibility
=
getParamByPrefix
(
annotationString
,
NoteField
.
TRANSPARENCY_ZOOM_LEVEL_VISIBILITY_OLD
.
getCommonName
()
+
":"
);
if
(
transparencyZoomLevelVisibility
==
null
)
{
return
;
}
else
{
logger
.
warn
(
"Deprecated parameter found: "
+
NoteField
.
TRANSPARENCY_ZOOM_LEVEL_VISIBILITY_OLD
.
getCommonName
()
+
". Use "
+
NoteField
.
TRANSPARENCY_ZOOM_LEVEL_VISIBILITY
.
getCommonName
());
}
}
if
(
element
.
getTransparencyLevel
()
==
null
||
element
.
getTransparencyLevel
().
isEmpty
())
{
element
.
setTransparencyLevel
(
transparencyZoomLevelVisibility
);
...
...
converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
View file @
223d7bc7
...
...
@@ -107,6 +107,18 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
}
}
@Test
public
void
testParseTransparencyDeprecated
()
throws
Exception
{
try
{
CellDesignerXmlParser
parser
=
new
CellDesignerXmlParser
();
Model
model
=
parser
.
createModel
(
new
ConverterParams
().
filename
(
"testFiles/model_with_transparency_old.xml"
));
assertFalse
(
model
.
getCompartments
().
get
(
0
).
getTransparencyLevel
().
isEmpty
());
}
catch
(
Exception
e
)
{
e
.
printStackTrace
();
throw
e
;
}
}
@Test
public
void
testParseVcard
()
throws
Exception
{
try
{
...
...
converter-CellDesigner/testFiles/model_with_transparency.xml
View file @
223d7bc7
...
...
@@ -164,7 +164,7 @@
<head>
<title/>
</head>
<body>
TransparencyZoomLevelVisibilit
y:0
<body>
SemanticZoomLevelTransparenc
y:0
</body>
</html>
</notes>
...
...
@@ -180,7 +180,7 @@
<head>
<title/>
</head>
<body>
TransparencyZoomLevelVisibilit
y:1
<body>
SemanticZoomLevelTransparenc
y:1
</body>
</html>
</notes>
...
...
@@ -196,7 +196,7 @@
<head>
<title/>
</head>
<body>
TransparencyZoomLevelVisibilit
y:2
<body>
SemanticZoomLevelTransparenc
y:2
</body>
</html>
</notes>
...
...
@@ -212,7 +212,7 @@
<head>
<title/>
</head>
<body>
TransparencyZoomLevelVisibilit
y:3
<body>
SemanticZoomLevelTransparenc
y:3
</body>
</html>
</notes>
...
...
converter-CellDesigner/testFiles/model_with_transparency_old.xml
0 → 100644
View file @
223d7bc7
<?xml version="1.0" encoding="UTF-8"?>
<sbml
xmlns=
"http://www.sbml.org/sbml/level2/version4"
xmlns:celldesigner=
"http://www.sbml.org/2001/ns/celldesigner"
level=
"2"
version=
"4"
>
<model
metaid=
"untitled"
id=
"untitled"
>
<annotation>
<celldesigner:extension>
<celldesigner:modelVersion>
4.0
</celldesigner:modelVersion>
<celldesigner:modelDisplay
sizeX=
"600"
sizeY=
"400"
/>
<celldesigner:listOfCompartmentAliases>
<celldesigner:compartmentAlias
id=
"ca1"
compartment=
"c1"
>
<celldesigner:class>
SQUARE
</celldesigner:class>
<celldesigner:bounds
x=
"15.0"
y=
"73.0"
w=
"137.0"
h=
"153.0"
/>
<celldesigner:namePoint
x=
"75.0"
y=
"190.5"
/>
<celldesigner:doubleLine
thickness=
"12.0"
outerWidth=
"2.0"
innerWidth=
"1.0"
/>
<celldesigner:paint
color=
"ffcccc00"
scheme=
"Color"
/>
<celldesigner:info
state=
"empty"
angle=
"-1.5707963267948966"
/>
</celldesigner:compartmentAlias>
<celldesigner:compartmentAlias
id=
"ca3"
compartment=
"c3"
>
<celldesigner:class>
SQUARE
</celldesigner:class>
<celldesigner:bounds
x=
"176.0"
y=
"30.0"
w=
"203.0"
h=
"129.0"
/>
<celldesigner:namePoint
x=
"269.0"
y=
"123.5"
/>
<celldesigner:doubleLine
thickness=
"12.0"
outerWidth=
"2.0"
innerWidth=
"1.0"
/>
<celldesigner:paint
color=
"ffcccc00"
scheme=
"Color"
/>
<celldesigner:info
state=
"empty"
angle=
"-1.5707963267948966"
/>
</celldesigner:compartmentAlias>
<celldesigner:compartmentAlias
id=
"ca4"
compartment=
"c4"
>
<celldesigner:class>
SQUARE
</celldesigner:class>
<celldesigner:bounds
x=
"443.0"
y=
"69.0"
w=
"149.0"
h=
"178.0"
/>
<celldesigner:namePoint
x=
"509.0"
y=
"211.5"
/>
<celldesigner:doubleLine
thickness=
"12.0"
outerWidth=
"2.0"
innerWidth=
"1.0"
/>
<celldesigner:paint
color=
"ffcccc00"
scheme=
"Color"
/>
<celldesigner:info
state=
"empty"
angle=
"-1.5707963267948966"
/>
</celldesigner:compartmentAlias>
<celldesigner:compartmentAlias
id=
"ca5"
compartment=
"c5"
>
<celldesigner:class>
SQUARE
</celldesigner:class>
<celldesigner:bounds
x=
"197.0"
y=
"219.0"
w=
"186.0"
h=
"129.0"
/>
<celldesigner:namePoint
x=
"281.5"
y=
"312.5"
/>
<celldesigner:doubleLine
thickness=
"12.0"
outerWidth=
"2.0"
innerWidth=
"1.0"
/>
<celldesigner:paint
color=
"ffcccc00"
scheme=
"Color"
/>
<celldesigner:info
state=
"empty"
angle=
"-1.5707963267948966"
/>
</celldesigner:compartmentAlias>
</celldesigner:listOfCompartmentAliases>
<celldesigner:listOfComplexSpeciesAliases/>
<celldesigner:listOfSpeciesAliases>
<celldesigner:speciesAlias
id=
"sa1"
species=
"s1"
compartmentAlias=
"ca1"
>
<celldesigner:activity>
inactive
</celldesigner:activity>
<celldesigner:bounds
x=
"34.0"
y=
"121.0"
w=
"80.0"
h=
"40.0"
/>
<celldesigner:font
size=
"12"
/>
<celldesigner:view
state=
"usual"
/>
<celldesigner:usualView>
<celldesigner:innerPosition
x=
"19.0"
y=
"48.0"
/>
<celldesigner:boxSize
width=
"80.0"
height=
"40.0"
/>
<celldesigner:singleLine
width=
"1.0"
/>
<celldesigner:paint
color=
"ffccffcc"
scheme=
"Color"
/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition
x=
"0.0"
y=
"0.0"
/>
<celldesigner:boxSize
width=
"80.0"
height=
"60.0"
/>
<celldesigner:singleLine
width=
"0.0"
/>
<celldesigner:paint
color=
"3fff0000"
scheme=
"Color"
/>
</celldesigner:briefView>
<celldesigner:info
state=
"empty"
angle=
"-1.5707963267948966"
/>
</celldesigner:speciesAlias>
<celldesigner:speciesAlias
id=
"sa2"
species=
"s2"
compartmentAlias=
"ca3"
>
<celldesigner:activity>
inactive
</celldesigner:activity>
<celldesigner:bounds
x=
"233.0"
y=
"57.0"
w=
"80.0"
h=
"40.0"
/>
<celldesigner:font
size=
"12"
/>
<celldesigner:view
state=
"usual"
/>
<celldesigner:usualView>
<celldesigner:innerPosition
x=
"57.0"
y=
"27.0"
/>
<celldesigner:boxSize
width=
"80.0"
height=
"40.0"
/>
<celldesigner:singleLine
width=
"1.0"
/>
<celldesigner:paint
color=
"ffccffcc"
scheme=
"Color"
/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition
x=
"0.0"
y=
"0.0"
/>
<celldesigner:boxSize
width=
"80.0"
height=
"60.0"
/>
<celldesigner:singleLine
width=
"0.0"
/>
<celldesigner:paint
color=
"3fff0000"
scheme=
"Color"
/>
</celldesigner:briefView>
<celldesigner:info
state=
"empty"
angle=
"-1.5707963267948966"
/>
</celldesigner:speciesAlias>
<celldesigner:speciesAlias
id=
"sa3"
species=
"s3"
compartmentAlias=
"ca4"
>
<celldesigner:activity>
inactive
</celldesigner:activity>
<celldesigner:bounds
x=
"473.0"
y=
"137.0"
w=
"80.0"
h=
"40.0"
/>
<celldesigner:font
size=
"12"
/>
<celldesigner:view
state=
"usual"
/>
<celldesigner:usualView>
<celldesigner:innerPosition
x=
"30.0"
y=
"68.0"
/>
<celldesigner:boxSize
width=
"80.0"
height=
"40.0"
/>
<celldesigner:singleLine
width=
"1.0"
/>
<celldesigner:paint
color=
"ffccffcc"
scheme=
"Color"
/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition
x=
"0.0"
y=
"0.0"
/>
<celldesigner:boxSize
width=
"80.0"
height=
"60.0"
/>
<celldesigner:singleLine
width=
"0.0"
/>
<celldesigner:paint
color=
"3fff0000"
scheme=
"Color"
/>
</celldesigner:briefView>
<celldesigner:info
state=
"empty"
angle=
"-1.5707963267948966"
/>
</celldesigner:speciesAlias>
<celldesigner:speciesAlias
id=
"sa4"
species=
"s4"
compartmentAlias=
"ca5"
>
<celldesigner:activity>
inactive
</celldesigner:activity>
<celldesigner:bounds
x=
"277.0"
y=
"263.0"
w=
"80.0"
h=
"40.0"
/>
<celldesigner:font
size=
"12"
/>
<celldesigner:view
state=
"usual"
/>
<celldesigner:usualView>
<celldesigner:innerPosition
x=
"80.0"
y=
"44.0"
/>
<celldesigner:boxSize
width=
"80.0"
height=
"40.0"
/>
<celldesigner:singleLine
width=
"1.0"
/>
<celldesigner:paint
color=
"ffccffcc"
scheme=
"Color"
/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition
x=
"0.0"
y=
"0.0"
/>
<celldesigner:boxSize
width=
"80.0"
height=
"60.0"
/>
<celldesigner:singleLine
width=
"0.0"
/>
<celldesigner:paint
color=
"3fff0000"
scheme=
"Color"
/>
</celldesigner:briefView>
<celldesigner:info
state=
"empty"
angle=
"-1.5707963267948966"
/>
</celldesigner:speciesAlias>
</celldesigner:listOfSpeciesAliases>
<celldesigner:listOfGroups/>
<celldesigner:listOfProteins>
<celldesigner:protein
id=
"pr1"
name=
"s1"
type=
"GENERIC"
/>
</celldesigner:listOfProteins>
<celldesigner:listOfGenes/>
<celldesigner:listOfRNAs/>
<celldesigner:listOfAntisenseRNAs/>
<celldesigner:listOfLayers/>
<celldesigner:listOfBlockDiagrams/>
</celldesigner:extension>
</annotation>
<listOfUnitDefinitions>
<unitDefinition
metaid=
"substance"
id=
"substance"
name=
"substance"
>
<listOfUnits>
<unit
metaid=
"CDMT00001"
kind=
"mole"
/>
</listOfUnits>
</unitDefinition>
<unitDefinition
metaid=
"volume"
id=
"volume"
name=
"volume"
>
<listOfUnits>
<unit
metaid=
"CDMT00002"
kind=
"litre"
/>
</listOfUnits>
</unitDefinition>
<unitDefinition
metaid=
"area"
id=
"area"
name=
"area"
>
<listOfUnits>
<unit
metaid=
"CDMT00003"
kind=
"metre"
exponent=
"2"
/>
</listOfUnits>
</unitDefinition>
<unitDefinition
metaid=
"length"
id=
"length"
name=
"length"
>
<listOfUnits>
<unit
metaid=
"CDMT00004"
kind=
"metre"
/>
</listOfUnits>
</unitDefinition>
<unitDefinition
metaid=
"time"
id=
"time"
name=
"time"
>
<listOfUnits>
<unit
metaid=
"CDMT00005"
kind=
"second"
/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment
metaid=
"default"
id=
"default"
size=
"1"
units=
"volume"
/>
<compartment
metaid=
"c1"
id=
"c1"
name=
"c1"
size=
"1"
units=
"volume"
outside=
"default"
>
<notes>
<html
xmlns=
"http://www.w3.org/1999/xhtml"
>
<head>
<title/>
</head>
<body>
TransparencyZoomLevelVisibility:0
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:name>
c1
</celldesigner:name>
</celldesigner:extension>
</annotation>
</compartment>
<compartment
metaid=
"c3"
id=
"c3"
name=
"c3"
size=
"1"
units=
"volume"
outside=
"default"
>
<notes>
<html
xmlns=
"http://www.w3.org/1999/xhtml"
>
<head>
<title/>
</head>
<body>
TransparencyZoomLevelVisibility:1
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:name>
c3
</celldesigner:name>
</celldesigner:extension>
</annotation>
</compartment>
<compartment
metaid=
"c4"
id=
"c4"
name=
"c4"
size=
"1"
units=
"volume"
outside=
"default"
>
<notes>
<html
xmlns=
"http://www.w3.org/1999/xhtml"
>
<head>
<title/>
</head>
<body>
TransparencyZoomLevelVisibility:2
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:name>
c4
</celldesigner:name>
</celldesigner:extension>
</annotation>
</compartment>
<compartment
metaid=
"c5"
id=
"c5"
name=
"c5"
size=
"1"
units=
"volume"
outside=
"default"
>
<notes>
<html
xmlns=
"http://www.w3.org/1999/xhtml"
>
<head>
<title/>
</head>
<body>
TransparencyZoomLevelVisibility:3
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:name>
c5
</celldesigner:name>
</celldesigner:extension>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species
metaid=
"s1"
id=
"s1"
name=
"s1"
compartment=
"c1"
initialAmount=
"0"
>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>
inside
</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>
PROTEIN
</celldesigner:class>
<celldesigner:proteinReference>
pr1
</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species
metaid=
"s2"
id=
"s2"
name=
"s1"
compartment=
"c3"
initialAmount=
"0"
>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>
inside
</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>
PROTEIN
</celldesigner:class>
<celldesigner:proteinReference>
pr1
</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species
metaid=
"s3"
id=
"s3"
name=
"s1"
compartment=
"c4"
initialAmount=
"0"
>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>
inside
</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>
PROTEIN
</celldesigner:class>
<celldesigner:proteinReference>
pr1
</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species
metaid=
"s4"
id=
"s4"
name=
"s1"
compartment=
"c5"
initialAmount=
"0"
>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>
inside
</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>
PROTEIN
</celldesigner:class>
<celldesigner:proteinReference>
pr1
</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
</listOfSpecies>
</model>
</sbml>
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