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Commit 223d7bc7 authored by Piotr Gawron's avatar Piotr Gawron
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TransparencyZoomLevelVisibility changed to SemanticZoomLevelTransparency

parent da0a20af
Pipeline #10027 failed with stage
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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>TransparencyZoomLevelVisibility:0
<body>SemanticZoomLevelTransparency:0
</body>
</html>
</notes>
......@@ -180,7 +180,7 @@
<head>
<title/>
</head>
<body>TransparencyZoomLevelVisibility:1
<body>SemanticZoomLevelTransparency:1
</body>
</html>
</notes>
......@@ -196,7 +196,7 @@
<head>
<title/>
</head>
<body>TransparencyZoomLevelVisibility:2
<body>SemanticZoomLevelTransparency:2
</body>
</html>
</notes>
......@@ -212,7 +212,7 @@
<head>
<title/>
</head>
<body>TransparencyZoomLevelVisibility:3
<body>SemanticZoomLevelTransparency: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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