Skip to content
Snippets Groups Projects
Commit e105c901 authored by Piotr Gawron's avatar Piotr Gawron
Browse files

line type is used on operator for boolean gates

parent 480fd3d7
No related branches found
No related tags found
1 merge request!898Resolve "unknown boolean reaction is not fully dotted"
Pipeline #13040 failed
Hide whitespace changes
Inline Side-by-side
CHANGELOG
+ 2
− 0
View file @ e105c901
...@@ -20,6 +20,8 @@ minerva (14.0.0~beta.0) unstable; urgency=low ...@@ -20,6 +20,8 @@ minerva (14.0.0~beta.0) unstable; urgency=low
"Edit Project", "Edit User" (#881) "Edit Project", "Edit User" (#881)
* Bug fix: all colors in boolean reaction (from CellDesigner) are processed * Bug fix: all colors in boolean reaction (from CellDesigner) are processed
properly (#907) properly (#907)
* Bug fix: proper line type for boolean reaction is used on the whole
reaction (#908)
* Bug fix: user with modify access to the project can edit it in admin panel * Bug fix: user with modify access to the project can edit it in admin panel
(#901) (#901)
......
converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
+ 1
− 0
View file @ e105c901
...@@ -914,6 +914,7 @@ public class ReactionFromXml { ...@@ -914,6 +914,7 @@ public class ReactionFromXml {
Point2D thirdPoint = pointTransformation.getPointOnLine(product.getLine().getPoints().get(0), Point2D thirdPoint = pointTransformation.getPointOnLine(product.getLine().getPoints().get(0),
product.getLine().getPoints().get(1), 0.6); product.getLine().getPoints().get(1), 0.6);
line.addPoint(pointTransformation.copyPoint(secondPoint)); line.addPoint(pointTransformation.copyPoint(secondPoint));
line.setType(product.getLine().getType());
operator.setLine(line); operator.setLine(line);
// center line // center line
......
converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
+ 15
− 2
View file @ e105c901
...@@ -3,12 +3,11 @@ package lcsb.mapviewer.converter.model.celldesigner; ...@@ -3,12 +3,11 @@ package lcsb.mapviewer.converter.model.celldesigner;
import static org.junit.Assert.*; import static org.junit.Assert.*;
import static org.mockito.Mockito.when; import static org.mockito.Mockito.when;
import java.awt.*; import java.awt.Color;
import java.awt.geom.*; import java.awt.geom.*;
import java.io.*; import java.io.*;
import java.nio.charset.StandardCharsets; import java.nio.charset.StandardCharsets;
import java.util.*; import java.util.*;
import java.util.List;
import org.apache.logging.log4j.LogManager; import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger; import org.apache.logging.log4j.Logger;
...@@ -20,6 +19,7 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException; ...@@ -20,6 +19,7 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.ConverterParams; import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.InvalidInputDataExecption; import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser; import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.graphics.PolylineData; import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.BioEntity; import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.compartment.Compartment; import lcsb.mapviewer.model.map.compartment.Compartment;
...@@ -786,5 +786,18 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions { ...@@ -786,5 +786,18 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
assertEquals(0, new ModelComparator().compare(model, model2)); assertEquals(0, new ModelComparator().compare(model, model2));
} }
@Test
public void testParseDottedBooleanReaction() throws Exception {
CellDesignerXmlParser parser = new CellDesignerXmlParser();
Model model = parser.createModel(new ConverterParams().filename("testFiles/reactions/boolean-colors.xml"));
Reaction r1 = model.getReactionByReactionId("re1");
Set<LineType> reactionTypes = new HashSet<>();
for (AbstractNode node : r1.getNodes()) {
reactionTypes.add(node.getLine().getType());
}
assertEquals("Whole reaction should use the same reaction type", 1, reactionTypes.size());
}
} }
converter-CellDesigner/testFiles/reactions/dotted-line-boolean.xml 0 → 100644
+ 218
− 0
View file @ e105c901
<?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:listOfComplexSpeciesAliases/>
<celldesigner:listOfSpeciesAliases>
<celldesigner:speciesAlias id="sa1" species="s1">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="121.0" y="102.0" w="80.0" h="40.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<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">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="126.0" y="254.0" w="80.0" h="40.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<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">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="463.0" y="180.0" w="80.0" h="40.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<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:protein id="pr2" name="s2" type="GENERIC"/>
<celldesigner:protein id="pr3" name="s3" 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="CDMT00004" kind="mole"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="volume" id="volume" name="volume">
<listOfUnits>
<unit metaid="CDMT00005" kind="litre"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="area" id="area" name="area">
<listOfUnits>
<unit metaid="CDMT00006" kind="metre" exponent="2"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="length" id="length" name="length">
<listOfUnits>
<unit metaid="CDMT00007" kind="metre"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="time" id="time" name="time">
<listOfUnits>
<unit metaid="CDMT00008" kind="second"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment metaid="default" id="default" size="1" units="volume"/>
</listOfCompartments>
<listOfSpecies>
<species metaid="s1" id="s1" name="s1" compartment="default" 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="s2" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr2</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s3" id="s3" name="s3" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr3</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
</listOfSpecies>
<listOfReactions>
<reaction metaid="re1" id="re1" reversible="false">
<annotation>
<celldesigner:extension>
<celldesigner:reactionType>BOOLEAN_LOGIC_GATE</celldesigner:reactionType>
<celldesigner:baseReactants>
<celldesigner:baseReactant species="s2" alias="sa2"/>
<celldesigner:baseReactant species="s1" alias="sa1"/>
</celldesigner:baseReactants>
<celldesigner:baseProducts>
<celldesigner:baseProduct species="s3" alias="sa3"/>
</celldesigner:baseProducts>
<celldesigner:connectScheme connectPolicy="direct"/>
<celldesigner:editPoints>286.66666666666663,199.66666666666666</celldesigner:editPoints>
<celldesigner:line width="1.0" color="ff000000"/>
<celldesigner:listOfGateMember>
<celldesigner:GateMember type="BOOLEAN_LOGIC_GATE_OR" aliases="sa2,sa1" modificationType="UNKNOWN_POSITIVE_INFLUENCE" targetLineIndex="-1,-1" editPoints="286.66666666666663,199.66666666666666">
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:line width="1.0" color="ff000000"/>
</celldesigner:GateMember>
<celldesigner:GateMember type="UNKNOWN_POSITIVE_INFLUENCE" aliases="sa2" targetLineIndex="-1,0">
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:line width="1.0" color="ff000000"/>
</celldesigner:GateMember>
<celldesigner:GateMember type="UNKNOWN_POSITIVE_INFLUENCE" aliases="sa1" targetLineIndex="-1,0">
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:line width="1.0" color="ff000000"/>
</celldesigner:GateMember>
</celldesigner:listOfGateMember>
</celldesigner:extension>
</annotation>
<listOfReactants>
<speciesReference metaid="CDMT00001" species="s2">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa2</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
<speciesReference metaid="CDMT00002" species="s1">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa1</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
</listOfReactants>
<listOfProducts>
<speciesReference metaid="CDMT00003" species="s3">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa3</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
</listOfProducts>
</reaction>
</listOfReactions>
</model>
</sbml>
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment