From e105c9018d8a7dd13abd0547c62f3d050ee6e002 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 23 Aug 2019 15:27:21 +0200
Subject: [PATCH] line type is used on operator for boolean gates
---
CHANGELOG | 2 +
.../reaction/ReactionFromXml.java | 1 +
.../CellDesignerXmlParserTest.java | 17 +-
.../reactions/dotted-line-boolean.xml | 218 ++++++++++++++++++
4 files changed, 236 insertions(+), 2 deletions(-)
create mode 100644 converter-CellDesigner/testFiles/reactions/dotted-line-boolean.xml
diff --git a/CHANGELOG b/CHANGELOG
index 018af25c4a..8d21a978c9 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -20,6 +20,8 @@ minerva (14.0.0~beta.0) unstable; urgency=low
"Edit Project", "Edit User" (#881)
* Bug fix: all colors in boolean reaction (from CellDesigner) are processed
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
(#901)
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
index 942ecfe62f..44bdb84127 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
@@ -914,6 +914,7 @@ public class ReactionFromXml {
Point2D thirdPoint = pointTransformation.getPointOnLine(product.getLine().getPoints().get(0),
product.getLine().getPoints().get(1), 0.6);
line.addPoint(pointTransformation.copyPoint(secondPoint));
+ line.setType(product.getLine().getType());
operator.setLine(line);
// center line
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
index 09b54e687f..63e4b455a0 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
@@ -3,12 +3,11 @@ package lcsb.mapviewer.converter.model.celldesigner;
import static org.junit.Assert.*;
import static org.mockito.Mockito.when;
-import java.awt.*;
+import java.awt.Color;
import java.awt.geom.*;
import java.io.*;
import java.nio.charset.StandardCharsets;
import java.util.*;
-import java.util.List;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -20,6 +19,7 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
+import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.compartment.Compartment;
@@ -786,5 +786,18 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
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());
+ }
+
}
diff --git a/converter-CellDesigner/testFiles/reactions/dotted-line-boolean.xml b/converter-CellDesigner/testFiles/reactions/dotted-line-boolean.xml
new file mode 100644
index 0000000000..1d8d3648a5
--- /dev/null
+++ b/converter-CellDesigner/testFiles/reactions/dotted-line-boolean.xml
@@ -0,0 +1,218 @@
+<?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>
--
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