Skip to content

GitLab

C
core
Commit 41725e7d authored by Piotr Gawron's avatar Piotr Gawron
Browse files
Options

import of complex with no border fixed

parent 221794ab
Pipeline #23754 failed with stage
    in 49 minutes and 59 seconds
    Hide whitespace changes
    Inline Side-by-side
    Showing with 144 additions and 3 deletions
    CHANGELOG
    View file @ 41725e7d
    minerva (14.0.11) stable; urgency=medium
    * Bug fix: miRTarBase was down and targetting by miRNA stopped working on new
    installations (#1207)
    * Bug fix: complex with no border was inproperly imported from CellDesigner
    (#1198)
    -- Piotr Gawron <piotr.gawron@uni.lu> Mon, 30 Mar 2020 10:00:00 +0200
    ......
    converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParser.java
    View file @ 41725e7d
    ......@@ -20,6 +20,7 @@ import lcsb.mapviewer.model.map.model.Model;
    import lcsb.mapviewer.model.map.model.ModelData;
    import lcsb.mapviewer.model.map.species.Complex;
    import lcsb.mapviewer.model.map.species.Species;
    import lcsb.mapviewer.modelutils.map.ElementUtils;
    /**
    * Parser of CellDesigner xml used for parsing complex aliases. Important: Only
    ......@@ -132,9 +133,13 @@ public class ComplexAliasXmlParser extends AbstractAliasXmlParser<Complex> {
    if (state.equalsIgnoreCase("usual")) {
    view = usualView;
    } else if (state.equalsIgnoreCase("brief")) {
    view = briefView;
    view = usualView;
    } else if (state.equalsIgnoreCase("complexnoborder")) {
    view = usualView;
    } else if (state.equalsIgnoreCase("complexparentbrief")) {
    view = briefView;
    } else {
    throw new InvalidXmlSchemaException(new ElementUtils().getElementTag(result)+"Don't know how to process state: " + state);
    }
    if (view != null) {
    ......
    converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java
    View file @ 41725e7d
    ......@@ -2,10 +2,9 @@ package lcsb.mapviewer.converter.model.celldesigner;
    import static org.junit.Assert.*;
    import java.awt.*;
    import java.awt.Color;
    import java.io.ByteArrayInputStream;
    import java.util.*;
    import java.util.List;
    import org.apache.logging.log4j.LogManager;
    import org.apache.logging.log4j.Logger;
    ......@@ -317,4 +316,12 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
    testXmlSerialization(model);
    }
    @Test
    public void testComplexNoBorder() throws Exception {
    CellDesignerXmlParser parser = new CellDesignerXmlParser();
    Model model = parser.createModel(new ConverterParams().filename("testFiles/problematic/complex_no_border.xml"));
    assertTrue(model.getElementByElementId("csa1").getWidth() > 0);
    testXmlSerialization(model);
    }
    }
    converter-CellDesigner/testFiles/problematic/complex_no_border.xml 0 → 100644
    View file @ 41725e7d
    <?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:listOfIncludedSpecies>
    <celldesigner:species id="s2" name="s2">
    <celldesigner:notes>
    <html xmlns="http://www.w3.org/1999/xhtml">
    <head>
    <title/>
    </head>
    <body/>
    </html>
    </celldesigner:notes>
    <celldesigner:annotation>
    <celldesigner:complexSpecies>s1</celldesigner:complexSpecies>
    <celldesigner:speciesIdentity>
    <celldesigner:class>PROTEIN</celldesigner:class>
    <celldesigner:proteinReference>pr1</celldesigner:proteinReference>
    </celldesigner:speciesIdentity>
    </celldesigner:annotation>
    </celldesigner:species>
    </celldesigner:listOfIncludedSpecies>
    <celldesigner:listOfCompartmentAliases/>
    <celldesigner:listOfComplexSpeciesAliases>
    <celldesigner:complexSpeciesAlias id="csa1" species="s1">
    <celldesigner:activity>inactive</celldesigner:activity>
    <celldesigner:bounds x="171.0" y="79.0" w="100.0" h="120.0"/>
    <celldesigner:font size="12"/>
    <celldesigner:view state="complexnoborder"/>
    <celldesigner:backupSize w="0.0" h="0.0"/>
    <celldesigner:backupView state="none"/>
    <celldesigner:usualView>
    <celldesigner:innerPosition x="0.0" y="0.0"/>
    <celldesigner:boxSize width="100.0" height="120.0"/>
    <celldesigner:singleLine width="2.0"/>
    <celldesigner:paint color="fff7f7f7" 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="2.0"/>
    <celldesigner:paint color="fff7f7f7" scheme="Color"/>
    </celldesigner:briefView>
    <celldesigner:info state="empty" angle="-1.5707963267948966"/>
    </celldesigner:complexSpeciesAlias>
    </celldesigner:listOfComplexSpeciesAliases>
    <celldesigner:listOfSpeciesAliases>
    <celldesigner:speciesAlias id="sa1" species="s2" complexSpeciesAlias="csa1">
    <celldesigner:activity>inactive</celldesigner:activity>
    <celldesigner:bounds x="183.0" y="91.0" w="80.0" h="40.0"/>
    <celldesigner:font size="12"/>
    <celldesigner:view state="usual"/>
    <celldesigner:usualView>
    <celldesigner:innerPosition x="12.0" y="12.0"/>
    <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="s2" 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"/>
    </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>COMPLEX</celldesigner:class>
    <celldesigner:name>s1</celldesigner:name>
    </celldesigner:speciesIdentity>
    </celldesigner:extension>
    </annotation>
    </species>
    </listOfSpecies>
    </model>
    </sbml>
    Markdown is supported
    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