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Commit 7d018c14 authored by Piotr Gawron's avatar Piotr Gawron
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problem with exporting proteins with modifications to xml

parent dac6636a
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2 merge requests!630WIP: Resolve "The privileges of a new user are not saved in some cases",!580Resolve "translating pdmap spring18 to SBML throws NPE"
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converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
+ 8
− 5
View file @ 7d018c14
......@@ -391,7 +391,7 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
}
List<String> annotations = new ArrayList<>();
for (MiriamData md: element.getMiriamData()) {
for (MiriamData md : element.getMiriamData()) {
annotations.add(md.toString());
}
Collections.sort(annotations);
......@@ -416,7 +416,6 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
}
modifications.add(modificationId);
}
Collections.sort(modifications);
multiDistinguisher += "\n" + StringUtils.join(modifications, ",");
}
multiDistinguisher += "\n" + element.getPositionToCompartment();
......@@ -432,7 +431,8 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
multiDistinguisher += "\n" + element.getCharge();
multiDistinguisher += "\n" + element.getHomodimer();
}
String result = element.getClass().getSimpleName() + "\n" + annotationNames+"\n"+element.getName() + "\n" + compartmentName + "\n"
String result = element.getClass().getSimpleName() + "\n" + annotationNames + "\n" + element.getName() + "\n"
+ compartmentName + "\n"
+ complexName
+ "\n" + multiDistinguisher;
return result;
......@@ -549,10 +549,13 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
private Map<String, String> modificationResidueIds = new HashMap<>();
private String getModificationResidueUniqueId(ModificationResidue mr) {
String result = modificationResidueIds.get(mr.getIdModificationResidue() + "_" + getSbmlIdKey(mr.getSpecies()));
SpeciesWithModificationResidue species = (SpeciesWithModificationResidue) mr.getSpecies();
String modificationId = "mod" + species.getModificationResidues().indexOf(mr);
String result = modificationResidueIds.get(modificationId + "_" + getSbmlIdKey(mr.getSpecies()));
if (result == null) {
result = "modification_residue_" + (modificationResidueCounter++);
modificationResidueIds.put(mr.getIdModificationResidue() + "_" + getSbmlIdKey(mr.getSpecies()), result);
modificationResidueIds.put(modificationId + "_" + getSbmlIdKey(mr.getSpecies()), result);
}
return result;
}
......
converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/CellDesignerToMultiExportTest.java
+ 8
− 0
View file @ 7d018c14
......@@ -23,6 +23,8 @@ import lcsb.mapviewer.converter.IConverter;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.field.SpeciesWithModificationResidue;
@RunWith(Parameterized.class)
public class CellDesignerToMultiExportTest {
......@@ -52,6 +54,12 @@ public class CellDesignerToMultiExportTest {
IConverter converter = new CellDesignerXmlParser();
Model model = converter.createModel(new ConverterParams().filename(filePath.toString()));
for (Element element: model.getElements()) {
if (element instanceof SpeciesWithModificationResidue) {
logger.debug(element.getElementId());
logger.debug(((SpeciesWithModificationResidue) element).getModificationResidues());
}
}
model.setName(null);
SbmlExporter sbmlExporter = new SbmlExporter();
......
converter-sbml/testFiles/cd_for_multi/problematic_modifications.xml 0 → 100644
+ 166
− 0
View file @ 7d018c14
<?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="A_comprehensive_Parkinsons_disease_map" id="A_comprehensive_Parkinsons_disease_map">
<annotation>
<celldesigner:extension>
<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
<celldesigner:modelDisplay sizeX="28928" sizeY="13893"/>
<celldesigner:listOfCompartmentAliases/>
<celldesigner:listOfComplexSpeciesAliases/>
<celldesigner:listOfSpeciesAliases>
<celldesigner:speciesAlias id="sa10102" species="s_id_sa10102">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="342.72727272727207" y="339.840909090909" w="100.0" h="40.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="100.0" height="40.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffccffcc" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="10232.727272727272" y="2304.840909090909"/>
<celldesigner:boxSize width="100.0" height="40.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffccffcc" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa6948" species="s_id_sa6948">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="192.5" y="444.9186829904356" w="98.0" h="45.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="98.0" height="45.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffccffcc" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="14925.5" y="9087.918682990436"/>
<celldesigner:boxSize width="98.0" height="45.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffccffcc" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
</celldesigner:listOfSpeciesAliases>
<celldesigner:listOfGroups/>
<celldesigner:listOfProteins>
<celldesigner:protein id="p_s_id_sa10102" name="generic_space_protein" type="GENERIC">
<celldesigner:listOfModificationResidues>
<celldesigner:modificationResidue angle="0.0" id="rs2" side="none"/>
<celldesigner:modificationResidue angle="0.0" id="rs3" side="none"/>
<celldesigner:modificationResidue angle="0.0" id="rs1" side="none"/>
</celldesigner:listOfModificationResidues>
</celldesigner:protein>
<celldesigner:protein id="p_s_id_sa10354" name="generic_space_protein" type="GENERIC">
<celldesigner:listOfModificationResidues>
<celldesigner:modificationResidue angle="0.0" id="rs1" side="none"/>
<celldesigner:modificationResidue angle="0.0" id="rs2" side="none"/>
<celldesigner:modificationResidue angle="0.0" id="rs3" side="none"/>
</celldesigner:listOfModificationResidues>
</celldesigner:protein>
<celldesigner:protein id="p_s_id_sa6948" name="generic_space_protein" type="GENERIC">
<celldesigner:listOfModificationResidues>
<celldesigner:modificationResidue angle="0.0" id="rs1" side="none"/>
<celldesigner:modificationResidue angle="0.0" id="rs2" side="none"/>
<celldesigner:modificationResidue angle="0.0" id="rs3" side="none"/>
</celldesigner:listOfModificationResidues>
</celldesigner:protein>
</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="CDMT00552" kind="mole"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="volume" id="volume" name="volume">
<listOfUnits>
<unit metaid="CDMT00553" kind="litre"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="area" id="area" name="area">
<listOfUnits>
<unit metaid="CDMT00554" kind="metre" exponent="2"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="length" id="length" name="length">
<listOfUnits>
<unit metaid="CDMT00555" kind="metre"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="time" id="time" name="time">
<listOfUnits>
<unit metaid="CDMT00556" kind="second"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment metaid="default" id="default" size="1" units="volume"/>
</listOfCompartments>
<listOfSpecies>
<species metaid="s_id_sa10102" id="s_id_sa10102" name="generic_space_protein" compartment="default" initialAmount="0" charge="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:hypothetical>true</celldesigner:hypothetical>
<celldesigner:proteinReference>p_s_id_sa10102</celldesigner:proteinReference>
<celldesigner:state>
<celldesigner:listOfModifications>
<celldesigner:modification residue="rs1" state="ubiquitinated"/>
</celldesigner:listOfModifications>
</celldesigner:state>
</celldesigner:speciesIdentity>
</celldesigner:extension>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#s_id_sa10102">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A36080"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="s_id_sa6948" id="s_id_sa6948" name="generic_space_protein" compartment="default" initialAmount="0" charge="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:hypothetical>true</celldesigner:hypothetical>
<celldesigner:proteinReference>p_s_id_sa6948</celldesigner:proteinReference>
<celldesigner:state>
<celldesigner:listOfModifications>
<celldesigner:modification residue="rs3" state="ubiquitinated"/>
</celldesigner:listOfModifications>
</celldesigner:state>
</celldesigner:speciesIdentity>
</celldesigner:extension>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#s_id_sa6948">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A36080"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
</listOfSpecies>
</model>
</sbml>
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