sbml id cannot contain ":" or "."

CHANGELOG

+minerva (15.1.1) stable; urgency=medium
+  * Bug fix: export to CD maps with species containing ":" or "." in species id
+    generated files that could not be opened in CellDesigner (#1363) 
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 23 Nov 2020 15:00:00 +0200
+
 minerva (15.1.0) stable; urgency=medium
   * Small improvement: information if species has activity, hypothetical flag
     set is available over REST API for element (#1379)

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollection.java

@@ -8,7 +8,10 @@ import org.apache.logging.log4j.Logger;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
 import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
+import lcsb.mapviewer.model.LogMarker;
+import lcsb.mapviewer.model.ProjectLogEntryType;
 import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.species.*;
 import lcsb.mapviewer.model.map.species.field.AbstractSiteModification;
 import lcsb.mapviewer.model.map.species.field.ModificationResidue;
@@ -23,7 +26,6 @@ public class CellDesignerElementCollection {
   /**
    * Default class logger
    */
-  @SuppressWarnings("unused")
   private static Logger logger = LogManager.getLogger();
 
   /**
@@ -66,7 +68,11 @@ public class CellDesignerElementCollection {
     } else {
       String sbmlId = getSbmlId(modelElement, true);
       if (sbmlIdByElement.get(sbmlId) == null) {
-        String id = "s_id_" + modelElement.getElementId();
+        String normalizedId = normalizeIdToCellDesigner(modelElement.getElementId());
+        if (!normalizedId.equals(modelElement.getElementId())) {
+          logger.warn(new LogMarker(ProjectLogEntryType.EXPORT_ISSUE, modelElement), "Invalid element id");
+        }
+        String id = "s_id_" + normalizeIdToCellDesigner(modelElement.getElementId());
         if (sbmlIdByElement.values().contains(id)) {
           throw new InvalidArgumentException("id duplicates");
         }
@@ -277,9 +283,20 @@ public class CellDesignerElementCollection {
       return null;
     }
     if (ca.getElementId().length() >= 2) {
-      return ca.getElementId();
+      return normalizeIdToCellDesigner(ca.getElementId());
     }
-    return "ca_prefix_issue_" + ca.getElementId();
+    return "ca_prefix_issue_" + normalizeIdToCellDesigner(ca.getElementId());
+  }
+
+  public String getModelId(Model model) {
+    if (model.getIdModel() == null) {
+      return null;
+    }
+    return normalizeIdToCellDesigner(model.getIdModel());
+  }
+
+  protected String normalizeIdToCellDesigner(String id) {
+    return id.replaceAll("[:\\.-]", "_");
   }
 
 }

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java

@@ -393,7 +393,8 @@ public class CellDesignerXmlParser extends Converter {
   }
 
   private void processModelRdfNode(Model model, Node node) throws InvalidXmlSchemaException {
-    XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser(CommonXmlParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
+    XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser(
+        CommonXmlParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
     model.addMiriamData(xmlAnnotationParser.parseRdfNode(node));
     model.addAuthors(xmlAnnotationParser.getAuthorsFromRdf(node));
     model.setCreationDate(xmlAnnotationParser.getCreateDateFromRdf(node));
@@ -635,7 +636,11 @@ public class CellDesignerXmlParser extends Converter {
           + "xmlns:celldesigner=\"http://www.sbml.org/2001/ns/celldesigner\" level=\"2\" version=\"4\">\n");
       result.append("<model ");
       if (model.getIdModel() != null) {
-        result.append("metaid=\"" + model.getIdModel() + "\" id=\"" + model.getIdModel() + "\"");
+        String id = elements.getModelId(model);
+        if (!id.equals(model.getIdModel())) {
+          logger.warn("Invalid map id: '" + model.getIdModel() + "' changed to '" + id + "'");
+        }
+        result.append("metaid=\"" + id + "\" id=\"" + id + "\"");
       }
       result.append(">\n");
 
@@ -729,7 +734,8 @@ public class CellDesignerXmlParser extends Converter {
 
     result.append("</celldesigner:extension>\n");
 
-    XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser(CommonXmlParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
+    XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser(
+        CommonXmlParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
     result.append(xmlAnnotationParser.dataSetToXmlString(model.getMiriamData(), model.getAuthors(),
         model.getCreationDate(), model.getModificationDates(), model.getIdModel()));
     result.append("</annotation>\n");

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollectionTest.java

 package lcsb.mapviewer.converter.model.celldesigner;
 
+import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertNotEquals;
 
 import org.apache.logging.log4j.LogManager;
@@ -54,4 +55,11 @@ public class CellDesignerElementCollectionTest extends CellDesignerTestFunctions
     assertNotEquals(collection.getElementId(p1), collection.getElementId(p2));
   }
 
+  @Test
+  public void testNormalizeToCd() {
+    CellDesignerElementCollection collection = new CellDesignerElementCollection();
+    assertFalse(collection.normalizeIdToCellDesigner("a.b").contains("."));
+    assertFalse(collection.normalizeIdToCellDesigner("a_b").contains("."));
+  }
+
 }

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/SbmlValidationTests.java

@@ -49,6 +49,7 @@ public class SbmlValidationTests extends CellDesignerTestFunctions {
     result.add(getTestSetFromFile("testFiles/reactions/modifier_with_operator.xml"));
     result.add(getTestSetFromFile("testFiles/problematic/problematic_reaction_name.xml"));
     result.add(getTestSetFromFile("testFiles/reactions/kinetics.xml"));
+    result.add(getTestSetFromFile("testFiles/problematic/invalid_sbml_id.xml"));
     result.add(emptyProteinNameTest());
     return result;
   }

converter-CellDesigner/testFiles/problematic/invalid_sbml_id.xml

+<?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="F007-inos.sbgn" id="F007-inos.sbgn">
+<notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body></body></html></notes><annotation>
+<celldesigner:extension>
+<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
+<celldesigner:modelDisplay sizeX="1632" sizeY="1188"/>
+<celldesigner:listOfIncludedSpecies>
+</celldesigner:listOfIncludedSpecies>
+<celldesigner:listOfCompartmentAliases>
+<celldesigner:compartmentAlias id="n1" compartment="s_id_n1">
+<celldesigner:class>SQUARE</celldesigner:class>
+<celldesigner:bounds x="36.73581314086914" y="921.4197998046875" w="1559.26416015625" h="250.22767639160156"/>
+<celldesigner:namePoint x="42.73581314086914" y="927.4197998046875"/>
+<celldesigner:doubleLine thickness="3.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="72EDEBE4" scheme="Color"/>
+</celldesigner:compartmentAlias>
+</celldesigner:listOfCompartmentAliases>
+<celldesigner:listOfComplexSpeciesAliases>
+</celldesigner:listOfComplexSpeciesAliases>
+<celldesigner:listOfSpeciesAliases>
+<celldesigner:speciesAlias id="n1__.__n0" species="s_id_n1__.__n0" compartmentAlias="n1" >
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="65.0" y="966.6474609375" w="86.0" h="46.0" />
+<celldesigner:font size="12"/><celldesigner:view state="usual"/>
+<celldesigner:usualView><celldesigner:innerPosition x="0" y="0"/><celldesigner:boxSize width="86.0" height="46.0"/><celldesigner:singleLine width="1.0"/><celldesigner:paint color="FFC8D8EB" scheme="Color"/></celldesigner:usualView>
+<celldesigner:briefView><celldesigner:innerPosition x="0" y="0"/><celldesigner:boxSize width="86.0" height="46.0"/><celldesigner:singleLine width="1.0"/><celldesigner:paint color="FFC8D8EB" scheme="Color"/></celldesigner:briefView>
+</celldesigner:speciesAlias>
+</celldesigner:listOfSpeciesAliases>
+<celldesigner:listOfProteins><celldesigner:protein id="p_s_id_n1__.__n0" name="STAT1_alpha_" type="GENERIC">
+<celldesigner:listOfModificationResidues><celldesigner:modificationResidue  id="3" name="Y701" angle="1.5973482732763293"></celldesigner:modificationResidue><celldesigner:modificationResidue  id="4" name="S727" angle="5.280262641519494"></celldesigner:modificationResidue></celldesigner:listOfModificationResidues>
+</celldesigner:protein>
+</celldesigner:listOfProteins>
+<celldesigner:listOfGenes></celldesigner:listOfGenes>
+<celldesigner:listOfRNAs></celldesigner:listOfRNAs>
+<celldesigner:listOfAntisenseRNAs></celldesigner:listOfAntisenseRNAs>
+<celldesigner:listOfLayers></celldesigner:listOfLayers>
+</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="#F007-inos.sbgn">
+<dcterms:modified rdf:parseType="Resource"></dcterms:modified>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+<listOfCompartments>
+<compartment metaid="s_id_n1" id="s_id_n1" name="NUCLEUS" size="1" units="volume" outside="default" >
+<notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>
+</body></html></notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:name>NUCLEUS</celldesigner:name>
+</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_n1">
+<dcterms:modified rdf:parseType="Resource"></dcterms:modified>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</compartment>
+<compartment metaid="default" id="default" name="" size="1" units="volume" >
+<notes><html xmlns="http://www.w3.org/1999/xhtml"><head><title/></head><body>
+</body></html></notes>
+<annotation>
+<celldesigner:extension>
+</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="#default">
+<dcterms:modified rdf:parseType="Resource"></dcterms:modified>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</compartment>
+</listOfCompartments>
+<listOfSpecies><species  name="STAT1_alpha_" id="s_id_n1__.__n0" metaid="s_id_n1__.__n0" initialConcentration="0.0" hasOnlySubstanceUnits="false" constant="false" boundaryCondition="false" compartment="s_id_n1"><annotation><celldesigner:extension><celldesigner:speciesIdentity><celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>p_s_id_n1__.__n0</celldesigner:proteinReference>
+<celldesigner:state>
+<celldesigner:homodimer>2</celldesigner:homodimer>
+<celldesigner:listOfModifications>
+<celldesigner:modification residue="3" state="phosphorylated"> </celldesigner:modification>
+<celldesigner:modification residue="4" state="phosphorylated"> </celldesigner:modification>
+</celldesigner:listOfModifications>
+</celldesigner:state>
+<celldesigner:name>STAT1_alpha_</celldesigner:name>
+</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_n1__.__n0">
+<dcterms:modified rdf:parseType="Resource"></dcterms:modified>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+</listOfSpecies>
+</model></sbml>