import of SBML crashed when there was no multi list of species types

af397630 · Piotr Gawron · 0cdb1cfc · af397630 · af397630 · af397630
Commit af397630 authored Jun 24, 2020 by Piotr Gawron
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -12,6 +12,8 @@ minerva (15.1.0) unstable; urgency=medium
    inside rectangle bounded by the polygon coordinates (#1096)
  * Bug fix: continuous refreshing list of project when uploading/removing
    project did not allow to change other project details (#996)
+  * Bug fix: when multi extension did not contain species type list import of
+    SBML crashed

 -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 18 Jun 2020 16:00:00 +0200


--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java
@@ -298,19 +298,31 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
  private String extractSBOTermFromSpecies(org.sbml.jsbml.Species species) {
    String sboTerm = species.getSBOTermID();
    MultiSpeciesPlugin multiExtension = (MultiSpeciesPlugin) species.getExtension("multi");
+    MultiSpeciesType speciesType = getMultiSpeciesType(multiExtension);
+    if (speciesType != null) {
+      String sboTerm2 = speciesType.getSBOTermID();
+      if (sboTerm != null && !sboTerm.isEmpty() && !sboTerm2.equals(sboTerm)) {
+        logger.warn("Different SBO terms defining species and speciesType: " + species.getId() + ". " + sboTerm + ";"
+            + sboTerm2);
+      } else {
+        sboTerm = sboTerm2;
+      }
+    }
+    return sboTerm;
+  }
+
+  private MultiSpeciesType getMultiSpeciesType(MultiSpeciesPlugin multiExtension) {
    if (multiExtension != null) {
-      MultiSpeciesType speciesType = getMultiPlugin().getListOfSpeciesTypes().get(multiExtension.getSpeciesType());
-      if (speciesType != null) {
-        String sboTerm2 = speciesType.getSBOTermID();
-        if (sboTerm != null && !sboTerm.isEmpty() && !sboTerm2.equals(sboTerm)) {
-          logger.warn("Different SBO terms defining species and speciesType: " + species.getId() + ". " + sboTerm + ";"
-              + sboTerm2);
-        } else {
-          sboTerm = sboTerm2;
+      MultiModelPlugin modelPlugin = getMultiPlugin();
+      if (modelPlugin != null) {
+        ListOf<MultiSpeciesType> listOfSpeciesTypes = modelPlugin.getListOfSpeciesTypes();
+        if (listOfSpeciesTypes != null) {
+          return listOfSpeciesTypes.get(multiExtension.getSpeciesType());
        }
      }
    }
-    return sboTerm;
+
+    return null;
  }

  private void assignModificationResiduesLayout(Element element) {

--- a/converter-sbml/testFiles/multi/multi_with_no_types.xml
+++ b/converter-sbml/testFiles/multi/multi_with_no_types.xml
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<!-- Created by minerva version Unknown on 2020-06-24 at 08:54:37 CEST with JSBML version 1.4. -->
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" multi:required="true" version="2" xmlns:multi="http://www.sbml.org/sbml/level3/version1/multi/version1">
+  <model id="id1" name="UNKNOWN DISEASE MAP">
+    <notes>
+      <body xmlns="http://www.w3.org/1999/xhtml">
+<p/>
+</body>
+    </notes>
+    <annotation>
+      <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="#id1">
+<dcterms:modified rdf:parseType="Resource"/>
+</rdf:Description>
+</rdf:RDF>
+    </annotation>
+    <listOfCompartments>
+      <compartment constant="false" id="default" multi:isType="false" size="1" spatialDimensions="3">
+        <notes>
+          <body xmlns="http://www.w3.org/1999/xhtml">
+<p/>
+</body>
+        </notes>
+        <annotation>
+          <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"/>
+</rdf:Description>
+</rdf:RDF>
+        </annotation>
+            </compartment>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species boundaryCondition="false" compartment="default" constant="false" hasOnlySubstanceUnits="false" id="species_0" initialConcentration="0" multi:speciesType="minerva_species_type_GenericProtein" name="SNCA" sboTerm="SBO:0000252">
+        <notes>
+          <body xmlns="http://www.w3.org/1999/xhtml">
+<p/>
+</body>
+        </notes>
+        <annotation>
+          <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="#species_0">
+<dcterms:modified rdf:parseType="Resource"/>
+</rdf:Description>
+</rdf:RDF>
+        </annotation>
+      </species>
+      <species boundaryCondition="false" compartment="default" constant="false" hasOnlySubstanceUnits="false" id="species_1" initialConcentration="0" multi:speciesType="minerva_species_type_GenericProtein" name="SNCA 2" sboTerm="SBO:0000252">
+        <notes>
+          <body xmlns="http://www.w3.org/1999/xhtml">
+<p/>
+</body>
+        </notes>
+        <annotation>
+          <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="#species_0">
+<dcterms:modified rdf:parseType="Resource"/>
+</rdf:Description>
+</rdf:RDF>
+        </annotation>
+      </species>
+    </listOfSpecies>
+    <listOfReactions>
+      <reaction id="r2" reversible="false" sboTerm="SBO:0000176">
+        <notes>
+          <body xmlns="http://www.w3.org/1999/xhtml">
+<p/>
+</body>
+        </notes>
+        <annotation>
+          <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="#r2">
+<dcterms:modified rdf:parseType="Resource"/>
+</rdf:Description>
+</rdf:RDF>
+        </annotation>
+              <listOfReactants>
+          <speciesReference constant="false" species="species_0"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference constant="false" species="species_1"/>
+        </listOfProducts>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>
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