diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java
index 1c8468a8c91b470457f3f135c62d2e77703e6137..bac6ee8c1366bd7bf3fac869ed70a06f089bc067 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java
@@ -65,6 +65,9 @@ public abstract class SbmlElementParser<T extends org.sbml.jsbml.Symbol> extends
}
used.add(source.getElementId());
AbstractReferenceGlyph glyph = idGlyphPair.getRight();
+ if (glyph.getId() == null || glyph.getId().equals("")) {
+ throw new InvalidInputDataExecption("Glyph for Species " + idGlyphPair.getLeft() + " doesn't have id");
+ }
Element elementWithLayout = source.copy();
elementWithLayout.setElementId(glyph.getId());
elementWithLayout.setX(glyph.getBoundingBox().getPosition().getX());
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
index e20a4566cc78d0351666ddf74b8e140950c42b61..12d77368fb7bafc34f9c98e42f3b2f59202c2869 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
@@ -40,6 +40,11 @@ public class SbmlParserTest {
assertFalse(compartment.getClass().equals(Compartment.class));
}
+ @Test(expected = InvalidInputDataExecption.class)
+ public void testInvalidSpeciesId() throws FileNotFoundException, InvalidInputDataExecption {
+ parser.createModel(new ConverterParams().filename("testFiles/invalid_layout_alias_without_id.xml"));
+ }
+
@Test
public void testParseUnits() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser.createModel(
diff --git a/converter-sbml/testFiles/invalid_layout_alias_without_id.xml b/converter-sbml/testFiles/invalid_layout_alias_without_id.xml
new file mode 100644
index 0000000000000000000000000000000000000000..ce53e764b6688bedad6005a0bea140bc28125e6a
--- /dev/null
+++ b/converter-sbml/testFiles/invalid_layout_alias_without_id.xml
@@ -0,0 +1,43 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" level="3" version="1" layout:required="false">
+ <model id="untitled" name="NEW DISEASE MAP">
+ <listOfUnitDefinitions>
+ <unitDefinition id="time" name="time"/>
+ <unitDefinition id="area" name="area"/>
+ <unitDefinition id="volume" name="volume"/>
+ <unitDefinition id="substance" name="substance"/>
+ <unitDefinition id="length" name="length"/>
+ </listOfUnitDefinitions>
+ <listOfSpecies>
+ <species sboTerm="SBO:0000252" id="species_6" name="F">
+ <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="#"/>
+ </rdf:RDF>
+ </annotation>
+ </species>
+ </listOfSpecies>
+ <listOfReactions>
+ </listOfReactions>
+ <layout:listOfLayouts xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+ <layout:layout layout:id="predicted_layout">
+ <layout:dimensions layout:width="762.238734102226" layout:height="293.472408203789"/>
+ <layout:listOfSpeciesGlyphs>
+ <layout:speciesGlyph layout:species="species_6">
+ <layout:boundingBox>
+ <layout:position layout:x="170" layout:y="228.75"/>
+ <layout:dimensions layout:width="80" layout:height="40"/>
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ </layout:listOfSpeciesGlyphs>
+ <layout:listOfTextGlyphs>
+ </layout:listOfTextGlyphs>
+ </layout:layout>
+ </layout:listOfLayouts>
+ </model>
+</sbml>