Commit de5c9e8d authored by Piotr Gawron's avatar Piotr Gawron
Browse files

error message is more informative when uploading sbml with invalid ids

parent af01620c
Pipeline #6376 passed with stage
in 1 minute and 52 seconds
......@@ -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());
......
......@@ -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(
......
<?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>
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