error message is more informative when uploading sbml with invalid ids

de5c9e8d · Piotr Gawron · af01620c · de5c9e8d · de5c9e8d · de5c9e8d
Commit de5c9e8d authored 6 years ago by Piotr Gawron
--- 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());

--- 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(

--- a/converter-sbml/testFiles/invalid_layout_alias_without_id.xml
+++ b/converter-sbml/testFiles/invalid_layout_alias_without_id.xml
+<?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>