From d9928f4bad2fb38e0c05894704fd220b886e48f8 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 7 Feb 2018 14:13:54 +0100
Subject: [PATCH] parsing of annotation added
---
.../model/sbml/SbmlBioEntityParser.java | 18 ++++++++++++----
.../converter/model/sbml/SbmlParserTest.java | 8 +++++++
.../small/compartment_with_annotation.xml | 21 +++++++++++++++++++
3 files changed, 43 insertions(+), 4 deletions(-)
create mode 100644 converter-sbml/testFiles/small/compartment_with_annotation.xml
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java
index ee333b6581..7ba0246982 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java
@@ -9,10 +9,12 @@ import org.apache.log4j.Logger;
import org.sbml.jsbml.AbstractNamedSBase;
import org.sbml.jsbml.Annotation;
import org.sbml.jsbml.ext.layout.Layout;
-import org.sbml.jsbml.util.NotImplementedException;
+import org.w3c.dom.Node;
import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
@@ -28,11 +30,19 @@ public class SbmlBioEntityParser extends XmlParser {
super();
}
- protected Set<MiriamData> parseAnnotation(Annotation annotation) {
+ protected Set<MiriamData> parseAnnotation(Annotation annotation) throws InvalidInputDataExecption {
+ XmlAnnotationParser parser = new XmlAnnotationParser();
+ Set<MiriamData> result = new HashSet<>();
if (annotation.getCVTermCount() > 0) {
- throw new NotImplementedException();
+ try {
+ Node node = getXmlDocumentFromString(annotation.getFullAnnotationString());
+ Node annotationNode = getNode("annotation", node);
+ Node rdfNode = getNode("rdf:RDF", annotationNode);
+ result.addAll(parser.parseRdfNode(rdfNode));
+ } catch (InvalidXmlSchemaException e) {
+ throw new InvalidInputDataExecption(e);
+ }
}
- Set<MiriamData> result = new HashSet<>();
return result;
}
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 19a431f9f7..e20a4566cc 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
@@ -138,4 +138,12 @@ public class SbmlParserTest {
}
+ @Test
+ public void testAnnotationsInComp() throws Exception {
+ Model model = parser.createModel(new ConverterParams().filename("testFiles/small/compartment_with_annotation.xml"));
+ assertNotNull(model);
+ assertEquals(1, model.getCompartments().size());
+ assertEquals(1, model.getCompartments().iterator().next().getMiriamData().size());
+ }
+
}
diff --git a/converter-sbml/testFiles/small/compartment_with_annotation.xml b/converter-sbml/testFiles/small/compartment_with_annotation.xml
new file mode 100644
index 0000000000..4498e84da9
--- /dev/null
+++ b/converter-sbml/testFiles/small/compartment_with_annotation.xml
@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
+ <model id="TestGEN">
+ <annotation/>
+ <listOfCompartments>
+ <compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+ <rdf:Description rdf:about="#">
+ <bqbiol:isVersionOf>
+ <rdf:Bag>
+ <rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
+ </rdf:Bag>
+ </bqbiol:isVersionOf>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </compartment>
+ </listOfCompartments>
+ </model>
+</sbml>
\ No newline at end of file
--
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