From 4888e2e08ebe3d14d9cbf42b4ee305f6a87be2f2 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Tue, 13 Oct 2009 07:59:38 +0000
Subject: [PATCH] SE-146 Schema validation for quantML files added
SVN: 12910
---
rtd_yeastx/build/build.xml | 1 +
rtd_yeastx/resource/examples/allFields.quantML | 2 +-
.../ch/systemsx/cisd/yeastx/quant/QuantMLParser.java | 12 +++++++++++-
3 files changed, 13 insertions(+), 2 deletions(-)
diff --git a/rtd_yeastx/build/build.xml b/rtd_yeastx/build/build.xml
index 304d58a568c..cc46a042d37 100644
--- a/rtd_yeastx/build/build.xml
+++ b/rtd_yeastx/build/build.xml
@@ -27,6 +27,7 @@
</fileset>
<fileset dir="source">
<include name="**/*.sql" />
+ <include name="**/*.xsd" />
</fileset>
</recursive-jar>
</target>
diff --git a/rtd_yeastx/resource/examples/allFields.quantML b/rtd_yeastx/resource/examples/allFields.quantML
index 58b62984f0f..8b6a654ad55 100644
--- a/rtd_yeastx/resource/examples/allFields.quantML
+++ b/rtd_yeastx/resource/examples/allFields.quantML
@@ -2,8 +2,8 @@
<quantML>
<msQuantification>
<source>msSoft</source>
- <valid>true</valid>
<comment>no comment</comment>
+ <valid>true</valid>
<registrationDate>04-Apr-1980 12:00:21</registrationDate>
<registrator>John Doe</registrator>
<concentration>
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/QuantMLParser.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/QuantMLParser.java
index 3fed98618f8..02c8cfd25b0 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/QuantMLParser.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/QuantMLParser.java
@@ -17,16 +17,23 @@
package ch.systemsx.cisd.yeastx.quant;
import java.io.File;
+import java.io.FileReader;
import java.io.IOException;
import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBException;
import javax.xml.bind.SchemaOutputResolver;
import javax.xml.bind.Unmarshaller;
+import javax.xml.bind.UnmarshallerHandler;
import javax.xml.transform.Result;
import javax.xml.transform.stream.StreamResult;
+import org.xml.sax.EntityResolver;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+
import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
+import ch.systemsx.cisd.common.utilities.XMLInfraStructure;
import ch.systemsx.cisd.yeastx.quant.dto.MSQuantificationsDTO;
/**
@@ -46,6 +53,9 @@ class QuantMLParser
private QuantMLParser()
{
this.unmarshaller = createUnmarshaller();
+ unmarshaller.setSchema(XMLInfraStructure.createSchema("/"
+ + QuantMLParser.class.getPackage().getName().replace('.', '/')
+ + "/quantml-schema.xsd"));
}
private static Unmarshaller createUnmarshaller()
@@ -90,7 +100,7 @@ class QuantMLParser
throw new IllegalArgumentException("Wrong type: " + object);
}
return (MSQuantificationsDTO) object;
- } catch (JAXBException ex)
+ } catch (Exception ex)
{
throw CheckedExceptionTunnel.wrapIfNecessary(ex);
}
--
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