-/**\r
-* Copyright (C) 2008 EDIT\r
-* European Distributed Institute of Taxonomy \r
-* http://www.e-taxonomy.eu\r
-*/\r
-\r
-package eu.etaxonomy.cdm.io.jaxb;\r
-\r
-import java.io.File;\r
-import java.io.IOException;\r
-import java.io.Writer;\r
-\r
-import javax.xml.bind.JAXBContext;\r
-import javax.xml.bind.JAXBException;\r
-import javax.xml.bind.Marshaller;\r
-import javax.xml.bind.Unmarshaller;\r
-import javax.xml.bind.helpers.DefaultValidationEventHandler;\r
-\r
-import org.apache.log4j.Logger;\r
-import org.xml.sax.SAXException;\r
-\r
-/**\r
- * Initializes a JaxbContext with one class (eu.etaxonomy.cdm.model.DataSet). \r
- * \r
- * @author a.babadshanjan\r
- */\r
-//Binds it to XML schemas found in /src/main/resources/schema/cdm (cdm.xsd, common.xsd, name.xsd).\r
-//There is a bit of magic with a resource resolver in eu.etaxonomy.cdm.io.jaxb\r
-//which allows to package the schemas into a jar file.\r
-public class CdmDocumentBuilder {\r
- \r
- private static final Logger logger = Logger.getLogger(CdmDocumentBuilder.class);\r
- \r
- private JAXBContext jaxbContext;\r
- private boolean formattedOutput = Boolean.TRUE;\r
- private String encoding = "UTF-8"; \r
- \r
-// public static String CDM_NAMESPACE = "eu.etaxonomy.cdm.model";\r
-// public static String[] CDM_SCHEMA_FILES = { "/schema/cdm/common.xsd",\r
-// "/schema/cdm/name.xsd",\r
-// "/schema/cdm/cdm.xsd" };\r
- \r
- public CdmDocumentBuilder() throws SAXException, JAXBException, IOException {\r
- \r
-// SchemaFactory schemaFactory = SchemaFactory.newInstance(XMLConstants.W3C_XML_SCHEMA_NS_URI);\r
-// schemaFactory.setResourceResolver(new CdmResourceResolver());\r
-// Source[] sources = new Source[CdmDocumentBuilder.CDM_SCHEMA_FILES.length];\r
-// \r
-// for(int i = 0; i < CdmDocumentBuilder.CDM_SCHEMA_FILES.length; i++) {\r
-// String schemaName = CdmDocumentBuilder.CDM_SCHEMA_FILES[i];\r
-// sources[i] = new StreamSource(this.getClass().getResourceAsStream(schemaName));\r
-// }\r
-// Schema cdmSchema = schemaFactory.newSchema(sources);\r
- \r
- jaxbContext = JAXBContext.newInstance(new Class[] {DataSet.class});\r
- if (logger.isDebugEnabled()) { logger.debug(jaxbContext.toString()); }\r
-\r
- }\r
- \r
- public CdmDocumentBuilder(boolean formattedOutput, String encoding) \r
- throws SAXException, JAXBException, IOException {\r
- \r
- this();\r
- this.formattedOutput = formattedOutput;\r
- this.encoding = encoding;\r
- }\r
- \r
- public void marshal(DataSet dataSet, Writer writer) throws JAXBException {\r
- \r
- Marshaller marshaller;\r
- marshaller = jaxbContext.createMarshaller();\r
- \r
- // For test purposes insert newlines to make the XML output readable\r
- marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, formattedOutput);\r
- \r
- marshaller.setProperty(Marshaller.JAXB_ENCODING, encoding);\r
- \r
- CdmMarshallerListener marshallerListener = new CdmMarshallerListener();\r
- marshaller.setListener(marshallerListener);\r
- \r
- // validate with explicit schema\r
- //marshaller.setSchema(cdmSchema);\r
- \r
- marshaller.setEventHandler(new DefaultValidationEventHandler());\r
-\r
- logger.info("Start marshalling");\r
- marshaller.marshal(dataSet, writer);\r
- \r
- }\r
-\r
- public DataSet unmarshal(DataSet dataSet, File file) throws JAXBException {\r
- \r
- Unmarshaller unmarshaller;\r
- unmarshaller = jaxbContext.createUnmarshaller();\r
- \r
- // DefaultValidationEventHandler implementation is part of the API and convenient for trouble-shooting.\r
- // It prints errors to System.out.\r
- //unmarshaller.setEventHandler(new DefaultValidationEventHandler());\r
-\r
- logger.info("Start unmarshalling");\r
- dataSet = (DataSet) unmarshaller.unmarshal(file);\r
- return dataSet;\r
- \r
- }\r
-\r
-// can only be used with JAXB 2.1\r
-// public void writeFile(DataSet dataSet, File file) throws JAXBException {\r
-// marshaller.marshal(dataSet, file);\r
-// }\r
-\r
-}\r
-\r
- \r
+/**
+ * Copyright (C) 2008 EDIT
+ * European Distributed Institute of Taxonomy
+ * http://www.e-taxonomy.eu
+ *
+ * The contents of this file are subject to the Mozilla Public License Version 1.1
+ * See LICENSE.TXT at the top of this package for the full license terms.
+ */
+
+package eu.etaxonomy.cdm.io.jaxb;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.io.UnsupportedEncodingException;
+import java.io.Writer;
+import java.net.URISyntaxException;
+
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.Marshaller;
+import javax.xml.bind.PropertyException;
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.parsers.SAXParser;
+import javax.xml.parsers.SAXParserFactory;
+import javax.xml.transform.Source;
+import javax.xml.transform.sax.SAXResult;
+import javax.xml.transform.sax.SAXSource;
+import javax.xml.transform.stream.StreamResult;
+import javax.xml.validation.Schema;
+import javax.xml.validation.SchemaFactory;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.apache.xml.resolver.tools.CatalogResolver;
+import org.springframework.core.io.ClassPathResource;
+import org.springframework.core.io.Resource;
+import org.springframework.oxm.UncategorizedMappingException;
+import org.springframework.oxm.XmlMappingException;
+import org.springframework.oxm.jaxb.Jaxb2Marshaller;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+import org.xml.sax.XMLReader;
+import org.xml.sax.helpers.XMLReaderFactory;
+
+import eu.etaxonomy.cdm.common.URI;
+import eu.etaxonomy.cdm.jaxb.CdmNamespacePrefixMapper;
+import eu.etaxonomy.cdm.jaxb.FormattedText;
+import eu.etaxonomy.cdm.jaxb.MultilanguageTextElement;
+
+/**
+ * Initializes a JaxbContext with one class (eu.etaxonomy.cdm.model.DataSet).
+ *
+ * @author a.babadshanjan, ben.clark
+ */
+//Binds it to XML schemas found in /src/main/resources/schema/cdm (cdm.xsd, common.xsd, name.xsd).
+//There is a bit of magic with a resource resolver in eu.etaxonomy.cdm.io.jaxb
+//which allows to package the schemas into a jar file.
+public class CdmDocumentBuilder extends Jaxb2Marshaller {
+
+ private static final Logger logger = LogManager.getLogger();
+ private boolean formattedOutput = Boolean.TRUE;
+ private String encoding = "UTF-8";
+
+ public static String CDM_NAMESPACE = "eu.etaxonomy.cdm.model";
+ public static String[] CDM_SCHEMA_FILES = { "/schema/cdm/agent.xsd",
+ "/schema/cdm/cdm.xsd",
+ "/schema/cdm/common.xsd",
+ "/schema/cdm/description.xsd",
+ "/schema/cdm/location.xsd",
+ "/schema/cdm/media.xsd",
+ "/schema/cdm/molecular.xsd",
+ "/schema/cdm/name.xsd",
+ "/schema/cdm/occurrence.xsd",
+ "/schema/cdm/reference.xsd",
+ "/schema/cdm/taxon.xsd"};
+ public static Class[] CONTEXT_CLASSES = {
+ DataSet.class,FormattedText.class,MultilanguageTextElement.class};
+
+ private Resource schemas[];
+
+ protected String[] getSchemaFiles() {
+ return CDM_SCHEMA_FILES;
+ }
+
+ protected Class[] getContextClasses() {
+ return CONTEXT_CLASSES;
+ }
+
+ public CdmDocumentBuilder() {
+ schemas = new Resource[CDM_SCHEMA_FILES.length];
+
+ for(int i = 0; i < CDM_SCHEMA_FILES.length; i++) {
+ schemas[i] = new ClassPathResource(CDM_SCHEMA_FILES[i]);
+ }
+
+ super.setSchemas(schemas);
+ super.setClassesToBeBound(CONTEXT_CLASSES);
+ super.setSchemaLanguage("http://www.w3.org/2001/XMLSchema");
+ }
+
+ public CdmDocumentBuilder(boolean formattedOutput, String encoding) {
+ this.formattedOutput = formattedOutput;
+ this.encoding = encoding;
+ }
+
+
+ @Override
+ protected void initJaxbMarshaller(Marshaller marshaller) throws JAXBException {
+ try {
+ marshaller.setProperty("com.sun.xml.bind.namespacePrefixMapper", new CdmNamespacePrefixMapper() );
+
+ // For test purposes insert newlines to make the XML output readable
+ marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, formattedOutput);
+ //marshaller.setProperty(Marshaller.JAXB_SCHEMA_LOCATION,"http://etaxonomy.eu/cdm/model/1.0 schema/cdm/cdm.xsd");
+ //marshaller.setProperty(Marshaller.JAXB_SCHEMA_LOCATION,"http://etaxonomy.eu/cdm/model/1.0 cdm.xsd");
+ marshaller.setProperty(Marshaller.JAXB_ENCODING, encoding);
+
+ CdmMarshallerListener marshallerListener = new CdmMarshallerListener();
+ marshaller.setListener(marshallerListener);
+ marshaller.setEventHandler(new WarningTolerantValidationEventHandler());
+ } catch(PropertyException pe) {
+ throw new JAXBException(pe.getMessage(),pe);
+ }
+ }
+
+ protected <T> T unmarshal(Class<T> clazz, InputSource input) {
+ SAXParserFactory saxParserFactory = SAXParserFactory.newInstance();
+ Schema schema;
+ try {
+ schema = createSchema();
+ saxParserFactory.setNamespaceAware(true);
+ saxParserFactory.setXIncludeAware(true);
+ saxParserFactory.setValidating(true);
+ saxParserFactory.setSchema(schema);
+
+ SAXParser saxParser = saxParserFactory.newSAXParser();
+ XMLReader xmlReader = saxParser.getXMLReader();
+ xmlReader.setEntityResolver(new CatalogResolver());
+ xmlReader.setErrorHandler(new DefaultErrorHandler());
+ SAXSource saxSource = new SAXSource( xmlReader, input);
+ saxSource.setSystemId(input.getSystemId());
+
+ return (T)super.unmarshal(saxSource);
+ } catch (IOException e) {
+ throw new UncategorizedMappingException(e.getMessage(), e);
+ } catch (SAXException e) {
+ throw new UncategorizedMappingException(e.getMessage(), e);
+ } catch (ParserConfigurationException e) {
+ throw new UncategorizedMappingException(e.getMessage(), e);
+ }
+ }
+
+ private Schema createSchema() throws SAXException, IOException {
+ //method created to avoid dependency of spring-xml like in earlier versions
+ //old implementation was schema = SchemaLoaderUtils.loadSchema(schemas, "http://www.w3.org/2001/XMLSchema");
+ //maybe we can improve this loading in future
+
+ String schemaLanguage = "http://www.w3.org/2001/XMLSchema";
+ Source[] schemaSources = new Source[schemas.length];
+ XMLReader reader = XMLReaderFactory.createXMLReader();
+ reader.setFeature("http://xml.org/sax/features/namespace-prefixes", true);
+ for (int i = 0; i < schemas.length; i++) {
+ schemaSources[i] = makeSchemaSource(reader, schemas[i]);// new ResourceSource(reader, schemas[i]);
+ }
+ SchemaFactory schemaFactory = SchemaFactory.newInstance(schemaLanguage);
+ return schemaFactory.newSchema(schemaSources);
+ }
+
+ private Source makeSchemaSource(XMLReader reader, Resource resource) throws IOException {
+ Source result = new SAXSource(reader, createInputSource(resource));
+ return result;
+ }
+
+ private static InputSource createInputSource(Resource resource) throws IOException {
+ InputSource inputSource = new InputSource(resource.getInputStream());
+ inputSource.setSystemId(getSystemId(resource));
+ return inputSource;
+ }
+
+ /** Retrieves the URL from the given resource as System ID. Returns <code>null</code> if it cannot be opened. */
+ private static String getSystemId(Resource resource) {
+ try {
+ return new URI(resource.getURL().toExternalForm()).toString();
+ }
+ catch (IOException ex) {
+ logger.debug("Could not get System ID from [" + resource + "], ex");
+ return null;
+ }
+ catch (URISyntaxException e) {
+ logger.debug("Could not get System ID from [" + resource + "], ex");
+ return null;
+ }
+ }
+
+ public <T> T unmarshal(Class<T> clazz,Reader reader) throws XmlMappingException {
+ InputSource source = new InputSource(reader);
+ return unmarshal(clazz,source);
+ }
+
+ public <T> T unmarshal(Class<T> clazz,Reader reader, String systemId) throws XmlMappingException {
+ InputSource input = new InputSource(reader);
+ input.setSystemId(systemId);
+ return unmarshal(clazz,input);
+ }
+
+ public <T> T unmarshal(Class<T> clazz, File file) throws XmlMappingException {
+
+ InputSource input;
+ try {
+ input = new InputSource(new InputStreamReader(new FileInputStream(file),encoding));
+ return unmarshal(clazz,input);
+ } catch (UnsupportedEncodingException e) {
+ throw new UncategorizedMappingException(e.getMessage(), e);
+ } catch (FileNotFoundException e) {
+ throw new UncategorizedMappingException(e.getMessage(), e);
+ }
+ }
+
+ public void marshal(DataSet dataSet, Writer writer) throws XmlMappingException {
+ logger.info("Start marshalling");
+ super.marshal(dataSet, new StreamResult(writer));
+ }
+
+ public void marshal(DataSet dataSet, StreamResult result) throws XmlMappingException {
+ logger.info("Start marshalling");
+ super.marshal(dataSet, result);
+ }
+
+ public void marshal(DataSet dataSet, SAXResult result) throws XmlMappingException {
+ logger.info("Start marshalling");
+ super.marshal(dataSet, result);
+ }
+}
\ No newline at end of file
BGBM BDI Projects / cdmlib.git / blobdiff