-/**\r
- * Copyright (C) 2008 EDIT\r
- * European Distributed Institute of Taxonomy\r
- * http://www.e-taxonomy.eu\r
- *\r
- * The contents of this file are subject to the Mozilla Public License Version 1.1\r
- * See LICENSE.TXT at the top of this package for the full license terms.\r
- */\r
-\r
-package eu.etaxonomy.cdm.io.jaxb;\r
-\r
-import java.io.File;\r
-import java.io.FileInputStream;\r
-import java.io.FileNotFoundException;\r
-import java.io.IOException;\r
-import java.io.InputStreamReader;\r
-import java.io.Reader;\r
-import java.io.UnsupportedEncodingException;\r
-import java.io.Writer;\r
-import eu.etaxonomy.cdm.common.URI;\r
-import java.net.URISyntaxException;\r
-\r
-import javax.xml.bind.JAXBException;\r
-import javax.xml.bind.Marshaller;\r
-import javax.xml.bind.PropertyException;\r
-import javax.xml.parsers.ParserConfigurationException;\r
-import javax.xml.parsers.SAXParser;\r
-import javax.xml.parsers.SAXParserFactory;\r
-import javax.xml.transform.Source;\r
-import javax.xml.transform.sax.SAXResult;\r
-import javax.xml.transform.sax.SAXSource;\r
-import javax.xml.transform.stream.StreamResult;\r
-import javax.xml.validation.Schema;\r
-import javax.xml.validation.SchemaFactory;\r
-\r
-import org.apache.logging.log4j.LogManager;import org.apache.logging.log4j.Logger;\r
-import org.apache.xml.resolver.tools.CatalogResolver;\r
-import org.springframework.core.io.ClassPathResource;\r
-import org.springframework.core.io.Resource;\r
-import org.springframework.oxm.UncategorizedMappingException;\r
-import org.springframework.oxm.XmlMappingException;\r
-import org.springframework.oxm.jaxb.Jaxb2Marshaller;\r
-import org.xml.sax.InputSource;\r
-import org.xml.sax.SAXException;\r
-import org.xml.sax.XMLReader;\r
-import org.xml.sax.helpers.XMLReaderFactory;\r
-\r
-import eu.etaxonomy.cdm.jaxb.CdmNamespacePrefixMapper;\r
-import eu.etaxonomy.cdm.jaxb.FormattedText;\r
-import eu.etaxonomy.cdm.jaxb.MultilanguageTextElement;\r
-\r
-/**\r
- * Initializes a JaxbContext with one class (eu.etaxonomy.cdm.model.DataSet).\r
- *\r
- * @author a.babadshanjan, ben.clark\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 extends Jaxb2Marshaller {\r
-\r
- private static final Logger logger = LogManager.getLogger(CdmDocumentBuilder.class);\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/agent.xsd",\r
- "/schema/cdm/cdm.xsd",\r
- "/schema/cdm/common.xsd",\r
- "/schema/cdm/description.xsd",\r
- "/schema/cdm/location.xsd",\r
- "/schema/cdm/media.xsd",\r
- "/schema/cdm/molecular.xsd",\r
- "/schema/cdm/name.xsd",\r
- "/schema/cdm/occurrence.xsd",\r
- "/schema/cdm/reference.xsd",\r
- "/schema/cdm/taxon.xsd"};\r
- public static Class[] CONTEXT_CLASSES = {DataSet.class,FormattedText.class,MultilanguageTextElement.class};\r
-\r
- private Resource schemas[];\r
-\r
- protected String[] getSchemaFiles() {\r
- return CDM_SCHEMA_FILES;\r
- }\r
-\r
- protected Class[] getContextClasses() {\r
- return CONTEXT_CLASSES;\r
- }\r
-\r
- public CdmDocumentBuilder() {\r
- schemas = new Resource[CDM_SCHEMA_FILES.length];\r
-\r
- for(int i = 0; i < CDM_SCHEMA_FILES.length; i++) {\r
- schemas[i] = new ClassPathResource(CDM_SCHEMA_FILES[i]);\r
- }\r
-\r
- super.setSchemas(schemas);\r
- super.setClassesToBeBound(CONTEXT_CLASSES);\r
- super.setSchemaLanguage("http://www.w3.org/2001/XMLSchema");\r
- }\r
-\r
- public CdmDocumentBuilder(boolean formattedOutput, String encoding) {\r
- this.formattedOutput = formattedOutput;\r
- this.encoding = encoding;\r
- }\r
-\r
-\r
- @Override\r
- protected void initJaxbMarshaller(Marshaller marshaller) throws JAXBException {\r
- try {\r
- marshaller.setProperty("com.sun.xml.bind.namespacePrefixMapper", new CdmNamespacePrefixMapper() );\r
-\r
- // For test purposes insert newlines to make the XML output readable\r
- marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, formattedOutput);\r
- //marshaller.setProperty(Marshaller.JAXB_SCHEMA_LOCATION,"http://etaxonomy.eu/cdm/model/1.0 schema/cdm/cdm.xsd");\r
- //marshaller.setProperty(Marshaller.JAXB_SCHEMA_LOCATION,"http://etaxonomy.eu/cdm/model/1.0 cdm.xsd");\r
- marshaller.setProperty(Marshaller.JAXB_ENCODING, encoding);\r
-\r
- CdmMarshallerListener marshallerListener = new CdmMarshallerListener();\r
- marshaller.setListener(marshallerListener);\r
- marshaller.setEventHandler(new WarningTolerantValidationEventHandler());\r
- } catch(PropertyException pe) {\r
- throw new JAXBException(pe.getMessage(),pe);\r
- }\r
- }\r
-\r
- protected <T> T unmarshal(Class<T> clazz, InputSource input) {\r
- SAXParserFactory saxParserFactory = SAXParserFactory.newInstance();\r
- Schema schema;\r
- try {\r
- schema = createSchema();\r
- saxParserFactory.setNamespaceAware(true);\r
- saxParserFactory.setXIncludeAware(true);\r
- saxParserFactory.setValidating(true);\r
- saxParserFactory.setSchema(schema);\r
-\r
- SAXParser saxParser = saxParserFactory.newSAXParser();\r
- XMLReader xmlReader = saxParser.getXMLReader();\r
- xmlReader.setEntityResolver(new CatalogResolver());\r
- xmlReader.setErrorHandler(new DefaultErrorHandler());\r
- SAXSource saxSource = new SAXSource( xmlReader, input);\r
- saxSource.setSystemId(input.getSystemId());\r
-\r
- return (T)super.unmarshal(saxSource);\r
- } catch (IOException e) {\r
- throw new UncategorizedMappingException(e.getMessage(), e);\r
- } catch (SAXException e) {\r
- throw new UncategorizedMappingException(e.getMessage(), e);\r
- } catch (ParserConfigurationException e) {\r
- throw new UncategorizedMappingException(e.getMessage(), e);\r
- }\r
- }\r
-\r
- private Schema createSchema() throws SAXException, IOException {\r
- //method created to avoid dependency of spring-xml like in earlier versions\r
- //old implementation was schema = SchemaLoaderUtils.loadSchema(schemas, "http://www.w3.org/2001/XMLSchema");\r
- //maybe we can improve this loading in future\r
-\r
- String schemaLanguage = "http://www.w3.org/2001/XMLSchema";\r
- Source[] schemaSources = new Source[schemas.length];\r
- XMLReader reader = XMLReaderFactory.createXMLReader();\r
- reader.setFeature("http://xml.org/sax/features/namespace-prefixes", true);\r
- for (int i = 0; i < schemas.length; i++) {\r
- schemaSources[i] = makeSchemaSource(reader, schemas[i]);// new ResourceSource(reader, schemas[i]);\r
- }\r
- SchemaFactory schemaFactory = SchemaFactory.newInstance(schemaLanguage);\r
- return schemaFactory.newSchema(schemaSources);\r
- }\r
-\r
- private Source makeSchemaSource(XMLReader reader, Resource resource) throws IOException {\r
- Source result = new SAXSource(reader, createInputSource(resource));\r
- return result;\r
- }\r
-\r
- private static InputSource createInputSource(Resource resource) throws IOException {\r
- InputSource inputSource = new InputSource(resource.getInputStream());\r
- inputSource.setSystemId(getSystemId(resource));\r
- return inputSource;\r
- }\r
-\r
- /** Retrieves the URL from the given resource as System ID. Returns <code>null</code> if it cannot be opened. */\r
- private static String getSystemId(Resource resource) {\r
- try {\r
- return new URI(resource.getURL().toExternalForm()).toString();\r
- }\r
- catch (IOException ex) {\r
- logger.debug("Could not get System ID from [" + resource + "], ex");\r
- return null;\r
- }\r
- catch (URISyntaxException e) {\r
- logger.debug("Could not get System ID from [" + resource + "], ex");\r
- return null;\r
- }\r
- }\r
-\r
-\r
- public <T> T unmarshal(Class<T> clazz,Reader reader) throws XmlMappingException {\r
- InputSource source = new InputSource(reader);\r
- return unmarshal(clazz,source);\r
- }\r
-\r
- public <T> T unmarshal(Class<T> clazz,Reader reader, String systemId) throws XmlMappingException {\r
- InputSource input = new InputSource(reader);\r
- input.setSystemId(systemId);\r
- return unmarshal(clazz,input);\r
- }\r
-\r
- public <T> T unmarshal(Class<T> clazz, File file) throws XmlMappingException {\r
-\r
- InputSource input;\r
- try {\r
- input = new InputSource(new InputStreamReader(new FileInputStream(file),encoding));\r
- return unmarshal(clazz,input);\r
- } catch (UnsupportedEncodingException e) {\r
- throw new UncategorizedMappingException(e.getMessage(), e);\r
- } catch (FileNotFoundException e) {\r
- throw new UncategorizedMappingException(e.getMessage(), e);\r
- }\r
-\r
- }\r
-\r
- public void marshal(DataSet dataSet, Writer writer) throws XmlMappingException {\r
- logger.info("Start marshalling");\r
- super.marshal(dataSet, new StreamResult(writer));\r
- }\r
-\r
- public void marshal(DataSet dataSet, StreamResult result) throws XmlMappingException {\r
- logger.info("Start marshalling");\r
- super.marshal(dataSet, result);\r
- }\r
-\r
- public void marshal(DataSet dataSet, SAXResult result) throws XmlMappingException {\r
- logger.info("Start marshalling");\r
- super.marshal(dataSet, result);\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