engine/compbio/engine/conf/RunnerConfigMarshaller.java

   1 /* Copyright (c) 2009 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0     \r
   4  * \r
   5  *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
   6  *  Apache License version 2 as published by the Apache Software Foundation\r
   7  * \r
   8  *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
   9  *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
  10  *  License for more details.\r
  11  * \r
  12  *  A copy of the license is in apache_license.txt. It is also available here:\r
  13  * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
  14  * \r
  15  * Any republication or derived work distributed in source code form\r
  16  * must include this copyright and license notice.\r
  17  */\r
  18 \r
  19 package compbio.engine.conf;\r
  20 \r
  21 import java.io.File;\r
  22 import java.io.IOException;\r
  23 import java.io.InputStream;\r
  24 import java.io.OutputStream;\r
  25 import java.util.ArrayList;\r
  26 import java.util.Arrays;\r
  27 import java.util.List;\r
  28 \r
  29 import javax.xml.bind.JAXBContext;\r
  30 import javax.xml.bind.JAXBElement;\r
  31 import javax.xml.bind.JAXBException;\r
  32 import javax.xml.bind.Marshaller;\r
  33 import javax.xml.bind.SchemaOutputResolver;\r
  34 import javax.xml.bind.Unmarshaller;\r
  35 import javax.xml.transform.Result;\r
  36 import javax.xml.transform.stream.StreamResult;\r
  37 import javax.xml.transform.stream.StreamSource;\r
  38 import javax.xml.validation.Schema;\r
  39 import javax.xml.validation.SchemaFactory;\r
  40 import javax.xml.validation.Validator;\r
  41 \r
  42 import org.apache.log4j.Logger;\r
  43 import org.xml.sax.SAXException;\r
  44 \r
  45 import compbio.util.SysPrefs;\r
  46 \r
  47 public class RunnerConfigMarshaller<T> {\r
  48 \r
  49         private static final Logger log = Logger\r
  50                         .getLogger(RunnerConfigMarshaller.class);\r
  51 \r
  52         private final JAXBContext ctx;\r
  53 \r
  54         @SuppressWarnings("all")\r
  55         public RunnerConfigMarshaller(Class<?> rootClass) throws JAXBException {\r
  56                 this(rootClass, null);\r
  57         }\r
  58 \r
  59         public RunnerConfigMarshaller(Class<?> rootClass, Class<?>... classes)\r
  60                         throws JAXBException {\r
  61 \r
  62                 if (classes != null) {\r
  63                         List<Class<?>> classesList = new ArrayList<Class<?>>(Arrays\r
  64                                         .asList(classes));\r
  65                         classesList.add(rootClass);\r
  66                         ctx = JAXBContext.newInstance(classesList.toArray(new Class<?>[0]));\r
  67                 } else {\r
  68                         ctx = JAXBContext.newInstance(rootClass);\r
  69                 }\r
  70         }\r
  71 \r
  72         public void write(Object xmlRootElement, OutputStream out)\r
  73                         throws JAXBException, IOException {\r
  74                 Marshaller marsh = ctx.createMarshaller();\r
  75                 marsh.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);\r
  76                 // disable validation\r
  77                 marsh.setSchema(null);\r
  78                 marsh.marshal(xmlRootElement, out);\r
  79         }\r
  80 \r
  81         public void writeAndValidate(Object xmlRootElement, String schemafile,\r
  82                         OutputStream out) throws JAXBException, IOException, SAXException {\r
  83                 Marshaller marsh = ctx.createMarshaller();\r
  84                 marsh.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);\r
  85                 marsh.setProperty(Marshaller.JAXB_NO_NAMESPACE_SCHEMA_LOCATION,\r
  86                                 schemafile);\r
  87                 marsh.setSchema(getSchema(schemafile));\r
  88                 marsh.marshal(xmlRootElement, out);\r
  89         }\r
  90 \r
  91         void generateSchema(String directoryForSchema, String schemaName)\r
  92                         throws JAXBException, IOException {\r
  93 \r
  94                 Marshaller marsh = ctx.createMarshaller();\r
  95                 marsh.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);\r
  96                 ctx.generateSchema(new MySchemaOutputResolver(directoryForSchema,\r
  97                                 schemaName));\r
  98         }\r
  99 \r
 100         public static Schema getSchema(String schemafile) throws SAXException {\r
 101                 // define the type of schema - we use W3C:\r
 102                 String schemaLang = "http://www.w3.org/2001/XMLSchema";\r
 103                 // get validation driver:\r
 104                 SchemaFactory factory = SchemaFactory.newInstance(schemaLang);\r
 105                 // create schema by reading it from an XSD file:\r
 106                 Schema schema = factory.newSchema(new StreamSource(schemafile));\r
 107                 return schema;\r
 108         }\r
 109 \r
 110         /**\r
 111          * \r
 112          * @return\r
 113          * @throws SAXException\r
 114          */\r
 115         public static Validator getValidator(String schemafile) throws SAXException {\r
 116                 Schema schema = getSchema(schemafile);\r
 117                 Validator validator = schema.newValidator();\r
 118                 return validator;\r
 119         }\r
 120 \r
 121         public static Validator getValidator(Schema schema) throws SAXException {\r
 122                 Validator validator = schema.newValidator();\r
 123                 return validator;\r
 124         }\r
 125 \r
 126         public static boolean validate(Validator validator, String document)\r
 127                         throws IOException, SAXException {\r
 128                 try {\r
 129                         // at last perform validation:\r
 130                         validator.validate(new StreamSource(document));\r
 131                 } catch (SAXException ex) {\r
 132                         ex.printStackTrace();\r
 133                         log.warn("SAXException validating xml" + ex.getMessage());\r
 134                         // we are here if the document is not valid:\r
 135                         // ... process validation error...\r
 136                         return false;\r
 137                 }\r
 138                 return true;\r
 139         }\r
 140 \r
 141         public <V> V readAndValidate(InputStream document, Class<V> resultElemType)\r
 142                         throws JAXBException, IOException, SAXException {\r
 143 \r
 144                 String schemaFile = Long.toHexString(System.nanoTime());\r
 145                 generateSchema(SysPrefs.getSystemTmpDir(), schemaFile);\r
 146 \r
 147                 Unmarshaller um = ctx.createUnmarshaller();\r
 148                 um.setSchema(getSchema(SysPrefs.getSystemTmpDir() + File.separator\r
 149                                 + schemaFile));\r
 150 \r
 151                 JAXBElement<V> rconfig = um.unmarshal(new StreamSource(document),\r
 152                                 resultElemType);\r
 153                 return rconfig.getValue();\r
 154         }\r
 155 \r
 156         static class MySchemaOutputResolver extends SchemaOutputResolver {\r
 157                 final String dir;\r
 158                 final String sname;\r
 159 \r
 160                 public MySchemaOutputResolver(String directory, String suggestedFileName) {\r
 161                         this.dir = directory;\r
 162                         this.sname = suggestedFileName;\r
 163                 }\r
 164 \r
 165                 @Override\r
 166                 public Result createOutput(String namespaceUri, String suggestedFileName)\r
 167                                 throws IOException {\r
 168                         return new StreamResult(new File(dir, this.sname));\r
 169                 }\r
 170         }\r
 171 \r
 172         @SuppressWarnings("all")\r
 173         public <V> V read(InputStream instream, Class<V> resultElemType)\r
 174                         throws JAXBException {\r
 175                 return read(instream, resultElemType, null);\r
 176         }\r
 177 \r
 178         public <V> V read(InputStream instream, Class<V> resultElemType,\r
 179                         Class<?>... classes) throws JAXBException {\r
 180                 if (instream == null) {\r
 181                         throw new NullPointerException("Input stream must be provided!");\r
 182                 }\r
 183                 JAXBContext ctx = null;\r
 184                 if (classes != null) {\r
 185                         List<Class<?>> classesList = new ArrayList<Class<?>>(Arrays\r
 186                                         .asList(classes));\r
 187                         classesList.add(resultElemType);\r
 188                         ctx = JAXBContext.newInstance(classesList.toArray(new Class<?>[0]));\r
 189                 } else {\r
 190                         ctx = JAXBContext.newInstance(resultElemType);\r
 191                 }\r
 192 \r
 193                 Unmarshaller um = ctx.createUnmarshaller();\r
 194                 JAXBElement<V> rconfig = um.unmarshal(new StreamSource(instream),\r
 195                                 resultElemType);\r
 196 \r
 197                 return rconfig.getValue();\r
 198         }\r
 199 \r
 200 }\r