// PathVisio, // a tool for data visualization and analysis using Biological Pathways // Copyright 2006-2011 BiGCaT Bioinformatics // // Licensed under the Apache License, Version 2.0 (the "License"); // you may not use this file except in compliance with the License. // You may obtain a copy of the License at // // http://www.apache.org/licenses/LICENSE-2.0 // // Unless required by applicable law or agreed to in writing, software // distributed under the License is distributed on an "AS IS" BASIS, // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. // See the License for the specific language governing permissions and // limitations under the License. // package org.wikipathways.applet; import java.io.ByteArrayOutputStream; import java.io.File; import java.io.FileOutputStream; import java.net.URL; import org.apache.commons.codec.binary.Base64; import org.apache.xmlrpc.client.XmlRpcClient; import org.apache.xmlrpc.client.XmlRpcClientConfigImpl; import org.apache.xmlrpc.client.XmlRpcSunHttpTransportFactory; import org.apache.xmlrpc.client.XmlRpcTransportFactory; import org.jdom.Document; import org.jdom.output.XMLOutputter; import org.pathvisio.core.model.ConverterException; import org.pathvisio.core.model.GpmlFormat; import org.pathvisio.core.model.ImageExporter; import org.pathvisio.core.model.Pathway; /** * Special exporter that uses the WikiPathways XMLRPC interface to * convert to SVG and other image formats. By letting the server * do all the heavy work, we don't need libraries such as Batik * in the Applet and thus we can keep the Applet small. */ public class WikiPathwaysExporter extends ImageExporter { URL rpcUrl; public WikiPathwaysExporter(URL rpcUrl, String type) { super(type); this.rpcUrl = rpcUrl; } public void doExport(File file, Pathway pathway) throws ConverterException { XmlRpcClientConfigImpl config = new XmlRpcClientConfigImpl(); config.setServerURL(rpcUrl); XmlRpcClient client = new XmlRpcClient(); XmlRpcTransportFactory ctf = new XmlRpcSunHttpTransportFactory(client); client.setTransportFactory(ctf); client.setConfig(config); try { Document doc = GpmlFormat.createJdom(pathway); XMLOutputter outputter = new XMLOutputter(); ByteArrayOutputStream out = new ByteArrayOutputStream(); outputter.output(doc, out); byte[] data = out.toByteArray(); byte[] data64 = Base64.encodeBase64(data); Object[] params = new Object[]{ data64, getDefaultExtension() }; byte[] converted64 = ((String)client.execute("WikiPathways.convertPathway", params)).getBytes(); Base64.decodeBase64(converted64); byte[] converted = Base64.decodeBase64(converted64); FileOutputStream fout = new FileOutputStream(file); fout.write(converted); fout.close(); } catch(Exception e) { throw new ConverterException(e); } } }