Java tutorial
/* * #%L * gitools-core * %% * Copyright (C) 2013 Universitat Pompeu Fabra - Biomedical Genomics group * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as * published by the Free Software Foundation, either version 3 of the * License, or (at your option) any later version. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public * License along with this program. If not, see * <http://www.gnu.org/licenses/gpl-3.0.html>. * #L% */ package org.gitools.resource; import org.apache.commons.io.IOUtils; import org.gitools.api.ApplicationContext; import org.gitools.api.PersistenceException; import org.gitools.api.analysis.IProgressMonitor; import org.gitools.api.plugins.IPlugin; import org.gitools.api.resource.IResource; import org.gitools.api.resource.IResourceLocator; import org.gitools.api.resource.ResourceReference; import org.gitools.api.resource.adapter.ResourceReferenceXmlAdapter; import javax.xml.bind.JAXBContext; import javax.xml.bind.Marshaller; import javax.xml.bind.Unmarshaller; import java.io.*; import java.util.ArrayList; import java.util.List; public abstract class AbstractXmlFormat<R extends IResource> extends AbstractResourceFormat<R> { private List<ResourceReference<? extends IResource>> dependencies; protected AbstractXmlFormat(String extension, Class<R> resourceClass) { super(extension, resourceClass); } @Override public boolean isContainer() { return true; } @Override public boolean isConfigurable() { return true; } @Override public boolean isDefaultExtension() { return true; } @Override protected void configureResource(IResourceLocator resourceLocator, IProgressMonitor progressMonitor) throws PersistenceException { } public void beforeRead(InputStream in, IResourceLocator resourceLocator, Unmarshaller unmarshaller, IProgressMonitor progressMonitor) throws PersistenceException { dependencies = new ArrayList<>(); unmarshaller.setAdapter(new ResourceReferenceXmlAdapter(dependencies, resourceLocator)); } public void beforeWrite(OutputStream out, IResourceLocator resourceLocator, R resource, Marshaller marshaller, IProgressMonitor progressMonitor) throws PersistenceException { dependencies = new ArrayList<>(); marshaller.setAdapter(ResourceReferenceXmlAdapter.class, new ResourceReferenceXmlAdapter(dependencies, resourceLocator)); } /** * Override this method if you want to modify the resource after reading it, just * before to close the stream. * * @param inputStream the open input stream * @param resourceLocator the resource locator * @param resource the entity * @param unmarshaller the unmarshaller * @param progressMonitor the progress monitor * @throws PersistenceException the persistence exception */ public void afterRead(InputStream inputStream, IResourceLocator resourceLocator, R resource, Unmarshaller unmarshaller, IProgressMonitor progressMonitor) throws PersistenceException { } @Override protected R readResource(IResourceLocator resourceLocator, IProgressMonitor progressMonitor) throws PersistenceException { R entity; try { List<Class> classList = new ArrayList<>(); classList.add(getResourceClass()); for (IPlugin p : ApplicationContext.getPluginManger().getPlugins()) { classList.add(p.getPluginClass()); } JAXBContext context = JAXBContext.newInstance(classList.toArray(new Class[classList.size()])); Unmarshaller unmarshaller = context.createUnmarshaller(); InputStream in = resourceLocator.openInputStream(progressMonitor); beforeRead(in, resourceLocator, unmarshaller, progressMonitor); entity = (R) unmarshaller.unmarshal(in); afterRead(in, resourceLocator, entity, unmarshaller, progressMonitor); in.close(); } catch (Exception e) { throw new PersistenceException(e); } return entity; } public void afterWrite(OutputStream out, IResourceLocator resourceLocator, R resource, Marshaller marshaller, IProgressMonitor progressMonitor) throws PersistenceException { // Force write the dependencies for (ResourceReference<? extends IResource> dependency : dependencies) { IResourceLocator dependencyLocator = resourceLocator .getReferenceLocator(dependency.getLocator().getName()); if (dependency.isChanged()) { // Rewrite the resource dependency.get(); ApplicationContext.getPersistenceManager().store(dependencyLocator, dependency.get(), dependency.getResourceFormat(), progressMonitor); } else { if (!resourceLocator.equals(resource.getLocator())) { // We are in a 'Save as...' String fromName = resource.getLocator().getBaseName(); String toName = resourceLocator.getBaseName(); String dependencyName = dependency.getLocator().getName().replace(toName, fromName); IResourceLocator fromLocator = resource.getLocator().getReferenceLocator(dependencyName); File output = dependencyLocator.getWriteFile(); // Copy file to file try { if (!output.exists()) { output.createNewFile(); } IOUtils.copy(fromLocator.openInputStream(progressMonitor), new FileOutputStream(output)); fromLocator.close(progressMonitor); dependencyLocator.close(progressMonitor); } catch (IOException e) { throw new PersistenceException(e); } //TODO Do this properly // Copy the mtabix file if it's present if (dependencyName.endsWith("tdm.gz")) { fromLocator = resource.getLocator().getReferenceLocator(dependencyName + ".mtabix"); output = new File(output.getParentFile(), dependency.getLocator().getName() + ".mtabix"); try { output.createNewFile(); IOUtils.copy(fromLocator.openInputStream(progressMonitor), new FileOutputStream(output)); fromLocator.close(progressMonitor); } catch (Exception e) { output.delete(); } } } } } } @Override protected void writeResource(IResourceLocator resourceLocator, R resource, IProgressMonitor monitor) throws PersistenceException { monitor.begin("Saving " + resourceLocator.getName(), 1); try { List<Class> classList = new ArrayList<>(); classList.add(getResourceClass()); for (IPlugin p : ApplicationContext.getPluginManger().getPlugins()) { classList.add(p.getPluginClass()); } JAXBContext context = JAXBContext.newInstance(classList.toArray(new Class[classList.size()])); Marshaller marshaller = context.createMarshaller(); marshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true); // Prepare to write beforeWrite(null, resourceLocator, resource, marshaller, monitor); // Marshal to a temporal file to create dependencies File tmpFile = File.createTempFile("gitools-" + resourceLocator.getName(), ".tmp"); marshaller.marshal(resource, tmpFile); // Write the XML OutputStream out = resourceLocator.openOutputStream(monitor); InputStream in = new FileInputStream(tmpFile); org.apache.commons.io.IOUtils.copy(in, out); // Write the dependencies afterWrite(out, resourceLocator, resource, marshaller, monitor); // Close everything in.close(); tmpFile.delete(); out.close(); } catch (Exception e) { throw new PersistenceException(e); } } }