/*
* #%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);
}
}
}