/*
* #%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.matrix.modulemap.format;
import org.gitools.api.PersistenceException;
import org.gitools.api.analysis.IProgressMonitor;
import org.gitools.api.modulemap.IModuleMap;
import org.gitools.api.resource.IResourceLocator;
import org.gitools.matrix.modulemap.HashModuleMap;
import org.gitools.utils.readers.text.CSVReader;
import javax.enterprise.context.ApplicationScoped;
import java.io.*;
import java.util.*;
@ApplicationScoped
public class IxmModuleMapFormat extends AbstractModuleMapFormat {
public static final String EXTENSION = "ixm";
public IxmModuleMapFormat() {
super(EXTENSION);
}
@Override
protected IModuleMap readResource(IResourceLocator resourceLocator, IProgressMonitor progressMonitor) throws PersistenceException {
try {
progressMonitor.begin("Loading modules...", resourceLocator.getContentLength());
InputStream in = resourceLocator.openInputStream(progressMonitor);
CSVReader parser = new CSVReader(new InputStreamReader(in));
progressMonitor.begin("Reading item names ...", 1);
List<String> items = Arrays.asList(parser.readNext());
progressMonitor.info(items.size() + " items");
progressMonitor.begin("Reading modules ...", 1);
String[] fields;
HashModuleMap moduleMap = new HashModuleMap();
while ((fields = parser.readNext()) != null) {
String module = fields[0];
for (int j = 1; j < fields.length; j++) {
int itemIndex = Integer.parseInt(fields[j]);
if (itemIndex >= 0 && itemIndex < items.size()) {
moduleMap.addMapping(module, items.get(itemIndex));
}
}
}
progressMonitor.info(moduleMap.getModules().size() + " modules and " + moduleMap.getItems().size() + " items annotated");
in.close();
return moduleMap;
} catch (Exception e) {
throw new PersistenceException(e);
}
}
@Override
protected void writeResource(IResourceLocator resourceLocator, IModuleMap moduleMap, IProgressMonitor progressMonitor) throws PersistenceException {
progressMonitor.begin("Saving modules...", moduleMap.getModules().size());
try {
OutputStream out = resourceLocator.openOutputStream(progressMonitor);
final PrintWriter pw = new PrintWriter(new OutputStreamWriter(out));
final Iterator<String> itemsIterator = moduleMap.getItems().iterator();
Map<String, Integer> itemsIndex = new HashMap<>();
int index = 0;
while (itemsIterator.hasNext()) {
String item = itemsIterator.next();
itemsIndex.put(item, index);
index++;
pw.print('"');
pw.print(item);
pw.print('"');
if (itemsIterator.hasNext()) {
pw.print("\t");
}
}
pw.print('\n');
for (String module : moduleMap.getModules()) {
pw.print('"');
pw.print(module);
pw.print('"');
for (String item : moduleMap.getMappingItems(module)) {
pw.print('\t');
pw.print(itemsIndex.get(item));
}
pw.print('\n');
progressMonitor.worked(1);
}
pw.close();
} catch (Exception e) {
throw new PersistenceException(e);
}
}
}