/*
* #%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 com.google.common.base.Joiner;
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.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import static com.google.common.collect.Lists.newArrayList;
@ApplicationScoped
public class GmxModuleMapFormat extends AbstractModuleMapFormat {
public static final String EXTENSION = "gmx";
private static Joiner TAB_JOINER = Joiner.on('\t');
public GmxModuleMapFormat() {
super(EXTENSION);
}
@Override
protected IModuleMap readResource(IResourceLocator resourceLocator, IProgressMonitor progressMonitor) throws PersistenceException {
progressMonitor.begin("Reading ...", 1);
HashModuleMap moduleMap = new HashModuleMap();
try {
InputStream in = resourceLocator.openInputStream(progressMonitor);
CSVReader parser = new CSVReader(new InputStreamReader(in));
// read column names
String[] modules = parser.readNext();
// Discard descriptions
parser.readNext();
String[] fields;
while ((fields = parser.readNext()) != null) {
if (fields.length > modules.length) {
throw new PersistenceException("Row with more columns than expected at line " + parser.getLineNumber());
}
for (int i = 0; i < fields.length; i++) {
moduleMap.addMapping(modules[i], fields[i]);
}
}
in.close();
progressMonitor.info(moduleMap.getModules().size() + " modules");
} catch (IOException e) {
throw new PersistenceException(e);
}
return moduleMap;
}
@Override
protected void writeResource(IResourceLocator resourceLocator, IModuleMap moduleMap, IProgressMonitor progressMonitor) throws PersistenceException {
progressMonitor.begin("Saving module map...", moduleMap.getModules().size());
try {
OutputStream out = resourceLocator.openOutputStream(progressMonitor);
PrintWriter pw = new PrintWriter(new OutputStreamWriter(out));
List<String> modules = newArrayList(moduleMap.getModules());
Map<String, List<String>> itemsMap = new HashMap<>();
int maxItemsPerModule = 0;
for (String module : modules) {
List<String> items = newArrayList(moduleMap.getMappingItems(module));
if (items.size() > maxItemsPerModule) {
maxItemsPerModule = items.size();
}
itemsMap.put(module, items);
}
// Module labels
pw.println(TAB_JOINER.join(modules));
// descriptions
for (int m = 1; m < modules.size(); m++) {
pw.append('\t');
}
pw.println();
// data
List<String> line = new ArrayList<>(modules.size());
for (int l=0; l < maxItemsPerModule; l++) {
for (String module : modules) {
List<String> items = itemsMap.get(module);
if (l >= items.size()) {
line.add("");
} else {
line.add(items.get(l));
}
}
pw.println(TAB_JOINER.join(line));
line.clear();
}
pw.close();
} catch (Exception e) {
throw new PersistenceException(e);
}
}
}