public static void extractGM(String pathToGMData) {
String directoryPath = DirectorySettings.getCacheDirectory().getAbsolutePath();
try {
File data = new File(pathToGMData);
ZipFile zipData = new ZipFile(data.getAbsolutePath());
Enumeration entries = zipData.entries();
while (entries.hasMoreElements()) {
ZipEntry entry = (ZipEntry) entries.nextElement();
if (entry.isDirectory()) {
(new File(directoryPath + File.separator + entry.getName())).mkdirs();
continue;
}
IOUtils.copy(
zipData.getInputStream(entry),
new FileOutputStream(directoryPath + File.separator + entry.getName()));
}
zipData.close();
FileWriter fstream =
new FileWriter(
DirectorySettings.getGeneManiaDirectory()
+ File.separator
+ DirectorySettings.GENEMANIA_CHECK_FILE);
BufferedWriter out = new BufferedWriter(fstream);
out.write("This file indicates that the GeneMANIA data has finished downloading.");
out.close();
if (!data.delete()) {
LOG.error("Couldn't delete GeneMANIA .zip: " + data.getAbsolutePath());
}
} catch (IOException ex) {
java.util.logging.Logger.getLogger(GenemaniaInfoRetriever.class.getName())
.log(Level.SEVERE, null, ex);
}
}
// returns invalid genes that were not set
public void setGenes(List<String> geneNames) {
try {
this.genes = getValidGenes(geneNames);
} catch (Exception ex) {
java.util.logging.Logger.getLogger(GenemaniaInfoRetriever.class.getName())
.log(Level.SEVERE, null, ex);
}
}