private void unzipPlugin(Path zip, Path target) throws IOException {
Files.createDirectories(target);
try (ZipInputStream zipInput = new ZipInputStream(Files.newInputStream(zip))) {
ZipEntry entry;
byte[] buffer = new byte[8192];
while ((entry = zipInput.getNextEntry()) != null) {
Path targetFile = target.resolve(entry.getName());
// be on the safe side: do not rely on that directories are always extracted
// before their children (although this makes sense, but is it guaranteed?)
Files.createDirectories(targetFile.getParent());
if (entry.isDirectory() == false) {
try (OutputStream out = Files.newOutputStream(targetFile)) {
int len;
while ((len = zipInput.read(buffer)) >= 0) {
out.write(buffer, 0, len);
}
}
}
zipInput.closeEntry();
}
}
}
public static byte[] input(String fileName) {
try {
return input(Files.newInputStream(IO.path(fileName)));
} catch (IOException e) {
return Exceptions.handle(byte[].class, e);
}
}
public static void main(String[] args) throws MessagingException, IOException {
Properties props = new Properties();
try (InputStream in = Files.newInputStream(Paths.get("mail", "mail.properties"))) {
props.load(in);
}
List<String> lines = Files.readAllLines(Paths.get(args[0]), Charset.forName("UTF-8"));
String from = lines.get(0);
String to = lines.get(1);
String subject = lines.get(2);
StringBuilder builder = new StringBuilder();
for (int i = 3; i < lines.size(); i++) {
builder.append(lines.get(i));
builder.append("\n");
}
Console console = System.console();
String password = new String(console.readPassword("Password: "));
Session mailSession = Session.getDefaultInstance(props);
// mailSession.setDebug(true);
MimeMessage message = new MimeMessage(mailSession);
message.setFrom(new InternetAddress(from));
message.addRecipient(RecipientType.TO, new InternetAddress(to));
message.setSubject(subject);
message.setText(builder.toString());
Transport tr = mailSession.getTransport();
try {
tr.connect(null, password);
tr.sendMessage(message, message.getAllRecipients());
} finally {
tr.close();
}
}
public static InputStream inputStream(String resource) {
Path path = path(resource);
try {
return Files.newInputStream(path);
} catch (IOException e) {
return Exceptions.handle(InputStream.class, "unable to open " + resource, e);
}
}
public static void main(String[] args) throws IOException {
Properties props = new Properties();
try (InputStream in = Files.newInputStream(Paths.get(args[0]))) {
props.load(in);
}
String url = props.remove("url").toString();
String result = doPost(url, props);
System.out.println(result);
}
public static long checksumBufferedInputStream(Path filename) throws IOException {
try (InputStream in = new BufferedInputStream(Files.newInputStream(filename))) {
CRC32 crc = new CRC32();
int c;
while ((c = in.read()) != -1) crc.update(c);
return crc.getValue();
}
}
/**
* Gets a connection from the properties specified in the file database.properties
*
* @return the database connection
*/
public static Connection getConnection() throws SQLException, IOException {
Properties props = new Properties();
try (InputStream in = Files.newInputStream(Paths.get("database.properties"))) {
props.load(in);
}
String drivers = props.getProperty("jdbc.drivers");
if (drivers != null) System.setProperty("jdbc.drivers", drivers);
String url = props.getProperty("jdbc.url");
String username = props.getProperty("jdbc.username");
String password = props.getProperty("jdbc.password");
return DriverManager.getConnection(url, username, password);
}
private void processFile(Path inGzPath, String conservedType) throws IOException {
BufferedReader br =
new BufferedReader(
new InputStreamReader(new GZIPInputStream(Files.newInputStream(inGzPath))));
String line = null;
String chromosome = "";
int start = 0, end = 0;
float value;
Map<String, String> attributes = new HashMap<>();
// ConservedRegion conservedRegion = null;
List<Float> values = new ArrayList<>();
ConservedRegionChunk conservedRegion = null;
while ((line = br.readLine()) != null) {
if (line.startsWith("fixedStep")) {
// new group, save last
if (conservedRegion != null) {
conservedRegion.setEnd(end);
conservedRegion =
new ConservedRegionChunk(
chromosome, start, end, conservedType, start / CHUNKSIZE, values);
fileSerializer.serialize(conservedRegion, getOutputFileName(chromosome));
}
// offset = 0;
attributes.clear();
String[] attrFields = line.split(" ");
String[] attrKeyValue;
for (String attrField : attrFields) {
if (!attrField.equalsIgnoreCase("fixedStep")) {
attrKeyValue = attrField.split("=");
attributes.put(attrKeyValue[0].toLowerCase(), attrKeyValue[1]);
}
}
chromosome = attributes.get("chrom").replace("chr", "");
start = Integer.parseInt(attributes.get("start"));
end = Integer.parseInt(attributes.get("start"));
values = new ArrayList<>(2000);
} else {
int startChunk = start / CHUNKSIZE;
end++;
int endChunk = end / CHUNKSIZE;
if (startChunk != endChunk) {
conservedRegion =
new ConservedRegionChunk(
chromosome, start, end - 1, conservedType, startChunk, values);
fileSerializer.serialize(conservedRegion, getOutputFileName(chromosome));
values.clear();
start = end;
}
value = Float.parseFloat(line.trim());
values.add(value);
}
}
// write last
conservedRegion =
new ConservedRegionChunk(chromosome, start, end, conservedType, start / CHUNKSIZE, values);
fileSerializer.serialize(conservedRegion, getOutputFileName(chromosome));
br.close();
}
