private static boolean exists(Path p) {
Path base = p.getParent();
String fileName = p.getFileName().toString();
return Arrays.asList(extensions)
.stream()
.anyMatch(it -> Files.exists(base.resolve(fileName + it)));
}
private static Set<ShardId> findAllShardsForIndex(Path indexPath) throws IOException {
Set<ShardId> shardIds = new HashSet<>();
if (Files.isDirectory(indexPath)) {
try (DirectoryStream<Path> stream = Files.newDirectoryStream(indexPath)) {
String currentIndex = indexPath.getFileName().toString();
for (Path shardPath : stream) {
if (Files.isDirectory(shardPath)) {
Integer shardId = Ints.tryParse(shardPath.getFileName().toString());
if (shardId != null) {
ShardId id = new ShardId(currentIndex, shardId);
shardIds.add(id);
}
}
}
}
}
return shardIds;
}
public void listInstalledPlugins(Terminal terminal) throws IOException {
Path[] plugins = getListInstalledPlugins();
terminal.println("Installed plugins in %s:", environment.pluginsFile().toAbsolutePath());
if (plugins == null || plugins.length == 0) {
terminal.println(" - No plugin detected");
} else {
for (Path plugin : plugins) {
terminal.println(" - " + plugin.getFileName());
}
}
}
@Override
public void parse() throws IOException {
if (conservedRegionPath == null
|| !Files.exists(conservedRegionPath)
|| !Files.isDirectory(conservedRegionPath)) {
throw new IOException(
"Conservation directory whether does not exist, is not a directory or cannot be read");
}
Map<String, Path> files = new HashMap<>();
String chromosome;
Set<String> chromosomes = new HashSet<>();
// Reading all files in phastCons folder
DirectoryStream<Path> directoryStream =
Files.newDirectoryStream(conservedRegionPath.resolve("phastCons"));
for (Path path : directoryStream) {
chromosome = path.getFileName().toString().split("\\.")[0].replace("chr", "");
chromosomes.add(chromosome);
files.put(chromosome + "phastCons", path);
}
// Reading all files in phylop folder
directoryStream = Files.newDirectoryStream(conservedRegionPath.resolve("phylop"));
for (Path path : directoryStream) {
chromosome = path.getFileName().toString().split("\\.")[0].replace("chr", "");
chromosomes.add(chromosome);
files.put(chromosome + "phylop", path);
}
/** Now we can iterate over all the chromosomes found and process the files */
logger.debug("Chromosomes found {}", chromosomes.toString());
for (String chr : chromosomes) {
logger.debug("Processing chromosome {}, file {}", chr, files.get(chr + "phastCons"));
processFile(files.get(chr + "phastCons"), "phastCons");
logger.debug("Processing chromosome {}, file {}", chr, files.get(chr + "phylop"));
processFile(files.get(chr + "phylop"), "phylop");
}
}
private int getNumberOfItems(Path quellOrdner) {
int retValue = 0;
try {
DirectoryStream<Path> qstream = Files.newDirectoryStream(quellOrdner);
for (Path qfile : qstream) {
if (Files.isDirectory(qfile)) {
getNumberOfItems(Paths.get(quellOrdner.toString() + "/" + qfile.getFileName()));
}
i++;
}
qstream.close();
} catch (IOException e) {
e.printStackTrace();
}
retValue = i;
return retValue;
}
public Set<String> findAllIndices() throws IOException {
if (nodePaths == null || locks == null) {
throw new IllegalStateException("node is not configured to store local location");
}
assert assertEnvIsLocked();
Set<String> indices = Sets.newHashSet();
for (NodePath nodePath : nodePaths) {
Path indicesLocation = nodePath.indicesPath;
if (Files.isDirectory(indicesLocation)) {
try (DirectoryStream<Path> stream = Files.newDirectoryStream(indicesLocation)) {
for (Path index : stream) {
if (Files.isDirectory(index)) {
indices.add(index.getFileName().toString());
}
}
}
}
}
return indices;
}
/**
* Tries to find all allocated shards for the given index on the current node. NOTE: This methods
* is prone to race-conditions on the filesystem layer since it might not see directories created
* concurrently or while it's traversing.
*
* @param index the index to filter shards
* @return a set of shard IDs
* @throws IOException if an IOException occurs
*/
public Set<ShardId> findAllShardIds(final Index index) throws IOException {
assert index != null;
if (nodePaths == null || locks == null) {
throw new IllegalStateException("node is not configured to store local location");
}
assert assertEnvIsLocked();
final Set<ShardId> shardIds = Sets.newHashSet();
String indexName = index.name();
for (final NodePath nodePath : nodePaths) {
Path location = nodePath.indicesPath;
if (Files.isDirectory(location)) {
try (DirectoryStream<Path> indexStream = Files.newDirectoryStream(location)) {
for (Path indexPath : indexStream) {
if (indexName.equals(indexPath.getFileName().toString())) {
shardIds.addAll(findAllShardsForIndex(indexPath));
}
}
}
}
}
return shardIds;
}
@Override
public void run() {
logger.debug("Register root " + startDir.toString());
try {
registerAll(startDir);
} catch (IOException ex) {
logger.error(ex.getMessage());
return;
}
if (isInterrupted()) return;
VOSync.debug("Sync local db with drive");
DbPool.goSql(
"Synching the local db with drive",
"select NAME from FILES",
new SqlWorker<Boolean>() {
@Override
public Boolean go(Connection conn, PreparedStatement stmt) throws SQLException {
ResultSet resSet = stmt.executeQuery();
while (resSet.next()) {
try {
String fileName = resSet.getString(1);
Path filePath =
FileSystems.getDefault().getPath(startDir.toString(), fileName.substring(1));
if (!filePath.toFile().exists()) {
logger.debug(
"Deleting file " + fileName + " existing in DB and not present on disk");
api.delete(fileName);
MetaHandler.delete(fileName);
}
} catch (DropboxException ex) {
}
}
resSet.close();
return true;
}
});
if (isInterrupted()) return;
VOSync.debug("Sync storage");
syncStorage();
logger.debug("Start watching");
while (!isInterrupted()) {
WatchKey key;
try {
key = watcher.take();
} catch (InterruptedException x) {
return;
}
Path dir = keys.get(key);
if (dir == null) {
System.err.println("WatchKey " + key.toString() + " not recognized!");
continue;
}
for (WatchEvent<?> event : key.pollEvents()) {
Kind<?> kind = event.kind();
// TBD - provide example of how OVERFLOW event is handled
if (kind == OVERFLOW) {
continue;
}
// Context for directory entry event is the file name of entry
WatchEvent<Path> ev = cast(event);
Path name = ev.context();
Path child = dir.resolve(name);
Path relativeDir = startDir.relativize(child);
String fileRelPath = "/" + fixPath(relativeDir.toString());
// print out event
logger.debug(event.kind().name() + ":" + child + " " + name + " " + key);
try {
if (Files.exists(child, new LinkOption[] {}) && Files.isHidden(child)) {
logger.error(
"Skipping hidden file " + child.getFileName()); // skip OS generated catalog files
} else {
if (event.kind() == ENTRY_CREATE) {
if (Files.isRegularFile(child, NOFOLLOW_LINKS)) { // file modified
uploadFile(fileRelPath, child);
} else if (Files.isDirectory(child, NOFOLLOW_LINKS)) { // directory contents changed
registerAll(child);
}
} else if (event.kind() == ENTRY_DELETE) {
logger.debug("Deleting " + fileRelPath);
api.delete(fileRelPath);
MetaHandler.delete(fileRelPath);
logger.debug("Deleted!");
} else if (event.kind() == ENTRY_MODIFY) {
if (Files.isRegularFile(child, NOFOLLOW_LINKS)) { // file modified
uploadFile(fileRelPath, child);
} else if (Files.isDirectory(child, NOFOLLOW_LINKS)) { // directory contents changed
// logger.debug("Renewing dir: "+relativeDir.toString());
// TODO update folder date
// MetaHandler.setFile(fileRelPath, child, rev);
}
}
}
} catch (IOException ex) {
ex.printStackTrace();
logger.error(ex.getMessage());
} catch (DropboxException ex) {
ex.printStackTrace();
logger.error(ex.getMessage());
}
}
boolean valid = key.reset();
if (!valid) keys.remove(key);
}
}
public void cnpStart(Path quellOrdner, Path zielOrdner) {
try {
DirectoryStream<Path> qstream = Files.newDirectoryStream(quellOrdner);
for (Path qfile : qstream) {
Path target = Paths.get(zielOrdner.toString() + "/" + qfile.getFileName());
if (abbruch) break;
if (Files.isDirectory(qfile) && !Files.exists(target)) {
Files.createDirectory(target);
textArea.append("Verzeichnis: " + qfile + " wurde erstellt" + System.lineSeparator());
cnpStart(
Paths.get(quellOrdner.toString() + "/" + qfile.getFileName()),
Paths.get(zielOrdner.toString() + "/" + qfile.getFileName()));
} else if (Files.isDirectory(qfile) && Files.exists(target)) {
textArea.append("Wechsle in Verzeichnis: " + qfile + System.lineSeparator());
cnpStart(
Paths.get(quellOrdner.toString() + "/" + qfile.getFileName()),
Paths.get(zielOrdner.toString() + "/" + qfile.getFileName()));
}
// Wenn die Datei noch nicht existiert
else if (!Files.exists(target)) {
textArea.append(
"Datei " + target.toString() + " wurde erstellt" + System.lineSeparator());
Files.copy(qfile, target, StandardCopyOption.REPLACE_EXISTING);
}
// Wenn Datei im Zielverzeichnis schon existiert
else if (Files.exists(target)) {
if (cAUeSchr) {
textArea.append(
"Datei "
+ target.toString()
+ " wird absolut überschrieben"
+ System.lineSeparator());
Files.copy(qfile, target, StandardCopyOption.REPLACE_EXISTING);
} else if (cUeSchr) {
if (checkAlter(
Paths.get(quellOrdner.toString() + "/" + qfile.getFileName()),
Paths.get(zielOrdner.toString() + "/" + qfile.getFileName()))) {
textArea.append(
target.toString()
+ " wird mit neuer Datei überschrieben"
+ System.lineSeparator());
Files.copy(qfile, target, StandardCopyOption.REPLACE_EXISTING);
} else {
textArea.append(
target.toString() + " alte Datei bleibt bestehen" + System.lineSeparator());
}
} else
textArea.append(
target.toString() + " alte Datei bleibt bestehen" + System.lineSeparator());
}
pbCounter++;
progressBar.setValue(pbCounter);
}
qstream.close();
} catch (IOException e) {
e.printStackTrace();
}
}
