public Path[] getListInstalledPlugins() throws IOException {
if (!Files.exists(environment.pluginsFile())) {
return new Path[0];
}
try (DirectoryStream<Path> stream = Files.newDirectoryStream(environment.pluginsFile())) {
return Iterators.toArray(stream.iterator(), Path.class);
}
}
@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 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;
}
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;
}
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();
}
}