public void setFastaFile(GridFile inputFile) {
GridFile old = this.fastaFile;
inputFiles.remove(inputFile.getUrl());
this.fastaFile = inputFile;
inputFiles.put(inputFile.getUrl(), null);
pcs.firePropertyChange("fastaFile", old, this.fastaFile);
pcs.firePropertyChange("inputFiles", null, inputFiles);
}
public GridFile getFolderListing(String url, int recursiveLevels)
throws RemoteFileSystemException {
if (url.equals(ServiceInterface.VIRTUAL_GRID_PROTOCOL_NAME + "://")) {
final GridFile root = new GridFile(url, -1L);
root.setVirtual(true);
root.setPath(url);
if (recursiveLevels == 0) {
return root;
}
for (final String key : plugins.keySet()) {
final GridFile vfs =
new GridFile(ServiceInterface.VIRTUAL_GRID_PROTOCOL_NAME + "://" + key, -1L);
vfs.setVirtual(true);
vfs.setPath(url + vfs.getName());
// vfs.setName(StringUtils.capitalize(key));
vfs.setName(key);
root.addChild(vfs);
}
return root;
}
try {
return getPlugin(url).createGridFile(url, recursiveLevels);
} catch (final InvalidPathException e) {
throw new RemoteFileSystemException(e);
}
}
public boolean isFolder(String file) throws RemoteFileSystemException {
final GridFile f = createGsiftpGridFile(file);
final Map<String, String> urls = DtoProperty.mapFromDtoPropertiesList(f.getUrls());
for (final String key : urls.keySet()) {
if (key.startsWith("gsiftp")) {
return user.getFileManager().isFolder(key);
}
}
throw new RemoteFileSystemException("IsFolder not supported for virtual file system.");
}
public String upload(DataHandler source, String filename) throws RemoteFileSystemException {
final GridFile f = createGsiftpGridFile(filename);
final Map<String, String> urls = DtoProperty.mapFromDtoPropertiesList(f.getUrls());
for (final String key : urls.keySet()) {
if (key.startsWith("gsiftp")) {
return user.getFileManager().upload(source, key);
}
}
throw new RemoteFileSystemException("Upload not supported for virtual file system.");
}
public long lastModified(String url) throws RemoteFileSystemException {
final GridFile f = createGsiftpGridFile(url);
final Map<String, String> urls = DtoProperty.mapFromDtoPropertiesList(f.getUrls());
for (final String key : urls.keySet()) {
if (key.startsWith("gsiftp")) {
return user.getFileManager().lastModified(key);
}
}
throw new RemoteFileSystemException("Last modified not supported for virtual file system.");
}
public GridFile createGridFile(String path, int recursiveLevels)
throws RemoteFileSystemException {
path = FileManager.removeTrailingSlash(path);
// Thread.dumpStack();
if (recursiveLevels > 1) {
throw new RuntimeException("Recursion levels greater than 1 not supported yet");
}
final String rightPart = path.substring(BASE.length());
if (rightPart.contains("//")) {
GridFile result = null;
// that means we everything before the // is the fqan and everything
// after is the path
final int i = rightPart.indexOf("//");
String fqanT = rightPart.substring(0, i);
final String restPath = rightPart.substring(i + 2);
if (!fqanT.startsWith("/")) {
fqanT = "/" + fqanT;
}
final Set<String> urls = resolveUrls(restPath, fqanT, true);
if (urls.size() == 0) {
// TODO not sure what to do
throw new RuntimeException("No real url found for virtual url.");
} else if (urls.size() == 1) {
result = new GridFile(urls.iterator().next(), -1L);
result.setVirtual(false);
result.setPath(path);
} else {
result = new GridFile(path, -1L);
result.setVirtual(true);
result.setPath(path);
}
if (recursiveLevels == 0) {
return result;
}
final Set<GridFile> childs = listGroup(fqanT, restPath, true);
for (final GridFile file : childs) {
if (file.isInaccessable()) {
result.addChild(file);
} else {
result.addChildren(file.getChildren());
}
}
final Map<String, Set<String>> temp = findDirectChildFqans(fqanT);
final Set<String> childFqans = temp.keySet();
for (final String fqan : childFqans) {
final Set<MountPoint> mps = user.getMountPoints(fqan);
// we need to remove all volatile mountpoints first, users are
// not interested in those
final Iterator<MountPoint> it = mps.iterator();
while (it.hasNext()) {
final MountPoint mp = it.next();
if (mp.isVolatileFileSystem()) {
it.remove();
}
}
if (mps.size() == 1) {
final GridFile file = new GridFile(mps.iterator().next());
file.setName(FileManager.getFilename(fqan));
final String pathNew =
(path + "/" + file.getName()).replace("///", "/").replace("//", "/") + "//";
file.setPath(pathNew);
file.setVirtual(true);
file.addSites(temp.get(fqan));
result.addChild(file);
} else {
final GridFile file =
new GridFile((BASE + fqan).replace("///", "/").replace("//", "/") + "//", fqan);
final String pathNew =
(path + "/" + file.getName()).replace("///", "/").replace("//", "/") + "//";
// String pathNew = file.getUrl();
file.setPath(pathNew);
for (final MountPoint mp : mps) {
// X.p("Add" + mp.getRootUrl());
file.addUrl(mp.getRootUrl(), GridFile.FILETYPE_MOUNTPOINT_PRIORITY);
}
file.setVirtual(true);
file.addSites(temp.get(fqan));
result.addChild(file);
}
}
return result;
}
final int index = BASE.length();
final String importantUrlPart = path.substring(index);
final String[] tokens = StringUtils.split(importantUrlPart, '/');
GridFile result = null;
if (tokens.length == 0) {
// means root of the groupfilesystem
result = new GridFile(path, -1L);
result.setVirtual(true);
result.setPath(path);
if (recursiveLevels == 0) {
return result;
}
for (final VO vo : new TreeSet<VO>(user.getFqans().values())) {
final GridFile f = new GridFile(BASE + "/" + vo.getVoName(), -1L);
f.setVirtual(true);
f.setPath(path + "/" + vo.getVoName());
for (final MountPoint mp : user.getMountPoints("/" + vo.getVoName())) {
f.addSite(mp.getSite());
f.addUrl(mp.getRootUrl(), GridFile.FILETYPE_MOUNTPOINT_PRIORITY);
}
result.addChild(f);
}
} else if (tokens.length == 1) {
// means is root of VO so we need to list potential files on all
// sites that support this vo
// and also all child vos
final String parentfqan = "/" + tokens[0];
final Set<String> urls = resolveUrls(path, parentfqan, true);
if (urls.size() == 1) {
result = new GridFile(urls.iterator().next(), -1L);
result.setVirtual(false);
result.setPath(path);
} else {
result = new GridFile(path, -1L);
result.setVirtual(true);
result.setPath(path);
for (final String u : urls) {
result.addUrl(u, GridFile.FILETYPE_MOUNTPOINT_PRIORITY);
}
}
if (recursiveLevels == 0) {
return result;
}
final Map<String, Set<String>> temp = findDirectChildFqans(parentfqan);
final Set<String> childFqans = temp.keySet();
for (final String fqan : childFqans) {
final Set<MountPoint> mps = Sets.newTreeSet(user.getMountPoints(fqan));
// we need to remove volatile mountpoints
final Iterator<MountPoint> it = mps.iterator();
while (it.hasNext()) {
final MountPoint mp = it.next();
if (mp.isVolatileFileSystem()) {
it.remove();
}
}
if (mps.size() == 1) {
final GridFile file = new GridFile(mps.iterator().next());
file.setName(FileManager.getFilename(fqan));
file.setPath(path + "/" + file.getName());
file.setVirtual(true);
file.addSites(temp.get(fqan));
result.addChild(file);
} else {
final GridFile file = new GridFile(BASE + fqan, fqan);
file.setPath(path + "/" + file.getName());
file.setVirtual(true);
file.addSites(temp.get(fqan));
for (final MountPoint mp : mps) {
file.addUrl(mp.getRootUrl(), GridFile.FILETYPE_MOUNTPOINT_PRIORITY);
}
file.addFqan(fqan);
result.addChild(file);
}
}
final Set<GridFile> files = listGroup("/" + tokens[0], "", true);
for (final GridFile file : files) {
if (file.isInaccessable()) {
result.addChild(file);
} else {
result.addChildren(file.getChildren());
}
}
} else {
String currentUrl = BASE;
String potentialFqan = "";
final Set<String> parentUrls = new HashSet<String>();
final Set<GridFile> children = new TreeSet<GridFile>();
for (final String token : tokens) {
currentUrl = currentUrl + "/" + token;
potentialFqan = potentialFqan + "/" + token;
if (!user.getFqans().keySet().contains(potentialFqan)) {
continue;
}
final String rest = path.substring(currentUrl.length());
final Set<String> urls = resolveUrls(rest, potentialFqan, true);
parentUrls.addAll(urls);
if (recursiveLevels == 1) {
final Set<GridFile> files = listGroup(potentialFqan, rest, false);
for (final GridFile file : files) {
if (file.isInaccessable()) {
children.add(file);
} else {
children.addAll(file.getChildren());
}
}
}
}
if (recursiveLevels == 1) {
final Map<String, Set<String>> temp = findDirectChildFqans(potentialFqan);
final Set<String> childFqans = temp.keySet();
for (final String fqan : childFqans) {
final Set<MountPoint> mps = user.getMountPoints(fqan);
// we need to remove volatile mountpoints
final Iterator<MountPoint> it = mps.iterator();
while (it.hasNext()) {
final MountPoint mp = it.next();
if (mp.isVolatileFileSystem()) {
it.remove();
}
}
if (mps.size() == 0) {
continue;
}
if (mps.size() == 1) {
final GridFile file = new GridFile(mps.iterator().next());
file.setName(FileManager.getFilename(fqan));
file.setPath(path + "/" + file.getName() + "//");
file.setVirtual(true);
file.addSites(temp.get(fqan));
children.add(file);
} else {
final GridFile file = new GridFile(BASE + fqan, fqan);
file.setPath(path + "/" + file.getName() + "//");
file.setVirtual(true);
file.addSites(temp.get(fqan));
children.add(file);
}
}
}
if (recursiveLevels == 0) {
myLogger.debug(
"Checking whether any of the possible real urls for virtual url " + path + " exist...");
// test whether files actually exist
if (parentUrls.size() > 0) {
final NamedThreadFactory tf = new NamedThreadFactory("realUrlCheckForVfs");
final ExecutorService executor = Executors.newFixedThreadPool(parentUrls.size(), tf);
// let's sort using last modified date, so that we can give
// the
// last file the highest priority
final Map<Long, String> temp = Collections.synchronizedMap(new TreeMap<Long, String>());
for (final String url : parentUrls) {
final Thread t =
new Thread() {
@Override
public void run() {
try {
final long ts = user.getFileManager().lastModified(url);
temp.put(ts, url);
myLogger.debug("File exists: " + url);
// boolean exists =
// user.getFileSystemManager()
// .fileExists(url);
// if (exists) {
// myLogger.debug("File exists: " + url);
// temp.add(url);
// } else {
// myLogger.debug("File does not exit: " +
// url);
// }
} catch (final Exception e) {
myLogger.debug(
"File does not exit: " + url + " - " + e.getLocalizedMessage());
}
}
};
executor.execute(t);
}
executor.shutdown();
try {
executor.awaitTermination(60, TimeUnit.SECONDS);
} catch (final InterruptedException e) {
}
if (temp.size() == 1) {
result = new GridFile(temp.values().iterator().next(), -1L);
result.setVirtual(false);
result.setPath(path);
} else {
result = new GridFile(path, -1L);
result.setVirtual(true);
result.setPath(path);
int i = 0;
for (final Long lm : temp.keySet()) {
result.addUrl(temp.get(lm), GridFile.FILETYPE_FOLDER_PRIORITY + i);
i = i + 1;
}
}
return result;
}
}
// xxx
if (parentUrls.size() == 1) {
final String url = parentUrls.iterator().next();
try {
final boolean isFolder = user.getFileManager().isFolder(url);
if (isFolder) {
result = new GridFile(url, -1L);
} else {
result = user.ls(url, 0);
}
result.setVirtual(false);
result.setPath(path);
} catch (Exception e) {
result = new GridFile(url, -1L);
GridFile error = new GridFile(url, false, e);
result.addChild(error);
}
} else {
result = new GridFile(path, -1L);
result.setVirtual(true);
result.setPath(path);
for (final String u : parentUrls) {
result.addUrl(u, GridFile.FILETYPE_FOLDER_PRIORITY);
}
}
result.addChildren(children);
}
return result;
}
public void filesSelected(Set<GridFile> files) {
if ((files == null) || (files.size() == 0)) {
getViewMenuItem().setEnabled(false);
getRefreshMenuItem().setEnabled(false);
getDownloadMenuItem().setEnabled(false);
getCreateFolderMenuItem().setEnabled(false);
getDeleteMenuItem().setEnabled(false);
getCopyMenuItem().setEnabled(false);
return;
}
if (files.size() == 1) {
if (files.iterator().next().isFolder()) {
getRefreshMenuItem().setEnabled(true);
final Clipboard cb = FileManager.FILE_TRANSFER_CLIPBOARD;
final Transferable t = cb.getContents(null);
if (t != null) {
final GridFile target = files.iterator().next();
if (target.isVirtual()) {
if (target.getUrls().size() == 1) {
if (target.getUrl().startsWith(ServiceInterface.VIRTUAL_GRID_PROTOCOL_NAME)) {
getPasteMenuItem().setEnabled(false);
} else {
getPasteMenuItem().setEnabled(true);
}
} else {
getPasteMenuItem().setEnabled(true);
}
} else {
getPasteMenuItem().setEnabled(true);
}
} else {
getPasteMenuItem().setEnabled(false);
}
} else {
getRefreshMenuItem().setEnabled(false);
getPasteMenuItem().setEnabled(false);
}
} else {
getRefreshMenuItem().setEnabled(false);
getPasteMenuItem().setEnabled(false);
}
boolean folder = false;
for (final GridFile file : files) {
if (file.isFolder()) {
folder = true;
}
if (file.isVirtual()) {
if (folder) {
getDownloadMenuItem().setEnabled(false);
if (getOpenMenuItem() != null) {
getOpenMenuItem().setEnabled(false);
}
getCreateFolderMenuItem().setEnabled(true);
} else {
if (file.getUrls().size() == 1) {
getDownloadMenuItem().setEnabled(true);
if (getOpenMenuItem() != null) {
getOpenMenuItem().setEnabled(true);
}
} else {
getDownloadMenuItem().setEnabled(false);
if (getOpenMenuItem() != null) {
getOpenMenuItem().setEnabled(false);
}
}
getCreateFolderMenuItem().setEnabled(false);
}
getDeleteMenuItem().setEnabled(false);
getCopyMenuItem().setEnabled(false);
return;
}
}
if (folder) {
getViewMenuItem().setEnabled(false);
if (getOpenMenuItem() != null) {
getOpenMenuItem().setEnabled(false);
}
} else {
getViewMenuItem().setEnabled(true);
if (getOpenMenuItem() != null) {
getOpenMenuItem().setEnabled(true);
}
}
getDownloadMenuItem().setEnabled(true);
getCreateFolderMenuItem().setEnabled(true);
getDeleteMenuItem().setEnabled(true);
getCopyMenuItem().setEnabled(true);
}