/**
* Upload files to the managed repository.
*
* <p>This is done by first passing in the possibly absolute local file paths. A common selection
* of those are chosen and passed back to the client.
*
* <p>As each file is written to the server, a message digest is kept updated of the bytes that
* are being written. These are then returned to the caller so they can be checked against the
* values found on the server.
*
* @param container The current import container we're to handle.
* @return A list of the client-side (i.e. local) hashes for each file.
*/
public List<String> uploadFilesToRepository(
final String[] srcFiles, final ImportProcessPrx proc) {
final byte[] buf = new byte[store.getDefaultBlockSize()];
final int fileTotal = srcFiles.length;
final List<String> checksums = new ArrayList<String>(fileTotal);
// TODO Fix with proper code instead of 10000L
final TimeEstimator estimator = new ProportionalTimeEstimatorImpl(10000L);
log.debug("Used files created:");
for (int i = 0; i < fileTotal; i++) {
try {
checksums.add(uploadFile(proc, srcFiles, i, checksumProviderFactory, estimator, buf));
} catch (ServerError e) {
log.error("Server error uploading file.", e);
break;
} catch (IOException e) {
log.error("I/O error uploading file.", e);
break;
}
}
return checksums;
}
/**
* Perform an image import uploading files if necessary.
*
* @param container The import container which houses all the configuration values and target for
* the import.
* @param index Index of the import in a set. <code>0</code> is safe if this is a singular import.
* @param numDone Number of imports completed in a set. <code>0</code> is safe if this is a
* singular import.
* @param total Total number of imports in a set. <code>1</code> is safe if this is a singular
* import.
* @return List of Pixels that have been imported.
* @throws FormatException If there is a Bio-Formats image file format error during import.
* @throws IOException If there is an I/O error.
* @throws ServerError If there is an error communicating with the OMERO server we're importing
* into.
* @since OMERO Beta 4.2.1.
*/
public List<Pixels> importImage(
final ImportContainer container, int index, int numDone, int total)
throws FormatException, IOException, Throwable {
HandlePrx handle;
for (FileExclusion exclusion : exclusions) {
Boolean veto = exclusion.suggestExclusion(store.getServiceFactory(), container);
if (Boolean.TRUE.equals(veto)) {
notifyObservers(
new ImportEvent.FILESET_EXCLUSION(
container.getFile().getAbsolutePath(), 0, container.getUsedFiles().length));
return Collections.emptyList();
}
}
final ImportProcessPrx proc = createImport(container);
final String[] srcFiles = container.getUsedFiles();
final List<String> checksums = new ArrayList<String>();
final byte[] buf = new byte[store.getDefaultBlockSize()];
final TimeEstimator estimator =
new ProportionalTimeEstimatorImpl(container.getUsedFilesTotalSize());
Map<Integer, String> failingChecksums = new HashMap<Integer, String>();
notifyObservers(
new ImportEvent.FILESET_UPLOAD_START(null, index, srcFiles.length, null, null, null));
for (int i = 0; i < srcFiles.length; i++) {
checksums.add(uploadFile(proc, srcFiles, i, checksumProviderFactory, estimator, buf));
}
try {
handle = proc.verifyUpload(checksums);
} catch (ChecksumValidationException cve) {
failingChecksums = cve.failingChecksums;
throw cve;
} finally {
try {
proc.close();
} catch (Exception e) {
log.warn("Exception while closing proc", e);
}
notifyObservers(
new ImportEvent.FILESET_UPLOAD_END(
null,
index,
srcFiles.length,
null,
null,
srcFiles,
checksums,
failingChecksums,
null));
}
// At this point the import is running, check handle for number of
// steps.
ImportCallback cb = null;
try {
cb = createCallback(proc, handle, container);
if (minutesToWait == 0) {
log.info("Disconnecting from import process...");
cb.close(false);
cb = null;
handle = null;
return Collections.emptyList(); // EARLY EXIT
}
if (minutesToWait < 0) {
while (true) {
if (cb.block(5000)) {
break;
}
}
} else {
cb.loop(minutesToWait * 30, 2000);
}
final ImportResponse rsp = cb.getImportResponse();
if (rsp == null) {
throw new Exception("Import failure");
}
return rsp.pixels;
} finally {
if (cb != null) {
cb.close(true); // Allow cb to close handle
} else if (handle != null) {
handle.close();
}
}
}
public String uploadFile(
final ImportProcessPrx proc, final String[] srcFiles, int index, TimeEstimator estimator)
throws ServerError, IOException {
final byte[] buf = new byte[store.getDefaultBlockSize()];
return uploadFile(proc, srcFiles, index, checksumProviderFactory, estimator, buf);
}