public void init(Helper helper) {
this.helper = helper;
if (!helper.getEventContext().isCurrentUserAdmin()) {
throw helper.cancel(new ERR(), new omero.SecurityViolation(), "not-admin");
}
log.debug("Looking repo " + repoUuid);
try {
String proposedName = "InternalRepository-" + repoUuid;
InternalRepositoryPrx[] proxies = reg.lookupRepositories();
for (InternalRepositoryPrx prx : proxies) {
Ice.Identity id = prx.ice_getIdentity();
if (proposedName.equals(id.name)) {
repo = prx;
log.debug("Found repo " + repoUuid);
break;
}
}
} catch (Exception e) {
throw helper.cancel(new ERR(), e, "registry-lookup", "repoUuid", repoUuid);
}
if (repo == null) {
throw helper.cancel(new Unknown(), null, "unknown-repo", "repoUuid", repoUuid);
}
this.helper.setSteps(1);
}
public void init(Helper helper) {
this.helper = helper;
helper.setSteps(5);
final ImportConfig config = new ImportConfig();
final String sessionUuid = helper.getEventContext().getCurrentSessionUuid();
if (!(location instanceof ManagedImportLocationI)) {
throw helper.cancel(
new ERR(), null, "bad-location", "location-type", location.getClass().getName());
}
ManagedImportLocationI managedLocation = (ManagedImportLocationI) location;
logPath = managedLocation.getLogFile();
logFilename = logPath.getFullFsPath();
MDC.put("fileset", logFilename);
file = ((ManagedImportLocationI) location).getTarget();
try {
sf = reg.getInternalServiceFactory(sessionUuid, "unused", 3, 1, clientUuid);
store = new OMEROMetadataStoreClient();
store.setCurrentLogFile(logFilename, token);
store.initialize(sf);
registerKeepAlive();
fileName = file.getFullFsPath();
shortName = file.getName();
format = null;
usedFiles = new String[] {fileName};
open(reader, store, file);
format = reader.getFormat();
if (reader.getUsedFiles() != null) {
usedFiles = reader.getUsedFiles();
}
if (usedFiles == null) {
throw new NullPointerException("usedFiles must be non-null");
}
// Process all information which has been passed in as annotations
detectKnownAnnotations();
// Now that we've possibly updated the settings object, copy out
// all the values needed by import.
userSpecifiedTarget = settings.userSpecifiedTarget;
userSpecifiedName =
settings.userSpecifiedName == null ? null : settings.userSpecifiedName.getValue();
userSpecifiedDescription =
settings.userSpecifiedDescription == null
? null
: settings.userSpecifiedDescription.getValue();
userPixels = settings.userSpecifiedPixels;
annotationList = settings.userSpecifiedAnnotationList;
doThumbnails = settings.doThumbnails == null ? true : settings.doThumbnails.getValue();
noStatsInfo = settings.noStatsInfo == null ? false : settings.noStatsInfo.getValue();
IFormatReader baseReader = reader.getImageReader().getReader();
if (log.isInfoEnabled()) {
log.info("File format: " + format);
log.info("Base reader: " + baseReader.getClass().getName());
}
notifyObservers(new ImportEvent.LOADED_IMAGE(shortName, 0, 0, 0));
formatString = baseReader.getClass().getSimpleName();
formatString = formatString.replace("Reader", "");
} catch (Cancel c) {
throw c;
} catch (Throwable t) {
throw helper.cancel(new ERR(), t, "error-on-init");
} finally {
MDC.clear();
}
}
