@Parameters({"target"})
@BeforeClass
public void setUp(String target) throws Exception {
log.info("METADATA VALIDATOR TARGET: " + target);
sf = new TestServiceFactory().proxy();
config = new ImportConfig();
// Let the user know at what level we're logging
ch.qos.logback.classic.Logger lociLogger =
(ch.qos.logback.classic.Logger) LoggerFactory.getLogger("loci");
ch.qos.logback.classic.Logger omeLogger =
(ch.qos.logback.classic.Logger) LoggerFactory.getLogger("ome.formats");
log.info(
String.format(
"Log levels -- Bio-Formats: %s OMERO.importer: %s",
lociLogger.getLevel(), omeLogger.getLevel()));
store = new OMEROMetadataStoreClient();
store.initialize(sf);
store.setEnumerationProvider(new TestEnumerationProvider());
store.setInstanceProvider(new BlitzInstanceProvider(store.getEnumerationProvider()));
minimalStore = new OMEROMetadataStoreClient();
minimalStore.initialize(sf);
minimalStore.setEnumerationProvider(new TestEnumerationProvider());
minimalStore.setInstanceProvider(
new BlitzInstanceProvider(minimalStore.getEnumerationProvider()));
wrapper = new OMEROWrapper(config);
wrapper.setMetadataOptions(new DefaultMetadataOptions(MetadataLevel.ALL));
minimalWrapper = new OMEROWrapper(config);
minimalWrapper.setMetadataOptions(new DefaultMetadataOptions(MetadataLevel.MINIMUM));
wrapper.setMetadataStore(store);
store.setReader(wrapper.getImageReader());
minimalStore.setReader(minimalWrapper.getImageReader());
}
public TestEngine(TestEngineConfig config)
throws CannotCreateSessionException, PermissionDeniedException, ServerError {
this.config = config;
ProxyFactory pf = new ProxyFactory(new OMEROMetadataStoreClient());
pf.addAdvice(interceptor);
pf.setProxyTargetClass(true);
store = (OMEROMetadataStoreClient) pf.getProxy();
wrapper = new OMEROWrapper(new ImportConfig());
login_url = config.getFeedbackLoginUrl();
login_username = config.getFeedbackLoginUsername();
login_password = config.getFeedbackLoginPassword();
message_url = config.getFeedbackMessageUrl();
comment_url = config.getCommentUrl();
// Login
if (config.getSessionKey() != null) {
store.initialize(config.getHostname(), config.getPort(), config.getSessionKey());
} else {
store.initialize(
config.getUsername(), config.getPassword(), config.getHostname(), config.getPort());
}
importLibrary = new ImportLibrary(store, wrapper);
}
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();
}
}