OMERO import example in Java

OmeroImport.java

import loci.formats.in.DefaultMetadataOptions;
import loci.formats.in.MetadataLevel;
import ome.formats.OMEROMetadataStoreClient;
import ome.formats.importer.ImportConfig;
import ome.formats.importer.cli.ErrorHandler;
import ome.formats.importer.cli.LoggingImportMonitor;
import omero.model.Dataset;

public class OmeroImport {

    public static void main(String[] args) throws Exception {
        if (args.length != 6) {
            System.err.println("Usage: OmeroImport <host> <port> " +
                    "<username> <password> <dataset_id> <path>");
            System.exit(1);
        }

        // Set up configuration parameters
        ImportConfig config = new ImportConfig();
        config.email.set("");
        config.sendFiles.set(true);
        config.sendReport.set(false);
        config.contOnError.set(false);
        config.debug.set(false);
        config.hostname.set(args[0]);
        config.port.set(Integer.parseInt(args[1]));
        config.username.set(args[2]);
        config.password.set(args[3]);
        config.targetClass.set(Dataset.class.getName());
        config.targetId.set(Long.parseLong(args[4]));

        // Create an array with the paths that we are going to check as being
        // an import candidate and subsequently import.
        String[] paths = new String[] { args[5] };

        // Create a new metadata store using the configuration we've set up,
        // this will log in to OMERO.
        OMEROMetadataStoreClient store = config.createStore();
        try {
            store.logVersionInfo(config.getIniVersionNumber());

            // Create a OMERO reader wrapper which encompasses the related
            // Bio-Formats functionality required for an OMERO import, an
            // import library which is responsible for actually performing an
            // OMERO import life cycle and an error handler which encompasses
            // all error reporting while an import is taking place.
            OMEROWrapper reader = new OMEROWrapper(config);
            ImportLibrary library = new ImportLibrary(store, reader);
            ErrorHandler handler = new ErrorHandler(config);

            // Add a logging observer to the import library which will print
            // to the log file (defaulting to STDOUT/STDERR) the status of the
            // import process.
            library.addObserver(new LoggingImportMonitor());

            // Calculate the candidates that are required for the import, which
            // is done with a metadata level of MINIMUM to avoid parsing and
            // populating all metadata during this process.
            ImportCandidates candidates =
                    new ImportCandidates(reader, paths, handler);

            // Up the metadata level to ALL so that the actual import itself
            // will be complete.
            reader.setMetadataOptions(
                    new DefaultMetadataOptions(MetadataLevel.ALL));
            boolean success = library.importCandidates(config, candidates);
            if (success) {
                System.exit(0);
            } else {
                System.exit(1);
            }
        } finally {
            store.logout();
        }
    }
}