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Only keep ReplacePolicy in ReplacePolicy.java
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@ppouchin
ppouchin committed Mar 11, 2024
1 parent fe52f30 commit cfc2a25
Showing 1 changed file with 9 additions and 244 deletions.
253 changes: 9 additions & 244 deletions src/main/java/fr/igred/omero/util/ReplacePolicy.java
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* Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/

package fr.igred.omero;


import fr.igred.omero.client.Browser;
import fr.igred.omero.client.Client;
import fr.igred.omero.client.GatewayWrapper;
import fr.igred.omero.exception.AccessException;
import fr.igred.omero.exception.ExceptionHandler;
import fr.igred.omero.exception.ServiceException;
import loci.formats.in.DefaultMetadataOptions;
import loci.formats.in.MetadataLevel;
import ome.formats.OMEROMetadataStoreClient;
import ome.formats.importer.ImportCandidates;
import ome.formats.importer.ImportConfig;
import ome.formats.importer.ImportContainer;
import ome.formats.importer.ImportLibrary;
import ome.formats.importer.OMEROWrapper;
import ome.formats.importer.cli.ErrorHandler;
import ome.formats.importer.cli.LoggingImportMonitor;
import omero.gateway.model.DataObject;
import omero.gateway.util.PojoMapper;
import omero.model.Pixels;

import java.io.IOException;
import java.lang.invoke.MethodHandles;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.logging.Logger;

import static java.util.stream.Collectors.toList;
package fr.igred.omero.util;


/**
* Generic class containing a DataObject (or a subclass) object.
*
* @param <T> Subclass of {@link DataObject}
* Policy to specify how to handle objects when they are replaced.
*/
public abstract class RepositoryObjectWrapper<T extends DataObject> extends AnnotatableWrapper<T> {

/**
* Constructor of the class RepositoryObjectWrapper.
*
* @param o The DataObject to wrap in the RepositoryObjectWrapper.
*/
protected RepositoryObjectWrapper(T o) {
super(o);
}


/**
* Method used for importing a number of import candidates.
*
* @param target The import target.
* @param library The importer.
* @param config The configuration information.
* @param candidates Hosts information about the files to import.
*
* @return The list of imported pixels.
*/
private static List<Pixels> importCandidates(DataObject target, ImportLibrary library, ImportConfig config, ImportCandidates candidates) {
List<Pixels> pixels = new ArrayList<>(0);

ExecutorService threadPool = Executors.newFixedThreadPool(config.parallelUpload.get());

List<ImportContainer> containers = candidates.getContainers();
if (containers != null) {
pixels = new ArrayList<>(containers.size());
for (int i = 0; i < containers.size(); i++) {
ImportContainer container = containers.get(i);
container.setTarget(target.asIObject());
List<Pixels> imported = new ArrayList<>(1);
try {
imported = library.importImage(container, threadPool, i);
} catch (Throwable e) {
String filename = container.getFile().getName();
String error = String.format("Error during image import for: %s", filename);
Logger.getLogger(MethodHandles.lookup().lookupClass().getName()).severe(error);
if (Boolean.FALSE.equals(config.contOnError.get())) {
return pixels;
}
}
pixels.addAll(imported);
}
}
threadPool.shutdown();
return pixels;
}


/**
* Imports all images candidates in the paths to the target in OMERO.
*
* @param client The client handling the connection.
* @param target The import target.
* @param threads The number of threads (same value used for filesets and uploads).
* @param paths Paths to the image files on the computer.
*
* @return If the import did not exit because of an error.
*
* @throws ServiceException Cannot connect to OMERO.
* @throws AccessException Cannot access data.
* @throws IOException Cannot read file.
*/
protected static boolean importImages(GatewayWrapper client, DataObject target, int threads, String... paths)
throws ServiceException, AccessException, IOException {
boolean success;

ImportConfig config = new ImportConfig();
String type = PojoMapper.getGraphType(target.getClass());
config.target.set(type + ":" + target.getId());
config.username.set(client.getUser().getUserName());
config.email.set(client.getUser().getEmail());
config.parallelFileset.set(threads);
config.parallelUpload.set(threads);

OMEROMetadataStoreClient store = client.getImportStore();
try (OMEROWrapper reader = new OMEROWrapper(config)) {
ExceptionHandler.ofConsumer(store, s -> s.logVersionInfo(config.getIniVersionNumber()))
.handleServerAndService("Cannot log version information during import.")
.rethrow();
reader.setMetadataOptions(new DefaultMetadataOptions(MetadataLevel.ALL));

ImportLibrary library = new ImportLibrary(store, reader);
library.addObserver(new LoggingImportMonitor());

ErrorHandler handler = new ErrorHandler(config);

ImportCandidates candidates = new ImportCandidates(reader, paths, handler);
success = library.importCandidates(config, candidates);
} finally {
client.closeImport();
}

return success;
}


/**
* Imports one image file to the target in OMERO.
*
* @param client The client handling the connection.
* @param target The import target.
* @param path Path to the image file on the computer.
*
* @return The list of IDs of the newly imported images.
*
* @throws ServiceException Cannot connect to OMERO.
* @throws AccessException Cannot access data.
* @throws IOException Cannot read file.
*/
protected static List<Long> importImage(GatewayWrapper client, DataObject target, String path)
throws ServiceException, AccessException, IOException {
ImportConfig config = new ImportConfig();
String type = PojoMapper.getGraphType(target.getClass());
config.target.set(type + ":" + target.getId());
config.username.set(client.getUser().getUserName());
config.email.set(client.getUser().getEmail());

Collection<Pixels> pixels;

OMEROMetadataStoreClient store = client.getImportStore();
try (OMEROWrapper reader = new OMEROWrapper(config)) {
ExceptionHandler.ofConsumer(store, s -> s.logVersionInfo(config.getIniVersionNumber()))
.handleServerAndService("Cannot log version information during import.")
.rethrow();
reader.setMetadataOptions(new DefaultMetadataOptions(MetadataLevel.ALL));

ImportLibrary library = new ImportLibrary(store, reader);
library.addObserver(new LoggingImportMonitor());

ErrorHandler handler = new ErrorHandler(config);

ImportCandidates candidates = new ImportCandidates(reader, new String[]{path}, handler);
pixels = importCandidates(target, library, config, candidates);
} finally {
client.closeImport();
}

return pixels.stream()
.map(pix -> pix.getImage().getId().getValue())
.distinct()
.collect(toList());
}


/**
* Gets the object name.
*
* @return See above.
*/
public abstract String getName();


/**
* Gets the object description
*
* @return See above.
*/
public abstract String getDescription();


/**
* Copies annotation links from some other object to this one.
* <p>Kept for API compatibility purposes.</p>
*
* @param client The client handling the connection.
* @param object Other repository object to copy annotations from.
*
* @throws ServiceException Cannot connect to OMERO.
* @throws AccessException Cannot access data.
* @throws ExecutionException A Facility can't be retrieved or instantiated.
*/
@SuppressWarnings("MethodOverloadsMethodOfSuperclass")
public void copyAnnotationLinks(Client client, RepositoryObjectWrapper<?> object)
throws AccessException, ServiceException, ExecutionException {
super.copyAnnotationLinks(client, object);
}


/**
* Reloads the object from OMERO.
*
* @param browser The data browser.
*
* @throws ServiceException Cannot connect to OMERO.
* @throws AccessException Cannot access data.
* @throws ExecutionException A Facility can't be retrieved or instantiated.
*/
public abstract void reload(Browser browser)
throws ServiceException, AccessException, ExecutionException;


/**
* Policy to specify how to handle objects when they are replaced.
*/
public enum ReplacePolicy {
/** Unlink objects only */
UNLINK,

/** Delete all objects */
DELETE,
public enum ReplacePolicy {
/** Unlink objects only */
UNLINK,

/** Delete orphaned objects */
DELETE_ORPHANED
}
/** Delete all objects */
DELETE,

/** Delete orphaned objects */
DELETE_ORPHANED
}

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