InstrumentProcessor.java example

Explorer
openmicroscopy-master
/*
 * ome.formats.model.InstrumentProcessor
 *
 *------------------------------------------------------------------------------
 *  Copyright (C) 2006-2008 University of Dundee. All rights reserved.
 *
 *
 *  This program is free software; you can redistribute it and/or modify
 *  it under the terms of the GNU General Public License as published by
 *  the Free Software Foundation; either version 2 of the License, or
 *  (at your option) any later version.
 *  This program is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU General Public License for more details.
 *
 *  You should have received a copy of the GNU General Public License along
 *  with this program; if not, write to the Free Software Foundation, Inc.,
 *  51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
 *
 *------------------------------------------------------------------------------
 */

package ome.formats.model;

import java.util.LinkedHashMap;
import java.util.List;

import ome.formats.Index;
import ome.util.LSID;
import omero.metadatastore.IObjectContainer;
import omero.model.Arc;
import omero.model.Detector;
import omero.model.Filament;
import omero.model.Instrument;
import omero.model.Laser;
import omero.model.OTF;
import omero.model.Objective;

import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
 * Processes the members of an Instrument (Objective, OTF, Arc Laser and
 * Filament) and ensures that the Instrument containers are present in the
 * container cache, adding them if they are missing.
 *
 * @author Chris Allan <callan at blackcat dot ca>
 *
 */
public class InstrumentProcessor implements ModelProcessor {
  /** Logger for this class */
  private Logger log = LoggerFactory.getLogger(InstrumentProcessor.class);

  /**
   * Processes the OMERO client side metadata store.
   * @param store OMERO metadata store to process.
   * @throws ModelException If there is an error during processing.
   */
  public void process(IObjectContainerStore store) throws ModelException {
    List<IObjectContainer> containers =
      store.getIObjectContainers(Detector.class);
    containers.addAll(store.getIObjectContainers(Objective.class));
    containers.addAll(store.getIObjectContainers(OTF.class));
    containers.addAll(store.getIObjectContainers(Arc.class));
    containers.addAll(store.getIObjectContainers(Laser.class));
    containers.addAll(store.getIObjectContainers(Filament.class));

    for (IObjectContainer container : containers) {
      Integer instrumentIndex = container.indexes.get(
          Index.INSTRUMENT_INDEX.getValue());
      Instrument instrument = (Instrument) store.getSourceObject(
          new LSID(Instrument.class, instrumentIndex));

      // If instrument is missing
      if (instrument == null) {
        LinkedHashMap<Index, Integer> indexes =
          new LinkedHashMap<Index, Integer>();
        indexes.put(Index.INSTRUMENT_INDEX, instrumentIndex);
        container = store.getIObjectContainer(Instrument.class, indexes);
        instrument = (Instrument) container.sourceObject;
      }
    }
  }

}