edu.harvard.med.iccbl.screensaver.io.libraries.MasterStockPlateMappingLoader.java Source code

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Here is the source code for edu.harvard.med.iccbl.screensaver.io.libraries.MasterStockPlateMappingLoader.java

Source

// $HeadURL$
// $Id$
//
// Copyright  2010 by the President and Fellows of Harvard College.
// 
// Screensaver is an open-source project developed by the ICCB-L and NSRB labs
// at Harvard Medical School. This software is distributed under the terms of
// the GNU General Public License.

package edu.harvard.med.iccbl.screensaver.io.libraries;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.util.Set;

import com.google.common.collect.Sets;
import org.apache.commons.cli.OptionBuilder;
import org.apache.commons.cli.ParseException;
import org.apache.log4j.Logger;

import edu.harvard.med.screensaver.db.DAOTransaction;
import edu.harvard.med.screensaver.db.DAOTransactionRollbackException;
import edu.harvard.med.screensaver.db.GenericEntityDAO;
import edu.harvard.med.screensaver.io.CommandLineApplication;
import edu.harvard.med.screensaver.model.libraries.CopyUsageType;
import edu.harvard.med.screensaver.model.libraries.Plate;
import edu.harvard.med.screensaver.model.libraries.Quadrant;
import edu.harvard.med.screensaver.model.libraries.StockPlateMapping;

/**
 * The file format for the loader is a CSV file with three fields per row:
 * <code>&lt;96-well stock plate number&gt;,&lt;stock plate number&gt;,&lt;quadrant&gt;</code> where &lt;quadrant&gt;
 * is the string value of a {@link Quadrant} enum value. The 96-well stock plates (referenced in the first field) may
 * only have copy plates with usage type {@link CopyUsageType#MASTER_STOCK_PLATES}.
 */
public class MasterStockPlateMappingLoader extends CommandLineApplication {
    private static final Logger log = Logger.getLogger(MasterStockPlateMappingLoader.class);

    @SuppressWarnings("static-access")
    public static void main(String[] args) throws IOException {
        final MasterStockPlateMappingLoader app = new MasterStockPlateMappingLoader(args);
        app.addCommandLineOption(OptionBuilder.isRequired().hasArg(true).withArgName("file")
                .withLongOpt("input-file")
                .withDescription(
                        "The path of a CSV file containing the stock plate mapping data (master stock plate number, stock plate number, quadrant")
                .create("f"));
        app.processOptions(true, false);
        GenericEntityDAO dao = (GenericEntityDAO) app.getSpringBean("genericEntityDao");
        dao.doInTransaction(new DAOTransaction() {
            @Override
            public void runTransaction() {
                try {
                    app.load();
                } catch (Exception e) {
                    throw new DAOTransactionRollbackException(e);
                }
            }
        });
    }

    public MasterStockPlateMappingLoader(String[] args) {
        super(args);
    }

    public void load() throws ParseException, IOException {
        File file = getCommandLineOptionValue("f", File.class);
        GenericEntityDAO dao = (GenericEntityDAO) getSpringBean("genericEntityDao");
        BufferedReader reader = new BufferedReader(new FileReader(file));
        String row = null;
        int nPlatesUpdated = 0;
        int nPlateNumbersUpdated = 0;
        while ((row = reader.readLine()) != null) {
            String[] fields = row.split(",");
            Integer masterStockPlateNumber = Integer.valueOf(fields[0]);
            Integer stockPlateNumber = Integer.valueOf(fields[1]);
            Quadrant quadrant = Quadrant.valueOf(fields[2]);
            Set<Plate> copyPlatesForPlateNumber = Sets
                    .newHashSet(dao.findEntitiesByProperty(Plate.class, "plateNumber", masterStockPlateNumber));
            int copiesUpdated = 0;
            for (Plate masterStockPlate : copyPlatesForPlateNumber) {
                log.debug("for plate: " + masterStockPlateNumber + ", found copy: "
                        + masterStockPlate.getCopy().getName() + ", usage type: "
                        + masterStockPlate.getCopy().getUsageType());
                if (masterStockPlate.getCopy().getUsageType() == CopyUsageType.MASTER_STOCK_PLATES) {
                    masterStockPlate.setStockPlateMapping(new StockPlateMapping(stockPlateNumber, quadrant));
                    log.info("updated plate " + masterStockPlate.getPlateNumber() + " copy "
                            + masterStockPlate.getCopy().getName() + " with "
                            + masterStockPlate.getStockPlateMapping());
                    ++nPlatesUpdated;
                    ++copiesUpdated;
                }
            }
            if (copiesUpdated == 0) {
                throw new IllegalArgumentException("plate " + masterStockPlateNumber
                        + " has no master stock plate copies, according to the copy usage types found");
            }
            ++nPlateNumbersUpdated;
        }
        log.info("updated " + nPlateNumbersUpdated + " plate number(s)");
        log.info("updated " + nPlatesUpdated + " plate(s)");
    }
}