org.obiba.genobyte.cli.OpenCommand.java Source code

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Here is the source code for org.obiba.genobyte.cli.OpenCommand.java

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/*******************************************************************************
 * Copyright 2007(c) Gnome Qubec. All rights reserved.
 * 
 * This file is part of GenoByte.
 * 
 * GenoByte 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 3
 * of the License, or (at your option) any later version.
 * 
 * GenoByte 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, see <http://www.gnu.org/licenses/>. 
 *******************************************************************************/
package org.obiba.genobyte.cli;

import org.apache.commons.cli.Option;
import org.apache.commons.cli.OptionBuilder;
import org.apache.commons.cli.ParseException;
import org.obiba.bitwise.BitwiseStore;
import org.obiba.bitwise.BitwiseStoreUtil;
import org.obiba.bitwise.util.BitwiseDiskUtil;
import org.obiba.genobyte.GenotypingStore;

/**
 * Base class for opening a GenotypingStore, extending classes should implement the {@link OpenCommand#openStore} method.
 */
public abstract class OpenCommand implements CliCommand {

    public boolean requiresOpenStore() {
        return false;
    }

    public boolean execute(Option opt, CliContext context) throws ParseException {
        String storeName = opt.getValue();
        if (context.getStore() != null) {
            context.getOutput().println("Closing current store.");
            context.getStore().close();
        }

        context.clear();
        context.getOutput().println("Opening store " + storeName + ".");
        GenotypingStore<?, ?, ?, ?> store = open(storeName);
        if (store == null) {
            context.getOutput().println("Store " + storeName + " does not exist");
            return false;
        }
        context.setStore(store);
        context.setActiveRecordStore(store.getSampleRecordStore());

        return false;
    }

    public Option getOption() {
        return OptionBuilder.withDescription("open the store <name>").withLongOpt("open").hasArg()
                .withArgName("name").create('o');
    }

    /**
     * Override this method and return an opened instance of the specified store name.
     *
     * @param samples the store holding the sample records
     * @param assays the store holding the assay records
     * @return an opened instance of the specified store 
     */
    abstract protected GenotypingStore<?, ?, ?, ?> openStore(BitwiseStore samples, BitwiseStore assays);

    /**
     * Opens both {@link BitwiseStore} instances and calls {@link OpenCommand#openStore(BitwiseStore, BitwiseStore)}.
     *
     * @param name the name of the store to open
     * @return an opened instance of the specified store 
     */
    protected GenotypingStore<?, ?, ?, ?> open(String name) {
        BitwiseStore sampleStore = null;
        BitwiseStore assayStore = null;
        String samplesName = name + "_samples";
        String assaysName = name + "_assays";
        if (BitwiseStoreUtil.getInstance().exists(samplesName)) {
            sampleStore = BitwiseStoreUtil.getInstance().open(samplesName);
            if (sampleStore == null) {
                throw new IllegalArgumentException("Cannot open store [" + samplesName + "]");
            }
        } else {
            // TODO: When a call to "exists" is made, the underlying directory is created. This will delete it.
            BitwiseDiskUtil.deleteStore(samplesName);
            return null;
        }
        if (BitwiseStoreUtil.getInstance().exists(assaysName)) {
            assayStore = BitwiseStoreUtil.getInstance().open(assaysName);
            if (assayStore == null) {
                throw new IllegalArgumentException("Cannot open store [" + assaysName + "]");
            }
        } else {
            BitwiseDiskUtil.deleteStore(assaysName);
            return null;
        }

        return openStore(sampleStore, assayStore);

    }
}