com.metamolecular.pubcouch.pubchem.Snapshot.java Source code

Introduction

Here is the source code for com.metamolecular.pubcouch.pubchem.Snapshot.java

Source

/*
 * PubCouch - A CouchDB Interface for PubChem
 *
 * Copyright (c) 2010 Metamolecular, LLC
 *
 * http://metamolecular.com
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */
package com.metamolecular.pubcouch.pubchem;

import com.metamolecular.pubcouch.record.DefaultRecordStreamer;
import com.metamolecular.pubcouch.record.Record;
import java.io.IOException;
import java.io.InputStream;
import java.io.SequenceInputStream;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.Enumeration;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.zip.GZIPInputStream;
import org.apache.commons.net.ftp.FTP;
import org.apache.commons.net.ftp.FTPClient;

/**
 *
 * @author Richard L. Apodaca <rapodaca at metamolecular.com>
 */
public class Snapshot extends Archive {

    private static String SUBSTANCES_DIR = "/pubchem/Substance/CURRENT-Full/SDF";
    private static String COMPOUNDS_DIR = "/pubchem/Compound/CURRENT-Full/SDF";

    public Snapshot() {
        super();
    }

    public Snapshot(FTPClient client) {
        super(client);
    }

    @Override
    public DefaultRecordStreamer getCompounds() throws IOException {
        client.changeWorkingDirectory(COMPOUNDS_DIR);

        return new DefaultRecordStreamer(getStream());
    }

    @Override
    public DefaultRecordStreamer getCompounds(int beginAfter) throws IOException {
        client.changeWorkingDirectory(COMPOUNDS_DIR);
        DefaultRecordStreamer result = new DefaultRecordStreamer(getStream(beginAfter));
        String key = "PUBCHEM_COMPOUND_CID";
        String value = String.valueOf(beginAfter);

        for (Record record : result) {
            if (record.get(key).equals(value)) {
                break;
            }
        }

        return result;
    }

    @Override
    public DefaultRecordStreamer getSubstances() throws IOException {
        client.changeWorkingDirectory(SUBSTANCES_DIR);

        return new DefaultRecordStreamer(getStream());
    }

    @Override
    public DefaultRecordStreamer getSubstances(int beginAfter) throws IOException {
        client.setConnectTimeout(1000);
        client.changeWorkingDirectory(SUBSTANCES_DIR);
        DefaultRecordStreamer result = new DefaultRecordStreamer(getStream(beginAfter));
        String key = "PUBCHEM_SUBSTANCE_ID";

        for (Record record : result) {
            int sid = 0;

            try {
                sid = Integer.parseInt(record.get(key));
            } catch (Exception e) {
                continue;
            }

            if (sid >= beginAfter) {
                break;
            }
        }

        return result;
    }

    public boolean completePendingCommand() throws IOException {
        return client.completePendingCommand();
    }

    public InputStream getStream() throws IOException {
        return new SequenceInputStream(new StreamEnumerator(getFilenames()));
    }

    private List<String> getFilenames() throws IOException {
        List<String> result = new ArrayList();
        String[] names = client.listNames();

        for (String name : names) {
            if (name.matches(".*\\.sdf\\.gz")) {
                result.add(name);
            }
        }

        Collections.sort(result);

        return result;
    }

    private InputStream getStream(int beginAfter) throws IOException {
        //    Compound_00000001_00025000.sdf.gz
        Pattern pattern = Pattern.compile("^(Substance|Compound)_(\\d{8})_(\\d{8})\\.sdf\\.gz");
        List<String> filenames = getFilenames();
        List<String> keep = new ArrayList();
        boolean check = true;

        for (String name : filenames) {
            Matcher matcher = pattern.matcher(name);

            if (matcher.matches()) {
                if (check) {
                    int start = Integer.parseInt(matcher.group(2));
                    int end = Integer.parseInt(matcher.group(3));

                    if (beginAfter >= start && beginAfter <= end) {
                        keep.add(name);
                        check = false;
                    }
                } else {
                    keep.add(name);
                }
            }
        }

        return new SequenceInputStream(new StreamEnumerator(keep));
    }

    private class StreamEnumerator implements Enumeration<InputStream> {
        private List<String> filenames;
        private int index;

        private StreamEnumerator(List<String> filenames) {
            this.filenames = filenames;
            this.index = 0;
        }

        public boolean hasMoreElements() {
            return index < filenames.size();
        }

        public InputStream nextElement() {
            System.out.println("loading next stream...");
            try {
                if (index != 0) {
                    System.out.println("complete pending");
                    Thread.sleep(1000);
                    client.completePendingCommand();
                    System.out.println("done");
                }
            } catch (Exception e) {
                e.printStackTrace();
            }
            InputStream result = null;

            try {
                client.setFileType(FTP.BINARY_FILE_TYPE);
                result = new GZIPInputStream(client.retrieveFileStream(filenames.get(index)));
            } catch (IOException e) {
                throw new RuntimeException(e);
            }

            index++;

            System.out.println("done");

            return result;
        }
    }
}