edu.scripps.fl.pubchem.PubChemFactory.java Source code

Introduction

Here is the source code for edu.scripps.fl.pubchem.PubChemFactory.java

Source

/*
 * Copyright 2010 The Scripps Research Institute
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package edu.scripps.fl.pubchem;

import java.io.IOException;
import java.io.InputStream;
import java.util.zip.GZIPInputStream;

import org.apache.commons.vfs.FileObject;
import org.apache.commons.vfs.VFS;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/*
 * @author Mark Southern (southern at scripps dot edu)
 */
public class PubChemFactory {

    private static final Logger log = LoggerFactory.getLogger(PubChemFactory.class);

    private static final String ftpUser = "anonymous";
    private static final String ftpPass = "scripps.edu";
    private static final String ftpHost = "ftp.ncbi.nlm.nih.gov";
    private static final String pubchemBioAssayUrlFormat = "ftp://%s:%s@ftp.ncbi.nlm.nih.gov/pubchem/Bioassay/CSV/%s/%s.zip";

    private static PubChemFactory instance;

    private PubChemFactory() {
    }

    public static PubChemFactory getInstance() {
        if (instance == null) {
            synchronized (PubChemFactory.class) { // 1
                if (instance == null) {
                    synchronized (PubChemFactory.class) { // 3
                        // inst = new Singleton(); //4
                        instance = new PubChemFactory();
                    }
                    // instance = inst; //5
                }
            }
        }
        return instance;
    }

    protected static String getAIDArchive(long aid) {
        long low = nextLowestMultiple(aid, 1000);
        return String.format("%07d_%07d", low + 1, low + 1000);
    }

    // http://mindprod.com/jgloss/round.html
    // rounding m down to multiple of n
    protected static long nextLowestMultiple(long m, long n) {
        long floor = m / n * n;
        return floor;
    }

    public InputStream getPubChemXmlDesc(long aid) throws IOException {
        String archive = getAIDArchive(aid);
        String sUrl = String.format(pubchemBioAssayUrlFormat, ftpUser, ftpPass, "Description", archive);
        String szip = String.format("zip:%s!/%s/%s.descr.xml.gz", sUrl, archive, aid);
        log.debug(sUrl);
        FileObject fo = VFS.getManager().resolveFile(szip);
        log.debug("Resolved file: " + szip);
        try {
            InputStream is = fo.getContent().getInputStream();
            return new GZIPInputStream(is);
        } catch (Exception e) {
            log.info("AID: " + aid + " is not in the ftp site.", e.getMessage());
            return null;
        }
    }

    public InputStream getPubChemCsv(long aid) throws IOException {
        String archive = getAIDArchive(aid);
        String sUrl = String.format(pubchemBioAssayUrlFormat, ftpUser, ftpPass, "Data", archive);
        String szip = String.format("zip:%s!/%s/%s.csv.gz", sUrl, archive, aid);
        log.debug(sUrl);
        FileObject fo = VFS.getManager().resolveFile(szip);
        log.debug("Resolved file: " + szip);
        InputStream is = fo.getContent().getInputStream();
        return new GZIPInputStream(is);
    }

}