org.ensembl.gti.seqstore.TestSeqStore.java Source code

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Here is the source code for org.ensembl.gti.seqstore.TestSeqStore.java

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/*
 * Copyright 2015 EMBL-European Bioinformatics 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 org.ensembl.gti.seqstore;

import java.io.BufferedReader;
import java.io.FileInputStream;
import java.io.FileReader;
import java.io.InputStreamReader;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Properties;
import java.util.zip.GZIPInputStream;

import org.apache.commons.lang.time.StopWatch;
import org.ensembl.gti.seqstore.database.EnaCramSeqStore;
import org.ensembl.gti.seqstore.database.JdbcSeqStore;
import org.ensembl.gti.seqstore.database.SeqStore;
import org.ensembl.gti.seqstore.database.cramstore.EnaCramSubmissionHandler;
import org.ensembl.gti.seqstore.server.MetaDataServer;
import org.ensembl.gti.seqstore.server.MetaDataServer.MetaDataServerOptions;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import com.beust.jcommander.JCommander;
import com.beust.jcommander.Parameter;

public class TestSeqStore {

    public static class TestSeqStoreOpts extends MetaDataServerOptions {

        public TestSeqStoreOpts() {
        }

        public TestSeqStoreOpts(Properties properties) {
            super(properties);
        }

        @Parameter(names = { "-implementation", "-i" }, description = "Implementation")
        private String implementation = "jdbc";

        @Parameter(names = { "-files", "-f" }, description = "Sequence files", required = true)
        private List<String> files;

        public String getImplementation() {
            return implementation;
        }

        public void setImplementation(String implementation) {
            this.implementation = implementation;
        }

        public List<String> getFiles() {
            return files;
        }

        public void setFiles(List<String> files) {
            this.files = files;
        }

    }

    public static final SeqStore buildSeqStore(TestSeqStoreOpts opts) {
        SeqStore store = null;
        switch (opts.getImplementation()) {
        case "jdbc":
            store = new JdbcSeqStore(
                    MetaDataServer.buildDataSource(opts.getDbUri(), opts.getDbUser(), opts.getDbPass()));
            break;
        case "ena":
            store = new EnaCramSeqStore(
                    MetaDataServer.buildDataSource(opts.getDbUri(), opts.getDbUser(), opts.getDbPass()),
                    new EnaCramSubmissionHandler(opts.getFtpUri(), opts.getSubmitUri(), opts.getCentre(),
                            opts.getSubmitUser(), opts.getSubmitPass()));
            break;
        }
        return store;
    }

    public static void main(String[] args) throws Exception {
        TestSeqStoreOpts opts = new TestSeqStoreOpts();
        new JCommander(opts, args);
        Logger log = LoggerFactory.getLogger(TestSeqStore.class);
        log.info("Building store " + opts.getImplementation());
        SeqStore store = buildSeqStore(opts);
        log.info("Built store of type " + store.getClass().getSimpleName() + ": starting session");
        long sessionId = store.startSession("testseqstore");
        StopWatch watch = new StopWatch();
        Map<String, Long> times = new HashMap<>();
        for (String file : opts.getFiles()) {
            log.info("Processing " + file);
            long time = 0;
            int n = 0;
            BufferedReader reader = null;
            if (file.endsWith(".gz")) {
                reader = new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(file))));
            } else {
                reader = new BufferedReader(new FileReader(file));
            }
            String line;
            StringBuilder seq = null;
            while ((line = reader.readLine()) != null) {
                if (line.charAt(0) == '>') {
                    n++;
                    time += processSeq(watch, seq, store, sessionId);
                    seq = new StringBuilder();
                } else if (seq != null) {
                    seq.append(line.trim());
                }
            }
            n++;
            time += processSeq(watch, seq, store, sessionId);
            reader.close();
            times.put(file, time);
            double secs = 1.0 * time / 1000;
            log.info(String.format("Completed processing %s: %d sequences in %.3f s (%.3f seq/s) ", file, n, secs,
                    n / secs));
        }
        log.info("Completed test");

    }

    private static long processSeq(StopWatch watch, StringBuilder seq, SeqStore store, long sessionId) {
        long time = 0;
        if (seq != null && seq.length() > 0) {
            String str = seq.toString();
            watch.reset();
            watch.start();
            store.storeSequence(sessionId, str);
            watch.stop();
            time = watch.getTime();
        }
        return time;
    }

}