edu.umn.msi.tropix.proteomics.idpicker.impl.IdPickerJobProcessorImpl.java Source code

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Here is the source code for edu.umn.msi.tropix.proteomics.idpicker.impl.IdPickerJobProcessorImpl.java

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/********************************************************************************
 * Copyright (c) 2009 Regents of the University of Minnesota
 *
 * This Software was written at the Minnesota Supercomputing Institute
 * http://msi.umn.edu
 *
 * All rights reserved. The following statement of license applies
 * only to this file, and and not to the other files distributed with it
 * or derived therefrom.  This file is made available under the terms of
 * the Eclipse Public License v1.0 which accompanies this distribution,
 * and is available at http://www.eclipse.org/legal/epl-v10.html
 *
 * Contributors:
 * Minnesota Supercomputing Institute - initial API and implementation
 *******************************************************************************/

package edu.umn.msi.tropix.proteomics.idpicker.impl;

import java.io.OutputStream;
import java.util.Iterator;
import java.util.List;
import java.util.Properties;

import org.globus.exec.generated.JobDescriptionType;

import com.google.common.base.Preconditions;
import com.google.common.collect.Iterables;
import com.google.common.collect.Lists;

import edu.umn.msi.tropix.common.io.InputContext;
import edu.umn.msi.tropix.common.io.PropertiesUtils;
import edu.umn.msi.tropix.common.io.PropertiesUtilsFactory;
import edu.umn.msi.tropix.common.io.ZipUtils;
import edu.umn.msi.tropix.common.io.ZipUtilsFactory;
import edu.umn.msi.tropix.common.jobqueue.jobprocessors.BaseExecutableJobProcessorImpl;
import edu.umn.msi.tropix.proteomics.idpicker.parameters.IdPickerParameters;

class IdPickerJobProcessorImpl extends BaseExecutableJobProcessorImpl {
    private static final ZipUtils ZIP_UTILS = ZipUtilsFactory.getInstance();
    private static final PropertiesUtils PROPERTIES_UTILS = PropertiesUtilsFactory.getInstance();
    private static final String DATABASE_PATH = "db.fasta";
    private Iterable<InputContext> pepXmlContexts;
    private InputContext databaseContext;
    private IdPickerParameters parameters;
    private FileMaskCreator fileMaskCreator;

    @Override
    protected void doPreprocessing() {
        databaseContext.get(getStagingDirectory().getOutputContext(DATABASE_PATH));

        fileMaskCreator = new FileMaskCreator(parameters);

        writeSampleDirectories();
        savePepXmlFiles();
        getStagingDirectory().getOutputContext("idpQonvert-files")
                .put(fileMaskCreator.getQonvertLines().getBytes());
        getStagingDirectory().getOutputContext("idpAssemble-files")
                .put(fileMaskCreator.getAssembleLines().getBytes());
        writeQonvertCfg();
        writeAssembleCfg();
        writeReportCfg();
        final JobDescriptionType jobDescription = getJobDescription().getJobDescriptionType();
        final List<String> arguments = Lists.newArrayList();
        jobDescription.setArgument(Iterables.toArray(arguments, String.class));
        jobDescription.setDirectory(getStagingDirectory().getAbsolutePath());
    }

    private void writeSampleDirectories() {
        for (final String sampleName : fileMaskCreator.getSampleNames()) {
            getStagingDirectory().makeDirectory(sampleName);
        }
    }

    private void putProperties(final Properties properties, final String name, final String value) {
        if (value != null) {
            properties.put(name, value);
        }
    }

    private void putProperties(final Properties properties, final String name, final Boolean value) {
        putProperties(properties, name, value == null ? null : Boolean.toString(value));
    }

    private void putProperties(final Properties properties, final String name, final Double value) {
        putProperties(properties, name, value == null ? null : Double.toString(value));
    }

    private void putProperties(final Properties properties, final String name, final Integer value) {
        putProperties(properties, name, value == null ? null : Integer.toString(value));
    }

    private void writeQonvertCfg() {
        final Properties properties = new Properties();
        putProperties(properties, "ProteinDatabase", DATABASE_PATH);
        putProperties(properties, "PreserveInputHierarchy", "true");
        putProperties(properties, "HasDecoyDatabase", parameters.getHasDecoyDatabase());
        if (parameters.getDecoyPrefix() != null) {
            putProperties(properties, "DecoyPrefix", parameters.getDecoyPrefix());
        }
        putProperties(properties, "NormalizeSearchScores", parameters.getNormalizeSearchScores());
        putProperties(properties, "OptimizeScoreWeights", parameters.getOptimizeScoreWeights());
        putProperties(properties, "MaxFDR", parameters.getMaxFDRQonvert());
        putProperties(properties, "MaxResultRank", parameters.getMaxResultRank());
        putProperties(properties, "OptimizeScorePermutations", parameters.getOptimizeScorePermutations());
        getStagingDirectory().getOutputContext("idpQonvert.cfg")
                .put(PROPERTIES_UTILS.toString(properties).getBytes());
    }

    private void writeAssembleCfg() {
        final Properties properties = new Properties();
        putProperties(properties, "MaxFDR", parameters.getMaxFDRAssemble());
        putProperties(properties, "MaxResultRank", parameters.getMaxResultRank());
        getStagingDirectory().getOutputContext("idpAssemble.cfg")
                .put(PROPERTIES_UTILS.toString(properties).getBytes());
    }

    private void writeReportCfg() {
        final Properties properties = new Properties();
        putProperties(properties, "MinDistinctPeptides", parameters.getMinDistinctPeptides());
        putProperties(properties, "MaxAmbiguousIds", parameters.getMaxAmbiguousIds());
        putProperties(properties, "MaxFDR", parameters.getMaxFDRReport());
        putProperties(properties, "MinAdditionalPeptides", parameters.getMinAdditionalPeptides());
        putProperties(properties, "MaxResultRank", parameters.getMaxResultRank());
        getStagingDirectory().getOutputContext("idpReport.cfg")
                .put(PROPERTIES_UTILS.toString(properties).getBytes());
    }

    @Override
    protected void doPostprocessing() {
        if (wasCompletedNormally()) {
            getResourceTracker().add(getStagingDirectory().getInputContext("combined-sources.xml"));
            final OutputStream zipOutputStream = getResourceTracker().newStream();
            ZIP_UTILS.zipDirectory(getStagingDirectory(), "combined-sources", zipOutputStream);
        }
    }

    private void savePepXmlFiles() {
        final Iterator<String> inputPathsIter = fileMaskCreator.getPepXmlPaths(getStagingDirectory().getSep())
                .iterator();
        for (InputContext pepXmlContext : pepXmlContexts) {
            Preconditions.checkState(inputPathsIter.hasNext());
            final String name = inputPathsIter.next();
            pepXmlContext.get(getStagingDirectory().getOutputContext(name));
        }
    }

    public void setPepXmlContexts(final Iterable<InputContext> pepXmlContexts) {
        this.pepXmlContexts = pepXmlContexts;
    }

    public void setDatabaseContext(final InputContext databaseContext) {
        this.databaseContext = databaseContext;
    }

    public void setParameters(final IdPickerParameters parameters) {
        this.parameters = parameters;
    }
}