edu.umn.msi.tropix.galaxy.service.GalaxyJobProcessorImpl.java Source code

Introduction

Here is the source code for edu.umn.msi.tropix.galaxy.service.GalaxyJobProcessorImpl.java

Source

/********************************************************************************
 * 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.galaxy.service;

import java.util.Iterator;

import org.apache.commons.io.FilenameUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.globus.exec.generated.JobDescriptionType;
import org.springframework.util.StringUtils;

import com.google.common.base.Preconditions;

import edu.umn.msi.tropix.common.io.InputContext;
import edu.umn.msi.tropix.common.io.InputContexts;
import edu.umn.msi.tropix.common.io.OutputContext;
import edu.umn.msi.tropix.common.jobqueue.jobprocessors.BaseExecutableJobProcessorFactoryImpl;
import edu.umn.msi.tropix.common.jobqueue.jobprocessors.BaseExecutableJobProcessorImpl;
import edu.umn.msi.tropix.common.xml.XMLUtility;
import edu.umn.msi.tropix.galaxy.inputs.RootInput;
import edu.umn.msi.tropix.galaxy.tool.ConfigFile;
import edu.umn.msi.tropix.galaxy.tool.Data;
import edu.umn.msi.tropix.galaxy.tool.Tool;
import edu.umn.msi.tropix.galaxy.xml.GalaxyXmlUtils;

class GalaxyJobProcessorImpl extends BaseExecutableJobProcessorImpl {
    private static final Log LOG = LogFactory.getLog(GalaxyJobProcessorImpl.class);
    private final GalaxyConverter galaxyConverter;
    private Iterable<InputContext> inputContexts;
    private Iterable<String> fileNames;
    private Tool tool;
    private RootInput rootInput;
    private ToolEvaluator toolEvaluator;

    GalaxyJobProcessorImpl(final GalaxyConverter galaxyConverter) {
        this.galaxyConverter = galaxyConverter;
    }

    void setInputContext(final Iterable<InputContext> inputContexts) {
        this.inputContexts = inputContexts;
    }

    void setFileNames(final Iterable<String> fileNames) {
        this.fileNames = fileNames;
    }

    void setTool(final Tool tool) {
        this.tool = tool;
    }

    void setRootInput(final RootInput rootInput) {
        this.rootInput = rootInput;
    }

    @Override
    protected void doPreprocessing() {
        final Iterator<String> fileNameIterator = fileNames.iterator();
        final Iterator<InputContext> inputContextsIterator = inputContexts.iterator();
        while (fileNameIterator.hasNext()) {
            Preconditions.checkState(inputContextsIterator.hasNext());
            final String fileName = fileNameIterator.next();
            LOG.debug(String.format("In preprocessing with filename %s", fileName));
            // Verify this write attempt isn't trying to write outside the specified staging directory.
            // Later this should be modified to let subdirectories be written.
            Preconditions.checkState(FilenameUtils.getName(fileName).equals(fileName));
            final OutputContext outputContext = getStagingDirectory().getOutputContext(fileName);
            inputContextsIterator.next().get(outputContext);
        }
        if (LOG.isDebugEnabled()) {
            LOG.debug("Pre Expanded Galaxy Tool");
            LOG.debug(GalaxyXmlUtils.serialize(tool));
            LOG.debug("RootInput");
            LOG.debug(GalaxyXmlUtils.serialize(rootInput));
        }
        final Context context = Contexts.expandPathsAndBuildContext(tool, rootInput, getStagingDirectory());
        toolEvaluator.resolve(tool, context);
        if (LOG.isDebugEnabled()) {
            LOG.debug("Expanded Galaxy Tool");
            LOG.debug(new XMLUtility<Tool>(Tool.class).toString(tool));
        }
        if (tool.getConfigfiles() != null) {
            for (final ConfigFile configFile : tool.getConfigfiles().getConfigfile()) {
                final String configFileName = configFile.getName();
                Preconditions.checkState(FilenameUtils.getName(configFileName).equals(configFileName));
                getStagingDirectory().getOutputContext(configFileName).put(configFile.getValue().getBytes());
            }
        }
        final JobDescriptionType jobDescription = getJobDescription().getJobDescriptionType();
        jobDescription.setDirectory(getStagingDirectory().getAbsolutePath());
        galaxyConverter.populateJobDescription(jobDescription, tool);
    }

    @Override
    protected void doPostprocessing() {
        if (wasCompletedNormally()) {
            final String standardError = InputContexts.toString(getStagingDirectory()
                    .getInputContext(BaseExecutableJobProcessorFactoryImpl.DEFAULT_STANDARD_ERROR_FILE_NAME));
            if (StringUtils.hasText(standardError)) {
                throw new IllegalStateException(
                        String.format("Problem executing galaxy tool, standard error was %s", standardError));
            }
        }
        for (final Data output : tool.getOutputs().getData()) {
            final InputContext inputContext = getStagingDirectory().getInputContext(output.getName());
            getResourceTracker().add(inputContext);
        }
    }

    public void setToolEvaluator(final ToolEvaluator toolEvaluator) {
        this.toolEvaluator = toolEvaluator;
    }

}