edu.mayo.mprc.mascot.MascotWorkPacket.java Source code

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Here is the source code for edu.mayo.mprc.mascot.MascotWorkPacket.java

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package edu.mayo.mprc.mascot;

import com.google.common.base.Charsets;
import com.google.common.io.Files;
import edu.mayo.mprc.daemon.worker.WorkPacket;
import edu.mayo.mprc.searchengine.EngineWorkPacket;
import edu.mayo.mprc.searchengine.SearchEngineResult;
import edu.mayo.mprc.utilities.progress.ProgressReporter;
import org.apache.log4j.Logger;

import java.io.File;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import java.util.regex.Pattern;

/**
 * Defines a Mascot search.
 */
public final class MascotWorkPacket extends EngineWorkPacket {
    private static final Logger LOGGER = Logger.getLogger(MascotWorkPacket.class);

    private static final long serialVersionUID = 20090402L;
    private String shortDbName;

    // USERNAME, USEREMAIL and LICENSE fields do not influence the result
    private static final Pattern DELETE_HEADERS = Pattern.compile("(?<=\n)(LICENSE|USERNAME|USEREMAIL)=[^\n]*\n");

    public static final String MASCOT_URL_FILENAME = "mascot_url.txt";

    public MascotWorkPacket(final boolean fromScratch) {
        super(fromScratch);
    }

    public MascotWorkPacket(final File outputFile, final String searchParams, final File inputFile,
            final String shortDbName, final boolean fromScratch, final boolean publishSearchFiles) {
        super(inputFile, outputFile, searchParams, null, publishSearchFiles, fromScratch);

        assert inputFile != null : "Mascot request cannot be created: The input file was null";
        assert shortDbName != null : "Mascot request cannot be created: Short database name was null";
        assert outputFile != null : "Mascot request cannot be created: The output file was null";
        assert searchParams != null : "Mascot request cannot be created: The search params have to be set";

        this.shortDbName = shortDbName;
    }

    public String getShortDbName() {
        return shortDbName;
    }

    @Override
    public String getStringDescriptionOfTask() {
        final StringBuilder description = new StringBuilder(100);
        String paramString = getSearchParams();
        paramString = DELETE_HEADERS.matcher(paramString).replaceAll("");
        description.append("Input:").append(getInputFile().getAbsolutePath()).append('\n').append("Database:")
                .append(getShortDbName()).append('\n').append("ParamFile:\n---\n").append(paramString)
                .append("---\n");
        return description.toString();
    }

    @Override
    public WorkPacket translateToCachePacket(final File cacheFolder) {
        return new MascotWorkPacket(canonicalOutput(cacheFolder), getSearchParams(), getInputFile(),
                getShortDbName(), isFromScratch(), false);
    }

    @Override
    public List<String> getOutputFiles() {
        return Arrays.asList(getOutputFile().getName(), MASCOT_URL_FILENAME);
    }

    @Override
    public void reportCachedResult(final ProgressReporter reporter, final File targetFolder,
            final List<String> outputFiles) {
        final File mascotUrlFile = new File(targetFolder, outputFiles.get(1));
        if (mascotUrlFile.exists()) {
            try {
                final String mascotUrl = Files.toString(mascotUrlFile, Charsets.UTF_8);
                reporter.reportProgress(new MascotResultUrl(mascotUrl));
            } catch (IOException ignore) {
                // SWALLOWED: not a big deal if we cannot report the mascot url
                LOGGER.warn("Cache could not find mascot URL information: " + mascotUrlFile.getAbsolutePath());
            }
        }

        reporter.reportProgress(new SearchEngineResult(new File(targetFolder, outputFiles.get(0))));
    }

}