Example usage for org.apache.hadoop.mapreduce TaskInputOutputContext getConfiguration

List of usage examples for org.apache.hadoop.mapreduce TaskInputOutputContext getConfiguration

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Introduction

In this page you can find the example usage for org.apache.hadoop.mapreduce TaskInputOutputContext getConfiguration.

Prototype

public Configuration getConfiguration();

Source Link

Document

Return the configuration for the job.

Usage

From source file:Payload.java

License:Open Source License

/** Shadow setup function
 *///from  w  w w. j  a v  a  2  s. co  m
private static void setup(TaskInputOutputContext task, String name) throws IOException {
    script = new Script();
    EggGlobal.script = script;
    EggIterator.script = script;
    EggContext.task = task;

    Scriptable global = script.newObject("EggGlobal", null);
    script.setGlobalScope(global);
    thisObj = script.newObject("EggContext", null);

    Object o = script.deserialize(task.getConfiguration(), name);
    if (o instanceof NativeObject) {
        NativeObject obj = (NativeObject) o;
        fmap = (Function) script.getProperty("map", obj);
        freduce = (Function) script.getProperty("reduce", obj);
        fsetup = (Function) script.getProperty("setup", obj);
        fcleanup = (Function) script.getProperty("cleanup", obj);
        if (fsetup != null)
            script.callFunction(fsetup, thisObj, null);
    } else if (o instanceof Function) {
        fmapred = (Function) o;
    }
}

From source file:be.ugent.intec.halvade.utils.HalvadeFileUtils.java

License:Open Source License

public static String downloadGFF(TaskInputOutputContext context, String id)
        throws IOException, URISyntaxException, InterruptedException {
    Configuration conf = context.getConfiguration();
    String refDir = HalvadeConf.getRefDirOnScratch(conf);
    String gff = HalvadeConf.getGff(context.getConfiguration());
    if (gff == null)
        return null;
    String gffSuffix = null;//ww  w.  j  av a  2s .  c o  m
    int si = gff.lastIndexOf('.');
    if (si > 0)
        gffSuffix = gff.substring(si);
    else
        throw new InterruptedException("Illegal filename for gff file: " + gff);
    Logger.DEBUG("suffix: " + gffSuffix);
    if (!refDir.endsWith("/"))
        refDir = refDir + "/";
    HalvadeFileLock lock = new HalvadeFileLock(context, refDir, GFF_LOCK);
    String gffFile = null;
    try {
        lock.getLock();

        ByteBuffer bytes = ByteBuffer.allocate(4);
        if (lock.read(bytes) > 0) {
            bytes.flip();
            long val = bytes.getInt();
            if (val == DEFAULT_LOCK_VAL)
                Logger.DEBUG("gff has been downloaded to local scratch: " + val);
            else {
                Logger.INFO("downloading missing gff file to local scratch");
                FileSystem fs = FileSystem.get(new URI(gff), conf);
                gffFile = findFile(refDir, gffSuffix, false);
                if (gffFile == null)
                    gffFile = refDir + id;

                attemptDownloadFileFromHDFS(context, fs, gff, gffFile + gffSuffix, RETRIES);
                Logger.INFO("FINISHED downloading the complete reference index to local scratch");
                bytes.clear();
                bytes.putInt(DEFAULT_LOCK_VAL).flip();
                lock.forceWrite(bytes);
            }
        } else {
            Logger.INFO("downloading missing gff file to local scratch");
            Logger.DEBUG("gff file: " + gff);
            FileSystem fs = FileSystem.get(new URI(gff), conf);
            gffFile = findFile(refDir, gffSuffix, false);
            if (gffFile == null)
                gffFile = refDir + id;
            attemptDownloadFileFromHDFS(context, fs, gff, gffFile + gffSuffix, RETRIES);
            Logger.INFO("FINISHED downloading the complete reference index to local scratch");
            bytes.clear();
            bytes.putInt(DEFAULT_LOCK_VAL).flip();
            lock.forceWrite(bytes);
        }

    } catch (InterruptedException ex) {
        Logger.EXCEPTION(ex);
    } finally {
        lock.releaseLock();
    }
    if (gffFile == null)
        gffFile = findFile(refDir, gffSuffix, false);
    return gffFile + gffSuffix;

}

From source file:be.ugent.intec.halvade.utils.HalvadeFileUtils.java

License:Open Source License

protected static String downloadAlignerIndex(TaskInputOutputContext context, String id, String refName,
        String refSuffix, String[] refFiles) throws IOException, URISyntaxException {
    Configuration conf = context.getConfiguration();
    String refDir = HalvadeConf.getRefDirOnScratch(conf);
    if (!refDir.endsWith("/"))
        refDir = refDir + "/";
    HalvadeFileLock lock = new HalvadeFileLock(context, refDir, REF_LOCK);
    String refBase = null;/* w  w w. j a  v a 2  s  .c o  m*/
    try {
        lock.getLock();

        ByteBuffer bytes = ByteBuffer.allocate(4);
        if (lock.read(bytes) > 0) {
            bytes.flip();
            long val = bytes.getInt();
            if (val == REF_BOTH)
                Logger.DEBUG("reference has been downloaded to local scratch: " + val);
            else {
                Logger.INFO("downloading missing reference index files to local scratch");
                String HDFSRef = HalvadeConf.getRefOnHDFS(conf);
                FileSystem fs = FileSystem.get(new URI(HDFSRef), conf);
                refBase = findFile(refDir, refSuffix, false); // refSuffix = HALVADE_BWA_SUFFIX
                boolean foundExisting = (refBase != null);
                if (!foundExisting)
                    refBase = refDir + refName + id; // refName = bwa_ref-

                for (String suffix : refFiles) { //  refFiles = BWA_REF_FILES
                    attemptDownloadFileFromHDFS(context, fs, HDFSRef + suffix, refBase + suffix, RETRIES);
                }
                Logger.INFO("FINISHED downloading the complete reference index to local scratch");
                if (!foundExisting) {
                    File f = new File(refBase + refSuffix);
                    f.createNewFile();
                    f = new File(refBase + HALVADE_GATK_SUFFIX);
                    f.createNewFile();
                }
                bytes.clear();
                bytes.putInt(REF_BOTH).flip();
                lock.forceWrite(bytes);
            }
        } else {
            Logger.INFO("downloading missing reference index files to local scratch");
            String HDFSRef = HalvadeConf.getRefOnHDFS(conf);
            FileSystem fs = FileSystem.get(new URI(HDFSRef), conf);
            refBase = findFile(refDir, refSuffix, false);
            boolean foundExisting = (refBase != null);
            if (!foundExisting)
                refBase = refDir + refName + id;

            for (String suffix : refFiles) {
                attemptDownloadFileFromHDFS(context, fs, HDFSRef + suffix, refBase + suffix, RETRIES);
            }
            Logger.INFO("FINISHED downloading the complete reference index to local scratch");
            if (!foundExisting) {
                File f = new File(refBase + refSuffix);
                f.createNewFile();
                f = new File(refBase + HALVADE_GATK_SUFFIX);
                f.createNewFile();
            }
            bytes.clear();
            bytes.putInt(REF_BOTH).flip();
            lock.forceWrite(bytes);
        }

    } catch (InterruptedException ex) {
        Logger.EXCEPTION(ex);
    } finally {
        lock.releaseLock();
    }
    if (refBase == null)
        refBase = findFile(refDir, refSuffix, false);
    return refBase + refFiles[0];
}

From source file:be.ugent.intec.halvade.utils.HalvadeFileUtils.java

License:Open Source License

public static String downloadGATKIndex(TaskInputOutputContext context, String id)
        throws IOException, URISyntaxException {
    Configuration conf = context.getConfiguration();
    String tmpDir = HalvadeConf.getScratchTempDir(conf);
    String refDir = HalvadeConf.getRefDirOnScratch(conf);
    if (!refDir.endsWith("/"))
        refDir = refDir + "/";
    HalvadeFileLock lock = new HalvadeFileLock(context, refDir, REF_LOCK);
    String refBase = null;//from  w  w w  .ja  v  a  2s.  co  m
    try {
        lock.getLock();

        ByteBuffer bytes = ByteBuffer.allocate(4);
        if (lock.read(bytes) > 0) {
            bytes.flip();
            long val = bytes.getInt();
            if (val == REF_BOTH || val == DEFAULT_LOCK_VAL)
                Logger.DEBUG("reference has been downloaded to local scratch: " + val);
            else {
                Logger.INFO("downloading missing reference index files to local scratch");
                String HDFSRef = HalvadeConf.getRefOnHDFS(conf);
                FileSystem fs = FileSystem.get(new URI(HDFSRef), conf);
                refBase = findFile(refDir, HALVADE_GATK_SUFFIX, false);
                boolean foundExisting = (refBase != null);
                if (!foundExisting)
                    refBase = refDir + "bwa_ref-" + id;

                for (String suffix : GATK_REF_FILES) {
                    attemptDownloadFileFromHDFS(context, fs, HDFSRef + suffix, refBase + suffix, RETRIES);
                }
                Logger.INFO("FINISHED downloading the complete reference index to local scratch");
                if (!foundExisting) {
                    File f = new File(refBase + HALVADE_GATK_SUFFIX);
                    f.createNewFile();
                }
                bytes.clear();
                bytes.putInt(DEFAULT_LOCK_VAL).flip();
                lock.forceWrite(bytes);
            }
        } else {
            Logger.INFO("downloading missing reference index files to local scratch");
            String HDFSRef = HalvadeConf.getRefOnHDFS(conf);
            FileSystem fs = FileSystem.get(new URI(HDFSRef), conf);
            refBase = findFile(refDir, HALVADE_GATK_SUFFIX, false);
            boolean foundExisting = (refBase != null);
            if (!foundExisting)
                refBase = refDir + "bwa_ref-" + id;

            for (String suffix : GATK_REF_FILES) {
                attemptDownloadFileFromHDFS(context, fs, HDFSRef + suffix, refBase + suffix, RETRIES);
            }
            Logger.INFO("FINISHED downloading the complete reference index to local scratch");
            if (!foundExisting) {
                File f = new File(refBase + HALVADE_GATK_SUFFIX);
                f.createNewFile();
            }
            bytes.clear();
            bytes.putInt(DEFAULT_LOCK_VAL).flip();
            lock.forceWrite(bytes);
        }

    } catch (InterruptedException ex) {
        Logger.EXCEPTION(ex);
    } finally {
        lock.releaseLock();
    }
    if (refBase == null)
        refBase = findFile(refDir, HALVADE_GATK_SUFFIX, false);
    return refBase + GATK_REF_FILES[0];
}

From source file:be.ugent.intec.halvade.utils.HalvadeFileUtils.java

License:Open Source License

public static String downloadSTARIndex(TaskInputOutputContext context, String id, boolean usePass2Genome)
        throws IOException, URISyntaxException {
    Configuration conf = context.getConfiguration();
    String tmpDir = HalvadeConf.getScratchTempDir(conf);
    String refDir = HalvadeConf.getRefDirOnScratch(conf);
    if (!refDir.endsWith("/"))
        refDir = refDir + "/";
    HalvadeFileLock lock = new HalvadeFileLock(context, tmpDir, STARG_LOCK);
    String refBase = null;//from www .  j  av a2 s . c  om
    try {
        lock.getLock();

        ByteBuffer bytes = ByteBuffer.allocate(4);
        if (lock.read(bytes) > 0) {
            bytes.flip();
            long val = bytes.getInt();
            if (val == DEFAULT_LOCK_VAL)
                Logger.DEBUG("reference has been downloaded to local scratch: " + val);
            else {
                Logger.INFO("downloading missing reference index files to local scratch");
                if (usePass2Genome)
                    Logger.DEBUG("using Pass2 genome");
                String HDFSRef = usePass2Genome ? HalvadeConf.getStarDirPass2HDFS(conf)
                        : HalvadeConf.getStarDirOnHDFS(conf);
                Logger.DEBUG("downloading STAR genome from: " + HDFSRef);
                FileSystem fs = FileSystem.get(new URI(HDFSRef), conf);
                refBase = findFile(refDir, usePass2Genome ? HALVADE_STAR_SUFFIX_P2 : HALVADE_STAR_SUFFIX_P1,
                        true);
                boolean foundExisting = (refBase != null);
                if (!foundExisting) {
                    refBase = refDir + id + "-star/";
                    //make dir
                    File makeRefDir = new File(refBase);
                    makeRefDir.mkdir();
                }
                Logger.DEBUG("STAR dir: " + refBase);
                if (!usePass2Genome) {
                    for (String suffix : STAR_REF_FILES) {
                        attemptDownloadFileFromHDFS(context, fs, HDFSRef + suffix, refBase + suffix, RETRIES);
                    }
                    for (String suffix : STAR_REF_OPTIONAL_FILES) {
                        if (fs.exists(new Path(HDFSRef + suffix)))
                            attemptDownloadFileFromHDFS(context, fs, HDFSRef + suffix, refBase + suffix,
                                    RETRIES);
                    }
                }
                Logger.INFO("FINISHED downloading the complete reference index to local scratch");
                if (!foundExisting) {
                    File f = new File(
                            refBase + (usePass2Genome ? HALVADE_STAR_SUFFIX_P2 : HALVADE_STAR_SUFFIX_P1));
                    f.createNewFile();
                }
                bytes.clear();
                bytes.putInt(DEFAULT_LOCK_VAL).flip();
                lock.forceWrite(bytes);
            }
        } else {
            Logger.INFO("downloading missing reference index files to local scratch");
            if (usePass2Genome)
                Logger.DEBUG("using Pass2 genome");
            String HDFSRef = usePass2Genome ? HalvadeConf.getStarDirPass2HDFS(conf)
                    : HalvadeConf.getStarDirOnHDFS(conf);
            Logger.DEBUG("downloading STAR genome from: " + HDFSRef);
            FileSystem fs = FileSystem.get(new URI(HDFSRef), conf);
            refBase = findFile(refDir, usePass2Genome ? HALVADE_STAR_SUFFIX_P2 : HALVADE_STAR_SUFFIX_P1, true);
            boolean foundExisting = (refBase != null);
            if (!foundExisting) {
                refBase = refDir + id + "-star/";
                //make dir
                File makeRefDir = new File(refBase);
                makeRefDir.mkdir();
            }
            Logger.DEBUG("STAR dir: " + refBase);
            if (!usePass2Genome) {
                for (String suffix : STAR_REF_FILES) {
                    attemptDownloadFileFromHDFS(context, fs, HDFSRef + suffix, refBase + suffix, RETRIES);
                }
                for (String suffix : STAR_REF_OPTIONAL_FILES) {
                    if (fs.exists(new Path(HDFSRef + suffix)))
                        attemptDownloadFileFromHDFS(context, fs, HDFSRef + suffix, refBase + suffix, RETRIES);
                }
            }
            Logger.INFO("FINISHED downloading the complete reference index to local scratch");
            if (!foundExisting) {
                File f = new File(refBase + (usePass2Genome ? HALVADE_STAR_SUFFIX_P2 : HALVADE_STAR_SUFFIX_P1));
                f.createNewFile();
            }
            bytes.clear();
            bytes.putInt(DEFAULT_LOCK_VAL).flip();
            lock.forceWrite(bytes);
        }

    } catch (InterruptedException ex) {
        Logger.EXCEPTION(ex);
    } finally {
        lock.releaseLock();
    }
    if (refBase == null)
        refBase = findFile(refDir, usePass2Genome ? HALVADE_STAR_SUFFIX_P2 : HALVADE_STAR_SUFFIX_P1, true);
    return refBase;
}

From source file:be.ugent.intec.halvade.utils.HalvadeFileUtils.java

License:Open Source License

public static String[] downloadSites(TaskInputOutputContext context, String id)
        throws IOException, URISyntaxException, InterruptedException {
    Configuration conf = context.getConfiguration();
    String tmpDir = HalvadeConf.getScratchTempDir(conf);
    String refDir = HalvadeConf.getRefDirOnScratch(conf);
    String HDFSsites[] = HalvadeConf.getKnownSitesOnHDFS(conf);
    String[] localSites = new String[HDFSsites.length];
    if (!refDir.endsWith("/"))
        refDir = refDir + "/";
    HalvadeFileLock lock = new HalvadeFileLock(context, refDir, DBSNP_LOCK);
    String refBase = null;/*from  w w  w .  j a  v a2 s  .  com*/
    try {
        lock.getLock();

        ByteBuffer bytes = ByteBuffer.allocate(4);
        if (lock.read(bytes) > 0) {
            bytes.flip();
            long val = bytes.getInt();
            if (val == DEFAULT_LOCK_VAL)
                Logger.DEBUG("dbSNP has been downloaded to local scratch: " + val);
            else {
                Logger.INFO("downloading missing dbSNP to local scratch");
                refBase = findFile(refDir, HALVADE_DBSNP_SUFFIX, true);
                boolean foundExisting = (refBase != null);
                if (!foundExisting) {
                    refBase = refDir + id + "-dbsnp/";
                    //make dir
                    File makeRefDir = new File(refBase);
                    makeRefDir.mkdir();
                }
                Logger.DEBUG("dbSNP dir: " + refBase);

                for (int i = 0; i < HDFSsites.length; i++) {
                    String fullName = HDFSsites[i];
                    String name = fullName.substring(fullName.lastIndexOf('/') + 1);
                    Logger.DEBUG("Downloading " + name);
                    FileSystem fs = FileSystem.get(new URI(fullName), conf);
                    attemptDownloadFileFromHDFS(context, fs, fullName, refBase + name, RETRIES);
                    localSites[i] = refBase + name;
                    // attempt to download .idx file
                    if (!foundExisting && fs.exists(new Path(fullName + ".idx")))
                        attemptDownloadFileFromHDFS(context, fs, fullName + ".idx", refBase + name + ".idx",
                                RETRIES);
                }

                Logger.INFO("finished downloading the new sites to local scratch");
                if (!foundExisting) {
                    File f = new File(refBase + HALVADE_DBSNP_SUFFIX);
                    f.createNewFile();
                }
                bytes.clear();
                bytes.putInt(DEFAULT_LOCK_VAL).flip();
                lock.forceWrite(bytes);
            }
        } else {
            Logger.INFO("downloading missing dbSNP to local scratch");
            refBase = findFile(refDir, HALVADE_DBSNP_SUFFIX, true);
            boolean foundExisting = (refBase != null);
            if (!foundExisting) {
                refBase = refDir + id + "-dbsnp/";
                //make dir
                File makeRefDir = new File(refBase);
                makeRefDir.mkdir();
            }
            Logger.DEBUG("dbSNP dir: " + refBase);

            for (int i = 0; i < HDFSsites.length; i++) {
                String fullName = HDFSsites[i];
                String name = fullName.substring(fullName.lastIndexOf('/') + 1);
                Logger.DEBUG("Downloading " + name);
                FileSystem fs = FileSystem.get(new URI(fullName), conf);
                attemptDownloadFileFromHDFS(context, fs, fullName, refBase + name, RETRIES);
                localSites[i] = refBase + name;
                // attempt to download .idx file
                if (!foundExisting && fs.exists(new Path(fullName + ".idx")))
                    attemptDownloadFileFromHDFS(context, fs, fullName + ".idx", refBase + name + ".idx",
                            RETRIES);
            }

            Logger.INFO("finished downloading the new sites to local scratch");
            if (!foundExisting) {
                File f = new File(refBase + HALVADE_DBSNP_SUFFIX);
                f.createNewFile();
            }
            bytes.clear();
            bytes.putInt(DEFAULT_LOCK_VAL).flip();
            lock.forceWrite(bytes);
        }
    } catch (InterruptedException ex) {
        Logger.EXCEPTION(ex);
    } finally {
        lock.releaseLock();
    }
    if (refBase == null) {
        refBase = findFile(refDir, HALVADE_DBSNP_SUFFIX, true);
        File dir = new File(refBase);
        File[] directoryListing = dir.listFiles();
        if (directoryListing != null) {
            int found = 0;
            for (int i = 0; i < HDFSsites.length; i++) {
                String fullName = HDFSsites[i];
                String name = fullName.substring(fullName.lastIndexOf('/') + 1);
                localSites[i] = refBase + name;
                if ((new File(localSites[i])).exists())
                    found++;
                else
                    Logger.DEBUG(name + " not found in local scratch");
            }
            if (found != HDFSsites.length) {
                throw new IOException(
                        refBase + " has different number of files: " + found + " vs " + localSites.length);
            }
        } else {
            throw new IOException(refBase + " has no files");
        }
    }
    return localSites;
}

From source file:com.asakusafw.runtime.stage.output.StageOutputDriver.java

License:Apache License

private static Map<String, ResultOutput<?>> prepareSinks(TaskInputOutputContext<?, ?, ?, ?> context) {
    assert context != null;
    Map<String, ResultOutput<?>> results = new HashMap<>();
    Configuration conf = context.getConfiguration();
    for (String name : conf.getStringCollection(K_NAMES)) {
        results.put(name, null);//from w  ww.j a  v a  2s.com
    }
    return results;
}

From source file:com.cloudera.oryx.als.computation.iterate.row.YState.java

License:Open Source License

synchronized void initialize(TaskInputOutputContext<?, ?, ?, ?> context, int currentPartition,
        int numPartitions) {

    Configuration conf = context.getConfiguration();

    LongSet expectedIDs;/*from   www .  j av a2s.c  om*/
    try {
        expectedIDs = ComputationDataUtils.readExpectedIDsFromPartition(currentPartition, numPartitions,
                conf.get(RowStep.POPULAR_KEY), context, conf);
    } catch (IOException e) {
        throw new IllegalStateException(e);
    }

    String yKey = conf.get(RowStep.Y_KEY_KEY);
    log.info("Reading X or Y from {}", yKey);

    Y = new LongObjectMap<float[]>();

    Iterable<MatrixRow> in;
    try {
        in = new AvroFileSource<MatrixRow>(Namespaces.toPath(yKey), (AvroType<MatrixRow>) ptype).read(conf);
    } catch (IOException e) {
        throw new IllegalStateException(e);
    }

    RealMatrix theYTY = null;
    int dimension = 0;
    long count = 0;
    for (MatrixRow record : in) {
        long keyID = record.getRowId();
        float[] vector = record.getValues();
        Preconditions.checkNotNull(vector, "Vector was null for %s?", keyID);

        if (theYTY == null) {
            dimension = vector.length;
            theYTY = new Array2DRowRealMatrix(dimension, dimension);
        }
        for (int row = 0; row < dimension; row++) {
            double rowValue = vector[row];
            for (int col = 0; col < dimension; col++) {
                theYTY.addToEntry(row, col, rowValue * vector[col]);
            }
        }

        if (expectedIDs == null || expectedIDs.contains(keyID)) {
            Y.put(keyID, vector);
        }

        if (++count % 1000 == 0) {
            context.progress();
        }
    }

    Preconditions.checkNotNull(theYTY);
    YTY = theYTY;
}

From source file:com.moz.fiji.mapreduce.impl.DirectFijiTableWriterContext.java

License:Apache License

/**
 * Constructs a new context that can write cells directly to a Fiji table.
 *
 * @param hadoopContext is the Hadoop {@link TaskInputOutputContext} that will be used to perform
 *     the writes./*  ww  w .java 2 s  . c  o m*/
 * @throws IOException on I/O error.
 */
public DirectFijiTableWriterContext(TaskInputOutputContext<?, ?, ?, ?> hadoopContext) throws IOException {
    super(hadoopContext);
    final Configuration conf = new Configuration(hadoopContext.getConfiguration());
    final FijiURI outputURI = FijiURI.newBuilder(conf.get(FijiConfKeys.FIJI_OUTPUT_TABLE_URI)).build();
    mFiji = Fiji.Factory.open(outputURI, conf);
    mTable = mFiji.openTable(outputURI.getTable());
    mWriter = mTable.getWriterFactory().openBufferedWriter();
    mEntityIdFactory = EntityIdFactory.getFactory(mTable.getLayout());
}

From source file:com.moz.fiji.mapreduce.impl.FijiTableContextFactory.java

License:Apache License

/**
 * Instantiates the configured FijiTableContext.
 *
 * @param taskContext Hadoop task context.
 * @return the configured FijiTableContext.
 * @throws IOException on I/O error.//from   ww w. ja  va  2 s  .co m
 */
public static FijiTableContext create(TaskInputOutputContext taskContext) throws IOException {
    final Configuration conf = taskContext.getConfiguration();
    final String className = conf.get(FijiConfKeys.FIJI_TABLE_CONTEXT_CLASS);
    if (className == null) {
        throw new IOException(String.format("FijiTableContext class missing from configuration (key '%s').",
                FijiConfKeys.FIJI_TABLE_CONTEXT_CLASS));
    }

    Throwable throwable = null;
    try {
        final Class<?> genericClass = Class.forName(className);
        final Class<? extends FijiTableContext> klass = genericClass.asSubclass(FijiTableContext.class);
        final Constructor<? extends FijiTableContext> constructor = klass
                .getConstructor(TaskInputOutputContext.class);
        final FijiTableContext context = constructor.newInstance(taskContext);
        return context;
    } catch (ClassCastException cce) {
        throwable = cce;
    } catch (ClassNotFoundException cnfe) {
        throwable = cnfe;
    } catch (NoSuchMethodException nsme) {
        throwable = nsme;
    } catch (InvocationTargetException ite) {
        throwable = ite;
    } catch (IllegalAccessException iae) {
        throwable = iae;
    } catch (InstantiationException ie) {
        throwable = ie;
    }
    throw new IOException(String.format("Error instantiating FijiTableWriter class '%s': %s.", className,
            throwable.getMessage()), throwable);
}