Examples with FlatMapFunction org.apache.spark.api.java.function.FlatMapFunction used on opensource projects

Example 1 with FlatMapFunction

use of org.apache.spark.api.java.function.FlatMapFunction in project deeplearning4j by deeplearning4j.

the class Word2Vec method train.

/**
     *  Training word2vec model on a given text corpus
     *
     * @param corpusRDD training corpus
     * @throws Exception
     */
public void train(JavaRDD<String> corpusRDD) throws Exception {
    log.info("Start training ...");
    if (workers > 0)
        corpusRDD.repartition(workers);
    // SparkContext
    final JavaSparkContext sc = new JavaSparkContext(corpusRDD.context());
    // Pre-defined variables
    Map<String, Object> tokenizerVarMap = getTokenizerVarMap();
    Map<String, Object> word2vecVarMap = getWord2vecVarMap();
    // Variables to fill in train
    final JavaRDD<AtomicLong> sentenceWordsCountRDD;
    final JavaRDD<List<VocabWord>> vocabWordListRDD;
    final JavaPairRDD<List<VocabWord>, Long> vocabWordListSentenceCumSumRDD;
    final VocabCache<VocabWord> vocabCache;
    final JavaRDD<Long> sentenceCumSumCountRDD;
    int maxRep = 1;
    // Start Training //
    //////////////////////////////////////
    log.info("Tokenization and building VocabCache ...");
    // Processing every sentence and make a VocabCache which gets fed into a LookupCache
    Broadcast<Map<String, Object>> broadcastTokenizerVarMap = sc.broadcast(tokenizerVarMap);
    TextPipeline pipeline = new TextPipeline(corpusRDD, broadcastTokenizerVarMap);
    pipeline.buildVocabCache();
    pipeline.buildVocabWordListRDD();
    // Get total word count and put into word2vec variable map
    word2vecVarMap.put("totalWordCount", pipeline.getTotalWordCount());
    // 2 RDDs: (vocab words list) and (sentence Count).Already cached
    sentenceWordsCountRDD = pipeline.getSentenceCountRDD();
    vocabWordListRDD = pipeline.getVocabWordListRDD();
    // Get vocabCache and broad-casted vocabCache
    Broadcast<VocabCache<VocabWord>> vocabCacheBroadcast = pipeline.getBroadCastVocabCache();
    vocabCache = vocabCacheBroadcast.getValue();
    log.info("Vocab size: {}", vocabCache.numWords());
    //////////////////////////////////////
    log.info("Building Huffman Tree ...");
    // Building Huffman Tree would update the code and point in each of the vocabWord in vocabCache
    /*
        We don't need to build tree here, since it was built earlier, at TextPipeline.buildVocabCache() call.
        
        Huffman huffman = new Huffman(vocabCache.vocabWords());
        huffman.build();
        huffman.applyIndexes(vocabCache);
        */
    //////////////////////////////////////
    log.info("Calculating cumulative sum of sentence counts ...");
    sentenceCumSumCountRDD = new CountCumSum(sentenceWordsCountRDD).buildCumSum();
    //////////////////////////////////////
    log.info("Mapping to RDD(vocabWordList, cumulative sentence count) ...");
    vocabWordListSentenceCumSumRDD = vocabWordListRDD.zip(sentenceCumSumCountRDD).setName("vocabWordListSentenceCumSumRDD");
    /////////////////////////////////////
    log.info("Broadcasting word2vec variables to workers ...");
    Broadcast<Map<String, Object>> word2vecVarMapBroadcast = sc.broadcast(word2vecVarMap);
    Broadcast<double[]> expTableBroadcast = sc.broadcast(expTable);
    /////////////////////////////////////
    log.info("Training word2vec sentences ...");
    FlatMapFunction firstIterFunc = new FirstIterationFunction(word2vecVarMapBroadcast, expTableBroadcast, vocabCacheBroadcast);
    @SuppressWarnings("unchecked") JavaRDD<Pair<VocabWord, INDArray>> indexSyn0UpdateEntryRDD = vocabWordListSentenceCumSumRDD.mapPartitions(firstIterFunc).map(new MapToPairFunction());
    // Get all the syn0 updates into a list in driver
    List<Pair<VocabWord, INDArray>> syn0UpdateEntries = indexSyn0UpdateEntryRDD.collect();
    // Instantiate syn0
    INDArray syn0 = Nd4j.zeros(vocabCache.numWords(), layerSize);
    // Updating syn0 first pass: just add vectors obtained from different nodes
    log.info("Averaging results...");
    Map<VocabWord, AtomicInteger> updates = new HashMap<>();
    Map<Long, Long> updaters = new HashMap<>();
    for (Pair<VocabWord, INDArray> syn0UpdateEntry : syn0UpdateEntries) {
        syn0.getRow(syn0UpdateEntry.getFirst().getIndex()).addi(syn0UpdateEntry.getSecond());
        // for proper averaging we need to divide resulting sums later, by the number of additions
        if (updates.containsKey(syn0UpdateEntry.getFirst())) {
            updates.get(syn0UpdateEntry.getFirst()).incrementAndGet();
        } else
            updates.put(syn0UpdateEntry.getFirst(), new AtomicInteger(1));
        if (!updaters.containsKey(syn0UpdateEntry.getFirst().getVocabId())) {
            updaters.put(syn0UpdateEntry.getFirst().getVocabId(), syn0UpdateEntry.getFirst().getAffinityId());
        }
    }
    // Updating syn0 second pass: average obtained vectors
    for (Map.Entry<VocabWord, AtomicInteger> entry : updates.entrySet()) {
        if (entry.getValue().get() > 1) {
            if (entry.getValue().get() > maxRep)
                maxRep = entry.getValue().get();
            syn0.getRow(entry.getKey().getIndex()).divi(entry.getValue().get());
        }
    }
    long totals = 0;
    log.info("Finished calculations...");
    vocab = vocabCache;
    InMemoryLookupTable<VocabWord> inMemoryLookupTable = new InMemoryLookupTable<VocabWord>();
    Environment env = EnvironmentUtils.buildEnvironment();
    env.setNumCores(maxRep);
    env.setAvailableMemory(totals);
    update(env, Event.SPARK);
    inMemoryLookupTable.setVocab(vocabCache);
    inMemoryLookupTable.setVectorLength(layerSize);
    inMemoryLookupTable.setSyn0(syn0);
    lookupTable = inMemoryLookupTable;
    modelUtils.init(lookupTable);
}

Example 2 with FlatMapFunction

use of org.apache.spark.api.java.function.FlatMapFunction in project beam by apache.

the class SparkGroupAlsoByWindowViaWindowSet method groupAlsoByWindow.

public static <K, InputT, W extends BoundedWindow> JavaDStream<WindowedValue<KV<K, Iterable<InputT>>>> groupAlsoByWindow(JavaDStream<WindowedValue<KV<K, Iterable<WindowedValue<InputT>>>>> inputDStream, final Coder<K> keyCoder, final Coder<WindowedValue<InputT>> wvCoder, final WindowingStrategy<?, W> windowingStrategy, final SparkRuntimeContext runtimeContext, final List<Integer> sourceIds) {
    final IterableCoder<WindowedValue<InputT>> itrWvCoder = IterableCoder.of(wvCoder);
    final Coder<InputT> iCoder = ((FullWindowedValueCoder<InputT>) wvCoder).getValueCoder();
    final Coder<? extends BoundedWindow> wCoder = ((FullWindowedValueCoder<InputT>) wvCoder).getWindowCoder();
    final Coder<WindowedValue<KV<K, Iterable<InputT>>>> wvKvIterCoder = FullWindowedValueCoder.of(KvCoder.of(keyCoder, IterableCoder.of(iCoder)), wCoder);
    final TimerInternals.TimerDataCoder timerDataCoder = TimerInternals.TimerDataCoder.of(windowingStrategy.getWindowFn().windowCoder());
    long checkpointDurationMillis = runtimeContext.getPipelineOptions().as(SparkPipelineOptions.class).getCheckpointDurationMillis();
    // we have to switch to Scala API to avoid Optional in the Java API, see: SPARK-4819.
    // we also have a broader API for Scala (access to the actual key and entire iterator).
    // we use coders to convert objects in the PCollection to byte arrays, so they
    // can be transferred over the network for the shuffle and be in serialized form
    // for checkpointing.
    // for readability, we add comments with actual type next to byte[].
    // to shorten line length, we use:
    //---- WV: WindowedValue
    //---- Iterable: Itr
    //---- AccumT: A
    //---- InputT: I
    DStream<Tuple2<ByteArray, byte[]>> /*Itr<WV<I>>*/
    pairDStream = inputDStream.transformToPair(new Function<JavaRDD<WindowedValue<KV<K, Iterable<WindowedValue<InputT>>>>>, JavaPairRDD<ByteArray, byte[]>>() {

        // we use mapPartitions with the RDD API because its the only available API
        // that allows to preserve partitioning.
        @Override
        public JavaPairRDD<ByteArray, byte[]> call(JavaRDD<WindowedValue<KV<K, Iterable<WindowedValue<InputT>>>>> rdd) throws Exception {
            return rdd.mapPartitions(TranslationUtils.functionToFlatMapFunction(WindowingHelpers.<KV<K, Iterable<WindowedValue<InputT>>>>unwindowFunction()), true).mapPartitionsToPair(TranslationUtils.<K, Iterable<WindowedValue<InputT>>>toPairFlatMapFunction(), true).mapPartitionsToPair(TranslationUtils.pairFunctionToPairFlatMapFunction(CoderHelpers.toByteFunction(keyCoder, itrWvCoder)), true);
        }
    }).dstream();
    PairDStreamFunctions<ByteArray, byte[]> pairDStreamFunctions = DStream.toPairDStreamFunctions(pairDStream, JavaSparkContext$.MODULE$.<ByteArray>fakeClassTag(), JavaSparkContext$.MODULE$.<byte[]>fakeClassTag(), null);
    int defaultNumPartitions = pairDStreamFunctions.defaultPartitioner$default$1();
    Partitioner partitioner = pairDStreamFunctions.defaultPartitioner(defaultNumPartitions);
    // use updateStateByKey to scan through the state and update elements and timers.
    DStream<Tuple2<ByteArray, Tuple2<StateAndTimers, List<byte[]>>>> /*WV<KV<K, Itr<I>>>*/
    firedStream = pairDStreamFunctions.updateStateByKey(new SerializableFunction1<scala.collection.Iterator<Tuple3</*K*/
    ByteArray, Seq<byte[]>, Option<Tuple2<StateAndTimers, /*WV<KV<K, Itr<I>>>*/
    List<byte[]>>>>>, scala.collection.Iterator<Tuple2</*K*/
    ByteArray, Tuple2<StateAndTimers, /*WV<KV<K, Itr<I>>>*/
    List<byte[]>>>>>() {

        @Override
        public scala.collection.Iterator<Tuple2</*K*/
        ByteArray, Tuple2<StateAndTimers, /*WV<KV<K, Itr<I>>>*/
        List<byte[]>>>> apply(final scala.collection.Iterator<Tuple3</*K*/
        ByteArray, Seq<byte[]>, Option<Tuple2<StateAndTimers, /*WV<KV<K, Itr<I>>>*/
        List<byte[]>>>>> iter) {
            //--- ACTUAL STATEFUL OPERATION:
            //
            // Input Iterator: the partition (~bundle) of a cogrouping of the input
            // and the previous state (if exists).
            //
            // Output Iterator: the output key, and the updated state.
            //
            // possible input scenarios for (K, Seq, Option<S>):
            // (1) Option<S>.isEmpty: new data with no previous state.
            // (2) Seq.isEmpty: no new data, but evaluating previous state (timer-like behaviour).
            // (3) Seq.nonEmpty && Option<S>.isDefined: new data with previous state.
            final SystemReduceFn<K, InputT, Iterable<InputT>, Iterable<InputT>, W> reduceFn = SystemReduceFn.buffering(((FullWindowedValueCoder<InputT>) wvCoder).getValueCoder());
            final OutputWindowedValueHolder<K, InputT> outputHolder = new OutputWindowedValueHolder<>();
            // use in memory Aggregators since Spark Accumulators are not resilient
            // in stateful operators, once done with this partition.
            final MetricsContainerImpl cellProvider = new MetricsContainerImpl("cellProvider");
            final CounterCell droppedDueToClosedWindow = cellProvider.getCounter(MetricName.named(SparkGroupAlsoByWindowViaWindowSet.class, GroupAlsoByWindowsAggregators.DROPPED_DUE_TO_CLOSED_WINDOW_COUNTER));
            final CounterCell droppedDueToLateness = cellProvider.getCounter(MetricName.named(SparkGroupAlsoByWindowViaWindowSet.class, GroupAlsoByWindowsAggregators.DROPPED_DUE_TO_LATENESS_COUNTER));
            AbstractIterator<Tuple2<ByteArray, Tuple2<StateAndTimers, List<byte[]>>>> /*WV<KV<K, Itr<I>>>*/
            outIter = new AbstractIterator<Tuple2</*K*/
            ByteArray, Tuple2<StateAndTimers, /*WV<KV<K, Itr<I>>>*/
            List<byte[]>>>>() {

                @Override
                protected Tuple2</*K*/
                ByteArray, Tuple2<StateAndTimers, /*WV<KV<K, Itr<I>>>*/
                List<byte[]>>> computeNext() {
                    // (possibly) previous-state and (possibly) new data.
                    while (iter.hasNext()) {
                        // for each element in the partition:
                        Tuple3<ByteArray, Seq<byte[]>, Option<Tuple2<StateAndTimers, List<byte[]>>>> next = iter.next();
                        ByteArray encodedKey = next._1();
                        K key = CoderHelpers.fromByteArray(encodedKey.getValue(), keyCoder);
                        Seq<byte[]> seq = next._2();
                        Option<Tuple2<StateAndTimers, List<byte[]>>> prevStateAndTimersOpt = next._3();
                        SparkStateInternals<K> stateInternals;
                        SparkTimerInternals timerInternals = SparkTimerInternals.forStreamFromSources(sourceIds, GlobalWatermarkHolder.get());
                        // get state(internals) per key.
                        if (prevStateAndTimersOpt.isEmpty()) {
                            // no previous state.
                            stateInternals = SparkStateInternals.forKey(key);
                        } else {
                            // with pre-existing state.
                            StateAndTimers prevStateAndTimers = prevStateAndTimersOpt.get()._1();
                            stateInternals = SparkStateInternals.forKeyAndState(key, prevStateAndTimers.getState());
                            Collection<byte[]> serTimers = prevStateAndTimers.getTimers();
                            timerInternals.addTimers(SparkTimerInternals.deserializeTimers(serTimers, timerDataCoder));
                        }
                        ReduceFnRunner<K, InputT, Iterable<InputT>, W> reduceFnRunner = new ReduceFnRunner<>(key, windowingStrategy, ExecutableTriggerStateMachine.create(TriggerStateMachines.stateMachineForTrigger(TriggerTranslation.toProto(windowingStrategy.getTrigger()))), stateInternals, timerInternals, outputHolder, new UnsupportedSideInputReader("GroupAlsoByWindow"), reduceFn, runtimeContext.getPipelineOptions());
                        // clear before potential use.
                        outputHolder.clear();
                        if (!seq.isEmpty()) {
                            // new input for key.
                            try {
                                Iterable<WindowedValue<InputT>> elementsIterable = CoderHelpers.fromByteArray(seq.head(), itrWvCoder);
                                Iterable<WindowedValue<InputT>> validElements = LateDataUtils.dropExpiredWindows(key, elementsIterable, timerInternals, windowingStrategy, droppedDueToLateness);
                                reduceFnRunner.processElements(validElements);
                            } catch (Exception e) {
                                throw new RuntimeException("Failed to process element with ReduceFnRunner", e);
                            }
                        } else if (stateInternals.getState().isEmpty()) {
                            // no input and no state -> GC evict now.
                            continue;
                        }
                        try {
                            // advance the watermark to HWM to fire by timers.
                            timerInternals.advanceWatermark();
                            // call on timers that are ready.
                            reduceFnRunner.onTimers(timerInternals.getTimersReadyToProcess());
                        } catch (Exception e) {
                            throw new RuntimeException("Failed to process ReduceFnRunner onTimer.", e);
                        }
                        // this is mostly symbolic since actual persist is done by emitting output.
                        reduceFnRunner.persist();
                        // obtain output, if fired.
                        List<WindowedValue<KV<K, Iterable<InputT>>>> outputs = outputHolder.get();
                        if (!outputs.isEmpty() || !stateInternals.getState().isEmpty()) {
                            StateAndTimers updated = new StateAndTimers(stateInternals.getState(), SparkTimerInternals.serializeTimers(timerInternals.getTimers(), timerDataCoder));
                            // persist Spark's state by outputting.
                            List<byte[]> serOutput = CoderHelpers.toByteArrays(outputs, wvKvIterCoder);
                            return new Tuple2<>(encodedKey, new Tuple2<>(updated, serOutput));
                        }
                    // an empty state with no output, can be evicted completely - do nothing.
                    }
                    return endOfData();
                }
            };
            // log if there's something to log.
            long lateDropped = droppedDueToLateness.getCumulative();
            if (lateDropped > 0) {
                LOG.info(String.format("Dropped %d elements due to lateness.", lateDropped));
                droppedDueToLateness.inc(-droppedDueToLateness.getCumulative());
            }
            long closedWindowDropped = droppedDueToClosedWindow.getCumulative();
            if (closedWindowDropped > 0) {
                LOG.info(String.format("Dropped %d elements due to closed window.", closedWindowDropped));
                droppedDueToClosedWindow.inc(-droppedDueToClosedWindow.getCumulative());
            }
            return scala.collection.JavaConversions.asScalaIterator(outIter);
        }
    }, partitioner, true, JavaSparkContext$.MODULE$.<Tuple2<StateAndTimers, List<byte[]>>>fakeClassTag());
    if (checkpointDurationMillis > 0) {
        firedStream.checkpoint(new Duration(checkpointDurationMillis));
    }
    // go back to Java now.
    JavaPairDStream<ByteArray, Tuple2<StateAndTimers, List<byte[]>>> /*WV<KV<K, Itr<I>>>*/
    javaFiredStream = JavaPairDStream.fromPairDStream(firedStream, JavaSparkContext$.MODULE$.<ByteArray>fakeClassTag(), JavaSparkContext$.MODULE$.<Tuple2<StateAndTimers, List<byte[]>>>fakeClassTag());
    // filter state-only output (nothing to fire) and remove the state from the output.
    return javaFiredStream.filter(new Function<Tuple2</*K*/
    ByteArray, Tuple2<StateAndTimers, /*WV<KV<K, Itr<I>>>*/
    List<byte[]>>>, Boolean>() {

        @Override
        public Boolean call(Tuple2</*K*/
        ByteArray, Tuple2<StateAndTimers, /*WV<KV<K, Itr<I>>>*/
        List<byte[]>>> t2) throws Exception {
            // filter output if defined.
            return !t2._2()._2().isEmpty();
        }
    }).flatMap(new FlatMapFunction<Tuple2</*K*/
    ByteArray, Tuple2<StateAndTimers, /*WV<KV<K, Itr<I>>>*/
    List<byte[]>>>, WindowedValue<KV<K, Iterable<InputT>>>>() {

        @Override
        public Iterable<WindowedValue<KV<K, Iterable<InputT>>>> call(Tuple2</*K*/
        ByteArray, Tuple2<StateAndTimers, /*WV<KV<K, Itr<I>>>*/
        List<byte[]>>> t2) throws Exception {
            // return in serialized form.
            return CoderHelpers.fromByteArrays(t2._2()._2(), wvKvIterCoder);
        }
    });
}

Example 3 with FlatMapFunction

use of org.apache.spark.api.java.function.FlatMapFunction in project gatk by broadinstitute.

the class VariantWalkerSpark method getVariantsFunction.

private static FlatMapFunction<Shard<VariantContext>, VariantWalkerContext> getVariantsFunction(final Broadcast<ReferenceMultiSource> bReferenceSource, final Broadcast<FeatureManager> bFeatureManager, final SAMSequenceDictionary sequenceDictionary, final int variantShardPadding) {
    return (FlatMapFunction<Shard<VariantContext>, VariantWalkerContext>) shard -> {
        SimpleInterval paddedInterval = shard.getInterval().expandWithinContig(variantShardPadding, sequenceDictionary);
        ReferenceDataSource reference = bReferenceSource == null ? null : new ReferenceMemorySource(bReferenceSource.getValue().getReferenceBases(null, paddedInterval), sequenceDictionary);
        FeatureManager features = bFeatureManager == null ? null : bFeatureManager.getValue();
        return StreamSupport.stream(shard.spliterator(), false).filter(v -> v.getStart() >= shard.getStart() && v.getStart() <= shard.getEnd()).map(v -> {
            final SimpleInterval variantInterval = new SimpleInterval(v);
            return new VariantWalkerContext(v, new ReadsContext(), new ReferenceContext(reference, variantInterval), new FeatureContext(features, variantInterval));
        }).iterator();
    };
}

Example 4 with FlatMapFunction

use of org.apache.spark.api.java.function.FlatMapFunction in project gatk by broadinstitute.

the class ReadsSparkSourceUnitTest method testPutPairsInSamePartition.

@Test(dataProvider = "readPairsAndPartitions")
public void testPutPairsInSamePartition(int numPairs, int numPartitions, int[] expectedReadsPerPartition) throws IOException {
    JavaSparkContext ctx = SparkContextFactory.getTestSparkContext();
    SAMFileHeader header = ArtificialReadUtils.createArtificialSamHeader();
    header.setSortOrder(SAMFileHeader.SortOrder.queryname);
    JavaRDD<GATKRead> reads = createPairedReads(ctx, header, numPairs, numPartitions);
    ReadsSparkSource readsSparkSource = new ReadsSparkSource(ctx);
    JavaRDD<GATKRead> pairedReads = readsSparkSource.putPairsInSamePartition(header, reads);
    List<List<GATKRead>> partitions = pairedReads.mapPartitions((FlatMapFunction<Iterator<GATKRead>, List<GATKRead>>) it -> Iterators.singletonIterator(Lists.newArrayList(it))).collect();
    assertEquals(partitions.size(), numPartitions);
    for (int i = 0; i < numPartitions; i++) {
        assertEquals(partitions.get(i).size(), expectedReadsPerPartition[i]);
    }
    assertEquals(Arrays.stream(expectedReadsPerPartition).sum(), numPairs * 2);
}

Example 5 with FlatMapFunction

use of org.apache.spark.api.java.function.FlatMapFunction in project beijingThirdPeriod by weidongcao.

the class SparkOperateBcp method run.

public static void run(TaskBean task) {
    logger.info("开始处理 {} 的BCP数据", task.getContentType());
    SparkConf conf = new SparkConf().setAppName(task.getContentType());
    JavaSparkContext sc = new JavaSparkContext(conf);
    JavaRDD<String> originalRDD = sc.textFile(task.getBcpPath());
    // 对BCP文件数据进行基本的处理，并生成ID(HBase的RowKey，Solr的Sid)
    JavaRDD<String[]> valueArrrayRDD = originalRDD.mapPartitions((FlatMapFunction<Iterator<String>, String[]>) iter -> {
        List<String[]> list = new ArrayList<>();
        while (iter.hasNext()) {
            String str = iter.next();
            String[] fields = str.split("\t");
            list.add(fields);
        }
        return list.iterator();
    });
    /*
         * 对数据进行过滤
         * 字段名数组里没有id字段(HBase的RowKey，Solr的Side)
         * BCP文件可能升级，添加了新的字段
         * FTP、IM_CHAT表新加了三个字段："service_code_out", "terminal_longitude", "terminal_latitude"
         * HTTP表新了了7个字段其中三个字段与上面相同："service_code_out", "terminal_longitude", "terminal_latitude"
         *      另外4个字段是："manufacturer_code", "zipname", "bcpname", "rownumber", "
         * 故过滤的时候要把以上情况考虑进去
         */
    JavaRDD<String[]> filterValuesRDD;
    filterValuesRDD = valueArrrayRDD.filter((Function<String[], Boolean>) (String[] strings) -> // BCP文件 没有新加字段，
    (task.getColumns().length + 1 == strings.length) || // BCP文件添加了新的字段，且只添加了三个字段
    ((task.getColumns().length + 1) == (strings.length + 3)) || // HTTP的BCP文件添加了新的字段，且添加了7个字段
    (BigDataConstants.CONTENT_TYPE_HTTP.equalsIgnoreCase(task.getContentType()) && ((task.getColumns().length + 1) == (strings.length + 3 + 4))));
    // BCP文件数据写入HBase
    bcpWriteIntoHBase(filterValuesRDD, task);
    sc.close();
}