Examples with BinaryDataFile org.apache.jena.dboe.base.file.BinaryDataFile used on opensource projects

Example 1 with BinaryDataFile

use of org.apache.jena.dboe.base.file.BinaryDataFile in project jena by apache.

the class ProcBuildNodeTableX method exec2.

/**
 * Pair<triples, indexed nodes>
 * @param sortThreads
 */
// [BULK] Output, not return.
private static Pair<Long, Long> exec2(String DB, XLoaderFiles loaderFiles, int sortThreads, String sortNodeTableArgs, List<String> datafiles) {
    // Threads - 1 parser, 1 builder, 2 sort.
    // Steps:
    // 1 - parser to and pipe terms to sort
    // 2 - sort
    // 3 - build node table from unique sort
    IRIProvider provider = SystemIRIx.getProvider();
    // SystemIRIx.setProvider(new IRIProviderAny());
    DatasetGraph dsg = DatabaseMgr.connectDatasetGraph(DB);
    DatasetGraphTDB dsgtdb = TDBInternal.getDatasetGraphTDB(dsg);
    NodeTable nt = dsgtdb.getTripleTable().getNodeTupleTable().getNodeTable();
    NodeTableTRDF nodeTable = (NodeTableTRDF) nt.baseNodeTable();
    OutputStream toSortOutputStream;
    InputStream fromSortInputStream;
    if (sortThreads <= 0)
        sortThreads = 2;
    // ** Step 2: The sort
    Process procSort;
    try {
        // LOG.info("Step : external sort");
        // Mutable list.
        List<String> sortCmd = new ArrayList<>(Arrays.asList("sort", "--temporary-directory=" + loaderFiles.TMPDIR, "--buffer-size=50%", "--parallel=" + sortThreads, "--unique", "--key=1,1"));
        if (BulkLoaderX.CompressSortNodeTableFiles)
            sortCmd.add("--compress-program=" + BulkLoaderX.gzipProgram());
        // if ( sortNodeTableArgs != null ) {}
        ProcessBuilder pb2 = new ProcessBuilder(sortCmd);
        pb2.environment().put("LC_ALL", "C");
        procSort = pb2.start();
        // To process.
        // Let the writer close it.
        toSortOutputStream = procSort.getOutputStream();
        // From process to the tree builder.
        // Let the reader side close it.
        fromSortInputStream = procSort.getInputStream();
    // // Debug sort process.
    // InputStream fromSortErrortStream = proc2.getErrorStream();
    // IOUtils.copy(fromSortErrortStream, System.err);
    } catch (Exception ex) {
        throw new RuntimeException(ex);
    }
    // ** Step 1 : write intermediate file (hash, thrift bytes).
    AtomicLong countParseTicks = new AtomicLong(-1);
    AtomicLong countIndexedNodes = new AtomicLong(-1);
    long tickPoint = BulkLoaderX.DataTick;
    int superTick = BulkLoaderX.DataSuperTick;
    Runnable task1 = () -> {
        ProgressMonitorOutput monitor = ProgressMonitorOutput.create(BulkLoaderX.LOG_Nodes, "Nodes", tickPoint, superTick);
        OutputStream output = IO.ensureBuffered(toSortOutputStream);
        // Counting.
        StreamRDF worker = new NodeHashTmpStream(output);
        ProgressStreamRDF stream = new ProgressStreamRDF(worker, monitor);
        monitor.start();
        String label = monitor.getLabel();
        datafiles.forEach(datafile -> {
            String basename = FileOps.basename(datafile);
            monitor.setLabel(basename);
            stream.start();
            RDFParser.source(datafile).parse(stream);
            stream.finish();
        });
        monitor.finish();
        monitor.setLabel(label);
        IO.flush(output);
        IO.close(output);
        long x = monitor.getTime();
        // long x = timer.endTimer();
        long count = monitor.getTicks();
        countParseTicks.set(count);
        double xSec = x / 1000.0;
        double rate = count / xSec;
        FmtLog.info(BulkLoaderX.LOG_Nodes, "%s Parse (nodes): %s seconds : %,d triples/quads %,.0f TPS", BulkLoaderX.StageMarker, Timer.timeStr(x), count, rate);
    };
    // [BULK] XXX AsyncParser.asyncParse(files, output)
    Thread thread1 = async(task1, "AsyncParser");
    // Step3: build node table.
    Runnable task3 = () -> {
        Timer timer = new Timer();
        // Don't start timer until sort send something
        // Process stream are already buffered.
        InputStream input = IO.ensureBuffered(fromSortInputStream);
        FileSet fileSet = new FileSet(dsgtdb.getLocation(), Names.nodeTableBaseName);
        BufferChannel blkState = FileFactory.createBufferChannel(fileSet, Names.extBptState);
        long idxTickPoint = BulkLoaderX.DataTick;
        int idxSuperTick = BulkLoaderX.DataSuperTick;
        ProgressMonitorOutput monitor = ProgressMonitorOutput.create(BulkLoaderX.LOG_Terms, "Index", idxTickPoint, idxSuperTick);
        // Library of tools!
        dsg.executeWrite(() -> {
            BinaryDataFile objectFile = nodeTable.getData();
            Iterator<Record> rIter = records(BulkLoaderX.LOG_Terms, input, objectFile);
            rIter = new ProgressIterator<>(rIter, monitor);
            // Record of (hash, nodeId)
            BPlusTree bpt1 = (BPlusTree) (nodeTable.getIndex());
            BPlusTreeParams bptParams = bpt1.getParams();
            RecordFactory factory = new RecordFactory(SystemTDB.LenNodeHash, NodeId.SIZE);
            // Wait until something has been received from the sort step
            rIter.hasNext();
            monitor.start();
            // .. then start the timer. It is closed after the transaction finishes.
            timer.startTimer();
            BPlusTree bpt2 = BPlusTreeRewriter.packIntoBPlusTree(rIter, bptParams, factory, blkState, bpt1.getNodeManager().getBlockMgr(), bpt1.getRecordsMgr().getBlockMgr());
            bpt2.sync();
            bpt1.sync();
            objectFile.sync();
            monitor.finish();
        });
        blkState.sync();
        IO.close(input);
        long x = timer.endTimer();
        long count = monitor.getTicks();
        countIndexedNodes.set(count);
        String rateStr = BulkLoaderX.rateStr(count, x);
        FmtLog.info(BulkLoaderX.LOG_Terms, "%s Index terms: %s seconds : %,d indexed RDF terms : %s PerSecond", BulkLoaderX.StageMarker, Timer.timeStr(x), count, rateStr);
    };
    Thread thread3 = async(task3, "AsyncBuild");
    try {
        int exitCode = procSort.waitFor();
        if (exitCode != 0) {
            String msg = IO.readWholeFileAsUTF8(procSort.getErrorStream());
            String logMsg = String.format("Sort RC = %d : Error: %s", exitCode, msg);
            Log.error(BulkLoaderX.LOG_Terms, logMsg);
            // ** Exit process
            System.exit(exitCode);
        } else
            BulkLoaderX.LOG_Terms.info("Sort finished");
    // I/O Stream toSortOutputStream and fromSortInputStream closed by
    // their users - step 1 and step 3.
    } catch (InterruptedException e) {
        BulkLoaderX.LOG_Nodes.error("Failed to cleanly wait-for the subprocess");
        throw new RuntimeException(e);
    }
    BulkLoaderX.waitFor(thread1);
    BulkLoaderX.waitFor(thread3);
    return Pair.create(countParseTicks.get(), countIndexedNodes.get());
}

Example 2 with BinaryDataFile

use of org.apache.jena.dboe.base.file.BinaryDataFile in project jena by apache.

the class LoaderOps method ntDataFile.

/**
 * Get the node storage for a {@Link NodeTable}
 */
public static TransBinaryDataFile ntDataFile(NodeTable nt) {
    NodeTableTRDF ntt = (NodeTableTRDF) (nt.baseNodeTable());
    BinaryDataFile bdf = ntt.getData();
    TransBinaryDataFile tbdf = (TransBinaryDataFile) bdf;
    return tbdf;
}

Example 3 with BinaryDataFile

use of org.apache.jena.dboe.base.file.BinaryDataFile in project jena by apache.

the class tdbdumpnodes method main.

public static void main(String... args) throws TException {
    if (args.length != 1) {
        System.err.println("Usage: tdbdumpnodes NodeFile -- e.g \"Database2/Data-0001/nodes-data.dat\"");
        System.exit(1);
    }
    String FN = args[0];
    URLConnection x;
    BinaryDataFile f = new BinaryDataFileRandomAccess(FN);
    f.open();
    TReadAppendFileTransport transport = new TReadAppendFileTransport(f);
    TProtocol protocol = TRDF.protocol(transport);
    transport.readPosition(0);
    // [0x        1BFEA0FD]
    // <http://data.europa.eu/esco/occupation/99492920-e5a5-4dba-9e5a-93193147198c>
    // [0x        1BFEA14C] ** Bad read ** don't know what type: 14
    // transport.readPosition(0x1BFEA0FD);
    long limit = f.length();
    // limit = 0x1C2092FF;
    System.out.printf("File length: %,d [0x%16X]\n", limit, limit);
    while (true) {
        long locn = transport.readPosition();
        if (locn >= limit)
            break;
        try {
            Node n = readOne(protocol);
            System.out.printf("[0x%16X] %s\n", locn, FmtUtils.stringForNode(n));
        } catch (Exception ex) {
            System.out.printf("[0x%16X] ** Bad read ** %s\n", locn, ex.getMessage());
            long jump = 100;
            long i = locn;
            for (; i < locn + jump; i++) {
                transport.readPosition(i);
                try {
                    Node n = readOne(protocol);
                    System.out.printf("Resync: %,d  [0x%16X] ==> [0x%16X]\n", i - locn, locn, i);
                    System.out.printf("[0x%16X] ** %s\n", locn, FmtUtils.stringForNode(n));
                } catch (Exception ex2) {
                }
            }
            if (locn - i >= jump)
                System.out.printf("No resync: %,d  [0x%16X] ==> [0x%16X]\n", i - locn, locn, i);
        // // Problems - back up and dump.
        // byte bytes[] = new byte[256];
        // int len = f.read(locn, bytes);
        // StringBuilder sBuff = new StringBuilder() ;
        // for ( int i = 0 ; i < len ; i++ ) {
        // byte b = bytes[i] ;
        // int hi = (b & 0xF0) >> 4 ;
        // int lo = b & 0xF ;
        // if ( i != 0 ) {
        // if (i % 20 == 0  )
        // sBuff.append("\n");
        // else
        // sBuff.append(" ");
        // }
        // sBuff.append(Chars.hexDigitsUC[hi]) ;
        // sBuff.append(Chars.hexDigitsUC[lo]) ;
        // }
        // String str = sBuff.toString();
        // if ( !str.endsWith("\n") )
        // str = str+"\n";
        // System.out.print(str);
        // System.exit(1);
        }
    }
}