Examples with EnvironmentConfig com.sleepycat.je.EnvironmentConfig used on opensource projects

Example 26 with EnvironmentConfig

use of com.sleepycat.je.EnvironmentConfig in project bboxdb by jnidzwetzki.

the class BDBTupleStore method open.

@Override
public void open() throws Exception {
    final EnvironmentConfig envConfig = new EnvironmentConfig();
    envConfig.setTransactional(USE_TRANSACTIONS);
    envConfig.setAllowCreate(true);
    environment = new Environment(dir, envConfig);
    Transaction txn = null;
    if (USE_TRANSACTIONS) {
        txn = environment.beginTransaction(null, null);
    }
    final DatabaseConfig dbConfig = new DatabaseConfig();
    dbConfig.setTransactional(USE_TRANSACTIONS);
    dbConfig.setAllowCreate(true);
    // dbConfig.setSortedDuplicates(true);
    dbConfig.setDeferredWrite(true);
    // dbConfig.setKeyPrefixing(true);
    // dbConfig.setNodeMaxEntries(128);
    database = environment.openDatabase(txn, "test", dbConfig);
    if (txn != null) {
        txn.commit();
    }
}

Example 27 with EnvironmentConfig

use of com.sleepycat.je.EnvironmentConfig in project jvarkit by lindenb.

the class NgsFilesScanner method doWork.

@Override
public int doWork(List<String> args) {
    boolean dump = false;
    EnvironmentConfig envCfg = new EnvironmentConfig();
    Environment env = null;
    if (bdbHome == null) {
        LOG.error("BDB home undefined");
        return -1;
    }
    if (!bdbHome.exists() || !bdbHome.isDirectory()) {
        LOG.error("BDB doesn't exist or is not a directory");
        return -1;
    }
    File root = new File("/");
    Cursor cursor = null;
    OutputStream xmlout = null;
    try {
        if (!dump && args.size() == 1) {
            root = new File(args.get(0));
        } else if (!(dump && args.isEmpty())) {
            LOG.error("illegal.number.of.arguments");
            return -1;
        }
        envCfg.setAllowCreate(!dump);
        envCfg.setReadOnly(dump);
        envCfg.setTransactional(false);
        LOG.info("Opening env " + bdbHome);
        env = new Environment(bdbHome, envCfg);
        // TransactionConfig txnCfg=new TransactionConfig();
        // this.txn=env.beginTransaction(null, txnCfg);
        LOG.info("Opening database " + DATABASE_NAME);
        DatabaseConfig cfg = new DatabaseConfig();
        cfg.setAllowCreate(!dump);
        cfg.setReadOnly(dump);
        cfg.setTransactional(false);
        this.database = env.openDatabase(this.txn, DATABASE_NAME, cfg);
        DatabaseEntry key = new DatabaseEntry();
        DatabaseEntry data = new DatabaseEntry();
        if (dump) {
            XMLEventFactory xef = XMLEventFactory.newFactory();
            XMLOutputFactory xof = XMLOutputFactory.newFactory();
            XMLInputFactory xif = XMLInputFactory.newFactory();
            xmlout = openFileOrStdoutAsStream(outputFile);
            XMLEventWriter out = xof.createXMLEventWriter(xmlout, "UTF-8");
            out.add(xef.createStartDocument("UTF-8", "1.0"));
            out.add(xef.createStartElement("", "", "ngs-files"));
            cursor = this.database.openCursor(this.txn, null);
            while (cursor.getNext(key, data, LockMode.DEFAULT) == OperationStatus.SUCCESS) {
                File file = new File(StringBinding.entryToString(key));
                if (isEntryShouldBeDeleted(file)) {
                    LOG.info("deleting entry for " + file);
                    // cursor.delete();//no env is read only
                    continue;
                }
                StringReader sr = new StringReader(StringBinding.entryToString(data));
                XMLEventReader xr = xif.createXMLEventReader(sr);
                while (xr.hasNext()) {
                    XMLEvent evt = xr.nextEvent();
                    if (evt.isStartDocument())
                        continue;
                    if (evt.isEndDocument())
                        break;
                    out.add(evt);
                }
                xr.close();
                sr.close();
            }
            cursor.close();
            out.add(xef.createEndElement("", "", "ngs-files"));
            out.add(xef.createEndDocument());
            out.flush();
            out.close();
            xmlout.flush();
            xmlout.close();
            xmlout = null;
        } else {
            recursive(root);
            // final cleanup
            cursor = this.database.openCursor(this.txn, null);
            while (cursor.getNext(key, data, LockMode.DEFAULT) == OperationStatus.SUCCESS) {
                File file = new File(StringBinding.entryToString(key));
                if (isEntryShouldBeDeleted(file)) {
                    LOG.info("deleting entry for " + file);
                    cursor.delete();
                }
            }
            cursor.close();
        }
        return 0;
    } catch (Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        if (cursor != null)
            try {
                cursor.close();
            } catch (Exception err) {
            }
        if (this.txn != null)
            try {
                this.txn.commit();
            } catch (Exception err) {
            }
        if (this.database != null)
            try {
                this.database.close();
            } catch (Exception err) {
            }
        if (env != null)
            try {
                env.close();
            } catch (Exception err) {
            }
        CloserUtil.close(xmlout);
    }
}

Example 28 with EnvironmentConfig

use of com.sleepycat.je.EnvironmentConfig in project jvarkit by lindenb.

the class LumpySort method doWork.

@Override
public int doWork(final List<String> args) {
    VariantContextWriter vcw = null;
    LineIterator vcfIn = null;
    Environment environment = null;
    Database variantsDb1 = null;
    final List<File> inputs = IOUtil.unrollFiles(args.stream().map(S -> new File(S)).collect(Collectors.toList()), ".vcf", ".vcf.gz");
    if (inputs.isEmpty()) {
        LOG.error("empty vcf list");
        return -1;
    }
    try {
        IOUtil.assertDirectoryIsWritable(this.bdbHomeDir);
        final Set<VCFHeaderLine> metaData = new HashSet<>();
        final Set<String> sampleNames = new TreeSet<>();
        final IntervalTreeMap<Boolean> intervalTreeMapBed;
        if (this.bedFile != null) {
            intervalTreeMapBed = new IntervalTreeMap<>();
            final BedLineCodec bedLineCodec = new BedLineCodec();
            final BufferedReader br = IOUtils.openFileForBufferedReading(this.bedFile);
            br.lines().map(L -> bedLineCodec.decode(L)).filter(L -> L != null).forEach(B -> intervalTreeMapBed.put(B.toInterval(), true));
            br.close();
        } else {
            intervalTreeMapBed = null;
        }
        for (int idx = 0; idx < inputs.size(); ++idx) {
            final File vcfFile = inputs.get(idx);
            LOG.info("Read header " + (idx + 1) + "/" + inputs.size());
            final VCFFileReader r = new VCFFileReader(vcfFile, false);
            final VCFHeader header = r.getFileHeader();
            if (!LumpyConstants.isLumpyHeader(header)) {
                LOG.error("doesn't look like a Lumpy-SV vcf header " + vcfFile);
                r.close();
                return -1;
            }
            if (!header.hasGenotypingData()) {
                LOG.error("No sample in " + vcfFile);
                r.close();
                return -1;
            }
            for (final String sampleName : header.getSampleNamesInOrder()) {
                if (sampleNames.contains(sampleName)) {
                    LOG.error("Sample found twice " + sampleName + " in " + vcfFile);
                    r.close();
                    return -1;
                }
                sampleNames.add(sampleName);
            }
            metaData.addAll(header.getMetaDataInInputOrder().stream().filter(H -> !H.getKey().equals("fileDate")).collect(Collectors.toSet()));
            r.close();
        }
        final VCFInfoHeaderLine nSampleInfoHeaderLine = new VCFInfoHeaderLine("NSAMPLES", 1, VCFHeaderLineType.Integer, "Number of affected samples.");
        metaData.add(nSampleInfoHeaderLine);
        final VCFFormatHeaderLine chromStartFormatHeaderLine = new VCFFormatHeaderLine("CB", 1, VCFHeaderLineType.Integer, "Original Variant POS");
        metaData.add(chromStartFormatHeaderLine);
        final VCFFormatHeaderLine chromEndFormatHeaderLine = new VCFFormatHeaderLine("CE", 1, VCFHeaderLineType.Integer, "Original Variant END");
        metaData.add(chromEndFormatHeaderLine);
        final VCFHeader outHeader = new VCFHeader(metaData, sampleNames);
        final VCFHeaderVersion[] versions = VCFHeaderVersion.values();
        this.vcfEncoder = new VCFEncoder(outHeader, false, true);
        this.vcfCodec.setVCFHeader(outHeader, versions[versions.length - 1]);
        /* open BDB env */
        final Transaction txn = null;
        environment = new Environment(this.bdbHomeDir, new EnvironmentConfig().setAllowCreate(true).setReadOnly(false));
        variantsDb1 = environment.openDatabase(txn, "variants1", new DatabaseConfig().setBtreeComparator(KeySorterComparator.class).setAllowCreate(true).setReadOnly(false).setTemporary(true));
        long total_variants = 0L;
        final LumpyVarBinding lumpVarBinding = new LumpyVarBinding();
        final KeySorterBinding keySorterBinding = new KeySorterBinding();
        for (int idx = 0; idx < inputs.size(); ++idx) {
            final long millisecstart = System.currentTimeMillis();
            final File vcfFile = inputs.get(idx);
            int nVariant = 0;
            final VCFFileReader r = new VCFFileReader(vcfFile, false);
            final List<Genotype> missing = new ArrayList<>(sampleNames.size());
            for (final String sn : sampleNames) {
                if (r.getFileHeader().getSampleNamesInOrder().contains(sn))
                    continue;
                missing.add(GenotypeBuilder.createMissing(sn, 2));
            }
            final CloseableIterator<VariantContext> iter = r.iterator();
            while (iter.hasNext()) {
                VariantContext ctx = iter.next();
                if (!this.keep_secondary) {
                    if (ctx.hasAttribute("SECONDARY"))
                        continue;
                }
                if (!this.variantFilter.test(ctx))
                    continue;
                if (intervalTreeMapBed != null && !intervalTreeMapBed.containsOverlapping(ctx))
                    continue;
                final List<Genotype> gtList = new ArrayList<>(ctx.getGenotypes());
                for (int gi = 0; gi < gtList.size(); gi++) {
                    Genotype g = gtList.get(gi);
                    final GenotypeBuilder gb;
                    if (this.do_genotype && isAvailableGenotype(g)) {
                        gb = new GenotypeBuilder(g.getSampleName(), ctx.getAlternateAlleles());
                        gb.attributes(g.getExtendedAttributes());
                    } else {
                        gb = new GenotypeBuilder(g);
                    }
                    gb.attribute(chromStartFormatHeaderLine.getID(), ctx.getStart());
                    gb.attribute(chromEndFormatHeaderLine.getID(), ctx.getEnd());
                    gtList.set(gi, gb.make());
                }
                gtList.addAll(missing);
                ctx = new VariantContextBuilder(ctx).genotypes(gtList).rmAttribute("PRPOS").make();
                final LumpyVar lvar = new LumpyVar(ctx, total_variants);
                final DatabaseEntry key = new DatabaseEntry();
                final DatabaseEntry data = new DatabaseEntry();
                lumpVarBinding.objectToEntry(lvar, data);
                keySorterBinding.objectToEntry(lvar.getSortKey(), key);
                if (variantsDb1.put(txn, key, data) != OperationStatus.SUCCESS) {
                    r.close();
                    LOG.error("insertion failed");
                    return -1;
                }
                nVariant++;
                total_variants++;
            }
            iter.close();
            r.close();
            LOG.info("Read  " + (idx + 1) + "/" + inputs.size() + " variants of " + vcfFile + " N=" + nVariant + " Total:" + total_variants + " That took: " + Duration.ofMillis(System.currentTimeMillis() - millisecstart));
            System.gc();
        }
        if (intervalTreeMapBed != null)
            intervalTreeMapBed.clear();
        System.gc();
        LOG.info("Writing output");
        final List<Allele> ALLELES_NO_CALLS = this.do_genotype ? Collections.singletonList(Allele.NO_CALL) : Arrays.asList(Allele.NO_CALL, Allele.NO_CALL);
        final Cursor cursor = variantsDb1.openCursor(txn, null);
        vcw = super.openVariantContextWriter(this.outputFile);
        vcw.writeHeader(outHeader);
        for (; ; ) {
            final DatabaseEntry key = new DatabaseEntry();
            final DatabaseEntry data = new DatabaseEntry();
            OperationStatus status = cursor.getNext(key, data, LockMode.DEFAULT);
            if (!status.equals(OperationStatus.SUCCESS))
                break;
            final LumpyVar first = lumpVarBinding.entryToObject(data);
            if (this.do_not_merge_ctx) {
                vcw.add(first.ctx);
                continue;
            }
            final KeySorter keySorter1 = keySorterBinding.entryToObject(key);
            final List<LumpyVar> buffer = new ArrayList<>();
            buffer.add(first);
            final DatabaseEntry key2 = new DatabaseEntry();
            final DatabaseEntry data2 = new DatabaseEntry();
            final Cursor cursor2 = cursor.dup(true);
            for (; ; ) {
                status = cursor2.getNext(key2, data2, LockMode.DEFAULT);
                if (!status.equals(OperationStatus.SUCCESS))
                    break;
                final KeySorter keySorter2 = keySorterBinding.entryToObject(key2);
                if (keySorter1.compare1(keySorter2) != 0) {
                    break;
                }
                final LumpyVar lv = lumpVarBinding.entryToObject(data2);
                if (lv.ctx.getStart() > first.ctx.getEnd()) {
                    break;
                }
                if (first.canMerge(lv)) {
                    buffer.add(lv);
                    cursor2.delete();
                }
            }
            cursor2.close();
            // delete 'first'
            cursor.delete();
            final int variantStartA = buffer.stream().mapToInt(V -> V.ctx.getStart()).min().getAsInt();
            final int variantStartB = (int) buffer.stream().mapToInt(V -> V.ctx.getStart()).average().getAsDouble();
            final int variantStartC = buffer.stream().mapToInt(V -> V.ctx.getStart()).max().getAsInt();
            final int variantEndA = buffer.stream().mapToInt(V -> V.ctx.getEnd()).min().getAsInt();
            final int variantEndB = (int) buffer.stream().mapToInt(V -> V.ctx.getEnd()).average().getAsDouble();
            final int variantEndC = buffer.stream().mapToInt(V -> V.ctx.getEnd()).max().getAsInt();
            final VariantContextBuilder vcb = new VariantContextBuilder("lumpymerge", first.ctx.getContig(), variantStartB, variantEndB, first.ctx.getAlleles());
            vcb.attribute("END", variantEndB);
            vcb.attribute("SVTYPE", first.ctx.getAttribute("SVTYPE"));
            vcb.attribute("SVLEN", (int) Percentile.median().evaluate(buffer.stream().mapToInt(V -> V.ctx.getEnd() - V.ctx.getStart())));
            vcb.attribute("CIPOS", Arrays.asList(variantStartB - variantStartA, variantStartC - variantStartB));
            vcb.attribute("CIEND", Arrays.asList(variantEndB - variantEndA, variantEndC - variantEndB));
            vcb.attribute("SU", buffer.stream().flatMap(V -> V.ctx.getGenotypes().stream()).mapToInt(G -> G.getAttributeAsInt("SU", 0)).sum());
            vcb.attribute("SR", buffer.stream().flatMap(V -> V.ctx.getGenotypes().stream()).mapToInt(G -> G.getAttributeAsInt("SR", 0)).sum());
            vcb.attribute("PE", buffer.stream().flatMap(V -> V.ctx.getGenotypes().stream()).mapToInt(G -> G.getAttributeAsInt("PE", 0)).sum());
            final Map<String, Genotype> sample2genotype = new HashMap<>(sampleNames.size());
            buffer.stream().flatMap(V -> V.ctx.getGenotypes().stream()).filter(G -> isAvailableGenotype(G)).forEach(G -> {
                sample2genotype.put(G.getSampleName(), G);
            });
            vcb.attribute(nSampleInfoHeaderLine.getID(), sample2genotype.size());
            for (final String sn : sampleNames) {
                if (!sample2genotype.containsKey(sn)) {
                    sample2genotype.put(sn, new GenotypeBuilder(sn, ALLELES_NO_CALLS).attribute("SU", 0).attribute("SR", 0).attribute("PE", 0).make());
                }
            }
            vcb.genotypes(sample2genotype.values());
            vcw.add(vcb.make());
        }
        cursor.close();
        vcw.close();
        vcw = null;
        variantsDb1.close();
        variantsDb1 = null;
        environment.close();
        environment = null;
        return 0;
    } catch (final Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(vcfIn);
        CloserUtil.close(vcw);
        CloserUtil.close(variantsDb1);
        CloserUtil.close(environment);
    }
}