Examples with DB org.mapdb.DB used on opensource projects

Example 6 with DB

use of org.mapdb.DB in project rskj by rsksmart.

the class IndexedBlockStoreTest method test8.

// leveldb + mapdb, multi branch, total re-branch test
@Test
public void test8() throws IOException {
    BigInteger bi = new BigInteger(32, new Random());
    String testDir = "test_db_" + bi;
    config.setDataBaseDir(testDir);
    DB indexDB = createMapDB(testDir);
    Map<Long, List<IndexedBlockStore.BlockInfo>> indexMap = createIndexMap(indexDB);
    KeyValueDataSource blocksDB = new LevelDbDataSource(config, "blocks");
    blocksDB.init();
    try {
        IndexedBlockStore indexedBlockStore = new IndexedBlockStore(indexMap, blocksDB, indexDB);
        Block genesis = Genesis.getInstance(config);
        List<Block> bestLine = getRandomChain(genesis.getHash().getBytes(), 1, 100);
        indexedBlockStore.saveBlock(genesis, genesis.getCumulativeDifficulty(), true);
        BlockDifficulty td = BlockDifficulty.ZERO;
        for (int i = 0; i < bestLine.size(); ++i) {
            Block newBlock = bestLine.get(i);
            td = td.add(newBlock.getCumulativeDifficulty());
            indexedBlockStore.saveBlock(newBlock, td, true);
        }
        byte[] forkParentHash = bestLine.get(60).getHash().getBytes();
        long forkParentNumber = bestLine.get(60).getNumber();
        List<Block> forkLine = getRandomChain(forkParentHash, forkParentNumber + 1, 10);
        for (int i = 0; i < forkLine.size(); ++i) {
            Block newBlock = forkLine.get(i);
            Block parentBlock = indexedBlockStore.getBlockByHash(newBlock.getParentHash().getBytes());
            td = indexedBlockStore.getTotalDifficultyForHash(parentBlock.getHash().getBytes());
            td = td.add(newBlock.getCumulativeDifficulty());
            indexedBlockStore.saveBlock(newBlock, td, false);
        }
        Block bestBlock = bestLine.get(bestLine.size() - 1);
        Block forkBlock = forkLine.get(forkLine.size() - 1);
        assertTrue(indexedBlockStore.getBestBlock().getNumber() == 100);
        indexedBlockStore.reBranch(forkBlock);
        assertTrue(indexedBlockStore.getBestBlock().getNumber() == 71);
        // Assert that all fork moved to the main line
        for (Block currBlock : forkLine) {
            Long number = currBlock.getNumber();
            Block chainBlock = indexedBlockStore.getChainBlockByNumber(number);
            assertEquals(currBlock.getShortHash(), chainBlock.getShortHash());
        }
        // Assert that all fork moved to the main line
        // re-branch back to previous line and assert that
        // all the block really moved
        bestBlock = bestLine.get(bestLine.size() - 1);
        indexedBlockStore.reBranch(bestBlock);
        for (Block currBlock : bestLine) {
            Long number = currBlock.getNumber();
            Block chainBlock = indexedBlockStore.getChainBlockByNumber(number);
            assertEquals(currBlock.getShortHash(), chainBlock.getShortHash());
        }
    } finally {
        blocksDB.close();
        indexDB.close();
        FileUtil.recursiveDelete(testDir);
    }
}

Example 7 with DB

use of org.mapdb.DB in project eol-globi-data by jhpoelen.

the class StudyImporterForCoetzer method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    if (org.apache.commons.lang.StringUtils.isBlank(getResourceArchiveURI())) {
        throw new StudyImporterException("failed to import [" + getDataset().getNamespace() + "]: no [archiveURL] specified");
    }
    DB db = DBMaker.newMemoryDirectDB().compressionEnable().transactionDisable().make();
    final HTreeMap<Integer, String> taxonMap = db.createHashMap("taxonMap").make();
    final HTreeMap<Integer, String> refMap = db.createHashMap("refMap").make();
    try {
        InputStream inputStream = DatasetUtil.getNamedResourceStream(getDataset(), "archive");
        ZipInputStream zipInputStream = new ZipInputStream(inputStream);
        ZipEntry entry;
        File taxonTempFile = null;
        File assocTempFile = null;
        File referencesTempFile = null;
        File distributionTempFile = null;
        while ((entry = zipInputStream.getNextEntry()) != null) {
            if (entry.getName().matches("(^|(.*/))taxon.txt$")) {
                taxonTempFile = FileUtils.saveToTmpFile(zipInputStream, entry);
            } else if (entry.getName().matches("(^|(.*/))description.txt$")) {
                assocTempFile = FileUtils.saveToTmpFile(zipInputStream, entry);
            } else if (entry.getName().matches("(^|(.*/))references.txt$")) {
                referencesTempFile = FileUtils.saveToTmpFile(zipInputStream, entry);
            } else if (entry.getName().matches("(^|(.*/))distribution.txt$")) {
                distributionTempFile = FileUtils.saveToTmpFile(zipInputStream, entry);
            } else {
                IOUtils.copy(zipInputStream, new NullOutputStream());
            }
        }
        IOUtils.closeQuietly(zipInputStream);
        if (taxonTempFile == null) {
            throw new StudyImporterException("failed to find expected [taxon.txt] resource");
        }
        if (assocTempFile == null) {
            throw new StudyImporterException("failed to find expected [description.txt] resource");
        }
        if (referencesTempFile == null) {
            throw new StudyImporterException("failed to find expected [references.txt] resource");
        }
        if (distributionTempFile == null) {
            throw new StudyImporterException("failed to find expected [distribution.txt] resource");
        }
        BufferedReader assocReader = FileUtils.getUncompressedBufferedReader(new FileInputStream(taxonTempFile), CharsetConstant.UTF8);
        LabeledCSVParser parser = CSVTSVUtil.createLabeledCSVParser(assocReader);
        parser.changeDelimiter('\t');
        String[] line;
        while ((line = parser.getLine()) != null) {
            taxonMap.put(Integer.parseInt(line[0]), nameFor(line));
        }
        LabeledCSVParser refs = CSVTSVUtil.createLabeledCSVParser(new FileInputStream(referencesTempFile));
        refs.changeDelimiter('\t');
        String[] refsLine;
        while ((refsLine = refs.getLine()) != null) {
            refMap.put(Integer.parseInt(refsLine[0]), refsLine[1]);
        }
        LabeledCSVParser assoc = CSVTSVUtil.createLabeledCSVParser(new FileInputStream(assocTempFile));
        assoc.changeDelimiter('\t');
        final Map<String, InteractType> interactTypeMap = new HashMap<String, InteractType>() {

            {
                put("Visits flowers of", InteractType.VISITS_FLOWERS_OF);
                put("Host of", InteractType.VISITS_FLOWERS_OF);
                put("Parasite of", InteractType.PARASITE_OF);
                put("Nests in", InteractType.INTERACTS_WITH);
            }
        };
        String[] assocLine;
        while ((assocLine = assoc.getLine()) != null) {
            final Integer taxonId = Integer.parseInt(assocLine[0]);
            final String[] parts = assocLine[2].split(":");
            if (parts.length > 1) {
                String interactionString = parts[0];
                String[] targetTaxonNames = parts[1].split(",");
                for (String targetTaxonName : targetTaxonNames) {
                    final String reference = refMap.get(taxonId);
                    final String sourceTaxonName = taxonMap.get(taxonId);
                    if (StringUtils.isNotBlank(reference) && StringUtils.isNotBlank(sourceTaxonName)) {
                        final Study study = nodeFactory.getOrCreateStudy(new StudyImpl(getSourceCitation() + reference, getSourceCitationLastAccessed(), null, reference));
                        final Specimen source = nodeFactory.createSpecimen(study, new TaxonImpl(StringUtils.trim(sourceTaxonName), null));
                        final Specimen target = nodeFactory.createSpecimen(study, new TaxonImpl(StringUtils.trim(targetTaxonName), null));
                        final InteractType relType = interactTypeMap.get(interactionString);
                        if (relType == null) {
                            throw new StudyImporterException("found unsupported interaction type [" + interactionString + "]");
                        }
                        source.interactsWith(target, relType);
                    }
                }
            }
        }
    } catch (IOException | NodeFactoryException e) {
        throw new StudyImporterException(e);
    }
    db.close();
}

Example 8 with DB

use of org.mapdb.DB in project mapdb by jankotek.

the class Issue418Test method test.

@Test
public void test() {
    final File tmp = TT.tempFile();
    for (int o = 0; o < 2; o++) {
        final DB db = DBMaker.fileDB(tmp).make();
        final DBConcurrentMap map = db.hashMap("foo").expireMaxSize(100).createOrOpen();
        for (int i = 0; i < TT.testScale() * 10000; i++) map.put("foo" + i, "bar" + i);
        db.commit();
        db.close();
    }
}

Example 9 with DB

use of org.mapdb.DB in project mapdb by jankotek.

the class IssueFromDatumbox method main.

@Test
public void main() throws IOException {
    // Pick one of the following lines to get a different error
    // fails every time - throws java.lang.NullPointerException
    String f = TT.tempFile().getPath();
    // File f = File.createTempFile("mapdb","db"); //fails every time - throws java.io.EOFException exception
    // String f = "/tmp/constantName"; //fails only in the first execution but NOT in any subsequent execution - throws java.lang.NullPointerException
    SomeObject x = new SomeObject();
    x.someValue = 10;
    x.someClass = SomeOtherClass.class;
    DB db = DBMaker.fileDB(f).make();
    Atomic.Var<Object> atomicVar = db.atomicVar("test").createOrOpen();
    atomicVar.set(x);
    db.close();
    db = DBMaker.fileDB(f).make();
    atomicVar = db.atomicVar("test").createOrOpen();
    x = (SomeObject) atomicVar.get();
    assertEquals(10, x.someValue);
    assertEquals(SomeOtherClass.class, x.someClass);
    db.close();
}

Example 10 with DB

use of org.mapdb.DB in project watchdog by TestRoots.

the class PersisterBase method createDatabase.

private DB createDatabase(final File file) {
    replaceClassLoader();
    DB database = DBMaker.newFileDB(file).closeOnJvmShutdown().make();
    isClosed = false;
    resetOldClassLoader();
    return database;
}