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

Example 1 with Environment

use of com.sleepycat.je.Environment in project OpenRefine by OpenRefine.

the class RefineBrokerImpl method init.

@Override
public void init(ServletConfig config) throws Exception {
    logger.trace("> init");
    super.init(config);
    timer = new Timer();
    expirer = new Expirer();
    timer.schedule(expirer, 0, LOCK_EXPIRATION_CHECK_DELAY);
    String dataDir = config.getInitParameter("refine.data");
    if (dataDir == null)
        dataDir = "data";
    File dataPath = new File(dataDir);
    if (!dataPath.exists())
        dataPath.mkdirs();
    EnvironmentConfig envConfig = new EnvironmentConfig();
    envConfig.setAllowCreate(true);
    envConfig.setTransactional(true);
    env = new Environment(dataPath, envConfig);
    StoreConfig storeConfig = new StoreConfig();
    storeConfig.setAllowCreate(true);
    storeConfig.setTransactional(true);
    projectStore = new EntityStore(env, "ProjectsStore", storeConfig);
    lockStore = new EntityStore(env, "LockStore", storeConfig);
    projectById = projectStore.getPrimaryIndex(String.class, Project.class);
    lockById = lockStore.getPrimaryIndex(String.class, Lock.class);
    locksByProject = lockStore.getSecondaryIndex(lockById, String.class, "pid");
    logger.trace("< init");
}

Example 2 with Environment

use of com.sleepycat.je.Environment in project GeoGig by boundlessgeo.

the class JEObjectDatabase method createDatabase.

protected Database createDatabase() {
    final String databaseName = "ObjectDatabase";
    Environment environment;
    try {
        environment = createEnvironment(readOnly);
    } catch (EnvironmentLockedException e) {
        throw new IllegalStateException("The repository is already open by another process for writing", e);
    }
    if (!environment.getDatabaseNames().contains(databaseName)) {
        if (readOnly) {
            environment.close();
            try {
                environment = createEnvironment(false);
            } catch (EnvironmentLockedException e) {
                throw new IllegalStateException(String.format("Environment open readonly but database %s does not exist.", databaseName));
            }
        }
        DatabaseConfig dbConfig = new DatabaseConfig();
        dbConfig.setAllowCreate(true);
        Database openDatabase = environment.openDatabase(null, databaseName, dbConfig);
        openDatabase.close();
        environment.flushLog(true);
        environment.close();
        environment = createEnvironment(readOnly);
    }
    // System.err.println("Opened ObjectDatabase at " + env.getHome()
    // + ". Environment read-only: " + environment.getConfig().getReadOnly()
    // + " database read only: " + this.readOnly);
    Database database;
    try {
        LOGGER.debug("Opening ObjectDatabase at {}", environment.getHome());
        DatabaseConfig dbConfig = new DatabaseConfig();
        dbConfig.setCacheMode(CacheMode.MAKE_COLD);
        // can result in a slightly smaller db size
        dbConfig.setKeyPrefixing(false);
        dbConfig.setReadOnly(readOnly);
        boolean transactional = environment.getConfig().getTransactional();
        dbConfig.setTransactional(transactional);
        dbConfig.setDeferredWrite(!transactional);
        database = environment.openDatabase(null, databaseName, dbConfig);
    } catch (RuntimeException e) {
        if (environment != null) {
            environment.close();
        }
        throw e;
    }
    this.env = environment;
    return database;
}

Example 3 with Environment

use of com.sleepycat.je.Environment in project vertigo by KleeGroup.

the class BerkeleyKVStorePlugin method buildFsEnvironment.

private static Environment buildFsEnvironment(final File dbFile, final boolean readOnly) {
    dbFile.mkdirs();
    final EnvironmentConfig fsEnvironmentConfig = new EnvironmentConfig().setConfigParam(EnvironmentConfig.LOG_MEM_ONLY, "false").setConfigParam(EnvironmentConfig.CLEANER_MIN_UTILIZATION, "90").setConfigParam(EnvironmentConfig.CLEANER_MIN_FILE_UTILIZATION, "50").setReadOnly(readOnly).setAllowCreate(!readOnly).setTransactional(!readOnly);
    return new Environment(dbFile, fsEnvironmentConfig);
}

Example 4 with Environment

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

the class Biostar92368 method doWork.

@Override
public int doWork(List<String> args) {
    if (this.dbHome == null) {
        LOG.error("Undefined DB-Home");
        return -1;
    }
    environment = null;
    EnvironmentConfig envCfg = new EnvironmentConfig();
    this.database = null;
    Transaction txn = null;
    PrintStream out = null;
    try {
        envCfg.setAllowCreate(true);
        this.environment = new Environment(dbHome, envCfg);
        DatabaseConfig cfg = new DatabaseConfig();
        cfg.setAllowCreate(true);
        cfg.setTemporary(true);
        this.database = environment.openDatabase(txn, "interactions", cfg);
        if (args.isEmpty()) {
            LOG.info("reading stdin");
            LineIterator r = IOUtils.openStdinForLineIterator();
            load(txn, r);
            CloserUtil.close(r);
        } else {
            for (String filename : args) {
                LOG.info("reading " + filename);
                LineIterator r = IOUtils.openURIForLineIterator(filename);
                load(txn, r);
                CloserUtil.close(r);
            }
        }
        out = super.openFileOrStdoutAsPrintStream(outputFile);
        DatabaseEntry key1 = new DatabaseEntry();
        DatabaseEntry data1 = new DatabaseEntry();
        DatabaseEntry key2 = new DatabaseEntry();
        DatabaseEntry data2 = new DatabaseEntry();
        Cursor c1 = this.database.openCursor(txn, null);
        Cursor c2 = this.database.openCursor(txn, null);
        while (c1.getNext(key1, data1, LockMode.DEFAULT) == OperationStatus.SUCCESS) {
            String prot1 = StringBinding.entryToString(key1);
            boolean first = true;
            while ((first ? c2.getFirst(key2, data2, LockMode.DEFAULT) : c2.getNext(key2, data2, LockMode.DEFAULT)) == OperationStatus.SUCCESS) {
                first = false;
                String prot2 = StringBinding.entryToString(key2);
                if (prot2.compareTo(prot1) <= 0)
                    continue;
                Stack<String> path = new Stack<String>();
                path.push(prot1);
                int depth = recursive(txn, prot2, path, -1, maxDepth);
                if (depth != -1) {
                    out.println(prot1 + "\t" + prot2 + "\t" + depth);
                } else {
                // System.out.println(prot1+"\t"+prot2+"\t"+depth);
                }
                if (out.checkError())
                    break;
            }
        }
        CloserUtil.close(c2);
        CloserUtil.close(c1);
        out.flush();
        out.close();
        return 0;
    } catch (Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(this.database);
        CloserUtil.close(this.environment);
    }
}

Example 5 with Environment

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

the class VcfAnnotWithBeacon method doWork.

@Override
public int doWork(final List<String> args) {
    try {
        if (this.bdbDir != null) {
            LOG.info("open BDB " + this.bdbDir);
            IOUtil.assertDirectoryIsWritable(this.bdbDir);
            final EnvironmentConfig envCfg = new EnvironmentConfig();
            envCfg.setAllowCreate(true);
            envCfg.setReadOnly(false);
            this.bdbEnv = new Environment(this.bdbDir, envCfg);
            final DatabaseConfig cfg = new DatabaseConfig();
            cfg.setAllowCreate(true);
            cfg.setReadOnly(false);
            this.beaconDatabase = this.bdbEnv.openDatabase(this.txn, "ga4ghBeaconBuffer", cfg);
        }
        return doVcfToVcf(args, outputFile);
    } catch (final Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(beaconDatabase);
        CloserUtil.close(bdbEnv);
    }
}