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

Example 16 with DatabaseConfig

use of com.sleepycat.je.DatabaseConfig 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 17 with DatabaseConfig

use of com.sleepycat.je.DatabaseConfig 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);
    }
}

Example 18 with DatabaseConfig

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

the class PubmedOrcidGraph method doWork.

@Override
public int doWork(final List<String> args) {
    if (!this.ncbiApiKey.isApiKeyDefined()) {
        LOG.error("NCBI API key is not defined");
        return -1;
    }
    InputStream in = null;
    XMLEventReader r = null;
    try {
        // open BDB
        final EnvironmentConfig envCfg = new EnvironmentConfig();
        envCfg.setAllowCreate(true);
        envCfg.setReadOnly(false);
        LOG.info("open BDB env...");
        this.environment = new Environment(this.bdbDir, envCfg);
        LOG.info("open BDB databases...");
        final DatabaseConfig config = new DatabaseConfig();
        config.setAllowCreate(true);
        config.setReadOnly(false);
        config.setTemporary(true);
        this.authorDatabase = this.environment.openDatabase(txn, "authors", config);
        this.articleDatabase = this.environment.openDatabase(txn, "articles", config);
        this.linkDatabase = this.environment.openDatabase(txn, "links", config);
        if (this.dumpStrangeOrcidFile != null) {
            this.errPrintWriter = super.openPathOrStdoutAsPrintStream(this.dumpStrangeOrcidFile);
        }
        if (this.input_is_orcid_id) {
            /* recursively scan authors */
            for (final String orcid : args) {
                scanOrcid(orcid, 0);
            }
            while (complete()) {
            // run...
            }
        } else {
            /* input is a efetch stream */
            final String inputName = oneFileOrNull(args);
            in = (inputName == null ? stdin() : IOUtils.openURIForReading(inputName));
            scanArticles(in, 0);
            in.close();
            in = null;
        }
        dumpGexf();
        this.errPrintWriter.flush();
        if (this.dumpStrangeOrcidFile != null) {
            this.errPrintWriter.close();
        }
        return 0;
    } catch (Exception e) {
        LOG.error(e);
        return -1;
    } finally {
        CloserUtil.close(in);
        CloserUtil.close(r);
        CloserUtil.close(authorDatabase);
        CloserUtil.close(articleDatabase);
        CloserUtil.close(linkDatabase);
        CloserUtil.close(environment);
    }
}

Example 19 with DatabaseConfig

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

the class PubmedAuthorGraph method doWork.

@Override
public int doWork(final List<String> args) {
    if (!this.ncbiApiKey.isApiKeyDefined()) {
        LOG.error("NCBI API key is not defined");
        return -1;
    }
    InputStream in = null;
    XMLEventReader r = null;
    try {
        // open BDB
        final EnvironmentConfig envCfg = new EnvironmentConfig();
        envCfg.setAllowCreate(true);
        envCfg.setReadOnly(false);
        LOG.info("open BDB env...");
        this.environment = new Environment(this.bdbDir, envCfg);
        LOG.info("open BDB databases...");
        final DatabaseConfig config = new DatabaseConfig();
        config.setAllowCreate(true);
        config.setReadOnly(false);
        config.setTemporary(true);
        this.authorDatabase = this.environment.openDatabase(txn, "authors", config);
        this.articleDatabase = this.environment.openDatabase(txn, "articles", config);
        /* input is a efetch stream */
        final String inputName = oneFileOrNull(args);
        in = (inputName == null ? stdin() : IOUtils.openURIForReading(inputName));
        scanArticles(in);
        in.close();
        in = null;
        dumpGexf();
        return 0;
    } catch (final Throwable e) {
        e.printStackTrace();
        LOG.error(e);
        return -1;
    } finally {
        CloserUtil.close(in);
        CloserUtil.close(r);
        CloserUtil.close(authorDatabase);
        CloserUtil.close(articleDatabase);
        CloserUtil.close(environment);
    }
}

Example 20 with DatabaseConfig

use of com.sleepycat.je.DatabaseConfig in project BIMserver by opensourceBIM.

the class BerkeleyKeyValueStore method openTable.

public boolean openTable(DatabaseSession databaseSession, String tableName, boolean transactional) throws BimserverDatabaseException {
    if (tables.containsKey(tableName)) {
        throw new BimserverDatabaseException("Table " + tableName + " already opened");
    }
    DatabaseConfig databaseConfig = new DatabaseConfig();
    databaseConfig.setKeyPrefixing(keyPrefixing);
    databaseConfig.setAllowCreate(false);
    boolean finalTransactional = transactional && useTransactions;
    // if (!transactional) {
    // databaseConfig.setCacheMode(CacheMode.EVICT_BIN);
    // }
    databaseConfig.setDeferredWrite(!finalTransactional);
    databaseConfig.setTransactional(finalTransactional);
    databaseConfig.setSortedDuplicates(false);
    Database database = environment.openDatabase(null, tableName, databaseConfig);
    if (database == null) {
        throw new BimserverDatabaseException("Table " + tableName + " not found in database");
    }
    tables.put(tableName, new TableWrapper(database, finalTransactional));
    return true;
}