@Override public Object validate(Object o) { // check whether argument is a String or not if (o instanceof String) { try { // lookup org in map Entry org = index.get(o.toString().toLowerCase()); String species = o.toString().toLowerCase(); while (org == null && species.lastIndexOf(" ") > 0) { species = species.substring(0, species.lastIndexOf(" ")).trim(); org = index.get(species); } // if org was found return taxid if (org != null) return org.getId(); } catch (DatabaseException dbe) { fireEventOccurred(new DatabaseErrorEvent(dbe.getMessage(), "[Validator - validate]")); } } // nothing was found or error return null; }
/** * Constructor for a customized message with extension. * * @param message * String * @param extension * String */ public DatabaseErrorEvent(String message, String extension) { super(message, extension); super.desc = "An error occurred with the persistent layer."; this.setLog4jLevel(Level.ERROR); }
+ path, "[BerkeleyEnv - constructor]")); DatabaseErrorEvent error = new DatabaseErrorEvent( Config.properties.getProperty("persistent.BerkeleyEnv.PermissionError") + dir.getPath(), "[BerkeleyEnv - constructor]"); error.setLog4jLevel(Level.FATAL); if (!dir.canRead()) { fireEventOccurred(error); DatabaseErrorEvent de = new DatabaseErrorEvent(dbe.getMessage(), "[BerkeleyEnv - constructor]"); fireEventOccurred(de);
fireEventOccurred(new DatabaseErrorEvent(dbe.getMessage(), "[Validator - validate]"));
/** * Sets the runtime cache size of the Berkeley persistent layer as a * absolute figure. * * @param size * long */ // fixme: can find no uses of this public void setCacheSize(long size) { try { myDbEnvironment.getMutableConfig().setCacheSize(size); } catch (IllegalArgumentException iae) { DatabaseErrorEvent de = new DatabaseErrorEvent(iae.getMessage(), "[BerkeleyEnv - setCacheSize]"); fireEventOccurred(de); } catch (DatabaseException dbe) { DatabaseErrorEvent de = new DatabaseErrorEvent(dbe.getMessage(), "[BerkeleyEnv - setCacheSize]"); fireEventOccurred(de); } }
/** * Sets the runtime cache size of the Berkeley persistent layer as a * percentage of Java Heap. * * @param percent * int */ // fixme: can find no uses of this public void setCachePercentage(int percent) { try { myDbEnvironment.getMutableConfig().setCachePercent(percent); myDbEnvironment.evictMemory(); } catch (IllegalArgumentException iae) { DatabaseErrorEvent de = new DatabaseErrorEvent(iae.getMessage(), "[BerkeleyEnv - setCache]"); fireEventOccurred(de); } catch (DatabaseException dbe) { DatabaseErrorEvent de = new DatabaseErrorEvent(dbe.getMessage(), "[BerkeleyEnv - setCache]"); fireEventOccurred(de); } }
@Override public void cleanup() { index = null; // if a database was opened close it if (store != null) { try { store.close(); store = null; } catch (DatabaseException dbe) { fireEventOccurred(new DatabaseErrorEvent(dbe.getMessage(), "[Validator - cleanup]")); } } if (myEnv != null) { try { // Finally, close environment. myEnv.close(); myEnv = null; } catch (DatabaseException dbe) { fireEventOccurred(new DatabaseErrorEvent(dbe.getMessage(), "[Validator - cleanup]")); } } }
bais.close(); } catch (IOException ioe) { DatabaseErrorEvent de = new DatabaseErrorEvent( ioe.getMessage(), topic); fireEventOccurred(de); DatabaseErrorEvent de = new DatabaseErrorEvent( dbe.getMessage(), topic); fireEventOccurred(de); cursor.close(); } catch (DatabaseException dbe) { DatabaseErrorEvent de = new DatabaseErrorEvent( dbe.getMessage(), topic); fireEventOccurred(de);
@Override public void cleanup() { index = null; // if a database was opened close it if (store != null) { try { store.close(); store = null; } catch (DatabaseException dbe) { fireEventOccurred(new DatabaseErrorEvent(dbe.getMessage(), "[Validator - cleanup]")); } } if (myEnv != null) { try { // Finally, close environment. myEnv.close(); myEnv = null; } catch (DatabaseException dbe) { fireEventOccurred(new DatabaseErrorEvent(dbe.getMessage(), "[Validator - cleanup]")); } } }
fireEventOccurred(new DatabaseErrorEvent(dbe.getMessage(), "[Validator - validate]")); } catch (FileNotFoundException fnfe) {
bais.close(); } catch (IOException ioe) { DatabaseErrorEvent de = new DatabaseErrorEvent( ioe.getMessage(), "[BerkeleyEnv - getSID]"); fireEventOccurred(de); DatabaseErrorEvent de = new DatabaseErrorEvent( dbe.getMessage(), "[BerkeleyEnv - getSID]"); fireEventOccurred(de); cursor.close(); } catch (DatabaseException dbe) { DatabaseErrorEvent de = new DatabaseErrorEvent( dbe.getMessage(), "[BerkeleyEnv - getSID]"); fireEventOccurred(de);
@Override public void commit() { try { // sync all secondary databases for (SecondaryDatabase d : secDatabases.values()) { d.sync(); } // sync all primary databases for (Database d : databases.values()) { d.sync(); } // sync all dup databases for (Database d : dupDatabases.values()) { d.sync(); } if (myDbEnvironment != null) { myDbEnvironment.sync(); myDbEnvironment.compress(); myDbEnvironment.evictMemory(); } } catch (DatabaseException dbe) { DatabaseErrorEvent de = new DatabaseErrorEvent(dbe.getMessage(), "[BerkeleyEnv - commit]"); fireEventOccurred(de); } }
fireEventOccurred(new DatabaseErrorEvent(dbe.getMessage(), "[Validator - validate]")); } catch (FileNotFoundException fnfe) {
/** * Inserts a key/data combination into corresponding database. * * @param c * Class * @param key * Object * @param data * byte[] */ public void insertIntoDatabase(Class<?> c, Object key, byte[] data) { // get database for data Database myDb = databases.get(c); if (myDb != null) { try { // convert key and data DatabaseEntry theKey = convert(key); DatabaseEntry theData = new DatabaseEntry(data); // insert into database myDb.put(null, theKey, theData); } catch (DatabaseException dbe) { DatabaseErrorEvent de = new DatabaseErrorEvent( dbe.getMessage(), "[BerkeleyEnv - insertIntoDatabase]"); fireEventOccurred(de); } } }
/** * Inserts a key/data combination into corresponding database. * * @param c * Class * @param key * Object * @param data * byte[] */ public void insertIntoDupDatabase(Class<?> c, Object key, byte[] data) { // get database for data Database myDb = dupDatabases.get(c); if (myDb != null) { try { // convert key and data DatabaseEntry theKey = convert(key); DatabaseEntry theData = new DatabaseEntry(data); // insert into database myDb.put(null, theKey, theData); } catch (DatabaseException dbe) { DatabaseErrorEvent de = new DatabaseErrorEvent( dbe.getMessage(), "[BerkeleyEnv - insertIntoDupDatabase]"); fireEventOccurred(de); } } }
/** * Deletes a value from a primary database for a given key and class. * * @param c * Class * @param key * Object * @return byte[] */ public boolean deleteFromDatabase(Class<?> c, Object key) { byte[] old = getFromDatabase(c, key); // get database for class Database myDb = databases.get(c); if (old != null && myDb != null) { try { // convert key DatabaseEntry theKey = convert(key); // perform delete if (myDb.delete(null, theKey) == OperationStatus.SUCCESS) { return true; } } catch (DatabaseException dbe) { DatabaseErrorEvent de = new DatabaseErrorEvent( dbe.getMessage(), "[BerkeleyEnv - deleteFromDatabase]"); fireEventOccurred(de); } } return false; }
DatabaseErrorEvent de = new DatabaseErrorEvent( dbe.getMessage(), "[BerkeleyEnv - existsInDatabase]"); fireEventOccurred(de);
/** * Returns value associated with a key in a database for a given class. * * @param c * Class * @param key * Object * @return byte[] */ public byte[] getFromDatabase(Class<?> c, Object key) { // get database for class Database myDb = databases.get(c); if (myDb != null) { try { // convert key DatabaseEntry theKey = convert(key); // contains return data DatabaseEntry theData = new DatabaseEntry(); // perform the get if (myDb.get(null, theKey, theData, LockMode.DEFAULT) == OperationStatus.SUCCESS) { return theData.getData(); } } catch (DatabaseException dbe) { DatabaseErrorEvent de = new DatabaseErrorEvent( dbe.getMessage(), "[BerkeleyEnv - getFromDatabase]"); fireEventOccurred(de); } } return null; }
DatabaseErrorEvent de = new DatabaseErrorEvent( dbe.getMessage(), "[BerkeleyDupBrowser - next]"); berkeley.fireEventOccurred(de);
DatabaseErrorEvent de = new DatabaseErrorEvent( dbe.getMessage(), "[BerkeleyEnv - deleteFromDupDatabase]"); cursor.close(); } catch (DatabaseException dbe) { DatabaseErrorEvent de = new DatabaseErrorEvent( dbe.getMessage(), "[BerkeleyEnv - deleteFromDupDatabase]");