/ - Diff - D-Net - D-Net project tracking tool

     	 * @throws MDStoreServiceException
     	 *             the MD store service exception
     	 */
     	private void verifyConsistency() throws MDStoreServiceException {
     	@Override
     	public void verifyConsistency() throws MDStoreServiceException {
     		if (this.getManagerTable() == null) {
     			if (!db.collectionExists(TABLE_NAME)) {
     				bootstrapManager();

     import org.apache.commons.logging.LogFactory;
     import org.springframework.beans.factory.annotation.Required;
     import eu.dnetlib.data.mdstore.MDStoreServiceException;
     import eu.dnetlib.data.mdstore.modular.connector.MDStoreDao;
     import eu.dnetlib.data.mdstore.modular.mongodb.MongoMDStore;
     import eu.dnetlib.enabling.tools.AbstractSchedulable;
-...
     	protected void doExecute() {
     		log.info("performing mdstore index check");
     		for (String mdId : getDao().listMDStores()) {
     			try {
     				log.info("ensureindex for mdStoreId:" + mdId);
     				((MongoMDStore) getDao().getMDStore(mdId)).ensureIndices();
     			} catch (Throwable e) {
     				log.warn("unable to reindex mdstore: " + mdId, e);
     		try {
     			for (String mdId : getDao().listMDStores()) {
     				try {
     					log.info("ensureindex for mdStoreId:" + mdId);
     					((MongoMDStore) getDao().getMDStore(mdId)).ensureIndices();
     				} catch (Throwable e) {
     					log.warn("unable to reindex mdstore: " + mdId, e);
+    				}
+    			}
     		} catch (MDStoreServiceException e) {
     			log.warn("unable to reindex mdstore ", e);
+    		}
     		log.info("mdstore index check completed");

     import com.mongodb.DBCollection;
     import com.mongodb.DBObject;
     import eu.dnetlib.data.mdstore.MDStoreServiceException;
     import eu.dnetlib.data.mdstore.modular.connector.MDStoreDao;
     import eu.dnetlib.data.mdstore.modular.mongodb.MongoMDStore;
     import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
-...
     	 * lookup locator.
     	 */
     	private ServiceLocator<ISLookUpService> lookupLocator;
     	/**
     	 * {@link Endpoint}
     	 */
     	private Endpoint endpoint;
     	/**
     	 * {@link EndpointReferenceBuilder}
     	 */
     	private EndpointReferenceBuilder<Endpoint> eprBuilder;
     	private EndpointReferenceBuilder<Endpoint> eprBuilder;
     	/**
     	 * MDStore dao.
     	 */
     	private MDStoreDao dao;
     	private boolean runOnStart;
     	public void runOnStart() {
     		if(isRunOnStart()) {
     	public void runOnStart() throws MDStoreServiceException {
     		if (isRunOnStart()) {
     			log.info("running mdStore metadata check on service start");
     			repairMetadata();
+    		}
-...
     	/**
     	 * Job execution method.
+    	 *
     	 * @throws MDStoreServiceException
     	 */
     	public void repairMetadata() {
     	public void repairMetadata() throws MDStoreServiceException {
     		DBCollection metadata = ((MongoMDStore) getDao().getMDStore("metadata")).getCollection();
     		if (metadata.findOne() != null) {
     			log.debug("mdStore metadata doesn't need to be repaired");
-...
+    		}
     		try {
     			List<String> mdStores = getLookupLocator().getService().quickSearchProfile(
     				"//RESOURCE_PROFILE[" +
     					".//RESOURCE_TYPE/@value='MDStoreDSResourceType' and " +
     					".//RESOURCE_URI/@value='" + getServiceAddress() + "']");
     					"//RESOURCE_PROFILE[" + ".//RESOURCE_TYPE/@value='MDStoreDSResourceType' and " + ".//RESOURCE_URI/@value='" + getServiceAddress() + "']");
     			log.debug("repairing mdstore metadata");
     			if(mdStores!=null){
     				for(String MDStoreProfile : mdStores)
     			if (mdStores != null) {
     				for (String MDStoreProfile : mdStores) {
     					metadata.save(getMdInfo(MDStoreProfile));
+    				}
+    			}
     			log.debug("FINISHED repairing mdstore metadata");
     		} catch(ISLookUpException e) {
     		} catch (ISLookUpException e) {
     			throw new RuntimeException(e);
     		} catch(DocumentException e ) {
     		} catch (DocumentException e) {
     			throw new RuntimeException(e);
+    		}
+    		}
+    	}
     	/**
     	 * Helper method, gets an MDStore profile and returns a DBObject.
+    	 *
+    	 *
     	 * @param MDStoreProfile
     	 * @return a DBObject representing the metadata informations
     	 * @throws DocumentException
-...
     		return dbo;
+    	}
     	private String getServiceAddress() {
     		return getEprBuilder().getAddress(getEndpoint()) + "?wsdl";
+    	}
+    	}
     	@Required
     	public void setEprBuilder(EndpointReferenceBuilder<Endpoint> eprBuilder) {
     	public void setEprBuilder(final EndpointReferenceBuilder<Endpoint> eprBuilder) {
     		this.eprBuilder = eprBuilder;
+    	}
     	public EndpointReferenceBuilder<Endpoint> getEprBuilder() {
     		return eprBuilder;
+    	}
     	@Required
     	public void setEndpoint(Endpoint endpoint) {
     	public void setEndpoint(final Endpoint endpoint) {
     		this.endpoint = endpoint;
+    	}
     	public Endpoint getEndpoint() {
     		return endpoint;
+    	}
+    	}
     	@Required
     	public void setDao(MDStoreDao dao) {
     	public void setDao(final MDStoreDao dao) {
     		this.dao = dao;
+    	}
-...
+    	}
     	@Required
     	public void setLookupLocator(ServiceLocator<ISLookUpService> lookupLocator) {
     	public void setLookupLocator(final ServiceLocator<ISLookUpService> lookupLocator) {
     		this.lookupLocator = lookupLocator;
+    	}
-...
+    	}
     	@Required
     	public void setRunOnStart(boolean runOnStart) {
     	public void setRunOnStart(final boolean runOnStart) {
     		this.runOnStart = runOnStart;
+    	}
-...
+    	}
+    }

+    		}
     		public String getFormat() {
     			return mdstoreDao.getMDStore(id).getFormat();
     			try {
     				return mdstoreDao.getMDStore(id).getFormat();
     			} catch (MDStoreServiceException e) {
     				return null;
+    			}
+    		}
     		public String getLayout() {
     			return mdstoreDao.getMDStore(id).getLayout();
     			try {
     				return mdstoreDao.getMDStore(id).getLayout();
     			} catch (MDStoreServiceException e) {
     				return null;
+    			}
+    		}
     		public String getInterpretation() {
     			return mdstoreDao.getMDStore(id).getInterpretation();
     			try {
     				return mdstoreDao.getMDStore(id).getInterpretation();
     			} catch (MDStoreServiceException e) {
     				return null;
+    			}
+    		}
     		public boolean getIndexed() {
-...
+    	}
     	@RequestMapping(value = "/inspector/mdstores.do")
     	public void mdstores(final Model model) {
     	public void mdstores(final Model model) throws MDStoreServiceException {
     		model.addAttribute("mdstores", MappedCollection.listMap(mdstoreDao.listMDStores(), new UnaryFunction<MDStoreDescription, String>() {
     			@Override

     	private MDStoreTransactionManager transactionManager;
     	@Override
     	public void execute(final BlackboardServerHandler handler, final BlackboardJob job) throws ISRegistryDocumentNotFoundException, ISRegistryException {
     	public void execute(final BlackboardServerHandler handler, final BlackboardJob job) throws ISRegistryDocumentNotFoundException, ISRegistryException,
     			MDStoreServiceException {
     		registryLocator.getService().deleteProfile(job.getParameters().get("id"));
     		String currentId = job.getParameters().get("id");
     		try {

     	private MDStoreTransactionManager transactionManager;
     	@Override
     	public void execute(final BlackboardServerHandler handler, final BlackboardJob job) throws ISRegistryException {
     	public void execute(final BlackboardServerHandler handler, final BlackboardJob job) throws ISRegistryException, MDStoreServiceException {
     		final String format = job.getParameters().get("format");
     		final String interpretation = job.getParameters().get("interpretation");
     		final String layout = job.getParameters().get("layout");

modules/cnr-modular-mdstore-service/trunk/src/main/java/eu/dnetlib/data/mdstore/modular/MDStoreRetriever.java
38	38
39	39	}
40	40
41		public Iterable<String> deliver(final String format, final String layout, final String interpretation) {
	41	public Iterable<String> deliver(final String format, final String layout, final String interpretation) throws MDStoreServiceException {
42	42	return Iterables.concat(Iterables.transform(dao.listMDStores(format, layout, interpretation), new Function<String, Iterable<String>>() {
43	43
44	44	@Override
...	...
81	81	return resultSetFactory;
82	82	}
83	83
	84	public void verifyConsistency() throws MDStoreServiceException {
	85	transactionManager.verifyConsistency();
	86	}
	87
84	88	}

     import java.util.List;
     import eu.dnetlib.data.mdstore.MDStoreServiceException;
     public interface MDStoreDao {
     	MDStore getMDStore(String mdId);
     	MDStore getMDStore(String mdId) throws MDStoreServiceException;
     	List<String> listMDStores();
     	List<String> listMDStores() throws MDStoreServiceException;
     	List<String> listMDStores(String format, String layout, String interpretation);
     	List<String> listMDStores(String format, String layout, String interpretation) throws MDStoreServiceException;
     	void createMDStore(String mdId, String format, String interpretation, String layout);
     	void createMDStore(String mdId, String format, String interpretation, String layout) throws MDStoreServiceException;
     	void deleteMDStore(String id);
     	void deleteMDStore(String id) throws MDStoreServiceException;
+    }

     public interface MDStoreTransactionManager {
     	/**
     	 * Verify consistency.
+    	 *
     	 * @throws MDStoreServiceException
     	 *             the MD store service exception
     	 */
     	public abstract void verifyConsistency() throws MDStoreServiceException;
     	/**
     	 * Creates the md store.
+    	 *
+    	 *
     	 * @param mdId
     	 *            the md id
     	 * @throws MDStoreServiceException
-...
     	/**
     	 * Drop md store.
+    	 *
+    	 *
     	 * @param mdId
     	 *            the md id
     	 * @throws MDStoreServiceException
-...
     	/**
     	 * Gets the MD store collection.
+    	 *
+    	 *
     	 * @param mdId
     	 *            the md id
     	 * @return the MD store collection
-...
     	/**
     	 * Start a new transaction for writing in the mdstore this will create a temporary mdstore in which save the content. and after finished
     	 * switch it to the existing one
+    	 *
+    	 *
     	 * @param mdId
     	 * @param refresh
     	 * @throws MDStoreServiceException
-...
     	/**
     	 * Commit the transaction
+    	 *
+    	 *
+    	 *
+    	 *
     	 * @param transactionId
     	 * @param mdId
     	 * @return
-...
     	/**
     	 * Book a a current mdstore, so the transaction manager can't delete during a possible commit, until the resultset associate has not
     	 * expired
+    	 *
+    	 *
     	 * @param mdStoreId
     	 * @return
     	 * @throws MDStoreServiceException
-...
     	/**
     	 * Return a JSON about the transaction assigned to a particular mdstore
+    	 *
+    	 *
     	 * @param mdStoreId
     	 * @return
     	 * @throws MDStoreServiceException
-...
     	/**
     	 * Manually drop an old collection assigned to a particular mdStore
+    	 *
+    	 *
     	 * @param mdId
     	 *            : the id of the mdStore
     	 * @param idToDrop
-...
     	/**
     	 * Manually drop an old collection assigned to a particular mdStore
+    	 *
+    	 *
     	 * @param mdId
     	 *            : the id of the mdStore
     	 * @param idToDrop
-...
     	/**
     	 * Start the garbage collection of the old mdstore not used
+    	 *
+    	 *
     	 * @throws MDStoreServiceException
     	 */
     	public abstract void garbage() throws MDStoreServiceException;

+    	}
     	@Override
     	public void start() {
     		try {
     			retriever.getDao().listMDStores();
     			retriever.verifyConsistency();
     		} catch (MDStoreServiceException e) {
+    		}
     		super.start();
+    	}
     	@Override
     	public List<String> getListOfMDStores() throws MDStoreServiceException {
     		return retriever.getDao().listMDStores();
+    	}

      */
     public class PostgresMDStore implements MDStore {
     	private static final int MAX_NUM_RECORD_BEFORE_COMMIT = 10000;
     	private static final int MAX_NUM_RECORD_BEFORE_COMMIT = 100;
     	/** The id. */
     	private String id;
-...
     	 */
     	@Override
     	public void truncate() {
     		Connection conn = null;
     		try {
     			Connection conn = datasource.getConnection();
     			conn = datasource.getConnection();
     			// DELETE ALL ITEM IN FIELDS
     			conn.setAutoCommit(false);
     			String sql = String.format("delete from  %s_fields", this.id);
-...
     		} catch (SQLException e) {
     			log.error("Erron on dropping table " + this.id);
     		} finally {
     			if (conn != null) {
     				try {
     					conn.close();
     				} catch (SQLException e) {
     					log.error("Error on get mdstore", e);
+    				}
+    			}
+    		}
+    	}
-...
     		final BlockingQueue<Object> queue = new ArrayBlockingQueue<Object>(80);
     		final Object sentinel = new Object();
     		Thread background = null;
     		Connection connection = null;
     		try {
     			final Connection conn = this.datasource.getConnection();
     			connection = this.datasource.getConnection();
     			final Connection conn = connection;
     			conn.setAutoCommit(false);
     			// DROP DISCARDED COLLECTION AT NEW FEEDING
     			String dropDiscardedCollectionQuery = String.format("delete from %s_discarded", this.id);
-...
     				@Override
     				public void run() {
     					int commitNumber = 0;
     					while (true) {
     						try {
     							Object record = queue.take();
     							if (record == sentinel) {
     								conn.commit();
     								updateSizeOnMetadataTable(conn);
     								if (conn != null) {
     									try {
     										conn.close();
     									} catch (SQLException e) {
     										log.error("Error on close mdstore", e);
+    									}
+    								}
     								break;
+    							}
     							safeFeedRecord((String) record, incremental, conn);
-...
+    							}
     						} catch (InterruptedException e) {
     							log.fatal("got exception in background thread", e);
     							if (conn != null) {
     								try {
     									conn.close();
     								} catch (SQLException e1) {
     									log.error("Error on close mdstore", e);
+    								}
+    							}
     							throw new IllegalStateException(e);
     						} catch (SQLException e) {
     							log.fatal("got exception in background thread", e);
     							if (conn != null) {
     								try {
     									conn.close();
     								} catch (SQLException e1) {
     									log.error("Error on close mdstore", e);
+    								}
+    							}
     							throw new IllegalStateException(e);
+    						}
+    					}
-...
     			});
     			background.start();
     		} catch (SQLException e) {
     			if (connection != null) {
     				try {
     					connection.close();
     				} catch (SQLException e1) {
     					log.error("Error on close mdstore", e);
+    				}
+    			}
     			throw new IllegalStateException(e);
+    		}
     		try {
-...
     	private void feedRecord(final String record, final boolean incremental, final Connection connection) {
     		final Map<String, String> recordProperties = getRecordParser().parseRecord(record);
     		log.debug("found props: " + recordProperties);
     		if (recordProperties.containsKey("id")) {
     			String p = "WITH upsert AS (UPDATE %s SET body=?, timestampdate=? WHERE recordid=? RETURNING *) "
-...
     				ps.executeUpdate();
     			} catch (SQLException e) {
     				log.error("Error on insert Element");
     				log.error("Error on insert Element", e);
+    			}
     		} else {
     			if (discardRecords) {
-...
     	 */
     	@Override
     	public void deleteRecord(final String recordId) {
     		Connection connection = null;
     		try {
     			Connection connection = this.datasource.getConnection();
     			connection = this.datasource.getConnection();
     			String sql = String.format("delete from %s where recordid = ?", this.id);
     			PreparedStatement ps = connection.prepareStatement(sql);
     			ps.setString(1, recordId);
     			ps.executeUpdate();
     		} catch (SQLException e) {
     			log.error("ERROR ON DELETING record ", e);
     		} finally {
     			if (connection != null) {
     				try {
     					connection.close();
     				} catch (SQLException e) {
     					log.error("Error on get mdstore", e);
+    				}
+    			}
+    		}
+    	}
-...
     	 */
     	@Override
     	public String getRecord(final String recordId) throws DocumentNotFoundException {
     		Connection connection = null;
     		try {
     			Connection connection = this.datasource.getConnection();
     			connection = this.datasource.getConnection();
     			String sql = String.format("select body from %s where recordid = ?", this.id);
     			PreparedStatement ps = connection.prepareStatement(sql);
     			ps.setString(1, recordId);
-...
     		} catch (SQLException e) {
     			log.error("ERROR ON DELETING record ", e);
     			return null;
     		} finally {
     			if (connection != null) {
     				try {
     					connection.close();
     				} catch (SQLException e) {
     					log.error("Error on get mdstore", e);
+    				}
+    			}
+    		}
+    	}

     	@Override
     	public List<String> getResult(final int fromPosition, final int toPosition) {
     		Connection connection = null;
     		try {
     			Connection connection = datasource.getConnection();
     			String sql = String.format("select %s from %s order by recordid limit %d offset %d", this.selectedField, this.mdid, (fromPosition - 1),
     					((toPosition - fromPosition) + 1));
     			connection = datasource.getConnection();
     			String sql = String.format("select %s from %s order by recordid limit %d offset %d", this.selectedField, this.mdid,
     					((toPosition - fromPosition) + 1), (fromPosition - 1));
     			List<String> output = new ArrayList<String>();
     			PreparedStatement ps = connection.prepareStatement(sql);
     			java.sql.ResultSet rs = ps.executeQuery();
-...
     		} catch (SQLException e) {
     			log.error(e);
     			return null;
     		} finally {
     			if (connection != null) {
     				try {
     					connection.close();
     				} catch (SQLException e) {
     					log.error("Error on close connection", e);
+    				}
+    			}
+    		}
+    	}

     	private Resource templateCollection;
     	/** The datasource. */
     	@Autowired
     	@javax.annotation.Resource(name = "mdstoreDataSource")
     	private DataSource datasource;
     	/** The mdstore dao. */
-...
     	 * @throws MDStoreServiceException
     	 *             the MD store service exception
     	 */
     	private void verifyConsistency() throws MDStoreServiceException {
     	@Override
     	public void verifyConsistency() throws MDStoreServiceException {
     		Connection connection = null;
     		try {
     			Connection connection = this.datasource.getConnection();
     			connection = this.datasource.getConnection();
     			if (!existsTable("metadata", connection)) {
     				mdstoreDAO.listMDStores();
+    			}
     			if (!existsTable(TRANSACTION_TABLE, connection)) {
     				log.debug(String.format("Table %s does not exist , Creating table", TRANSACTION_TABLE));
     				createTable(templateTransaction, connection, TRANSACTION_TABLE);
-...
     				log.debug(String.format("Table %s does not exist , Creating table", READLOCK_TABLE));
     				createTable(templateReadLock, connection, READLOCK_TABLE);
+    			}
     		} catch (SQLException e) {
     			log.error("Error during verify consistency ", e);
     		} finally {
     			if (connection != null) {
     				try {
     					connection.close();
     				} catch (SQLException e) {
     					log.error("Error on close connection", e);
     					throw new MDStoreServiceException(e);
+    				}
+    			}
+    		}
+    	}
-...
     	/*
     	 * (non-Javadoc)
+    	 *
+    	 *
     	 * @see eu.dnetlib.data.mdstore.modular.connector.MDStoreTransactionManager#createMDStore(java.lang.String)
     	 */
     	@Override
-...
     	/*
     	 * (non-Javadoc)
+    	 *
+    	 *
     	 * @see eu.dnetlib.data.mdstore.modular.connector.MDStoreTransactionManager#dropMDStore(java.lang.String)
     	 */
     	@Override
     	public void dropMDStore(final String mdId) throws MDStoreServiceException {
     		Connection connection = null;
     		try {
     			Connection connection = this.datasource.getConnection();
     			connection = this.datasource.getConnection();
     			verifyConsistency();
     			connection.setAutoCommit(true);
     			String sql = String.format("select current_table from %s where mdid = ?", METADATA_TABLE);
-...
     		} catch (SQLException e) {
     			log.error("ERROR ON DROP MDSTORE " + mdId, e);
     			throw new MDStoreServiceException("ERROR ON DROP MDSTORE " + mdId, e);
     		} finally {
     			if (connection != null) {
     				try {
     					connection.close();
     				} catch (SQLException e) {
     					log.error("Error on close connection", e);
     					throw new MDStoreServiceException(e);
+    				}
+    			}
+    		}
+    	}
     	/*
     	 * (non-Javadoc)
+    	 *
+    	 *
     	 * @see eu.dnetlib.data.mdstore.modular.connector.MDStoreTransactionManager#getMDStoreCollection(java.lang.String)
     	 */
     	@Override
     	public String getMDStoreCollection(final String mdId) throws MDStoreServiceException {
     		Connection connection = null;
     		try {
     			connection = this.datasource.getConnection();
     			verifyConsistency();
     			Connection connection = this.datasource.getConnection();
     			String table = getCurrentTable(mdId, connection);
     			if (!existsTable(table, connection))
     				throw new MDStoreServiceException(String.format("ERROR on GET MDSTORE: unable to find the current mdstore associated on %s", mdId));
-...
     		} catch (SQLException e) {
     			log.error("ERROR ON GET MDSTORE " + mdId, e);
     			throw new MDStoreServiceException("ERROR ON GET MDSTORE " + mdId, e);
     		} finally {
     			if (connection != null) {
     				try {
     					connection.close();
     				} catch (SQLException e) {
     					log.error("Error on close connection", e);
     					throw new MDStoreServiceException(e);
+    				}
+    			}
+    		}
+    	}
-...
     	/*
     	 * (non-Javadoc)
+    	 *
+    	 *
     	 * @see eu.dnetlib.data.mdstore.modular.connector.MDStoreTransactionManager#startTransaction(java.lang.String, boolean)
     	 */
     	@Override
     	public String startTransaction(final String mdId, final boolean refresh) throws MDStoreServiceException {
     		Connection connection = null;
     		try {
     			connection = this.datasource.getConnection();
     			verifyConsistency();
     			Connection connection = this.datasource.getConnection();
     			String table = getCurrentTable(mdId, connection);
     			if (mdId.contains("_")) {
     				table = StringUtils.substringBefore(mdId, "_").replace("-", "_");
-...
     			return table;
     		} catch (SQLException e) {
     			throw new MDStoreServiceException("Error on creating transaction ", e);
     		} finally {
     			if (connection != null) {
     				try {
     					connection.close();
     				} catch (SQLException e) {
     					log.error("Error on close connection", e);
     					throw new MDStoreServiceException(e);
+    				}
+    			}
+    		}
+    	}
     	/**
-...
     	 *             the MD store service exception
     	 */
     	public String getMDStoreForTransaction(final String transactionId) throws MDStoreServiceException {
     		Connection connection = null;
     		try {
     			connection = this.datasource.getConnection();
     			verifyConsistency();
     			String sql = String.format("select mdstoreid from %s where id=?", TRANSACTION_TABLE);
     			Connection connection = this.datasource.getConnection();
     			PreparedStatement statement = connection.prepareStatement(sql);
     			statement.setString(1, transactionId);
     			ResultSet rs = statement.executeQuery();
-...
     			return rs.getString(1);
     		} catch (SQLException e) {
     			return null;
     		} finally {
     			if (connection != null) {
     				try {
     					connection.close();
     				} catch (SQLException e) {
     					log.error("Error on close connection", e);
     					throw new MDStoreServiceException(e);
+    				}
+    			}
+    		}
+    	}
     	/*
     	 * (non-Javadoc)
+    	 *
+    	 *
     	 * @see eu.dnetlib.data.mdstore.modular.connector.MDStoreTransactionManager#commit(java.lang.String, java.lang.String)
     	 */
     	@Override
-...
     	 *             the MD store service exception
     	 */
     	private void dropEntriesInTransaction(final String tableName, final String mdId) throws MDStoreServiceException {
     		Connection connection = null;
     		try {
     			Connection connection = this.datasource.getConnection();
     			connection = this.datasource.getConnection();
     			String sql = String.format("delete from %s where id=? and mdstoreid=?", TRANSACTION_TABLE);
     			PreparedStatement ps = connection.prepareStatement(sql);
     			ps.setString(1, tableName);
-...
     			ps.executeUpdate();
     		} catch (SQLException e) {
     			throw new MDStoreServiceException("Error on deleting transaction table");
     		} finally {
     			if (connection != null) {
     				try {
     					connection.close();
     				} catch (SQLException e) {
     					log.error("Error on close connection", e);
     					throw new MDStoreServiceException(e);
+    				}
+    			}
+    		}
+    	}
-...
     		String sql_delete_fields = String.format("DROP table IF EXISTS  %s_fields", tableName);
     		String sql_delete_discarded = String.format("DROP table IF EXISTS %s_discarded", tableName);
     		String sql_delete_table = String.format("DROP table IF EXISTS %s", tableName);
     		Connection connection = null;
     		try {
     			Connection connection = this.datasource.getConnection();
     			connection = this.datasource.getConnection();
     			connection.prepareStatement(sql_delete_fields).executeUpdate();
     			connection.prepareStatement(sql_delete_discarded).executeUpdate();
     			connection.prepareStatement(sql_delete_table).executeUpdate();
     		} catch (SQLException e) {
     			throw new MDStoreServiceException("error on drop old table ", e);
     		} finally {
     			if (connection != null) {
     				try {
     					connection.close();
     				} catch (SQLException e) {
     					log.error("Error on close connection", e);
     					throw new MDStoreServiceException(e);
+    				}
+    			}
+    		}
+    	}
-...
     	 *             the MD store service exception
     	 */
     	private String retreiveCurrentId(final String mdId) throws MDStoreServiceException {
     		Connection connection = null;
     		try {
     			Connection connection = this.datasource.getConnection();
     			connection = this.datasource.getConnection();
     			String sql = String.format("select current_table from %s where mdid=?", METADATA_TABLE);
     			PreparedStatement st = connection.prepareStatement(sql);
     			st.setString(1, mdId);
-...
     			return rs.getString("current_table");
     		} catch (SQLException e) {
     			throw new MDStoreServiceException("Error on retrieve the current table from metadata for mdId " + mdId, e);
     		} finally {
     			if (connection != null) {
     				try {
     					connection.close();
     				} catch (SQLException e) {
     					log.error("Error on close connection", e);
     					throw new MDStoreServiceException(e);
+    				}
+    			}
+    		}
+    	}
-...
     	 *             the MD store service exception
     	 */
     	private void updateCurrentTable(final String transactionId, final String mdId) throws MDStoreServiceException {
     		Connection connection = null;
     		try {
     			Connection connection = this.datasource.getConnection();
     			connection = this.datasource.getConnection();
     			String sql = String.format("update %s set current_table=? where mdid=?", METADATA_TABLE);
     			PreparedStatement st = connection.prepareStatement(sql);
     			st.setString(1, transactionId);
-...
     			st.executeUpdate();
     		} catch (SQLException e) {
     			throw new MDStoreServiceException("Error on update metadata table, for commit on metadata", e);
     		} finally {
     			if (connection != null) {
     				try {
     					connection.close();
     				} catch (SQLException e) {
     					log.error("Error on close connection", e);
     					throw new MDStoreServiceException(e);
+    				}
+    			}
+    		}
+    	}
     	/*
     	 * (non-Javadoc)
+    	 *
+    	 *
     	 * @see eu.dnetlib.data.mdstore.modular.connector.MDStoreTransactionManager#readMdStore(java.lang.String)
     	 */
     	@Override
     	public String readMdStore(final String mdStoreId) throws MDStoreServiceException {
     		Connection connection = null;
     		try {
     			Connection connection = this.datasource.getConnection();
     			connection = this.datasource.getConnection();
     			String currentTableName = getCurrentTable(mdStoreId, connection);
     			String p = "WITH upsert AS (UPDATE %s SET dateofread=? WHERE id=? and mdstoreid=? RETURNING *) "
     					+ " INSERT INTO %s (id, mdstoreid, dateofread) SELECT ?,?,?  WHERE NOT EXISTS (SELECT * FROM upsert)";
-...
     			ps.setString(5, mdStoreId);
     			ps.setTimestamp(6, new Timestamp(System.currentTimeMillis()));
     			ps.executeUpdate();
     			return mdStoreId;
     		} catch (SQLException e) {
     			throw new MDStoreServiceException("Error on lock mdstore ", e);
     		} finally {
     			if (connection != null) {
     				try {
     					connection.close();
     				} catch (SQLException e) {
     					log.error("Error on close connection", e);
     					throw new MDStoreServiceException(e);
+    				}
+    			}
+    		}
     		return null;
+    	}
     	/*
     	 * (non-Javadoc)
+    	 *
+    	 *
     	 * @see eu.dnetlib.data.mdstore.modular.connector.MDStoreTransactionManager#getInfoForCurrentMdStore(java.lang.String)
     	 */
     	@Override
     	public MDStoreManagerInfo getInfoForCurrentMdStore(final String mdStoreId) throws MDStoreServiceException {
     		Connection connection = null;
     		try {
     			connection = this.datasource.getConnection();
     			MDStoreManagerInfo info = new MDStoreManagerInfo();
     			String currenttable = getCurrentTable(mdStoreId, this.datasource.getConnection());
-...
     			List<MDStoreExpiredInfo> infoExpired = getJdbcTemplateObject().query(sql, new Object[] { mdStoreId }, new MDStoreReadLockInfo());
     			sql = String.format("select * from %s where mdstoreid=?", TRANSACTION_TABLE);
     			List<MDStoreTransactionInfo> infotransactions = getJdbcTemplateObject().query(sql, new Object[] { mdStoreId }, new MDStoreTransactionMapper());
     			Connection connection = this.datasource.getConnection();
     			if (infotransactions != null) {
     				for (MDStoreTransactionInfo i : infotransactions) {
     					i.setSize(getSizeOfTable(i.getId(), connection));
-...
     			return info;
     		} catch (SQLException e) {
     			throw new MDStoreServiceException(e);
     		} finally {
     			if (connection != null) {
     				try {
     					connection.close();
     				} catch (SQLException e) {
     					log.error("Error on close connection", e);
     					throw new MDStoreServiceException(e);
+    				}
+    			}
+    		}
+    	}
-...
     	/*
     	 * (non-Javadoc)
+    	 *
+    	 *
     	 * @see eu.dnetlib.data.mdstore.modular.connector.MDStoreTransactionManager#dropUsed(java.lang.String, java.lang.String)
     	 */
     	@Override
     	public Boolean dropUsed(final String mdId, final String idToDrop) throws MDStoreServiceException {
     		Connection conn = null;
     		try {
     			Connection conn = this.datasource.getConnection();
     			conn = this.datasource.getConnection();
     			String sql = "delete from readlock where id=? and mdstoreid=?";
     			PreparedStatement statement = conn.prepareStatement(sql);
     			log.info("deleting collection from readlock table:" + idToDrop);
     			statement.setString(1, idToDrop);
     			statement.setString(2, mdId);
     			statement.executeUpdate();
     			dropCollection(idToDrop);
     			String currentTable = getCurrentTable(mdId, conn);
     			if (!currentTable.equals(idToDrop)) {
     				dropCollection(idToDrop);
+    			}
     			return true;
     		} catch (SQLException e) {
     			throw new MDStoreServiceException("Unable to delete a readlock table with id:" + idToDrop, e);
     		} finally {
     			if (conn != null) {
     				try {
     					conn.close();
     				} catch (SQLException e) {
     					log.error("Error on close connection", e);
     					throw new MDStoreServiceException(e);
+    				}
+    			}
+    		}
+    	}
     	/*
     	 * (non-Javadoc)
+    	 *
+    	 *
     	 * @see eu.dnetlib.data.mdstore.modular.connector.MDStoreTransactionManager#dropTransaction(java.lang.String, java.lang.String)
     	 */
     	@Override
     	public Boolean dropTransaction(final String mdId, final String idToDrop) throws MDStoreServiceException {
     		Connection conn = null;
     		try {
     			Connection conn = this.datasource.getConnection();
     			conn = this.datasource.getConnection();
     			String sql = "delete from transactions where id=? and mdstoreid=?";
     			PreparedStatement statement = conn.prepareStatement(sql);
     			log.info("deleting collection from transactions table:" + idToDrop);
-...
     			return true;
     		} catch (SQLException e) {
     			throw new MDStoreServiceException("Unable to delete a transaction table with id:" + idToDrop, e);
     		} finally {
     			if (conn != null) {
     				try {
     					conn.close();
     				} catch (SQLException e) {
     					log.error("Error on close connection", e);
     					throw new MDStoreServiceException(e);
+    				}
+    			}
+    		}
+    	}
     	/*
     	 * (non-Javadoc)
+    	 *
+    	 *
     	 * @see eu.dnetlib.data.mdstore.modular.connector.MDStoreTransactionManager#garbage()
     	 */
     	@Override
     	public void garbage() throws MDStoreServiceException {
     		verifyConsistency();
     		String findOldStoresql = "select r.id from readlock r, metadata m where r.mdstoreid = m.mdid and r.id != current_table and extract (day from (now() - r.dateofread)) >=?";
     		Connection conn = null;
     		try {
     			conn = this.datasource.getConnection();
     			log.info("Start garbage collection of the unused mdstore");
     			Connection conn = this.datasource.getConnection();
     			PreparedStatement ps = conn.prepareStatement(findOldStoresql);
     			ps.setInt(1, expiredDays);
     			ResultSet rs = ps.executeQuery();
-...
     		} catch (SQLException e) {
     			throw new MDStoreServiceException("Unable to start garbage of the mdstores", e);
     		} finally {
     			if (conn != null) {
     				try {
     					conn.close();
     				} catch (SQLException e) {
     					log.error("Error on close connection", e);
     					throw new MDStoreServiceException(e);
+    				}
+    			}
+    		}
+    	}

     public class MDStoreDaoPostgresImpl implements MDStoreDao {
     	/** The datasource. */
     	@Autowired
     	@javax.annotation.Resource(name = "mdstoreDataSource")
     	private DataSource datasource;
     	/** The metadata table. */
-...
     	 */
     	@Override
     	public MDStore getMDStore(final String mdId) throws MDStoreServiceException {
     		Connection conn = null;
     		try {
     			Connection conn = datasource.getConnection();
     			conn = datasource.getConnection();
     			verifyConsistency(conn);
     			String mdProfileID = transactionManager.getMDStoreForTransaction(mdId);
     			String sql = String.format("select * from %s where %s = ?", METADATA_TABLE, MDIDColumnName);
     			String sql = String.format("select * from %s where %s = ? or current_table= ?", METADATA_TABLE, MDIDColumnName);
     			if (mdProfileID != null) {
     				sql = String.format("select * from %s where %s = ?", METADATA_TABLE, MDIDColumnName);
+    			}
     			PreparedStatement ps = conn.prepareStatement(sql);
     			if (mdProfileID != null) {
     				ps.setString(1, mdProfileID);
     			} else {
     				ps.setString(1, mdId);
     				ps.setString(2, mdId);
+    			}
     			ResultSet rs = ps.executeQuery();
     			if (!rs.next()) throw new MDStoreServiceException("Collection not found for MDStoreID :" + (mdProfileID != null ? mdProfileID : mdId));
-...
     		} catch (Exception e) {
     			log.error("Error on get mdstore", e);
     			throw new MDStoreServiceException(e);
     		} finally {
     			if (conn != null) {
     				try {
     					conn.close();
     				} catch (SQLException e) {
     					log.error("Error on close connection", e);
     					throw new MDStoreServiceException(e);
+    				}
+    			}
+    		}
+    	}
-...
     	 */
     	@Override
     	public List<String> listMDStores() throws MDStoreServiceException {
     		Connection conn = null;
     		try {
     			Connection conn = datasource.getConnection();
     			conn = datasource.getConnection();
     			verifyConsistency(conn);
     			String query = "select  " + MDIDColumnName + "  from metadata";
     			PreparedStatement st = conn.prepareStatement(query);
-...
     		} catch (Exception e) {
     			log.error("Error on listing mdstore", e);
     			throw new MDStoreServiceException(e);
     		} finally {
     			if (conn != null) {
     				try {
     					conn.close();
     				} catch (SQLException e) {
     					log.error("Error on close connection", e);
     					throw new MDStoreServiceException(e);
+    				}
+    			}
+    		}
+    	}
-...
     	 */
     	@Override
     	public List<String> listMDStores(final String format, final String layout, final String interpretation) throws MDStoreServiceException {
     		Connection conn = null;
     		try {
     			Connection conn = datasource.getConnection();
     			conn = datasource.getConnection();
     			verifyConsistency(conn);
     			String query = "select  " + MDIDColumnName + "  from metadata where lower(format) = ? and lower(layout) = ? and lower(interpretation) = ?";
     			PreparedStatement st = conn.prepareStatement(query);
-...
     		} catch (Exception e) {
     			log.error("Error on listing mdstore", e);
     			throw new MDStoreServiceException(e);
     		} finally {
     			if (conn != null) {
     				try {
     					conn.close();
     				} catch (SQLException e) {
     					log.error("Error on close connection", e);
     					throw new MDStoreServiceException(e);
+    				}
+    			}
+    		}
+    	}
-...
     	 */
     	@Override
     	public void createMDStore(final String mdId, final String format, final String interpretation, final String layout) throws MDStoreServiceException {
     		Connection conn = null;
     		try {
     			Connection conn = datasource.getConnection();
     			conn = datasource.getConnection();
     			verifyConsistency(conn);
     			String query = "insert into  " + METADATA_TABLE + "  values (?,?,?,?,?,?)";
     			String query = "insert into  " + METADATA_TABLE + "  values (?,?,?,?,?,?,?)";
     			PreparedStatement st = conn.prepareStatement(query);
     			st.setString(1, mdId);
     			st.setString(2, format);
-...
     			st.setString(5, "mdstore_" + idName.replace("-", "_"));
     			st.setInt(6, 0);
     			st.setInt(7, 0);
     			log.debug(st.toString());
     			st.executeUpdate();
     			final StringTemplate templateCollection = new StringTemplate(IOUtils.toString(getTemplateCollection().getInputStream()));
-...
     		} catch (Exception e) {
     			log.error("Error on inserting mdstore", e);
     			throw new MDStoreServiceException(e);
     		} finally {
     			if (conn != null) {
     				try {
     					conn.close();
     				} catch (SQLException e) {
     					log.error("Error on close connection", e);
     					throw new MDStoreServiceException(e);
+    				}
+    			}
+    		}
+    	}
-...
     	 */
     	@Override
     	public void deleteMDStore(final String mdId) throws MDStoreServiceException {
     		Connection conn = null;
     		try {
     			Connection conn = datasource.getConnection();
     			conn = datasource.getConnection();
     			verifyConsistency(conn);
     			// RETREIVE THE CURRENT USED TABLE ON METADATA
     			String sql = String.format("select * from %s where %s = ?", METADATA_TABLE, MDIDColumnName);
-...
     		} catch (Exception e) {
     			log.error("Error on deleting mdstore", e);
     			throw new MDStoreServiceException(e);
     		} finally {
     			if (conn != null) {
     				try {
     					conn.close();
     				} catch (SQLException e) {
     					log.error("Error on close connection", e);
     					throw new MDStoreServiceException(e);
+    				}
+    			}
+    		}
+    	}

     package eu.dnetlib.data.mdstore.modular.inspector;
     import static eu.dnetlib.miscutils.collections.MappedCollection.listMap;
     import java.io.StringReader;
     import java.util.HashMap;
     import java.util.List;
     import java.util.Map;
     import javax.annotation.Resource;
     import org.apache.commons.logging.Log;
     import org.apache.commons.logging.LogFactory;
     import org.dom4j.Document;
     import org.dom4j.DocumentException;
     import org.dom4j.io.SAXReader;
     import org.springframework.stereotype.Controller;
     import org.springframework.ui.Model;
     import org.springframework.web.bind.annotation.RequestMapping;
     import org.springframework.web.bind.annotation.RequestMethod;
     import org.springframework.web.bind.annotation.RequestParam;
     import com.google.common.base.Function;
     import com.google.common.collect.Lists;
     import eu.dnetlib.data.mdstore.MDStoreServiceException;
     import eu.dnetlib.data.mdstore.modular.MDStoreFeeder;
     import eu.dnetlib.data.mdstore.modular.connector.MDStore;
     import eu.dnetlib.data.mdstore.modular.connector.MDStoreDao;
     import eu.dnetlib.data.mdstore.modular.connector.MDStoreManagerInfo;
     import eu.dnetlib.data.mdstore.modular.connector.MDStoreTransactionManager;
     import eu.dnetlib.enabling.inspector.AbstractInspectorController;
     import eu.dnetlib.enabling.resultset.ResultSetListener;
     import eu.dnetlib.miscutils.collections.MappedCollection;
     import eu.dnetlib.miscutils.functional.UnaryFunction;
     import eu.dnetlib.miscutils.functional.xml.TryIndentXmlString;
     @Controller
     public class MDStorePostgresInspector extends AbstractInspectorController {
     	private static final Log log = LogFactory.getLog(MDStorePostgresInspector.class); // NOPMD by marko on 11/24/08 5:02 PM
     	@Resource(name = "postgresMDStoreDao")
     	private MDStoreDao mdstoreDao;
     	@Resource(name = "postgresTransactionManager")
     	private MDStoreTransactionManager transactionManager;
     	@Resource
     	private MDStoreFeeder feeder;
     	class MDStoreDescription {
     		private String id;
     		private int size;
     		public MDStoreDescription(final String id, final int size) {
     			super();
     			this.id = id;
     			this.size = size;
+    		}
     		public String getFormat() {
     			try {
     				return mdstoreDao.getMDStore(id).getFormat();
     			} catch (MDStoreServiceException e) {
     				return null;
+    			}
+    		}
     		public String getLayout() {
     			try {
     				return mdstoreDao.getMDStore(id).getLayout();
     			} catch (MDStoreServiceException e) {
     				return null;
+    			}
+    		}
     		public String getInterpretation() {
     			try {
     				return mdstoreDao.getMDStore(id).getInterpretation();
     			} catch (MDStoreServiceException e) {
     				return null;
+    			}
+    		}
     		public boolean getIndexed() {
     			return true;
+    		}
     		public String getId() {
     			return id;
+    		}
     		public void setId(final String id) {
     			this.id = id;
+    		}
     		public int getSize() {
     			return size;
+    		}
     		public void setSize(final int size) {
     			this.size = size;
+    		}
+    	}
     	@RequestMapping(value = "/inspector/mdstores.do")
     	public void mdstores(final Model model) throws MDStoreServiceException {
     		model.addAttribute("mdstores", MappedCollection.listMap(mdstoreDao.listMDStores(), new UnaryFunction<MDStoreDescription, String>() {
     			@Override
     			public MDStoreDescription evaluate(final String arg) {
     				try {
     					String currentid = transactionManager.getMDStoreCollection(arg);
     					MDStore mdstore = mdstoreDao.getMDStore(currentid);
     					return new MDStoreDescription(arg, mdstore.getSize());
     				} catch (MDStoreServiceException e) {
     					return null;
+    				}
+    			}
     		}));
+    	}
     	@RequestMapping(value = "/inspector/mdstore.do", method = RequestMethod.GET)
     	public void mdstore(final Model model,
     			@RequestParam("id") final String id,
     			@RequestParam(value = "start", required = false) final Integer startParam,
     			@RequestParam(value = "regex", required = false) final String regex) throws MDStoreServiceException {
     		int pageSize = 10;
     		int start = 0;
     		if (startParam != null) {
     			start = startParam;
+    		}
     		String currentId = transactionManager.getMDStoreCollection(id);
     		MDStore mdstore = mdstoreDao.getMDStore(currentId);
     		ResultSetListener rs = mdstore.deliver(null, null, regex);
     		Function<String, Map<String, String>> function = new Function<String, Map<String, String>>() {
     			private SAXReader reader = new SAXReader();
     			@Override
     			public Map<String, String> apply(final String input) {
     				try {

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Revision 30928

Added by Sandro La Bruzzo over 9 years ago