org.opencb.cellbase.lib.indexer

Class IndexManager

java.lang.Object

org.opencb.cellbase.lib.indexer.IndexManager

public class IndexManager
extends Object

Constructor Summary

Constructors

Constructor and Description
IndexManager(CellBaseConfiguration configuration)

Method Summary

Modifier and Type	Method and Description
void	createMongoDBIndexes(String collectionName, String databaseName, boolean dropIndexesFirst) Create indexes for specified collection.
void	createMongoDBIndexes(String data, String speciesName, String assemblyName, boolean dropIndexesFirst) Create indexes.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

IndexManager

public IndexManager(CellBaseConfiguration configuration)

Method Detail

createMongoDBIndexes

public void createMongoDBIndexes(String data,
                                 String speciesName,
                                 String assemblyName,
                                 boolean dropIndexesFirst)
                          throws CellbaseException,
                                 IOException

Create indexes. Exception thrown if species or assembly is incorrect. NULL assembly value will default to first assembly in the config file.

Parameters:

data - list of collections to index

speciesName - name of species

assemblyName - name of assembly

dropIndexesFirst - if TRUE, deletes the index before creating a new one. FALSE, no index is created if it already exists.

Throws:

IOException - if configuration file can't be read

CellbaseException - if indexes file isn't found, or invalid input

createMongoDBIndexes

public void createMongoDBIndexes(String collectionName,
                                 String databaseName,
                                 boolean dropIndexesFirst)
                          throws IOException,
                                 CellbaseException

Create indexes for specified collection. Use by the load to create indexes. Will throw an exception if given database does not already exist.

Parameters:

collectionName - create indexes for this collection

databaseName - name of database

dropIndexesFirst - if TRUE, deletes the index before creating a new one. FALSE, no index is created if it already exists.

Throws:

IOException - if configuration file can't be read

CellbaseException - if indexes file isn't found