org.apache.ctakes.core.cc

Class AbstractJdbcWriter

java.lang.Object

org.apache.uima.resource.Resource_ImplBase

org.apache.uima.resource.ConfigurableResource_ImplBase

org.apache.uima.collection.CasConsumer_ImplBase

org.apache.ctakes.core.cc.AbstractJdbcWriter

All Implemented Interfaces:

org.apache.uima.collection.base_cpm.CasObjectProcessor, org.apache.uima.collection.base_cpm.CasProcessor, org.apache.uima.collection.CasConsumer, org.apache.uima.resource.ConfigurableResource, org.apache.uima.resource.Resource

Direct Known Subclasses:

JdbcWriterTemplate

public abstract class AbstractJdbcWriter
extends org.apache.uima.collection.CasConsumer_ImplBase

Write cas to a database using jdbc

Since:

1/8/2015

Version:

%I%

Author:

SPF , chip-nlp

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected static interface	AbstractJdbcWriter.FieldInfo
protected static interface	AbstractJdbcWriter.TableInfo
protected static class	AbstractJdbcWriter.TableSqlInfo

Field Summary

Fields

Modifier and Type	Field and Description
protected Map<String,AbstractJdbcWriter.TableSqlInfo>	_tableSqlInfoMap
static String	PARAM_DB_CONN_RESRC

Fields inherited from interface org.apache.uima.resource.Resource

PARAM_AGGREGATE_SOFA_MAPPINGS, PARAM_CONFIG_MANAGER, PARAM_CONFIG_PARAM_SETTINGS, PARAM_EXTERNAL_OVERRIDE_SETTINGS, PARAM_PERFORMANCE_TUNING_SETTINGS, PARAM_RESOURCE_MANAGER, PARAM_UIMA_CONTEXT

Constructor Summary

Constructors

Constructor and Description
AbstractJdbcWriter()

Method Summary

Modifier and Type	Method and Description
void	collectionProcessComplete(org.apache.uima.util.ProcessTrace arg0) closes the PreparedStatements
protected static String	createRowInsertSql(String tableName, AbstractJdbcWriter.FieldInfo... fieldInfos)
protected abstract Collection<AbstractJdbcWriter.TableInfo>	getTableInfos() Called from initialize()
protected Map<String,AbstractJdbcWriter.TableSqlInfo>	getTableSqlInfoMap()
void	initialize()
void	processCas(org.apache.uima.cas.CAS aCAS)
protected static void	setFieldInfoValue(Map<AbstractJdbcWriter.FieldInfo,Object> fieldInfoMap, AbstractJdbcWriter.FieldInfo fieldInfo, Object value) This is a safety method to set values of fieldInfoMaps instead of doing a direct .put in the map.
protected abstract void	writeJCasInformation(org.apache.uima.jcas.JCas jcas, int encounterNum, long patientNum, String providerId, Timestamp startDate) The main "process" method, called from processCas
protected static int	writeTableRow(PreparedStatement preparedStatement, int batchSize, Map<? extends AbstractJdbcWriter.FieldInfo,Object> fieldInfoMap) Adds a new row of values to a batch in the prepared statement.

Methods inherited from class org.apache.uima.collection.CasConsumer_ImplBase

batchProcessComplete, destroy, getProcessingResourceMetaData, initialize, isReadOnly, isStateless, processCas, reconfigure, typeSystemInit

Methods inherited from class org.apache.uima.resource.ConfigurableResource_ImplBase

getConfigParameterValue, getConfigParameterValue, setConfigParameterValue, setConfigParameterValue

Methods inherited from class org.apache.uima.resource.Resource_ImplBase

getCasManager, getLogger, getMetaData, getResourceManager, getUimaContext, getUimaContextAdmin, setLogger, setMetaData

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.apache.uima.resource.ConfigurableResource

getConfigParameterValue, getConfigParameterValue, setConfigParameterValue, setConfigParameterValue

Methods inherited from interface org.apache.uima.resource.Resource

getLogger, getMetaData, getResourceManager, getUimaContext, getUimaContextAdmin, setLogger

Field Detail

PARAM_DB_CONN_RESRC

public static final String PARAM_DB_CONN_RESRC

See Also:

Constant Field Values

_tableSqlInfoMap

protected final Map<String,AbstractJdbcWriter.TableSqlInfo> _tableSqlInfoMap

Constructor Detail

AbstractJdbcWriter

public AbstractJdbcWriter()

Method Detail

initialize

public void initialize()
                throws org.apache.uima.resource.ResourceInitializationException

Overrides:

initialize in class org.apache.uima.collection.CasConsumer_ImplBase

Throws:

org.apache.uima.resource.ResourceInitializationException

collectionProcessComplete

public void collectionProcessComplete(org.apache.uima.util.ProcessTrace arg0)
                               throws org.apache.uima.resource.ResourceProcessException,
                                      IOException

closes the PreparedStatements

Specified by:

collectionProcessComplete in interface org.apache.uima.collection.base_cpm.CasProcessor

Overrides:

collectionProcessComplete in class org.apache.uima.collection.CasConsumer_ImplBase

Throws:

org.apache.uima.resource.ResourceProcessException

IOException

processCas

public void processCas(org.apache.uima.cas.CAS aCAS)
                throws org.apache.uima.resource.ResourceProcessException

Throws:

org.apache.uima.resource.ResourceProcessException

getTableInfos

protected abstract Collection<AbstractJdbcWriter.TableInfo> getTableInfos()

Called from initialize()

Returns:

Table Info Objects for all tables of interest

writeJCasInformation

protected abstract void writeJCasInformation(org.apache.uima.jcas.JCas jcas,
                                             int encounterNum,
                                             long patientNum,
                                             String providerId,
                                             Timestamp startDate)
                                      throws SQLException

The main "process" method, called from processCas

Parameters:

jcas - -

encounterNum - -

patientNum - -

providerId - -

startDate - -

Throws:

SQLException - if implementations throw SQLException

getTableSqlInfoMap

protected Map<String,AbstractJdbcWriter.TableSqlInfo> getTableSqlInfoMap()

Returns:

the map of table name to table sql info objects

setFieldInfoValue

protected static void setFieldInfoValue(Map<AbstractJdbcWriter.FieldInfo,Object> fieldInfoMap,
                                        AbstractJdbcWriter.FieldInfo fieldInfo,
                                        Object value)

This is a safety method to set values of fieldInfoMaps instead of doing a direct .put in the map. an IllegalArgumentException will be thrown if the given value is not the same class type as what the given FieldInfo wants

Parameters:

fieldInfoMap - map in which to set the value

fieldInfo - key

value - value

writeTableRow

protected static int writeTableRow(PreparedStatement preparedStatement,
                                   int batchSize,
                                   Map<? extends AbstractJdbcWriter.FieldInfo,Object> fieldInfoMap)
                            throws SQLException

Adds a new row of values to a batch in the prepared statement. If the number of rows hits a maximum size (100) then the batch is executed.

Parameters:

preparedStatement - -

batchSize - the current batch row count in the prepared statement

fieldInfoMap - for row value assignment

Returns:

new batchCount (incremented by one or reset to zero)

Throws:

SQLException - if a PreparedStatement call throws one or if there is a type, value mismatch in fieldInfoMap

createRowInsertSql

protected static String createRowInsertSql(String tableName,
                                           AbstractJdbcWriter.FieldInfo... fieldInfos)
                                    throws SQLDataException

Parameters:

tableName - -

fieldInfos - -

Returns:

-

Throws:

SQLDataException