org.apache.ctakes.core.cc

Class JdbcWriterTemplate

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

org.apache.ctakes.core.cc.JdbcWriterTemplate

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

@PipeBitInfo(name="JDBC Writer (Template)",
             description="Stores extracted information and document metadata in a database.",
             role=WRITER,
             dependencies={DOCUMENT_ID,IDENTIFIED_ANNOTATION})
public class JdbcWriterTemplate
extends AbstractJdbcWriter

Template Cas Consumer to write a table to a sql database using jdbc

Since:

1/8/2015

Version:

%I%

Author:

SPF , chip-nlp

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	JdbcWriterTemplate.I2b2FieldInfo

Nested classes/interfaces inherited from class org.apache.ctakes.core.cc.AbstractJdbcWriter

AbstractJdbcWriter.FieldInfo, AbstractJdbcWriter.TableInfo, AbstractJdbcWriter.TableSqlInfo

Field Summary

Fields

Modifier and Type	Field and Description
static String	PARAM_VECTOR_TABLE
protected static String	SPAN_END_LABEL
protected static String	SPAN_START_LABEL

Fields inherited from class org.apache.ctakes.core.cc.AbstractJdbcWriter

_tableSqlInfoMap, 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
JdbcWriterTemplate()

Method Summary

Modifier and Type	Method and Description
protected String	createBlob(org.apache.uima.jcas.JCas jcas, IdentifiedAnnotation annotation) I2b2 wants annotation begin and end offsets plus the covered text
protected Collection<AbstractJdbcWriter.TableInfo>	getTableInfos() Called from initialize()
void	initialize()
protected void	saveAnnotations(org.apache.uima.jcas.JCas jcas, Map<JdbcWriterTemplate.I2b2FieldInfo,Object> fieldInfoValues, String cui, String preferredText, Iterable<IdentifiedAnnotation> annotations, boolean saveAffirmed)
protected void	writeJCasInformation(org.apache.uima.jcas.JCas jcas, int encounterNum, long patientNum, String providerId, Timestamp startDate) The main "process" method, called from processCas

Methods inherited from class org.apache.ctakes.core.cc.AbstractJdbcWriter

collectionProcessComplete, createRowInsertSql, getTableSqlInfoMap, processCas, setFieldInfoValue, writeTableRow

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_VECTOR_TABLE

public static final String PARAM_VECTOR_TABLE

See Also:

Constant Field Values

SPAN_START_LABEL

protected static final String SPAN_START_LABEL

See Also:

Constant Field Values

SPAN_END_LABEL

protected static final String SPAN_END_LABEL

See Also:

Constant Field Values

Constructor Detail

JdbcWriterTemplate

public JdbcWriterTemplate()

Method Detail

initialize

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

Overrides:

initialize in class AbstractJdbcWriter

Throws:

org.apache.uima.resource.ResourceInitializationException

getTableInfos

protected Collection<AbstractJdbcWriter.TableInfo> getTableInfos()

Called from initialize()

Specified by:

getTableInfos in class AbstractJdbcWriter

Returns:

Table Info Objects for all tables of interest

writeJCasInformation

protected 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

Specified by:

writeJCasInformation in class AbstractJdbcWriter

Parameters:

jcas - -

encounterNum - -

patientNum - -

providerId - -

startDate - -

Throws:

SQLException - if implementations throw SQLException

saveAnnotations

protected void saveAnnotations(org.apache.uima.jcas.JCas jcas,
                               Map<JdbcWriterTemplate.I2b2FieldInfo,Object> fieldInfoValues,
                               String cui,
                               String preferredText,
                               Iterable<IdentifiedAnnotation> annotations,
                               boolean saveAffirmed)
                        throws SQLException

Parameters:

jcas - -

fieldInfoValues - -

cui - -

preferredText - -

annotations - -

saveAffirmed - -

Throws:

SQLException

createBlob

protected String createBlob(org.apache.uima.jcas.JCas jcas,
                            IdentifiedAnnotation annotation)

I2b2 wants annotation begin and end offsets plus the covered text

Parameters:

jcas - in case the blob needs to obtain annotation information from the jcas

annotation - -

Returns:

a blob with encoded text span and covered text of the annotation