org.apache.ctakes.core.cc

Class JdbcWriterTemplate

java.lang.Object

CasConsumer_ImplBase

org.apache.ctakes.core.cc.AbstractJdbcWriter

org.apache.ctakes.core.cc.JdbcWriterTemplate

public class JdbcWriterTemplate
extends AbstractJdbcWriter

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

Since:

1/8/2015

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
private static class	JdbcWriterTemplate.I2b2Concept A more useful representation of umls concept for our purposes - we don't want repeat cuis for multiple tuis
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
private java.lang.String	_tableName
private static Logger	LOGGER
static java.lang.String	PARAM_VECTOR_TABLE
private static java.lang.String	SPAN_END_LABEL
private static java.lang.String	SPAN_START_LABEL

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

_tableSqlInfoMap, PARAM_DB_CONN_RESRC

Constructor Summary

Constructors

Constructor and Description
JdbcWriterTemplate()

Method Summary

Methods

Modifier and Type	Method and Description
private static java.lang.String	createBlob(IdentifiedAnnotation annotation)
private static java.util.Collection<JdbcWriterTemplate.I2b2Concept>	createI2b2Concepts(java.lang.Iterable<UmlsConcept> umlsConcepts) I2b2 only cares about Cui & preferred text.
protected java.util.Collection<AbstractJdbcWriter.TableInfo>	getTableInfos() Called from initialize()
void	initialize()
private void	saveAnnotations(java.util.Map<JdbcWriterTemplate.I2b2FieldInfo,java.lang.Object> fieldInfoValues, java.lang.String cui, java.lang.String preferredText, java.lang.Iterable<IdentifiedAnnotation> annotations, boolean saveAffirmed)
private void	saveEntities(JCas jcas, int encounterNum, long patientNum, java.lang.String providerId, java.sql.Timestamp startDate)
private void	saveI2b2Concept(java.util.Map<JdbcWriterTemplate.I2b2FieldInfo,java.lang.Object> fieldInfoValues, JdbcWriterTemplate.I2b2Concept i2b2Concept, java.lang.Iterable<IdentifiedAnnotation> annotations)
protected void	writeJCasInformation(JCas jcas, int encounterNum, long patientNum, java.lang.String providerId, java.sql.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 java.lang.Object

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

Field Detail

LOGGER

private static final Logger LOGGER

PARAM_VECTOR_TABLE

public static final java.lang.String PARAM_VECTOR_TABLE

See Also:

Constant Field Values

SPAN_START_LABEL

private static final java.lang.String SPAN_START_LABEL

See Also:

Constant Field Values

SPAN_END_LABEL

private static final java.lang.String SPAN_END_LABEL

See Also:

Constant Field Values

_tableName

private java.lang.String _tableName

Constructor Detail

JdbcWriterTemplate

public JdbcWriterTemplate()

Method Detail

initialize

public void initialize()
                throws ResourceInitializationException

Overrides:

initialize in class AbstractJdbcWriter

Throws:

ResourceInitializationException

getTableInfos

protected java.util.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(JCas jcas,
                        int encounterNum,
                        long patientNum,
                        java.lang.String providerId,
                        java.sql.Timestamp startDate)
                             throws java.sql.SQLException

The main "process" method, called from processCas

Specified by:

writeJCasInformation in class AbstractJdbcWriter

Parameters:

jcas - -

encounterNum - -

patientNum - -

providerId - -

startDate - -

Throws:

java.sql.SQLException - if implementations throw SQLException

saveEntities

private void saveEntities(JCas jcas,
                int encounterNum,
                long patientNum,
                java.lang.String providerId,
                java.sql.Timestamp startDate)
                   throws java.sql.SQLException

Throws:

java.sql.SQLException

saveI2b2Concept

private void saveI2b2Concept(java.util.Map<JdbcWriterTemplate.I2b2FieldInfo,java.lang.Object> fieldInfoValues,
                   JdbcWriterTemplate.I2b2Concept i2b2Concept,
                   java.lang.Iterable<IdentifiedAnnotation> annotations)
                      throws java.sql.SQLException

Throws:

java.sql.SQLException

saveAnnotations

private void saveAnnotations(java.util.Map<JdbcWriterTemplate.I2b2FieldInfo,java.lang.Object> fieldInfoValues,
                   java.lang.String cui,
                   java.lang.String preferredText,
                   java.lang.Iterable<IdentifiedAnnotation> annotations,
                   boolean saveAffirmed)
                      throws java.sql.SQLException

Throws:

java.sql.SQLException

createBlob

private static java.lang.String createBlob(IdentifiedAnnotation annotation)

Parameters:

annotation - -

Returns:

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

createI2b2Concepts

private static java.util.Collection<JdbcWriterTemplate.I2b2Concept> createI2b2Concepts(java.lang.Iterable<UmlsConcept> umlsConcepts)

I2b2 only cares about Cui & preferred text. A Cui may belong to multiple Tuis, making multiple UmlsConcept objects (one per tui). I2b2 does NOT want multiple rows of a single Cui just because it has multiple tuis.

Parameters:

umlsConcepts - -

Returns:

-