de.sekmi.histream.i2b2

Class I2b2Inserter

java.lang.Object

de.sekmi.histream.impl.AbstractObservationHandler

de.sekmi.histream.i2b2.I2b2Inserter

All Implemented Interfaces:

ObservationHandler, Plugin, Closeable, AutoCloseable, Consumer<Observation>

public class I2b2Inserter
extends AbstractObservationHandler
implements ObservationHandler, Closeable, Plugin

Inserts observations in to the i2b2 observation_fact table.

Need to specify default provider id for i2b2 in property 'nullProvider'. Null values in providerId will be be replaced with this value and stored in provider_id column.

locationId is stored as location_cd, null-values are stored as '@'.

valtype_cd: N numeric, B stored in observation_blob, T text, '@' no value, 'NLP' NLP result xml objects. Undocumented but used in demodata: D: datetime "YYYY-MM-DD HH:mm" stored in tval_char, "YYYYMMDD.HHmm0" stored in nval_num.

The most difficult part is handling the instance_num field. By default, i2b2 uses a four byte signed integer for instance_num. Incrementing instance_num for every record would lead eventually to a number overflow. The primary key consists of patient_num,concept_cd,modifier_cd,start_date,encounter_num,instance_num,provider_id. Ideally, instance_num should be unique to encounter_num and start_date, but there is no realistic way to keep track per start_date, since observations can come in in any order. Therefore, we keep track of the maximum instance_num per encounter in the visit store (which caches visits anyways) and increase the instance_num only for observations with modifiers.

Author:

R.W.Majeed

Constructor Summary

Constructors

Constructor and Description
I2b2Inserter()

Method Summary

Modifier and Type	Method and Description
void	acceptOrException(Observation o)
void	close()
int	getInsertCount()
void	open(Connection connection, DataDialect dialect) Initialize the database connection
boolean	purgeSource(String sourceId) Deletes all observations with the given sourceId
boolean	purgeVisit(int encounter_num) Deletes all observations for the given encounter_num
void	resetInsertCount()
void	setMeta(String key, String value)

Methods inherited from class de.sekmi.histream.impl.AbstractObservationHandler

accept, getErrorCount, reportError, resetErrorCount, setErrorHandler

Methods inherited from class java.lang.Object

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

Methods inherited from interface de.sekmi.histream.ObservationHandler

accept, setErrorHandler

Methods inherited from interface java.util.function.Consumer

andThen

Methods inherited from interface de.sekmi.histream.Plugin

newInstance

Constructor Detail

I2b2Inserter

public I2b2Inserter()

Method Detail

purgeSource

public boolean purgeSource(String sourceId)
                    throws SQLException

Deletes all observations with the given sourceId

Parameters:

sourceId - source id

Returns:

true if observations were found and deleted, false if no matching observations were found.

Throws:

SQLException - if the DELETE statement failed

purgeVisit

public boolean purgeVisit(int encounter_num)
                   throws SQLException

Deletes all observations for the given encounter_num

Parameters:

encounter_num - encounter number (e.g. observation_fact.encounter_num)

Returns:

true if observations were found and deleted, false if no matching observations were found.

Throws:

SQLException - if the DELETE statement failed.

open

public void open(Connection connection,
                 DataDialect dialect)
          throws SQLException

Initialize the database connection

Parameters:

connection - database connection for insertions

dialect - data dialect for i2b2

Throws:

SQLException - if preparation/initialisation failed

acceptOrException

public void acceptOrException(Observation o)
                       throws ObservationException

Specified by:

acceptOrException in class AbstractObservationHandler

Throws:

ObservationException

close

public void close()
           throws IOException

Specified by:

close in interface Plugin

Specified by:

close in interface Closeable

Specified by:

close in interface AutoCloseable

Throws:

IOException

setMeta

public void setMeta(String key,
                    String value)

Specified by:

setMeta in interface ObservationHandler

getInsertCount

public int getInsertCount()

resetInsertCount

public void resetInsertCount()