de.sekmi.histream.i2b2

Class I2b2ExtractorFactory

java.lang.Object

de.sekmi.histream.i2b2.I2b2ExtractorFactory

All Implemented Interfaces:

ObservationExtractor, AutoCloseable

public class I2b2ExtractorFactory
extends Object
implements AutoCloseable, ObservationExtractor

Extract observations from i2b2.

Allows simple queries against the i2b2 observation_fact table and retrieval of facts.

TODO add/use interface from histream-core XXX TODO allow to map patient_num -> Patient and encounter_num -> Encounter, this must be done before the extension is accessed

Author:

R.W.Majeed

Field Summary

Fields

Modifier and Type	Field and Description
static String	ALLOW_WILDCARD_CONCEPT_CODES Boolean feature whether to allow wildcard concept keys.

Constructor Summary

Constructors

Constructor and Description
I2b2ExtractorFactory(DataSource crc_ds, ObservationFactory factory)

Method Summary

Modifier and Type	Method and Description
void	close()
I2b2Extractor	extract(Instant start_min, Instant start_max, Iterable<String> notations)
ObservationFactory	getObservationFactory()
void	setFeature(String feature, Object value)
void	setPatientLookup(Function<Integer,? extends Patient> lookup)
void	setProperty(String property, Object value)
void	setVisitLookup(Function<Integer,? extends Visit> lookup)

Methods inherited from class java.lang.Object

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

Field Detail

ALLOW_WILDCARD_CONCEPT_CODES

public static String ALLOW_WILDCARD_CONCEPT_CODES

Boolean feature whether to allow wildcard concept keys.

Use with caution: Unexpected results might happen if wildcard concepts overlap. (Such as query fails, duplicate facts, etc.)

Constructor Detail

I2b2ExtractorFactory

public I2b2ExtractorFactory(DataSource crc_ds,
                            ObservationFactory factory)
                     throws SQLException

Throws:

SQLException

Method Detail

getObservationFactory

public ObservationFactory getObservationFactory()

setPatientLookup

public void setPatientLookup(Function<Integer,? extends Patient> lookup)

setVisitLookup

public void setVisitLookup(Function<Integer,? extends Visit> lookup)

setFeature

public void setFeature(String feature,
                       Object value)

setProperty

public void setProperty(String property,
                        Object value)

close

public void close()

Specified by:

close in interface AutoCloseable

extract

public I2b2Extractor extract(Instant start_min,
                             Instant start_max,
                             Iterable<String> notations)
                      throws IOException

Specified by:

extract in interface ObservationExtractor

Throws:

IOException