A C D E F G I L M O P R S T U

A

acceptOrException(Observation) - Method in class de.sekmi.histream.i2b2.I2b2Inserter

ALLOW_WILDCARD_CONCEPT_CODES - Static variable in class de.sekmi.histream.i2b2.I2b2ExtractorFactory

Boolean feature whether to allow wildcard concept keys.

C

close() - Method in class de.sekmi.histream.i2b2.I2b2Extractor

close() - Method in class de.sekmi.histream.i2b2.I2b2ExtractorFactory

close() - Method in class de.sekmi.histream.i2b2.I2b2Inserter

close() - Method in class de.sekmi.histream.i2b2.ont.Import

close() - Method in class de.sekmi.histream.i2b2.PostgresExtension

config - Variable in class de.sekmi.histream.i2b2.PostgresExtension

copyProperties(Map<String, String>, String, Properties) - Static method in class de.sekmi.histream.i2b2.PostgresExtension

Each key in src that starts with keyPrefix is copied (without the prefix) and its value to dest

createInstance(Observation) - Method in class de.sekmi.histream.i2b2.PostgresPatientStore

createInstance(Object...) - Method in class de.sekmi.histream.i2b2.PostgresPatientStore

createInstance(Observation) - Method in class de.sekmi.histream.i2b2.PostgresVisitStore

createInstance(Object...) - Method in class de.sekmi.histream.i2b2.PostgresVisitStore

D

DataDialect - Class in de.sekmi.histream.i2b2

Configuration of exact meaning of values in observation_fact table.

DataDialect() - Constructor for class de.sekmi.histream.i2b2.DataDialect

db - Variable in class de.sekmi.histream.i2b2.PostgresExtension

de.sekmi.histream.i2b2 - package de.sekmi.histream.i2b2

Connectors for i2b2 integration.

de.sekmi.histream.i2b2.ont - package de.sekmi.histream.i2b2.ont

Interfaces to i2b2 ontology

decodeLocationCd(String) - Method in class de.sekmi.histream.i2b2.DataDialect

decodeModifierCd(String) - Method in class de.sekmi.histream.i2b2.DataDialect

decodeValueFlagCd(String) - Method in class de.sekmi.histream.i2b2.DataDialect

deleteWhereSourceId(String) - Method in class de.sekmi.histream.i2b2.PostgresExtension

deleteWhereSourceId(String) - Method in class de.sekmi.histream.i2b2.PostgresPatientStore

deleteWhereSourceId(String) - Method in class de.sekmi.histream.i2b2.PostgresVisitStore

dump() - Method in class de.sekmi.histream.i2b2.I2b2Extractor

E

encodeLocationCd(String) - Method in class de.sekmi.histream.i2b2.DataDialect

encodeOperator(Value) - Method in class de.sekmi.histream.i2b2.DataDialect

encodeProviderId(String) - Method in class de.sekmi.histream.i2b2.DataDialect

encodeUnitCd(String) - Method in class de.sekmi.histream.i2b2.DataDialect

encodeValueFlagCd(Value) - Method in class de.sekmi.histream.i2b2.DataDialect

errorHandler(SQLException) - Method in class de.sekmi.histream.i2b2.I2b2Extractor

Retrieves errors during the get() operation.

extract(Timestamp, Timestamp, Iterable<String>) - Method in class de.sekmi.histream.i2b2.I2b2ExtractorFactory

Extract observations for given concept codes with observation.start between start_min and start_end.

extract(Instant, Instant, Iterable<String>) - Method in class de.sekmi.histream.i2b2.I2b2ExtractorFactory

F

findVisit(String) - Method in class de.sekmi.histream.i2b2.PostgresVisitStore

Find a visit.

flush() - Method in class de.sekmi.histream.i2b2.PostgresExtension

Write updates to disk.

flush() - Method in class de.sekmi.histream.i2b2.PostgresPatientStore

flush() - Method in class de.sekmi.histream.i2b2.PostgresVisitStore

G

get() - Method in class de.sekmi.histream.i2b2.I2b2Extractor

getAliasIds(Patient) - Method in class de.sekmi.histream.i2b2.PostgresPatientStore

getCause() - Method in exception de.sekmi.histream.i2b2.UncheckedSQLException

getConnection(Map<String, String>, String[]) - Static method in class de.sekmi.histream.i2b2.PostgresExtension

getDefaultProviderId() - Method in class de.sekmi.histream.i2b2.DataDialect

getFetchSize() - Method in class de.sekmi.histream.i2b2.PostgresExtension

Get the configuration setting for fetchSize if configured.

getInsertCount() - Method in class de.sekmi.histream.i2b2.I2b2Inserter

getInstanceTypes() - Method in class de.sekmi.histream.i2b2.PostgresPatientStore

getInstanceTypes() - Method in class de.sekmi.histream.i2b2.PostgresVisitStore

getMeta(String) - Method in class de.sekmi.histream.i2b2.I2b2Extractor

getNullLocationCd() - Method in class de.sekmi.histream.i2b2.DataDialect

getNullModifierCd() - Method in class de.sekmi.histream.i2b2.DataDialect

getNullUnitCd() - Method in class de.sekmi.histream.i2b2.DataDialect

getNullValueFlagCd() - Method in class de.sekmi.histream.i2b2.DataDialect

getNullValueTypeCd() - Method in class de.sekmi.histream.i2b2.DataDialect

getNum() - Method in class de.sekmi.histream.i2b2.I2b2Patient

getNum() - Method in class de.sekmi.histream.i2b2.I2b2Visit

getObservationFactory() - Method in class de.sekmi.histream.i2b2.I2b2ExtractorFactory

getPatientNum() - Method in class de.sekmi.histream.i2b2.I2b2Visit

I

I2b2Extractor - Class in de.sekmi.histream.i2b2

Retrieves observations from i2b2.

I2b2ExtractorFactory - Class in de.sekmi.histream.i2b2

Extract observations from i2b2.

I2b2ExtractorFactory(DataSource, ObservationFactory) - Constructor for class de.sekmi.histream.i2b2.I2b2ExtractorFactory

I2b2Inserter - Class in de.sekmi.histream.i2b2

Inserts observations in to the i2b2 observation_fact table.

I2b2Inserter(Map<String, String>) - Constructor for class de.sekmi.histream.i2b2.I2b2Inserter

I2b2Inserter(DataSource, Map<String, String>) - Constructor for class de.sekmi.histream.i2b2.I2b2Inserter

I2b2Patient - Class in de.sekmi.histream.i2b2

I2b2 patient.

I2b2Patient(int) - Constructor for class de.sekmi.histream.i2b2.I2b2Patient

I2b2Patient(int, Patient.Sex, DateTimeAccuracy, DateTimeAccuracy) - Constructor for class de.sekmi.histream.i2b2.I2b2Patient

I2b2Visit - Class in de.sekmi.histream.i2b2

I2b2 visit.

I2b2Visit(int, int) - Constructor for class de.sekmi.histream.i2b2.I2b2Visit

Import - Class in de.sekmi.histream.i2b2.ont

Import ontology data into i2b2.

Import(Map<String, String>) - Constructor for class de.sekmi.histream.i2b2.ont.Import

Connect to the i2b2 database.

inaccurateSqlTimestamp(DateTimeAccuracy) - Static method in class de.sekmi.histream.i2b2.PostgresExtension

isDefaultProviderId(String) - Method in class de.sekmi.histream.i2b2.DataDialect

isNullLocationCd(String) - Method in class de.sekmi.histream.i2b2.DataDialect

L

loadMaxInstanceNums() - Method in class de.sekmi.histream.i2b2.PostgresVisitStore

M

main(String[]) - Static method in class de.sekmi.histream.i2b2.ont.Import

merge(Patient, String, ExternalSourceType) - Method in class de.sekmi.histream.i2b2.PostgresPatientStore

O

openDatabase(String[]) - Method in class de.sekmi.histream.i2b2.PostgresExtension

Open a database connection using configuration properties with the given prefixes.

openDatabase(DataSource) - Method in class de.sekmi.histream.i2b2.PostgresExtension

Open a database connection using a data source

P

PostgresExtension<T> - Class in de.sekmi.histream.i2b2

Extension with database connectivity.

PostgresExtension(Map<String, String>) - Constructor for class de.sekmi.histream.i2b2.PostgresExtension

PostgresPatientStore - Class in de.sekmi.histream.i2b2

Patient cache which synchronizes with i2b2 patient_dimension and patient_mapping tables.

PostgresPatientStore(Map<String, String>) - Constructor for class de.sekmi.histream.i2b2.PostgresPatientStore

Construct new postgres patient store.

PostgresPatientStore(DataSource, Map<String, String>) - Constructor for class de.sekmi.histream.i2b2.PostgresPatientStore

Create a patient store using a DataSource.

PostgresVisitStore - Class in de.sekmi.histream.i2b2

Visit cache which synchronizes with an i2b2 visit_dimension table.

PostgresVisitStore(Map<String, String>) - Constructor for class de.sekmi.histream.i2b2.PostgresVisitStore

Create a visit store using configuration settings.

PostgresVisitStore(DataSource, Map<String, String>) - Constructor for class de.sekmi.histream.i2b2.PostgresVisitStore

Create a visit store using a DataSource.

prepareStatement(Connection, String) - Method in class de.sekmi.histream.i2b2.I2b2ExtractorFactory

prepareStatements() - Method in class de.sekmi.histream.i2b2.PostgresExtension

prepareStatements() - Method in class de.sekmi.histream.i2b2.PostgresPatientStore

prepareStatements() - Method in class de.sekmi.histream.i2b2.PostgresVisitStore

processOntology() - Method in class de.sekmi.histream.i2b2.ont.Import

purge(String) - Method in class de.sekmi.histream.i2b2.PostgresPatientStore

purgeSource(String) - Method in class de.sekmi.histream.i2b2.I2b2Inserter

Deletes all observations with the given sourceId

purgeVisit(int) - Method in class de.sekmi.histream.i2b2.I2b2Inserter

Deletes all observations for the given encounter_num

R

resetInsertCount() - Method in class de.sekmi.histream.i2b2.I2b2Inserter

retrieve(String) - Method in class de.sekmi.histream.i2b2.PostgresPatientStore

S

setFeature(String, Object) - Method in class de.sekmi.histream.i2b2.I2b2ExtractorFactory

setMeta(String, String) - Method in class de.sekmi.histream.i2b2.I2b2Inserter

setNum(int) - Method in class de.sekmi.histream.i2b2.I2b2Patient

setOntology(Ontology) - Method in class de.sekmi.histream.i2b2.ont.Import

setProperty(String, Object) - Method in class de.sekmi.histream.i2b2.I2b2ExtractorFactory

size() - Method in class de.sekmi.histream.i2b2.PostgresPatientStore

Returns the number of patients which are currently available in memory.

size() - Method in class de.sekmi.histream.i2b2.PostgresVisitStore

T

toString() - Method in class de.sekmi.histream.i2b2.I2b2Visit

U

UncheckedSQLException - Exception in de.sekmi.histream.i2b2

UncheckedSQLException(SQLException) - Constructor for exception de.sekmi.histream.i2b2.UncheckedSQLException

A C D E F G I L M O P R S T U