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

A

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

C

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

context - Variable in class de.sekmi.histream.i2b2.services.HiveServer

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

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

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

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

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

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

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

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

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

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

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

H

HiveServer - Class in de.sekmi.histream.i2b2.services

Provides REST interfaces to emulate an i2b2 server.

HiveServer() - Constructor for class de.sekmi.histream.i2b2.services.HiveServer

I

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

invoke(Source) - Method in class de.sekmi.histream.i2b2.services.HiveServer

L

loadMainScript() - Method in class de.sekmi.histream.i2b2.services.HiveServer

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

loadScipts() - Method in class de.sekmi.histream.i2b2.services.HiveServer

M

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

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

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.

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

reloadChangesLoop() - Method in class de.sekmi.histream.i2b2.services.HiveServer

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

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

S

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

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

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