A B C D E F G H I J L M N O P Q R S T U V X

A

AbstractFileInfo - Class in edu.emory.cci.aiw.cvrg.eureka.etl.job

An abstract base class to hold information found about an uploaded file during the validation process.

AbstractFileQueryResultsHandler - Class in edu.emory.cci.aiw.cvrg.eureka.etl.dest

AbstractFileQueryResultsHandler(DestinationEntity, EtlProperties) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.dest.AbstractFileQueryResultsHandler

AppModule - Class in edu.emory.cci.aiw.cvrg.eureka.etl.config

B

BackEndContextListener - Class in edu.emory.cci.aiw.cvrg.eureka.etl.config

Loaded up on application initialization, sets up the application with Guice injector and any other bootup processes.

BackEndContextListener() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.config.BackEndContextListener

C

cleanup() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dest.AbstractFileQueryResultsHandler

Called by AbstractFileQueryResultsHandler.close() to give subclasses an opportunity to clean up resources that they have created.

cleanup() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dest.PatientSetExtractorQueryResultsHandler

cleanup() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dest.PatientSetSenderQueryResultsHandler

close() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.config.EntityManagerExecutor

close() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dao.JpaEurekaDeidConfigDao

close() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dest.AbstractFileQueryResultsHandler

Calls AbstractFileQueryResultsHandler.cleanup(), and then closes the output stream that is passed into AbstractFileQueryResultsHandler.start(java.io.OutputStream, java.util.Collection).

close() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dest.TabularFileQueryResultsHandler

close() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDataSourceBackend

close() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.ksb.PropositionDefinitionFinder

close() - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataProvider

Closes any underlying resources needed to read the data.

close() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.XlsxDataProvider

ConceptResource - Class in edu.emory.cci.aiw.cvrg.eureka.etl.resource

ConceptResource(EtlProperties) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.resource.ConceptResource

ConfigDao<E extends ConfigEntity> - Interface in edu.emory.cci.aiw.cvrg.eureka.etl.dao

ConfigDTOExtractorVisitor - Interface in edu.emory.cci.aiw.cvrg.eureka.etl.resource

ConfigurationError - Error in edu.emory.cci.aiw.cvrg.eureka.etl.config

configure() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.config.AppModule

constantSpecs(String, String, String, String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDataSourceBackend

contextDestroyed(ServletContextEvent) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.config.BackEndContextListener

contextInitialized(ServletContextEvent) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.config.BackEndContextListener

CPT - Class in edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet

Hold information about a patient's CPT codes.

CPT() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.CPT

create(HttpServletRequest, EtlDestination) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.DestinationResource

create(EtlDestination) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.Destinations

D

DataInserter - Class in edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet

Inserts data into a Protempa database.

DataInserter(Connection) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataInserter

Build a new object with the given configuration.

DataInserterException - Exception in edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet

Thrown if there are any issues when inserting data from the input source to the Protempa data source.

DataInserterException(Throwable) - Constructor for exception edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataInserterException

Create exception with the given Throwabler as the root cause.

DataProvider - Interface in edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet

An interface to provide functionality needed to provide data for upload to a PROTEMPA schema.

DataProviderException - Exception in edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet

Exception thrown when the data provider can not properly parse or fetch the data needed.

DataValidator - Class in edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet

Validates the incoming data before it is pushed to the Protempa database.

DataValidator(File) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataValidator

DeidPerPatientParamsDao - Interface in edu.emory.cci.aiw.cvrg.eureka.etl.dao

delete(HttpServletRequest, String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.DestinationResource

deleteAll(DestinationEntity) - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.dao.DeidPerPatientParamsDao

deleteAll(DestinationEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dao.JpaDeidPerPatientParamsDao

destinationConfigFile(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.config.EtlProperties

DestinationDao - Interface in edu.emory.cci.aiw.cvrg.eureka.etl.dao

DestinationDTOExtractorVisitor - Class in edu.emory.cci.aiw.cvrg.eureka.etl.resource

DestinationDTOExtractorVisitor(EtlProperties, AuthorizedUserEntity, EtlGroupDao) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.resource.DestinationDTOExtractorVisitor

DestinationResource - Class in edu.emory.cci.aiw.cvrg.eureka.etl.resource

DestinationResource(EtlProperties, AuthorizedUserDao, DestinationDao, EtlGroupDao) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.resource.DestinationResource

Destinations - Class in edu.emory.cci.aiw.cvrg.eureka.etl.resource

Destinations(EtlProperties, AuthorizedUserEntity, DestinationDao, EtlGroupDao) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.resource.Destinations

doDelete(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.OutputResource

doExecute(EntityManager) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.config.EntityManagerExecutor

doExecute(EntityManager) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.config.JobRepairerExecutor

doGet(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.OutputResource

doRepair(JobEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.config.JobRepairer

E

edu.emory.cci.aiw.cvrg.eureka.etl.config - package edu.emory.cci.aiw.cvrg.eureka.etl.config

edu.emory.cci.aiw.cvrg.eureka.etl.dao - package edu.emory.cci.aiw.cvrg.eureka.etl.dao

edu.emory.cci.aiw.cvrg.eureka.etl.dest - package edu.emory.cci.aiw.cvrg.eureka.etl.dest

edu.emory.cci.aiw.cvrg.eureka.etl.dsb - package edu.emory.cci.aiw.cvrg.eureka.etl.dsb

edu.emory.cci.aiw.cvrg.eureka.etl.job - package edu.emory.cci.aiw.cvrg.eureka.etl.job

edu.emory.cci.aiw.cvrg.eureka.etl.ksb - package edu.emory.cci.aiw.cvrg.eureka.etl.ksb

edu.emory.cci.aiw.cvrg.eureka.etl.resource - package edu.emory.cci.aiw.cvrg.eureka.etl.resource

edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet - package edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet

Encounter - Class in edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet

Hold information about a patient's encounter.

Encounter() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Encounter

EntityManagerExecutor - Class in edu.emory.cci.aiw.cvrg.eureka.etl.config

EntityManagerExecutor(String) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.config.EntityManagerExecutor

ETL - Class in edu.emory.cci.aiw.cvrg.eureka.etl.job

This class actually runs Protempa.

ETL(EtlProperties, JobDao, DestinationDao, EtlGroupDao, ProtempaDestinationFactory, Provider<EntityManager>) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.job.ETL

EtlException - Exception in edu.emory.cci.aiw.cvrg.eureka.etl.job

An ETL exception is thrown when job execution has failed.

EtlException() - Constructor for exception edu.emory.cci.aiw.cvrg.eureka.etl.job.EtlException

EtlException(Throwable) - Constructor for exception edu.emory.cci.aiw.cvrg.eureka.etl.job.EtlException

EtlException(String) - Constructor for exception edu.emory.cci.aiw.cvrg.eureka.etl.job.EtlException

EtlException(String, Throwable) - Constructor for exception edu.emory.cci.aiw.cvrg.eureka.etl.job.EtlException

EtlGroupDao - Interface in edu.emory.cci.aiw.cvrg.eureka.etl.dao

EtlProperties - Class in edu.emory.cci.aiw.cvrg.eureka.etl.config

Contains methods to fetch configuration information for the application.

EtlProperties() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.config.EtlProperties

ETLServletModule - Class in edu.emory.cci.aiw.cvrg.eureka.etl.config

A Guice configuration module for setting up the web infrastructure and binding appropriate implementations to interfaces.

ETLServletModule(EtlProperties) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.config.ETLServletModule

EurekaDataSourceBackend - Class in edu.emory.cci.aiw.cvrg.eureka.etl.dsb

Data source backend for Eureka!.

EurekaDataSourceBackend() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDataSourceBackend

EurekaDeidConfig - Interface in edu.emory.cci.aiw.cvrg.eureka.etl.dest

EurekaDeidConfigDao - Interface in edu.emory.cci.aiw.cvrg.eureka.etl.dao

EurekaDeidConfigFactory - Interface in edu.emory.cci.aiw.cvrg.eureka.etl.dest

EurekaDelimitedFileDataSourceBackend - Class in edu.emory.cci.aiw.cvrg.eureka.etl.dsb

EurekaDelimitedFileDataSourceBackend() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDelimitedFileDataSourceBackend

EurekaFileDataSourceBackend - Interface in edu.emory.cci.aiw.cvrg.eureka.etl.dsb

EurekaFixedWidthFileDataSourceBackend - Class in edu.emory.cci.aiw.cvrg.eureka.etl.dsb

EurekaFixedWidthFileDataSourceBackend() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaFixedWidthFileDataSourceBackend

EurekaIndexOnProperty - Class in edu.emory.cci.aiw.cvrg.eureka.etl.dest

EurekaProtempaConfigurations - Class in edu.emory.cci.aiw.cvrg.eureka.etl.config

EurekaProtempaConfigurations(EtlProperties) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.config.EurekaProtempaConfigurations

eventSpecs(String, String, String, String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDataSourceBackend

ExcelSpreadsheetBackendPropertyValidator - Class in edu.emory.cci.aiw.cvrg.eureka.etl.dsb

ExcelSpreadsheetBackendPropertyValidator() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.ExcelSpreadsheetBackendPropertyValidator

execute() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.config.EntityManagerExecutor

F

FileBackendPropertyValidator - Class in edu.emory.cci.aiw.cvrg.eureka.etl.dsb

FileBackendPropertyValidator() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.FileBackendPropertyValidator

FileResource - Class in edu.emory.cci.aiw.cvrg.eureka.etl.resource

FileResource(EtlProperties, AuthorizedUserDao, SourceConfigDao, EtlGroupDao) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.resource.FileResource

FileSupport - Class in edu.emory.cci.aiw.cvrg.eureka.etl.dest

FileSupport() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.dest.FileSupport

FileWarning - Class in edu.emory.cci.aiw.cvrg.eureka.etl.job

Contains information about warnings found in an uploaded file.

find(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.ksb.PropositionDefinitionFinder

findAll(Collection<String>) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.ksb.PropositionDefinitionFinder

finish() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dest.PatientSetExtractorQueryResultsHandler

finish() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dest.PatientSetSenderQueryResultsHandler

finish() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dest.TabularFileQueryResultsHandler

format(Object, StringBuffer, FieldPosition) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dest.TableColumnSpecFormat

FromConfigFile - Class in edu.emory.cci.aiw.cvrg.eureka.etl.resource

fromDestId(String) - Static method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.ToConfigFile

fromSourceConfigId(String) - Static method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.ToConfigFile

G

get() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.job.TaskProvider

getAcceptedMimetypes() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.FileBackendPropertyValidator

getAll() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dao.JpaDestinationDao

getAll(HttpServletRequest, DestinationType) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.DestinationResource

getAll() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.Destinations

Gets all configs for which the current user has read permissions.

getAll(HttpServletRequest, String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.JobResource

getAll(HttpServletRequest) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.SourceConfigResource

getAllCohortDestinations() - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.dao.DestinationDao

getAllCohortDestinations() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dao.JpaDestinationDao

getAllCohorts() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.Destinations

getAllI2B2Destinations() - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.dao.DestinationDao

getAllI2B2Destinations() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dao.JpaDestinationDao

getAllI2B2s() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.Destinations

getAllPatientSetExtractorDestinations() - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.dao.DestinationDao

getAllPatientSetExtractorDestinations() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dao.JpaDestinationDao

getAllPatientSetExtractors() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.Destinations

getAllPatientSetSenderDestinations() - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.dao.DestinationDao

getAllPatientSetSenderDestinations() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dao.JpaDestinationDao

getAllPatientSetSenders() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.Destinations

getAllTabularFileDestinations() - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.dao.DestinationDao

getAllTabularFileDestinations() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dao.JpaDestinationDao

getAllTabularFiles() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.Destinations

getByKeyId(String) - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.dao.DeidPerPatientParamsDao

getByKeyId(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dao.JpaDeidPerPatientParamsDao

getByName(String) - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.dao.ConfigDao

Gets a configuration by name.

getByName(String) - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.dao.EtlGroupDao

getByName(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dao.JpaDestinationDao

getByName(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dao.JpaEtlGroupDao

getByName(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dao.JpaSourceConfigDao

getCptCodes() - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataProvider

Get a list of CPT codes from the data.

getCptCodes() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.XlsxDataProvider

getCptProcedureCodesRootFullName() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDataSourceBackend

getDatabaseId() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDataSourceBackend

getDataFile() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.XlsxDataProvider

getDateOfBirth() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Patient

Get the patient's date of birth.

getDefaultPositionPerFile(File) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDelimitedFileDataSourceBackend

getDefaultPositionPerFile(File) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaFixedWidthFileDataSourceBackend

getDestination(HttpServletRequest, String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.DestinationResource

getDestinationConfigDirectory() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.config.EtlProperties

getDiagnosisCodesRootFullName() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDataSourceBackend

getDischargeDisposition() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Encounter

Get the encounter's discharge disposition.

getEncounterId() - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Observation

Get the unique identifier for the encounter with which the observation is associated.

getEncounters() - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataProvider

Get a list of encounters from the data.

getEncounters() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.XlsxDataProvider

getEnd() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Encounter

Get the encounter's end date.

getEntityId() - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Observation

Get the unique identifier for the entity associated with the observation.

getEtlDestination() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.DestinationDTOExtractorVisitor

getFilename() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDataSourceBackend

getFilename() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDelimitedFileDataSourceBackend

getFilename() - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaFileDataSourceBackend

getFilename() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaFixedWidthFileDataSourceBackend

getFilter() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.job.Task

getFirstName() - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Person

Get the person's first name.

getFlag() - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.ObservationWithResult

Get the flag for the result.

getGender() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Patient

Get the patient's gender.

getIcd9Diagnoses() - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataProvider

Get a list of ICD9 Diagnostic codes from the data.

getIcd9Diagnoses() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.XlsxDataProvider

getIcd9ProcedureCodesRootFullName() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDataSourceBackend

getIcd9Procedures() - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataProvider

Get a list of ICD9 Procedure codes from the data.

getIcd9Procedures() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.XlsxDataProvider

getId() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Encounter

Get the encounter's unique identifier.

getId() - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Observation

Get the unique identifier for the observation.

getId() - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Person

Get the person's unique identifier.

getInjector() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.config.BackEndContextListener

getInstance(DestinationEntity) - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.dest.EurekaDeidConfigFactory

getInstance(DestinationEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dest.JpaEurekaDeidConfigFactory

getInstance(Long, boolean) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dest.ProtempaDestinationFactory

getInstance(DestinationEntity, boolean) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dest.ProtempaDestinationFactory

getJob(HttpServletRequest, Long) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.JobResource

getJobStats(HttpServletRequest, Long, String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.JobResource

getJobStatsRoot(HttpServletRequest, Long) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.JobResource

getJobStatus(JobFilter) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.JobResource

getKeyType() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDataSourceBackend

getKeyType() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDelimitedFileDataSourceBackend

getKeyType() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaFixedWidthFileDataSourceBackend

getKeyTypeDisplayName() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDataSourceBackend

getKeyTypeDisplayName() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDelimitedFileDataSourceBackend

getKeyTypeDisplayName() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaFixedWidthFileDataSourceBackend

getLabs() - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataProvider

Get a list of lab results from the data.

getLabs() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.XlsxDataProvider

getLabsRootFullName() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDataSourceBackend

getLanguage() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Patient

Get the language spoken by the patient.

getLastName() - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Person

Get the person's last name.

getLatestJob(HttpServletRequest) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.JobResource

getLatestWithFilter(JobFilter) - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.dao.JobDao

getLatestWithFilter(JobFilter) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dao.JpaJobDao

getMaritalStatus() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Patient

Get the patient's marital status.

getMedicationOrdersRootFullName() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDataSourceBackend

getMedications() - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataProvider

Get a list of medication from the data.

getMedications() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.XlsxDataProvider

getOffset(String, DestinationEntity) - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.dao.EurekaDeidConfigDao

getOffset(String, DestinationEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dao.JpaEurekaDeidConfigDao

getOne(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.Destinations

Gets the specified source extractDTO.

getOrCreatePatientParams(String, DestinationEntity) - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.dao.EurekaDeidConfigDao

getOrCreatePatientParams(String, DestinationEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dao.JpaEurekaDeidConfigDao

getOutputDirectory() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.config.EtlProperties

getOutputName(DestinationEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dest.FileSupport

getOutputName(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dest.FileSupport

getPatientId() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Encounter

Get the unique identifier for the patient associated with this encounter.

getPatients() - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataProvider

Get a list of patients from the data.

getPatients() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.XlsxDataProvider

getPrompts() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.job.Task

getPropertyName() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dest.EurekaIndexOnProperty

getProposition(String, String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.ConceptResource

getPropositionsBySearchKey(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.ksb.PropositionDefinitionFinder

getPropositionsGet(String, List<String>, String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.ConceptResource

getPropositionsInTheOntologyBySearchKey(String, String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.ConceptResource

getPropositionsPost(String, List<String>, String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.ConceptResource

getProviderId() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Encounter

Get the unique identifier for the provider associated with this encounter.

getProviders() - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataProvider

Get a list of providers from the data.

getProviders() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.XlsxDataProvider

getProxyCallbackServer() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.config.EtlProperties

getQueryResultsHandler(Query, DataSource, KnowledgeSource) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dest.PatientSetExtractorDestination

getQueryResultsHandler(Query, DataSource, KnowledgeSource) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dest.PatientSetSenderDestination

getQueryResultsHandler(Query, DataSource, KnowledgeSource) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dest.TabularFileDestination

getRace() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Patient

Get the patient's race.

getRandom() - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.dao.EurekaDeidConfigDao

getRandom() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dao.JpaEurekaDeidConfigDao

getRank() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Icd9Diagnosis

getResultAsNum() - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.ObservationWithResult

Get the results as a number.

getResultAsStr() - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.ObservationWithResult

Get the results as a string.

getSampleUrl() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDataSourceBackend

getSearchLimit() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.config.EtlProperties

getSource(HttpServletRequest, String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.SourceConfigResource

getSourceConfigDirectory() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.config.EtlProperties

getStart() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Encounter

Get the encounter's start date.

getSupportedPropositionIds(DataSource, KnowledgeSource) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dest.PatientSetExtractorDestination

getSupportedPropositionIds(DataSource, KnowledgeSource) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dest.PatientSetSenderDestination

getTaskThreadPoolSize() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.config.EtlProperties

Gets the size of the thread pool created to run Protempa tasks.

getTimestamp() - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Observation

Get the date of the observation.

getType() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Encounter

Get the encounter's type.

getUnits() - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.ObservationWithResult

Get the units used to measure the results.

getUploadedDirectory() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.config.EtlProperties

getUrl() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.config.EtlProperties

getValidationEvents() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataValidator

Get the validation events generated after validate() is called.

getVitals() - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataProvider

Get a list of vitals from the data.

getVitals() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.XlsxDataProvider

getVitalsRootFullName() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDataSourceBackend

getWithFilter(JobFilter) - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.dao.JobDao

Gets a list of jobs that meet the given filter criteria.

getWithFilter(JobFilter) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dao.JpaJobDao

getWithFilterDesc(JobFilter) - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.dao.JobDao

getWithFilterDesc(JobFilter) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dao.JpaJobDao

H

handleQueryResult(String, List<Proposition>, Map<Proposition, List<Proposition>>, Map<Proposition, List<Proposition>>, Map<UniqueId, Proposition>) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dest.PatientSetExtractorQueryResultsHandler

handleQueryResult(String, List<Proposition>, Map<Proposition, List<Proposition>>, Map<Proposition, List<Proposition>>, Map<UniqueId, Proposition>) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dest.PatientSetSenderQueryResultsHandler

handleQueryResult(String, List<Proposition>, Map<Proposition, List<Proposition>>, Map<Proposition, List<Proposition>>, Map<UniqueId, Proposition>) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dest.TabularFileQueryResultsHandler

I

Icd9Diagnosis - Class in edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet

Bean to hold information about ICD9 Diagnosis codes.

Icd9Diagnosis() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Icd9Diagnosis

Icd9Procedure - Class in edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet

Bean class to hold information about ICD9 procedures codes.

Icd9Procedure() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Icd9Procedure

initialize(BackendInstanceSpec) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDataSourceBackend

initialize(BackendInstanceSpec) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDelimitedFileDataSourceBackend

initialize(BackendInstanceSpec) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaFixedWidthFileDataSourceBackend

insertCptCodes(List<CPT>) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataInserter

Insert the given list of CPT codes to a target database using the given connection.

insertEncounters(List<Encounter>) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataInserter

Insert the given list of encounters to a target database using the given connection.

insertIcd9Diagnoses(List<Icd9Diagnosis>) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataInserter

Insert the given list of ICD9 diagnosis codes to a target database using the given connection.

insertIcd9Procedures(List<Icd9Procedure>) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataInserter

Insert the given list of ICD9 procedure codes to a target database using the given connection.

insertLabs(List<Lab>) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataInserter

Insert the given list of lab results to a target database using the given connection.

insertMedications(List<Medication>) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataInserter

Insert the given list of medications to a target database using the given connection.

insertPatients(List<Patient>) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataInserter

Insert a list of patients to the data base using the given connection.

insertProviders(List<Provider>) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataInserter

Insert the given list of providers to a target database using the given connection.

insertVitals(List<Vital>) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataInserter

Insert the given list of vital signs to a target database using the given connection.

isFailed() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataValidator

isGroupExecute() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dao.ResolvedPermissions

isGroupRead() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dao.ResolvedPermissions

isGroupWrite() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dao.ResolvedPermissions

isUpdateData() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.job.Task

J

JobDao - Interface in edu.emory.cci.aiw.cvrg.eureka.etl.dao

A data access object interface to retrieve and store information about Protempa ETL jobs.

JobEventDao - Interface in edu.emory.cci.aiw.cvrg.eureka.etl.dao

JobRepairer - Class in edu.emory.cci.aiw.cvrg.eureka.etl.config

On startup, repairs jobs that were running when Eureka backend was shut down.

JobRepairer(EntityManager) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.config.JobRepairer

JobRepairerExecutor - Class in edu.emory.cci.aiw.cvrg.eureka.etl.config

JobRepairerExecutor(String) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.config.JobRepairerExecutor

JobResource - Class in edu.emory.cci.aiw.cvrg.eureka.etl.resource

JobResource(JobDao, TaskManager, AuthorizedUserDao, DestinationDao, EtlProperties, ProtempaDestinationFactory, Provider<EntityManager>) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.resource.JobResource

JpaDeidPerPatientParamsDao - Class in edu.emory.cci.aiw.cvrg.eureka.etl.dao

Implements the JobDao interface, with the use of JPA entity managers.

JpaDeidPerPatientParamsDao(Provider<EntityManager>) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.dao.JpaDeidPerPatientParamsDao

Construct instance with the given EntityManager provider.

JpaDestinationDao - Class in edu.emory.cci.aiw.cvrg.eureka.etl.dao

JpaDestinationDao(Provider<EntityManager>) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.dao.JpaDestinationDao

JpaEtlGroupDao - Class in edu.emory.cci.aiw.cvrg.eureka.etl.dao

JpaEtlGroupDao(Provider<EntityManager>) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.dao.JpaEtlGroupDao

JpaEtlUserDao - Class in edu.emory.cci.aiw.cvrg.eureka.etl.dao

An implementation of the AuthorizedUserDao interface, backed by JPA entities and queries.

JpaEtlUserDao(Provider<EntityManager>) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.dao.JpaEtlUserDao

Create an object with the give entity manager.

JpaEurekaDeidConfigDao - Class in edu.emory.cci.aiw.cvrg.eureka.etl.dao

JpaEurekaDeidConfigFactory - Class in edu.emory.cci.aiw.cvrg.eureka.etl.dest

JpaEurekaDeidConfigFactory(EurekaDeidConfigDao) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.dest.JpaEurekaDeidConfigFactory

JpaJobDao - Class in edu.emory.cci.aiw.cvrg.eureka.etl.dao

Implements the JobDao interface, with the use of JPA entity managers.

JpaJobDao(Provider<EntityManager>) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.dao.JpaJobDao

Construct instance with the given EntityManager provider.

JpaJobEventDao - Class in edu.emory.cci.aiw.cvrg.eureka.etl.dao

Implements the JobDao interface, with the use of JPA entity managers.

JpaJobEventDao(Provider<EntityManager>) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.dao.JpaJobEventDao

Construct instance with the given EntityManager provider.

JpaRoleDao - Class in edu.emory.cci.aiw.cvrg.eureka.etl.dao

A RoleDao implementation, backed by JPA entities and queries.

JpaRoleDao(Provider<EntityManager>) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.dao.JpaRoleDao

Create a new object with the given entity manager.

JpaSourceConfigDao - Class in edu.emory.cci.aiw.cvrg.eureka.etl.dao

JpaSourceConfigDao(Provider<EntityManager>) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.dao.JpaSourceConfigDao

L

Lab - Class in edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet

Holds results information about lab tests performed during an encounter.

Lab() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Lab

load(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.config.EurekaProtempaConfigurations

M

Medication - Class in edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet

Bean class to hold informationa bout medications during an encounter.

Medication() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Medication

N

NewProtempaException - Exception in edu.emory.cci.aiw.cvrg.eureka.etl.job

O

Observation - Interface in edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet

Observations related to a patient's encounter.

ObservationWithResult - Interface in edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet

Observations for a patient's encounter, including results of the observation.

outputDirectory(String, String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.config.EtlProperties

outputFileDirectory(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.config.EtlProperties

OutputResource - Class in edu.emory.cci.aiw.cvrg.eureka.etl.resource

Operations related to a data file (doPost, status, etc)

OutputResource(EtlProperties, DestinationDao, FileSupport) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.resource.OutputResource

Create an object with the give data access object.

outputTempDirectory(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.config.EtlProperties

P

parseDefaultTimestamp(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDelimitedFileDataSourceBackend

parseDefaultTimestamp(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaFixedWidthFileDataSourceBackend

parseObject(String, ParsePosition) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dest.TableColumnSpecFormat

Patient - Class in edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet

Holds information about a patient.

Patient() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Patient

PatientSetExtractorDestination - Class in edu.emory.cci.aiw.cvrg.eureka.etl.dest

PatientSetExtractorQueryResultsHandler - Class in edu.emory.cci.aiw.cvrg.eureka.etl.dest

PatientSetSender - Class in edu.emory.cci.aiw.cvrg.eureka.etl.dest

PatientSetSenderDestination - Class in edu.emory.cci.aiw.cvrg.eureka.etl.dest

PatientSetSenderQueryResultsHandler - Class in edu.emory.cci.aiw.cvrg.eureka.etl.dest

Person - Interface in edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet

A person related to an encounter, such as a provider or a patient.

primitiveParameterSpecs(String, String, String, String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDataSourceBackend

PropositionDefinitionFinder - Class in edu.emory.cci.aiw.cvrg.eureka.etl.ksb

PropositionDefinitionFinder(String, EtlProperties) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.ksb.PropositionDefinitionFinder

PropositionFinderException - Exception in edu.emory.cci.aiw.cvrg.eureka.etl.ksb

PropositionFinderException(Throwable) - Constructor for exception edu.emory.cci.aiw.cvrg.eureka.etl.ksb.PropositionFinderException

PropositionFinderException(String) - Constructor for exception edu.emory.cci.aiw.cvrg.eureka.etl.ksb.PropositionFinderException

ProtempaDestinationFactory - Class in edu.emory.cci.aiw.cvrg.eureka.etl.dest

ProtempaDestinationFactory(DestinationDao, DeidPerPatientParamsDao, EtlProperties, EurekaDeidConfigFactory) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.dest.ProtempaDestinationFactory

Provider - Class in edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet

Holds information about a provider during a patient's visit.

Provider() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Provider

Q

queueTask(Long, List<PropositionDefinition>, List<String>, Filter, boolean, Configuration) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.job.TaskManager

R

readPropositions(Set<String>, Set<String>, Filter, QueryResultsHandler) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDataSourceBackend

repairIfNeeded() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.config.JobRepairer

resolveDestinationPermissions(AuthorizedUserEntity, DestinationEntity) - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.dao.EtlGroupDao

resolveDestinationPermissions(AuthorizedUserEntity, DestinationEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dao.JpaEtlGroupDao

ResolvedPermissions - Class in edu.emory.cci.aiw.cvrg.eureka.etl.dao

ResolvedPermissions(boolean, boolean, boolean) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.dao.ResolvedPermissions

resolveSourceConfigPermissions(AuthorizedUserEntity, SourceConfigEntity) - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.dao.EtlGroupDao

resolveSourceConfigPermissions(AuthorizedUserEntity, SourceConfigEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dao.JpaEtlGroupDao

RoleDao - Interface in edu.emory.cci.aiw.cvrg.eureka.etl.dao

A data access object interface for working with RoleEntity objects in the data store.

RoleResource - Class in edu.emory.cci.aiw.cvrg.eureka.etl.resource

A RESTful end-point for working with RoleEntity objects.

RoleResource(RoleDao) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.resource.RoleResource

Create a RoleResource object with the given RoleDao

run() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.job.Task

S

searchPropositions(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.ksb.PropositionDefinitionFinder

searchPropositionsInTheOntology(String, String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.ConceptResource

setAcceptedMimetypes(String[]) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.FileBackendPropertyValidator

setCptProcedureCodesRootFullName(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDataSourceBackend

setCpts(List<CPT>) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataValidator

Set the list of CPT codes to validate.

setDatabaseId(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDataSourceBackend

setDateOfBirth(Date) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Patient

Set the patient's date of birth.

setDiagnosisCodesRootFullName(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDataSourceBackend

setDischargeDisposition(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Encounter

Set the encounter's discharge disposition.

setEncounterId(Long) - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Observation

Set the unique identifier for the encounter with which the observation is associated.

setEncounters(List<Encounter>) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataValidator

Set the list of encounters to validate.

setEnd(Date) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Encounter

Set the encounter's end date.

setEntityId(String) - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Observation

Set the unique identifier for the entity associated with the observation.

setFilename(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDataSourceBackend

setFilename(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDelimitedFileDataSourceBackend

setFilename(String) - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaFileDataSourceBackend

setFilename(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaFixedWidthFileDataSourceBackend

setFilter(Filter) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.job.Task

setFirstName(String) - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Person

Set the person's first name.

setFlag(String) - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.ObservationWithResult

Set the flag for the result.

setGender(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Patient

Set the patient's gender.

setIcd9Diagnoses(List<Icd9Diagnosis>) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataValidator

Set the list of ICD9 Diagnosis codes to validate.

setIcd9ProcedureCodesRootFullName(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDataSourceBackend

setIcd9Procedures(List<Icd9Procedure>) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataValidator

Set the list of ICD9 procedure codes to validate.

setId(Long) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Encounter

Set the encounter's unique identifier.

setId(String) - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Observation

Set the unique identifier for the observation.

setId(Long) - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Person

Set the person's unique identifier.

setLabs(List<Lab>) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataValidator

Set the list of labs to validate.

setLabsRootFullName(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDataSourceBackend

setLanguage(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Patient

Set the language spoken by the patient.

setLastName(String) - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Person

Set the person's last name.

setMaritalStatus(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Patient

Set the patient's marital status.

setMedicationOrdersRootFullName(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDataSourceBackend

setMedications(List<Medication>) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataValidator

Set the list of medications to validate.

setPatientId(Long) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Encounter

Set the unique identifier for the patient associated with this encounter.

setPatients(List<Patient>) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataValidator

Set the list of patients to validate.

setPrompts(Configuration) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.job.Task

setProviderId(Long) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Encounter

Set the unique identifier for the provider associated with this encounter.

setProviders(List<Provider>) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataValidator

Set the list of providers to validate

setRace(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Patient

Set the patient's race.

setRank(int) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Icd9Diagnosis

setResultAsNum(Double) - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.ObservationWithResult

Set the results as a number

setResultAsStr(String) - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.ObservationWithResult

Set the results as a string.

setSampleUrl(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDataSourceBackend

setStart(Date) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Encounter

Set the encounter's start date.

setTimestamp(Date) - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Observation

Set the date of the observation.

setType(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Encounter

Set the encounter's type.

setUnits(String) - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.ObservationWithResult

Set the units used to measure the results.

setUpdateData(boolean) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.job.Task

setVitals(List<Vital>) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataValidator

Set the list of vitals to validate.

setVitalsRootFullName(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDataSourceBackend

shutdown() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.job.TaskManager

shutdownNow() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.job.TaskManager

SourceConfigDao - Interface in edu.emory.cci.aiw.cvrg.eureka.etl.dao

SourceConfigResource - Class in edu.emory.cci.aiw.cvrg.eureka.etl.resource

SourceConfigResource(EtlProperties, AuthorizedUserDao, SourceConfigDao, EtlGroupDao) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.resource.SourceConfigResource

stagedSpecs(String, String, String, String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDataSourceBackend

start(Collection<PropositionDefinition>) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dest.AbstractFileQueryResultsHandler

Creates an output stream and calls AbstractFileQueryResultsHandler.start(java.io.OutputStream, java.util.Collection).

start(OutputStream, Collection<PropositionDefinition>) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dest.AbstractFileQueryResultsHandler

Called by AbstractFileQueryResultsHandler.start(java.util.Collection) to given subclasses an opportunity to create resources and access the output stream.

start(OutputStream, Collection<PropositionDefinition>) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dest.PatientSetExtractorQueryResultsHandler

start(OutputStream, Collection<PropositionDefinition>) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dest.PatientSetSenderQueryResultsHandler

start(Collection<PropositionDefinition>) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dest.TabularFileQueryResultsHandler

submit(HttpServletRequest, JobRequest) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.JobResource

T

TableColumnSpecFormat - Class in edu.emory.cci.aiw.cvrg.eureka.etl.dest

TableColumnSpecFormat(String) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.dest.TableColumnSpecFormat

TableColumnSpecFormat(String, Format) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.dest.TableColumnSpecFormat

TabularFileDestination - Class in edu.emory.cci.aiw.cvrg.eureka.etl.dest

TabularFileQueryResultsHandler - Class in edu.emory.cci.aiw.cvrg.eureka.etl.dest

Task - Class in edu.emory.cci.aiw.cvrg.eureka.etl.job

TaskManager - Class in edu.emory.cci.aiw.cvrg.eureka.etl.job

TaskManager(Provider<Task>, EtlProperties) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.job.TaskManager

TaskProvider - Class in edu.emory.cci.aiw.cvrg.eureka.etl.job

TaskProvider(JobDao, ETL, Provider<EntityManager>) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.job.TaskProvider

TextPlainBackendPropertyValidator - Class in edu.emory.cci.aiw.cvrg.eureka.etl.dsb

TextPlainBackendPropertyValidator() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.TextPlainBackendPropertyValidator

toComm(AuthorizedRoleEntity, HttpServletRequest) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.RoleResource

toComm(AuthorizedUserEntity, HttpServletRequest) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.UserResource

ToConfigFile - Class in edu.emory.cci.aiw.cvrg.eureka.etl.resource

toDestId(File) - Static method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.FromConfigFile

toEntity(User) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.UserResource

toSourceConfigId(File) - Static method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.FromConfigFile

toString() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.job.AbstractFileInfo

U

update(DeidPerPatientParams) - Method in interface edu.emory.cci.aiw.cvrg.eureka.etl.dao.EurekaDeidConfigDao

update(DeidPerPatientParams) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dao.JpaEurekaDeidConfigDao

update(HttpServletRequest, EtlDestination) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.DestinationResource

update(EtlDestination) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.Destinations

upload(HttpServletRequest, String, String, InputStream, FormDataContentDisposition) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.FileResource

uploadedDirectory(String, String) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.config.EtlProperties

UriBackendPropertyValidator - Class in edu.emory.cci.aiw.cvrg.eureka.etl.dsb

UriBackendPropertyValidator() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.UriBackendPropertyValidator

UserResource - Class in edu.emory.cci.aiw.cvrg.eureka.etl.resource

RESTful end-point for UserEntity related methods.

UserResource(AuthorizedUserDao, RoleDao) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.resource.UserResource

Create a UserResource object with a User DAO and a Role DAO.

V

validate() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dest.PatientSetExtractorQueryResultsHandler

validate() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dest.PatientSetSenderQueryResultsHandler

validate() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dest.TabularFileQueryResultsHandler

validate(String, Object) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.FileBackendPropertyValidator

validate(String, Object) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.UriBackendPropertyValidator

validate() - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.DataValidator

Run all the validation routines for the data we have.

validateData(KnowledgeSource) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.dsb.EurekaDataSourceBackend

visit(CohortDestinationEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.DestinationDTOExtractorVisitor

visit(I2B2DestinationEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.DestinationDTOExtractorVisitor

visit(Neo4jDestinationEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.DestinationDTOExtractorVisitor

visit(PatientSetExtractorDestinationEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.DestinationDTOExtractorVisitor

visit(PatientSetSenderDestinationEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.DestinationDTOExtractorVisitor

visit(TabularFileDestinationEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.etl.resource.DestinationDTOExtractorVisitor

Vital - Class in edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet

Holds information about vital signs taken during a patient's visit.

Vital() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.Vital

X

XlsxDataProvider - Class in edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet

An implementation of the DataProvider interface, using an Excel workbook as the data source.

XlsxDataProvider(File, Locale) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.etl.spreadsheet.XlsxDataProvider

Create the data provider from the given data file.

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