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

A

AbstractConverter - Class in edu.emory.cci.aiw.cvrg.eureka.services.conversion

AbstractPropositionFinder<K> - Class in edu.emory.cci.aiw.cvrg.eureka.services.finder

AbstractPropositionFinder(PropositionRetriever<K>) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.finder.AbstractPropositionFinder

AbstractValueThresholdGroupEntityConverter - Class in edu.emory.cci.aiw.cvrg.eureka.services.conversion

addPropositionId(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.PropositionDefinitionConverterVisitor

addUser(UserRequest, UriInfo) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.UserRequestResource

Add a new user to the system.

addUser(User, UriInfo) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.UserResource

Add a new user to the system.

AppPropertyResource - Class in edu.emory.cci.aiw.cvrg.eureka.services.resource

AppPropertyResource(ServiceProperties) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.resource.AppPropertyResource

asValue(DataElementEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.AbstractConverter

asValue(DataElementEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.DataElementConversionSupport

asValue(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.DataElementConversionSupport

asValueCompString(DataElementEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.AbstractConverter

asValueCompString(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.DataElementConversionSupport

asValueCompString(DataElementEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.DataElementConversionSupport

asValueString(DataElementEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.AbstractConverter

asValueString(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.DataElementConversionSupport

asValueString(DataElementEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.DataElementConversionSupport

AuthenticationMethodDao - Interface in edu.emory.cci.aiw.cvrg.eureka.services.dao

AuthenticationMethodResource - Class in edu.emory.cci.aiw.cvrg.eureka.services.resource

AuthenticationMethodResource(AuthenticationMethodDao) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.resource.AuthenticationMethodResource

C

CategorizationConverter - Class in edu.emory.cci.aiw.cvrg.eureka.services.conversion

CategorizationConverter() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.conversion.CategorizationConverter

CategorizationTranslator - Class in edu.emory.cci.aiw.cvrg.eureka.services.translation

Translates categorical data elements (UI element) into categorization propositions.

CategorizationTranslator(DataElementEntityDao, SystemPropositionFinder, SourceConfigResource) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.translation.CategorizationTranslator

changePassword(String, String) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.clients.I2b2Client

changePassword(String, String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.clients.I2b2RestClient

changePassword(HttpServletRequest, PasswordChangeRequest) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.UserResource

Changes a user's password.

ConfigListener - Class in edu.emory.cci.aiw.cvrg.eureka.services.config

Set up the Guice dependency injection engine.

ConfigListener() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.config.ConfigListener

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

ConversionSupport - Class in edu.emory.cci.aiw.cvrg.eureka.services.conversion

ConversionSupport() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.conversion.ConversionSupport

convert(CategoryEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.CategorizationConverter

convert(FrequencyEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.FrequencyNotValueThresholdConverter

convert(FrequencyEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.FrequencyValueThresholdConverter

convert(SystemProposition) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.SystemPropositionConverter

convert(ValueThresholdGroupEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.ValueThresholdsCompoundLowLevelAbstractionConverter

convert(ValueThresholdGroupEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.ValueThresholdsLowLevelAbstractionConverter

create(DataElement) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.DataElementResource

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

createDestination(EtlDestination) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClient

createDestination(EtlDestination) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClientImpl

D

DataElementConversionSupport - Class in edu.emory.cci.aiw.cvrg.eureka.services.conversion

DataElementConversionSupport() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.conversion.DataElementConversionSupport

DataElementEntityDao - Interface in edu.emory.cci.aiw.cvrg.eureka.services.dao

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

DataElementEntityTranslatorVisitor - Class in edu.emory.cci.aiw.cvrg.eureka.services.translation

DataElementEntityTranslatorVisitor(SystemPropositionTranslator, SequenceTranslator, CategorizationTranslator, FrequencyTranslator, ValueThresholdsTranslator) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.translation.DataElementEntityTranslatorVisitor

DataElementResource - Class in edu.emory.cci.aiw.cvrg.eureka.services.resource

PropositionCh

DataElementResource(DataElementEntityDao, UserDao, DataElementEntityTranslatorVisitor, SummarizingDataElementEntityTranslatorVisitor, DataElementTranslatorVisitor) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.resource.DataElementResource

DataElementTranslatorVisitor - Class in edu.emory.cci.aiw.cvrg.eureka.services.translation

DataElementTranslatorVisitor(SystemPropositionTranslator, SequenceTranslator, CategorizationTranslator, FrequencyTranslator, ValueThresholdsTranslator) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.translation.DataElementTranslatorVisitor

delete(Long, String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.DataElementResource

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

deleteDestination(String) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClient

deleteDestination(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClientImpl

deleteOutput(String) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClient

deleteOutput(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClientImpl

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

DestinationResource(EtlClient, UserDao, ConversionSupport) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.resource.DestinationResource

DestinationToEtlDestinationVisitor - Class in edu.emory.cci.aiw.cvrg.eureka.services.conversion

DestinationToEtlDestinationVisitor(ConversionSupport) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.conversion.DestinationToEtlDestinationVisitor

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

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

E

edu.emory.cci.aiw.cvrg.eureka.services.authentication - package edu.emory.cci.aiw.cvrg.eureka.services.authentication

edu.emory.cci.aiw.cvrg.eureka.services.clients - package edu.emory.cci.aiw.cvrg.eureka.services.clients

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

edu.emory.cci.aiw.cvrg.eureka.services.conversion - package edu.emory.cci.aiw.cvrg.eureka.services.conversion

This package implements conversion of Eureka! derived data elements to Protempa proposition definitions.

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

edu.emory.cci.aiw.cvrg.eureka.services.email - package edu.emory.cci.aiw.cvrg.eureka.services.email

edu.emory.cci.aiw.cvrg.eureka.services.entity - package edu.emory.cci.aiw.cvrg.eureka.services.entity

edu.emory.cci.aiw.cvrg.eureka.services.finder - package edu.emory.cci.aiw.cvrg.eureka.services.finder

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

edu.emory.cci.aiw.cvrg.eureka.services.translation - package edu.emory.cci.aiw.cvrg.eureka.services.translation

edu.emory.cci.aiw.cvrg.eureka.services.util - package edu.emory.cci.aiw.cvrg.eureka.services.util

EmailException - Exception in edu.emory.cci.aiw.cvrg.eureka.services.email

To be thrown when there are any errors in initializing an email sender, or in sending the email.

EmailException(String) - Constructor for exception edu.emory.cci.aiw.cvrg.eureka.services.email.EmailException

Create an exception with the given message.

EmailException(Throwable) - Constructor for exception edu.emory.cci.aiw.cvrg.eureka.services.email.EmailException

Create an exception with the given Throwable as the root cause.

EmailSender - Interface in edu.emory.cci.aiw.cvrg.eureka.services.email

An interface that defines how emails can be sent out from the application.

EtlClient - Interface in edu.emory.cci.aiw.cvrg.eureka.services.config

EtlClientImpl - Class in edu.emory.cci.aiw.cvrg.eureka.services.config

EtlClientImpl(ServiceProperties) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClientImpl

EtlDestinationToDestinationVisitor - Class in edu.emory.cci.aiw.cvrg.eureka.services.conversion

EtlDestinationToDestinationVisitor(ConversionSupport) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.conversion.EtlDestinationToDestinationVisitor

F

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

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

FileResource(EtlClient) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.resource.FileResource

Create an object with the give data access object.

find(String, K) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.finder.AbstractPropositionFinder

Retrieves a proposition definition from the PropositionRetriever specified in this object's constructor.

find(String, K) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.finder.PropositionFinder

Finds the proposition definition for the given user and key.

findAll(String, List<String>, Boolean) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.finder.SystemPropositionFinder

Finds all of the system elements given by the keys for the given user

FreeMarkerEmailSender - Class in edu.emory.cci.aiw.cvrg.eureka.services.email

Implements the EmailSender interface with FreeMarker templates.

FreeMarkerEmailSender(ServiceProperties, Session) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.email.FreeMarkerEmailSender

Default constructor, creates a FreeMarker configuration object.

FrequencyConverter - Interface in edu.emory.cci.aiw.cvrg.eureka.services.conversion

FrequencyNotValueThresholdConverter - Class in edu.emory.cci.aiw.cvrg.eureka.services.conversion

FrequencyNotValueThresholdConverter() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.conversion.FrequencyNotValueThresholdConverter

FrequencyTranslator - Class in edu.emory.cci.aiw.cvrg.eureka.services.translation

FrequencyTranslator(DataElementEntityDao, TimeUnitDao, SystemPropositionFinder, ValueComparatorDao, FrequencyTypeDao, SourceConfigResource) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.translation.FrequencyTranslator

FrequencyTypeDao - Interface in edu.emory.cci.aiw.cvrg.eureka.services.dao

FrequencyTypeResource - Class in edu.emory.cci.aiw.cvrg.eureka.services.resource

FrequencyTypeResource(FrequencyTypeDao) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.resource.FrequencyTypeResource

FrequencyValueThresholdConverter - Class in edu.emory.cci.aiw.cvrg.eureka.services.conversion

FrequencyValueThresholdConverter() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.conversion.FrequencyValueThresholdConverter

G

generatePassword() - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.util.PasswordGenerator

generatePassword() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.util.PasswordGeneratorImpl

get(Long) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.AuthenticationMethodResource

get(HttpServletRequest, String, boolean) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.DataElementResource

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

get(Long) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.FrequencyTypeResource

get(Long) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.LoginTypeResource

get(Long) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.OAuthProviderResource

get(Long) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.RelationOperatorResource

get(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.SourceConfigResource

get(String, boolean) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.SystemElementResource

get(Long) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.ThresholdsOperatorResource

get(Long) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.TimeUnitResource

get(Long) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.ValueComparatorResource

getActivationEmailSubject() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.ServiceProperties

Get the activation email subject line.

getAll() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.AuthenticationMethodResource

getAll(HttpServletRequest, boolean) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.DataElementResource

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

Gets all of the destinations for a user

getAll() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.LoginTypeResource

getAll() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.OAuthProviderResource

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

Gets all of the system elements for a user

getAll() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.SystemElementResource

Gets all of the system elements for a user

getAll() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.ThresholdsOperatorResource

getAllAsc() - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.dao.FrequencyTypeDao

getAllAsc() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.dao.JpaFrequencyTypeDao

getAllAsc() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.dao.JpaRelationOperatorDao

getAllAsc() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.dao.JpaTimeUnitDao

getAllAsc() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.dao.JpaValueComparatorDao

getAllAsc() - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.dao.RelationOperatorDao

getAllAsc() - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.dao.TimeUnitDao

getAllAsc() - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.dao.ValueComparatorDao

getAllAsc() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.FrequencyTypeResource

getAllAsc() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.RelationOperatorResource

getAllAsc() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.TimeUnitResource

getAllAsc() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.ValueComparatorResource

getAppPropertiesLinks() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.ServiceProperties

Gets the appPropertiesLinks.

getAppPropertiesLinks() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.AppPropertyResource

getAppPropertiesModes() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.ServiceProperties

Gets the appPropertiesModes.

getAppPropertiesModes() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.AppPropertyResource

getAppPropertiesRegistration() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.ServiceProperties

Gets the appPropertiesRegistration.

getAppPropertiesRegistration() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.AppPropertyResource

getByAttributePrincipal(AttributePrincipal) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.dao.JpaUserDao

getByAttributePrincipal(AttributePrincipal) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.dao.UserDao

Get a user object, given the user name.

getByHttpServletRequest(HttpServletRequest) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.dao.JpaUserDao

getByHttpServletRequest(HttpServletRequest) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.dao.UserDao

getByName(AuthenticationMethod) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.dao.AuthenticationMethodDao

Gets a value definition match operator based on the name attribute.

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

Gets a value definition match operator based on the name attribute.

getByName(AuthenticationMethod) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.dao.JpaAuthenticationMethodDao

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

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

getByName(LoginType) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.dao.JpaLoginTypeDao

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

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

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

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

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

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

Get a user object, given the user name.

getByName(LoginType) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.dao.LoginTypeDao

Gets a value definition match operator based on the name attribute.

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

Gets a value definition match operator based on the name attribute.

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

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

Gets a value definition match operator based on the name attribute.

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

Gets a value comparator based on the name attribute.

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

Gets a value comparator based on the name attribute.

getByName(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.AuthenticationMethodResource

getByName(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.FrequencyTypeResource

getByName(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.LoginTypeResource

getByName(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.OAuthProviderResource

getByName(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.RelationOperatorResource

getByName(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.ThresholdsOperatorResource

getByName(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.TimeUnitResource

getByName(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.ValueComparatorResource

getByUserAndKey(Long, String) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.dao.DataElementEntityDao

Gets a user-defined data element entity based on the "key" attribute.

getByUserAndKey(Long, String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.dao.JpaDataElementEntityDao

getByUserId(Long) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.dao.DataElementEntityDao

Gets a list of user-defined data element entities for the given user ID.

getByUserId(Long) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.dao.JpaDataElementEntityDao

getByUsername(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.dao.JpaUserDao

getByUsername(String) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.dao.UserDao

getByVerificationCode(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.dao.JpaLocalUserDao

getByVerificationCode(String) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.dao.LocalUserDao

Get a user by the verification code.

getCache() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.finder.AbstractPropositionFinder

getCache() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.finder.SystemPropositionFinder

getCacheManager() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.finder.AbstractPropositionFinder

getCacheManager() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.finder.SystemPropositionFinder

getCohortDestinations() - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClient

getCohortDestinations() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClientImpl

getDataElement() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.translation.DataElementEntityTranslatorVisitor

getDataElement() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.translation.SummarizingDataElementEntityTranslatorVisitor

getDataElementEntity() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.translation.DataElementTranslatorVisitor

getDefault() - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.dao.FrequencyTypeDao

getDefault() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.dao.JpaFrequencyTypeDao

getDefault() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.dao.JpaRelationOperatorDao

getDefault() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.dao.JpaTimeUnitDao

getDefault() - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.dao.RelationOperatorDao

getDefault() - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.dao.TimeUnitDao

getDefaultSystemPropositions() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.ServiceProperties

Gets the default list of system propositions for the application.

getDestination(String) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClient

getDestination(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClientImpl

getDestination() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.EtlDestinationToDestinationVisitor

getDestinations() - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClient

getDestinations() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClientImpl

getEtlDestination() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.DestinationToEtlDestinationVisitor

getEtlUrl() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.ServiceProperties

Get the URL for the eureka-protempa-etl application.

getFromEmailAddress() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.ServiceProperties

Get email address in the From header.

getGitHubOAuthKey() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.ServiceProperties

getGitHubOAuthSecret() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.ServiceProperties

getGlobusOAuthKey() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.ServiceProperties

getGlobusOAuthSecret() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.ServiceProperties

getGoogleOAuthKey() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.ServiceProperties

getGoogleOAuthSecret() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.ServiceProperties

getI2b2AdminPassword() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.ServiceProperties

Gets the i2b2 admin password from application.properties.

getI2b2AdminUser() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.ServiceProperties

Gets the i2b2 admin username from application.properties.

getI2B2Destinations() - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClient

getI2B2Destinations() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClientImpl

getI2b2Domain() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.ServiceProperties

Gets the i2b2 domain from application.properties.

getI2b2URL() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.ServiceProperties

Gets the i2b2 rest URL from application.properties.

getInjector() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.ConfigListener

getInstance(PropositionDefinitionConverterVisitor, List<DataElementEntity>) - Static method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.PropositionDefinitionCollector

getJob(Long) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClient

getJob(Long) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClientImpl

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

getJobs() - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClient

getJobs() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClientImpl

getJobsByUser(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.JobResource

Get a list of jobs associated with user referred to by the given unique identifier.

getJobsDesc() - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClient

getJobsDesc() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClientImpl

getJobStats(Long, String) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClient

getJobStats(Long, String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClientImpl

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

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

getJobStatus(JobFilter) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClient

getJobStatus(JobFilter) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClientImpl

getLdapUserEntityInstance() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.entity.UserEntityFactory

getLocalUserEntityInstance() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.entity.UserEntityFactory

getMe(HttpServletRequest) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.UserResource

Get a user using the username.

getNode() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.ServicesNodeToEtlNodeVisitor

getOAuthUserEntityInstance() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.entity.UserEntityFactory

getOutput(String) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClient

getOutput(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClientImpl

getParams(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.SourceConfigResource

getParamsList() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.SourceConfigResource

getPasswordChangeEmailSubject() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.ServiceProperties

Get the password change email subject line.

getPasswordResetEmailSubject() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.ServiceProperties

Gets the subject line for a password reset email.

getPatientSetExtractorDestinations() - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClient

getPatientSetExtractorDestinations() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClientImpl

getPrimaryProposition() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.PropositionDefinitionConverterVisitor

getPrimaryPropositionDefinition() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.CategorizationConverter

getPrimaryPropositionDefinition() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.FrequencyNotValueThresholdConverter

getPrimaryPropositionDefinition() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.FrequencyValueThresholdConverter

getPrimaryPropositionDefinition() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.SystemPropositionConverter

getPrimaryPropositionDefinition() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.ValueThresholdsCompoundLowLevelAbstractionConverter

getPrimaryPropositionDefinition() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.ValueThresholdsLowLevelAbstractionConverter

getPrimaryPropositionId() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.CategorizationConverter

getPrimaryPropositionId() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.FrequencyNotValueThresholdConverter

getPrimaryPropositionId() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.FrequencyValueThresholdConverter

getPrimaryPropositionId() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.PropositionDefinitionConverterVisitor

getPrimaryPropositionId() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.SystemPropositionConverter

getPrimaryPropositionId() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.ValueThresholdsCompoundLowLevelAbstractionConverter

getPrimaryPropositionId() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.ValueThresholdsLowLevelAbstractionConverter

getPropositionDefinition(String, String) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClient

Gets a proposition definition with a specified id for a source configuration.

getPropositionDefinition(String, String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClientImpl

Gets a proposition definition with a specified id for a specified user.

getPropositionDefinitions(String, List<String>, Boolean) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClient

Gets all of the proposition definitions given by the key IDs for the given source configuration.

getPropositionDefinitions(String, List<String>, Boolean) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClientImpl

Gets all of the proposition definitions given by the key IDs for the given user.

getPropositionDefinitions() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.PropositionDefinitionConverterVisitor

getPropositionSearchResults(String, String) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClient

getPropositionSearchResults(String, String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClientImpl

getPropositionSearchResultsBySearchKey(String, String) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClient

getPropositionSearchResultsBySearchKey(String, String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClientImpl

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

getProxyCallbackServer() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.ServiceProperties

getRegistrationTimeout() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.ServiceProperties

Get the number of hours to keep a user registration without verification, before deleting it from the database.

getResourceUrl() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.clients.I2b2RestClient

getResourceUrl() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClientImpl

getRole(Long) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.RoleResource

Get a role by the role's identification number.

getRoleByName(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.dao.JpaRoleDao

getRoleByName(String) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.dao.RoleDao

Get a role, given the name of that role.

getRoles() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.RoleResource

Get a list of all the roles available in the system.

getServicesUrl(HttpServletRequest) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.ServiceProperties

Get the base URL for the services layer for external users.

getSourceConfig(String) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClient

getSourceConfig(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClientImpl

getSourceConfigs() - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClient

getSourceConfigs() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClientImpl

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

Get the status of the most recent job process for the given user.

getSystemElementsBySearchKey(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.SystemElementResource

getSystemType() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.util.PropositionDefinitionTypeVisitor

getToShowPropDefs() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.PropositionDefinitionCollector

getTwitterOAuthKey() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.ServiceProperties

getTwitterOAuthSecret() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.ServiceProperties

getUserById(HttpServletRequest, Long) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.UserResource

Get a user by the user's identification number.

getUserEntity() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.util.UserRequestToUserEntityVisitor

getUserEntity() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.util.UserToUserEntityVisitor

getUserOrSystemByUserAndKey(Long, String) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.dao.DataElementEntityDao

Gets a system proposition definition that has been loaded previously into the database.

getUserOrSystemByUserAndKey(Long, String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.dao.JpaDataElementEntityDao

getUserPropDefs() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.PropositionDefinitionCollector

getUsers() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.UserResource

Get a list of all users in the system.

getVerificationEmailSubject() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.ServiceProperties

Get the verification email subject line.

getVerificationUrl() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.ServiceProperties

Get the verification base URL, to be used in sending a verification email to the user.

I

I2b2Client - Interface in edu.emory.cci.aiw.cvrg.eureka.services.clients

I2b2RestClient - Class in edu.emory.cci.aiw.cvrg.eureka.services.clients

I2b2RestClient(ServiceProperties) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.clients.I2b2RestClient

J

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

REST operations related to jobs submitted by the user.

JobResource(UserDao, PropositionDefinitionConverterVisitor, DataElementEntityDao, EtlClient, ServiceProperties) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.resource.JobResource

Construct a new job resource with the given job update thread.

JpaAuthenticationMethodDao - Class in edu.emory.cci.aiw.cvrg.eureka.services.dao

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

JpaDataElementEntityDao - Class in edu.emory.cci.aiw.cvrg.eureka.services.dao

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

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

Create an object with the given entity manager provider.

JpaFrequencyTypeDao - Class in edu.emory.cci.aiw.cvrg.eureka.services.dao

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

JpaLocalUserDao - Class in edu.emory.cci.aiw.cvrg.eureka.services.dao

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

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

Create an object with the give entity manager.

JpaLoginTypeDao - Class in edu.emory.cci.aiw.cvrg.eureka.services.dao

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

JpaOAuthProviderDao - Class in edu.emory.cci.aiw.cvrg.eureka.services.dao

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

JpaRelationOperatorDao - Class in edu.emory.cci.aiw.cvrg.eureka.services.dao

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

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

A RoleDao implementation, backed by JPA entities and queries.

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

Create a new object with the given entity manager.

JpaThresholdsOperatorDao - Class in edu.emory.cci.aiw.cvrg.eureka.services.dao

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

JpaTimeUnitDao - Class in edu.emory.cci.aiw.cvrg.eureka.services.dao

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

JpaUserDao - Class in edu.emory.cci.aiw.cvrg.eureka.services.dao

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

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

Create an object with the give entity manager.

JpaValueComparatorDao - Class in edu.emory.cci.aiw.cvrg.eureka.services.dao

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

L

LocalUserDao - Interface in edu.emory.cci.aiw.cvrg.eureka.services.dao

LoginTypeDao - Interface in edu.emory.cci.aiw.cvrg.eureka.services.dao

LoginTypeResource - Class in edu.emory.cci.aiw.cvrg.eureka.services.resource

LoginTypeResource(LoginTypeDao) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.resource.LoginTypeResource

M

main(String[]) - Static method in class edu.emory.cci.aiw.cvrg.eureka.services.util.SuperUserDefaultPasswordGenerator

O

OAuthProviderDao - Interface in edu.emory.cci.aiw.cvrg.eureka.services.dao

OAuthProviderResource - Class in edu.emory.cci.aiw.cvrg.eureka.services.resource

OAuthProviderResource(OAuthProviderDao) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.resource.OAuthProviderResource

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

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

OutputResource(EtlClient) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.resource.OutputResource

Create an object with the give data access object.

P

PasswordGenerator - Interface in edu.emory.cci.aiw.cvrg.eureka.services.util

An interface that defines the ability to generate random passwords.

PasswordGeneratorImpl - Class in edu.emory.cci.aiw.cvrg.eureka.services.util

An implementation of PasswordGenerator that uses a secure random number to generate the password.

PasswordGeneratorImpl() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.util.PasswordGeneratorImpl

PasswordResetResource - Class in edu.emory.cci.aiw.cvrg.eureka.services.resource

PasswordResetResource(LocalUserDao, EmailSender, I2b2Client, PasswordGenerator, ServiceProperties) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.resource.PasswordResetResource

PropositionDefinitionCollector - Class in edu.emory.cci.aiw.cvrg.eureka.services.conversion

PropositionDefinitionConverterVisitor - Class in edu.emory.cci.aiw.cvrg.eureka.services.conversion

PropositionDefinitionConverterVisitor(SystemPropositionConverter, CategorizationConverter, SequenceConverter, ValueThresholdsLowLevelAbstractionConverter, ValueThresholdsCompoundLowLevelAbstractionConverter, FrequencyNotValueThresholdConverter, FrequencyValueThresholdConverter) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.conversion.PropositionDefinitionConverterVisitor

PropositionDefinitionTypeVisitor - Class in edu.emory.cci.aiw.cvrg.eureka.services.util

PropositionDefinitionTypeVisitor() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.util.PropositionDefinitionTypeVisitor

PropositionFinder<K> - Interface in edu.emory.cci.aiw.cvrg.eureka.services.finder

Finds proposition definitions.

PropositionFindException - Exception in edu.emory.cci.aiw.cvrg.eureka.services.finder

Represents errors in retrieving proposition definitions.

PropositionFindException() - Constructor for exception edu.emory.cci.aiw.cvrg.eureka.services.finder.PropositionFindException

PropositionFindException(String) - Constructor for exception edu.emory.cci.aiw.cvrg.eureka.services.finder.PropositionFindException

PropositionFindException(String, Throwable) - Constructor for exception edu.emory.cci.aiw.cvrg.eureka.services.finder.PropositionFindException

PropositionFindException(Throwable) - Constructor for exception edu.emory.cci.aiw.cvrg.eureka.services.finder.PropositionFindException

PropositionRetriever<K> - Interface in edu.emory.cci.aiw.cvrg.eureka.services.finder

Interface for accessing sources of proposition definitions.

PropositionTranslator<E extends DataElement,P extends DataElementEntity> - Interface in edu.emory.cci.aiw.cvrg.eureka.services.translation

Translates a UI data element into a proposition as understood by the service layer data model.

PropositionUtil - Class in edu.emory.cci.aiw.cvrg.eureka.services.util

Provides common utility functions operating on DataElementEntitys.

putUser(HttpServletRequest, User, Long) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.UserResource

Put an updated user to the system.

R

RelationOperatorDao - Interface in edu.emory.cci.aiw.cvrg.eureka.services.dao

RelationOperatorResource - Class in edu.emory.cci.aiw.cvrg.eureka.services.resource

RelationOperatorResource(RelationOperatorDao) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.resource.RelationOperatorResource

resetPassword(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.PasswordResetResource

Reset the given user's password.

retrieve(String, K) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.finder.PropositionRetriever

Retrieves a proposition definition with the specified id and for the specified user.

retrieve(String, String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.finder.SystemPropositionRetriever

retrieveAll(String, List<String>, Boolean) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.finder.SystemPropositionRetriever

Retrieves all of the system elements given by the keys for the given user

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

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

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

A RESTful end-point for working with Role objects.

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

Create a RoleResource object with the given RoleDao

S

searchSystemElements(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.SystemElementResource

sendActivationMessage(UserEntity) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.email.EmailSender

Send an activation email to the user.

sendActivationMessage(UserEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.email.FreeMarkerEmailSender

sendPasswordChangeMessage(UserEntity) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.email.EmailSender

Send a password change email to the user.

sendPasswordChangeMessage(UserEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.email.FreeMarkerEmailSender

sendPasswordResetMessage(UserEntity, String) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.email.EmailSender

Send a password reset email to the user.

sendPasswordResetMessage(UserEntity, String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.email.FreeMarkerEmailSender

sendVerificationMessage(UserEntity) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.email.EmailSender

Send a verification email to the user.

sendVerificationMessage(UserEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.email.FreeMarkerEmailSender

Sends a verification email.

SequenceTranslator - Class in edu.emory.cci.aiw.cvrg.eureka.services.translation

Translates from sequences (UI data element) to high-level abstractions.

SequenceTranslator(DataElementEntityDao, TimeUnitDao, RelationOperatorDao, SystemPropositionFinder, ValueComparatorDao, SourceConfigResource) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.translation.SequenceTranslator

ServiceProperties - Class in edu.emory.cci.aiw.cvrg.eureka.services.config

Looks up the application properties file (application.properties) and presents the values contained in the file to the rest of the application.

ServiceProperties() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.config.ServiceProperties

ServicesAuthenticationSupport - Class in edu.emory.cci.aiw.cvrg.eureka.services.authentication

ServicesAuthenticationSupport() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.authentication.ServicesAuthenticationSupport

ServicesNodeToEtlNodeVisitor - Class in edu.emory.cci.aiw.cvrg.eureka.services.conversion

ServicesNodeToEtlNodeVisitor() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.conversion.ServicesNodeToEtlNodeVisitor

setAppPropertiesLinks(AppPropertiesLinks) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.ServiceProperties

Sets the appPropertiesLinks.

setAppPropertiesModes(AppPropertiesModes) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.ServiceProperties

Sets the appPropertiesModes.

setAppPropertiesRegistration(AppPropertiesRegistration) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.ServiceProperties

Sets the appPropertiesRegistration.

setConverterVisitor(PropositionDefinitionConverterVisitor) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.CategorizationConverter

setConverterVisitor(PropositionDefinitionConverterVisitor) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.FrequencyValueThresholdConverter

setConverterVisitor(PropositionDefinitionConverterVisitor) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.ValueThresholdsCompoundLowLevelAbstractionConverter

setConverterVisitor(PropositionDefinitionConverterVisitor) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.ValueThresholdsLowLevelAbstractionConverter

setVisitor(PropositionDefinitionConverterVisitor) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.FrequencyNotValueThresholdConverter

shutdown() - Method in class edu.emory.cci.aiw.cvrg.eureka.services.finder.AbstractPropositionFinder

shutdown() - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.finder.PropositionFinder

Performs any clean-up operations for the finder.

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

SourceConfigResource(EtlClient) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.resource.SourceConfigResource

sourceId(DataElementEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.AbstractConverter

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

Create a new job (by uploading a new file).

submitJob(JobRequest) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClient

submitJob(JobRequest) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClientImpl

SummarizingDataElementEntityTranslatorVisitor - Class in edu.emory.cci.aiw.cvrg.eureka.services.translation

SummarizingDataElementEntityTranslatorVisitor() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.translation.SummarizingDataElementEntityTranslatorVisitor

SuperUserDefaultPasswordGenerator - Class in edu.emory.cci.aiw.cvrg.eureka.services.util

SuperUserDefaultPasswordGenerator() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.util.SuperUserDefaultPasswordGenerator

SystemElementResource - Class in edu.emory.cci.aiw.cvrg.eureka.services.resource

SystemElementResource(SystemPropositionFinder, SourceConfigResource, ServiceProperties, EtlClient) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.resource.SystemElementResource

SystemPropositionConverter - Class in edu.emory.cci.aiw.cvrg.eureka.services.conversion

SystemPropositionConverter() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.conversion.SystemPropositionConverter

SystemPropositionFinder - Class in edu.emory.cci.aiw.cvrg.eureka.services.finder

SystemPropositionFinder(SystemPropositionRetriever) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.finder.SystemPropositionFinder

SystemPropositionRetriever - Class in edu.emory.cci.aiw.cvrg.eureka.services.finder

Retrieves proposition definitions from the ETL layer.

SystemPropositionRetriever(EtlClient) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.finder.SystemPropositionRetriever

SystemPropositionTranslator - Class in edu.emory.cci.aiw.cvrg.eureka.services.translation

SystemPropositionTranslator(DataElementEntityDao, SourceConfigResource, SystemPropositionFinder) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.translation.SystemPropositionTranslator

T

ThresholdsOperatorDao - Interface in edu.emory.cci.aiw.cvrg.eureka.services.dao

ThresholdsOperatorResource - Class in edu.emory.cci.aiw.cvrg.eureka.services.resource

ThresholdsOperatorResource(ThresholdsOperatorDao) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.resource.ThresholdsOperatorResource

TimeUnitDao - Interface in edu.emory.cci.aiw.cvrg.eureka.services.dao

TimeUnitResource - Class in edu.emory.cci.aiw.cvrg.eureka.services.resource

TimeUnitResource(TimeUnitDao) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.resource.TimeUnitResource

toDataElementKey(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.ConversionSupport

toDataElementKey(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.DataElementConversionSupport

toPropositionId(DataElementEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.AbstractConverter

toPropositionId(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.ConversionSupport

toPropositionId(DataElementEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.ConversionSupport

toPropositionId(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.DataElementConversionSupport

toPropositionId(DataElementEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.DataElementConversionSupport

toPropositionIdWrapped(DataElementEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.AbstractConverter

toPropositionIdWrapped(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.ConversionSupport

toPropositionIdWrapped(DataElementEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.ConversionSupport

toPropositionIdWrapped(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.DataElementConversionSupport

toPropositionIdWrapped(DataElementEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.DataElementConversionSupport

toSystemElement(String, PropositionDefinition, boolean, SystemPropositionFinder) - Static method in class edu.emory.cci.aiw.cvrg.eureka.services.util.PropositionUtil

Wraps a proposition definition into a proposition wrapper.

toSystemProposition(PropositionDefinition, Long) - Static method in class edu.emory.cci.aiw.cvrg.eureka.services.util.PropositionUtil

translateFromElement(Category) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.translation.CategorizationTranslator

translateFromElement(Frequency) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.translation.FrequencyTranslator

translateFromElement(E) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.translation.PropositionTranslator

Translates the given data element to a proposition understood by the services layer data model.

translateFromElement(Sequence) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.translation.SequenceTranslator

translateFromElement(SystemElement) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.translation.SystemPropositionTranslator

translateFromElement(ValueThresholds) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.translation.ValueThresholdsTranslator

translateFromProposition(CategoryEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.translation.CategorizationTranslator

translateFromProposition(FrequencyEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.translation.FrequencyTranslator

translateFromProposition(P) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.translation.PropositionTranslator

Translates the given proposition entity into a data element understood by the webapp layer.

translateFromProposition(SequenceEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.translation.SequenceTranslator

translateFromProposition(SystemProposition) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.translation.SystemPropositionTranslator

translateFromProposition(ValueThresholdGroupEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.translation.ValueThresholdsTranslator

U

update(HttpServletRequest, DataElement) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.DataElementResource

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

updateDestination(EtlDestination) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClient

updateDestination(EtlDestination) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClientImpl

upload(String, String, String, InputStream) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClient

upload(String, String, String, InputStream) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClientImpl

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

UserDao - Interface in edu.emory.cci.aiw.cvrg.eureka.services.dao

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

UserEntityFactory - Class in edu.emory.cci.aiw.cvrg.eureka.services.entity

UserEntityFactory(LoginTypeDao, AuthenticationMethodDao) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.entity.UserEntityFactory

UserRequestResource - Class in edu.emory.cci.aiw.cvrg.eureka.services.resource

RESTful end-point for new user registration-related methods.

UserRequestResource(UserDao, LocalUserDao, RoleDao, EmailSender, OAuthProviderDao, LoginTypeDao, AuthenticationMethodDao) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.resource.UserRequestResource

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

UserRequestToUserEntityVisitor - Class in edu.emory.cci.aiw.cvrg.eureka.services.util

UserRequestToUserEntityVisitor(OAuthProviderDao, RoleDao, LoginTypeDao, AuthenticationMethodDao) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.util.UserRequestToUserEntityVisitor

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

RESTful end-point for UserEntity related methods.

UserResource(UserDao, LocalUserDao, RoleDao, EmailSender, I2b2Client, OAuthProviderDao, LoginTypeDao, AuthenticationMethodDao, ServiceProperties) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.resource.UserResource

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

UserToUserEntityVisitor - Class in edu.emory.cci.aiw.cvrg.eureka.services.util

UserToUserEntityVisitor(OAuthProviderDao, RoleDao, LoginTypeDao, AuthenticationMethodDao) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.util.UserToUserEntityVisitor

V

validatePropositions(ValidationRequest) - Method in interface edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClient

validatePropositions(ValidationRequest) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.config.EtlClientImpl

ValueComparatorDao - Interface in edu.emory.cci.aiw.cvrg.eureka.services.dao

ValueComparatorResource - Class in edu.emory.cci.aiw.cvrg.eureka.services.resource

ValueComparatorResource(ValueComparatorDao) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.resource.ValueComparatorResource

ValueThresholdsCompoundLowLevelAbstractionConverter - Class in edu.emory.cci.aiw.cvrg.eureka.services.conversion

ValueThresholdsCompoundLowLevelAbstractionConverter() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.conversion.ValueThresholdsCompoundLowLevelAbstractionConverter

ValueThresholdsLowLevelAbstractionConverter - Class in edu.emory.cci.aiw.cvrg.eureka.services.conversion

ValueThresholdsLowLevelAbstractionConverter() - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.conversion.ValueThresholdsLowLevelAbstractionConverter

ValueThresholdsTranslator - Class in edu.emory.cci.aiw.cvrg.eureka.services.translation

ValueThresholdsTranslator(ValueComparatorDao, ThresholdsOperatorDao, TranslatorSupport, TimeUnitDao, RelationOperatorDao) - Constructor for class edu.emory.cci.aiw.cvrg.eureka.services.translation.ValueThresholdsTranslator

verifyUser(String) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.resource.UserRequestResource

Mark a local user as verified.

visit(CohortDestination) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.DestinationToEtlDestinationVisitor

visit(I2B2Destination) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.DestinationToEtlDestinationVisitor

visit(Neo4jDestination) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.DestinationToEtlDestinationVisitor

visit(PatientSetExtractorDestination) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.DestinationToEtlDestinationVisitor

visit(EtlCohortDestination) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.EtlDestinationToDestinationVisitor

visit(EtlI2B2Destination) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.EtlDestinationToDestinationVisitor

visit(EtlNeo4jDestination) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.EtlDestinationToDestinationVisitor

visit(EtlPatientSetExtractorDestination) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.EtlDestinationToDestinationVisitor

visit(SystemProposition) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.PropositionDefinitionConverterVisitor

visit(CategoryEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.PropositionDefinitionConverterVisitor

visit(SequenceEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.PropositionDefinitionConverterVisitor

visit(ValueThresholdGroupEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.PropositionDefinitionConverterVisitor

visit(FrequencyEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.PropositionDefinitionConverterVisitor

visit(Literal) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.ServicesNodeToEtlNodeVisitor

visit(UnaryOperator) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.ServicesNodeToEtlNodeVisitor

visit(BinaryOperator) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.conversion.ServicesNodeToEtlNodeVisitor

visit(SystemProposition) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.translation.DataElementEntityTranslatorVisitor

visit(CategoryEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.translation.DataElementEntityTranslatorVisitor

visit(SequenceEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.translation.DataElementEntityTranslatorVisitor

visit(FrequencyEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.translation.DataElementEntityTranslatorVisitor

visit(ValueThresholdGroupEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.translation.DataElementEntityTranslatorVisitor

visit(SystemElement) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.translation.DataElementTranslatorVisitor

visit(Category) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.translation.DataElementTranslatorVisitor

visit(Sequence) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.translation.DataElementTranslatorVisitor

visit(Frequency) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.translation.DataElementTranslatorVisitor

visit(ValueThresholds) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.translation.DataElementTranslatorVisitor

visit(SystemProposition) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.translation.SummarizingDataElementEntityTranslatorVisitor

visit(CategoryEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.translation.SummarizingDataElementEntityTranslatorVisitor

visit(SequenceEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.translation.SummarizingDataElementEntityTranslatorVisitor

visit(FrequencyEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.translation.SummarizingDataElementEntityTranslatorVisitor

visit(ValueThresholdGroupEntity) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.translation.SummarizingDataElementEntityTranslatorVisitor

visit(Collection<? extends PropositionDefinition>) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.util.PropositionDefinitionTypeVisitor

visit(ConstantDefinition) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.util.PropositionDefinitionTypeVisitor

visit(EventDefinition) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.util.PropositionDefinitionTypeVisitor

visit(HighLevelAbstractionDefinition) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.util.PropositionDefinitionTypeVisitor

visit(LowLevelAbstractionDefinition) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.util.PropositionDefinitionTypeVisitor

visit(SequentialTemporalPatternDefinition) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.util.PropositionDefinitionTypeVisitor

visit(PrimitiveParameterDefinition) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.util.PropositionDefinitionTypeVisitor

visit(SliceDefinition) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.util.PropositionDefinitionTypeVisitor

visit(CompoundLowLevelAbstractionDefinition) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.util.PropositionDefinitionTypeVisitor

visit(ContextDefinition) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.util.PropositionDefinitionTypeVisitor

visit(LocalUserRequest) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.util.UserRequestToUserEntityVisitor

visit(LdapUserRequest) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.util.UserRequestToUserEntityVisitor

visit(OAuthUserRequest) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.util.UserRequestToUserEntityVisitor

visit(LocalUser) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.util.UserToUserEntityVisitor

visit(LdapUser) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.util.UserToUserEntityVisitor

visit(OAuthUser) - Method in class edu.emory.cci.aiw.cvrg.eureka.services.util.UserToUserEntityVisitor

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