Index (Eureka! Client 1.0-Alpha-3 API)

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

A

AbstractDestinationVisitor - Class in org.eurekaclinical.eureka.client.comm
AbstractDestinationVisitor() - Constructor for class org.eurekaclinical.eureka.client.comm.AbstractDestinationVisitor
accept(NodeVisitor) - Method in class org.eurekaclinical.eureka.client.comm.BinaryOperator
accept(PhenotypeVisitor) - Method in class org.eurekaclinical.eureka.client.comm.Category
accept(DestinationVisitor) - Method in class org.eurekaclinical.eureka.client.comm.CohortDestination
accept(DestinationVisitor) - Method in class org.eurekaclinical.eureka.client.comm.Destination
accept(PhenotypeVisitor) - Method in class org.eurekaclinical.eureka.client.comm.Frequency
accept(DestinationVisitor) - Method in class org.eurekaclinical.eureka.client.comm.I2B2Destination
accept(UserVisitor) - Method in class org.eurekaclinical.eureka.client.comm.LdapUser
accept(UserRequestVisitor) - Method in class org.eurekaclinical.eureka.client.comm.LdapUserRequest
accept(NodeVisitor) - Method in class org.eurekaclinical.eureka.client.comm.Literal
accept(UserVisitor) - Method in class org.eurekaclinical.eureka.client.comm.LocalUser
accept(UserRequestVisitor) - Method in class org.eurekaclinical.eureka.client.comm.LocalUserRequest
accept(DestinationVisitor) - Method in class org.eurekaclinical.eureka.client.comm.Neo4jDestination
accept(NodeVisitor) - Method in class org.eurekaclinical.eureka.client.comm.Node
accept(UserVisitor) - Method in class org.eurekaclinical.eureka.client.comm.OAuthUser
accept(UserRequestVisitor) - Method in class org.eurekaclinical.eureka.client.comm.OAuthUserRequest
accept(DestinationVisitor) - Method in class org.eurekaclinical.eureka.client.comm.PatientSetExtractorDestination
accept(PhenotypeVisitor) - Method in interface org.eurekaclinical.eureka.client.comm.PhenotypeVisitable
accept(PhenotypeVisitor) - Method in class org.eurekaclinical.eureka.client.comm.Sequence
accept(PhenotypeVisitor) - Method in class org.eurekaclinical.eureka.client.comm.SystemPhenotype
accept(NodeVisitor) - Method in class org.eurekaclinical.eureka.client.comm.UnaryOperator
accept(UserRequestVisitor) - Method in interface org.eurekaclinical.eureka.client.comm.UserRequestVisitable: Performs some processing on a user entity.
accept(UserVisitor) - Method in interface org.eurekaclinical.eureka.client.comm.UserVisitable: Performs some processing on a user entity.
accept(PhenotypeVisitor) - Method in class org.eurekaclinical.eureka.client.comm.ValueThresholds
AuthenticationMethod - Enum in org.eurekaclinical.eureka.client.comm.authentication
AuthenticationMethod - Class in org.eurekaclinical.eureka.client.comm
AuthenticationMethod() - Constructor for class org.eurekaclinical.eureka.client.comm.AuthenticationMethod
authenticationMethod() - Method in class org.eurekaclinical.eureka.client.comm.LdapUser
authenticationMethod() - Method in class org.eurekaclinical.eureka.client.comm.LdapUserRequest
authenticationMethod() - Method in class org.eurekaclinical.eureka.client.comm.LocalUser
authenticationMethod() - Method in class org.eurekaclinical.eureka.client.comm.LocalUserRequest
authenticationMethod() - Method in class org.eurekaclinical.eureka.client.comm.OAuthUser
authenticationMethod() - Method in class org.eurekaclinical.eureka.client.comm.OAuthUserRequest
authenticationMethod() - Method in class org.eurekaclinical.eureka.client.comm.User
authenticationMethod() - Method in class org.eurekaclinical.eureka.client.comm.UserRequest

B

BinaryOperator - Class in org.eurekaclinical.eureka.client.comm
BinaryOperator() - Constructor for class org.eurekaclinical.eureka.client.comm.BinaryOperator
BinaryOperator.Op - Enum in org.eurekaclinical.eureka.client.comm

C

Category - Class in org.eurekaclinical.eureka.client.comm: Container class for the categorical user-created phenotype from the UI.
Category() - Constructor for class org.eurekaclinical.eureka.client.comm.Category
Category.CategoricalType - Enum in org.eurekaclinical.eureka.client.comm
changePassword(String, String) - Method in class org.eurekaclinical.eureka.client.EurekaClient
Cohort - Class in org.eurekaclinical.eureka.client.comm
Cohort() - Constructor for class org.eurekaclinical.eureka.client.comm.Cohort
CohortDestination - Class in org.eurekaclinical.eureka.client.comm
CohortDestination() - Constructor for class org.eurekaclinical.eureka.client.comm.CohortDestination
createDestination(Destination) - Method in class org.eurekaclinical.eureka.client.EurekaClient

D

DefaultSourceConfigOption - Class in org.eurekaclinical.eureka.client.comm
DefaultSourceConfigOption() - Constructor for class org.eurekaclinical.eureka.client.comm.DefaultSourceConfigOption
deleteDestination(Long, String) - Method in class org.eurekaclinical.eureka.client.EurekaClient
deleteUserPhenotype(Long, Long) - Method in class org.eurekaclinical.eureka.client.EurekaClient
deserialize(JsonParser, DeserializationContext) - Method in class org.eurekaclinical.eureka.client.comm.json.SourceConfigOptionValueDeserializer
deserializeWithType(JsonParser, DeserializationContext, TypeDeserializer) - Method in class org.eurekaclinical.eureka.client.comm.json.SourceConfigOptionValueDeserializer
Destination - Class in org.eurekaclinical.eureka.client.comm: The configuration for a Protempa run, including the input data store information, the output i2b2 data store information, ontology information, and other related items.
Destination() - Constructor for class org.eurekaclinical.eureka.client.comm.Destination
DestinationType - Enum in org.eurekaclinical.eureka.client.comm
DestinationVisitor - Interface in org.eurekaclinical.eureka.client.comm

E

EMPTY_SECTION_ARRAY - Static variable in class org.eurekaclinical.eureka.client.comm.SourceConfig
equals(Object) - Method in class org.eurekaclinical.eureka.client.comm.PatientSet
EurekaClient - Class in org.eurekaclinical.eureka.client
EurekaClient(String) - Constructor for class org.eurekaclinical.eureka.client.EurekaClient

F

FileSourceConfigOption - Class in org.eurekaclinical.eureka.client.comm
FileSourceConfigOption() - Constructor for class org.eurekaclinical.eureka.client.comm.FileSourceConfigOption
Frequency - Class in org.eurekaclinical.eureka.client.comm
Frequency() - Constructor for class org.eurekaclinical.eureka.client.comm.Frequency

G

getAbbrevDisplayName() - Method in class org.eurekaclinical.eureka.client.comm.PropositionWrapper: Gets the phenotype definition's abbreviated display name.
getAcceptedMimetypes() - Method in class org.eurekaclinical.eureka.client.comm.FileSourceConfigOption
getAcceptedMimetypes() - Method in class org.eurekaclinical.eureka.client.comm.SourceConfigParams.Upload
getAlgorithmSourceBackends() - Method in class org.eurekaclinical.eureka.client.comm.SourceConfig
getAliasPropositionId() - Method in class org.eurekaclinical.eureka.client.comm.PatientSetExtractorDestination
getAtLeast() - Method in class org.eurekaclinical.eureka.client.comm.Frequency
getCategoricalType() - Method in class org.eurekaclinical.eureka.client.comm.Category
getCategoricalType() - Method in class org.eurekaclinical.eureka.client.comm.PhenotypeField
getChildren() - Method in class org.eurekaclinical.eureka.client.comm.Category
getChildren() - Method in class org.eurekaclinical.eureka.client.comm.PropositionWrapper: Gets this phenotype definition's children, if any.
getChildren() - Method in class org.eurekaclinical.eureka.client.comm.SystemPhenotype
getChildrenToParents() - Method in class org.eurekaclinical.eureka.client.comm.Statistics
getCohort() - Method in class org.eurekaclinical.eureka.client.comm.CohortDestination
getCohortDestinations() - Method in class org.eurekaclinical.eureka.client.EurekaClient
getCounts() - Method in class org.eurekaclinical.eureka.client.comm.Statistics
getCreated() - Method in class org.eurekaclinical.eureka.client.comm.Phenotype
getCreated() - Method in class org.eurekaclinical.eureka.client.comm.PropositionWrapper: Gets the creation date of this phenotype definition.
getCreated() - Method in class org.eurekaclinical.eureka.client.comm.User
getCreatedAt() - Method in class org.eurekaclinical.eureka.client.comm.Destination
getDataSourceBackends() - Method in class org.eurekaclinical.eureka.client.comm.SourceConfig
getDateRangePhenotypeKey() - Method in class org.eurekaclinical.eureka.client.comm.JobSpec
getDbPath() - Method in class org.eurekaclinical.eureka.client.comm.Neo4jDestination
getDepartment() - Method in class org.eurekaclinical.eureka.client.comm.User
getDepartment() - Method in class org.eurekaclinical.eureka.client.comm.UserRequest: Get the user's department.
getDescription() - Method in class org.eurekaclinical.eureka.client.comm.AuthenticationMethod
getDescription() - Method in class org.eurekaclinical.eureka.client.comm.Destination
getDescription() - Method in class org.eurekaclinical.eureka.client.comm.LoginType
getDescription() - Method in class org.eurekaclinical.eureka.client.comm.Phenotype
getDescription() - Method in class org.eurekaclinical.eureka.client.comm.SourceConfigOption
getDestination(String) - Method in class org.eurekaclinical.eureka.client.EurekaClient
getDestinationId() - Method in class org.eurekaclinical.eureka.client.comm.Job
getDestinationId() - Method in class org.eurekaclinical.eureka.client.comm.JobListRow
getDestinationId() - Method in class org.eurekaclinical.eureka.client.comm.JobSpec
getDestinations() - Method in class org.eurekaclinical.eureka.client.EurekaClient
getDisplayName() - Method in class org.eurekaclinical.eureka.client.comm.Link
getDisplayName() - Method in class org.eurekaclinical.eureka.client.comm.Phenotype
getDisplayName() - Method in class org.eurekaclinical.eureka.client.comm.PropositionWrapper: Gets the phenotype definition's display name.
getDisplayName() - Method in class org.eurekaclinical.eureka.client.comm.SourceConfig
getDisplayName() - Method in class org.eurekaclinical.eureka.client.comm.SourceConfig.Section
getDisplayName() - Method in class org.eurekaclinical.eureka.client.comm.SourceConfigOption
getEarliestDate() - Method in class org.eurekaclinical.eureka.client.comm.JobSpec
getEarliestDateSide() - Method in class org.eurekaclinical.eureka.client.comm.JobSpec
getEmail() - Method in class org.eurekaclinical.eureka.client.comm.User
getEmail() - Method in class org.eurekaclinical.eureka.client.comm.UserRequest: Get the user's email address.
getExceptionStackTrace() - Method in class org.eurekaclinical.eureka.client.comm.JobEvent
getFinish() - Method in class org.eurekaclinical.eureka.client.comm.Literal
getFinishedDate() - Method in class org.eurekaclinical.eureka.client.comm.JobListRow
getFinishedDateFormatted() - Method in class org.eurekaclinical.eureka.client.comm.JobListRow
getFinishTimestamp() - Method in class org.eurekaclinical.eureka.client.comm.Job
getFirstName() - Method in class org.eurekaclinical.eureka.client.comm.User
getFirstName() - Method in class org.eurekaclinical.eureka.client.comm.UserRequest: Get the user's first name.
getFrequencyType() - Method in class org.eurekaclinical.eureka.client.comm.Frequency
getFrom() - Method in class org.eurekaclinical.eureka.client.comm.JobFilter
getFullName() - Method in class org.eurekaclinical.eureka.client.comm.User
getFullName() - Method in class org.eurekaclinical.eureka.client.comm.UserRequest
getHasDuration() - Method in class org.eurekaclinical.eureka.client.comm.PhenotypeField
getHasPropertyConstraint() - Method in class org.eurekaclinical.eureka.client.comm.PhenotypeField
getI2B2Destinations() - Method in class org.eurekaclinical.eureka.client.EurekaClient
getId() - Method in class org.eurekaclinical.eureka.client.comm.AuthenticationMethod
getId() - Method in class org.eurekaclinical.eureka.client.comm.Cohort
getId() - Method in class org.eurekaclinical.eureka.client.comm.Destination: Get the unique identifier for the configuration.
getId() - Method in class org.eurekaclinical.eureka.client.comm.Job
getId() - Method in class org.eurekaclinical.eureka.client.comm.JobEvent
getId() - Method in class org.eurekaclinical.eureka.client.comm.LoginType
getId() - Method in class org.eurekaclinical.eureka.client.comm.Node
getId() - Method in class org.eurekaclinical.eureka.client.comm.Phenotype
getId() - Method in class org.eurekaclinical.eureka.client.comm.PhenotypeField
getId() - Method in class org.eurekaclinical.eureka.client.comm.PropositionWrapper: Returns a user phenotype definition's id.
getId() - Method in class org.eurekaclinical.eureka.client.comm.SourceConfig
getId() - Method in class org.eurekaclinical.eureka.client.comm.SourceConfig.Section
getId() - Method in class org.eurekaclinical.eureka.client.comm.SourceConfigParams
getId() - Method in class org.eurekaclinical.eureka.client.comm.UserRequest: Get the request's unique identifier.
getIsConsecutive() - Method in class org.eurekaclinical.eureka.client.comm.Frequency
getIsWithin() - Method in class org.eurekaclinical.eureka.client.comm.Frequency
getJob(Long) - Method in class org.eurekaclinical.eureka.client.EurekaClient
getJobEvents() - Method in class org.eurekaclinical.eureka.client.comm.Job: Gets job events, assumed in order of occurrence.
getJobId() - Method in class org.eurekaclinical.eureka.client.comm.JobFilter
getJobId() - Method in class org.eurekaclinical.eureka.client.comm.JobListRow
getJobs() - Method in class org.eurekaclinical.eureka.client.EurekaClient
getJobsDesc() - Method in class org.eurekaclinical.eureka.client.EurekaClient
getJobStats(Long, String) - Method in class org.eurekaclinical.eureka.client.EurekaClient
getKey() - Method in class org.eurekaclinical.eureka.client.comm.Phenotype
getKey() - Method in class org.eurekaclinical.eureka.client.comm.PropositionWrapper: Returns a system phenotype definition's id string.
getKnowledgeSourceBackends() - Method in class org.eurekaclinical.eureka.client.comm.SourceConfig
getLastLogin() - Method in class org.eurekaclinical.eureka.client.comm.User
getLastModified() - Method in class org.eurekaclinical.eureka.client.comm.Phenotype
getLastModified() - Method in class org.eurekaclinical.eureka.client.comm.PropositionWrapper: Gets the last modified date of this phenotype definition.
getLastName() - Method in class org.eurekaclinical.eureka.client.comm.User
getLastName() - Method in class org.eurekaclinical.eureka.client.comm.UserRequest: Get the user's last name.
getLatest() - Method in class org.eurekaclinical.eureka.client.comm.JobFilter
getLatestDate() - Method in class org.eurekaclinical.eureka.client.comm.JobSpec
getLatestDateSide() - Method in class org.eurekaclinical.eureka.client.comm.JobSpec
getLatestJob() - Method in class org.eurekaclinical.eureka.client.EurekaClient
getLeftNode() - Method in class org.eurekaclinical.eureka.client.comm.BinaryOperator
getLinks() - Method in class org.eurekaclinical.eureka.client.comm.Destination
getLinks() - Method in class org.eurekaclinical.eureka.client.comm.Job
getLinks() - Method in class org.eurekaclinical.eureka.client.comm.JobListRow
getLoginType() - Method in enum org.eurekaclinical.eureka.client.comm.authentication.AuthenticationMethod
getLoginType() - Method in class org.eurekaclinical.eureka.client.comm.User
getLoginType() - Method in class org.eurekaclinical.eureka.client.comm.UserRequest
getLowerComp() - Method in class org.eurekaclinical.eureka.client.comm.ValueThreshold
getLowerUnits() - Method in class org.eurekaclinical.eureka.client.comm.ValueThreshold
getLowerValue() - Method in class org.eurekaclinical.eureka.client.comm.ValueThreshold
getMaxDuration() - Method in class org.eurekaclinical.eureka.client.comm.PhenotypeField
getMaxDurationUnits() - Method in class org.eurekaclinical.eureka.client.comm.PhenotypeField
getMe() - Method in class org.eurekaclinical.eureka.client.EurekaClient
getMessage() - Method in class org.eurekaclinical.eureka.client.comm.JobEvent
getMessages() - Method in class org.eurekaclinical.eureka.client.comm.JobListRow
getMinDuration() - Method in class org.eurekaclinical.eureka.client.comm.PhenotypeField
getMinDurationUnits() - Method in class org.eurekaclinical.eureka.client.comm.PhenotypeField
getMostRecentMessage() - Method in class org.eurekaclinical.eureka.client.comm.JobListRow
getName() - Method in class org.eurekaclinical.eureka.client.comm.AuthenticationMethod
getName() - Method in class org.eurekaclinical.eureka.client.comm.Destination
getName() - Method in class org.eurekaclinical.eureka.client.comm.JobSpec
getName() - Method in class org.eurekaclinical.eureka.client.comm.Literal
getName() - Method in class org.eurekaclinical.eureka.client.comm.LoginType
getName() - Method in class org.eurekaclinical.eureka.client.comm.PatientSet
getName() - Method in class org.eurekaclinical.eureka.client.comm.SourceConfigOption
getName() - Method in class org.eurekaclinical.eureka.client.comm.SourceConfigParams
getName() - Method in class org.eurekaclinical.eureka.client.comm.SourceConfigParams.Upload
getName() - Method in class org.eurekaclinical.eureka.client.comm.ValueThresholds
getNewPassword() - Method in class org.eurekaclinical.eureka.client.comm.PasswordChangeRequest
getNode() - Method in class org.eurekaclinical.eureka.client.comm.Cohort
getNode() - Method in class org.eurekaclinical.eureka.client.comm.UnaryOperator
getNumberOfKeys() - Method in class org.eurekaclinical.eureka.client.comm.Statistics
getOAuthProvider() - Method in class org.eurekaclinical.eureka.client.comm.OAuthUser
getOAuthProvider() - Method in class org.eurekaclinical.eureka.client.comm.OAuthUserRequest
getOldPassword() - Method in class org.eurekaclinical.eureka.client.comm.PasswordChangeRequest
getOp() - Method in class org.eurekaclinical.eureka.client.comm.BinaryOperator
getOp() - Method in class org.eurekaclinical.eureka.client.comm.UnaryOperator
getOptions() - Method in class org.eurekaclinical.eureka.client.comm.SourceConfig.Section
getOrganization() - Method in class org.eurekaclinical.eureka.client.comm.User
getOrganization() - Method in class org.eurekaclinical.eureka.client.comm.UserRequest: Get the user's organization.
getOutput(String) - Method in class org.eurekaclinical.eureka.client.EurekaClient
getOwnerUserId() - Method in class org.eurekaclinical.eureka.client.comm.Destination: Get the unique identifier for the owner of the configuration.
getOwnerUsername() - Method in class org.eurekaclinical.eureka.client.comm.SourceConfig
getPassword() - Method in class org.eurekaclinical.eureka.client.comm.LocalUser
getPassword() - Method in class org.eurekaclinical.eureka.client.comm.LocalUserRequest: Get the user's password.
getPasswordExpiration() - Method in class org.eurekaclinical.eureka.client.comm.LocalUser
getPatients() - Method in class org.eurekaclinical.eureka.client.comm.PatientSet
getPhenotype() - Method in class org.eurekaclinical.eureka.client.comm.Frequency
getPhenotype() - Method in class org.eurekaclinical.eureka.client.comm.ValueThreshold
getPhenotypeDescription() - Method in class org.eurekaclinical.eureka.client.comm.PhenotypeField
getPhenotypeDisplayName() - Method in class org.eurekaclinical.eureka.client.comm.PhenotypeField
getPhenotypeField() - Method in class org.eurekaclinical.eureka.client.comm.RelatedPhenotypeField
getPhenotypeFields() - Method in class org.eurekaclinical.eureka.client.comm.Destination
getPhenotypeKey() - Method in class org.eurekaclinical.eureka.client.comm.PhenotypeField
getPhenotypes(String[], boolean) - Method in class org.eurekaclinical.eureka.client.EurekaClient
getPrimaryPhenotype() - Method in class org.eurekaclinical.eureka.client.comm.Sequence
getPrompts() - Method in class org.eurekaclinical.eureka.client.comm.JobSpec
getProperties() - Method in class org.eurekaclinical.eureka.client.comm.PropositionWrapper: Gets this phenotype definition's properties, if any.
getProperties() - Method in class org.eurekaclinical.eureka.client.comm.SystemPhenotype
getProperty() - Method in class org.eurekaclinical.eureka.client.comm.PhenotypeField
getPropertyType() - Method in class org.eurekaclinical.eureka.client.comm.SourceConfigOption
getPropertyValue() - Method in class org.eurekaclinical.eureka.client.comm.PhenotypeField
getPropositionIds() - Method in class org.eurekaclinical.eureka.client.comm.JobSpec
getProviderUsername() - Method in class org.eurekaclinical.eureka.client.comm.OAuthUser
getProviderUsername() - Method in class org.eurekaclinical.eureka.client.comm.OAuthUserRequest
getRelatedPhenotypes() - Method in class org.eurekaclinical.eureka.client.comm.Sequence
getRelatedPhenotypes() - Method in class org.eurekaclinical.eureka.client.comm.ValueThreshold
getRelationMaxCount() - Method in class org.eurekaclinical.eureka.client.comm.RelatedPhenotypeField
getRelationMaxUnits() - Method in class org.eurekaclinical.eureka.client.comm.RelatedPhenotypeField
getRelationMinCount() - Method in class org.eurekaclinical.eureka.client.comm.RelatedPhenotypeField
getRelationMinUnits() - Method in class org.eurekaclinical.eureka.client.comm.RelatedPhenotypeField
getRelationOperator() - Method in class org.eurekaclinical.eureka.client.comm.RelatedPhenotypeField
getRelationOperator() - Method in class org.eurekaclinical.eureka.client.comm.ValueThreshold
getRequiredConcepts() - Method in class org.eurekaclinical.eureka.client.comm.Destination
getResourceUrl() - Method in class org.eurekaclinical.eureka.client.EurekaClient
getRightNode() - Method in class org.eurekaclinical.eureka.client.comm.BinaryOperator
getRole(Long) - Method in class org.eurekaclinical.eureka.client.EurekaClient
getRoleByName(String) - Method in class org.eurekaclinical.eureka.client.EurekaClient
getRoles() - Method in class org.eurekaclinical.eureka.client.EurekaClient
getSampleUrl() - Method in class org.eurekaclinical.eureka.client.comm.SourceConfigParams.Upload
getSequentialPhenotype() - Method in class org.eurekaclinical.eureka.client.comm.RelatedPhenotypeField
getSequentialPhenotypeSource() - Method in class org.eurekaclinical.eureka.client.comm.RelatedPhenotypeField
getSourceConfig(String) - Method in class org.eurekaclinical.eureka.client.EurekaClient
getSourceConfigId() - Method in class org.eurekaclinical.eureka.client.comm.Job
getSourceConfigId() - Method in class org.eurekaclinical.eureka.client.comm.JobListRow
getSourceConfigId() - Method in class org.eurekaclinical.eureka.client.comm.JobSpec
getSourceConfigParams() - Method in class org.eurekaclinical.eureka.client.EurekaClient
getSourceConfigs() - Method in class org.eurekaclinical.eureka.client.EurekaClient
getSourceId() - Method in class org.eurekaclinical.eureka.client.comm.SourceConfigParams.Upload
getStart() - Method in class org.eurekaclinical.eureka.client.comm.Literal
getStartedDate() - Method in class org.eurekaclinical.eureka.client.comm.JobListRow
getStartedDateFormatted() - Method in class org.eurekaclinical.eureka.client.comm.JobListRow
getStartTimestamp() - Method in class org.eurekaclinical.eureka.client.comm.Job
getState() - Method in class org.eurekaclinical.eureka.client.comm.JobFilter
getState() - Method in class org.eurekaclinical.eureka.client.comm.JobListRow
getStatus() - Method in exception org.eurekaclinical.eureka.client.comm.exception.PhenotypeHandlingException
getStatus() - Method in class org.eurekaclinical.eureka.client.comm.Job
getStatus() - Method in class org.eurekaclinical.eureka.client.comm.JobEvent
getStatus() - Method in class org.eurekaclinical.eureka.client.comm.JobListRow
getSystemPhenotype(String, boolean) - Method in class org.eurekaclinical.eureka.client.EurekaClient
getSystemPhenotypes() - Method in class org.eurekaclinical.eureka.client.EurekaClient
getSystemPhenotypes(List<String>, boolean) - Method in class org.eurekaclinical.eureka.client.EurekaClient
getSystemPhenotypeSearchResults(String) - Method in class org.eurekaclinical.eureka.client.EurekaClient
getSystemPhenotypeSearchResultsBySearchKey(String) - Method in class org.eurekaclinical.eureka.client.EurekaClient
getSystemType() - Method in class org.eurekaclinical.eureka.client.comm.SystemPhenotype
getTermSourceBackends() - Method in class org.eurekaclinical.eureka.client.comm.SourceConfig
getThresholdsOperator() - Method in class org.eurekaclinical.eureka.client.comm.ValueThresholds
getTimeStamp() - Method in class org.eurekaclinical.eureka.client.comm.JobEvent
getTitle() - Method in class org.eurekaclinical.eureka.client.comm.User
getTitle() - Method in class org.eurekaclinical.eureka.client.comm.UserRequest: Get the user's title.
getTo() - Method in class org.eurekaclinical.eureka.client.comm.JobFilter
getType() - Method in class org.eurekaclinical.eureka.client.comm.Destination
getType() - Method in class org.eurekaclinical.eureka.client.comm.Phenotype
getType() - Method in class org.eurekaclinical.eureka.client.comm.PhenotypeField
getType() - Method in class org.eurekaclinical.eureka.client.comm.PropositionWrapper: Gets the type of a user phenotype definition.
getUpdatedAt() - Method in class org.eurekaclinical.eureka.client.comm.Destination
getUploads() - Method in class org.eurekaclinical.eureka.client.comm.SourceConfigParams
getUpperComp() - Method in class org.eurekaclinical.eureka.client.comm.ValueThreshold
getUpperUnits() - Method in class org.eurekaclinical.eureka.client.comm.ValueThreshold
getUpperValue() - Method in class org.eurekaclinical.eureka.client.comm.ValueThreshold
getUrl() - Method in class org.eurekaclinical.eureka.client.comm.Link
getUserById(Long) - Method in class org.eurekaclinical.eureka.client.EurekaClient
getUserId() - Method in class org.eurekaclinical.eureka.client.comm.JobFilter
getUserId() - Method in class org.eurekaclinical.eureka.client.comm.Phenotype
getUserId() - Method in class org.eurekaclinical.eureka.client.comm.PropositionWrapper: Returns a user phenotype definition's user id.
getUsername() - Method in class org.eurekaclinical.eureka.client.comm.Job
getUsername() - Method in class org.eurekaclinical.eureka.client.comm.PatientSet
getUsername() - Method in class org.eurekaclinical.eureka.client.comm.UserRequest: Gets the user's unique username.
getUserPhenotype(String, boolean) - Method in class org.eurekaclinical.eureka.client.EurekaClient
getUserPhenotypes(boolean) - Method in class org.eurekaclinical.eureka.client.EurekaClient
getUsers() - Method in class org.eurekaclinical.eureka.client.EurekaClient
getValue() - Method in class org.eurekaclinical.eureka.client.comm.SourceConfigOption
getValueThresholds() - Method in class org.eurekaclinical.eureka.client.comm.ValueThresholds
getVerificationCode() - Method in class org.eurekaclinical.eureka.client.comm.LocalUser
getVerifyEmail() - Method in class org.eurekaclinical.eureka.client.comm.UserRequest: Set the user's email address verification.
getVerifyPassword() - Method in class org.eurekaclinical.eureka.client.comm.LocalUserRequest: Get the password verification.
getWithinAtLeast() - Method in class org.eurekaclinical.eureka.client.comm.Frequency
getWithinAtLeast() - Method in class org.eurekaclinical.eureka.client.comm.ValueThreshold
getWithinAtLeastUnit() - Method in class org.eurekaclinical.eureka.client.comm.ValueThreshold
getWithinAtLeastUnits() - Method in class org.eurekaclinical.eureka.client.comm.Frequency
getWithinAtMost() - Method in class org.eurekaclinical.eureka.client.comm.Frequency
getWithinAtMost() - Method in class org.eurekaclinical.eureka.client.comm.ValueThreshold
getWithinAtMostUnit() - Method in class org.eurekaclinical.eureka.client.comm.ValueThreshold
getWithinAtMostUnits() - Method in class org.eurekaclinical.eureka.client.comm.Frequency

H

hashCode() - Method in class org.eurekaclinical.eureka.client.comm.PatientSet

I

I2B2Destination - Class in org.eurekaclinical.eureka.client.comm
I2B2Destination() - Constructor for class org.eurekaclinical.eureka.client.comm.I2B2Destination
isActive() - Method in class org.eurekaclinical.eureka.client.comm.User
isExecute() - Method in class org.eurekaclinical.eureka.client.comm.Destination
isExecute() - Method in class org.eurekaclinical.eureka.client.comm.SourceConfig
isGetStatisticsSupported() - Method in class org.eurekaclinical.eureka.client.comm.Destination
isGetStatisticsSupported() - Method in class org.eurekaclinical.eureka.client.comm.Job
isGetStatisticsSupported() - Method in class org.eurekaclinical.eureka.client.comm.JobListRow
isInSystem() - Method in class org.eurekaclinical.eureka.client.comm.Phenotype
isInSystem() - Method in class org.eurekaclinical.eureka.client.comm.PhenotypeField
isInSystem() - Method in class org.eurekaclinical.eureka.client.comm.PropositionWrapper: Gets whether this phenotype definition is a system or user data element definition.
isInSystem() - Method in class org.eurekaclinical.eureka.client.comm.SystemPhenotype
isInternalNode() - Method in class org.eurekaclinical.eureka.client.comm.Phenotype
isJobConceptListSupported() - Method in class org.eurekaclinical.eureka.client.comm.Destination
isJobSubmitted() - Method in class org.eurekaclinical.eureka.client.comm.JobListRow
isParent() - Method in class org.eurekaclinical.eureka.client.comm.PropositionWrapper: Returns whether this phenotype definition has children.
isParent() - Method in class org.eurekaclinical.eureka.client.comm.SystemPhenotype
isPrompt() - Method in class org.eurekaclinical.eureka.client.comm.SourceConfigOption
isRead() - Method in class org.eurekaclinical.eureka.client.comm.Destination
isRead() - Method in class org.eurekaclinical.eureka.client.comm.SourceConfig
isRequired() - Method in class org.eurekaclinical.eureka.client.comm.SourceConfigOption
isRequired() - Method in class org.eurekaclinical.eureka.client.comm.SourceConfigParams.Upload
isSummarized() - Method in class org.eurekaclinical.eureka.client.comm.Phenotype
isSummarized() - Method in class org.eurekaclinical.eureka.client.comm.PropositionWrapper: Gets whether or not the children of this proposition are included in the message.
isUpdateData() - Method in class org.eurekaclinical.eureka.client.comm.JobSpec
isVerified() - Method in class org.eurekaclinical.eureka.client.comm.LocalUser
isWrite() - Method in class org.eurekaclinical.eureka.client.comm.Destination
isWrite() - Method in class org.eurekaclinical.eureka.client.comm.SourceConfig

J

Job - Class in org.eurekaclinical.eureka.client.comm
Job() - Constructor for class org.eurekaclinical.eureka.client.comm.Job
JobEvent - Class in org.eurekaclinical.eureka.client.comm
JobEvent() - Constructor for class org.eurekaclinical.eureka.client.comm.JobEvent
JobFilter - Class in org.eurekaclinical.eureka.client.comm: A communication class used by the service layer to send filter criteria to the ETL layer for job status retrieval tasks.
JobFilter(Long, Long, String, Date, Date, Boolean) - Constructor for class org.eurekaclinical.eureka.client.comm.JobFilter: Create an instance with the given parameters.
JobFilter(String) - Constructor for class org.eurekaclinical.eureka.client.comm.JobFilter: Creates a filter by parsing the given string for the needed values.
JobListRow - Class in org.eurekaclinical.eureka.client.comm: A communication bean to transfer information about a job status.
JobListRow() - Constructor for class org.eurekaclinical.eureka.client.comm.JobListRow
JobSpec - Class in org.eurekaclinical.eureka.client.comm: Hold information about a user's file upload.
JobSpec() - Constructor for class org.eurekaclinical.eureka.client.comm.JobSpec
JobSpec.Side - Enum in org.eurekaclinical.eureka.client.comm
JobStatus - Enum in org.eurekaclinical.eureka.client.comm: The different types of job events that are recorded.

L

LdapUser - Class in org.eurekaclinical.eureka.client.comm
LdapUser() - Constructor for class org.eurekaclinical.eureka.client.comm.LdapUser
LdapUserRequest - Class in org.eurekaclinical.eureka.client.comm
LdapUserRequest() - Constructor for class org.eurekaclinical.eureka.client.comm.LdapUserRequest
Link - Class in org.eurekaclinical.eureka.client.comm
Link() - Constructor for class org.eurekaclinical.eureka.client.comm.Link
Literal - Class in org.eurekaclinical.eureka.client.comm
Literal() - Constructor for class org.eurekaclinical.eureka.client.comm.Literal
LocalUser - Class in org.eurekaclinical.eureka.client.comm
LocalUser() - Constructor for class org.eurekaclinical.eureka.client.comm.LocalUser
LocalUserRequest - Class in org.eurekaclinical.eureka.client.comm
LocalUserRequest() - Constructor for class org.eurekaclinical.eureka.client.comm.LocalUserRequest
LoginType - Enum in org.eurekaclinical.eureka.client.comm.authentication
LoginType - Class in org.eurekaclinical.eureka.client.comm
LoginType() - Constructor for class org.eurekaclinical.eureka.client.comm.LoginType

M

messages() - Method in class org.eurekaclinical.eureka.client.comm.Job: Return a list of messages generated by the job.

N

Neo4jDestination - Class in org.eurekaclinical.eureka.client.comm
Neo4jDestination() - Constructor for class org.eurekaclinical.eureka.client.comm.Neo4jDestination
Node - Class in org.eurekaclinical.eureka.client.comm
Node() - Constructor for class org.eurekaclinical.eureka.client.comm.Node
NodeVisitor - Interface in org.eurekaclinical.eureka.client.comm

O

OAuthUser - Class in org.eurekaclinical.eureka.client.comm
OAuthUser() - Constructor for class org.eurekaclinical.eureka.client.comm.OAuthUser
OAuthUserRequest - Class in org.eurekaclinical.eureka.client.comm
OAuthUserRequest() - Constructor for class org.eurekaclinical.eureka.client.comm.OAuthUserRequest
org.eurekaclinical.eureka.client - package org.eurekaclinical.eureka.client
org.eurekaclinical.eureka.client.comm - package org.eurekaclinical.eureka.client.comm
org.eurekaclinical.eureka.client.comm.authentication - package org.eurekaclinical.eureka.client.comm.authentication
org.eurekaclinical.eureka.client.comm.exception - package org.eurekaclinical.eureka.client.comm.exception
org.eurekaclinical.eureka.client.comm.json - package org.eurekaclinical.eureka.client.comm.json

P

PasswordChangeRequest - Class in org.eurekaclinical.eureka.client.comm
PasswordChangeRequest() - Constructor for class org.eurekaclinical.eureka.client.comm.PasswordChangeRequest
PatientSet - Class in org.eurekaclinical.eureka.client.comm
PatientSet() - Constructor for class org.eurekaclinical.eureka.client.comm.PatientSet
PatientSetExtractorDestination - Class in org.eurekaclinical.eureka.client.comm
PatientSetExtractorDestination() - Constructor for class org.eurekaclinical.eureka.client.comm.PatientSetExtractorDestination
Phenotype - Class in org.eurekaclinical.eureka.client.comm: A user-created phenotype from the UI.
Phenotype(Phenotype.Type) - Constructor for class org.eurekaclinical.eureka.client.comm.Phenotype
Phenotype.Type - Enum in org.eurekaclinical.eureka.client.comm
PhenotypeField - Class in org.eurekaclinical.eureka.client.comm
PhenotypeField() - Constructor for class org.eurekaclinical.eureka.client.comm.PhenotypeField
PhenotypeField(Phenotype) - Constructor for class org.eurekaclinical.eureka.client.comm.PhenotypeField
PhenotypeHandlingException - Exception in org.eurekaclinical.eureka.client.comm.exception
PhenotypeHandlingException(Response.Status, String) - Constructor for exception org.eurekaclinical.eureka.client.comm.exception.PhenotypeHandlingException
PhenotypeHandlingException(Response.Status, String, Throwable) - Constructor for exception org.eurekaclinical.eureka.client.comm.exception.PhenotypeHandlingException
PhenotypeHandlingException(Response.Status, Throwable) - Constructor for exception org.eurekaclinical.eureka.client.comm.exception.PhenotypeHandlingException
PhenotypeVisitable - Interface in org.eurekaclinical.eureka.client.comm
PhenotypeVisitor - Interface in org.eurekaclinical.eureka.client.comm
PropositionWrapper - Class in org.eurekaclinical.eureka.client.comm: Represents messages containing phenotype definitions.
PropositionWrapper() - Constructor for class org.eurekaclinical.eureka.client.comm.PropositionWrapper: Creates the message object.
PropositionWrapper.Type - Enum in org.eurekaclinical.eureka.client.comm
proxyDelete(String) - Method in class org.eurekaclinical.eureka.client.EurekaClient
proxyGet(String, MultivaluedMap) - Method in class org.eurekaclinical.eureka.client.EurekaClient
proxyPost(String, String) - Method in class org.eurekaclinical.eureka.client.EurekaClient
proxyPut(String, String) - Method in class org.eurekaclinical.eureka.client.EurekaClient

R

RelatedPhenotypeField - Class in org.eurekaclinical.eureka.client.comm
RelatedPhenotypeField() - Constructor for class org.eurekaclinical.eureka.client.comm.RelatedPhenotypeField

S

saveUserPhenotype(Phenotype) - Method in class org.eurekaclinical.eureka.client.EurekaClient
Section() - Constructor for class org.eurekaclinical.eureka.client.comm.SourceConfig.Section
Sequence - Class in org.eurekaclinical.eureka.client.comm: Container class for the sequence user-created phenotype from the UI.
Sequence() - Constructor for class org.eurekaclinical.eureka.client.comm.Sequence
setAbbrevDisplayName(String) - Method in class org.eurekaclinical.eureka.client.comm.PropositionWrapper: Sets the phenotype definition's abbreviated display name.
setAcceptedMimetypes(String[]) - Method in class org.eurekaclinical.eureka.client.comm.FileSourceConfigOption
setAcceptedMimetypes(String[]) - Method in class org.eurekaclinical.eureka.client.comm.SourceConfigParams.Upload
setActive(boolean) - Method in class org.eurekaclinical.eureka.client.comm.User
setAlgorithmSourceBackends(SourceConfig.Section[]) - Method in class org.eurekaclinical.eureka.client.comm.SourceConfig
setAliasPropositionId(String) - Method in class org.eurekaclinical.eureka.client.comm.PatientSetExtractorDestination
setAtLeast(Integer) - Method in class org.eurekaclinical.eureka.client.comm.Frequency
setCategoricalType(Category.CategoricalType) - Method in class org.eurekaclinical.eureka.client.comm.Category
setCategoricalType(Category.CategoricalType) - Method in class org.eurekaclinical.eureka.client.comm.PhenotypeField
setChildren(List<PhenotypeField>) - Method in class org.eurekaclinical.eureka.client.comm.Category
setChildren(List<PropositionWrapper>) - Method in class org.eurekaclinical.eureka.client.comm.PropositionWrapper: Sets this phenotype definition's children.
setChildren(List<SystemPhenotype>) - Method in class org.eurekaclinical.eureka.client.comm.SystemPhenotype
setChildrenToParents(Map<String, String>) - Method in class org.eurekaclinical.eureka.client.comm.Statistics
setCohort(Cohort) - Method in class org.eurekaclinical.eureka.client.comm.CohortDestination
setCounts(Map<String, Integer>) - Method in class org.eurekaclinical.eureka.client.comm.Statistics
setCreated(Date) - Method in class org.eurekaclinical.eureka.client.comm.Phenotype
setCreated(Date) - Method in class org.eurekaclinical.eureka.client.comm.PropositionWrapper: Sets the creation date of this phenotype definition.
setCreated(Date) - Method in class org.eurekaclinical.eureka.client.comm.User
setCreatedAt(Date) - Method in class org.eurekaclinical.eureka.client.comm.Destination
setDataSourceBackends(SourceConfig.Section[]) - Method in class org.eurekaclinical.eureka.client.comm.SourceConfig
setDateRangePhenotypeKey(String) - Method in class org.eurekaclinical.eureka.client.comm.JobSpec
setDbPath(String) - Method in class org.eurekaclinical.eureka.client.comm.Neo4jDestination
setDepartment(String) - Method in class org.eurekaclinical.eureka.client.comm.User
setDepartment(String) - Method in class org.eurekaclinical.eureka.client.comm.UserRequest: Set the user's department.
setDescription(String) - Method in class org.eurekaclinical.eureka.client.comm.AuthenticationMethod
setDescription(String) - Method in class org.eurekaclinical.eureka.client.comm.Destination
setDescription(String) - Method in class org.eurekaclinical.eureka.client.comm.LoginType
setDescription(String) - Method in class org.eurekaclinical.eureka.client.comm.Phenotype
setDescription(String) - Method in class org.eurekaclinical.eureka.client.comm.SourceConfigOption
setDestinationId(String) - Method in class org.eurekaclinical.eureka.client.comm.Job
setDestinationId(String) - Method in class org.eurekaclinical.eureka.client.comm.JobListRow
setDestinationId(String) - Method in class org.eurekaclinical.eureka.client.comm.JobSpec
setDisplayName(String) - Method in class org.eurekaclinical.eureka.client.comm.Link
setDisplayName(String) - Method in class org.eurekaclinical.eureka.client.comm.Phenotype
setDisplayName(String) - Method in class org.eurekaclinical.eureka.client.comm.PropositionWrapper: Sets the phenotype definition's display name.
setDisplayName(String) - Method in class org.eurekaclinical.eureka.client.comm.SourceConfig.Section
setDisplayName(String) - Method in class org.eurekaclinical.eureka.client.comm.SourceConfig
setDisplayName(String) - Method in class org.eurekaclinical.eureka.client.comm.SourceConfigOption
setEarliestDate(Date) - Method in class org.eurekaclinical.eureka.client.comm.JobSpec
setEarliestDateSide(JobSpec.Side) - Method in class org.eurekaclinical.eureka.client.comm.JobSpec
setEmail(String) - Method in class org.eurekaclinical.eureka.client.comm.User
setEmail(String) - Method in class org.eurekaclinical.eureka.client.comm.UserRequest: Set the user's email address.
setExceptionStackTrace(String) - Method in class org.eurekaclinical.eureka.client.comm.JobEvent
setExecute(boolean) - Method in class org.eurekaclinical.eureka.client.comm.Destination
setExecute(boolean) - Method in class org.eurekaclinical.eureka.client.comm.SourceConfig
setFinish(Date) - Method in class org.eurekaclinical.eureka.client.comm.Literal
setFinishedDate(Date) - Method in class org.eurekaclinical.eureka.client.comm.JobListRow
setFinishTimestamp(Date) - Method in class org.eurekaclinical.eureka.client.comm.Job
setFirstName(String) - Method in class org.eurekaclinical.eureka.client.comm.User
setFirstName(String) - Method in class org.eurekaclinical.eureka.client.comm.UserRequest: Set the user's first name.
setFrequencyType(Long) - Method in class org.eurekaclinical.eureka.client.comm.Frequency
setFullName(String) - Method in class org.eurekaclinical.eureka.client.comm.User
setFullName(String) - Method in class org.eurekaclinical.eureka.client.comm.UserRequest
setGetStatisticsSupported(boolean) - Method in class org.eurekaclinical.eureka.client.comm.Destination
setGetStatisticsSupported(boolean) - Method in class org.eurekaclinical.eureka.client.comm.Job
setGetStatisticsSupported(boolean) - Method in class org.eurekaclinical.eureka.client.comm.JobListRow
setHasDuration(Boolean) - Method in class org.eurekaclinical.eureka.client.comm.PhenotypeField
setHasPropertyConstraint(Boolean) - Method in class org.eurekaclinical.eureka.client.comm.PhenotypeField
setId(Long) - Method in class org.eurekaclinical.eureka.client.comm.AuthenticationMethod
setId(Long) - Method in class org.eurekaclinical.eureka.client.comm.Cohort
setId(Long) - Method in class org.eurekaclinical.eureka.client.comm.Destination: Set the unique identifier for the configuration.
setId(Long) - Method in class org.eurekaclinical.eureka.client.comm.Job
setId(Long) - Method in class org.eurekaclinical.eureka.client.comm.JobEvent
setId(Long) - Method in class org.eurekaclinical.eureka.client.comm.LoginType
setId(Long) - Method in class org.eurekaclinical.eureka.client.comm.Node
setId(Long) - Method in class org.eurekaclinical.eureka.client.comm.Phenotype
setId(Long) - Method in class org.eurekaclinical.eureka.client.comm.PhenotypeField
setId(Long) - Method in class org.eurekaclinical.eureka.client.comm.PropositionWrapper: Sets a user phenotype definition's id.
setId(String) - Method in class org.eurekaclinical.eureka.client.comm.SourceConfig.Section
setId(String) - Method in class org.eurekaclinical.eureka.client.comm.SourceConfig
setId(String) - Method in class org.eurekaclinical.eureka.client.comm.SourceConfigParams
setId(Long) - Method in class org.eurekaclinical.eureka.client.comm.UserRequest: Set the user's unique identifier.
setInSystem(boolean) - Method in class org.eurekaclinical.eureka.client.comm.Phenotype
setInSystem(boolean) - Method in class org.eurekaclinical.eureka.client.comm.PropositionWrapper: Sets whether this phenotype definition is a aystem or user data element definition.
setInternalNode(boolean) - Method in class org.eurekaclinical.eureka.client.comm.Phenotype
setIsConsecutive(Boolean) - Method in class org.eurekaclinical.eureka.client.comm.Frequency
setIsWithin(Boolean) - Method in class org.eurekaclinical.eureka.client.comm.Frequency
setJobConceptListSupported(boolean) - Method in class org.eurekaclinical.eureka.client.comm.Destination
setJobEvents(List<JobEvent>) - Method in class org.eurekaclinical.eureka.client.comm.Job: Sets job events, assumed in order of occurrence.
setJobId(Long) - Method in class org.eurekaclinical.eureka.client.comm.JobListRow
setKey(String) - Method in class org.eurekaclinical.eureka.client.comm.Phenotype
setKey(String) - Method in class org.eurekaclinical.eureka.client.comm.PropositionWrapper: Sets a system phenotype definition's id string.
setKnowledgeSourceBackends(SourceConfig.Section[]) - Method in class org.eurekaclinical.eureka.client.comm.SourceConfig
setLastLogin(Date) - Method in class org.eurekaclinical.eureka.client.comm.User
setLastModified(Date) - Method in class org.eurekaclinical.eureka.client.comm.Phenotype
setLastModified(Date) - Method in class org.eurekaclinical.eureka.client.comm.PropositionWrapper: Sets the last modified date of this phenotype definition.
setLastName(String) - Method in class org.eurekaclinical.eureka.client.comm.User
setLastName(String) - Method in class org.eurekaclinical.eureka.client.comm.UserRequest: Set the user's last name.
setLatestDate(Date) - Method in class org.eurekaclinical.eureka.client.comm.JobSpec
setLatestDateSide(JobSpec.Side) - Method in class org.eurekaclinical.eureka.client.comm.JobSpec
setLeftNode(Node) - Method in class org.eurekaclinical.eureka.client.comm.BinaryOperator
setLinks(List<Link>) - Method in class org.eurekaclinical.eureka.client.comm.Destination
setLinks(List<Link>) - Method in class org.eurekaclinical.eureka.client.comm.Job
setLinks(List<Link>) - Method in class org.eurekaclinical.eureka.client.comm.JobListRow
setLoginType(LoginType) - Method in class org.eurekaclinical.eureka.client.comm.User
setLoginType(LoginType) - Method in class org.eurekaclinical.eureka.client.comm.UserRequest
setLowerComp(Long) - Method in class org.eurekaclinical.eureka.client.comm.ValueThreshold
setLowerUnits(String) - Method in class org.eurekaclinical.eureka.client.comm.ValueThreshold
setLowerValue(String) - Method in class org.eurekaclinical.eureka.client.comm.ValueThreshold
setMaxDuration(Integer) - Method in class org.eurekaclinical.eureka.client.comm.PhenotypeField
setMaxDurationUnits(Long) - Method in class org.eurekaclinical.eureka.client.comm.PhenotypeField
setMessage(String) - Method in class org.eurekaclinical.eureka.client.comm.JobEvent
setMessages(List<String>) - Method in class org.eurekaclinical.eureka.client.comm.JobListRow
setMinDuration(Integer) - Method in class org.eurekaclinical.eureka.client.comm.PhenotypeField
setMinDurationUnits(Long) - Method in class org.eurekaclinical.eureka.client.comm.PhenotypeField
setName(AuthenticationMethod) - Method in class org.eurekaclinical.eureka.client.comm.AuthenticationMethod
setName(String) - Method in class org.eurekaclinical.eureka.client.comm.Destination
setName(String) - Method in class org.eurekaclinical.eureka.client.comm.JobSpec
setName(String) - Method in class org.eurekaclinical.eureka.client.comm.Literal
setName(LoginType) - Method in class org.eurekaclinical.eureka.client.comm.LoginType
setName(String) - Method in class org.eurekaclinical.eureka.client.comm.PatientSet
setName(String) - Method in class org.eurekaclinical.eureka.client.comm.SourceConfigOption
setName(String) - Method in class org.eurekaclinical.eureka.client.comm.SourceConfigParams
setName(String) - Method in class org.eurekaclinical.eureka.client.comm.SourceConfigParams.Upload
setName(String) - Method in class org.eurekaclinical.eureka.client.comm.ValueThresholds
setNewPassword(String) - Method in class org.eurekaclinical.eureka.client.comm.PasswordChangeRequest
setNode(Node) - Method in class org.eurekaclinical.eureka.client.comm.Cohort
setNode(Node) - Method in class org.eurekaclinical.eureka.client.comm.UnaryOperator
setNumberOfKeys(Integer) - Method in class org.eurekaclinical.eureka.client.comm.Statistics
setOAuthProvider(Long) - Method in class org.eurekaclinical.eureka.client.comm.OAuthUser
setOAuthProvider(String) - Method in class org.eurekaclinical.eureka.client.comm.OAuthUserRequest
setOldPassword(String) - Method in class org.eurekaclinical.eureka.client.comm.PasswordChangeRequest
setOp(BinaryOperator.Op) - Method in class org.eurekaclinical.eureka.client.comm.BinaryOperator
setOp(UnaryOperator.Op) - Method in class org.eurekaclinical.eureka.client.comm.UnaryOperator
setOptions(SourceConfigOption[]) - Method in class org.eurekaclinical.eureka.client.comm.SourceConfig.Section
setOrganization(String) - Method in class org.eurekaclinical.eureka.client.comm.User
setOrganization(String) - Method in class org.eurekaclinical.eureka.client.comm.UserRequest: Set the user's organization.
setOwnerUserId(Long) - Method in class org.eurekaclinical.eureka.client.comm.Destination: Set the unique identifier for the owner of the configuration.
setOwnerUsername(String) - Method in class org.eurekaclinical.eureka.client.comm.SourceConfig
setParent(boolean) - Method in class org.eurekaclinical.eureka.client.comm.PropositionWrapper: Sets whether this phenotype definition has children.
setParent(boolean) - Method in class org.eurekaclinical.eureka.client.comm.SystemPhenotype
setPassword(String) - Method in class org.eurekaclinical.eureka.client.comm.LocalUser
setPassword(String) - Method in class org.eurekaclinical.eureka.client.comm.LocalUserRequest: Set the user's password.
setPasswordExpiration(Date) - Method in class org.eurekaclinical.eureka.client.comm.LocalUser
setPatients(Set<String>) - Method in class org.eurekaclinical.eureka.client.comm.PatientSet
setPhenotype(PhenotypeField) - Method in class org.eurekaclinical.eureka.client.comm.Frequency
setPhenotype(PhenotypeField) - Method in class org.eurekaclinical.eureka.client.comm.ValueThreshold
setPhenotypeDescription(String) - Method in class org.eurekaclinical.eureka.client.comm.PhenotypeField
setPhenotypeDisplayName(String) - Method in class org.eurekaclinical.eureka.client.comm.PhenotypeField
setPhenotypeField(PhenotypeField) - Method in class org.eurekaclinical.eureka.client.comm.RelatedPhenotypeField
setPhenotypeFields(PhenotypeField[]) - Method in class org.eurekaclinical.eureka.client.comm.Destination
setPhenotypeKey(String) - Method in class org.eurekaclinical.eureka.client.comm.PhenotypeField
setPrimaryPhenotype(PhenotypeField) - Method in class org.eurekaclinical.eureka.client.comm.Sequence
setPrompt(boolean) - Method in class org.eurekaclinical.eureka.client.comm.SourceConfigOption
setPrompts(SourceConfig) - Method in class org.eurekaclinical.eureka.client.comm.JobSpec
setProperties(List<String>) - Method in class org.eurekaclinical.eureka.client.comm.PropositionWrapper: Sets this phenotype definition's properties.
setProperties(List<String>) - Method in class org.eurekaclinical.eureka.client.comm.SystemPhenotype
setProperty(String) - Method in class org.eurekaclinical.eureka.client.comm.PhenotypeField
setPropertyType(SourceConfigOption.BackendPropertyType) - Method in class org.eurekaclinical.eureka.client.comm.SourceConfigOption
setPropertyValue(String) - Method in class org.eurekaclinical.eureka.client.comm.PhenotypeField
setPropositionIds(List<String>) - Method in class org.eurekaclinical.eureka.client.comm.JobSpec
setProviderUsername(String) - Method in class org.eurekaclinical.eureka.client.comm.OAuthUser
setProviderUsername(String) - Method in class org.eurekaclinical.eureka.client.comm.OAuthUserRequest
setRead(boolean) - Method in class org.eurekaclinical.eureka.client.comm.Destination
setRead(boolean) - Method in class org.eurekaclinical.eureka.client.comm.SourceConfig
setRelatedPhenotypes(List<RelatedPhenotypeField>) - Method in class org.eurekaclinical.eureka.client.comm.Sequence
setRelatedPhenotypes(List<PhenotypeField>) - Method in class org.eurekaclinical.eureka.client.comm.ValueThreshold
setRelationMaxCount(Integer) - Method in class org.eurekaclinical.eureka.client.comm.RelatedPhenotypeField
setRelationMaxUnits(Long) - Method in class org.eurekaclinical.eureka.client.comm.RelatedPhenotypeField
setRelationMinCount(Integer) - Method in class org.eurekaclinical.eureka.client.comm.RelatedPhenotypeField
setRelationMinUnits(Long) - Method in class org.eurekaclinical.eureka.client.comm.RelatedPhenotypeField
setRelationOperator(Long) - Method in class org.eurekaclinical.eureka.client.comm.RelatedPhenotypeField
setRelationOperator(Long) - Method in class org.eurekaclinical.eureka.client.comm.ValueThreshold
setRequired(boolean) - Method in class org.eurekaclinical.eureka.client.comm.SourceConfigOption
setRequired(boolean) - Method in class org.eurekaclinical.eureka.client.comm.SourceConfigParams.Upload
setRequiredConcepts(List<String>) - Method in class org.eurekaclinical.eureka.client.comm.Destination
setRightNode(Node) - Method in class org.eurekaclinical.eureka.client.comm.BinaryOperator
setSampleUrl(String) - Method in class org.eurekaclinical.eureka.client.comm.SourceConfigParams.Upload
setSequentialPhenotype(String) - Method in class org.eurekaclinical.eureka.client.comm.RelatedPhenotypeField
setSequentialPhenotypeSource(Long) - Method in class org.eurekaclinical.eureka.client.comm.RelatedPhenotypeField
setSourceConfigId(String) - Method in class org.eurekaclinical.eureka.client.comm.Job
setSourceConfigId(String) - Method in class org.eurekaclinical.eureka.client.comm.JobListRow
setSourceConfigId(String) - Method in class org.eurekaclinical.eureka.client.comm.JobSpec
setSourceId(String) - Method in class org.eurekaclinical.eureka.client.comm.SourceConfigParams.Upload
setStart(Date) - Method in class org.eurekaclinical.eureka.client.comm.Literal
setStartedDate(Date) - Method in class org.eurekaclinical.eureka.client.comm.JobListRow
setStartTimestamp(Date) - Method in class org.eurekaclinical.eureka.client.comm.Job
setStatus(JobStatus) - Method in class org.eurekaclinical.eureka.client.comm.Job
setStatus(JobStatus) - Method in class org.eurekaclinical.eureka.client.comm.JobEvent
setStatus(JobStatus) - Method in class org.eurekaclinical.eureka.client.comm.JobListRow
setSummarized(boolean) - Method in class org.eurekaclinical.eureka.client.comm.Phenotype
setSummarized(boolean) - Method in class org.eurekaclinical.eureka.client.comm.PropositionWrapper: Sets whether or not the children of this proposition are included in the message.
setSystemType(SystemType) - Method in class org.eurekaclinical.eureka.client.comm.SystemPhenotype
setTermSourceBackends(SourceConfig.Section[]) - Method in class org.eurekaclinical.eureka.client.comm.SourceConfig
setThresholdsOperator(Long) - Method in class org.eurekaclinical.eureka.client.comm.ValueThresholds
setTimeStamp(Date) - Method in class org.eurekaclinical.eureka.client.comm.JobEvent
setTitle(String) - Method in class org.eurekaclinical.eureka.client.comm.User
setTitle(String) - Method in class org.eurekaclinical.eureka.client.comm.UserRequest: Set the user's title
setType(Phenotype.Type) - Method in class org.eurekaclinical.eureka.client.comm.PhenotypeField
setType(PropositionWrapper.Type) - Method in class org.eurekaclinical.eureka.client.comm.PropositionWrapper: Sets the type of a user phenotype definition.
setUpdatedAt(Date) - Method in class org.eurekaclinical.eureka.client.comm.Destination
setUpdateData(boolean) - Method in class org.eurekaclinical.eureka.client.comm.JobSpec
setUploads(SourceConfigParams.Upload[]) - Method in class org.eurekaclinical.eureka.client.comm.SourceConfigParams
setUpperComp(Long) - Method in class org.eurekaclinical.eureka.client.comm.ValueThreshold
setUpperUnits(String) - Method in class org.eurekaclinical.eureka.client.comm.ValueThreshold
setUpperValue(String) - Method in class org.eurekaclinical.eureka.client.comm.ValueThreshold
setUrl(String) - Method in class org.eurekaclinical.eureka.client.comm.Link
setUserId(Long) - Method in class org.eurekaclinical.eureka.client.comm.Phenotype
setUserId(Long) - Method in class org.eurekaclinical.eureka.client.comm.PropositionWrapper: Sets a user phenotype definition's user id.
setUsername(String) - Method in class org.eurekaclinical.eureka.client.comm.Job
setUsername(String) - Method in class org.eurekaclinical.eureka.client.comm.PatientSet
setUsername(String) - Method in class org.eurekaclinical.eureka.client.comm.UserRequest: Sets the user's unique username.
setValue(Object) - Method in class org.eurekaclinical.eureka.client.comm.SourceConfigOption
setValueThresholds(List<ValueThreshold>) - Method in class org.eurekaclinical.eureka.client.comm.ValueThresholds
setVerificationCode(String) - Method in class org.eurekaclinical.eureka.client.comm.LocalUser
setVerified(boolean) - Method in class org.eurekaclinical.eureka.client.comm.LocalUser
setVerifyEmail(String) - Method in class org.eurekaclinical.eureka.client.comm.UserRequest: Set the user's email address verification.
setVerifyPassword(String) - Method in class org.eurekaclinical.eureka.client.comm.LocalUserRequest: Set the password verification.
setWithinAtLeast(Integer) - Method in class org.eurekaclinical.eureka.client.comm.Frequency
setWithinAtLeast(Integer) - Method in class org.eurekaclinical.eureka.client.comm.ValueThreshold
setWithinAtLeastUnit(Long) - Method in class org.eurekaclinical.eureka.client.comm.ValueThreshold
setWithinAtLeastUnits(Long) - Method in class org.eurekaclinical.eureka.client.comm.Frequency
setWithinAtMost(Integer) - Method in class org.eurekaclinical.eureka.client.comm.Frequency
setWithinAtMost(Integer) - Method in class org.eurekaclinical.eureka.client.comm.ValueThreshold
setWithinAtMostUnit(Long) - Method in class org.eurekaclinical.eureka.client.comm.ValueThreshold
setWithinAtMostUnits(Long) - Method in class org.eurekaclinical.eureka.client.comm.Frequency
setWrite(boolean) - Method in class org.eurekaclinical.eureka.client.comm.Destination
setWrite(boolean) - Method in class org.eurekaclinical.eureka.client.comm.SourceConfig
SourceConfig - Class in org.eurekaclinical.eureka.client.comm
SourceConfig() - Constructor for class org.eurekaclinical.eureka.client.comm.SourceConfig
SourceConfig.Section - Class in org.eurekaclinical.eureka.client.comm
SourceConfigOption - Class in org.eurekaclinical.eureka.client.comm
SourceConfigOption() - Constructor for class org.eurekaclinical.eureka.client.comm.SourceConfigOption
SourceConfigOption.BackendPropertyType - Enum in org.eurekaclinical.eureka.client.comm
SourceConfigOptionValueDeserializer - Class in org.eurekaclinical.eureka.client.comm.json: Acts like the default deserializer for untyped objects, except if the default deserializer returns an Integer, convert into a Long.
SourceConfigOptionValueDeserializer() - Constructor for class org.eurekaclinical.eureka.client.comm.json.SourceConfigOptionValueDeserializer
SourceConfigParams - Class in org.eurekaclinical.eureka.client.comm
SourceConfigParams() - Constructor for class org.eurekaclinical.eureka.client.comm.SourceConfigParams
SourceConfigParams.Upload - Class in org.eurekaclinical.eureka.client.comm
Statistics - Class in org.eurekaclinical.eureka.client.comm
Statistics() - Constructor for class org.eurekaclinical.eureka.client.comm.Statistics
submitJob(JobSpec) - Method in class org.eurekaclinical.eureka.client.EurekaClient
SystemPhenotype - Class in org.eurekaclinical.eureka.client.comm
SystemPhenotype() - Constructor for class org.eurekaclinical.eureka.client.comm.SystemPhenotype
SystemType - Enum in org.eurekaclinical.eureka.client.comm

T

toJobListRow() - Method in class org.eurekaclinical.eureka.client.comm.Job
toQueryParam() - Method in class org.eurekaclinical.eureka.client.comm.JobFilter: Convert the filter object into a string appropriate to be passed as a request parameter.
toString() - Method in class org.eurekaclinical.eureka.client.comm.AuthenticationMethod
toString() - Method in class org.eurekaclinical.eureka.client.comm.BinaryOperator
toString() - Method in class org.eurekaclinical.eureka.client.comm.Category
toString() - Method in class org.eurekaclinical.eureka.client.comm.Cohort
toString() - Method in class org.eurekaclinical.eureka.client.comm.Destination
toString() - Method in class org.eurekaclinical.eureka.client.comm.Frequency
toString() - Method in class org.eurekaclinical.eureka.client.comm.Job
toString() - Method in class org.eurekaclinical.eureka.client.comm.Literal
toString() - Method in class org.eurekaclinical.eureka.client.comm.LoginType
toString() - Method in class org.eurekaclinical.eureka.client.comm.Node
toString() - Method in class org.eurekaclinical.eureka.client.comm.PatientSet
toString() - Method in class org.eurekaclinical.eureka.client.comm.Phenotype
toString() - Method in class org.eurekaclinical.eureka.client.comm.PhenotypeField
toString() - Method in class org.eurekaclinical.eureka.client.comm.PropositionWrapper: Represents field values for debugging purposes.
toString() - Method in class org.eurekaclinical.eureka.client.comm.RelatedPhenotypeField
toString() - Method in class org.eurekaclinical.eureka.client.comm.Sequence
toString() - Method in class org.eurekaclinical.eureka.client.comm.SourceConfig
toString() - Method in class org.eurekaclinical.eureka.client.comm.SystemPhenotype
toString() - Method in class org.eurekaclinical.eureka.client.comm.UnaryOperator
toString() - Method in class org.eurekaclinical.eureka.client.comm.UserRequest
toString() - Method in class org.eurekaclinical.eureka.client.comm.ValueThreshold
toString() - Method in class org.eurekaclinical.eureka.client.comm.ValueThresholds

U

UnaryOperator - Class in org.eurekaclinical.eureka.client.comm
UnaryOperator() - Constructor for class org.eurekaclinical.eureka.client.comm.UnaryOperator
UnaryOperator.Op - Enum in org.eurekaclinical.eureka.client.comm
updateDestination(Destination) - Method in class org.eurekaclinical.eureka.client.EurekaClient
updateUser(User, Long) - Method in class org.eurekaclinical.eureka.client.EurekaClient
updateUserPhenotype(Long, Phenotype) - Method in class org.eurekaclinical.eureka.client.EurekaClient
Upload() - Constructor for class org.eurekaclinical.eureka.client.comm.SourceConfigParams.Upload
upload(String, String, String, InputStream) - Method in class org.eurekaclinical.eureka.client.EurekaClient
UriSourceConfigOption - Class in org.eurekaclinical.eureka.client.comm
UriSourceConfigOption() - Constructor for class org.eurekaclinical.eureka.client.comm.UriSourceConfigOption
User - Class in org.eurekaclinical.eureka.client.comm
User() - Constructor for class org.eurekaclinical.eureka.client.comm.User
UserRequest - Class in org.eurekaclinical.eureka.client.comm: A bean holding information about a user's registration request.
UserRequest() - Constructor for class org.eurekaclinical.eureka.client.comm.UserRequest: Default constructor, calls super()
userRequestToAuthenticationMethod(UserRequest) - Static method in enum org.eurekaclinical.eureka.client.comm.authentication.AuthenticationMethod
UserRequestVisitable - Interface in org.eurekaclinical.eureka.client.comm
UserRequestVisitor - Interface in org.eurekaclinical.eureka.client.comm
userToAuthenticationMethod(User) - Static method in enum org.eurekaclinical.eureka.client.comm.authentication.AuthenticationMethod
UserVisitable - Interface in org.eurekaclinical.eureka.client.comm
UserVisitor - Interface in org.eurekaclinical.eureka.client.comm

V

validate() - Method in class org.eurekaclinical.eureka.client.comm.LocalUser
validate() - Method in class org.eurekaclinical.eureka.client.comm.LocalUserRequest
validate() - Method in class org.eurekaclinical.eureka.client.comm.OAuthUser
validate() - Method in class org.eurekaclinical.eureka.client.comm.OAuthUserRequest
validate() - Method in class org.eurekaclinical.eureka.client.comm.User: Validate a User object.
validate() - Method in class org.eurekaclinical.eureka.client.comm.UserRequest: Validate a UserRequest object.
valueOf(String) - Static method in enum org.eurekaclinical.eureka.client.comm.authentication.AuthenticationMethod: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.eurekaclinical.eureka.client.comm.authentication.LoginType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.eurekaclinical.eureka.client.comm.BinaryOperator.Op: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.eurekaclinical.eureka.client.comm.Category.CategoricalType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.eurekaclinical.eureka.client.comm.DestinationType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.eurekaclinical.eureka.client.comm.JobSpec.Side: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.eurekaclinical.eureka.client.comm.JobStatus: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.eurekaclinical.eureka.client.comm.Phenotype.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.eurekaclinical.eureka.client.comm.PropositionWrapper.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.eurekaclinical.eureka.client.comm.SourceConfigOption.BackendPropertyType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.eurekaclinical.eureka.client.comm.SystemType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.eurekaclinical.eureka.client.comm.UnaryOperator.Op: Returns the enum constant of this type with the specified name.
values() - Static method in enum org.eurekaclinical.eureka.client.comm.authentication.AuthenticationMethod: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.eurekaclinical.eureka.client.comm.authentication.LoginType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.eurekaclinical.eureka.client.comm.BinaryOperator.Op: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.eurekaclinical.eureka.client.comm.Category.CategoricalType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.eurekaclinical.eureka.client.comm.DestinationType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.eurekaclinical.eureka.client.comm.JobSpec.Side: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.eurekaclinical.eureka.client.comm.JobStatus: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.eurekaclinical.eureka.client.comm.Phenotype.Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.eurekaclinical.eureka.client.comm.PropositionWrapper.Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.eurekaclinical.eureka.client.comm.SourceConfigOption.BackendPropertyType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.eurekaclinical.eureka.client.comm.SystemType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.eurekaclinical.eureka.client.comm.UnaryOperator.Op: Returns an array containing the constants of this enum type, in the order they are declared.
ValueThreshold - Class in org.eurekaclinical.eureka.client.comm
ValueThreshold() - Constructor for class org.eurekaclinical.eureka.client.comm.ValueThreshold
ValueThresholds - Class in org.eurekaclinical.eureka.client.comm
ValueThresholds() - Constructor for class org.eurekaclinical.eureka.client.comm.ValueThresholds
visit(CohortDestination) - Method in interface org.eurekaclinical.eureka.client.comm.DestinationVisitor
visit(I2B2Destination) - Method in interface org.eurekaclinical.eureka.client.comm.DestinationVisitor
visit(Neo4jDestination) - Method in interface org.eurekaclinical.eureka.client.comm.DestinationVisitor
visit(PatientSetExtractorDestination) - Method in interface org.eurekaclinical.eureka.client.comm.DestinationVisitor
visit(Literal) - Method in interface org.eurekaclinical.eureka.client.comm.NodeVisitor
visit(UnaryOperator) - Method in interface org.eurekaclinical.eureka.client.comm.NodeVisitor
visit(BinaryOperator) - Method in interface org.eurekaclinical.eureka.client.comm.NodeVisitor
visit(SystemPhenotype) - Method in interface org.eurekaclinical.eureka.client.comm.PhenotypeVisitor
visit(Category) - Method in interface org.eurekaclinical.eureka.client.comm.PhenotypeVisitor
visit(Sequence) - Method in interface org.eurekaclinical.eureka.client.comm.PhenotypeVisitor
visit(Frequency) - Method in interface org.eurekaclinical.eureka.client.comm.PhenotypeVisitor
visit(ValueThresholds) - Method in interface org.eurekaclinical.eureka.client.comm.PhenotypeVisitor
visit(LocalUserRequest) - Method in interface org.eurekaclinical.eureka.client.comm.UserRequestVisitor: Processes a local user request entity.
visit(LdapUserRequest) - Method in interface org.eurekaclinical.eureka.client.comm.UserRequestVisitor: Processes an LDAP user request entity.
visit(OAuthUserRequest) - Method in interface org.eurekaclinical.eureka.client.comm.UserRequestVisitor: Processes an OAuth user request entity.
visit(LocalUser) - Method in interface org.eurekaclinical.eureka.client.comm.UserVisitor: Processes a local user entity.
visit(LdapUser) - Method in interface org.eurekaclinical.eureka.client.comm.UserVisitor: Processes an LDAP user entity.
visit(OAuthUser) - Method in interface org.eurekaclinical.eureka.client.comm.UserVisitor: Processes an OAuth user entity.

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