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

AbstractTabularDestination - Class in org.eurekaclinical.eureka.client.comm

AbstractTabularDestination() - Constructor for class org.eurekaclinical.eureka.client.comm.AbstractTabularDestination

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(NodeVisitor) - Method in class org.eurekaclinical.eureka.client.comm.Literal

accept(DestinationVisitor) - Method in class org.eurekaclinical.eureka.client.comm.Neo4jDestination

accept(NodeVisitor) - Method in class org.eurekaclinical.eureka.client.comm.Node

accept(DestinationVisitor) - Method in class org.eurekaclinical.eureka.client.comm.PatientSetExtractorDestination

accept(DestinationVisitor) - Method in class org.eurekaclinical.eureka.client.comm.PatientSetSenderDestination

accept(PhenotypeVisitor) - Method in interface org.eurekaclinical.eureka.client.comm.PhenotypeVisitable

accept(DestinationVisitor) - Method in class org.eurekaclinical.eureka.client.comm.RelDbDestination

accept(PhenotypeVisitor) - Method in class org.eurekaclinical.eureka.client.comm.Sequence

accept(PhenotypeVisitor) - Method in class org.eurekaclinical.eureka.client.comm.SystemPhenotype

accept(DestinationVisitor) - Method in class org.eurekaclinical.eureka.client.comm.TabularFileDestination

accept(NodeVisitor) - Method in class org.eurekaclinical.eureka.client.comm.UnaryOperator

accept(PhenotypeVisitor) - Method in class org.eurekaclinical.eureka.client.comm.ValueThresholds

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

createDestination(Destination) - Method in class org.eurekaclinical.eureka.client.EurekaProxyClient

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

deleteDestination(Long, String) - Method in class org.eurekaclinical.eureka.client.EurekaProxyClient

deleteUserPhenotype(Long, Long) - Method in class org.eurekaclinical.eureka.client.EurekaClient

deleteUserPhenotype(Long, Long) - Method in class org.eurekaclinical.eureka.client.EurekaProxyClient

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

EurekaProxyClient - Class in org.eurekaclinical.eureka.client

EurekaProxyClient(String) - Constructor for class org.eurekaclinical.eureka.client.EurekaProxyClient

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

getAliasFieldName() - Method in class org.eurekaclinical.eureka.client.comm.PatientSetExtractorDestination

getAliasFieldName() - Method in class org.eurekaclinical.eureka.client.comm.PatientSetSenderDestination

getAliasFieldNameProperty() - Method in class org.eurekaclinical.eureka.client.comm.PatientSetExtractorDestination

getAliasFieldNameProperty() - Method in class org.eurekaclinical.eureka.client.comm.PatientSetSenderDestination

getAliasPatientIdProperty() - Method in class org.eurekaclinical.eureka.client.comm.PatientSetExtractorDestination

getAliasPatientIdProperty() - Method in class org.eurekaclinical.eureka.client.comm.PatientSetSenderDestination

getAliasPropositionId() - Method in class org.eurekaclinical.eureka.client.comm.PatientSetExtractorDestination

getAliasPropositionId() - Method in class org.eurekaclinical.eureka.client.comm.PatientSetSenderDestination

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

getCohortDestinations() - Method in class org.eurekaclinical.eureka.client.EurekaProxyClient

getColumnName() - Method in class org.eurekaclinical.eureka.client.comm.TableColumn

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.

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

getDescription() - Method in class org.eurekaclinical.eureka.client.comm.Destination

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

getDestination(String) - Method in class org.eurekaclinical.eureka.client.EurekaProxyClient

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

getDestinations() - Method in class org.eurekaclinical.eureka.client.EurekaProxyClient

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

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

getFormat() - Method in class org.eurekaclinical.eureka.client.comm.TableColumn

getFrequencyType() - Method in class org.eurekaclinical.eureka.client.comm.Frequency

getFrom() - Method in class org.eurekaclinical.eureka.client.comm.JobFilter

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

getI2B2Destinations() - Method in class org.eurekaclinical.eureka.client.EurekaProxyClient

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.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

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

getJob(Long) - Method in class org.eurekaclinical.eureka.client.EurekaProxyClient

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

getJobs() - Method in class org.eurekaclinical.eureka.client.EurekaProxyClient

getJobsDesc() - Method in class org.eurekaclinical.eureka.client.EurekaClient

getJobsDesc() - Method in class org.eurekaclinical.eureka.client.EurekaProxyClient

getJobStats(Long, String) - Method in class org.eurekaclinical.eureka.client.EurekaClient

getJobStats(Long, String) - Method in class org.eurekaclinical.eureka.client.EurekaProxyClient

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

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.

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

getLatestJob() - Method in class org.eurekaclinical.eureka.client.EurekaProxyClient

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

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

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.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.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

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

getOutput(String) - Method in class org.eurekaclinical.eureka.client.EurekaClient

getOutput(String) - Method in class org.eurekaclinical.eureka.client.EurekaProxyClient

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

getPath() - Method in class org.eurekaclinical.eureka.client.comm.TableColumn

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

getPatientSetService() - Method in class org.eurekaclinical.eureka.client.comm.PatientSetSenderDestination

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

getPhenotypes(String[], boolean) - Method in class org.eurekaclinical.eureka.client.EurekaProxyClient

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

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

getResourceUrl() - Method in class org.eurekaclinical.eureka.client.EurekaProxyClient

getRightNode() - Method in class org.eurekaclinical.eureka.client.comm.BinaryOperator

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

getSourceConfig(String) - Method in class org.eurekaclinical.eureka.client.EurekaProxyClient

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

getSourceConfigParams() - Method in class org.eurekaclinical.eureka.client.EurekaProxyClient

getSourceConfigs() - Method in class org.eurekaclinical.eureka.client.EurekaClient

getSourceConfigs() - Method in class org.eurekaclinical.eureka.client.EurekaProxyClient

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

getSystemPhenotype(String, boolean) - Method in class org.eurekaclinical.eureka.client.EurekaProxyClient

getSystemPhenotypes() - Method in class org.eurekaclinical.eureka.client.EurekaClient

getSystemPhenotypes(List<String>, boolean) - Method in class org.eurekaclinical.eureka.client.EurekaClient

getSystemPhenotypes() - Method in class org.eurekaclinical.eureka.client.EurekaProxyClient

getSystemPhenotypes(List<String>, boolean) - Method in class org.eurekaclinical.eureka.client.EurekaProxyClient

getSystemPhenotypeSearchResults(String) - Method in class org.eurekaclinical.eureka.client.EurekaClient

getSystemPhenotypeSearchResults(String) - Method in class org.eurekaclinical.eureka.client.EurekaProxyClient

getSystemPhenotypeSearchResultsBySearchKey(String) - Method in class org.eurekaclinical.eureka.client.EurekaClient

getSystemPhenotypeSearchResultsBySearchKey(String) - Method in class org.eurekaclinical.eureka.client.EurekaProxyClient

getSystemType() - Method in class org.eurekaclinical.eureka.client.comm.SystemPhenotype

getTableColumns() - Method in class org.eurekaclinical.eureka.client.comm.AbstractTabularDestination

getTableName() - Method in class org.eurekaclinical.eureka.client.comm.TableColumn

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

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

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

getUserPhenotype(String, boolean) - Method in class org.eurekaclinical.eureka.client.EurekaClient

getUserPhenotype(String, boolean) - Method in class org.eurekaclinical.eureka.client.EurekaProxyClient

getUserPhenotypes(boolean) - Method in class org.eurekaclinical.eureka.client.EurekaClient

getUserPhenotypes(boolean) - Method in class org.eurekaclinical.eureka.client.EurekaProxyClient

getValue() - Method in class org.eurekaclinical.eureka.client.comm.SourceConfigOption

getValueThresholds() - Method in class org.eurekaclinical.eureka.client.comm.ValueThresholds

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

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

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

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

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

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.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

PatientSetSenderDestination - Class in org.eurekaclinical.eureka.client.comm

PatientSetSenderDestination() - Constructor for class org.eurekaclinical.eureka.client.comm.PatientSetSenderDestination

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

R

RelatedPhenotypeField - Class in org.eurekaclinical.eureka.client.comm

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

RelDbDestination - Class in org.eurekaclinical.eureka.client.comm

RelDbDestination() - Constructor for class org.eurekaclinical.eureka.client.comm.RelDbDestination

S

saveUserPhenotype(Phenotype) - Method in class org.eurekaclinical.eureka.client.EurekaClient

saveUserPhenotype(Phenotype) - Method in class org.eurekaclinical.eureka.client.EurekaProxyClient

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

setAlgorithmSourceBackends(SourceConfig.Section[]) - Method in class org.eurekaclinical.eureka.client.comm.SourceConfig

setAliasFieldName(String) - Method in class org.eurekaclinical.eureka.client.comm.PatientSetExtractorDestination

setAliasFieldName(String) - Method in class org.eurekaclinical.eureka.client.comm.PatientSetSenderDestination

setAliasFieldNameProperty(String) - Method in class org.eurekaclinical.eureka.client.comm.PatientSetExtractorDestination

setAliasFieldNameProperty(String) - Method in class org.eurekaclinical.eureka.client.comm.PatientSetSenderDestination

setAliasPatientIdProperty(String) - Method in class org.eurekaclinical.eureka.client.comm.PatientSetExtractorDestination

setAliasPatientIdProperty(String) - Method in class org.eurekaclinical.eureka.client.comm.PatientSetSenderDestination

setAliasPropositionId(String) - Method in class org.eurekaclinical.eureka.client.comm.PatientSetExtractorDestination

setAliasPropositionId(String) - Method in class org.eurekaclinical.eureka.client.comm.PatientSetSenderDestination

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

setColumnName(String) - Method in class org.eurekaclinical.eureka.client.comm.TableColumn

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.

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

setDescription(String) - Method in class org.eurekaclinical.eureka.client.comm.Destination

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

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

setFormat(String) - Method in class org.eurekaclinical.eureka.client.comm.TableColumn

setFrequencyType(Long) - Method in class org.eurekaclinical.eureka.client.comm.Frequency

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.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.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

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

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.

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

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(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(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

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

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

setPath(String) - Method in class org.eurekaclinical.eureka.client.comm.TableColumn

setPatients(Set<String>) - Method in class org.eurekaclinical.eureka.client.comm.PatientSet

setPatientSetService(String) - Method in class org.eurekaclinical.eureka.client.comm.PatientSetSenderDestination

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

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

setTableColumns(List<TableColumn>) - Method in class org.eurekaclinical.eureka.client.comm.AbstractTabularDestination

setTableName(String) - Method in class org.eurekaclinical.eureka.client.comm.TableColumn

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

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

setValue(Object) - Method in class org.eurekaclinical.eureka.client.comm.SourceConfigOption

setValueThresholds(List<ValueThreshold>) - Method in class org.eurekaclinical.eureka.client.comm.ValueThresholds

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

submitJob(JobSpec) - Method in class org.eurekaclinical.eureka.client.EurekaProxyClient

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

TableColumn - Class in org.eurekaclinical.eureka.client.comm

TableColumn() - Constructor for class org.eurekaclinical.eureka.client.comm.TableColumn

TabularFileDestination - Class in org.eurekaclinical.eureka.client.comm

TabularFileDestination() - Constructor for class org.eurekaclinical.eureka.client.comm.TabularFileDestination

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.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.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.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

updateDestination(Destination) - Method in class org.eurekaclinical.eureka.client.EurekaProxyClient

updateUser(User, Long) - Method in class org.eurekaclinical.eureka.client.EurekaClient

updateUser(User, Long) - Method in class org.eurekaclinical.eureka.client.EurekaProxyClient

updateUserPhenotype(Long, Phenotype) - Method in class org.eurekaclinical.eureka.client.EurekaClient

updateUserPhenotype(Long, Phenotype) - Method in class org.eurekaclinical.eureka.client.EurekaProxyClient

Upload() - Constructor for class org.eurekaclinical.eureka.client.comm.SourceConfigParams.Upload

upload(String, String, String, InputStream) - Method in class org.eurekaclinical.eureka.client.EurekaClient

upload(String, String, String, InputStream) - Method in class org.eurekaclinical.eureka.client.EurekaProxyClient

UriSourceConfigOption - Class in org.eurekaclinical.eureka.client.comm

UriSourceConfigOption() - Constructor for class org.eurekaclinical.eureka.client.comm.UriSourceConfigOption

V

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.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(PatientSetSenderDestination) - Method in interface org.eurekaclinical.eureka.client.comm.DestinationVisitor

visit(TabularFileDestination) - Method in interface org.eurekaclinical.eureka.client.comm.DestinationVisitor

visit(RelDbDestination) - 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

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