Index (Bunsen Parent 0.4.2 API)

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

A

AbstractConceptMaps<T extends org.hl7.fhir.instance.model.api.IBaseResource,C extends AbstractConceptMaps<T,C>> - Class in com.cerner.bunsen.codes.base: This is a partial implementation of logic to manage FHIR ConceptMaps.
AbstractConceptMaps(SparkSession, FhirVersionEnum, Dataset<UrlAndVersion>, Dataset<T>, Dataset<Mapping>, Encoder<T>) - Constructor for class com.cerner.bunsen.codes.base.AbstractConceptMaps
AbstractValueSets<T extends org.hl7.fhir.instance.model.api.IBaseResource,C extends AbstractValueSets<T,C>> - Class in com.cerner.bunsen.codes.base: This is a partial implementation of logic to manage FHIR ValueSets.
AbstractValueSets(SparkSession, FhirVersionEnum, Dataset<UrlAndVersion>, Dataset<T>, Dataset<Value>, Encoder<T>) - Constructor for class com.cerner.bunsen.codes.base.AbstractValueSets
addCode(String, String, String) - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets.Builder: Adds a code under the given reference name to the value set.
addDescendantsOf(String, String, String, String) - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets.Builder: Add "descendants" of a given code value, that is code values that are transitively subsumed by the given value in the given hierarchy.
addDescendantsOf(String, String, String, String, String) - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets.Builder: Add "descendants" of a given code value, that is code values that are transitively subsumed by the given value in the given hierarchy.
addReference(String, String) - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets.Builder: Add a "reference" to a value set, that is, create a user-defined reference name for a value set of codes.
addReference(String, String, String) - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets.Builder: Add a "reference" to a value set, that is, create a user-defined reference name for a value set of codes.
addToConceptMap(T, Dataset<Mapping>) - Method in class com.cerner.bunsen.codes.base.AbstractConceptMaps: Adds the given mappings to the concept map.
addToConceptMap(ConceptMap, Dataset<Mapping>) - Method in class com.cerner.bunsen.r4.codes.ConceptMaps
addToConceptMap(ConceptMap, Dataset<Mapping>) - Method in class com.cerner.bunsen.stu3.codes.ConceptMaps
addToValueSet(T, Dataset<Value>) - Method in class com.cerner.bunsen.codes.base.AbstractValueSets: Adds the given values to the given value set instance.
addToValueSet(ValueSet, Dataset<Value>) - Method in class com.cerner.bunsen.r4.codes.ValueSets
addToValueSet(ValueSet, Dataset<Value>) - Method in class com.cerner.bunsen.stu3.codes.ValueSets
Ancestor - Class in com.cerner.bunsen.codes: A JavaBean to represent a ancestor row from one value to another.
Ancestor() - Constructor for class com.cerner.bunsen.codes.Ancestor: Nullary constructor so Spark can encode this class as a bean.
Ancestor(String, String, String, String, String, String) - Constructor for class com.cerner.bunsen.codes.Ancestor: Constructs a Ancestor instance.
ANCESTORS_TABLE - Static variable in class com.cerner.bunsen.codes.Hierarchies: Default table name where expanded ancestor information is stored.
AncestorValue() - Constructor for class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets.AncestorValue: Nullary constructor so Spark can encode this as a bean.
AncestorValue(String, String, String, String, String) - Constructor for class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets.AncestorValue: Constructs an ancestor value bean.

B

broadcast(Set<String>, boolean) - Method in class com.cerner.bunsen.codes.base.AbstractConceptMaps: Broadcast mappings stored in the given conceptMaps instance that match the given conceptMapUris.
broadcast(Map<String, String>) - Method in class com.cerner.bunsen.codes.base.AbstractConceptMaps: Broadcast mappings stored in the given conceptMaps instance that match the given conceptMapUris.
broadcast(Map<String, String>) - Method in class com.cerner.bunsen.r4.codes.ConceptMaps
broadcast(Map<String, String>) - Method in class com.cerner.bunsen.stu3.codes.ConceptMaps
BroadcastableConceptMap - Class in com.cerner.bunsen.codes.broadcast: A broadcastable concept map available in Spark operations or user-defined functions.
BroadcastableConceptMap(String, List<Mapping>, List<BroadcastableConceptMap>) - Constructor for class com.cerner.bunsen.codes.broadcast.BroadcastableConceptMap: Constructs the broadcastable concept map.
BroadcastableConceptMap.CodeValue - Class in com.cerner.bunsen.codes.broadcast: A specific code instance, identified by system and value, that has been broadcast.
BroadcastableMappings - Class in com.cerner.bunsen.codes.broadcast: A collection of BroadcastableConceptMaps that is usable in Spark transformations or UDFs.
BroadcastableMappings(Map<String, BroadcastableConceptMap>) - Constructor for class com.cerner.bunsen.codes.broadcast.BroadcastableMappings
BroadcastableValueSets - Class in com.cerner.bunsen.codes.broadcast: An immutable collection of value sets that can be broadcast for use in Spark transformations or user-defined functions.
BroadcastableValueSets.AncestorValue - Class in com.cerner.bunsen.codes.broadcast: Bean-style class to represent ancestor values locally and as Spark datasets.
BroadcastableValueSets.Builder - Class in com.cerner.bunsen.codes.broadcast
BroadcastableValueSets.Reference - Class in com.cerner.bunsen.codes.broadcast: Bean-style class to represent a reference to a value set.
build(SparkSession, AbstractValueSets) - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets.Builder: Returns broadcastable value sets by loading reference data that was added to this builder and the default value sets.
build(SparkSession, AbstractValueSets, Hierarchies) - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets.Builder: Returns broadcastable value sets by loading reference data that was added to this builder and the given value sets.
Builder() - Constructor for class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets.Builder
Bundles - Class in com.cerner.bunsen: Utilities to work with FHIR bundles.
Bundles.BundleContainer - Class in com.cerner.bunsen: A wrapper class for bundles that supports the use of Bundles from various FHIR versions in Spark RDDs.

C

com.cerner.bunsen - package com.cerner.bunsen: Core API for using FHIR in Apache Spark.
com.cerner.bunsen.codes - package com.cerner.bunsen.codes: Common for working with FHIR concept maps.
com.cerner.bunsen.codes.base - package com.cerner.bunsen.codes.base: Base classes for working with ConceptMaps and ValueSets.
com.cerner.bunsen.codes.broadcast - package com.cerner.bunsen.codes.broadcast: Support to broadcast code mappings that are useful to query or transform FHIR data in Spark.
com.cerner.bunsen.codes.systems - package com.cerner.bunsen.codes.systems: Support for importing LOINC and SNOMED terminology systems.
com.cerner.bunsen.r4.codes - package com.cerner.bunsen.r4.codes: Support for FHIR R4 ConceptMap and ValueSet resources.
com.cerner.bunsen.r4.python - package com.cerner.bunsen.r4.python: Support for Python-specific wrapper functions.
com.cerner.bunsen.shaded - package com.cerner.bunsen.shaded: This JAR contains only the bunsen-core project and its shaded dependencies for simple use with Apache Spark.
com.cerner.bunsen.stu3.codes - package com.cerner.bunsen.stu3.codes: Support for FHIR STU3 ConceptMap and ValueSet resources.
com.cerner.bunsen.stu3.python - package com.cerner.bunsen.stu3.python: Support for Python-specific wrapper functions.
CONCEPT_MAP_TABLE - Static variable in class com.cerner.bunsen.codes.base.AbstractConceptMaps: Defalt table name where concept maps are stored.
conceptMapEncoder - Variable in class com.cerner.bunsen.codes.base.AbstractConceptMaps
conceptMaps - Variable in class com.cerner.bunsen.codes.base.AbstractConceptMaps
ConceptMaps - Class in com.cerner.bunsen.r4.codes: An immutable collection of FHIR ConceptMaps.
ConceptMaps(SparkSession, Dataset<UrlAndVersion>, Dataset<ConceptMap>, Dataset<Mapping>) - Constructor for class com.cerner.bunsen.r4.codes.ConceptMaps
ConceptMaps - Class in com.cerner.bunsen.stu3.codes: An immutable collection of FHIR ConceptMaps.
ConceptMaps(SparkSession, Dataset<UrlAndVersion>, Dataset<ConceptMap>, Dataset<Mapping>) - Constructor for class com.cerner.bunsen.stu3.codes.ConceptMaps
contextFor(FhirVersionEnum) - Static method in class com.cerner.bunsen.FhirEncoders: Returns the FHIR context for the given version.
currentValueSets() - Static method in class com.cerner.bunsen.ValueSetUdfs: Returns the broadcast variable of the current valuesets so they can be used in other user-defined functions.

E

equals(Object) - Method in class com.cerner.bunsen.codes.Ancestor
equals(Object) - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets.AncestorValue
equals(Object) - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets.Reference
equals(Object) - Method in class com.cerner.bunsen.codes.Hierarchies.HierarchicalElement
equals(Object) - Method in class com.cerner.bunsen.codes.Mapping
equals(Object) - Method in class com.cerner.bunsen.codes.UrlAndVersion
equals(Object) - Method in class com.cerner.bunsen.codes.Value
EQUIVALENT - Static variable in class com.cerner.bunsen.codes.Mapping: Equivalent constant definition.
expandMappings(ConceptMap) - Static method in class com.cerner.bunsen.r4.codes.ConceptMaps: Given a concept map, returns a list of mapping records it contains.
expandMappings(ConceptMap) - Static method in class com.cerner.bunsen.stu3.codes.ConceptMaps: Given a concept map, returns a list of mapping records it contains.
expandValues(ValueSet) - Static method in class com.cerner.bunsen.r4.codes.ValueSets: Given a value set, returns a list of value records it contains.
expandValues(ValueSet) - Static method in class com.cerner.bunsen.stu3.codes.ValueSets: Given a value set, returns a list of value records it contains.
extractEntry(SparkSession, JavaRDD<Bundles.BundleContainer>, Class<T>) - Method in class com.cerner.bunsen.Bundles: Extracts the given resource type from the RDD of bundles and returns it as a Dataset of that type.
extractEntry(SparkSession, JavaRDD<Bundles.BundleContainer>, String) - Method in class com.cerner.bunsen.Bundles: Extracts the given resource type from the RDD of bundles and returns it as a Dataset of that type.
extractEntry(SparkSession, JavaRDD<Bundles.BundleContainer>, String, FhirEncoders) - Method in class com.cerner.bunsen.Bundles: Extracts the given resource type from the RDD of bundles and returns it as a Dataset of that type.
extractResource(String) - Method in class com.cerner.bunsen.Bundles.BundleContainer: Returns a list containing the resources of the given name that exist in the bundle.

F

FhirEncoders - Class in com.cerner.bunsen: Spark Encoders for FHIR Resources.
FhirEncoders(FhirContext, DataTypeMappings) - Constructor for class com.cerner.bunsen.FhirEncoders: Consumers should generally use the FhirEncoders.forStu3() or FhirEncoders.forR4() methods, but this is made available for test purposes and additional experimental mappings.
FhirEncoders.Builder - Class in com.cerner.bunsen: Encoder builder.
fhirVersion - Variable in class com.cerner.bunsen.codes.base.AbstractConceptMaps
fhirVersion - Variable in class com.cerner.bunsen.codes.base.AbstractValueSets
forR4() - Static method in class com.cerner.bunsen.Bundles
forR4() - Static method in class com.cerner.bunsen.FhirEncoders: Returns a builder to create encoders for FHIR R4.
forStu3() - Static method in class com.cerner.bunsen.Bundles
forStu3() - Static method in class com.cerner.bunsen.FhirEncoders: Returns a builder to create encoders for FHIR STU3.
forVersion(FhirVersionEnum) - Static method in class com.cerner.bunsen.FhirEncoders: Returns a builder to create encoders for the given FHIR version.
fromJson(Dataset<Row>, String) - Method in class com.cerner.bunsen.Bundles: Returns an RDD of bundles loaded from the given dataset that has JSON-encoded bundles in the given column.
fromJson(Dataset<String>) - Method in class com.cerner.bunsen.Bundles: Returns an RDD of bundles loaded from the given dataset of JSON-encoded bundles.
fromXml(Dataset<Row>, String) - Method in class com.cerner.bunsen.Bundles: Returns an RDD of bundles loaded from the given dataset that has XML-encoded bundles in the given column.
fromXml(Dataset<String>) - Method in class com.cerner.bunsen.Bundles: Returns an RDD of bundles loaded from the given dataset of XML-encoded bundles.
Functions - Class in com.cerner.bunsen.r4.python: Common functions for working with FHIR resources.
Functions() - Constructor for class com.cerner.bunsen.r4.python.Functions
Functions - Class in com.cerner.bunsen.stu3.python: Common functions for working with FHIR resources.
Functions() - Constructor for class com.cerner.bunsen.stu3.python.Functions

G

getAncestors() - Method in class com.cerner.bunsen.codes.Hierarchies: Returns a dataset of all ancestors in this collection.
getAncestorSystem() - Method in class com.cerner.bunsen.codes.Ancestor: Returns the code system that owns the ancestor value.
getAncestorSystem() - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets.AncestorValue: Returns the system of the ancestor code.
getAncestorSystem() - Method in class com.cerner.bunsen.codes.Hierarchies.HierarchicalElement: Returns the ancestor system.
getAncestorValue() - Method in class com.cerner.bunsen.codes.Ancestor: Returns the ancestor value.
getAncestorValue() - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets.AncestorValue: Returns the value of the ancestor code.
getAncestorValue() - Method in class com.cerner.bunsen.codes.Hierarchies.HierarchicalElement: Returns the ancestor value.
getBroadcastConceptMap(String) - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableMappings: Returns the broadcastable concept map for the concept map with the given URI.
getBundle() - Method in class com.cerner.bunsen.Bundles.BundleContainer: Returns the contained FHIR bundle.
getConceptMap(String, String) - Method in class com.cerner.bunsen.codes.base.AbstractConceptMaps: Returns the concept map with the given uri and version, or null if there is no such map.
getConceptMapEncoder() - Static method in class com.cerner.bunsen.r4.codes.ConceptMaps: Returns the encoder for concept maps.
getConceptMapEncoder() - Static method in class com.cerner.bunsen.stu3.codes.ConceptMaps: Returns the encoder for concept maps.
getConceptMapUri() - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableConceptMap: Returns the URI for the concept map.
getConceptMapUri() - Method in class com.cerner.bunsen.codes.Mapping: Returns the URI for the FHIR concept map that owns this mapping.
getConceptMapVersion() - Method in class com.cerner.bunsen.codes.Mapping: Returns the version of the FHIR concept map that owns this mapping.
getDefault(SparkSession) - Static method in class com.cerner.bunsen.codes.Hierarchies: Returns the collection of ancestors from the default database and table.
getDefault(SparkSession) - Static method in class com.cerner.bunsen.r4.codes.ConceptMaps: Returns the collection of concept maps from the default database and tables.
getDefault(SparkSession) - Static method in class com.cerner.bunsen.r4.codes.ValueSets: Returns the collection of value sets from the default database and tables.
getDefault(SparkSession) - Static method in class com.cerner.bunsen.stu3.codes.ConceptMaps: Returns the collection of concept maps from the default database and tables.
getDefault(SparkSession) - Static method in class com.cerner.bunsen.stu3.codes.ValueSets: Returns the collection of value sets from the default database and tables.
getDescendantSystem() - Method in class com.cerner.bunsen.codes.Ancestor: Returns the code system that owns the descendant value.
getDescendantSystem() - Method in class com.cerner.bunsen.codes.Hierarchies.HierarchicalElement: Returns the descendant system.
getDescendantValue() - Method in class com.cerner.bunsen.codes.Ancestor: Returns the descendant value.
getDescendantValue() - Method in class com.cerner.bunsen.codes.Hierarchies.HierarchicalElement: Returns the descendant value.
getEmpty(SparkSession) - Static method in class com.cerner.bunsen.codes.Hierarchies: Returns an empty Hierarchies instance.
getEmpty(SparkSession) - Static method in class com.cerner.bunsen.r4.codes.ConceptMaps: Returns an empty ConceptMaps instance.
getEmpty(SparkSession) - Static method in class com.cerner.bunsen.r4.codes.ValueSets: Returns an empty ValueSets instance.
getEmpty(SparkSession) - Static method in class com.cerner.bunsen.stu3.codes.ConceptMaps: Returns an empty ConceptMaps instance.
getEmpty(SparkSession) - Static method in class com.cerner.bunsen.stu3.codes.ValueSets: Returns an empty ValueSets instance.
getEquivalence() - Method in class com.cerner.bunsen.codes.Mapping: Returns the equivalence for the mapping.
getFhirVersion() - Method in class com.cerner.bunsen.FhirEncoders: Returns the version of FHIR used by encoders produced by this instance.
getFromDatabase(SparkSession, String) - Static method in class com.cerner.bunsen.codes.Hierarchies: Returns the collection of ancestors from the table in the given database.
getFromDatabase(SparkSession, String) - Static method in class com.cerner.bunsen.r4.codes.ConceptMaps: Returns the collection of concept maps from the tables in the given database.
getFromDatabase(SparkSession, String) - Static method in class com.cerner.bunsen.r4.codes.ValueSets: Returns the collection of value sets from the tables in the given database.
getFromDatabase(SparkSession, String) - Static method in class com.cerner.bunsen.stu3.codes.ConceptMaps: Returns the collection of concept maps from the tables in the given database.
getFromDatabase(SparkSession, String) - Static method in class com.cerner.bunsen.stu3.codes.ValueSets: Returns the collection of value sets from the tables in the given database.
getHierarchicalElementEncoder() - Static method in class com.cerner.bunsen.codes.Hierarchies: Returns the encoder for hierarchical elements.
getLatestMappings(Set<String>, boolean) - Method in class com.cerner.bunsen.codes.base.AbstractConceptMaps: Returns a dataset with the latest mappings for each valueset here.
getLatestValues(Set<String>, boolean) - Method in class com.cerner.bunsen.codes.base.AbstractValueSets: Returns a dataset with the latest values for each valueset of the given uris.
getLatestVersions(boolean) - Method in class com.cerner.bunsen.codes.base.AbstractConceptMaps: Returns the latest versions of all concept maps.
getLatestVersions(Set<String>, boolean) - Method in class com.cerner.bunsen.codes.base.AbstractConceptMaps: Returns the latest versions of a given set of concept maps.
getLatestVersions(boolean) - Method in class com.cerner.bunsen.codes.base.AbstractValueSets: Returns the latest version of all value sets.
getLatestVersions(Set<String>, boolean) - Method in class com.cerner.bunsen.codes.base.AbstractValueSets: Returns the latest versions of a given set of value sets.
getLatestVersions() - Method in class com.cerner.bunsen.codes.Hierarchies: Returns the latest version of all hierarchies.
getLatestVersions(Set<String>) - Method in class com.cerner.bunsen.codes.Hierarchies: Returns latest versions of the given hierarchies.
getMappingEncoder() - Static method in class com.cerner.bunsen.r4.codes.ConceptMaps: Returns the encoder for mappings.
getMappingEncoder() - Static method in class com.cerner.bunsen.stu3.codes.ConceptMaps: Returns the encoder for mappings.
getMappings() - Method in class com.cerner.bunsen.codes.base.AbstractConceptMaps: Returns a dataset of all mappings in this collection.
getMappings(String, String) - Method in class com.cerner.bunsen.codes.base.AbstractConceptMaps: Returns the mappings for the given URI and version.
getMappings(Map<String, String>) - Method in class com.cerner.bunsen.codes.base.AbstractConceptMaps: Returns a dataset with the mappings for each uri and version.
getMaps() - Method in class com.cerner.bunsen.codes.base.AbstractConceptMaps: Returns a dataset of concept maps to inspect metadata.
getMembers() - Method in class com.cerner.bunsen.codes.Hierarchies: Returns a dataset of UrlAndVersion members of this collection.
getOrCreate() - Method in class com.cerner.bunsen.FhirEncoders.Builder: Get or create an FhirEncoders instance that matches the builder's configuration.
getReferenceName() - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets.AncestorValue: Returns the value set reference name.
getReferenceName() - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets.Reference: Returns the value set reference name.
getReferenceNames() - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets: Returns the reference names in the value set.
getSourceSystem() - Method in class com.cerner.bunsen.codes.Mapping: Returns the code system for the source code.
getSourceValue() - Method in class com.cerner.bunsen.codes.Mapping: Returns the code value for the source code.
getSourceValueSet() - Method in class com.cerner.bunsen.codes.Mapping: Returns the valueset for all source values in this mapping.
getSystem() - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableConceptMap.CodeValue: Returns the code system.
getSystem() - Method in class com.cerner.bunsen.codes.Value: Returns the code system that owns this value.
getTarget(String, String) - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableConceptMap: Returns the target list of code values, or an empty list.
getTargetSystem() - Method in class com.cerner.bunsen.codes.Mapping: Returns the code system for the target code.
getTargetValue() - Method in class com.cerner.bunsen.codes.Mapping: Returns the code value for the target code.
getTargetValueSet() - Method in class com.cerner.bunsen.codes.Mapping: Returns the valueset for all target values in this mapping.
getUri() - Method in class com.cerner.bunsen.codes.Ancestor: Returns the hierarchy URI that owns this value.
getUri() - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets.AncestorValue: Returns the URI of the hierarchy that owns this ancestor value.
getUriAndVersionEncoder() - Static method in class com.cerner.bunsen.codes.Hierarchies: Returns the encoder for UrlAndVersion tuples.
getUrl() - Method in class com.cerner.bunsen.codes.UrlAndVersion
getUrlAndVersionEncoder() - Static method in class com.cerner.bunsen.codes.base.AbstractConceptMaps: Returns the encoder for UrlAndVersion tuples.
getUrlAndVersionEncoder() - Static method in class com.cerner.bunsen.codes.base.AbstractValueSets: Returns the encoder for UrlAndVersion tuples.
getUrlAndVersions(Dataset<T>) - Method in class com.cerner.bunsen.codes.base.AbstractConceptMaps: Returns a simple dataset of URL and versions of concept maps.
getUrlAndVersions(Dataset<T>) - Method in class com.cerner.bunsen.codes.base.AbstractValueSets: Returns a dataset of distinct URL and version tuples.
getValue() - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableConceptMap.CodeValue: Returns the code value.
getValue() - Method in class com.cerner.bunsen.codes.Value: Returns the value.
getValueEncoder() - Static method in class com.cerner.bunsen.codes.base.AbstractValueSets: Returns the encoder for values.
getValues() - Method in class com.cerner.bunsen.codes.base.AbstractValueSets: Returns a dataset of all values in this collection.
getValues(String, String) - Method in class com.cerner.bunsen.codes.base.AbstractValueSets: Returns the values for the given URI and version.
getValues(Map<String, String>) - Method in class com.cerner.bunsen.codes.base.AbstractValueSets: Returns a dataset with the values for each element in the map of uri to version.
getValues(String) - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets: Returns a map of code systems to the set of code values within those systems used by the given valueset reference.
getValueSet(String, String) - Method in class com.cerner.bunsen.codes.base.AbstractValueSets: Returns the value set with the given uri and version, or null if there is no such value set.
getValueSetEncoder() - Static method in class com.cerner.bunsen.r4.codes.ValueSets: Returns the encoder for value sets.
getValueSetEncoder() - Static method in class com.cerner.bunsen.stu3.codes.ValueSets: Returns the encoder for value sets.
getValueSets() - Method in class com.cerner.bunsen.codes.base.AbstractValueSets: Returns a dataset of value sets to inspect metadata.
getValueSetUri() - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets.Reference: Returns the value set uri that defines this reference relationship.
getValueSetUri() - Method in class com.cerner.bunsen.codes.Value: Returns the URI for this FHIR value set that owns this value.
getValueSetVersion() - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets.Reference: Returns the value set version that defines this reference relationship.
getValueSetVersion() - Method in class com.cerner.bunsen.codes.Value: Returns the version for this FHIR value set that owns this value.
getVersion() - Method in class com.cerner.bunsen.codes.Ancestor: Returns the hierarchy version that owns this value.
getVersion() - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets.AncestorValue: Returns the version of the hierarchy that owns this ancestor value.
getVersion() - Method in class com.cerner.bunsen.codes.UrlAndVersion
getVersion() - Method in class com.cerner.bunsen.codes.Value: Returns the version of the code system that owns this value.

H

hasCode(String, String, String) - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets: Returns true if the value set with the given reference name includes the given code value.
hasDuplicateUrlAndVersions(Dataset<UrlAndVersion>) - Method in class com.cerner.bunsen.codes.base.AbstractConceptMaps: Returns true if the UrlAndVersions of new value sets contains duplicates with the current ValueSets.
hasDuplicateUrlAndVersions(Dataset<UrlAndVersion>) - Method in class com.cerner.bunsen.codes.base.AbstractValueSets: Returns true if the UrlAndVersions if the membersToCheck has any duplicates with the members of this value sets instance.
hashCode() - Method in class com.cerner.bunsen.codes.Ancestor
hashCode() - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets.AncestorValue
hashCode() - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets.Reference
hashCode() - Method in class com.cerner.bunsen.codes.Hierarchies.HierarchicalElement
hashCode() - Method in class com.cerner.bunsen.codes.Mapping
hashCode() - Method in class com.cerner.bunsen.codes.UrlAndVersion
hashCode() - Method in class com.cerner.bunsen.codes.Value
HierarchicalElement() - Constructor for class com.cerner.bunsen.codes.Hierarchies.HierarchicalElement: Nullary constructor so Spark can encode this class as a bean.
HierarchicalElement(String, String, String, String) - Constructor for class com.cerner.bunsen.codes.Hierarchies.HierarchicalElement: Constructs a Hierarchies.HierarchicalElement instance.
Hierarchies - Class in com.cerner.bunsen.codes: An immutable collection of hierarchical systems.
Hierarchies.HierarchicalElement - Class in com.cerner.bunsen.codes: A JavaBean to represent an element in a hierarchical system from which transitive ancestors can be computed.
HIERARCHIES_DATABASE - Static variable in class com.cerner.bunsen.codes.Hierarchies: Default database name where the ancestor information is stored.
HIERARCHY_URI_PREFIX - Static variable in class com.cerner.bunsen.codes.Hierarchies: A URI prefix for hierarchical systems.

L

loadFromDirectory(SparkSession, String, int) - Method in class com.cerner.bunsen.Bundles: Returns an RDD of bundles loaded from the given path.
Loinc - Class in com.cerner.bunsen.codes.systems: Support for LOINC.
Loinc() - Constructor for class com.cerner.bunsen.codes.systems.Loinc
LOINC_CODE_SYSTEM_URI - Static variable in class com.cerner.bunsen.codes.systems.Loinc: LOINC code system URI.
LOINC_HIERARCHY_URI - Static variable in class com.cerner.bunsen.codes.systems.Loinc: Hierarchy URI used for LOINC is-a relationships.

M

Mapping - Class in com.cerner.bunsen.codes: A JavaBean to represent a mapping row from one value to another.
Mapping() - Constructor for class com.cerner.bunsen.codes.Mapping: Nullary constructor so Spark can encode this class as a bean.
Mapping(String, String, String, String, String, String, String, String, String) - Constructor for class com.cerner.bunsen.codes.Mapping: Constructs a Mapping instance.
MAPPING_DATABASE - Static variable in class com.cerner.bunsen.codes.base.AbstractConceptMaps: Default database name where mapping information is stored.
MAPPING_ENCODER - Static variable in class com.cerner.bunsen.codes.base.AbstractConceptMaps: An encoder for serializing mappings.
MAPPING_TABLE - Static variable in class com.cerner.bunsen.codes.base.AbstractConceptMaps: Default table name where expanded mapping information is stored.
mappings - Variable in class com.cerner.bunsen.codes.base.AbstractConceptMaps
members - Variable in class com.cerner.bunsen.codes.base.AbstractConceptMaps
members - Variable in class com.cerner.bunsen.codes.base.AbstractValueSets: URI and Version metadata used to preserve uniqueness among value sets.

N

newBuilder() - Static method in class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets: Returns a BroadcastableValueSets builder.
newInstance(SparkSession, Dataset<UrlAndVersion>, Dataset<T>, Dataset<Mapping>) - Method in class com.cerner.bunsen.codes.base.AbstractConceptMaps: Returns a new instance of this ConceptMaps type with the given parameters.
newInstance(SparkSession, Dataset<UrlAndVersion>, Dataset<ConceptMap>, Dataset<Mapping>) - Method in class com.cerner.bunsen.r4.codes.ConceptMaps
newInstance(SparkSession, Dataset<UrlAndVersion>, Dataset<ConceptMap>, Dataset<Mapping>) - Method in class com.cerner.bunsen.stu3.codes.ConceptMaps

O

of(Class<T>) - Method in class com.cerner.bunsen.FhirEncoders: Returns an encoder for the given FHIR resource.
of(String) - Method in class com.cerner.bunsen.FhirEncoders: Returns an encoder for the given FHIR resource by name, as defined by the FHIR specification.

P

popUdf(SparkSession) - Static method in class com.cerner.bunsen.ValueSetUdfs: Pops a BroadcastableValueSets from the user-defined function stack.
pushUdf(SparkSession, BroadcastableValueSets) - Static method in class com.cerner.bunsen.ValueSetUdfs: Pushes an "in_valueset" UDF that uses the given BroadcastableValueSets for its content.
pushUdf(SparkSession, Broadcast<BroadcastableValueSets>) - Static method in class com.cerner.bunsen.ValueSetUdfs: Pushes an "in_valueset" UDF that uses an already broadcast instance of BroadcastableValueSets for its content.

R

readMultiaxialHierarchyFile(SparkSession, String) - Static method in class com.cerner.bunsen.codes.systems.Loinc: Reads the LOINC mutliaxial hierarchy file and converts it to a Hierarchies.HierarchicalElement dataset.
readRelationshipFile(SparkSession, String) - Static method in class com.cerner.bunsen.codes.systems.Snomed: Reads a Snomed relationship file and converts it to a Hierarchies.HierarchicalElement dataset.
Reference() - Constructor for class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets.Reference: Nullary constructor so Spark can encode this class as a bean.
Reference(String, String, String) - Constructor for class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets.Reference: Constructs a BroadcastableValueSets.Reference value.
resourceToJson(Resource) - Static method in class com.cerner.bunsen.r4.python.Functions: Converts a resource to its JSON representation.
resourceToJson(Resource) - Static method in class com.cerner.bunsen.stu3.python.Functions: Converts a resource to its JSON representation.
resourceToXml(Resource) - Static method in class com.cerner.bunsen.r4.python.Functions: Converts a resource to its XML representation.
resourceToXml(Resource) - Static method in class com.cerner.bunsen.stu3.python.Functions: Converts a resource to its XML representation.

S

saveAsDatabase(SparkSession, JavaRDD<Bundles.BundleContainer>, String, String...) - Method in class com.cerner.bunsen.Bundles: Saves an RDD of bundles as a database, where each table has the resource name.
setAncestorSystem(String) - Method in class com.cerner.bunsen.codes.Ancestor: Sets the code system that owns the ancestor value.
setAncestorSystem(String) - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets.AncestorValue: Sets the system of the ancestor code.
setAncestorSystem(String) - Method in class com.cerner.bunsen.codes.Hierarchies.HierarchicalElement: Sets the ancestor system.
setAncestorValue(String) - Method in class com.cerner.bunsen.codes.Ancestor: Sets the ancestor value.
setAncestorValue(String) - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets.AncestorValue: Sets the value of the ancestor code.
setAncestorValue(String) - Method in class com.cerner.bunsen.codes.Hierarchies.HierarchicalElement: Sets the ancestor value.
setConceptMapUri(String) - Method in class com.cerner.bunsen.codes.Mapping: Sets the URI for the FHIR concept map that owns this mapping.
setConceptMapVersion(String) - Method in class com.cerner.bunsen.codes.Mapping: Sets the version of the FHIR concept map that owns this mapping.
setDescendantSystem(String) - Method in class com.cerner.bunsen.codes.Ancestor: Sets the code system that owns the descendant value.
setDescendantSystem(String) - Method in class com.cerner.bunsen.codes.Hierarchies.HierarchicalElement: Sets the descendant system.
setDescendantValue(String) - Method in class com.cerner.bunsen.codes.Ancestor: Sets the descendant value.
setDescendantValue(String) - Method in class com.cerner.bunsen.codes.Hierarchies.HierarchicalElement: Sets the descendant value.
setEquivalence(String) - Method in class com.cerner.bunsen.codes.Mapping: Sets the equivalence for the mapping.
setReferenceName(String) - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets.AncestorValue: Sets the value set reference name.
setReferenceName(String) - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets.Reference: Sets the value set reference name.
setSourceSystem(String) - Method in class com.cerner.bunsen.codes.Mapping: Sets the code system for the source code.
setSourceValue(String) - Method in class com.cerner.bunsen.codes.Mapping: Sets the code value for the source code.
setSourceValueSet(String) - Method in class com.cerner.bunsen.codes.Mapping: Sets the valueset for all source values in this mapping.
setSystem(String) - Method in class com.cerner.bunsen.codes.Value: Sets the code system that owns this value.
setTargetSystem(String) - Method in class com.cerner.bunsen.codes.Mapping: Sets the code system for the target code.
setTargetValue(String) - Method in class com.cerner.bunsen.codes.Mapping: Sets the code value for the target code.
setTargetValueSet(String) - Method in class com.cerner.bunsen.codes.Mapping: Sets the valueset for all target values in this mapping.
setUri(String) - Method in class com.cerner.bunsen.codes.Ancestor: Sets the hierarchy URI that owns this value.
setUri(String) - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets.AncestorValue: Sets the URI of the concept map that owns this ancestor value.
setUrl(String) - Method in class com.cerner.bunsen.codes.UrlAndVersion
setValue(String) - Method in class com.cerner.bunsen.codes.Value: Sets the value.
setValueSetUri(String) - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets.Reference: Sets the value set uri that defines this reference relationship.
setValueSetUri(String) - Method in class com.cerner.bunsen.codes.Value: Sets the URI for this FHIR value set that owns this value.
setValueSetVersion(String) - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets.Reference: Sets the value set version that defines this reference relationship.
setValueSetVersion(String) - Method in class com.cerner.bunsen.codes.Value: Sets the version for this FHIR value set that owns this value.
setVersion(String) - Method in class com.cerner.bunsen.codes.Ancestor: Sets the hierarchy version that owns this value.
setVersion(String) - Method in class com.cerner.bunsen.codes.broadcast.BroadcastableValueSets.AncestorValue: Sets the version of the hierarchy that owns this ancestor value.
setVersion(String) - Method in class com.cerner.bunsen.codes.UrlAndVersion
setVersion(String) - Method in class com.cerner.bunsen.codes.Value: Sets the version of the code system that owns this value.
Shaded - Class in com.cerner.bunsen.shaded: This JAR contains only the bunsen-core project and its shaded dependencies for simple use with Apache Spark.
Shaded() - Constructor for class com.cerner.bunsen.shaded.Shaded
Snomed - Class in com.cerner.bunsen.codes.systems: Support for SNOMED CT.
Snomed() - Constructor for class com.cerner.bunsen.codes.systems.Snomed
SNOMED_CODE_SYSTEM_URI - Static variable in class com.cerner.bunsen.codes.systems.Snomed: SNOMED code system URI.
SNOMED_HIERARCHY_URI - Static variable in class com.cerner.bunsen.codes.systems.Snomed: Hierarchy URI used for SNOMED is-a relationships.
spark - Variable in class com.cerner.bunsen.codes.base.AbstractConceptMaps
spark - Variable in class com.cerner.bunsen.codes.base.AbstractValueSets
SUBSUMES - Static variable in class com.cerner.bunsen.codes.Mapping: Subsumes constant definition.

T

TABLE_NAME_PATTERN - Static variable in class com.cerner.bunsen.codes.base.AbstractConceptMaps
TABLE_NAME_PATTERN - Static variable in class com.cerner.bunsen.codes.base.AbstractValueSets
toBundle(Dataset<? extends Resource>) - Static method in class com.cerner.bunsen.r4.python.Functions: Returns a bundle containing all resources in the dataset.
toBundle(Dataset<? extends Resource>) - Static method in class com.cerner.bunsen.stu3.python.Functions: Returns a bundle containing all resources in the dataset.
toJson(Dataset<?>, String) - Static method in class com.cerner.bunsen.r4.python.Functions: Converts a set of FHIR resources to JSON.
toJson(Dataset<?>, String) - Static method in class com.cerner.bunsen.stu3.python.Functions: Converts a set of FHIR resources to JSON.
toJsonBundle(Dataset<? extends Resource>) - Static method in class com.cerner.bunsen.r4.python.Functions: Returns a JSON string representing the resources as a bundle.
toJsonBundle(Dataset<? extends Resource>) - Static method in class com.cerner.bunsen.stu3.python.Functions: Returns a JSON string representing the resources as a bundle.

U

URL_AND_VERSION_ENCODER - Static variable in class com.cerner.bunsen.codes.base.AbstractConceptMaps
URL_AND_VERSION_ENCODER - Static variable in class com.cerner.bunsen.codes.base.AbstractValueSets
UrlAndVersion - Class in com.cerner.bunsen.codes: URI and version tuple used to uniquely identify a concept map, value set, or hierarchy.
UrlAndVersion(String, String) - Constructor for class com.cerner.bunsen.codes.UrlAndVersion
UrlAndVersion() - Constructor for class com.cerner.bunsen.codes.UrlAndVersion: Nullary constructor for use in Spark data sets.

V

Value - Class in com.cerner.bunsen.codes: A JavaBean to represent a value row of a value set.
Value() - Constructor for class com.cerner.bunsen.codes.Value: Nullary constructor so Spark can encode this class as a bean.
Value(String, String, String, String, String) - Constructor for class com.cerner.bunsen.codes.Value: Constructs a Value instance.
VALUE_ENCODER - Static variable in class com.cerner.bunsen.codes.base.AbstractValueSets: An encoder for serializing values.
VALUE_SETS_DATABASE - Static variable in class com.cerner.bunsen.codes.base.AbstractValueSets: Default database name where the value sets information is stored.
VALUE_SETS_TABLE - Static variable in class com.cerner.bunsen.codes.base.AbstractValueSets: Default table name where value sets metadata is stored.
values - Variable in class com.cerner.bunsen.codes.base.AbstractValueSets
VALUES_TABLE - Static variable in class com.cerner.bunsen.codes.base.AbstractValueSets: Default table name where the expanded values information is stored.
valueSetDatasetFromDirectory(String) - Method in class com.cerner.bunsen.codes.base.AbstractValueSets: Returns a dataset of ValueSet from the content stored at the given directory.
valueSetEncoder - Variable in class com.cerner.bunsen.codes.base.AbstractValueSets
valueSets - Variable in class com.cerner.bunsen.codes.base.AbstractValueSets
ValueSets - Class in com.cerner.bunsen.r4.codes: An immutable collection of FHIR ValueSets.
ValueSets - Class in com.cerner.bunsen.stu3.codes: An immutable collection of FHIR ValueSets.
ValueSetUdfs - Class in com.cerner.bunsen: Support for user-defined functions that use valuesets.
ValueSetUdfs() - Constructor for class com.cerner.bunsen.ValueSetUdfs

W

withConceptMaps(Dataset<T>) - Method in class com.cerner.bunsen.codes.base.AbstractConceptMaps: Returns a new ConceptMaps instance that includes the given maps.
withConceptMaps(T...) - Method in class com.cerner.bunsen.codes.base.AbstractConceptMaps: Returns a new ConceptMaps instance that includes the given map.
withConceptMaps(List<T>) - Method in class com.cerner.bunsen.codes.base.AbstractConceptMaps: Returns a new ConceptMaps instance that includes the given maps.
withConceptMaps(Dataset<T>, Dataset<Mapping>) - Method in class com.cerner.bunsen.codes.base.AbstractConceptMaps
withConceptMaps(Dataset<ConceptMap>) - Method in class com.cerner.bunsen.r4.codes.ConceptMaps
withConceptMaps(Dataset<ConceptMap>) - Method in class com.cerner.bunsen.stu3.codes.ConceptMaps
withDisjointMapsFromDirectory(String) - Method in class com.cerner.bunsen.codes.base.AbstractConceptMaps: Returns all concept maps that are disjoint with concept maps stored in the default database and adds them to our collection.
withDisjointMapsFromDirectory(String, String) - Method in class com.cerner.bunsen.codes.base.AbstractConceptMaps: Returns all concept maps that are disjoint with concept maps stored in the default database and adds them to our collection.
withDisjointValueSetsFromDirectory(String) - Method in class com.cerner.bunsen.codes.base.AbstractValueSets: Returns all value sets that are disjoint with value sets stored in the default database and adds them to our collection.
withDisjointValueSetsFromDirectory(String, String) - Method in class com.cerner.bunsen.codes.base.AbstractValueSets: Returns all value sets that are disjoint with value sets stored in the given database and adds them to our collection.
withExpandedMap(T, Dataset<Mapping>) - Method in class com.cerner.bunsen.codes.base.AbstractConceptMaps: Returns a new ConceptMaps instance that includes the given map and expanded mappings.
withHierarchies(Hierarchies) - Method in class com.cerner.bunsen.codes.Hierarchies: Returns a new hierarchies instance with the given hierarchies.
withHierarchyElements(String, String, Dataset<Hierarchies.HierarchicalElement>) - Method in class com.cerner.bunsen.codes.Hierarchies: Returns a new hierarchies instance with the transitive ancestors computed from the given dataset of Hierarchies.HierarchicalElement.
withLoincHierarchy(SparkSession, Hierarchies, String, String) - Static method in class com.cerner.bunsen.codes.systems.Loinc: Returns a Hierarchies instance with the specified multiaxial hierarchy.
withMapsFromDirectory(String) - Method in class com.cerner.bunsen.codes.base.AbstractConceptMaps: Reads all concept maps from a given directory and adds them to our collection.
withRelationships(SparkSession, Hierarchies, String, String) - Static method in class com.cerner.bunsen.codes.systems.Snomed: Returns a ConceptMaps instance with the specified multiaxial hierarchy.
withValueSets(Dataset<T>) - Method in class com.cerner.bunsen.codes.base.AbstractValueSets: Returns a new ValueSets instance that includes the given value sets.
withValueSets(T...) - Method in class com.cerner.bunsen.codes.base.AbstractValueSets: Returns a new ValueSets instance that includes the given value sets.
withValueSets(List<T>) - Method in class com.cerner.bunsen.codes.base.AbstractValueSets: Returns a new ValueSets instance that includes the given value sets.
withValueSets(Dataset<ValueSet>) - Method in class com.cerner.bunsen.r4.codes.ValueSets: Returns a new ValueSets instance that includes the given value sets.
withValueSets(Dataset<ValueSet>) - Method in class com.cerner.bunsen.stu3.codes.ValueSets: Returns a new ValueSets instance that includes the given value sets.
withValueSetsFromDirectory(String) - Method in class com.cerner.bunsen.codes.base.AbstractValueSets: Reads all value sets from a given directory and adds them to our collection.
writeToDatabase(String) - Method in class com.cerner.bunsen.codes.base.AbstractConceptMaps: Writes the updated concept maps to a database using the default "mappings" and "conceptmaps" table names.
writeToDatabase() - Method in class com.cerner.bunsen.codes.base.AbstractValueSets: Writes the the value sets to the default database "ontologies" using default table names: "values", and "valuesets".
writeToDatabase(String) - Method in class com.cerner.bunsen.codes.base.AbstractValueSets: Writes the value sets to the given database using default table names: "values", "valuesets", and "ancestors".
writeToDatabase() - Method in class com.cerner.bunsen.codes.Hierarchies: Writes the ancestors to the default database "ontologies" using the default table "ancestors".
writeToDatabase(String) - Method in class com.cerner.bunsen.codes.Hierarchies: Writes the ancestors to the given database using the default table name "ancestors".
writeToTables(String, String) - Method in class com.cerner.bunsen.codes.base.AbstractConceptMaps: Writes mappings to the given tables.
writeToTables(String, String) - Method in class com.cerner.bunsen.codes.base.AbstractValueSets: Writes value sets to the given tables.
writeToTables(String) - Method in class com.cerner.bunsen.codes.Hierarchies: Writes the ancestors to the given table.

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