com.cerner.bunsen

Class Bundles

java.lang.Object

com.cerner.bunsen.Bundles

public class Bundles
extends Object

Utilities to work with FHIR bundles.

Constructor Summary

Constructors

Constructor and Description
Bundles()

Method Summary

Modifier and Type	Method and Description
static <T extends org.hl7.fhir.instance.model.api.IBaseResource> org.apache.spark.sql.Dataset<T>	extractEntry(org.apache.spark.sql.SparkSession spark, org.apache.spark.api.java.JavaRDD<org.hl7.fhir.dstu3.model.Bundle> bundles, Class<T> resourceClass) Extracts the given resource type from the RDD of bundles and returns it as a Dataset of that type.
static <T extends org.hl7.fhir.instance.model.api.IBaseResource> org.apache.spark.sql.Dataset<T>	extractEntry(org.apache.spark.sql.SparkSession spark, org.apache.spark.api.java.JavaRDD<org.hl7.fhir.dstu3.model.Bundle> bundles, String resourceName) Extracts the given resource type from the RDD of bundles and returns it as a Dataset of that type.
static <T extends org.hl7.fhir.instance.model.api.IBaseResource> org.apache.spark.sql.Dataset<T>	extractEntry(org.apache.spark.sql.SparkSession spark, org.apache.spark.api.java.JavaRDD<org.hl7.fhir.dstu3.model.Bundle> bundles, String resourceName, FhirEncoders encoders) Extracts the given resource type from the RDD of bundles and returns it as a Dataset of that type.
static org.apache.spark.api.java.JavaRDD<org.hl7.fhir.dstu3.model.Bundle>	loadFromDirectory(org.apache.spark.sql.SparkSession spark, String path, int minPartitions) Returns an RDD of bundles loaded from the given path.
static void	saveAsDatabase(org.apache.spark.sql.SparkSession spark, org.apache.spark.api.java.JavaRDD<org.hl7.fhir.dstu3.model.Bundle> bundles, String database, String... resourceNames) Saves an RDD of bundles as a database, where each table has the resource name.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Bundles

public Bundles()

Method Detail

loadFromDirectory

public static org.apache.spark.api.java.JavaRDD<org.hl7.fhir.dstu3.model.Bundle> loadFromDirectory(org.apache.spark.sql.SparkSession spark,
                                                                                                   String path,
                                                                                                   int minPartitions)

Returns an RDD of bundles loaded from the given path.

Parameters:

spark - the spark session

path - a path to a directory of FHIR Bundles

minPartitions - a suggested value for the minimal number of partitions

Returns:

an RDD of FHIR Bundles

extractEntry

public static <T extends org.hl7.fhir.instance.model.api.IBaseResource> org.apache.spark.sql.Dataset<T> extractEntry(org.apache.spark.sql.SparkSession spark,
                                                                                                                     org.apache.spark.api.java.JavaRDD<org.hl7.fhir.dstu3.model.Bundle> bundles,
                                                                                                                     Class<T> resourceClass)

Extracts the given resource type from the RDD of bundles and returns it as a Dataset of that type.

Type Parameters:

T - the type of the resource being extracted from the bundles.

Parameters:

spark - the spark session

bundles - an RDD of FHIR Bundles

resourceClass - the type of resource to extract.

Returns:

a dataset of the given resource

extractEntry

public static <T extends org.hl7.fhir.instance.model.api.IBaseResource> org.apache.spark.sql.Dataset<T> extractEntry(org.apache.spark.sql.SparkSession spark,
                                                                                                                     org.apache.spark.api.java.JavaRDD<org.hl7.fhir.dstu3.model.Bundle> bundles,
                                                                                                                     String resourceName)

Extracts the given resource type from the RDD of bundles and returns it as a Dataset of that type.

Type Parameters:

T - the type of the resource being extracted from the bundles.

Parameters:

spark - the spark session

bundles - an RDD of FHIR Bundles

resourceName - the FHIR name of the resource type to extract (e.g., condition, patient, etc).

Returns:

a dataset of the given resource

extractEntry

public static <T extends org.hl7.fhir.instance.model.api.IBaseResource> org.apache.spark.sql.Dataset<T> extractEntry(org.apache.spark.sql.SparkSession spark,
                                                                                                                     org.apache.spark.api.java.JavaRDD<org.hl7.fhir.dstu3.model.Bundle> bundles,
                                                                                                                     String resourceName,
                                                                                                                     FhirEncoders encoders)

Extracts the given resource type from the RDD of bundles and returns it as a Dataset of that type.

Type Parameters:

T - the type of the resource being extracted from the bundles.

Parameters:

spark - the spark session

bundles - an RDD of FHIR Bundles

resourceName - the FHIR name of the resource type to extract (e.g., condition, patient. etc).

encoders - the Encoders instance defining how the resources are encoded.

Returns:

a dataset of the given resource

saveAsDatabase

public static void saveAsDatabase(org.apache.spark.sql.SparkSession spark,
                                  org.apache.spark.api.java.JavaRDD<org.hl7.fhir.dstu3.model.Bundle> bundles,
                                  String database,
                                  String... resourceNames)

Saves an RDD of bundles as a database, where each table has the resource name. This offers a simple way to load and query bundles in a system, although users with more sophisticated ETL operations may want to explicitly write different entities.

Note this will access the given RDD of bundles once per resource name, so consumers with enough memory should consider calling JavaRDD.cache() so that RDD is not recomputed for each.

Parameters:

spark - the spark session

bundles - an RDD of FHIR Bundles

database - the name of the database to write to

resourceNames - names of resources to be extracted from the bundle and written