org.apache.beam.sdk.io.gcp.healthcare

Class FhirIO

java.lang.Object

org.apache.beam.sdk.io.gcp.healthcare.FhirIO

public class FhirIO
extends java.lang.Object

FhirIO provides an API for reading and writing resources to Google Cloud Healthcare Fhir API.

Reading

FHIR resources can be read with FhirIO.Read, which supports use cases where you have a $PCollection of message IDs. This is appropriate for reading the Fhir notifications from a Pub/Sub subscription with PubsubIO.readStrings() or in cases where you have a manually prepared list of messages that you need to process (e.g. in a text file read with TextIO*) .

Fetch Resource contents from Fhir Store based on the PCollection of message ID strings FhirIO.Read.Result where one can call FhirIO.Read.Result.getResources() to retrieve a PCollection containing the successfully fetched Strings and/or FhirIO.Read.Result.getFailedReads()* to retrieve a PCollection of HealthcareIOError* containing the resource ID that could not be fetched and the exception as a HealthcareIOError, this can be used to write to the dead letter storage system of your choosing. This error handling is mainly to transparently surface errors where the upstream PCollection* contains IDs that are not valid or are not reachable due to permissions issues.

Writing

Write Resources can be written to FHIR with two different methods: Import or Execute Bundle.

Execute Bundle This is best for use cases where you are writing to a non-empty FHIR store with other clients or otherwise need referential integrity (e.g. A Streaming HL7v2 to FHIR ETL pipeline).

Import This is best for use cases where you are populating an empty FHIR store with no other clients. It is faster than the execute bundles method but does not respect referential integrity and the resources are not written transactionally (e.g. a historicaly backfill on a new FHIR store) This requires each resource to contain a client provided ID. It is important that when using import you give the appropriate permissions to the Google Cloud Healthcare Service Agent.

See Also:

https://cloud.google.com/healthcare/docs/reference/rest/v1beta1/projects.locations.datasets.fhirStores.fhir/executeBundle>, https://cloud.google.com/healthcare/docs/how-tos/permissions-healthcare-api-gcp-products#fhir_store_cloud_storage_permissions>, https://cloud.google.com/healthcare/docs/reference/rest/v1beta1/projects.locations.datasets.fhirStores/import> A {@link PCollection} of {@link String} can be ingested into an Fhir store using {@link FhirIO.Write#fhirStoresImport(String, String, String, FhirIO.Import.ContentStructure)} This will return a {@link FhirIO.Write.Result} on which you can call {@link FhirIO.Write.Result#getFailedBodies()} to retrieve a {@link PCollection} of {@link HealthcareIOError} containing the {@link String} that failed to be ingested and the exception.

Example

{@code
 Pipeline pipeline = ...

 // Tail the FHIR store by retrieving resources based on Pub/Sub notifications.
 FhirIO.Read.Result readResult = p
   .apply("Read FHIR notifications",
     PubsubIO.readStrings().fromSubscription(options.getNotificationSubscription()))
   .apply(FhirIO.readResources());

 // happily retrived messages
 PCollection resources = readResult.getResources();
 // message IDs that couldn't be retrieved + error context
 PCollection> failedReads = readResult.getFailedReads();

 failedReads.apply("Write Message IDs / Stacktrace for Failed Reads to BigQuery",
     BigQueryIO
         .write()
         .to(option.getBQFhirExecuteBundlesDeadLetterTable())
         .withFormatFunction(new HealthcareIOErrorToTableRow()));

 output = resources.apply("Happy path transformations", ...);
 FhirIO.Write.Result writeResult =
     output.apply("Execute FHIR Bundles", FhirIO.executeBundles(options.getExistingFhirStore()));

 PCollection> failedBundles = writeResult.getFailedInsertsWithErr();

 failedBundles.apply("Write failed bundles to BigQuery",
     BigQueryIO
         .write()
         .to(option.getBQFhirExecuteBundlesDeadLetterTable())
         .withFormatFunction(new HealthcareIOErrorToTableRow()));

 // Alternatively you could use import for high throughput to a new store.
 FhirIO.Write.Result writeResult =
     output.apply("Import FHIR Resources", FhirIO.executeBundles(options.getNewFhirStore()));
 }***
 

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	FhirIO.ExecuteBundles The type Execute bundles.
static class	FhirIO.Import Writes each bundle of elements to a new-line delimited JSON file on GCS and issues a fhirStores.import Request for that file.
static class	FhirIO.Read The type Read.
static class	FhirIO.Write The type Write.

Constructor Summary

Constructors

Constructor and Description
FhirIO()

Method Summary

Modifier and Type	Method and Description
static FhirIO.Import	importResources(java.lang.String fhirStore, java.lang.String tempDir, java.lang.String deadLetterDir, FhirIO.Import.ContentStructure contentStructure) Import resources.
static FhirIO.Import	importResources(ValueProvider<java.lang.String> fhirStore, ValueProvider<java.lang.String> tempDir, ValueProvider<java.lang.String> deadLetterDir, FhirIO.Import.ContentStructure contentStructure) Import resources.
static FhirIO.Read	readResources() Read resources from a PCollection of resource IDs (e.g.

Methods inherited from class java.lang.Object

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

Constructor Detail

FhirIO

public FhirIO()

Method Detail

readResources

public static FhirIO.Read readResources()

Read resources from a PCollection of resource IDs (e.g. when subscribing the pubsub notifications)

Returns:

the read

See Also:

FhirIO.Read

importResources

public static FhirIO.Import importResources(java.lang.String fhirStore,
                                            java.lang.String tempDir,
                                            java.lang.String deadLetterDir,
                                            @Nullable
                                            FhirIO.Import.ContentStructure contentStructure)

Import resources. Intended for use on empty FHIR stores

Parameters:

fhirStore - the fhir store

tempDir - the temp dir

deadLetterDir - the dead letter dir

contentStructure - the content structure

Returns:

the import

See Also:

FhirIO.Import

importResources

public static FhirIO.Import importResources(ValueProvider<java.lang.String> fhirStore,
                                            ValueProvider<java.lang.String> tempDir,
                                            ValueProvider<java.lang.String> deadLetterDir,
                                            @Nullable
                                            FhirIO.Import.ContentStructure contentStructure)

Import resources. Intended for use on empty FHIR stores

Parameters:

fhirStore - the fhir store

tempDir - the temp dir

deadLetterDir - the dead letter dir

contentStructure - the content structure

Returns:

the import

See Also:

FhirIO.Import