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 FHIR resource names in the format of projects/{p}/locations/{l}/datasets/{d}/fhirStores/{f}/fhir/{resourceType}/{id}. 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 resources that you need to process (e.g. in a text file read with TextIO*) .

Get Resource contents from the FHIR Store based on the PCollection of FHIR resource name strings FhirIO.Read.Result where one can call FhirIO.Read.Result.getResources() to retrieve a PCollection containing the successfully fetched json resources as Strings and/or FhirIO.Read.Result.getFailedReads() to retrieve a PCollection of HealthcareIOError containing the resources 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 FHIR resources that are not valid or are not reachable due to permissions issues. Additionally, you can query an entire FHIR Patient resource's compartment (resources that refer to the patient, and are referred to by the patient) by calling FhirIO.getPatientEverything to execute a FHIR GetPatientEverythingRequest.

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 historical 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.

Export This is to export FHIR resources from a FHIR store to Google Cloud Storage or BigQuery. The output resources are in ndjson (newline delimited json) of FHIR resources. It is important that when using export you give the appropriate permissions to the Google Cloud Healthcare Service Agent.

Deidentify This is to de-identify FHIR resources from a source FHIR store and write the result to a destination FHIR store. It is important that the destination store must already exist.

Search This is to search FHIR resources within a given FHIR store. The inputs are individual FHIR Search queries, represented by the FhirSearchParameter class. The outputs are results of each Search, represented as a Json array of FHIR resources in string form, with pagination handled, and an optional input key.

See Also:

https://cloud.google.com/healthcare/docs/reference/rest/v1/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/v1/projects.locations.datasets.fhirStores/import>, https://cloud.google.com/healthcare/docs/reference/rest/v1/projects.locations.datasets.fhirStores/export>, https://cloud.google.com/healthcare/docs/reference/rest/v1/projects.locations.datasets.fhirStores/deidentify>, https://cloud.google.com/healthcare/docs/reference/rest/v1/projects.locations.datasets.fhirStores/search> 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 resources
 PCollection resources = readResult.getResources();
 // resource paths that couldn't be retrieved + error context
 PCollection> failedReads = readResult.getFailedReads();

 failedReads.apply("Write Resources / 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()));

 // Export FHIR resources to Google Cloud Storage or BigQuery.
 String fhirStoreName = ...;
 String exportUri = ...; // "gs://..." or "bq://..."
 PCollection resources =
     pipeline.apply(FhirIO.exportResources(fhirStoreName, exportUri));

 // De-identify FHIR resources.
 String sourceFhirStoreName = ...;
 String destinationFhirStoreName = ...;
 DeidentifyConfig deidConfig = new DeidentifyConfig(); // use default DeidentifyConfig
 pipeline.apply(FhirIO.deidentify(fhirStoreName, destinationFhirStoreName, deidConfig));

 // Search FHIR resources using an "OR" query.
 Map queries = new HashMap<>();
 queries.put("name", "Alice,Bob");
 FhirSearchParameter searchParameter = FhirSearchParameter.of("Patient", queries);
 PCollection> searchQueries =
 pipeline.apply(
      Create.of(searchParameter)
            .withCoder(FhirSearchParameterCoder.of(StringUtf8Coder.of())));
 FhirIO.Search.Result searchResult =
      searchQueries.apply(FhirIO.searchResources(options.getFhirStore()));
 PCollection resources = searchResult.getResources(); // JsonArray of results

 // Search FHIR resources using an "AND" query with a key.
 Map> listQueries = new HashMap<>();
 listQueries.put("name", Arrays.asList("Alice", "Bob"));
 FhirSearchParameter> listSearchParameter =
      FhirSearchParameter.of("Patient", "Alice-Bob-Search", listQueries);
 PCollection>> listSearchQueries =
 pipeline.apply(
      Create.of(listSearchParameter)
            .withCoder(FhirSearchParameterCoder.of(ListCoder.of(StringUtf8Coder.of()))));
 FhirIO.Search.Result listSearchResult =
      searchQueries.apply(FhirIO.searchResources(options.getFhirStore()));
 PCollection> listResource =
      listSearchResult.getKeyedResources(); // KV<"Alice-Bob-Search", JsonArray of results>

 

Updates to the I/O connector code

For any significant updates to this I/O connector, please consider involving corresponding code reviewers mentioned here.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	FhirIO.Deidentify Deidentify FHIR resources from a FHIR store to a destination FHIR store.
static class	FhirIO.ExecuteBundles The type Execute bundles.
static class	FhirIO.ExecuteBundlesResult ExecuteBundlesResult contains both successfully executed bundles and information help debugging failed executions (eg metadata & error msgs).
static class	FhirIO.Export Export FHIR resources from a FHIR store to new line delimited json files on GCS or BigQuery.
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.Search<T> The type Search.
static class	FhirIO.Write The type Write.

Constructor Summary

Constructors

Constructor and Description
FhirIO()

Method Summary

Modifier and Type	Method and Description
static FhirIO.Deidentify	deidentify(java.lang.String sourceFhirStore, java.lang.String destinationFhirStore, com.google.api.services.healthcare.v1.model.DeidentifyConfig deidConfig) Deidentify FHIR resources.
static FhirIO.Deidentify	deidentify(ValueProvider<java.lang.String> sourceFhirStore, ValueProvider<java.lang.String> destinationFhirStore, ValueProvider<com.google.api.services.healthcare.v1.model.DeidentifyConfig> deidConfig) Deidentify FHIR resources.
static FhirIO.Export	exportResources(java.lang.String fhirStore, java.lang.String exportUri) Export resources to GCS.
static FhirIO.Export	exportResources(ValueProvider<java.lang.String> fhirStore, ValueProvider<java.lang.String> exportUri)
static FhirIOPatientEverything	getPatientEverything() Get the patient compartment for a FHIR Patient using the GetPatientEverything/$everything API.
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.
static FhirIO.Search<java.lang.String>	searchResources(java.lang.String fhirStore) Search resources from a Fhir store with String parameter values.
static FhirIO.Search<?>	searchResourcesWithGenericParameters(java.lang.String fhirStore) Search resources from a Fhir store with any type of parameter values.

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

searchResources

public static FhirIO.Search<java.lang.String> searchResources(java.lang.String fhirStore)

Search resources from a Fhir store with String parameter values.

Returns:

the search

See Also:

FhirIO.Search

searchResourcesWithGenericParameters

public static FhirIO.Search<?> searchResourcesWithGenericParameters(java.lang.String fhirStore)

Search resources from a Fhir store with any type of parameter values.

Returns:

the search

See Also:

FhirIO.Search

importResources

public static FhirIO.Import importResources(java.lang.String fhirStore,
                                            java.lang.String tempDir,
                                            java.lang.String deadLetterDir,
                                            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,
                                            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

exportResources

public static FhirIO.Export exportResources(java.lang.String fhirStore,
                                            java.lang.String exportUri)

Export resources to GCS. Intended for use on non-empty FHIR stores

Parameters:

fhirStore - the fhir store, in the format: projects/project_id/locations/location_id/datasets/dataset_id/fhirStores/fhir_store_id

exportUri - the destination GCS dir or BigQuery dataset, in the format: gs://YOUR_BUCKET_NAME/path/to/a/dir | bq://PROJECT_ID.BIGQUERY_DATASET_ID

Returns:

the export

See Also:

FhirIO.Export

exportResources

public static FhirIO.Export exportResources(ValueProvider<java.lang.String> fhirStore,
                                            ValueProvider<java.lang.String> exportUri)

See Also:

exportResources(String, String)

deidentify

public static FhirIO.Deidentify deidentify(java.lang.String sourceFhirStore,
                                           java.lang.String destinationFhirStore,
                                           com.google.api.services.healthcare.v1.model.DeidentifyConfig deidConfig)

Deidentify FHIR resources. Intended for use on non-empty FHIR stores

Parameters:

sourceFhirStore - the source fhir store, in the format: projects/project_id/locations/location_id/datasets/dataset_id/fhirStores/fhir_store_id

destinationFhirStore - the destination fhir store to write de-identified resources, in the format: projects/project_id/locations/location_id/datasets/dataset_id/fhirStores/fhir_store_id

deidConfig - the DeidentifyConfig

Returns:

the deidentify

See Also:

FhirIO.Deidentify

deidentify

public static FhirIO.Deidentify deidentify(ValueProvider<java.lang.String> sourceFhirStore,
                                           ValueProvider<java.lang.String> destinationFhirStore,
                                           ValueProvider<com.google.api.services.healthcare.v1.model.DeidentifyConfig> deidConfig)

Deidentify FHIR resources. Intended for use on non-empty FHIR stores

Parameters:

sourceFhirStore - the source fhir store, in the format: projects/project_id/locations/location_id/datasets/dataset_id/fhirStores/fhir_store_id

destinationFhirStore - the destination fhir store to write de-identified resources, in the format: projects/project_id/locations/location_id/datasets/dataset_id/fhirStores/fhir_store_id

deidConfig - the DeidentifyConfig

Returns:

the deidentify

See Also:

FhirIO.Deidentify

getPatientEverything

public static FhirIOPatientEverything getPatientEverything()

Get the patient compartment for a FHIR Patient using the GetPatientEverything/$everything API.

Returns:

the patient everything

See Also:

, FhirIOPatientEverything