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

Class HttpHealthcareApiClient

java.lang.Object

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

All Implemented Interfaces:

java.io.Serializable, HealthcareApiClient

public class HttpHealthcareApiClient
extends java.lang.Object
implements HealthcareApiClient, java.io.Serializable

A client that talks to the Cloud Healthcare API through HTTP requests. This client is created mainly to encapsulate the unserializable dependencies, since most generated classes are not serializable in the HTTP client.

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	HttpHealthcareApiClient.AuthenticatedRetryInitializer
static class	HttpHealthcareApiClient.FhirResourcePagesIterator The type FhirResourcePagesIterator for methods which return paged output.
static class	HttpHealthcareApiClient.HealthcareHttpException Wraps HttpResponse in an exception with a statusCode field for use with HealthcareIOError.
static class	HttpHealthcareApiClient.HL7v2MessagePages

Constructor Summary

Constructors

Constructor and Description
HttpHealthcareApiClient() Instantiates a new Http healthcare api client.
HttpHealthcareApiClient(CloudHealthcare client) Instantiates a new Http healthcare api client.

Method Summary

Modifier and Type	Method and Description
DicomStore	createDicomStore(java.lang.String dataset, java.lang.String name) Create a DicomStore.
DicomStore	createDicomStore(java.lang.String dataset, java.lang.String name, @Nullable java.lang.String pubsubTopic) Create a DicomStore with a PubSub listener.
FhirStore	createFhirStore(java.lang.String dataset, java.lang.String name, java.lang.String version) Create FHIR Store.
FhirStore	createFhirStore(java.lang.String dataset, java.lang.String name, java.lang.String version, @Nullable java.lang.String pubsubTopic) Create FHIR Store with a PubSub topic listener.
Message	createHL7v2Message(java.lang.String hl7v2Store, Message msg) Creates an HL7v2 message.
Hl7V2Store	createHL7v2Store(java.lang.String dataset, java.lang.String name) Create hl 7 v 2 store hl 7 v 2 store.
Operation	deidentifyFhirStore(java.lang.String sourcefhirStore, java.lang.String destinationFhirStore, DeidentifyConfig deidConfig) Deidentify a GCP FHIR Store and write the result into a new FHIR Store.
Empty	deleteDicomStore(java.lang.String name) Delete a Dicom Store.
Empty	deleteFhirStore(java.lang.String name) Delete Fhir store.
Empty	deleteHL7v2Message(java.lang.String msgName) Deletes an HL7v2 message.
Empty	deleteHL7v2Store(java.lang.String name) Deletes an HL7v2 store.
HttpBody	executeFhirBundle(java.lang.String fhirStore, java.lang.String bundle) Execute fhir bundle http body.
Operation	exportFhirResourceToBigQuery(java.lang.String fhirStore, java.lang.String bigQueryDatasetUri) Export a FHIR Resource to BigQuery.
Operation	exportFhirResourceToGcs(java.lang.String fhirStore, java.lang.String gcsDestinationPrefix) Export a FHIR Resource to GCS.
Instant	getEarliestHL7v2SendTime(java.lang.String hl7v2Store, @Nullable java.lang.String filter) Gets the earliest HL7v2 send time.
Message	getHL7v2Message(java.lang.String msgName) Gets HL7v2 message.
Hl7V2Store	getHL7v2Store(java.lang.String storeName) Gets HL7v2 store.
com.google.api.client.json.JsonFactory	getJsonFactory()
Instant	getLatestHL7v2SendTime(java.lang.String hl7v2Store, @Nullable java.lang.String filter) Gets the latest HL7v2 send time.
HttpBody	getPatientEverything(java.lang.String resourceName, @Nullable java.util.Map<java.lang.String,java.lang.Object> filters, java.lang.String pageToken) Fhir get patient everything http body.
Operation	importFhirResource(java.lang.String fhirStore, java.lang.String gcsSourcePath, @Nullable java.lang.String contentStructure) Importing a FHIR resource from GCS.
IngestMessageResponse	ingestHL7v2Message(java.lang.String hl7v2Store, Message msg) Ingest an HL7v2 message.
java.util.List<FhirStore>	listAllFhirStores(java.lang.String dataset) List all FHIR stores in a dataset.
ListMessagesResponse	makeHL7v2ListRequest(java.lang.String hl7v2Store, @Nullable java.lang.String filter, @Nullable java.lang.String orderBy, @Nullable java.lang.String pageToken) Make hl 7 v 2 list request list messages response.
ListMessagesResponse	makeSendTimeBoundHL7v2ListRequest(java.lang.String hl7v2Store, Instant start, @Nullable Instant end, @Nullable java.lang.String otherFilter, @Nullable java.lang.String orderBy, @Nullable java.lang.String pageToken) Time Bound HL7v2 list request.
Operation	pollOperation(Operation operation, java.lang.Long sleepMs) Poll operation.
HttpBody	readFhirResource(java.lang.String resourceName) Read fhir resource http body.
java.lang.String	retrieveDicomStudyMetadata(java.lang.String dicomWebPath) Retrieve DicomStudyMetadata.
HttpBody	searchFhirResource(java.lang.String fhirStore, java.lang.String resourceType, @Nullable java.util.Map<java.lang.String,java.lang.Object> parameters, java.lang.String pageToken) Search fhir resource http body.
Empty	uploadToDicomStore(java.lang.String webPath, java.lang.String filePath) Upload to a Dicom Store.

Methods inherited from class java.lang.Object

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

Constructor Detail

HttpHealthcareApiClient

public HttpHealthcareApiClient()
                        throws java.io.IOException

Instantiates a new Http healthcare api client.

Throws:

java.io.IOException - the io exception

HttpHealthcareApiClient

public HttpHealthcareApiClient(CloudHealthcare client)
                        throws java.io.IOException

Instantiates a new Http healthcare api client.

Parameters:

client - the client

Throws:

java.io.IOException - the io exception

Method Detail

getJsonFactory

public com.google.api.client.json.JsonFactory getJsonFactory()

createHL7v2Store

public Hl7V2Store createHL7v2Store(java.lang.String dataset,
                                   java.lang.String name)
                            throws java.io.IOException

Description copied from interface: HealthcareApiClient

Create hl 7 v 2 store hl 7 v 2 store.

Specified by:

createHL7v2Store in interface HealthcareApiClient

Parameters:

dataset - The dataset to create the HL7v2 store in.

name - The name of the store to be created.

Returns:

Empty.

Throws:

java.io.IOException - The IO Exception.

createFhirStore

public FhirStore createFhirStore(java.lang.String dataset,
                                 java.lang.String name,
                                 java.lang.String version)
                          throws java.io.IOException

Description copied from interface: HealthcareApiClient

Create FHIR Store.

Specified by:

createFhirStore in interface HealthcareApiClient

Parameters:

dataset - The name of the Dataset for the FHIR store to be created in.

name - The name of the FHIR store.

version - The version of the FHIR store (DSTU2, STU3, R4).

Throws:

java.io.IOException - The IO Exception.

createFhirStore

public FhirStore createFhirStore(java.lang.String dataset,
                                 java.lang.String name,
                                 java.lang.String version,
                                 @Nullable java.lang.String pubsubTopic)
                          throws java.io.IOException

Description copied from interface: HealthcareApiClient

Create FHIR Store with a PubSub topic listener.

Specified by:

createFhirStore in interface HealthcareApiClient

Parameters:

dataset - The name of Dataset for the FHIR store to be created in.

name - The name of the FHIR store.

version - The version of the FHIR store (DSTU2, STU3, R4).

pubsubTopic - The pubsub topic listening to the FHIR store.

Throws:

java.io.IOException - The IO Exception.

listAllFhirStores

public java.util.List<FhirStore> listAllFhirStores(java.lang.String dataset)
                                            throws java.io.IOException

Description copied from interface: HealthcareApiClient

List all FHIR stores in a dataset.

Specified by:

listAllFhirStores in interface HealthcareApiClient

Parameters:

dataset - The dataset, in the format: projects/project_id/locations/location_id/datasets/dataset_id

Returns:

A list of all FHIR stores in the dataset.

Throws:

java.io.IOException - The IO Exception.

deleteHL7v2Store

public Empty deleteHL7v2Store(java.lang.String name)
                       throws java.io.IOException

Description copied from interface: HealthcareApiClient

Deletes an HL7v2 store.

Specified by:

deleteHL7v2Store in interface HealthcareApiClient

Parameters:

name - The HL7v2 store to be deleted.

Returns:

Empty.

Throws:

java.io.IOException - The IO Exception.

deleteFhirStore

public Empty deleteFhirStore(java.lang.String name)
                      throws java.io.IOException

Description copied from interface: HealthcareApiClient

Delete Fhir store.

Specified by:

deleteFhirStore in interface HealthcareApiClient

Parameters:

name - The FHIR store to be deleted.

Returns:

Empty.

Throws:

java.io.IOException - The IO Exception.

retrieveDicomStudyMetadata

public java.lang.String retrieveDicomStudyMetadata(java.lang.String dicomWebPath)
                                            throws java.io.IOException

Description copied from interface: HealthcareApiClient

Retrieve DicomStudyMetadata.

Specified by:

retrieveDicomStudyMetadata in interface HealthcareApiClient

Parameters:

dicomWebPath - The Dicom Web Path to retrieve the metadata from.

Returns:

The study metadata.

Throws:

java.io.IOException - The IO Exception.

createDicomStore

public DicomStore createDicomStore(java.lang.String dataset,
                                   java.lang.String name)
                            throws java.io.IOException

Description copied from interface: HealthcareApiClient

Create a DicomStore.

Specified by:

createDicomStore in interface HealthcareApiClient

Parameters:

dataset - The dataset that the Dicom Store should be in, in the format: projects/project_id/locations/location_id/datasets/dataset_id.

name - The name of the Dicom Store to be created.

Returns:

Empty.

Throws:

java.io.IOException - The IO Exception.

deleteDicomStore

public Empty deleteDicomStore(java.lang.String name)
                       throws java.io.IOException

Description copied from interface: HealthcareApiClient

Delete a Dicom Store.

Specified by:

deleteDicomStore in interface HealthcareApiClient

Parameters:

name - The name of the Dicom Store to be deleted.

Returns:

Empty.

Throws:

java.io.IOException - The IO Exception.

uploadToDicomStore

public Empty uploadToDicomStore(java.lang.String webPath,
                                java.lang.String filePath)
                         throws java.io.IOException,
                                java.net.URISyntaxException

Description copied from interface: HealthcareApiClient

Upload to a Dicom Store.

Specified by:

uploadToDicomStore in interface HealthcareApiClient

Parameters:

webPath - String format of webPath to upload into.

filePath - filePath of file to upload.

Returns:

Empty.

Throws:

java.io.IOException - The IO Exception.

java.net.URISyntaxException

createDicomStore

public DicomStore createDicomStore(java.lang.String dataset,
                                   java.lang.String name,
                                   @Nullable java.lang.String pubsubTopic)
                            throws java.io.IOException

Description copied from interface: HealthcareApiClient

Create a DicomStore with a PubSub listener.

Specified by:

createDicomStore in interface HealthcareApiClient

Parameters:

dataset - The dataset that the Dicom Store should be in, in the format: projects/project_id/locations/location_id/datasets/dataset_id

name - The name of the Dicom Store to be created.

pubsubTopic - Name of PubSub topic connected with the Dicom store.

Returns:

Empty.

Throws:

java.io.IOException - The IO Exception.

getEarliestHL7v2SendTime

public Instant getEarliestHL7v2SendTime(java.lang.String hl7v2Store,
                                        @Nullable java.lang.String filter)
                                 throws java.io.IOException

Description copied from interface: HealthcareApiClient

Gets the earliest HL7v2 send time.

Specified by:

getEarliestHL7v2SendTime in interface HealthcareApiClient

Parameters:

hl7v2Store - The HL7v2 store.

filter - the filter to be matched on.

Returns:

The earliest HL7v2 send time.

Throws:

java.io.IOException - The IO Exception.

getLatestHL7v2SendTime

public Instant getLatestHL7v2SendTime(java.lang.String hl7v2Store,
                                      @Nullable java.lang.String filter)
                               throws java.io.IOException

Description copied from interface: HealthcareApiClient

Gets the latest HL7v2 send time.

Specified by:

getLatestHL7v2SendTime in interface HealthcareApiClient

Parameters:

hl7v2Store - The HL7v2 store.

filter - The filter to be matched on.

Returns:

The latest HL7v2 send time.

Throws:

java.io.IOException - The IO Exception.

makeSendTimeBoundHL7v2ListRequest

public ListMessagesResponse makeSendTimeBoundHL7v2ListRequest(java.lang.String hl7v2Store,
                                                              Instant start,
                                                              @Nullable Instant end,
                                                              @Nullable java.lang.String otherFilter,
                                                              @Nullable java.lang.String orderBy,
                                                              @Nullable java.lang.String pageToken)
                                                       throws java.io.IOException

Description copied from interface: HealthcareApiClient

Time Bound HL7v2 list request.

Specified by:

makeSendTimeBoundHL7v2ListRequest in interface HealthcareApiClient

Parameters:

hl7v2Store - The HL7v2 store.

start - Start time.

end - End time.

otherFilter - The filter outside of the sendTime.

orderBy - Order by.

pageToken - The page token.

Returns:

HTTP List response.

Throws:

java.io.IOException - The IO Exception.

makeHL7v2ListRequest

public ListMessagesResponse makeHL7v2ListRequest(java.lang.String hl7v2Store,
                                                 @Nullable java.lang.String filter,
                                                 @Nullable java.lang.String orderBy,
                                                 @Nullable java.lang.String pageToken)
                                          throws java.io.IOException

Description copied from interface: HealthcareApiClient

Make hl 7 v 2 list request list messages response.

Specified by:

makeHL7v2ListRequest in interface HealthcareApiClient

Parameters:

hl7v2Store - The HL7v2 Store.

filter - The Filter.

orderBy - Order by.

pageToken - The Page Token.

Returns:

HTTP List response.

Throws:

java.io.IOException - The IO Exception.

getHL7v2Message

public Message getHL7v2Message(java.lang.String msgName)
                        throws java.io.IOException

Gets HL7v2 message.

Specified by:

getHL7v2Message in interface HealthcareApiClient

Parameters:

msgName - the msg name

Returns:

the message

Throws:

java.io.IOException - the io exception

java.text.ParseException - the parse exception

deleteHL7v2Message

public Empty deleteHL7v2Message(java.lang.String msgName)
                         throws java.io.IOException

Description copied from interface: HealthcareApiClient

Deletes an HL7v2 message.

Specified by:

deleteHL7v2Message in interface HealthcareApiClient

Parameters:

msgName - The message name to be deleted.

Returns:

Empty.

Throws:

java.io.IOException - The IO Exception.

getHL7v2Store

public Hl7V2Store getHL7v2Store(java.lang.String storeName)
                         throws java.io.IOException

Gets HL7v2 store.

Specified by:

getHL7v2Store in interface HealthcareApiClient

Parameters:

storeName - the store name

Returns:

the HL7v2 store

Throws:

java.io.IOException - the io exception

ingestHL7v2Message

public IngestMessageResponse ingestHL7v2Message(java.lang.String hl7v2Store,
                                                Message msg)
                                         throws java.io.IOException

Description copied from interface: HealthcareApiClient

Ingest an HL7v2 message.

Specified by:

ingestHL7v2Message in interface HealthcareApiClient

Parameters:

hl7v2Store - The HL7v2 store of the message.

msg - The message.

Returns:

Empty.

Throws:

java.io.IOException - The IO Exception.

createHL7v2Message

public Message createHL7v2Message(java.lang.String hl7v2Store,
                                  Message msg)
                           throws java.io.IOException

Description copied from interface: HealthcareApiClient

Creates an HL7v2 message.

Specified by:

createHL7v2Message in interface HealthcareApiClient

Parameters:

hl7v2Store - The HL7v2 store to create a message in.

msg - The message to create.

Returns:

Empty.

Throws:

java.io.IOException - The IO Exception.

importFhirResource

public Operation importFhirResource(java.lang.String fhirStore,
                                    java.lang.String gcsSourcePath,
                                    @Nullable java.lang.String contentStructure)
                             throws java.io.IOException

Description copied from interface: HealthcareApiClient

Importing a FHIR resource from GCS.

Specified by:

importFhirResource in interface HealthcareApiClient

Parameters:

fhirStore - the FhirStore to import into.

gcsSourcePath - the GCS Path of resource.

contentStructure - The content structure.

Returns:

Empty.

Throws:

java.io.IOException - the io exception

exportFhirResourceToGcs

public Operation exportFhirResourceToGcs(java.lang.String fhirStore,
                                         java.lang.String gcsDestinationPrefix)
                                  throws java.io.IOException

Description copied from interface: HealthcareApiClient

Export a FHIR Resource to GCS.

Specified by:

exportFhirResourceToGcs in interface HealthcareApiClient

Parameters:

fhirStore - the FhirStore of the resource.

gcsDestinationPrefix - GCS Destination Prefix to export to.

Returns:

Empty.

Throws:

java.io.IOException - The IO Exception.

exportFhirResourceToBigQuery

public Operation exportFhirResourceToBigQuery(java.lang.String fhirStore,
                                              java.lang.String bigQueryDatasetUri)
                                       throws java.io.IOException

Description copied from interface: HealthcareApiClient

Export a FHIR Resource to BigQuery.

Specified by:

exportFhirResourceToBigQuery in interface HealthcareApiClient

Parameters:

fhirStore - the FhirStore of the resource.

bigQueryDatasetUri - The BQ Dataset URI to export to.

Returns:

Empty.

Throws:

java.io.IOException - The IO Exception.

deidentifyFhirStore

public Operation deidentifyFhirStore(java.lang.String sourcefhirStore,
                                     java.lang.String destinationFhirStore,
                                     DeidentifyConfig deidConfig)
                              throws java.io.IOException

Description copied from interface: HealthcareApiClient

Deidentify a GCP FHIR Store and write the result into a new FHIR Store.

Specified by:

deidentifyFhirStore in interface HealthcareApiClient

Parameters:

sourcefhirStore - the FhirStore to be deidentified.

destinationFhirStore - the FhirStore that the deidentified data will be written to.

deidConfig - the deidCongig specifying form of deidentification.

Returns:

Empty.

Throws:

java.io.IOException - The IO Exception.

pollOperation

public Operation pollOperation(Operation operation,
                               java.lang.Long sleepMs)
                        throws java.lang.InterruptedException,
                               java.io.IOException

Description copied from interface: HealthcareApiClient

Poll operation.

Specified by:

pollOperation in interface HealthcareApiClient

Parameters:

operation - to be polled.

sleepMs - length of time to wait between requests.

Returns:

HTTP Request (that returns status of operation).

Throws:

java.io.IOException - The IO Exception.

java.lang.InterruptedException

executeFhirBundle

public HttpBody executeFhirBundle(java.lang.String fhirStore,
                                  java.lang.String bundle)
                           throws java.io.IOException

Description copied from interface: HealthcareApiClient

Execute fhir bundle http body.

Specified by:

executeFhirBundle in interface HealthcareApiClient

Parameters:

fhirStore - the fhir store

bundle - the bundle

Returns:

the http body

Throws:

java.io.IOException - The IO Exception.

readFhirResource

public HttpBody readFhirResource(java.lang.String resourceName)
                          throws java.io.IOException

Description copied from interface: HealthcareApiClient

Read fhir resource http body.

Specified by:

readFhirResource in interface HealthcareApiClient

Parameters:

resourceName - the resource name, in format projects/{p}/locations/{l}/datasets/{d}/fhirStores/{f}/fhir/{resourceType}/{id}

Returns:

the http body

Throws:

java.io.IOException - The IO Exception.

searchFhirResource

public HttpBody searchFhirResource(java.lang.String fhirStore,
                                   java.lang.String resourceType,
                                   @Nullable java.util.Map<java.lang.String,java.lang.Object> parameters,
                                   java.lang.String pageToken)
                            throws java.io.IOException

Description copied from interface: HealthcareApiClient

Search fhir resource http body.

Specified by:

searchFhirResource in interface HealthcareApiClient

Parameters:

fhirStore - the fhir store

resourceType - the resource type

parameters - The parameters (in the form of key-value pairs).

Returns:

the http body

Throws:

java.io.IOException - The IO Exception.

getPatientEverything

public HttpBody getPatientEverything(java.lang.String resourceName,
                                     @Nullable java.util.Map<java.lang.String,java.lang.Object> filters,
                                     java.lang.String pageToken)
                              throws java.io.IOException

Description copied from interface: HealthcareApiClient

Fhir get patient everything http body.

Specified by:

getPatientEverything in interface HealthcareApiClient

Parameters:

resourceName - the resource name, in format projects/{p}/locations/{l}/datasets/{d}/fhirStores/{f}/fhir/{resourceType}/{id}

filters - optional request filters (in key value pairs).

Returns:

the http body

Throws:

java.io.IOException - The IO Exception.