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

Interface HealthcareApiClient

All Known Implementing Classes:

HttpHealthcareApiClient

public interface HealthcareApiClient

Defines a client to communicate with the GCP HCLS API (version v1).

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, 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, 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 store) Delete Fhir store.
Empty	deleteHL7v2Message(java.lang.String msgName) Deletes an HL7v2 message.
Empty	deleteHL7v2Store(java.lang.String store) 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 a Hl7v2 message by its name from a Hl7v2 store.
Hl7V2Store	getHL7v2Store(java.lang.String storeName) Gets an HL7v2 store.
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.

Method Detail

getHL7v2Message

Message getHL7v2Message(java.lang.String msgName)
                 throws java.io.IOException,
                        java.text.ParseException

Gets a Hl7v2 message by its name from a Hl7v2 store.

Parameters:

msgName - The message name to be retrieved.

Returns:

The HL7v2 message.

Throws:

java.io.IOException - The IO Exception.

java.text.ParseException - The Parse Exception.

deleteHL7v2Message

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

Deletes an HL7v2 message.

Parameters:

msgName - The message name to be deleted.

Returns:

Empty.

Throws:

java.io.IOException - The IO Exception.

getHL7v2Store

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

Gets an HL7v2 store.

Parameters:

storeName - The store name to be retrieved.

Returns:

The HL7v2 store.

Throws:

java.io.IOException - The IO Exception.

getEarliestHL7v2SendTime

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

Gets the earliest HL7v2 send time.

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

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

Gets the latest HL7v2 send time.

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

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

Time Bound HL7v2 list request.

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

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

Make hl 7 v 2 list request list messages response.

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.

ingestHL7v2Message

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

Ingest an HL7v2 message.

Parameters:

hl7v2Store - The HL7v2 store of the message.

msg - The message.

Returns:

Empty.

Throws:

java.io.IOException - The IO Exception.

createHL7v2Message

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

Creates an HL7v2 message.

Parameters:

hl7v2Store - The HL7v2 store to create a message in.

msg - The message to create.

Returns:

Empty.

Throws:

java.io.IOException - The IO Exception.

deleteHL7v2Store

Empty deleteHL7v2Store(java.lang.String store)
                throws java.io.IOException

Deletes an HL7v2 store.

Parameters:

store - The HL7v2 store to be deleted.

Returns:

Empty.

Throws:

java.io.IOException - The IO Exception.

importFhirResource

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

Importing a FHIR resource from GCS.

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

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

Export a FHIR Resource to GCS.

Parameters:

fhirStore - the FhirStore of the resource.

gcsDestinationPrefix - GCS Destination Prefix to export to.

Returns:

Empty.

Throws:

java.io.IOException - The IO Exception.

exportFhirResourceToBigQuery

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

Export a FHIR Resource to BigQuery.

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

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

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

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

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

Poll operation.

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

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

Execute fhir bundle http body.

Parameters:

fhirStore - the fhir store

bundle - the bundle

Returns:

the http body

Throws:

java.io.IOException - The IO Exception.

HttpHealthcareApiClient.HealthcareHttpException

readFhirResource

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

Read fhir resource http body.

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

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

Search fhir resource http body.

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

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

Fhir get patient everything http body.

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.

createHL7v2Store

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

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

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

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

Create FHIR Store with a PubSub topic listener.

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.

createFhirStore

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

Create FHIR Store.

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.

listAllFhirStores

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

List all FHIR stores in a dataset.

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.

deleteFhirStore

Empty deleteFhirStore(java.lang.String store)
               throws java.io.IOException

Delete Fhir store.

Parameters:

store - The FHIR store to be deleted.

Returns:

Empty.

Throws:

java.io.IOException - The IO Exception.

retrieveDicomStudyMetadata

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

Retrieve DicomStudyMetadata.

Parameters:

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

Returns:

The study metadata.

Throws:

java.io.IOException - The IO Exception.

createDicomStore

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

Create a DicomStore.

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.

createDicomStore

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

Create a DicomStore with a PubSub listener.

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.

deleteDicomStore

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

Delete a Dicom Store.

Parameters:

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

Returns:

Empty.

Throws:

java.io.IOException - The IO Exception.

uploadToDicomStore

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

Upload to a Dicom Store.

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