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| <div class="subTitle">org.apache.beam.sdk.io.gcp.healthcare</div> |
| <h2 title="Class FhirIO" class="title">Class FhirIO</h2> |
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| <ul class="inheritance"> |
| <li>java.lang.Object</li> |
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| <li>org.apache.beam.sdk.io.gcp.healthcare.FhirIO</li> |
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| <pre>public class <span class="typeNameLabel">FhirIO</span> |
| extends java.lang.Object</pre> |
| <div class="block"><a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.html" title="class in org.apache.beam.sdk.io.gcp.healthcare"><code>FhirIO</code></a> provides an API for reading and writing resources to <a |
| href="https://cloud.google.com/healthcare/docs/concepts/fhir">Google Cloud Healthcare Fhir API. |
| </a> |
| |
| <h3>Reading</h3> |
| |
| <p>FHIR resources can be read with <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Read.html" title="class in org.apache.beam.sdk.io.gcp.healthcare"><code>FhirIO.Read</code></a>, which supports use cases where you have a |
| $<a href="../../../../../../../org/apache/beam/sdk/values/PCollection.html" title="class in org.apache.beam.sdk.values"><code>PCollection</code></a> 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 <a href="../../../../../../../org/apache/beam/sdk/io/gcp/pubsub/PubsubIO.html#readStrings--"><code>PubsubIO.readStrings()</code></a> 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 <a href="../../../../../../../org/apache/beam/sdk/io/TextIO.html" title="class in org.apache.beam.sdk.io"><code>TextIO</code></a>*) . |
| |
| <p>Get Resource contents from the FHIR Store based on the <a href="../../../../../../../org/apache/beam/sdk/values/PCollection.html" title="class in org.apache.beam.sdk.values"><code>PCollection</code></a> of FHIR resource |
| name strings <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Read.Result.html" title="class in org.apache.beam.sdk.io.gcp.healthcare"><code>FhirIO.Read.Result</code></a> where one can call <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Read.Result.html#getResources--"><code>FhirIO.Read.Result.getResources()</code></a> to |
| retrieve a <a href="../../../../../../../org/apache/beam/sdk/values/PCollection.html" title="class in org.apache.beam.sdk.values"><code>PCollection</code></a> containing the successfully fetched json resources as <code>String</code>s and/or <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Read.Result.html#getFailedReads--"><code>FhirIO.Read.Result.getFailedReads()</code></a> to retrieve a <a href="../../../../../../../org/apache/beam/sdk/values/PCollection.html" title="class in org.apache.beam.sdk.values"><code>PCollection</code></a> of |
| <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/HealthcareIOError.html" title="class in org.apache.beam.sdk.io.gcp.healthcare"><code>HealthcareIOError</code></a> containing the resources that could not be fetched and the exception as |
| a <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/HealthcareIOError.html" title="class in org.apache.beam.sdk.io.gcp.healthcare"><code>HealthcareIOError</code></a>, 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 <a href="../../../../../../../org/apache/beam/sdk/values/PCollection.html" title="class in org.apache.beam.sdk.values"><code>PCollection</code></a> contains FHIR resources that are not valid or are not reachable due to permissions |
| issues. |
| |
| <p>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 <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.html#getPatientEverything--"><code>getPatientEverything()</code></a> to execute a FHIR GetPatientEverythingRequest. |
| |
| <h3>Writing</h3> |
| |
| <p>Write Resources can be written to FHIR with a couple of different methods: including Import or |
| Execute Bundle. |
| |
| <ul> |
| <li><a |
| href="https://cloud.google.com/healthcare/docs/reference/rest/v1/projects.locations.datasets.fhirStores.fhir/executeBundle">Execute |
| Bundle</a> |
| <p>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). |
| <li><a |
| href="https://cloud.google.com/healthcare/docs/reference/rest/v1/projects.locations.datasets.fhirStores/import">Import</a> |
| <p>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 <a |
| href="https://cloud.google.com/healthcare/docs/how-tos/permissions-healthcare-api-gcp-products#fhir_store_cloud_storage_permissions">permissions</a> |
| to the Google Cloud Healthcare Service Agent. |
| <li><a |
| href="https://cloud.google.com/healthcare/docs/reference/rest/v1/projects.locations.datasets.fhirStores/export">Export</a> |
| <p>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 <a |
| href="https://cloud.google.com/healthcare/docs/how-tos/permissions-healthcare-api-gcp-products#fhir_store_cloud_storage_permissions">permissions</a> |
| to the Google Cloud Healthcare Service Agent. |
| <li><a |
| href="https://cloud.google.com/healthcare/docs/reference/rest/v1/projects.locations.datasets.fhirStores/deidentify">Deidentify</a> |
| <p>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. |
| <li><a |
| href="https://cloud.google.com/healthcare/docs/reference/rest/v1/projects.locations.datasets.fhirStores/search">Search</a> |
| <p>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. |
| </ul> |
| |
| <p>A <a href="../../../../../../../org/apache/beam/sdk/values/PCollection.html" title="class in org.apache.beam.sdk.values"><code>PCollection</code></a> of <code>String</code> can be ingested into an Fhir store using <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Write.html#fhirStoresImport-java.lang.String-java.lang.String-java.lang.String-org.apache.beam.sdk.io.gcp.healthcare.FhirIO.Import.ContentStructure-"><code>FhirIO.Write.fhirStoresImport(String, String, String, FhirIO.Import.ContentStructure)</code></a> This will |
| return a <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Write.Result.html" title="class in org.apache.beam.sdk.io.gcp.healthcare"><code>FhirIO.Write.Result</code></a> on which you can call <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Write.Result.html#getFailedBodies--"><code>FhirIO.Write.Result.getFailedBodies()</code></a> to retrieve a <a href="../../../../../../../org/apache/beam/sdk/values/PCollection.html" title="class in org.apache.beam.sdk.values"><code>PCollection</code></a> of <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/HealthcareIOError.html" title="class in org.apache.beam.sdk.io.gcp.healthcare"><code>HealthcareIOError</code></a> containing the <code>String</code> that failed to be ingested and the exception. |
| |
| <p>Example |
| |
| <pre><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<String> resources = readResult.getResources(); |
| // resource paths that couldn't be retrieved + error context |
| PCollection<HealthcareIOError<String>> 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<HealthcareIOError<String>> 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<String> 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<String, String> queries = new HashMap<>(); |
| queries.put("name", "Alice,Bob"); |
| FhirSearchParameter<String> searchParameter = FhirSearchParameter.of("Patient", queries); |
| PCollection<FhirSearchParameter<String>> searchQueries = |
| pipeline.apply( |
| Create.of(searchParameter) |
| .withCoder(FhirSearchParameterCoder.of(StringUtf8Coder.of()))); |
| FhirIO.Search.Result searchResult = |
| searchQueries.apply(FhirIO.searchResources(options.getFhirStore())); |
| PCollection<JsonArray> resources = searchResult.getResources(); // JsonArray of results |
| |
| // Search FHIR resources using an "AND" query with a key. |
| Map<String, List<String>> listQueries = new HashMap<>(); |
| listQueries.put("name", Arrays.asList("Alice", "Bob")); |
| FhirSearchParameter<List<String>> listSearchParameter = |
| FhirSearchParameter.of("Patient", "Alice-Bob-Search", listQueries); |
| PCollection<FhirSearchParameter<List<String>>> listSearchQueries = |
| pipeline.apply( |
| Create.of(listSearchParameter) |
| .withCoder(FhirSearchParameterCoder.of(ListCoder.of(StringUtf8Coder.of())))); |
| FhirIO.Search.Result listSearchResult = |
| searchQueries.apply(FhirIO.searchResources(options.getFhirStore())); |
| PCollection<KV<String, JsonArray>> listResource = |
| listSearchResult.getKeyedResources(); // KV<"Alice-Bob-Search", JsonArray of results> |
| |
| </code></pre> |
| |
| <h3>Updates to the I/O connector code</h3> |
| |
| For any significant updates to this I/O connector, please consider involving corresponding code |
| reviewers mentioned <a |
| href="https://github.com/apache/beam/blob/master/sdks/java/io/google-cloud-platform/OWNERS"> |
| here</a>.</div> |
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| <th class="colFirst" scope="col">Modifier and Type</th> |
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| </tr> |
| <tr class="altColor"> |
| <td class="colFirst"><code>static class </code></td> |
| <td class="colLast"><code><span class="memberNameLink"><a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Deidentify.html" title="class in org.apache.beam.sdk.io.gcp.healthcare">FhirIO.Deidentify</a></span></code> |
| <div class="block">Deidentify FHIR resources from a FHIR store to a destination FHIR store.</div> |
| </td> |
| </tr> |
| <tr class="rowColor"> |
| <td class="colFirst"><code>static class </code></td> |
| <td class="colLast"><code><span class="memberNameLink"><a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.ExecuteBundles.html" title="class in org.apache.beam.sdk.io.gcp.healthcare">FhirIO.ExecuteBundles</a></span></code> |
| <div class="block">The type Execute bundles.</div> |
| </td> |
| </tr> |
| <tr class="altColor"> |
| <td class="colFirst"><code>static class </code></td> |
| <td class="colLast"><code><span class="memberNameLink"><a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.ExecuteBundlesResult.html" title="class in org.apache.beam.sdk.io.gcp.healthcare">FhirIO.ExecuteBundlesResult</a></span></code> |
| <div class="block">ExecuteBundlesResult contains both successfully executed bundles and information help debugging |
| failed executions (eg metadata & error msgs).</div> |
| </td> |
| </tr> |
| <tr class="rowColor"> |
| <td class="colFirst"><code>static class </code></td> |
| <td class="colLast"><code><span class="memberNameLink"><a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Export.html" title="class in org.apache.beam.sdk.io.gcp.healthcare">FhirIO.Export</a></span></code> |
| <div class="block">Export FHIR resources from a FHIR store to new line delimited json files on GCS or BigQuery.</div> |
| </td> |
| </tr> |
| <tr class="altColor"> |
| <td class="colFirst"><code>static class </code></td> |
| <td class="colLast"><code><span class="memberNameLink"><a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Import.html" title="class in org.apache.beam.sdk.io.gcp.healthcare">FhirIO.Import</a></span></code> |
| <div class="block">Writes each bundle of elements to a new-line delimited JSON file on GCS and issues a |
| fhirStores.import Request for that file.</div> |
| </td> |
| </tr> |
| <tr class="rowColor"> |
| <td class="colFirst"><code>static class </code></td> |
| <td class="colLast"><code><span class="memberNameLink"><a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Read.html" title="class in org.apache.beam.sdk.io.gcp.healthcare">FhirIO.Read</a></span></code> |
| <div class="block">The type Read.</div> |
| </td> |
| </tr> |
| <tr class="altColor"> |
| <td class="colFirst"><code>static class </code></td> |
| <td class="colLast"><code><span class="memberNameLink"><a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Search.html" title="class in org.apache.beam.sdk.io.gcp.healthcare">FhirIO.Search</a><<a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Search.html" title="type parameter in FhirIO.Search">T</a>></span></code> |
| <div class="block">The type Search.</div> |
| </td> |
| </tr> |
| <tr class="rowColor"> |
| <td class="colFirst"><code>static class </code></td> |
| <td class="colLast"><code><span class="memberNameLink"><a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Write.html" title="class in org.apache.beam.sdk.io.gcp.healthcare">FhirIO.Write</a></span></code> |
| <div class="block">The type Write.</div> |
| </td> |
| </tr> |
| </table> |
| </li> |
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| <td class="colOne"><code><span class="memberNameLink"><a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.html#FhirIO--">FhirIO</a></span>()</code> </td> |
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| <th class="colLast" scope="col">Method and Description</th> |
| </tr> |
| <tr id="i0" class="altColor"> |
| <td class="colFirst"><code>static <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Deidentify.html" title="class in org.apache.beam.sdk.io.gcp.healthcare">FhirIO.Deidentify</a></code></td> |
| <td class="colLast"><code><span class="memberNameLink"><a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.html#deidentify-java.lang.String-java.lang.String-com.google.api.services.healthcare.v1.model.DeidentifyConfig-">deidentify</a></span>(java.lang.String sourceFhirStore, |
| java.lang.String destinationFhirStore, |
| com.google.api.services.healthcare.v1.model.DeidentifyConfig deidConfig)</code> |
| <div class="block">Deidentify FHIR resources.</div> |
| </td> |
| </tr> |
| <tr id="i1" class="rowColor"> |
| <td class="colFirst"><code>static <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Deidentify.html" title="class in org.apache.beam.sdk.io.gcp.healthcare">FhirIO.Deidentify</a></code></td> |
| <td class="colLast"><code><span class="memberNameLink"><a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.html#deidentify-org.apache.beam.sdk.options.ValueProvider-org.apache.beam.sdk.options.ValueProvider-org.apache.beam.sdk.options.ValueProvider-">deidentify</a></span>(<a href="../../../../../../../org/apache/beam/sdk/options/ValueProvider.html" title="interface in org.apache.beam.sdk.options">ValueProvider</a><java.lang.String> sourceFhirStore, |
| <a href="../../../../../../../org/apache/beam/sdk/options/ValueProvider.html" title="interface in org.apache.beam.sdk.options">ValueProvider</a><java.lang.String> destinationFhirStore, |
| <a href="../../../../../../../org/apache/beam/sdk/options/ValueProvider.html" title="interface in org.apache.beam.sdk.options">ValueProvider</a><com.google.api.services.healthcare.v1.model.DeidentifyConfig> deidConfig)</code> |
| <div class="block">Deidentify FHIR resources.</div> |
| </td> |
| </tr> |
| <tr id="i2" class="altColor"> |
| <td class="colFirst"><code>static <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Export.html" title="class in org.apache.beam.sdk.io.gcp.healthcare">FhirIO.Export</a></code></td> |
| <td class="colLast"><code><span class="memberNameLink"><a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.html#exportResources-java.lang.String-java.lang.String-">exportResources</a></span>(java.lang.String fhirStore, |
| java.lang.String exportUri)</code> |
| <div class="block">Export resources to GCS.</div> |
| </td> |
| </tr> |
| <tr id="i3" class="rowColor"> |
| <td class="colFirst"><code>static <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Export.html" title="class in org.apache.beam.sdk.io.gcp.healthcare">FhirIO.Export</a></code></td> |
| <td class="colLast"><code><span class="memberNameLink"><a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.html#exportResources-org.apache.beam.sdk.options.ValueProvider-org.apache.beam.sdk.options.ValueProvider-">exportResources</a></span>(<a href="../../../../../../../org/apache/beam/sdk/options/ValueProvider.html" title="interface in org.apache.beam.sdk.options">ValueProvider</a><java.lang.String> fhirStore, |
| <a href="../../../../../../../org/apache/beam/sdk/options/ValueProvider.html" title="interface in org.apache.beam.sdk.options">ValueProvider</a><java.lang.String> exportUri)</code> </td> |
| </tr> |
| <tr id="i4" class="altColor"> |
| <td class="colFirst"><code>static <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIOPatientEverything.html" title="class in org.apache.beam.sdk.io.gcp.healthcare">FhirIOPatientEverything</a></code></td> |
| <td class="colLast"><code><span class="memberNameLink"><a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.html#getPatientEverything--">getPatientEverything</a></span>()</code> |
| <div class="block">Get the patient compartment for a FHIR Patient using the GetPatientEverything/$everything API.</div> |
| </td> |
| </tr> |
| <tr id="i5" class="rowColor"> |
| <td class="colFirst"><code>static <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Import.html" title="class in org.apache.beam.sdk.io.gcp.healthcare">FhirIO.Import</a></code></td> |
| <td class="colLast"><code><span class="memberNameLink"><a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.html#importResources-java.lang.String-java.lang.String-java.lang.String-org.apache.beam.sdk.io.gcp.healthcare.FhirIO.Import.ContentStructure-">importResources</a></span>(java.lang.String fhirStore, |
| java.lang.String tempDir, |
| java.lang.String deadLetterDir, |
| <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Import.ContentStructure.html" title="enum in org.apache.beam.sdk.io.gcp.healthcare">FhirIO.Import.ContentStructure</a> contentStructure)</code> |
| <div class="block">Import resources.</div> |
| </td> |
| </tr> |
| <tr id="i6" class="altColor"> |
| <td class="colFirst"><code>static <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Import.html" title="class in org.apache.beam.sdk.io.gcp.healthcare">FhirIO.Import</a></code></td> |
| <td class="colLast"><code><span class="memberNameLink"><a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.html#importResources-org.apache.beam.sdk.options.ValueProvider-org.apache.beam.sdk.options.ValueProvider-org.apache.beam.sdk.options.ValueProvider-org.apache.beam.sdk.io.gcp.healthcare.FhirIO.Import.ContentStructure-">importResources</a></span>(<a href="../../../../../../../org/apache/beam/sdk/options/ValueProvider.html" title="interface in org.apache.beam.sdk.options">ValueProvider</a><java.lang.String> fhirStore, |
| <a href="../../../../../../../org/apache/beam/sdk/options/ValueProvider.html" title="interface in org.apache.beam.sdk.options">ValueProvider</a><java.lang.String> tempDir, |
| <a href="../../../../../../../org/apache/beam/sdk/options/ValueProvider.html" title="interface in org.apache.beam.sdk.options">ValueProvider</a><java.lang.String> deadLetterDir, |
| <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Import.ContentStructure.html" title="enum in org.apache.beam.sdk.io.gcp.healthcare">FhirIO.Import.ContentStructure</a> contentStructure)</code> |
| <div class="block">Import resources.</div> |
| </td> |
| </tr> |
| <tr id="i7" class="rowColor"> |
| <td class="colFirst"><code>static <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Read.html" title="class in org.apache.beam.sdk.io.gcp.healthcare">FhirIO.Read</a></code></td> |
| <td class="colLast"><code><span class="memberNameLink"><a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.html#readResources--">readResources</a></span>()</code> |
| <div class="block">Read resources from a PCollection of resource IDs (e.g.</div> |
| </td> |
| </tr> |
| <tr id="i8" class="altColor"> |
| <td class="colFirst"><code>static <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Search.html" title="class in org.apache.beam.sdk.io.gcp.healthcare">FhirIO.Search</a><java.lang.String></code></td> |
| <td class="colLast"><code><span class="memberNameLink"><a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.html#searchResources-java.lang.String-">searchResources</a></span>(java.lang.String fhirStore)</code> |
| <div class="block">Search resources from a Fhir store with String parameter values.</div> |
| </td> |
| </tr> |
| <tr id="i9" class="rowColor"> |
| <td class="colFirst"><code>static <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Search.html" title="class in org.apache.beam.sdk.io.gcp.healthcare">FhirIO.Search</a><?></code></td> |
| <td class="colLast"><code><span class="memberNameLink"><a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.html#searchResourcesWithGenericParameters-java.lang.String-">searchResourcesWithGenericParameters</a></span>(java.lang.String fhirStore)</code> |
| <div class="block">Search resources from a Fhir store with any type of parameter values.</div> |
| </td> |
| </tr> |
| </table> |
| <ul class="blockList"> |
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| <h3>Methods inherited from class java.lang.Object</h3> |
| <code>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</code></li> |
| </ul> |
| </li> |
| </ul> |
| </li> |
| </ul> |
| </div> |
| <div class="details"> |
| <ul class="blockList"> |
| <li class="blockList"> |
| <!-- ========= CONSTRUCTOR DETAIL ======== --> |
| <ul class="blockList"> |
| <li class="blockList"><a name="constructor.detail"> |
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| </a> |
| <h3>Constructor Detail</h3> |
| <a name="FhirIO--"> |
| <!-- --> |
| </a> |
| <ul class="blockListLast"> |
| <li class="blockList"> |
| <h4>FhirIO</h4> |
| <pre>public FhirIO()</pre> |
| </li> |
| </ul> |
| </li> |
| </ul> |
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| <ul class="blockList"> |
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| <h3>Method Detail</h3> |
| <a name="readResources--"> |
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| <h4>readResources</h4> |
| <pre>public static <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Read.html" title="class in org.apache.beam.sdk.io.gcp.healthcare">FhirIO.Read</a> readResources()</pre> |
| <div class="block">Read resources from a PCollection of resource IDs (e.g. when subscribing the pubsub |
| notifications)</div> |
| <dl> |
| <dt><span class="returnLabel">Returns:</span></dt> |
| <dd>the read</dd> |
| <dt><span class="seeLabel">See Also:</span></dt> |
| <dd><a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Read.html" title="class in org.apache.beam.sdk.io.gcp.healthcare"><code>FhirIO.Read</code></a></dd> |
| </dl> |
| </li> |
| </ul> |
| <a name="searchResources-java.lang.String-"> |
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| <h4>searchResources</h4> |
| <pre>public static <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Search.html" title="class in org.apache.beam.sdk.io.gcp.healthcare">FhirIO.Search</a><java.lang.String> searchResources(java.lang.String fhirStore)</pre> |
| <div class="block">Search resources from a Fhir store with String parameter values.</div> |
| <dl> |
| <dt><span class="returnLabel">Returns:</span></dt> |
| <dd>the search</dd> |
| <dt><span class="seeLabel">See Also:</span></dt> |
| <dd><a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Search.html" title="class in org.apache.beam.sdk.io.gcp.healthcare"><code>FhirIO.Search</code></a></dd> |
| </dl> |
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| <h4>searchResourcesWithGenericParameters</h4> |
| <pre>public static <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Search.html" title="class in org.apache.beam.sdk.io.gcp.healthcare">FhirIO.Search</a><?> searchResourcesWithGenericParameters(java.lang.String fhirStore)</pre> |
| <div class="block">Search resources from a Fhir store with any type of parameter values.</div> |
| <dl> |
| <dt><span class="returnLabel">Returns:</span></dt> |
| <dd>the search</dd> |
| <dt><span class="seeLabel">See Also:</span></dt> |
| <dd><a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Search.html" title="class in org.apache.beam.sdk.io.gcp.healthcare"><code>FhirIO.Search</code></a></dd> |
| </dl> |
| </li> |
| </ul> |
| <a name="importResources-java.lang.String-java.lang.String-java.lang.String-org.apache.beam.sdk.io.gcp.healthcare.FhirIO.Import.ContentStructure-"> |
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| </a> |
| <ul class="blockList"> |
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| <h4>importResources</h4> |
| <pre>public static <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Import.html" title="class in org.apache.beam.sdk.io.gcp.healthcare">FhirIO.Import</a> importResources(java.lang.String fhirStore, |
| java.lang.String tempDir, |
| java.lang.String deadLetterDir, |
| <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Import.ContentStructure.html" title="enum in org.apache.beam.sdk.io.gcp.healthcare">FhirIO.Import.ContentStructure</a> contentStructure)</pre> |
| <div class="block">Import resources. Intended for use on empty FHIR stores</div> |
| <dl> |
| <dt><span class="paramLabel">Parameters:</span></dt> |
| <dd><code>fhirStore</code> - the fhir store</dd> |
| <dd><code>tempDir</code> - the temp dir</dd> |
| <dd><code>deadLetterDir</code> - the dead letter dir</dd> |
| <dd><code>contentStructure</code> - the content structure</dd> |
| <dt><span class="returnLabel">Returns:</span></dt> |
| <dd>the import</dd> |
| <dt><span class="seeLabel">See Also:</span></dt> |
| <dd><a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Import.html" title="class in org.apache.beam.sdk.io.gcp.healthcare"><code>FhirIO.Import</code></a></dd> |
| </dl> |
| </li> |
| </ul> |
| <a name="importResources-org.apache.beam.sdk.options.ValueProvider-org.apache.beam.sdk.options.ValueProvider-org.apache.beam.sdk.options.ValueProvider-org.apache.beam.sdk.io.gcp.healthcare.FhirIO.Import.ContentStructure-"> |
| <!-- --> |
| </a> |
| <ul class="blockList"> |
| <li class="blockList"> |
| <h4>importResources</h4> |
| <pre>public static <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Import.html" title="class in org.apache.beam.sdk.io.gcp.healthcare">FhirIO.Import</a> importResources(<a href="../../../../../../../org/apache/beam/sdk/options/ValueProvider.html" title="interface in org.apache.beam.sdk.options">ValueProvider</a><java.lang.String> fhirStore, |
| <a href="../../../../../../../org/apache/beam/sdk/options/ValueProvider.html" title="interface in org.apache.beam.sdk.options">ValueProvider</a><java.lang.String> tempDir, |
| <a href="../../../../../../../org/apache/beam/sdk/options/ValueProvider.html" title="interface in org.apache.beam.sdk.options">ValueProvider</a><java.lang.String> deadLetterDir, |
| <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Import.ContentStructure.html" title="enum in org.apache.beam.sdk.io.gcp.healthcare">FhirIO.Import.ContentStructure</a> contentStructure)</pre> |
| <div class="block">Import resources. Intended for use on empty FHIR stores</div> |
| <dl> |
| <dt><span class="paramLabel">Parameters:</span></dt> |
| <dd><code>fhirStore</code> - the fhir store</dd> |
| <dd><code>tempDir</code> - the temp dir</dd> |
| <dd><code>deadLetterDir</code> - the dead letter dir</dd> |
| <dd><code>contentStructure</code> - the content structure</dd> |
| <dt><span class="returnLabel">Returns:</span></dt> |
| <dd>the import</dd> |
| <dt><span class="seeLabel">See Also:</span></dt> |
| <dd><a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Import.html" title="class in org.apache.beam.sdk.io.gcp.healthcare"><code>FhirIO.Import</code></a></dd> |
| </dl> |
| </li> |
| </ul> |
| <a name="exportResources-java.lang.String-java.lang.String-"> |
| <!-- --> |
| </a> |
| <ul class="blockList"> |
| <li class="blockList"> |
| <h4>exportResources</h4> |
| <pre>public static <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Export.html" title="class in org.apache.beam.sdk.io.gcp.healthcare">FhirIO.Export</a> exportResources(java.lang.String fhirStore, |
| java.lang.String exportUri)</pre> |
| <div class="block">Export resources to GCS. Intended for use on non-empty FHIR stores</div> |
| <dl> |
| <dt><span class="paramLabel">Parameters:</span></dt> |
| <dd><code>fhirStore</code> - the fhir store, in the format: |
| projects/project_id/locations/location_id/datasets/dataset_id/fhirStores/fhir_store_id</dd> |
| <dd><code>exportUri</code> - the destination GCS dir or BigQuery dataset, in the format: |
| gs://YOUR_BUCKET_NAME/path/to/a/dir | bq://PROJECT_ID.BIGQUERY_DATASET_ID</dd> |
| <dt><span class="returnLabel">Returns:</span></dt> |
| <dd>the export</dd> |
| <dt><span class="seeLabel">See Also:</span></dt> |
| <dd><a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Export.html" title="class in org.apache.beam.sdk.io.gcp.healthcare"><code>FhirIO.Export</code></a></dd> |
| </dl> |
| </li> |
| </ul> |
| <a name="exportResources-org.apache.beam.sdk.options.ValueProvider-org.apache.beam.sdk.options.ValueProvider-"> |
| <!-- --> |
| </a> |
| <ul class="blockList"> |
| <li class="blockList"> |
| <h4>exportResources</h4> |
| <pre>public static <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Export.html" title="class in org.apache.beam.sdk.io.gcp.healthcare">FhirIO.Export</a> exportResources(<a href="../../../../../../../org/apache/beam/sdk/options/ValueProvider.html" title="interface in org.apache.beam.sdk.options">ValueProvider</a><java.lang.String> fhirStore, |
| <a href="../../../../../../../org/apache/beam/sdk/options/ValueProvider.html" title="interface in org.apache.beam.sdk.options">ValueProvider</a><java.lang.String> exportUri)</pre> |
| <dl> |
| <dt><span class="seeLabel">See Also:</span></dt> |
| <dd><a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.html#exportResources-java.lang.String-java.lang.String-"><code>exportResources(String, String)</code></a></dd> |
| </dl> |
| </li> |
| </ul> |
| <a name="deidentify-java.lang.String-java.lang.String-com.google.api.services.healthcare.v1.model.DeidentifyConfig-"> |
| <!-- --> |
| </a> |
| <ul class="blockList"> |
| <li class="blockList"> |
| <h4>deidentify</h4> |
| <pre>public static <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Deidentify.html" title="class in org.apache.beam.sdk.io.gcp.healthcare">FhirIO.Deidentify</a> deidentify(java.lang.String sourceFhirStore, |
| java.lang.String destinationFhirStore, |
| com.google.api.services.healthcare.v1.model.DeidentifyConfig deidConfig)</pre> |
| <div class="block">Deidentify FHIR resources. Intended for use on non-empty FHIR stores</div> |
| <dl> |
| <dt><span class="paramLabel">Parameters:</span></dt> |
| <dd><code>sourceFhirStore</code> - the source fhir store, in the format: |
| projects/project_id/locations/location_id/datasets/dataset_id/fhirStores/fhir_store_id</dd> |
| <dd><code>destinationFhirStore</code> - 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</dd> |
| <dd><code>deidConfig</code> - the DeidentifyConfig</dd> |
| <dt><span class="returnLabel">Returns:</span></dt> |
| <dd>the deidentify</dd> |
| <dt><span class="seeLabel">See Also:</span></dt> |
| <dd><a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Deidentify.html" title="class in org.apache.beam.sdk.io.gcp.healthcare"><code>FhirIO.Deidentify</code></a></dd> |
| </dl> |
| </li> |
| </ul> |
| <a name="deidentify-org.apache.beam.sdk.options.ValueProvider-org.apache.beam.sdk.options.ValueProvider-org.apache.beam.sdk.options.ValueProvider-"> |
| <!-- --> |
| </a> |
| <ul class="blockList"> |
| <li class="blockList"> |
| <h4>deidentify</h4> |
| <pre>public static <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Deidentify.html" title="class in org.apache.beam.sdk.io.gcp.healthcare">FhirIO.Deidentify</a> deidentify(<a href="../../../../../../../org/apache/beam/sdk/options/ValueProvider.html" title="interface in org.apache.beam.sdk.options">ValueProvider</a><java.lang.String> sourceFhirStore, |
| <a href="../../../../../../../org/apache/beam/sdk/options/ValueProvider.html" title="interface in org.apache.beam.sdk.options">ValueProvider</a><java.lang.String> destinationFhirStore, |
| <a href="../../../../../../../org/apache/beam/sdk/options/ValueProvider.html" title="interface in org.apache.beam.sdk.options">ValueProvider</a><com.google.api.services.healthcare.v1.model.DeidentifyConfig> deidConfig)</pre> |
| <div class="block">Deidentify FHIR resources. Intended for use on non-empty FHIR stores</div> |
| <dl> |
| <dt><span class="paramLabel">Parameters:</span></dt> |
| <dd><code>sourceFhirStore</code> - the source fhir store, in the format: |
| projects/project_id/locations/location_id/datasets/dataset_id/fhirStores/fhir_store_id</dd> |
| <dd><code>destinationFhirStore</code> - 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</dd> |
| <dd><code>deidConfig</code> - the DeidentifyConfig</dd> |
| <dt><span class="returnLabel">Returns:</span></dt> |
| <dd>the deidentify</dd> |
| <dt><span class="seeLabel">See Also:</span></dt> |
| <dd><a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIO.Deidentify.html" title="class in org.apache.beam.sdk.io.gcp.healthcare"><code>FhirIO.Deidentify</code></a></dd> |
| </dl> |
| </li> |
| </ul> |
| <a name="getPatientEverything--"> |
| <!-- --> |
| </a> |
| <ul class="blockListLast"> |
| <li class="blockList"> |
| <h4>getPatientEverything</h4> |
| <pre>public static <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIOPatientEverything.html" title="class in org.apache.beam.sdk.io.gcp.healthcare">FhirIOPatientEverything</a> getPatientEverything()</pre> |
| <div class="block">Get the patient compartment for a FHIR Patient using the GetPatientEverything/$everything API.</div> |
| <dl> |
| <dt><span class="returnLabel">Returns:</span></dt> |
| <dd>the patient everything</dd> |
| <dt><span class="seeLabel">See Also:</span></dt> |
| <dd><a |
| href=https://cloud.google.com/healthcare-api/docs/reference/rest/v1/projects.locations.datasets.fhirStores.fhir/Patient-everything></a>, |
| <a href="../../../../../../../org/apache/beam/sdk/io/gcp/healthcare/FhirIOPatientEverything.html" title="class in org.apache.beam.sdk.io.gcp.healthcare"><code>FhirIOPatientEverything</code></a></dd> |
| </dl> |
| </li> |
| </ul> |
| </li> |
| </ul> |
| </li> |
| </ul> |
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