Azure Deidentification client library for Java - version 1.0.0-beta.1

Azure Deidentification client library for Java.

This package contains Microsoft Azure Deidentification client library which is a managed service that enables users to tag, redact, or surrogate health data.

Documentation

Various documentation is available to help you get started

• API reference documentation
• Product documentation

Getting started

Prerequisites

• Java Development Kit (JDK) with version 8 or above
• Azure Subscription

Adding the package to your product

<dependency>
    <groupId>com.azure</groupId>
    <artifactId>azure-health-deidentification</artifactId>
    <version>1.0.0-beta.1</version>
</dependency>

Authentication

Azure Identity package provides the default implementation for authenticating the client.

Key concepts

Operation Modes:

• Tag: Will return a structure of offset and length with the PHI category of the related text spans.
• Redact: Will return output text with placeholder stubbed text. ex. [name]
• Surrogate: Will return output text with synthetic replacements.
  • My name is John Smith
  • My name is Tom Jones

Examples

The following sections provide several code snippets covering some of the most common Azure Deidentification client use cases, including:

• Create a DeidentificationClient
• Calling deidentification endpoint
• Creating deidentification Job
• Process deidentification Job
• List deidentification Jobs
• List completed files

Create a DeidentificationClient

Create a DeidentificationClient using the DEID_SERVICE_ENDPOINT environment variable.

DeidentificationClientBuilder deidentificationClientbuilder = new DeidentificationClientBuilder()
    .endpoint(Configuration.getGlobalConfiguration().get("DEID_SERVICE_ENDPOINT", "endpoint"))
    .httpClient(HttpClient.createDefault())
    .httpLogOptions(new HttpLogOptions().setLogLevel(HttpLogDetailLevel.BASIC));

DeidentificationClient deidentificationClient = deidentificationClientbuilder.buildClient();

Calling Deidentification endpoint

Calling the realtime endpoint with an input.

String inputText = "Hello, my name is John Smith.";

DeidentificationContent content = new DeidentificationContent(inputText);

DeidentificationResult result = deidentificationClient.deidentify(content);

System.out.println("Deidentified output: " + result.getOutputText());
// Deidentified output: Hello, my name is Harley Billiard.

Creating Deidentification Job

Creating a Deidentification Job using STORAGE_ACCOUNT_NAME and STORAGE_CONTAINER_NAME environment variables.

String storageLocation = "https://" + Configuration.getGlobalConfiguration().get("STORAGE_ACCOUNT_NAME") + ".blob.core.windows.net/" + Configuration.getGlobalConfiguration().get("STORAGE_CONTAINER_NAME");
String jobName = "MyJob-" + Instant.now().toEpochMilli();
String outputFolder = "_output";
String inputPrefix = "example_patient_1";
SourceStorageLocation sourceStorageLocation = new SourceStorageLocation(storageLocation, inputPrefix);

DeidentificationJob job = new DeidentificationJob(sourceStorageLocation, new TargetStorageLocation(storageLocation, outputFolder));
job.setOperation(OperationType.SURROGATE);
job.setDataType(DocumentDataType.PLAINTEXT);

Process Deidentification Job

Create and poll job until it is completed.

DeidentificationJob result = deidentificationClient.beginCreateJob(jobName, job)
    .waitForCompletion()
    .getValue();
System.out.println(jobName + " - " + result.getStatus());
// MyJob-1719953889301 - Succeeded

List Deidentification Jobs

List and process deidentification jobs

PagedIterable<DeidentificationJob> jobs = deidentificationClient.listJobs();
for (DeidentificationJob currentJob : jobs) {
    System.out.println(currentJob.getName() + " - " + currentJob.getStatus());
    // MyJob-1719953889301 - Succeeded
}

List completed files

List the files which are completed by a job.

PagedIterable<DocumentDetails> reports = deidentificationClient.listJobDocuments(jobName);

for (DocumentDetails currentFile : reports) {
    System.out.println(currentFile.getId() + " - " + currentFile.getOutput().getPath());
    // c45dcd5e-e3ce-4ff2-80b6-a8bbeb47f878 - _output/MyJob-1719954393623/example_patient_1/visit_summary.txt
    // e55a1aa2-8eba-4515-b070-1fd3d005008b - _output/MyJob-1719954393623/example_patient_1/doctor_dictation.txt
}

Troubleshooting

Next steps

Contributing

For details on contributing to this repository, see the contributing guide.

1. Fork it
2. Create your feature branch (git checkout -b my-new-feature)
3. Commit your changes (git commit -am 'Add some feature')
4. Push to the branch (git push origin my-new-feature)
5. Create new Pull Request