azure-health-deidentification 1.1.0b1
Microsoft Corporation Azure Health Deidentification Client Library for Python
License: MIT License
Requires Python: >=3.9
Keywords: azure, azure sdk

# Azure Health Data Services de-identification service client library for Python

This package contains a client library for the de-identification service in Azure Health Data Services which 
enables users to tag, redact, or surrogate health data containing Protected Health Information (PHI).
For more on service functionality and important usage considerations, see [the de-identification service overview][product_documentation].

This library supports API versions `2025-07-15-preview` and earlier.

Use the client library for the de-identification service to:
- Discover PHI in unstructured text
- Replace PHI in unstructured text with placeholder values
- Replace PHI in unstructured text with realistic surrogate values
- Manage asynchronous jobs to de-identify documents in Azure Storage

[Source code](https://github.com/Azure/azure-sdk-for-python/tree/main/sdk/healthdataaiservices/azure-health-deidentification/azure/health/deidentification)
| [Package (PyPI)](https://pypi.org/project/azure-health-deidentification)
| [API reference documentation](https://learn.microsoft.com/python/api/overview/azure/health-deidentification)
| [Product documentation][product_documentation]
| [Samples][samples]

## Getting started

### Prequisites

- Python 3.9 or later is required to use this package.
- Install [pip][pip].
- You need an [Azure subscription][azure_sub] to use this package.
- [Deploy the de-identification service][deid_quickstart].
- [Configure Azure role-based access control (RBAC)][deid_rbac] for the operations you will perform.

### Install the package

```bash
python -m pip install azure-health-deidentification
```

### Authentication
To authenticate with the de-identification service, install [`azure-identity`][azure_identity_pip]:

```bash
python -m pip install azure.identity
```

You can use [DefaultAzureCredential][default_azure_credential] to automatically find the best credential to use at runtime.

You will need a **service URL** to instantiate a client object. You can find the service URL for a particular resource in the [Azure portal][azure_portal], or using the [Azure CLI][azure_cli].
Here's an example of setting an environment variable in Bash using Azure CLI:

```bash
# Get the service URL for the resource
export HEALTHDATAAISERVICES_DEID_SERVICE_ENDPOINT=$(az deidservice show --name "<resource-name>" --resource-group "<resource-group-name>" --query "properties.serviceUrl")
```

Optionally, save the service URL as an environment variable named `HEALTHDATAAISERVICES_DEID_SERVICE_ENDPOINT` for the sample client initialization code.

Create a client with the endpoint and credential:
<!-- SNIPPET: examples.create_client -->

```python
from azure.health.deidentification import DeidentificationClient
from azure.identity import DefaultAzureCredential
import os


endpoint = os.environ["HEALTHDATAAISERVICES_DEID_SERVICE_ENDPOINT"]
credential = DefaultAzureCredential()
client = DeidentificationClient(endpoint, credential)
```

<!-- END SNIPPET -->

## Key concepts

### De-identification operations:
Given an input text, the de-identification service can perform four main operations:
- `Tag` returns the category and location within the text of detected PHI entities.
- `Redact` returns output text where detected PHI entities are replaced with placeholder text. For example, `John` would be replaced with `[name]`.
- `Surrogate` returns output text where detected PHI entities are replaced with realistic replacement values. For example, `My name is John Smith` could become `My name is Tom Jones`.
- `SurrogateOnly` returns output text where user-defined PHI entities are replaced with realistic replacement values.

### String Encoding
When using the `Tag` operation, the service will return the locations of PHI entities in the input text. These locations will be represented as offsets and lengths, each of which is a [StringIndex][string_index] containing
three properties corresponding to three different text encodings. **Python applications should use the `code_point` property.**

For more on text encoding, see [Character encoding in .NET][character_encoding].

### Available endpoints
There are two ways to interact with the de-identification service. You can send text directly, or you can create jobs 
to de-identify documents in Azure Storage.

You can de-identify text directly using the `DeidentificationClient`:
<!-- SNIPPET: deidentify_text_surrogate.surrogate -->

```python
from azure.health.deidentification import DeidentificationClient
from azure.health.deidentification.models import (
    DeidentificationContent,
    DeidentificationOperationType,
    DeidentificationResult,
)
from azure.identity import DefaultAzureCredential
import os

endpoint = os.environ["HEALTHDATAAISERVICES_DEID_SERVICE_ENDPOINT"]
credential = DefaultAzureCredential()
client = DeidentificationClient(endpoint, credential)

body = DeidentificationContent(
    input_text="Hello, my name is John Smith.", operation_type=DeidentificationOperationType.SURROGATE
)
result: DeidentificationResult = client.deidentify_text(body)
print(f'\nOriginal Text:     "{body.input_text}"')
print(f'Surrogated Text:   "{result.output_text}"')  # Surrogated output: Hello, my name is <synthetic name>.
```

<!-- END SNIPPET -->

To de-identify documents in Azure Storage, you'll need a storage account with a container to which the 
de-identification service has been granted an appropriate role. See [Tutorial: Configure Azure Storage to de-identify documents][deid_configure_storage]
for prerequisites and configuration options. You can upload the files in the [test data folder][test_data] as blobs, like: `https://<storageaccount>.blob.core.windows.net/<container>/example_patient_1/doctor_dictation.txt`.

You can create jobs to de-identify documents in the source Azure Storage account and container with an optional input prefix. If there's no input prefix, all blobs in the container will be de-identified. Azure Storage blobs can use `/` in the blob name to emulate a folder or directory layout. For more on blob naming, see [Naming and Referencing Containers, Blobs, and Metadata][blob_names]. The files you've uploaded can be de-identified by providing `example_patient_1` as the input prefix:
```
<container>/
├── example_patient_1/
       └──doctor_dictation.txt
       └──row-2-data.txt
       └──visit-summary.txt
```

Your target Azure Storage account and container where documents will be written can be the same as the source, or a different account or container. In the examples below, the source and target account and container are the same. You can specify an output prefix to indicate where the job's output documents should be written (defaulting to `_output`). Each document processed by the job will have the same relative blob name with the input prefix replaced by the output prefix:
```
<container>/
├── example_patient_1/
       └──doctor_dictation.txt
       └──row-2-data.txt
       └──visit-summary.txt
├── _output/
       └──doctor_dictation.txt
       └──row-2-data.txt
       └──visit-summary.txt
```

Set the following environment variables, updating the storage account and container with real values:
```bash
export HEALTHDATAAISERVICES_STORAGE_ACCOUNT_LOCATION="https://<storageaccount>.blob.core.windows.net/<container>"
export INPUT_PREFIX="example_patient_1"
export OUTPUT_PREFIX="_output"
```

The client exposes a `begin_deidentify_documents` method that returns a [LROPoller](https://learn.microsoft.com/python/api/azure-core/azure.core.polling.lropoller) instance. You can get the result of the operation by calling `result()`, optionally passing in a `timeout` value in seconds:
<!-- SNIPPET: deidentify_documents.sample -->

```python
from azure.health.deidentification import DeidentificationClient
from azure.health.deidentification.models import (
    DeidentificationJob,
    DeidentificationOperationType,
    SourceStorageLocation,
    TargetStorageLocation,
)
from azure.identity import DefaultAzureCredential
import os
import uuid

endpoint = os.environ["HEALTHDATAAISERVICES_DEID_SERVICE_ENDPOINT"]
storage_location = os.environ["HEALTHDATAAISERVICES_STORAGE_ACCOUNT_LOCATION"]
inputPrefix = os.environ.get("INPUT_PREFIX", "example_patient_1")
outputPrefix = os.environ.get("OUTPUT_PREFIX", "_output")

credential = DefaultAzureCredential()

client = DeidentificationClient(endpoint, credential)

jobname = f"sample-job-{uuid.uuid4().hex[:8]}"

job = DeidentificationJob(
    operation_type=DeidentificationOperationType.SURROGATE,
    source_location=SourceStorageLocation(
        location=storage_location,
        prefix=inputPrefix,
    ),
    target_location=TargetStorageLocation(location=storage_location, prefix=outputPrefix, overwrite=True),
)

finished_job: DeidentificationJob = client.begin_deidentify_documents(jobname, job).result(timeout=120)

print(f"Job Name:   {finished_job.job_name}")
print(f"Job Status: {finished_job.status}")
print(f"File Count: {finished_job.summary.total_count if finished_job.summary is not None else 0}")
```

<!-- END SNIPPET -->

## Examples
The following sections provide code samples covering some of the most common client use cases, including: 

- [Discover PHI in unstructured text](#discover-phi-in-unstructured-text)
- [Replace PHI in unstructured text with placeholder values](#replace-phi-in-unstructured-text-with-placeholder-values)
- [Replace PHI in unstructured text with realistic surrogate values](#replace-phi-in-unstructured-text-with-realistic-surrogate-values)
- [Replace only specific PHI entities with surrogate values](#replace-only-specific-phi-entities-with-surrogate-values)

See the [samples][samples] for code files illustrating common patterns, including creating and managing jobs to de-identify documents in Azure Storage. 

### Discover PHI in unstructured text
When you specify the `TAG` operation, the service will return information about the PHI entities it detects. You can use this information to customize your de-identification workflow:
<!-- SNIPPET: deidentify_text_tag.tag -->

```python
from azure.health.deidentification import DeidentificationClient
from azure.health.deidentification.models import (
    DeidentificationContent,
    DeidentificationOperationType,
    DeidentificationResult,
)
from azure.identity import DefaultAzureCredential
import os

endpoint = os.environ["HEALTHDATAAISERVICES_DEID_SERVICE_ENDPOINT"]
credential = DefaultAzureCredential()
client = DeidentificationClient(endpoint, credential)

body = DeidentificationContent(
    input_text="Hello, I'm Dr. John Smith.", operation_type=DeidentificationOperationType.TAG
)
result: DeidentificationResult = client.deidentify_text(body)
print(f'\nOriginal Text:    "{body.input_text}"')

if result.tagger_result and result.tagger_result.entities:
    print(f"Tagged Entities:")
    for entity in result.tagger_result.entities:
        print(
            f'\tEntity Text: "{entity.text}", Entity Category: "{entity.category}", Offset: "{entity.offset.code_point}", Length: "{entity.length.code_point}"'
        )
else:
    print("\tNo tagged entities found.")
```

<!-- END SNIPPET -->

### Replace PHI in unstructured text with placeholder values
When you specify the `REDACT` operation, the service will replace the PHI entities it detects with placeholder values. You can learn more about [redaction customization][deid_redact]. 
<!-- SNIPPET: deidentify_text_redact.redact -->

```python
from azure.health.deidentification import DeidentificationClient
from azure.health.deidentification.models import (
    DeidentificationContent,
    DeidentificationOperationType,
    DeidentificationResult,
)
from azure.identity import DefaultAzureCredential
import os

endpoint = os.environ["HEALTHDATAAISERVICES_DEID_SERVICE_ENDPOINT"]
credential = DefaultAzureCredential()
client = DeidentificationClient(endpoint, credential)

body = DeidentificationContent(
    input_text="It's great to work at Contoso.", operation_type=DeidentificationOperationType.REDACT
)
result: DeidentificationResult = client.deidentify_text(body)
print(f'\nOriginal Text:   "{body.input_text}"')
print(f'Redacted Text:   "{result.output_text}"')  # Redacted output: "It's great to work at [organization]."
```

<!-- END SNIPPET -->

### Replace PHI in unstructured text with realistic surrogate values
The default operation is the `SURROGATE` operation. Using this operation, the service will replace the PHI entities it detects with realistic surrogate values:
<!-- SNIPPET: deidentify_text_surrogate.surrogate -->

```python
from azure.health.deidentification import DeidentificationClient
from azure.health.deidentification.models import (
    DeidentificationContent,
    DeidentificationOperationType,
    DeidentificationResult,
)
from azure.identity import DefaultAzureCredential
import os

endpoint = os.environ["HEALTHDATAAISERVICES_DEID_SERVICE_ENDPOINT"]
credential = DefaultAzureCredential()
client = DeidentificationClient(endpoint, credential)

body = DeidentificationContent(
    input_text="Hello, my name is John Smith.", operation_type=DeidentificationOperationType.SURROGATE
)
result: DeidentificationResult = client.deidentify_text(body)
print(f'\nOriginal Text:     "{body.input_text}"')
print(f'Surrogated Text:   "{result.output_text}"')  # Surrogated output: Hello, my name is <synthetic name>.
```

<!-- END SNIPPET -->

### Replace only specific PHI entities with surrogate values
The `SURROGATE_ONLY` operation returns output text where user-defined PHI entities are replaced with realistic replacement values.
<!-- SNIPPET: deidentify_text_surrogate_only.surrogate_only -->

```python
from azure.health.deidentification import DeidentificationClient
from azure.health.deidentification.models import (
    DeidentificationContent,
    DeidentificationCustomizationOptions,
    DeidentificationOperationType,
    DeidentificationResult,
    PhiCategory,
    SimplePhiEntity,
    TaggedPhiEntities,
    TextEncodingType,
)
from azure.identity import DefaultAzureCredential
import os

endpoint = os.environ["HEALTHDATAAISERVICES_DEID_SERVICE_ENDPOINT"]
credential = DefaultAzureCredential()
client = DeidentificationClient(endpoint, credential)

# Define the entities to be surrogated - targeting "John Smith" at position 18-28
tagged_entities = TaggedPhiEntities(
    encoding=TextEncodingType.CODE_POINT,
    entities=[SimplePhiEntity(category=PhiCategory.PATIENT, offset=18, length=10)],
)

# Use SurrogateOnly operation with input locale specification
body = DeidentificationContent(
    input_text="Hello, my name is John Smith.",
    operation_type=DeidentificationOperationType.SURROGATE_ONLY,
    tagged_entities=tagged_entities,
    customizations=DeidentificationCustomizationOptions(
        input_locale="en-US"  # Specify input text locale for better PHI detection
    ),
)

result: DeidentificationResult = client.deidentify_text(body)
print(f'\nOriginal Text:        "{body.input_text}"')
print(f'Surrogate Only Text:  "{result.output_text}"')  # Surrogated output: Hello, my name is <synthetic name>.
```

<!-- END SNIPPET -->

### Troubleshooting
The `DeidentificationClient` raises various `AzureError` [exceptions][azure_error]. For example, if you
provide an invalid service URL, an `ServiceRequestError` would be raised with a message indicating the failure cause.
In the following code snippet, the error is handled and displayed:
<!-- SNIPPET: examples.handle_error -->

```python
from azure.core.exceptions import AzureError
from azure.health.deidentification.models import (
    DeidentificationContent,
)


error_client = DeidentificationClient("https://contoso.deid.azure.com", credential)
body = DeidentificationContent(input_text="Hello, I'm Dr. John Smith.")

try:
    error_client.deidentify_text(body)
except AzureError as e:
    print("\nError: " + e.message)
```

<!-- END SNIPPET -->

If you encounter an error indicating that the service is unable to access source or target storage in a de-identification job:
- Ensure you [assign a managed identity][deid_managed_identity] to your de-identification service
- Ensure you [assign appropriate permissions][deid_rbac] to the managed identity to access the storage account

## Next steps

Find a bug, or have feedback? Raise an issue with the [Health Deidentification][github_issue_label] label.

## Troubleshooting

- **Unable to Access Source or Target Storage**
  - Ensure you create your deid service with a system assigned managed identity
  - Ensure your storage account has given permissions to that managed identity

## Contributing

This project welcomes contributions and suggestions. Most contributions require
you to agree to a Contributor License Agreement (CLA) declaring that you have
the right to, and actually do, grant us the rights to use your contribution.
For details, visit https://cla.microsoft.com.

When you submit a pull request, a CLA-bot will automatically determine whether
you need to provide a CLA and decorate the PR appropriately (e.g., label,
comment). Simply follow the instructions provided by the bot. You will only
need to do this once across all repos using our CLA.

This project has adopted the
[Microsoft Open Source Code of Conduct][code_of_conduct]. For more information,
see the Code of Conduct FAQ or contact opencode@microsoft.com with any
additional questions or comments.

<!-- LINKS -->
[code_of_conduct]: https://opensource.microsoft.com/codeofconduct/
[product_documentation]: https://learn.microsoft.com/azure/healthcare-apis/deidentification/
[azure_identity_pip]: https://pypi.org/project/azure-identity/
[default_azure_credential]: https://github.com/Azure/azure-sdk-for-python/tree/main/sdk/identity/azure-identity#defaultazurecredential
[pip]: https://pypi.org/project/pip/
[azure_sub]: https://azure.microsoft.com/free/
[deid_quickstart]: https://learn.microsoft.com/azure/healthcare-apis/deidentification/quickstart
[string_index]: https://github.com/Azure/azure-sdk-for-python/blob/main/sdk/healthdataaiservices/azure-health-deidentification/azure/health/deidentification/models/_models.py#L548
[character_encoding]: https://learn.microsoft.com/dotnet/standard/base-types/character-encoding-introduction
[deid_redact]: https://learn.microsoft.com/azure/healthcare-apis/deidentification/redaction-format
[deid_rbac]: https://learn.microsoft.com/azure/healthcare-apis/deidentification/manage-access-rbac
[deid_managed_identity]: https://learn.microsoft.com/azure/healthcare-apis/deidentification/managed-identities
[deid_configure_storage]: https://learn.microsoft.com/azure/healthcare-apis/deidentification/configure-storage
[azure_cli]: https://learn.microsoft.com/cli/azure/healthcareapis/deidservice?view=azure-cli-latest
[azure_portal]: https://ms.portal.azure.com
[azure_error]: https://learn.microsoft.com/python/api/azure-core/azure.core.exceptions.azureerror
[samples]: https://github.com/Azure/azure-sdk-for-python/tree/main/sdk/healthdataaiservices/azure-health-deidentification/samples
[github_issue_label]: https://github.com/Azure/azure-sdk-for-python/labels/Health%20Deidentification
[blob_names]: https://learn.microsoft.com/rest/api/storageservices/naming-and-referencing-containers--blobs--and-metadata#blob-names
[test_data]: https://github.com/Azure/azure-sdk-for-python/tree/main/sdk/healthdataaiservices/azure-health-deidentification/tests/data