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Cloud Healthcare API Python Samples

===============================================================================

.. image:: https://gstatic.com/cloudssh/images/open-btn.png

:target: https://console.cloud.google.com/cloudshell/open?git_repo=https://github.com/GoogleCloudPlatform/python-docs-samples&page=editor&open_in_editor=healthcare/api-client/fhir/README.rst

This directory contains samples for Cloud Healthcare API. `Cloud Healthcare API`_ implements healthcare-native protocols and formats to accelerate ingestion, storage, analysis, and integration of healthcare data with cloud-based applications.

- See the `migration guide`_ for information about migrating to Python client library v0.25.1.

.. _migration guide: https://cloud.google.com/vision/docs/python-client-migration

.. _Cloud Healthcare API: https://cloud.google.com/healthcare/docs

Setup

-------------------------------------------------------------------------------

Authentication

++++++++++++++

This sample requires you to have authentication setup. Refer to the

`Authentication Getting Started Guide`_ for instructions on setting up

credentials for applications.

.. _Authentication Getting Started Guide:

https://cloud.google.com/docs/authentication/getting-started

Install Dependencies

++++++++++++++++++++

#. Clone python-docs-samples and change directory to the sample directory you want to use.

.. code-block:: bash

$ git clone https://github.com/GoogleCloudPlatform/python-docs-samples.git

#. Install `pip`_ and `virtualenv`_ if you do not already have them. You may want to refer to the `Python Development Environment Setup Guide`_ for Google Cloud Platform for instructions.

.. _Python Development Environment Setup Guide:

https://cloud.google.com/python/setup

#. Create a virtualenv. Samples are compatible with Python 2.7 and 3.4+.

.. code-block:: bash

$ virtualenv env

$ source env/bin/activate

#. Install the dependencies needed to run the samples.

.. code-block:: bash

$ pip install -r requirements.txt

.. _pip: https://pip.pypa.io/

.. _virtualenv: https://virtualenv.pypa.io/

Samples

-------------------------------------------------------------------------------

FHIR stores

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

.. image:: https://gstatic.com/cloudssh/images/open-btn.png

:target: https://console.cloud.google.com/cloudshell/open?git_repo=https://github.com/GoogleCloudPlatform/python-docs-samples&page=editor&open_in_editor=healthcare/api-client/fhir/fhir_stores.py,healthcare/api-client/fhir/README.rst

To run this sample:

.. code-block:: bash

$ python fhir_stores.py

usage: fhir_stores.py [-h] [--service_account_json SERVICE_ACCOUNT_JSON]

[--project_id PROJECT_ID] [--cloud_region CLOUD_REGION]

[--dataset_id DATASET_ID]

[--fhir_store_id FHIR_STORE_ID]

[--pubsub_topic PUBSUB_TOPIC] [--gcs_uri GCS_URI]

[--member MEMBER] [--role ROLE]

{create-fhir-store,delete-fhir-store,get-fhir-store,list-fhir-stores,patch-fhir-store,import-fhir-store,export-fhir-store-gcs,get_iam_policy,set_iam_policy}

...

positional arguments:

{create-fhir-store,delete-fhir-store,get-fhir-store,list-fhir-stores,patch-fhir-store,import-fhir-store,export-fhir-store-gcs,get_iam_policy,set_iam_policy}

create-fhir-store Creates a new FHIR store within the parent dataset.

delete-fhir-store Deletes the specified FHIR store.

get-fhir-store Gets the specified FHIR store.

list-fhir-stores Lists the FHIR stores in the given dataset.

patch-fhir-store Updates the FHIR store.

import-fhir-store Import resources into the FHIR store by copying them

from the specified source.

export-fhir-store-gcs

Export resources to a Google Cloud Storage bucket by

copying them from the FHIR store.

get_iam_policy Gets the IAM policy for the specified FHIR store.

set_iam_policy Sets the IAM policy for the specified FHIR store. A

single member will be assigned a single role. A member

can be any of: - allUsers, that is, anyone -

allAuthenticatedUsers, anyone authenticated with a

Google account - user:email, as in

'user:somebody@example.com' - group:email, as in

'group:admins@example.com' - domain:domainname, as in

'domain:example.com' - serviceAccount:email, as in

'serviceAccount:my-other-

app@appspot.gserviceaccount.com' A role can be any IAM

role, such as 'roles/viewer', 'roles/owner', or

'roles/editor'

optional arguments:

-h, --help show this help message and exit

--service_account_json SERVICE_ACCOUNT_JSON

Path to service account JSON file.

--project_id PROJECT_ID

GCP cloud project name

--cloud_region CLOUD_REGION

GCP cloud region

--dataset_id DATASET_ID

Name of dataset

--fhir_store_id FHIR_STORE_ID

Name of FHIR store

--pubsub_topic PUBSUB_TOPIC

The Cloud Pub/Sub topic where notifications of changes

are published

--gcs_uri GCS_URI URI for a Google Cloud Storage directory from which

filesshould be import or to which result filesshould

be written (e.g., "bucket-

id/path/to/destination/dir").

--member MEMBER Member to add to IAM policy (e.g.

"domain:example.com")

--role ROLE IAM Role to give to member (e.g. "roles/viewer")

FHIR resources

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

.. image:: https://gstatic.com/cloudssh/images/open-btn.png

:target: https://console.cloud.google.com/cloudshell/open?git_repo=https://github.com/GoogleCloudPlatform/python-docs-samples&page=editor&open_in_editor=healthcare/api-client/fhir/fhir_resources.py,healthcare/api-client/fhir/README.rst

To run this sample:

.. code-block:: bash

$ python fhir_resources.py

usage: fhir_resources.py [-h] [--service_account_json SERVICE_ACCOUNT_JSON]

[--base_url BASE_URL] [--project_id PROJECT_ID]

[--cloud_region CLOUD_REGION]

[--dataset_id DATASET_ID]

[--fhir_store_id FHIR_STORE_ID]

[--resource_type RESOURCE_TYPE]

[--resource_id RESOURCE_ID] [--bundle BUNDLE]

[--uri_prefix URI_PREFIX] [--version_id VERSION_ID]

{create-resource,delete-resource,conditional-delete-resource,get-resource,list-resource-history,export-resources,execute_bundle,get-resource-history,delete-resource-purge,update-resource,conditional-update-resource,patch-resource,conditional-patch-resource,search-resources-get,search-resources-post,get-patient-everything,get-metadata}

...

positional arguments:

{create-patient,create-encounter,create-observation,delete-resource,conditional-delete-resource,get-resource,list-resource-history,export-resources,execute_bundle,get-resource-history,delete-resource-purge,update-resource,conditional-update-resource,patch-resource,conditional-patch-resource,search-resources-get,search-resources-post,get-patient-everything,get-metadata}

create-patient Creates a new Patient resource in a FHIR store.

create-encounter Creates a new Encounter resource in a FHIR store.

create-observation Creates a new Observation resource in a FHIR store.

delete-resource Creates a new resource in a FHIR store.

conditional-delete-resource

Deletes an existing resource specified by search

criteria.

get-resource Gets a FHIR resource.

list-resource-history

Gets the history of a resource.

export-resources Exports resources in a FHIR store.

export-resources Exports resources in a FHIR store.

execute_bundle Executes the operations in the given bundle.

get-resource-history

Gets a version resource.

delete-resource-purge

Deletes versions of a resource (excluding current

version).

update-resource Updates an existing resource.

conditional-update-resource

Updates an existing resource specified by search

criteria.

patch-resource Updates part of an existing resource.

conditional-patch-resource

Updates part of an existing resource.

search-resources-get

Searches resources in the given FHIR store using the

searchResources GET method.

search-resources-post

Searches resources in the given FHIR store using the

searchResources GET method.

get-patient-everything

Gets all the resources in the patient compartment.

get-metadata Gets the capabilities statement for a FHIR store.

optional arguments:

-h, --help show this help message and exit

--service_account_json SERVICE_ACCOUNT_JSON

Path to service account JSON file.

--base_url BASE_URL Healthcare API URL.

--project_id PROJECT_ID

GCP project name

--cloud_region CLOUD_REGION

GCP region

--dataset_id DATASET_ID

Name of dataset

--fhir_store_id FHIR_STORE_ID

Name of FHIR store

--resource_type RESOURCE_TYPE

The type of resource. First letter must be capitalized

--resource_id RESOURCE_ID

Name of a FHIR resource

--patient_id PATIENT_ID

Identifier for a Patient resource. Can be used as a reference for an Encounter/Observation

--encounter_id ENCOUNTER_ID

Identifier for an Encounter resource. Can be used as a reference for an Observation

--bundle BUNDLE Name of file containing bundle of operations to

execute

--uri_prefix URI_PREFIX

Prefix of gs:// URIs for import and export

--version_id VERSION_ID

Version of a FHIR resource

The client library

-------------------------------------------------------------------------------

This sample uses the `Google Cloud Client Library for Python`_.

You can read the documentation for more details on API usage and use GitHub

to `browse the source`_ and `report issues`_.

.. _Google Cloud Client Library for Python:

https://googlecloudplatform.github.io/google-cloud-python/

.. _browse the source:

https://github.com/GoogleCloudPlatform/google-cloud-python

.. _report issues:

https://github.com/GoogleCloudPlatform/google-cloud-python/issues

.. _Google Cloud SDK: https://cloud.google.com/sdk/