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Cloud Healthcare API beta FHIR updates (GoogleCloudPlatform#2639)
* Cloud Healthcare API beta FHIR updates * Format fixes. * Run black * Fix lint * Remove modified Patient.json from PR * Address review comments. * Fix conditional tests so that they don't detect multiple resources * Fix lint issues * Skip delete blob in test if it was already deleted * fix lint and disable two conditional tests * lint fix Co-authored-by: Leah E. Cole <[email protected]>
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‎healthcare/api-client/fhir/README.rst.in

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# This file is used to generate README.rst
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.. This file is automatically generated. Do not edit this file directly.
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product:
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name: Cloud Healthcare API
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short_name: Healthcare API
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url: https://cloud.google.com/healthcare/docs
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description: >
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`Cloud Healthcare API`_ implements healthcare-native protocols and formats
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to accelerate ingestion, storage, analysis, and integration of healthcare
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data with cloud-based applications.
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Cloud Healthcare API Python Samples
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===============================================================================
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- See the `migration guide`_ for information about migrating to Python client library v0.25.1.
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.. image:: https://gstatic.com/cloudssh/images/open-btn.png
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: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
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.. _migration guide: https://cloud.google.com/vision/docs/python-client-migration
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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.
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- See the `migration guide`_ for information about migrating to Python client library v0.25.1.
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setup:
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- auth
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- install_deps
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.. _migration guide: https://cloud.google.com/vision/docs/python-client-migration
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samples:
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- name: FHIR stores
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file: fhir_stores.py
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show_help: True
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- name: FHIR resources
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file: fhir_resources.py
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show_help: True
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cloud_client_library: true
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folder: healthcare/api-client/fhir
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.. _Cloud Healthcare API: https://cloud.google.com/healthcare/docs
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Setup
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-------------------------------------------------------------------------------
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Authentication
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++++++++++++++
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This sample requires you to have authentication setup. Refer to the
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`Authentication Getting Started Guide`_ for instructions on setting up
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credentials for applications.
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.. _Authentication Getting Started Guide:
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https://cloud.google.com/docs/authentication/getting-started
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Install Dependencies
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++++++++++++++++++++
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#. Clone python-docs-samples and change directory to the sample directory you want to use.
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.. code-block:: bash
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$ git clone https://github.com/GoogleCloudPlatform/python-docs-samples.git
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#. 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.
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.. _Python Development Environment Setup Guide:
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https://cloud.google.com/python/setup
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#. Create a virtualenv. Samples are compatible with Python 2.7 and 3.4+.
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.. code-block:: bash
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$ virtualenv env
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$ source env/bin/activate
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#. Install the dependencies needed to run the samples.
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.. code-block:: bash
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$ pip install -r requirements.txt
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.. _pip: https://pip.pypa.io/
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.. _virtualenv: https://virtualenv.pypa.io/
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Samples
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-------------------------------------------------------------------------------
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FHIR stores
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+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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.. image:: https://gstatic.com/cloudssh/images/open-btn.png
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: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
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To run this sample:
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.. code-block:: bash
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$ python fhir_stores.py
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usage: fhir_stores.py [-h] [--service_account_json SERVICE_ACCOUNT_JSON]
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[--project_id PROJECT_ID] [--cloud_region CLOUD_REGION]
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[--dataset_id DATASET_ID]
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[--fhir_store_id FHIR_STORE_ID]
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[--pubsub_topic PUBSUB_TOPIC] [--gcs_uri GCS_URI]
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[--member MEMBER] [--role ROLE]
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{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}
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...
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positional arguments:
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{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}
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create-fhir-store Creates a new FHIR store within the parent dataset.
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delete-fhir-store Deletes the specified FHIR store.
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get-fhir-store Gets the specified FHIR store.
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list-fhir-stores Lists the FHIR stores in the given dataset.
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patch-fhir-store Updates the FHIR store.
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import-fhir-store Import resources into the FHIR store by copying them
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from the specified source.
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export-fhir-store-gcs
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Export resources to a Google Cloud Storage bucket by
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copying them from the FHIR store.
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get_iam_policy Gets the IAM policy for the specified FHIR store.
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set_iam_policy Sets the IAM policy for the specified FHIR store. A
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single member will be assigned a single role. A member
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can be any of: - allUsers, that is, anyone -
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allAuthenticatedUsers, anyone authenticated with a
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Google account - user:email, as in
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'user:[email protected]' - group:email, as in
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'group:[email protected]' - domain:domainname, as in
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'domain:example.com' - serviceAccount:email, as in
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'serviceAccount:my-other-
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[email protected]' A role can be any IAM
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role, such as 'roles/viewer', 'roles/owner', or
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'roles/editor'
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optional arguments:
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-h, --help show this help message and exit
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--service_account_json SERVICE_ACCOUNT_JSON
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Path to service account JSON file.
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--project_id PROJECT_ID
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GCP cloud project name
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--cloud_region CLOUD_REGION
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GCP cloud region
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--dataset_id DATASET_ID
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Name of dataset
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--fhir_store_id FHIR_STORE_ID
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Name of FHIR store
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--pubsub_topic PUBSUB_TOPIC
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The Cloud Pub/Sub topic where notifications of changes
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are published
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--gcs_uri GCS_URI URI for a Google Cloud Storage directory from which
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filesshould be import or to which result filesshould
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be written (e.g., "bucket-
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id/path/to/destination/dir").
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--member MEMBER Member to add to IAM policy (e.g.
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"domain:example.com")
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--role ROLE IAM Role to give to member (e.g. "roles/viewer")
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FHIR resources
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+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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.. image:: https://gstatic.com/cloudssh/images/open-btn.png
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: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
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To run this sample:
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.. code-block:: bash
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$ python fhir_resources.py
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usage: fhir_resources.py [-h] [--service_account_json SERVICE_ACCOUNT_JSON]
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[--base_url BASE_URL] [--project_id PROJECT_ID]
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[--cloud_region CLOUD_REGION]
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[--dataset_id DATASET_ID]
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[--fhir_store_id FHIR_STORE_ID]
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[--resource_type RESOURCE_TYPE]
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[--resource_id RESOURCE_ID] [--bundle BUNDLE]
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[--uri_prefix URI_PREFIX] [--version_id VERSION_ID]
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{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}
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...
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positional arguments:
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{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}
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create-patient Creates a new Patient resource in a FHIR store.
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create-encounter Creates a new Encounter resource in a FHIR store.
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create-observation Creates a new Observation resource in a FHIR store.
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delete-resource Creates a new resource in a FHIR store.
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conditional-delete-resource
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Deletes an existing resource specified by search
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criteria.
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get-resource Gets a FHIR resource.
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list-resource-history
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Gets the history of a resource.
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export-resources Exports resources in a FHIR store.
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export-resources Exports resources in a FHIR store.
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execute_bundle Executes the operations in the given bundle.
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get-resource-history
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Gets a version resource.
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delete-resource-purge
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Deletes versions of a resource (excluding current
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version).
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update-resource Updates an existing resource.
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conditional-update-resource
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Updates an existing resource specified by search
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criteria.
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patch-resource Updates part of an existing resource.
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conditional-patch-resource
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Updates part of an existing resource.
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search-resources-get
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Searches resources in the given FHIR store using the
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searchResources GET method.
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search-resources-post
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Searches resources in the given FHIR store using the
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searchResources GET method.
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get-patient-everything
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Gets all the resources in the patient compartment.
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get-metadata Gets the capabilities statement for a FHIR store.
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optional arguments:
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-h, --help show this help message and exit
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--service_account_json SERVICE_ACCOUNT_JSON
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Path to service account JSON file.
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--base_url BASE_URL Healthcare API URL.
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--project_id PROJECT_ID
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GCP project name
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--cloud_region CLOUD_REGION
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GCP region
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--dataset_id DATASET_ID
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Name of dataset
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--fhir_store_id FHIR_STORE_ID
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Name of FHIR store
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--resource_type RESOURCE_TYPE
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The type of resource. First letter must be capitalized
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--resource_id RESOURCE_ID
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Name of a FHIR resource
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--patient_id PATIENT_ID
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Identifier for a Patient resource. Can be used as a reference for an Encounter/Observation
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--encounter_id ENCOUNTER_ID
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Identifier for an Encounter resource. Can be used as a reference for an Observation
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--bundle BUNDLE Name of file containing bundle of operations to
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execute
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--uri_prefix URI_PREFIX
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Prefix of gs:// URIs for import and export
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--version_id VERSION_ID
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Version of a FHIR resource
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The client library
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-------------------------------------------------------------------------------
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This sample uses the `Google Cloud Client Library for Python`_.
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You can read the documentation for more details on API usage and use GitHub
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to `browse the source`_ and `report issues`_.
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.. _Google Cloud Client Library for Python:
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https://googlecloudplatform.github.io/google-cloud-python/
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.. _browse the source:
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https://github.com/GoogleCloudPlatform/google-cloud-python
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.. _report issues:
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https://github.com/GoogleCloudPlatform/google-cloud-python/issues
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.. _Google Cloud SDK: https://cloud.google.com/sdk/

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