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Add CHC API alpha datasets and FHIR samples and tests. (#1783)
* Add CHC API datasets samples and tests. * Add CHC API alpha FHIR samples and tests * Fix lint error. ./fhir_resources.py:330:80: E501 line too long (91 > 79 characters) resource_path = '{}/datasets/{}/fhirStores/{}/resources/Patient/{}/$everything'.format( * Fix lint errors. ./fhir_resources_test.py:22:1: E402 module level import not at top of file import datasets ^ ./fhir_resources_test.py:23:1: E402 module level import not at top of file import fhir_stores ^ ./fhir_resources_test.py:24:1: E402 module level import not at top of file import fhir_resources ^ * Fix lint errors. ./fhir_stores.py:85:80: E501 line too long (82 > 79 characters) fhir_store_name = 'projects/{}/locations/{}/datasets/{}/fhirStores/{}'.format( ^ ./fhir_stores.py:111:80: E501 line too long (82 > 79 characters) fhir_store_name = 'projects/{}/locations/{}/datasets/{}/fhirStores/{}'.format( ^ ./fhir_stores.py:340:5: E303 too many blank lines (2) command = parser.add_subparsers(dest='command') ^ ./fhir_stores.py:347:80: E501 line too long (81 > 79 characters) command.add_parser('export-fhir-resource', help=import_fhir_resource.__doc__) ^ ./fhir_stores.py:348:80: E501 line too long (81 > 79 characters) command.add_parser('import-fhir-resource', help=export_fhir_resource.__doc__) ^ ./fhir_stores.py:349:1: W293 blank line contains whitespace * Fix lint errors. ./fhir_stores_test.py:22:1: E402 module level import not at top of file import datasets ^ ./fhir_stores_test.py:23:1: E402 module level import not at top of file import fhir_stores * Remove blank line. * Remove blank line. * Remove blank line. * Remove blank line.
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‎healthcare/api-client/datasets/README.rst

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.. This file is automatically generated. Do not edit this file directly.
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Cloud Healthcare API Python Samples
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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/datasets/README.rst
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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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.. _migration guide: https://cloud.google.com/vision/docs/python-client-migration
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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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Authentication
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++++++++++++++
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Authentication for this service is done via an `API Key`_. To obtain an API
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Key:
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1. Open the `Cloud Platform Console`_
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2. Make sure that billing is enabled for your project.
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3. From the **Credentials** page, create a new **API Key** or use an existing
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one for your project.
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.. _API Key:
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https://developers.google.com/api-client-library/python/guide/aaa_apikeys
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.. _Cloud Console: https://console.cloud.google.com/project?_
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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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Datasets
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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/datasets/datasets.py,healthcare/api-client/datasets/README.rst
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To run this sample:
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.. code-block:: bash
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$ python datasets.py
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usage: datasets.py [-h] --service_account_json SERVICE_ACCOUNT_JSON --api_key
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API_KEY --project_id PROJECT_ID --cloud_region CLOUD_REGION
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--dataset_id DATASET_ID [--time_zone TIME_ZONE]
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[--destination_dataset_id DESTINATION_DATASET_ID]
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[--whitelist_tags WHITELIST_TAGS]
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{create-dataset,delete-dataset,get-dataset,list-datasets,patch-dataset,deidentify-dataset}
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...
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positional arguments:
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{create-dataset,delete-dataset,get-dataset,list-datasets,patch-dataset,deidentify-dataset}
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create-dataset Creates a dataset.
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delete-dataset Deletes a dataset.
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get-dataset Gets any metadata associated with a dataset.
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list-datasets Lists the datasets in the project.
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patch-dataset Updates dataset metadata.
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deidentify-dataset Creates a new dataset containing de-identified data
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from the source dataset.
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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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--api_key API_KEY Your API key.
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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 cloud region
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--dataset_id DATASET_ID
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Name of dataset
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--time_zone TIME_ZONE
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The default timezone used by a dataset
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--destination_dataset_id DESTINATION_DATASET_ID
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The name of the new dataset where the de-identified
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data will be written
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--whitelist_tags WHITELIST_TAGS
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The data to whitelist, for example "PatientID" or
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"StudyInstanceUID"
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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/

‎healthcare/api-client/datasets/README.rst.in

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# This file is used to generate README.rst
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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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- See the `migration guide`_ for information about migrating to Python client library v0.25.1.
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.. _migration guide: https://cloud.google.com/vision/docs/python-client-migration
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setup:
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- auth
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- auth_api_key
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- install_deps
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samples:
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- name: Datasets
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file: datasets.py
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show_help: True
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cloud_client_library: true
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folder: healthcare/api-client/datasets

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