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Regenerated healtcare README.rst files (#2132)
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‎healthcare/api-client/datasets/README.rst

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Original file line numberDiff line numberDiff line change
@@ -31,21 +31,6 @@ 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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@@ -94,29 +79,42 @@ To run this sample:
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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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usage: datasets.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] [--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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[--keeplist_tags KEEPLIST_TAGS] [--member MEMBER]
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[--role ROLE]
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{create-dataset,delete-dataset,get-dataset,list-datasets,patch-dataset,get_iam_policy,set_iam_policy,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,delete-dataset,get-dataset,list-datasets,patch-dataset,get_iam_policy,set_iam_policy,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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get_iam_policy Gets the IAM policy for the specified dataset.
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set_iam_policy Sets the IAM policy for the specified dataset. 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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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
@@ -128,9 +126,12 @@ To run this sample:
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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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--keeplist_tags KEEPLIST_TAGS
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The data to keeplist, for example "PatientID" or
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"StudyInstanceUID"
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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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‎healthcare/api-client/dicom/README.rst

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Original file line numberDiff line numberDiff line change
@@ -31,21 +31,6 @@ credentials for applications.
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.. _Authentication Getting Started Guide:
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https://cloud.google.com/docs/authentication/getting-started
3333

34-
Authentication
35-
++++++++++++++
36-
37-
Authentication for this service is done via an `API Key`_. To obtain an API
38-
Key:
39-
40-
1. Open the `Cloud Platform Console`_
41-
2. Make sure that billing is enabled for your project.
42-
3. From the **Credentials** page, create a new **API Key** or use an existing
43-
one for your project.
44-
45-
.. _API Key:
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https://developers.google.com/api-client-library/python/guide/aaa_apikeys
47-
.. _Cloud Console: https://console.cloud.google.com/project?_
48-
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Install Dependencies
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++++++++++++++++++++
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@@ -95,22 +80,36 @@ To run this sample:
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$ python dicom_stores.py
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usage: dicom_stores.py [-h] [--service_account_json SERVICE_ACCOUNT_JSON]
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[--api_key API_KEY] [--project_id PROJECT_ID]
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[--cloud_region CLOUD_REGION] [--dataset_id DATASET_ID]
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[--project_id PROJECT_ID] [--cloud_region CLOUD_REGION]
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[--dataset_id DATASET_ID]
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[--dicom_store_id DICOM_STORE_ID]
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[--pubsub_topic PUBSUB_TOPIC] [--uri_prefix URI_PREFIX]
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[--content_uri CONTENT_URI]
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[--export_format {FORMAT_UNSPECIFIED,DICOM,JSON_BIGQUERY_IMPORT}]
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{create-dicom-store,delete-dicom-store,get-dicom-store,list-dicom-stores,patch-dicom-store,export-dicom-store,import-dicom-store}
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[--member MEMBER] [--role ROLE]
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{create-dicom-store,delete-dicom-store,get-dicom-store,list-dicom-stores,patch-dicom-store,get_iam_policy,set_iam_policy,export-dicom-store,import-dicom-store}
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...
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positional arguments:
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{create-dicom-store,delete-dicom-store,get-dicom-store,list-dicom-stores,patch-dicom-store,export-dicom-store,import-dicom-store}
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{create-dicom-store,delete-dicom-store,get-dicom-store,list-dicom-stores,patch-dicom-store,get_iam_policy,set_iam_policy,export-dicom-store,import-dicom-store}
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create-dicom-store Creates a new DICOM store within the parent dataset.
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delete-dicom-store Deletes the specified DICOM store.
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get-dicom-store Gets the specified DICOM store.
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list-dicom-stores Lists the DICOM stores in the given dataset.
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patch-dicom-store Updates the DICOM store.
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get_iam_policy Gets the IAM policy for the specified dicom store.
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set_iam_policy Sets the IAM policy for the specified dicom 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'
114113
export-dicom-store Export data to a Google Cloud Storage bucket by
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copying it from the DICOM store.
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import-dicom-store Import data into the DICOM store by copying it from
@@ -120,7 +119,6 @@ To run this sample:
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-h, --help show this help message and exit
121120
--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
@@ -144,6 +142,66 @@ To run this sample:
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Specifies the output format. If the format is
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unspecified, thedefault functionality is to export to
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DICOM.
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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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DICOMweb
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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/dicom/dicomweb.py,healthcare/api-client/dicom/README.rst
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To run this sample:
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.. code-block:: bash
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$ python dicomweb.py
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usage: dicomweb.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] [--dataset_id DATASET_ID]
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[--dicom_store_id DICOM_STORE_ID] [--dcm_file DCM_FILE]
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[--study_uid STUDY_UID]
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{dicomweb-store-instance,dicomweb-search-instance,dicomweb-retrieve-study,dicomweb-delete-study}
172+
...
173+
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positional arguments:
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{dicomweb-store-instance,dicomweb-search-instance,dicomweb-retrieve-study,dicomweb-delete-study}
176+
dicomweb-store-instance
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Handles the POST requests specified in the DICOMweb
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standard.
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dicomweb-search-instance
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Handles the GET requests specified in DICOMweb
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standard.
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dicomweb-retrieve-study
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Handles the GET requests specified in the DICOMweb
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standard.
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dicomweb-delete-study
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Handles DELETE requests equivalent to the GET requests
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specified in the WADO-RS standard.
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optional arguments:
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-h, --help show this help message and exit
191+
--service_account_json SERVICE_ACCOUNT_JSON
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Path to service account JSON file.
193+
--base_url BASE_URL Healthcare API URL
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--project_id PROJECT_ID
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GCP project name
196+
--cloud_region CLOUD_REGION
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GCP region
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--dataset_id DATASET_ID
199+
Name of dataset
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--dicom_store_id DICOM_STORE_ID
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Name of DICOM store
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--dcm_file DCM_FILE File name for DCM file to store.
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--study_uid STUDY_UID
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Unique identifier for a study.
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@@ -164,4 +222,4 @@ to `browse the source`_ and `report issues`_.
164222
https://github.com/GoogleCloudPlatform/google-cloud-python/issues
165223

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167-
.. _Google Cloud SDK: https://cloud.google.com/sdk/
225+
.. _Google Cloud SDK: https://cloud.google.com/sdk/

‎healthcare/api-client/fhir/README.rst

Lines changed: 59 additions & 24 deletions
Original file line numberDiff line numberDiff line change
@@ -31,21 +31,6 @@ credentials for applications.
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.. _Authentication Getting Started Guide:
3232
https://cloud.google.com/docs/authentication/getting-started
3333

34-
Authentication
35-
++++++++++++++
36-
37-
Authentication for this service is done via an `API Key`_. To obtain an API
38-
Key:
39-
40-
1. Open the `Cloud Platform Console`_
41-
2. Make sure that billing is enabled for your project.
42-
3. From the **Credentials** page, create a new **API Key** or use an existing
43-
one for your project.
44-
45-
.. _API Key:
46-
https://developers.google.com/api-client-library/python/guide/aaa_apikeys
47-
.. _Cloud Console: https://console.cloud.google.com/project?_
48-
4934
Install Dependencies
5035
++++++++++++++++++++
5136

@@ -95,26 +80,44 @@ To run this sample:
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$ python fhir_stores.py
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usage: fhir_stores.py [-h] [--service_account_json SERVICE_ACCOUNT_JSON]
98-
[--api_key API_KEY] [--project_id PROJECT_ID]
99-
[--cloud_region CLOUD_REGION] [--dataset_id DATASET_ID]
83+
[--project_id PROJECT_ID] [--cloud_region CLOUD_REGION]
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[--dataset_id DATASET_ID]
10085
[--fhir_store_id FHIR_STORE_ID]
101-
[--pubsub_topic PUBSUB_TOPIC]
102-
{create-fhir-store,delete-fhir-store,get-fhir-store,list-fhir-stores,patch-fhir-store}
86+
[--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}
10389
...
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positional arguments:
106-
{create-fhir-store,delete-fhir-store,get-fhir-store,list-fhir-stores,patch-fhir-store}
92+
{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}
10793
create-fhir-store Creates a new FHIR store within the parent dataset.
10894
delete-fhir-store Deletes the specified FHIR store.
10995
get-fhir-store Gets the specified FHIR store.
11096
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
101+
Export resources to a Google Cloud Storage bucket by
102+
copying them from the FHIR store.
103+
get_iam_policy Gets the IAM policy for the specified FHIR store.
104+
set_iam_policy Sets the IAM policy for the specified FHIR store. A
105+
single member will be assigned a single role. A member
106+
can be any of: - allUsers, that is, anyone -
107+
allAuthenticatedUsers, anyone authenticated with a
108+
Google account - user:email, as in
109+
'user:[email protected]' - group:email, as in
110+
'group:[email protected]' - domain:domainname, as in
111+
'domain:example.com' - serviceAccount:email, as in
112+
'serviceAccount:my-other-
113+
[email protected]' A role can be any IAM
114+
role, such as 'roles/viewer', 'roles/owner', or
115+
'roles/editor'
112116
113117
optional arguments:
114118
-h, --help show this help message and exit
115119
--service_account_json SERVICE_ACCOUNT_JSON
116120
Path to service account JSON file.
117-
--api_key API_KEY Your API key.
118121
--project_id PROJECT_ID
119122
GCP cloud project name
120123
--cloud_region CLOUD_REGION
@@ -126,6 +129,13 @@ To run this sample:
126129
--pubsub_topic PUBSUB_TOPIC
127130
The Cloud Pub/Sub topic where notifications of changes
128131
are published
132+
--gcs_uri GCS_URI URI for a Google Cloud Storage directory from which
133+
filesshould be import or to which result filesshould
134+
be written (e.g., "bucket-
135+
id/path/to/destination/dir").
136+
--member MEMBER Member to add to IAM policy (e.g.
137+
"domain:example.com")
138+
--role ROLE IAM Role to give to member (e.g. "roles/viewer")
129139
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131141
@@ -150,17 +160,36 @@ To run this sample:
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[--dataset_id DATASET_ID]
151161
[--fhir_store_id FHIR_STORE_ID]
152162
[--resource_type RESOURCE_TYPE]
153-
[--resource_id RESOURCE_ID]
154-
{create-resource,delete-resource,get-resource,update-resource,patch-resource,search-resources-get,search-resources-post,get-patient-everything,get-metadata}
163+
[--resource_id RESOURCE_ID] [--bundle BUNDLE]
164+
[--uri_prefix URI_PREFIX] [--version_id VERSION_ID]
165+
{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}
155166
...
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positional arguments:
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{create-resource,delete-resource,get-resource,update-resource,patch-resource,search-resources-get,search-resources-post,get-patient-everything,get-metadata}
169+
{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}
159170
create-resource Creates a new resource in a FHIR store.
160171
delete-resource Creates a new resource in a FHIR store.
172+
conditional-delete-resource
173+
Deletes an existing resource specified by search
174+
criteria.
161175
get-resource Gets a FHIR resource.
176+
list-resource-history
177+
Gets the history of a resource.
178+
export-resources Exports resources in a FHIR store.
179+
export-resources Exports resources in a FHIR store.
180+
execute_bundle Executes the operations in the given bundle.
181+
get-resource-history
182+
Gets a version resource.
183+
delete-resource-purge
184+
Deletes versions of a resource (excluding current
185+
version).
162186
update-resource Updates an existing resource.
187+
conditional-update-resource
188+
Updates an existing resource specified by search
189+
criteria.
163190
patch-resource Updates part of an existing resource..
191+
conditional-patch-resource
192+
Updates part of an existing resource..
164193
search-resources-get
165194
Searches resources in the given FHIR store using the
166195
searchResources GET method.
@@ -188,6 +217,12 @@ To run this sample:
188217
The type of resource. First letter must be capitalized
189218
--resource_id RESOURCE_ID
190219
Name of a FHIR resource
220+
--bundle BUNDLE Name of file containing bundle of operations to
221+
execute
222+
--uri_prefix URI_PREFIX
223+
Prefix of gs:// URIs for import and export
224+
--version_id VERSION_ID
225+
Version of a FHIR resource
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