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Regenerated healtcare README.rst files #2132

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Regenerated healtcare README.rst files #2132

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49 changes: 25 additions & 24 deletions 49 healthcare/api-client/datasets/README.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -31,21 +31,6 @@ credentials for applications.
.. _Authentication Getting Started Guide:
https://cloud.google.com/docs/authentication/getting-started

Authentication
++++++++++++++

Authentication for this service is done via an `API Key`_. To obtain an API
Key:

1. Open the `Cloud Platform Console`_
2. Make sure that billing is enabled for your project.
3. From the **Credentials** page, create a new **API Key** or use an existing
one for your project.

.. _API Key:
https://developers.google.com/api-client-library/python/guide/aaa_apikeys
.. _Cloud Console: https://console.cloud.google.com/project?_

Install Dependencies
++++++++++++++++++++

Expand Down Expand Up @@ -94,29 +79,42 @@ To run this sample:

$ python datasets.py

usage: datasets.py [-h] --service_account_json SERVICE_ACCOUNT_JSON --api_key
API_KEY --project_id PROJECT_ID --cloud_region CLOUD_REGION
--dataset_id DATASET_ID [--time_zone TIME_ZONE]
usage: datasets.py [-h] [--service_account_json SERVICE_ACCOUNT_JSON]
[--project_id PROJECT_ID] [--cloud_region CLOUD_REGION]
[--dataset_id DATASET_ID] [--time_zone TIME_ZONE]
[--destination_dataset_id DESTINATION_DATASET_ID]
[--whitelist_tags WHITELIST_TAGS]
{create-dataset,delete-dataset,get-dataset,list-datasets,patch-dataset,deidentify-dataset}
[--keeplist_tags KEEPLIST_TAGS] [--member MEMBER]
[--role ROLE]
{create-dataset,delete-dataset,get-dataset,list-datasets,patch-dataset,get_iam_policy,set_iam_policy,deidentify-dataset}
...

positional arguments:
{create-dataset,delete-dataset,get-dataset,list-datasets,patch-dataset,deidentify-dataset}
{create-dataset,delete-dataset,get-dataset,list-datasets,patch-dataset,get_iam_policy,set_iam_policy,deidentify-dataset}
create-dataset Creates a dataset.
delete-dataset Deletes a dataset.
get-dataset Gets any metadata associated with a dataset.
list-datasets Lists the datasets in the project.
patch-dataset Updates dataset metadata.
get_iam_policy Gets the IAM policy for the specified dataset.
set_iam_policy Sets the IAM policy for the specified dataset. 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'
deidentify-dataset Creates a new dataset containing de-identified data
from the source dataset.

optional arguments:
-h, --help show this help message and exit
--service_account_json SERVICE_ACCOUNT_JSON
Path to service account JSON file.
--api_key API_KEY Your API key.
--project_id PROJECT_ID
GCP project name
--cloud_region CLOUD_REGION
Expand All @@ -128,9 +126,12 @@ To run this sample:
--destination_dataset_id DESTINATION_DATASET_ID
The name of the new dataset where the de-identified
data will be written
--whitelist_tags WHITELIST_TAGS
The data to whitelist, for example "PatientID" or
--keeplist_tags KEEPLIST_TAGS
The data to keeplist, for example "PatientID" or
"StudyInstanceUID"
--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")



Expand Down
100 changes: 79 additions & 21 deletions 100 healthcare/api-client/dicom/README.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -31,21 +31,6 @@ credentials for applications.
.. _Authentication Getting Started Guide:
https://cloud.google.com/docs/authentication/getting-started

Authentication
++++++++++++++

Authentication for this service is done via an `API Key`_. To obtain an API
Key:

1. Open the `Cloud Platform Console`_
2. Make sure that billing is enabled for your project.
3. From the **Credentials** page, create a new **API Key** or use an existing
one for your project.

.. _API Key:
https://developers.google.com/api-client-library/python/guide/aaa_apikeys
.. _Cloud Console: https://console.cloud.google.com/project?_

Install Dependencies
++++++++++++++++++++

Expand Down Expand Up @@ -95,22 +80,36 @@ To run this sample:
$ python dicom_stores.py

usage: dicom_stores.py [-h] [--service_account_json SERVICE_ACCOUNT_JSON]
[--api_key API_KEY] [--project_id PROJECT_ID]
[--cloud_region CLOUD_REGION] [--dataset_id DATASET_ID]
[--project_id PROJECT_ID] [--cloud_region CLOUD_REGION]
[--dataset_id DATASET_ID]
[--dicom_store_id DICOM_STORE_ID]
[--pubsub_topic PUBSUB_TOPIC] [--uri_prefix URI_PREFIX]
[--content_uri CONTENT_URI]
[--export_format {FORMAT_UNSPECIFIED,DICOM,JSON_BIGQUERY_IMPORT}]
{create-dicom-store,delete-dicom-store,get-dicom-store,list-dicom-stores,patch-dicom-store,export-dicom-store,import-dicom-store}
[--member MEMBER] [--role ROLE]
{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}
...

positional arguments:
{create-dicom-store,delete-dicom-store,get-dicom-store,list-dicom-stores,patch-dicom-store,export-dicom-store,import-dicom-store}
{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}
create-dicom-store Creates a new DICOM store within the parent dataset.
delete-dicom-store Deletes the specified DICOM store.
get-dicom-store Gets the specified DICOM store.
list-dicom-stores Lists the DICOM stores in the given dataset.
patch-dicom-store Updates the DICOM store.
get_iam_policy Gets the IAM policy for the specified dicom store.
set_iam_policy Sets the IAM policy for the specified dicom 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'
export-dicom-store Export data to a Google Cloud Storage bucket by
copying it from the DICOM store.
import-dicom-store Import data into the DICOM store by copying it from
Expand All @@ -120,7 +119,6 @@ To run this sample:
-h, --help show this help message and exit
--service_account_json SERVICE_ACCOUNT_JSON
Path to service account JSON file.
--api_key API_KEY Your API key
--project_id PROJECT_ID
GCP project name
--cloud_region CLOUD_REGION
Expand All @@ -144,6 +142,66 @@ To run this sample:
Specifies the output format. If the format is
unspecified, thedefault functionality is to export to
DICOM.
--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")



DICOMweb
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

.. 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/dicom/dicomweb.py,healthcare/api-client/dicom/README.rst




To run this sample:

.. code-block:: bash

$ python dicomweb.py

usage: dicomweb.py [-h] [--service_account_json SERVICE_ACCOUNT_JSON]
[--base_url BASE_URL] [--project_id PROJECT_ID]
[--cloud_region CLOUD_REGION] [--dataset_id DATASET_ID]
[--dicom_store_id DICOM_STORE_ID] [--dcm_file DCM_FILE]
[--study_uid STUDY_UID]
{dicomweb-store-instance,dicomweb-search-instance,dicomweb-retrieve-study,dicomweb-delete-study}
...

positional arguments:
{dicomweb-store-instance,dicomweb-search-instance,dicomweb-retrieve-study,dicomweb-delete-study}
dicomweb-store-instance
Handles the POST requests specified in the DICOMweb
standard.
dicomweb-search-instance
Handles the GET requests specified in DICOMweb
standard.
dicomweb-retrieve-study
Handles the GET requests specified in the DICOMweb
standard.
dicomweb-delete-study
Handles DELETE requests equivalent to the GET requests
specified in the WADO-RS standard.

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
--dicom_store_id DICOM_STORE_ID
Name of DICOM store
--dcm_file DCM_FILE File name for DCM file to store.
--study_uid STUDY_UID
Unique identifier for a study.



Expand All @@ -164,4 +222,4 @@ to `browse the source`_ and `report issues`_.
https://github.com/GoogleCloudPlatform/google-cloud-python/issues


.. _Google Cloud SDK: https://cloud.google.com/sdk/
.. _Google Cloud SDK: https://cloud.google.com/sdk/
83 changes: 59 additions & 24 deletions 83 healthcare/api-client/fhir/README.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -31,21 +31,6 @@ credentials for applications.
.. _Authentication Getting Started Guide:
https://cloud.google.com/docs/authentication/getting-started

Authentication
++++++++++++++

Authentication for this service is done via an `API Key`_. To obtain an API
Key:

1. Open the `Cloud Platform Console`_
2. Make sure that billing is enabled for your project.
3. From the **Credentials** page, create a new **API Key** or use an existing
one for your project.

.. _API Key:
https://developers.google.com/api-client-library/python/guide/aaa_apikeys
.. _Cloud Console: https://console.cloud.google.com/project?_

Install Dependencies
++++++++++++++++++++

Expand Down Expand Up @@ -95,26 +80,44 @@ To run this sample:
$ python fhir_stores.py

usage: fhir_stores.py [-h] [--service_account_json SERVICE_ACCOUNT_JSON]
[--api_key API_KEY] [--project_id PROJECT_ID]
[--cloud_region CLOUD_REGION] [--dataset_id DATASET_ID]
[--project_id PROJECT_ID] [--cloud_region CLOUD_REGION]
[--dataset_id DATASET_ID]
[--fhir_store_id FHIR_STORE_ID]
[--pubsub_topic PUBSUB_TOPIC]
{create-fhir-store,delete-fhir-store,get-fhir-store,list-fhir-stores,patch-fhir-store}
[--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}
{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.
--api_key API_KEY Your API key.
--project_id PROJECT_ID
GCP cloud project name
--cloud_region CLOUD_REGION
Expand All @@ -126,6 +129,13 @@ To run this sample:
--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")



Expand All @@ -150,17 +160,36 @@ To run this sample:
[--dataset_id DATASET_ID]
[--fhir_store_id FHIR_STORE_ID]
[--resource_type RESOURCE_TYPE]
[--resource_id RESOURCE_ID]
{create-resource,delete-resource,get-resource,update-resource,patch-resource,search-resources-get,search-resources-post,get-patient-everything,get-metadata}
[--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-resource,delete-resource,get-resource,update-resource,patch-resource,search-resources-get,search-resources-post,get-patient-everything,get-metadata}
{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}
create-resource Creates a new 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.
Expand Down Expand Up @@ -188,6 +217,12 @@ To run this sample:
The type of resource. First letter must be capitalized
--resource_id RESOURCE_ID
Name of a FHIR resource
--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



Expand Down
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