Name: dos-indexd-lambda
Owner: Data Biosphere
Description: Access indexd using GA4GH DOS
Created: 2018-02-06 19:51:49.0
Updated: 2018-02-07 03:40:36.0
Pushed: 2018-02-07 03:54:41.0
Homepage: https://mkc9oddwq0.execute-api.us-west-2.amazonaws.com/api/
Size: 555
Language: Jupyter Notebook
GitHub Committers
| User | Most Recent Commit | # Commits |
|---|---|---|
| David Steinberg | 2018-02-28 02:18:29.0 | 4 |
Other Committers
| User | Most Recent Commit | # Commits |
|---|
This presents an Amazon Lambda microservice following the Data Object Service(view the OpenAPI description!). It allows data in indexd to be accessed using Data Object Service APIs.
A development version of this service is available at https://mkc9oddwq0.execute-api.us-west-2.amazonaws.com/api/ . To make proper use of the service, one can either use cURL or an HTTP client to write API requests following the OpenAPI description.
ll request the first page of Data Objects from the service.
-X POST --header 'Content-Type: application/json' --header 'Accept: application/json' -d '{}' 'https://mkc9oddwq0.execute-api.us-west-2.amazonaws.com/api/ga4gh/dos/v1/dataobjects/list'
There is also a Python client available, that makes it easier to use the service from code.
ga4gh.dos.client import Client
nt = Client("https://mkc9oddwq0.execute-api.us-west-2.amazonaws.com/api/")
l_client = client.client
ls = client.models
l_client.ListDataObjects(body={}).result()
For more information refer to the Data Object Service.
This software is being actively developed to provide the greatest level of feature parity between DOS and indexd. It also presents an area to explore features that might extend the DOS API. Current development items can be seen in the Issues.
The Data Object Service can present many of the features of indexd naturally. This lambda should present a useful client for the latest releases of the indexd API.
In addition, the DOS schemas may be extended to present features available in indexd, but not yet in DOS.
The gateway portion of the AWS Lambda microservice is provided by chalice. So to manage deployment and to develop you'll need to install chalice.
Once you have installed chalice, you can download and deploy your own version of the service.
install chalice
clone https://github.com/DataBiosphere/dos-indexd-lambda.git
os-indexd-lambda
ice deploy
Chalice will return a HTTP location that you can issue DOS requests to. You can then use HTTP requests in the style of the Data Object Service.
A Python client for the Data Object Service is made available here. Install this client and then view the example in Example Usage. This notebook will guide you through basic read access to data in indexd via DOS.
If you have a problem accessing the service or deploying it for yourself, please head over to the Issues to let us know!