Story #11876

Updated by Tom Morris almost 4 years ago

As an R programmer I'd like to have the ability to query the Arvados APIs directly from R using a package which integrates well with and is published with the rest of the Bioconductor packages. The SDK should ideally allow me to do everything a Python programmer can do using the Python SDK, but as a first step should allow me to allow to find collections and files in Keep using filtering on metadata, load the files into R, process them and then write the results back to a collection. As an optional second stage, it'd be useful to be able to submit CWL jobs and monitor their progress.

The SDK should work on Windows, OS X, and Linux, which implies that depending on arv-mount Possible starting points for file reading design inspiration include Illumina's BaseSpaceR package and writing is not an acceptable option.

There are two relevant packages,
SevenBridges "sevenbridges" and Illumina's "BaseSpaceR", which could be used for a) design ideas and b) starting points for implementation (they are both Apache licensed). sevenbridges package.

http://bioconductor.org/packages/release/bioc/html/BaseSpaceR.html
https://developer.basespace.illumina.com/docs/content/documentation/sdk-samples/r-sdk-overview
http://bioconductor.org/packages/release/bioc/html/sevenbridges.html
https://github.com/sbg/sevenbridges-r
http://bioconductor.org/packages/release/bioc/html/BaseSpaceR.html
https://developer.basespace.illumina.com/docs/content/documentation/sdk-samples/r-sdk-overview


A potential supporting component might be googleAuthR http://code.markedmondson.me/googleAuthR/ which could be used in a similar way to googleComputeEngineR https://cloudyr.github.io/googleComputeEngineR/ and other packages which are layered on it.

-----------

Design sketch - create new client library for API server functions, but use HTTP or arv-mount access to get data rather than implementing Keep support.
googleAuthR can be used for API generation and response parsing, but needs to be reworked to not assume Google authentication or endpoints. Instead of the OAuth2 dance, it needs to be able to use an API token.

The full Arvados API currently consists of 24 object types (plus 24 list types for those objects) and 223 methods. There are create, delete, destroy, get, list, show, and update methods for each object type and then another 26 methods which are used once or twice each.

Test comparisons: Python Java - 8K lines in 472 20 tests, Golang - 4K lines in 213 tests,

Python - 8K lines in 472 tests

Object Types to be supported in initial version:

ApiClient
ApiClientAuthorization
AuthorizedKey
Collection
Container
ContainerRequest
Group (user groups & projects)
Link

Log ?
User ?
Workflow

Object Types not needed initially:

ApiClient
ApiClientAuthorization
AuthorizedKey
Human
Job
JobTask
KeepDisk
KeepService
Link
Log
Node
PipelineInstance
PipelineTemplate
Repository
Specimen
Trait
User
UserAgreement
VirtualMachine


Workflow

Miscellaneous Arvados API methods:

1 accessible
1 activate
1 auth
2 cancel
1 contents
1 create_system_auth
3 current
1 get_all_logins
1 get_all_permissions
1 get_permissions
2 lock
1 logins
1 new
2 ping
1 provenance
1 queue
1 queue_size
1 setup
1 sign
1 signatures
1 system
1 trash
1 unlock
1 unsetup
1 untrash
1 used_by

Back