Story #11876

Updated by Tom Morris about 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.

Possible starting points for design inspiration include Illumina's BaseSpaceR package and SevenBridges 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

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.

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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.

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

Object Types

ApiClient
ApiClientAuthorization
AuthorizedKey
Collection
Container
ContainerRequest
Group
Human
Job
JobTask
KeepDisk
KeepService
Link
Log
Node
PipelineInstance
PipelineTemplate
Repository
Specimen
Trait
User
UserAgreement
VirtualMachine
Workflow

Miscellaneous 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

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