getwilds/proofr

Client for the PROOF API

proofr's Issues

Set curl timeout so users don't have to wait so long for timeout failure if PROOF API down or not accessible

without this the timeout length is unbearably long, probably 15 sec or so

timeout_ms

Add docs in help for securely managing authentication

In the documentation of proof_authenticate(username, password) we might want to include some suggestions for how to not write your hutch password as inline code as a reminder or help for newbies.

documentation small thing - pak::pak("rcromwell")

hi,

finally started testing PROOF

on this page: https://getwilds.org/proofr/articles/proofr.html#rcromwell-setup

there's a chunk that looks like this

if (!requireNamespace("rcromwell", quietly=TRUE)) {
  install.packages("pak")
  pak::pak("rcromwell")
}

The line pak::pak("rcromwell") should read pak::pak("getwilds/rcromwell")

Testing more now...

thanks!

Janet

replace any links pointing to proof api repo with something else or remove

since proof api repo is private

Write more tests covering major points of the exported fxns

Add wait param to proof_status to wait for up

Surface error messages from PROOF API if useful to users

Not going to CRAN, right?

@vortexing We do not intend this package to ever go to CRAN, correct?

I assume not since it's very specific to hutch

Token handling

• Dont set as env var by deafult anymore when running auth function
• Allow for passing in token as param

to support shiny flow

dependency on rstudioapi

Followed instructions, rstudioapi did not get installed correctly as a dependency.

> pak::pak("getwilds/proofr:v0.2")
Error in loadNamespace(x) : there is no package called ‘rstudioapi’

`> sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: x86_64-apple-darwin20
Running under: macOS Sonoma 14.4.1

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Los_Angeles
tzcode source: internal

attached base packages:
[1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached):
[1] compiler_4.4.0 R6_2.5.1 fastmap_1.1.1 cli_3.6.2 htmltools_0.5.8.1
[6] tools_4.4.0 rstudioapi_0.16.0 yaml_2.3.8 rmarkdown_2.26 knitr_1.46
[11] xfun_0.43 digest_0.6.35 rlang_1.1.3 pak_0.7.2 evaluate_0.23 `

Change proof_start to use slurm_account as body param instead of pi_name

see https://github.com/FredHutch/proof-api/#post-cromwell-server and https://proof-api.fredhutch.org/

confirming with dan

If you have a proof server running...

... via the shiny app, can we provide some guidance about how to then connect to that server via proofr in R? Do we need to make a new server via proofr? Can you get your token from the app? I'd hope not, right?

Document server up time of 7 days

If a user submits a job to their proof based cromwell server, and it is still running when the 7 days are up, is that job interrupted at all?

No, Jobs keep running even if the cromwell server is unavailable.

So we can document that they don't need to worry about the 7 day thing, BUT they do need to have a server up and running to get data back out - unless they do it manually on the cluster presumably?

see also FredHutch/shiny-cromwell#24 getwilds/rcromwell#27

httr -> httr2

• vcr on cran only has support for httr, not httr2. httr2 support is in the works but not ready quite yet.
• rcromwell uses vcr.
• which means we need to use httr in rcromwell and this pkg for now

move to httr2 once vcr has support for it on github at least (& cran before rcromwell goes to cran)

@export proof_header

proof_header() should be exported, right? Since it's in the vignette?

rcromwell <--> proofr integration

Right now the way the integration works is to set headers globally for any httr requests. That could be a problem if other requests are being made - we only want Authorization headers with the proof token sent to the proof API servers

PROOF API token caching

ideally we securely store the API token for users so they dont have to manage it themselves, perhaps with https://keyring.r-lib.org/ or similar, but keyring is a heavy dependency

there's helper fxns in httr2 that could be used perhaps https://github.com/r-lib/httr2/blob/f7c3fee04c120d0d84c6ad1fd169fa822c6dfdff/R/secret.R#L12

For now, just ask the user to store their token themselves