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Home Page: http://getwilds.org/proofr/
License: Other
Client for the PROOF API
Home Page: http://getwilds.org/proofr/
License: Other
without this the timeout length is unbearably long, probably 15 sec or so
timeout_ms
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.
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
since proof api repo is private
@vortexing We do not intend this package to ever go to CRAN, correct?
I assume not since it's very specific to hutch
to support shiny flow
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 `
see https://github.com/FredHutch/proof-api/#post-cromwell-server and https://proof-api.fredhutch.org/
confirming with dan
... 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?
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?
vcr
on cran only has support for httr
, not httr2
. httr2
support is in the works but not ready quite yet.rcromwell
uses vcr
.httr
in rcromwell
and this pkg for nowmove to httr2
once vcr
has support for it on github at least (& cran before rcromwell
goes to cran)
proof_header()
should be exported, right? Since it's in the vignette?
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
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
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