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[Bug fix] : Fixed gsub issue in write.config.SIPNET #3275

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merged 9 commits into from
May 17, 2024
Merged

[Bug fix] : Fixed gsub issue in write.config.SIPNET #3275

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24bd159
added checks for cpruncmd and cpoutcmd
meetagrawal09 Mar 10, 2024
dfbb52d
fixed typo
meetagrawal09 Mar 10, 2024
db0c32a
bug fix
meetagrawal09 Mar 10, 2024
7357e3f
Merge branch 'develop' into develop
meetagrawal09 Mar 12, 2024
dff4163
Merge branch 'PecanProject:develop' into develop
meetagrawal09 Mar 23, 2024
b8ef634
Merge branch 'develop' into develop
meetagrawal09 May 4, 2024
2aab647
bug fix
meetagrawal09 May 17, 2024
33b4b5a
updated condition
meetagrawal09 May 17, 2024
aa0a709
Merge branch 'develop' into develop
mdietze May 17, 2024
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1 change: 1 addition & 0 deletions models/sipnet/R/write.configs.SIPNET.R
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Expand Up @@ -73,6 +73,7 @@ write.config.SIPNET <- function(defaults, trait.values, settings, run.id, inputs
cpruncmd <- cpoutcmd <- rmoutdircmd <- rmrundircmd <- ""
if (!is.null(settings$host$rabbitmq)) {
#rsync cmd from remote to local host.
settings$host$rabbitmq$cpfcmd <- if(settings$host$rabbitmq$cpfcmd == NULL) "" else settings$host$rabbitmq$cpfcmd
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@meetagrawal09 this syntax doesn't work in R. First, if(settings$host$rabbitmq$cpfcmd == NULL) throws an "argument is of length zero" error if the variable is NULL and should be replaced with is.null(). Second, the if ... else syntax should be replaced with the ifelse() function.

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Or the null-coalescing operator %||% as I showed above—it’s made for exactly this case

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Don't know but this operator did not work for me. Shows me the below error.

Error in settings$host$rabbitmq$cpfcmd %||% "" :  could not find function "%||%"

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@infotroph infotroph May 17, 2024 •
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Oh, hm.
(1) You'll need to import it[1] from rlang with #' @importFrom rlang %||% or just copy in the definition: function (x, y) { if (is.null(x)) y else x} ...
(2) ...which reminds me that %||% only works on scalars. @mdietze does your point about ifelse mean cpfcmd might have legnth >1? If so my advice was bad to start with and ifelse seems cleaner.

[1] (%||% has been added to base R in 4.4.0, so a few version bumps from now we'll be able to use it with no import)

cpruncmd <- gsub("@OUTDIR@", settings$host$rundir, settings$host$rabbitmq$cpfcmd)
cpruncmd <- gsub("@OUTFOLDER@", rundir, cpruncmd)

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