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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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10 changes: 7 additions & 3 deletions models/sipnet/R/write.configs.SIPNET.R
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Original file line number Diff line number Diff line change
Expand Up @@ -102,8 +102,12 @@ write.config.SIPNET <- function(defaults, trait.values, settings, run.id, inputs
jobsh <- gsub("@BINARY@", settings$model$binary, jobsh)
jobsh <- gsub("@REVISION@", settings$model$revision, jobsh)

jobsh <- gsub("@CPRUNCMD@", cpruncmd, jobsh)
jobsh <- gsub("@CPOUTCMD@", cpoutcmd, jobsh)
if(!is.identical(cpruncmd, character(0)) {
jobsh <- gsub("@CPRUNCMD@", cpruncmd, jobsh)
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Couple questions:

  • are we sure that if these variables aren't defined in the pecan.xmxl that they'll be set to character(0)?
  • If these variables don't exist, are we sure the job.sh will run correctly with the text of these tags left in the shell script? looking at the template job, it seems like they should be removed (i.e. gsubbed with an empty string)

    pecan/models/template/inst/template_geo.job

    Line 46 in 4564337

    @CPRUNCMD@

If the right thing to do is gsub with an empty string, and the is.identical is assuming the default is an empty string, this begs the question of why the default case is failing

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The code segment responsible to set the value of cpruncmd is write.configs.SIPNET.R#L76-L77.

Here since we don't set the value for settings$host$rabbitmq$cpfcmd as part of settings file that means on addressing this variable we get NULL. gsub returns a character(0) value when the target string is NULL.

Basically the line transforms to :

cpruncmd <- gsub("@OUTDIR@", settings$host$rundir, NULL)

which is why a check for this is needed in place.

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@meetagrawal09 I agree with your diagnosis, but I think the issue should be fixed on lines 76-77 rather than here. Maybe that could be something like cpruncmd <- gsub("@OUTDIR@", settings$host$rundir, settings$host$rabbitmq$cpfcmd %||% ""), then the replacements on lines 105-106 remain unconditional?

}
if(!is.identical(cpoutcmd, character(0)) {
jobsh <- gsub("@CPOUTCMD@", cpoutcmd, jobsh)
}
jobsh <- gsub("@RMOUTDIRCMD@", rmoutdircmd, jobsh)
jobsh <- gsub("@RMRUNDIRCMD@", rmrundircmd, jobsh)

Expand Down Expand Up @@ -630,4 +634,4 @@ remove.config.SIPNET <- function(main.outdir, settings) {
} else {
print("*** WARNING: Removal of files on remote host not yet implemented ***")
}
} # remove.config.SIPNET
} # remove.config.SIPNET