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resolve 500 error with Rlabkey 3.0.0 #123

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resolve 500 error with Rlabkey 3.0.0 #123

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29b8c7b
Merge pull request #1 from RGLab/main
jgbaum Nov 23, 2023
42e5beb
added command to disable Waf encoding for versions of Rlabkey >= 3.0.0
jgbaum Nov 27, 2023
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8 changes: 8 additions & 0 deletions R/ISCon-cytometry.R
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Original file line number Diff line number Diff line change
Expand Up @@ -51,6 +51,14 @@ ISCon$set(
which = "public",
name = "summarizeCyto",
value = function() {

# set Waf encoding FALSE for Rlabkey versions greater or equal to 3.0.0
# this needs to be repeated in the helper functions that make use of
# labkey.executeSql
if (packageVersion('Rlabkey') >= '3.0.0') {
labkey.setWafEncoding(FALSE)
}

# retrieve stats
nSamples <- suppressWarnings(labkey.executeSql(
folderPath = self$config$labkey.url.path,
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13 changes: 13 additions & 0 deletions R/ISCon-geneExpression.R
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Expand Up @@ -24,6 +24,12 @@ ISCon$set(
)
}

# set Waf encoding FALSE for Rlabkey versions greater or equal to 3.0.0
# this needs to be repeated in the helper functions that make use of
# labkey.executeSql
if (packageVersion('Rlabkey') >= '3.0.0') {
labkey.setWafEncoding(FALSE)
}

## MAIN
if (is.null(self$cache[[private$.constants$matrices]]) | reload) {
Expand Down Expand Up @@ -622,6 +628,13 @@ ISCon$set(
cacheinfo <- .getCacheInfo(outputType, annotation)
cache_name <- .getMatrixCacheName(matrixName, outputType, annotation)

# set Waf encoding FALSE for Rlabkey versions greater or equal to 3.0.0
# this needs to be repeated in the helper functions that make use of
# labkey.executeSql
if (packageVersion('Rlabkey') >= '3.0.0') {
labkey.setWafEncoding(FALSE)
}

if (!(matrixName %in% self$cache[[private$.constants$matrices]]$name)) {
stop("Invalid gene expression matrix name")
}
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7 changes: 7 additions & 0 deletions R/ISCon.R
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Expand Up @@ -360,6 +360,13 @@ ISCon$set(
labkey.url.path <- .get_url_path(study)
curlOptions <- .set_curl_options(login, password)

# set Waf encoding FALSE for Rlabkey versions greater or equal to 3.0.0
# this needs to be repeated in the helper functions that make use of
# labkey.executeSql
if (packageVersion('Rlabkey') >= '3.0.0') {
labkey.setWafEncoding(FALSE)
}

# set fields
self$config <- list(
labkey.url.base = labkey.url.base,
Expand Down