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Fix URIs matching error in sdrfToNfConf.R #46

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merged 13 commits into from
May 20, 2024
Merged

Fix URIs matching error in sdrfToNfConf.R #46

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1878c16
Update sdrfToNfConf.R
pmb59 May 15, 2024
46cc6c0
fix value of 'missing_uri_files', when 'uri_select' is not a data.fra…
pmb59 May 17, 2024
5bf6d5c
rm blank space
pmb59 May 17, 2024
b06765b
add R script check GitHub Action
pmb59 May 17, 2024
120fe6b
update actions versions
pmb59 May 17, 2024
d4d3acd
edit G-Action dependencies
pmb59 May 17, 2024
46edf8e
rm devtools from dependencies
pmb59 May 17, 2024
367ae96
fix dependencies
pmb59 May 17, 2024
3760df1
modify dependencies
pmb59 May 17, 2024
141c2d7
install devtools related dependencies
pmb59 May 17, 2024
af63c2a
pin r version
pmb59 May 17, 2024
07395a4
Update sdrfToNfConf_test.yml
pmb59 May 17, 2024
ba945b1
Removing github action - we can address this in another pull-request
pmb59 May 20, 2024
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6 changes: 3 additions & 3 deletions bin/sdrfToNfConf.R
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Original file line number Diff line number Diff line change
Expand Up @@ -162,7 +162,7 @@ for ( n in names(opt) ) {
}

################################################################################
# First round SDRF field checks: before we know about field content
# First round SDRF field checks: before we know about field content
################################################################################

# Load the SDRF
Expand Down Expand Up @@ -1077,14 +1077,14 @@ configs <- lapply(species_list, function(species){
}else{

# For each library we check if there is a fastq URI that can supply the file
uri_select <- apply(species.protocol.sdrf[,uri_cols], 2, function(x) basename(x) == files)
uri_select <- apply(species.protocol.sdrf[,uri_cols], 2, function(x) basename(x) == files)

if (is.data.frame(uri_select) || is.matrix(uri_select)) {
# the following line gives an error: dim(X) must have a positive length
# if not a matrix or a data.frame
missing_uri_files <- files[which(! apply(apply(species.protocol.sdrf[,uri_cols], 2, function(x) basename(x) == files), 1, any))]
} else {
missing_uri_files <- files[which(! apply(as.data.frame( apply(species.protocol.sdrf[,uri_cols], 2, function(x) basename(x) == files) ), 1, any))]
missing_uri_files <- files[which(! any(apply(species.protocol.sdrf[, uri_cols], 2, function(x) basename(x) == files)) )]
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Can you please explain briefly what are you trying to do here.. So I know what I understood from code is right..

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Hi @anilthanki Did you have a look to the description of the PR?

Basically, in this chunk for each library it is checked if there is a fastq URI that can supply the file. The error was in the fix for the case when uri_select is not a matrix or a data.frame

}

if (length(missing_uri_files) > 0){
Expand Down
8 changes: 4 additions & 4 deletions bin/utils.R
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@@ -1,5 +1,5 @@
pinfo <- function(...) {
cat(paste0("[INFO ",format(Sys.time(), format="%d/%m-%H:%M"),"] ",...,"\n"))
cat(paste0("[INFO ", format(Sys.time(), format="%d/%m-%H:%M"),"] ",...,"\n"))
}

perror <- function(...) {
Expand All @@ -10,14 +10,14 @@ pwarning <- function(...) {
cat(paste0("[WARNING] ",...,"\n"),file=stderr())
}

read.tsv <- function(f,header=TRUE, comment.char="", nrows=-1L,fill=FALSE, quote="\"", colClasses=NULL, drop=NULL) {
read.tsv <- function(f, header=TRUE, comment.char="", nrows=-1L,fill=FALSE, quote="\"", colClasses=NULL, drop=NULL) {
tsv.data <- NULL

suppressPackageStartupMessages(require(data.table))

fread(input=f,sep = "\t", nrows=nrows, header=header,check.names=FALSE,data.table=FALSE,fill=fill,drop=drop, quote=quote,colClasses=colClasses)
fread(input=f, sep = "\t", nrows=nrows, header=header, check.names=FALSE,data.table=FALSE, fill=fill, drop=drop, quote=quote, colClasses=colClasses)
}

write.tsv <- function(x, file, header=TRUE){
fwrite(x,file=file,sep="\t",row.names=FALSE,col.names=header,quote=FALSE,verbose=FALSE)
}
}