used to merge a meta data CSV (generated from SQL) with QTIP measurements CSV.

merge_left.R

options = commandArgs(trailingOnly = TRUE)
file1 = options[1]  #QTIP file
file2 = options[2]  #SQL query file
field_name = options[3] #not used - replace with what column name to use
outpath = options[4] #name of output file

file1.df = read.csv(file1, header = TRUE, stringsAsFactors = FALSE)
file2.df = read.csv(file2, header = TRUE, stringsAsFactors = FALSE)

get.filename = function(x) {
  splitted = strsplit(x, split = "/")[[1]]
  return(splitted[length(splitted)])
}

file1.df = file1.df[-1,]
file1.df$filename = sapply(file1.df$filename, get.filename)
file2.df$filename = sapply(file2.df$full_path, get.filename)

features.query = merge(file1.df, file2.df, by = "filename")

write.csv(features.query, file = outpath, row.names = FALSE, quote = FALSE)