Commit a81c652e authored by mmassaviol's avatar mmassaviol
Browse files

Debug error turning many floats to scientific format

parent 331979e9
......@@ -3,7 +3,6 @@
# Accepts one parameters: path to sag yaml configuration file
# Usage: Rscript /path/to/sag.yaml
args = commandArgs(trailingOnly=TRUE)
source("tools.R")
library(yaml)
......@@ -33,7 +32,7 @@ generate_page_input <- function(res, cnt) {
}
if(cnt$type == "text") {
res <- res + '\t\ttextInput("'+ cnt$name +'", label = "'+ cnt$label +'", value = "'+ cnt$value +'", width = "'+ 'auto' +'")'
res <- res + '\t\ttextInput("'+ cnt$name +'", label = "'+ cnt$label +'", value = "'+ format(cnt$value, scientific=F) +'", width = "'+ 'auto' +'")'
}
if(cnt$type == "textArea") {
......@@ -43,7 +42,7 @@ generate_page_input <- function(res, cnt) {
}
if(cnt$type == "numeric") {
res <- res + '\t\tnumericInput("'+ cnt$name +'", label = "'+ cnt$label +'", min = '+ cnt$min +', max = '+ cnt$max +', step = '+ cnt$step +', width = "'+ 'auto' +'", value = '+ cnt$value +')'
res <- res + '\t\tnumericInput("'+ cnt$name +'", label = "'+ cnt$label +'", min = '+ cnt$min +', max = '+ cnt$max +', step = '+ cnt$step +', width = "'+ 'auto' +'", value = '+ format(cnt$value, scientific=F) +')'
}
if(cnt$type == "slider") {
......@@ -421,7 +420,7 @@ generate_pages_server <- function() {
if(cnt$type == 'text' || cnt$type == 'textArea' || cnt$type == "input_dir" || cnt$type == "output_dir") {
genR <- genR + '\t\tif(!is.na(as.numeric(input$' + id + '))) {\n'
genR <- genR + '\t\t\tres = paste0(res, paste("' + id + ':", input$' + id + ', "\\n", sep = " "))\n'
genR <- genR + '\t\t\tres = paste0(res, paste("' + id + ':", format(input$' + id + ', scientific=F), "\\n", sep = " "))\n'
genR <- genR + '\t\t} else {\n'
genR <- genR + '\t\t\tres = paste0(res, paste("' + id + ':", paste0(\'\"\', input$' + id + ', \'\"\'), "\\n", sep = " "))\n'
genR <- genR + '\t\t}'
......@@ -429,7 +428,7 @@ generate_pages_server <- function() {
}
if(cnt$type == 'numeric') {
genR <- genR + '\t\tif(!is.na(as.numeric(input$' + id + '))) {\n'
genR <- genR + '\t\t\tres = paste0(res, paste("' + id + ':", input$' + id + ', "\\n", sep = " "))\n'
genR <- genR + '\t\t\tres = paste0(res, paste("' + id + ':", format(input$' + id + ', scientific=F), "\\n", sep = " "))\n'
genR <- genR + '\t\t} else {\n'
genR <- genR + '\t\t\tres = paste0(res, paste("' + id + ':", paste0(\'\"\', input$' + id + ', \'\"\'), "\\n", sep = " "))\n'
genR <- genR + '\t\t}'
......@@ -541,10 +540,10 @@ generate_pages_server <- function() {
save_params <- save_params + '\tres = ""'
save_params <- save_params + resG
#save_params <- save_params + '\t\tres = paste0(res, paste("final_step:", paste0(\'\"\', input$final_step, \'\"\'), "\\n", sep = " "))\n\n'
save_params <- save_params + '\ta = yaml.load_file("/workflow/params.total.yml")\n'
save_params <- save_params + '\ta = yaml.load_file("/workflow/params.total.yml", handlers=list("float#fix"=function(x){ format(x,scientific=F)}))\n'
save_params <- save_params + '\tp = a[["params"]]\n'
save_params <- save_params + '\ta["params"] = NULL\n'
save_params <- save_params + '\tb = yaml.load(res)\n'
save_params <- save_params + '\tb = yaml.load(res, handlers=list("float#fix"=function(x){ format(x,scientific=F)}))\n'
save_params <- save_params + '\tpnotb = subset(names(p), !(names(p)%in%names(b)))\n'
save_params <- save_params + '\td = list()\n'
save_params <- save_params + '\td$params = c(p[pnotb],b)\n'
......@@ -554,10 +553,10 @@ generate_pages_server <- function() {
save_params <- save_params + '\t\treturn(result)\n'
save_params <- save_params + '\t}\n'
save_params <- save_params + '\td = c(d,a)\n'
save_params <- save_params + '\tget_samples = yaml.load(system(paste0("python3 /workflow/get_samples.py ",input$sample_dir," ",input$SeOrPe),intern = T))\n'
save_params <- save_params + '\td$samples = get_samples$samples\n'
save_params <- save_params + '\td$params$sample_suffix = get_samples$suffix\n'
save_params <- save_params + '\twrite_yaml(d,path_param,handlers=list(logical = logical))\n'
#save_params <- save_params + '\tget_samples = yaml.load(system(paste0("python3 /workflow/get_samples.py ",input$sample_dir," ",input$SeOrPe),intern = T))\n'
#save_params <- save_params + '\td$samples = get_samples$samples\n'
#save_params <- save_params + '\td$params$sample_suffix = get_samples$suffix\n'
save_params <- save_params + '\twrite_yaml(d,path_param,handlers=list(logical = logical,"float#fix"=function(x){ format(x,scientific=F) }))\n'
save_params <- save_params + '\t}\n\n'
res <- save_params
......@@ -568,7 +567,7 @@ generate_pages_server <- function() {
res <- res + '\t}\n'
res <- res + '\telse if (input$force_from=="all"){ return("--forcerun all") }\n'
res <- res + '\telse {\n'
res <- res + '\t\tparams = yaml.load_file(paste0(input$results_dir,"/params.yml"))\n'
res <- res + '\t\tparams = yaml.load_file(paste0(input$results_dir,"/params.yml"), handlers=list("float#fix"=function(x){ format(x,scientific=F)}))\n'
res <- res + '\t\toutputs = params[["outputs"]]\n'
res <- res + '\t\ttool = params[["params"]][[force_from]]\n'
res <- res + '\t\tif (length(outputs[[tool]])==1)\n'
......@@ -618,7 +617,7 @@ generate_pages_server <- function() {
res <- res + '\t\tsystem(paste0("rm ",input$results_dir,"/rulegraph*"))\n\n'
res <- res + '\t\toutUI = tryCatch({\n'
res <- res + '\t\t\tsystem(paste0("snakemake -s /workflow/Snakefile --configfile ",input$results_dir,"/params.yml -d ",input$results_dir," all --rulegraph > ",input$results_dir,"/rulegraph",i,".dot"),intern=T)\n'
res <- res + '\t\t\tsystem(paste0("snakemake -s /workflow/Snakefile --configfile ",input$results_dir,"/params.yml -d ",input$results_dir," all --rulegraph 1> ",input$results_dir,"/rulegraph",i,".dot"),intern=T)\n'
res <- res + '\t\t\tsystem(paste0("cat ",input$results_dir,"/rulegraph",i,".dot | dot -Tsvg -Gratio=0.75 > ",input$results_dir,"/rulegraph",i,".svg"),intern=T)\n'
res <- res + '\t\t\ttagList(img(src = paste0("results/rulegraph",i,".svg") ,alt = "Rulegraph of Snakemake jobs",style="max-width: 100%;height: auto;display: block;margin: auto"))},\n'
res <- res + '\t\terror = function(e){\n'
......@@ -973,7 +972,7 @@ generate_app <- function() {
res <- res + 'reload = function(dossierAnalyse,session,output){\n'
res <- res + '\t# if params exists reload them\n'
res <- res + '\tif (file.exists(paste0(dossierAnalyse,"/params.yml"))){\n'
res <- res + '\t\tparams = read_yaml(paste0(dossierAnalyse,"/params.yml"))\n'
res <- res + '\t\tparams = read_yaml(paste0(dossierAnalyse,"/params.yml"), handlers=list("float#fix"=function(x){ format(x,scientific=F)}))\n'
res <- res + '\t\tfor (param in names(params$params_info)){\n'
res <- res + '\t\t\tif (params$params_info[[param]]$type == "text" || params$params_info[[param]]$type == "input_dir" || params$params_info[[param]]$type == "output_dir"){\n'
res <- res + '\t\t\t\tupdateTextInput(session, param, value = params[["params"]][[param]])\n'
......
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