Commit c774dd66 authored by svolant's avatar svolant
Browse files

modif curdir

parent 3f989bb8
......@@ -541,6 +541,7 @@ PCAPlot_meta <-function(input,dds, group_init, n = min(500, nrow(counts(dds))),
else Kval = val
ind_kept = which(as.character(group)%in%Kval)
# save(val,Kval,dds,group_init,type.trans,VarInt,ind_kept,file="testLDA")
## Get the group corresponding to the modalities
group = group[ind_kept]
nb = length(unique((group)))
......
......@@ -812,5 +812,3 @@ Plot_Visu_Tree <- function(input,resDiff,CT_Norm_OTU,taxo_table)
return(res)
}
......@@ -30,7 +30,7 @@ shinyServer(function(input, output,session) {
## Reactive target
values <- reactiveValues(TargetWorking = target,labeled=NULL,fastq_names_only=NULL,R1fastQ=NULL,R2fastQ=NULL,
json_name=json_name,num=0,pass=pass,login_email = NULL,is.valid =NULL,
biom_masque = NULL,tree_masque=NULL,masque_key = NULL,paths_fastq_tmp=NULL)
biom_masque = NULL,tree_masque=NULL,masque_key = NULL,paths_fastq_tmp=NULL,curdir=curdir)
## Counts file
dataInputCounts <-reactive({
......@@ -719,7 +719,7 @@ shinyServer(function(input, output,session) {
CMP = CheckMasque(input, values)
Error = CMP$Error
isJSONalreadyExist = file.exists(paste(curdir,"www","masque","doing",basename(json_name),sep= .Platform$file.sep))
isJSONalreadyExist = file.exists(paste(values$curdir,"www","masque","doing",basename(json_name),sep= .Platform$file.sep))
if(is.null(Error) && !isJSONalreadyExist)
{
......@@ -1139,7 +1139,7 @@ shinyServer(function(input, output,session) {
Error = CMP$Error
if(is.null(Error) && isolate(values$num)<100){
progress_file = paste(curdir,"www","masque","doing",paste(basename(file_path_sans_ext(json_name)),"_progress",".txt",sep=""),sep= .Platform$file.sep)
progress_file = paste(values$curdir,"www","masque","doing",paste(basename(file_path_sans_ext(json_name)),"_progress",".txt",sep=""),sep= .Platform$file.sep)
if(file.exists(progress_file))
{
pf = read_lines(progress_file)
......@@ -1170,7 +1170,7 @@ shinyServer(function(input, output,session) {
#
# passOK = FALSE;status = NULL;file = NULL
# print("OK")
# json_files = list.files(paste(curdir,"www","masque",sep= .Platform$file.sep),pattern = "json",recursive = TRUE)
# json_files = list.files(paste(values$curdir,"www","masque",sep= .Platform$file.sep),pattern = "json",recursive = TRUE)
# allpass = gsub(gsub(json_files,pattern = ".*file",replacement = ""),pattern = ".json",replacement = "")
#
# print(allpass)
......@@ -1179,7 +1179,7 @@ shinyServer(function(input, output,session) {
# passOK = any(isolate(input$password)==allpass)
# if(passOK){
# ind = which(isolate(input$password)==allpass)
# file = paste(curdir,"www","masque",json_files[ind],sep= .Platform$file.sep)
# file = paste(values$curdir,"www","masque",json_files[ind],sep= .Platform$file.sep)
# status = gsub(json_files[ind],pattern = "/.*",replacement = "")
# }
# }
......@@ -1194,7 +1194,7 @@ shinyServer(function(input, output,session) {
#
# passOK = FALSE;status = NULL;file = NULL
#
# json_files = list.files(paste(curdir,"www","masque",sep= .Platform$file.sep),pattern = "json",recursive = TRUE)
# json_files = list.files(paste(values$curdir,"www","masque",sep= .Platform$file.sep),pattern = "json",recursive = TRUE)
# allpass = gsub(gsub(json_files,pattern = ".*file",replacement = ""),pattern = ".json",replacement = "")
#
# print(allpass)
......@@ -1203,7 +1203,7 @@ shinyServer(function(input, output,session) {
# passOK = any(isolate(values$pass)==allpass)
# if(passOK){
# ind = which(values$pass==allpass)
# file = paste(curdir,"www","masque",json_files[ind],sep= .Platform$file.sep)
# file = paste(values$curdir,"www","masque",json_files[ind],sep= .Platform$file.sep)
# status = gsub(json_files[ind],pattern = "/.*",replacement = "")
# }
# }
......@@ -1215,7 +1215,7 @@ shinyServer(function(input, output,session) {
observeEvent(input$Check_project,{
values$masque_key = input$password
resbox = Project_box_result(values$masque_key,curdir)
resbox = Project_box_result(values$masque_key,values$curdir)
PS = resbox$PS
passOK = PS$passOK
......@@ -1245,7 +1245,7 @@ shinyServer(function(input, output,session) {
observeEvent(input$Check_project_over,{
values$masque_key = values$pass
resbox = Project_box_result(values$masque_key,curdir)
resbox = Project_box_result(values$masque_key,values$curdir)
PS = resbox$PS
passOK = PS$passOK
......@@ -1292,7 +1292,7 @@ shinyServer(function(input, output,session) {
# folder_name = basename(file_path_sans_ext(json_file))
# print(folder_name)
# ### Paste file name as folder
# annot_process = paste(curdir,"www","masque","done",folder_name,"shaman_annotation_process.tsv",sep= .Platform$file.sep)
# annot_process = paste(values$curdir,"www","masque","done",folder_name,"shaman_annotation_process.tsv",sep= .Platform$file.sep)
#
# if(file.exists(annot_process))
# {
......@@ -1323,7 +1323,7 @@ shinyServer(function(input, output,session) {
# hideElement("project_over",anim=TRUE)
#
# json_file = PS$file
# error_file = paste(curdir,"www","masque","error",paste(basename(file_path_sans_ext(json_file)),"_error",".txt",sep=""),sep= .Platform$file.sep)
# error_file = paste(values$curdir,"www","masque","error",paste(basename(file_path_sans_ext(json_file)),"_error",".txt",sep=""),sep= .Platform$file.sep)
# print(error_file)
# if(file.exists(error_file)){error_message = read_lines(error_file)}
#
......@@ -1372,7 +1372,7 @@ shinyServer(function(input, output,session) {
output$masque_status_key <-renderUI({
res = NULL
resbox = Project_box_result(values$masque_key,curdir)
resbox = Project_box_result(values$masque_key,values$curdir)
# if(resbox$PS$status=='done') showElement("MasqueToShaman",anim=TRUE)
# if(resbox$PS$status!='done') hideElement("MasqueToShaman",anim=TRUE)
......@@ -1388,7 +1388,7 @@ shinyServer(function(input, output,session) {
# folder_name = basename(file_path_sans_ext(json_file))
# print(folder_name)
# ### Paste file name as folder
# annot_process = paste(curdir,"www","masque","done",folder_name,"shaman_annotation_process.tsv",sep= .Platform$file.sep)
# annot_process = paste(values$curdir,"www","masque","done",folder_name,"shaman_annotation_process.tsv",sep= .Platform$file.sep)
#
# if(file.exists(annot_process))
# {
......@@ -1417,7 +1417,7 @@ shinyServer(function(input, output,session) {
# if(PS$status=="error"){
#
# json_file = PS$file
# error_file = paste(curdir,"www","masque","error",paste(basename(file_path_sans_ext(json_file)),"_error",".txt",sep=""),sep= .Platform$file.sep)
# error_file = paste(values$curdir,"www","masque","error",paste(basename(file_path_sans_ext(json_file)),"_error",".txt",sep=""),sep= .Platform$file.sep)
# print(error_file)
# if(file.exists(error_file)){error_message = read_lines(error_file)}
#
......@@ -1445,7 +1445,7 @@ shinyServer(function(input, output,session) {
res = NULL
if(PS$status=="doing"){
json_file = PS$file
progress_file = paste(curdir,"www","masque","doing",paste(basename(file_path_sans_ext(json_file)),"_progress",".txt",sep=""),sep= .Platform$file.sep)
progress_file = paste(values$curdir,"www","masque","doing",paste(basename(file_path_sans_ext(json_file)),"_progress",".txt",sep=""),sep= .Platform$file.sep)
if(file.exists(progress_file))
{
pf = read_lines(progress_file)
......@@ -1464,7 +1464,7 @@ shinyServer(function(input, output,session) {
output$build_process_table <- DT::renderDataTable({
folder_name = paste('file',values$masque_key,sep="")
build_process = paste(curdir,"www","masque","done",folder_name,"shaman_build_process.tsv",sep= .Platform$file.sep)
build_process = paste(values$curdir,"www","masque","done",folder_name,"shaman_build_process.tsv",sep= .Platform$file.sep)
if(file.exists(build_process))
{
bp = read.csv(build_process,sep="\t",header=TRUE)
......@@ -1588,8 +1588,8 @@ shinyServer(function(input, output,session) {
observeEvent(input$RunResMasque,{
updateSelectInput(session, "FileFormat","",selected = "fileBiom")
reset("fileBiom"); reset("fileTree")
values$biom_masque = paste(curdir,"www","masque","done",basename(file_path_sans_ext(json_name)),paste("shaman_",input$masque_database,".biom",sep=""),sep= .Platform$file.sep)
values$tree_masque = paste(curdir,"www","masque","done",basename(file_path_sans_ext(json_name)),paste("shaman_tree_",input$masque_database,".nhx",sep=""),sep= .Platform$file.sep)
values$biom_masque = paste(values$curdir,"www","masque","done",basename(file_path_sans_ext(json_name)),paste("shaman_",input$masque_database,".biom",sep=""),sep= .Platform$file.sep)
values$tree_masque = paste(values$curdir,"www","masque","done",basename(file_path_sans_ext(json_name)),paste("shaman_tree_",input$masque_database,".nhx",sep=""),sep= .Platform$file.sep)
})
......@@ -1598,7 +1598,7 @@ shinyServer(function(input, output,session) {
output$Download_masque_zip <- downloadHandler(
filename = function() { paste("SHAMAN_",values$masque_key,'.zip',sep="")},
content = function(file){
zip_file = paste(curdir,"www","masque","done",paste("file",values$masque_key,".zip",sep=""),sep= .Platform$file.sep)
zip_file = paste(values$curdir,"www","masque","done",paste("file",values$masque_key,".zip",sep=""),sep= .Platform$file.sep)
if(file.exists(zip_file)){file.copy(zip_file, file)}
}
)
......
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