Commit 3f989bb8 authored by svolant's avatar svolant
Browse files

correction error message masque

parent 7026a73d
...@@ -100,7 +100,7 @@ Project_box_result <- function(masque_key,curdir){ ...@@ -100,7 +100,7 @@ Project_box_result <- function(masque_key,curdir){
} }
if(PS$status=="error"){ if(PS$status=="error"){
error_message = "Failed"
json_file = PS$file json_file = PS$file
error_file = paste(curdir,"www","masque","error",paste('file',masque_key,"_error",".txt",sep=""),sep= .Platform$file.sep) error_file = paste(curdir,"www","masque","error",paste('file',masque_key,"_error",".txt",sep=""),sep= .Platform$file.sep)
......
...@@ -41,7 +41,10 @@ shinyServer(function(input, output,session) { ...@@ -41,7 +41,10 @@ shinyServer(function(input, output,session) {
if (is.null(inFile)) return(NULL) if (is.null(inFile)) return(NULL)
try(read.csv(inFile$datapath,sep=input$sepcount,header=TRUE,check.names=FALSE)->data,silent=T) tryCatch(read.csv(inFile$datapath,sep=input$sepcount,header=TRUE,check.names=FALSE)->data,
error=function(e) sendSweetAlert(messageId="ErrorCounts",
title = "Oops",
text=paste("Your file can not be read in SHAMAN.\n \n",e),type ="error"))
if(!is.null(data)){ if(!is.null(data)){
colnames(data) = gsub("-",".",colnames(data)) colnames(data) = gsub("-",".",colnames(data))
...@@ -63,7 +66,10 @@ shinyServer(function(input, output,session) { ...@@ -63,7 +66,10 @@ shinyServer(function(input, output,session) {
if(input$TypeTaxo=="Table") if(input$TypeTaxo=="Table")
{ {
try(read.csv(inFile$datapath,sep=input$septaxo,header=TRUE)->data,silent=T) tryCatch(read.csv(inFile$datapath,sep=input$septaxo,header=TRUE)->data,
error=function(e) sendSweetAlert(messageId="ErrorTaxo",
title = "Oops",
text=paste("Your file can not be read in SHAMAN.\n \n",e),type ="error"))
## Rownames ## Rownames
if(!is.null(data)) if(!is.null(data))
...@@ -80,7 +86,11 @@ shinyServer(function(input, output,session) { ...@@ -80,7 +86,11 @@ shinyServer(function(input, output,session) {
if(input$TypeTaxo=="RDP") if(input$TypeTaxo=="RDP")
{ {
data = read_rdp(inFile$datapath,input$RDP_th) tryCatch(read_rdp(inFile$datapath,input$RDP_th)->data,
error=function(e) sendSweetAlert(messageId="ErrorRDP",
title = "Oops",
text=paste("Your file can not be read in SHAMAN.\n \n",e),type ="error"))
} }
## Add NA ## Add NA
...@@ -99,10 +109,18 @@ shinyServer(function(input, output,session) { ...@@ -99,10 +109,18 @@ shinyServer(function(input, output,session) {
inFile <- input$fileBiom inFile <- input$fileBiom
if (!is.null(inFile) && is.null(values$biom_masque)) { if (!is.null(inFile) && is.null(values$biom_masque)) {
try(read_biom(inFile$datapath)->data,silent=T) tryCatch(read_biom(inFile$datapath)->data,
} error=function(e) sendSweetAlert(messageId="ErrorBiom1",
if (!is.null(values$biom_masque) && file.exists(values$biom_masque)) try(read_biom(values$biom_masque)->data,silent=T) title = "Oops",
text=paste("Your file can not be read in SHAMAN.\n \n",e),type ="error"))
}
if (!is.null(values$biom_masque) && file.exists(values$biom_masque)){
tryCatch(read_biom(values$biom_masque)->data,
error=function(e) sendSweetAlert(messageId="ErrorBiom2",
title = "Oops",
text=paste("Your file can not be read in SHAMAN.\n \n",e),type ="error"))
}
return(data) return(data)
}) })
...@@ -223,7 +241,10 @@ shinyServer(function(input, output,session) { ...@@ -223,7 +241,10 @@ shinyServer(function(input, output,session) {
if (is.null(inFile)) return(NULL) if (is.null(inFile)) return(NULL)
data = read.csv(inFile$datapath,sep=input$sepsize,header=TRUE) tryCatch(read.csv(inFile$datapath,sep=input$sepsize,header=TRUE)->data,
error=function(e) sendSweetAlert(messageId="ErrorSizeFactor",
title = "Oops",
text=paste("Your file can not be read in SHAMAN.\n \n",e),type ="error"))
return(as.data.frame(data)) return(as.data.frame(data))
}) })
...@@ -492,25 +513,37 @@ shinyServer(function(input, output,session) { ...@@ -492,25 +513,37 @@ shinyServer(function(input, output,session) {
output$TabBoxData <- renderUI({ output$TabBoxData <- renderUI({
tree = dataInputTree()$data tree = dataInputTree()$data
data=dataInput()$data data=dataInput()$data
if(!is.null(data$counts) && !is.null(data$taxo) && nrow(data$counts)>0 && nrow(data$taxo)>0 && !is.null(tree)) res=NULL
if(!is.null(tree))
{ {
tabBox(id="id_tabboxdata",width = NULL, selected = "Count table", res = tabBox(id="id_tabboxdata",style=" visibility: hidden;",width = NULL, selected = "Count table",
tabPanel("Count table",DT::dataTableOutput("DataCounts")), tabPanel("Count table",DT::dataTableOutput("DataCounts")),
tabPanel("Taxonomy",DT::dataTableOutput("DataTaxo")), tabPanel("Taxonomy",DT::dataTableOutput("DataTaxo")),
tabPanel("Summary",h5(strong("Percentage of annotation")),htmlOutput("SummaryView"), tabPanel("Summary",h5(strong("Percentage of annotation")),htmlOutput("SummaryView"),
br(),h5(strong("Number of features by level:")),plotOutput("SummaryViewBarplot",width = 1200,height=500)), br(),h5(strong("Number of features by level:")),plotOutput("SummaryViewBarplot",width = 1200,height=500)),
tabPanel("Phylogeny", PhyloTreeMetaROutput('PhyloTreeMetaR')) tabPanel("Phylogeny", PhyloTreeMetaROutput('PhyloTreeMetaR'))
) )
} }
else if(!is.null(data$counts) && !is.null(data$taxo) && nrow(data$counts)>0 && nrow(data$taxo)>0) else if(is.null(tree))
{ {
tabBox(id="id_tabboxdata",width = NULL, selected = "Count table", res = tabBox(id="id_tabboxdata",width = NULL, selected = "Count table",
tabPanel("Count table",DT::dataTableOutput("DataCounts")), tabPanel("Count table",DT::dataTableOutput("DataCounts")),
tabPanel("Taxonomy",DT::dataTableOutput("DataTaxo")), tabPanel("Taxonomy",DT::dataTableOutput("DataTaxo")),
tabPanel("Summary",h5(strong("Percentage of annotation")),htmlOutput("SummaryView"), tabPanel("Summary",h5(strong("Percentage of annotation")),htmlOutput("SummaryView"),
br(),h5(strong("Number of features by level:")),plotOutput("SummaryViewBarplot",width = 1200,height=500)) br(),h5(strong("Number of features by level:")),plotOutput("SummaryViewBarplot",width = 1200,height=500))
) )
} }
return(res)
})
observe({
data=dataInput()$data
if(!is.null(data$counts) && !is.null(data$taxo) && nrow(data$counts)>0 && nrow(data$taxo)>0)
{
showElement("tabboxdata_col",anim=TRUE)
} else hideElement("tabboxdata_col",anim=TRUE)
}) })
...@@ -519,11 +552,15 @@ shinyServer(function(input, output,session) { ...@@ -519,11 +552,15 @@ shinyServer(function(input, output,session) {
}) })
output$SummaryView <- renderGvis({ output$SummaryView <- renderGvis({
data = dataInput()$data tmp = dataInput()
data = tmp$data
taxo = data$taxo taxo = data$taxo
counts = data$counts counts = data$counts
check = tmp$check
cond = (!is.null(data$counts) && nrow(data$counts)>0 && !is.null(data$taxo) && nrow(data$taxo)>0 && is.null(check$CheckTaxo$Error) && is.null(check$CheckCounts$Error))
res = NULL res = NULL
if(!is.null(data$counts) && !is.null(data$taxo) && nrow(data$counts)>0 && nrow(data$taxo)>0) if(cond)
{ {
taxo = rbind(taxo,rep(NA,ncol(taxo))) taxo = rbind(taxo,rep(NA,ncol(taxo)))
#tmpPercent = round(apply(is.na(taxo),2,table)["FALSE",]/(nrow(taxo)-1)*100,2) #tmpPercent = round(apply(is.na(taxo),2,table)["FALSE",]/(nrow(taxo)-1)*100,2)
...@@ -552,11 +589,15 @@ shinyServer(function(input, output,session) { ...@@ -552,11 +589,15 @@ shinyServer(function(input, output,session) {
output$SummaryViewBarplot <- renderPlot({ output$SummaryViewBarplot <- renderPlot({
data = dataInput()$data tmp = dataInput()
data = tmp$data
taxo = data$taxo taxo = data$taxo
counts = data$counts counts = data$counts
check = tmp$check
cond = (!is.null(data$counts) && nrow(data$counts)>0 && !is.null(data$taxo) && nrow(data$taxo)>0 && is.null(check$CheckTaxo$Error) && is.null(check$CheckCounts$Error))
res = NULL res = NULL
if(!is.null(data$counts) && !is.null(data$taxo) && nrow(data$counts)>0 && nrow(data$taxo)>0) if(cond)
{ {
colors=rep(c("#1f77b4","#aec7e8","#ff7f0e","#ffbb78", "#2ca02c","#98df8a","#d62728","#ff9896","#9467bd","#c5b0d5","#8c564b", colors=rep(c("#1f77b4","#aec7e8","#ff7f0e","#ffbb78", "#2ca02c","#98df8a","#d62728","#ff9896","#9467bd","#c5b0d5","#8c564b",
"#c49c94","#e377c2","#f7b6d2","#7f7f7f", "#c7c7c7","#bcbd22","#dbdb8d","#17becf","#9edae5"),ceiling(ncol(taxo)/20)) "#c49c94","#e377c2","#f7b6d2","#7f7f7f", "#c7c7c7","#bcbd22","#dbdb8d","#17becf","#9edae5"),ceiling(ncol(taxo)/20))
...@@ -635,25 +676,7 @@ shinyServer(function(input, output,session) { ...@@ -635,25 +676,7 @@ shinyServer(function(input, output,session) {
# return(list(target = target, labeled=labeled)) # return(list(target = target, labeled=labeled))
}) })
# ## Select a folder (for MASQUE)
# observeEvent(
# ignoreNULL = TRUE,
# eventExpr = {
# input$directory
# },
# handlerExpr = {
# # if (input$directory > 0) {
# # condition prevents handler execution on initial app launch
#
# # launch the directory selection dialog with initial path read from the widget
# path = choose.dir(default = readDirectoryInput(session, 'directory'))
#
# # update the widget value
# updateDirectoryInput(session, 'directory', value = path)
# # }
# }
# )
############################################################# #############################################################
...@@ -661,17 +684,7 @@ shinyServer(function(input, output,session) { ...@@ -661,17 +684,7 @@ shinyServer(function(input, output,session) {
## MASQUE ## MASQUE
## ##
############################################################# #############################################################
## Select a folder (for MASQUE)
shinyDirChoose(input, 'dir', roots = c(dir=""),filetypes = c('', 'fastq','gz','fgz'))
# output$dirSel <- renderText({
# print(input$dir2)
# home <- normalizePath("~")
# home <- ""
# path_glob = file.path(home, paste(unlist(dir()$path[-1]), collapse = .Platform$file.sep))
# })
#
observeEvent(input$dir,{ observeEvent(input$dir,{
...@@ -685,17 +698,9 @@ shinyServer(function(input, output,session) { ...@@ -685,17 +698,9 @@ shinyServer(function(input, output,session) {
} }
}) })
# ## Create a fasta file containing the contaminant
# path <- reactive({
#
# home <- normalizePath("~")
# home <- ""
# file.path(home, paste(unlist(dir()$path[-1]), collapse = .Platform$file.sep),"*.f*q*")
# })
CreateFasta <- reactive({ CreateFasta <- reactive({
seq = NULL seq = NULL
tmp = tempdir() tmp = tempdir()
...@@ -708,7 +713,9 @@ shinyServer(function(input, output,session) { ...@@ -708,7 +713,9 @@ shinyServer(function(input, output,session) {
}) })
observeEvent(input$submit,{
## Action with submit button
MasqueSubmit <- eventReactive(input$submit,{
CMP = CheckMasque(input, values) CMP = CheckMasque(input, values)
Error = CMP$Error Error = CMP$Error
...@@ -781,9 +788,20 @@ shinyServer(function(input, output,session) { ...@@ -781,9 +788,20 @@ shinyServer(function(input, output,session) {
) )
} }
})
observeEvent(input$submit,{
tryCatch(MasqueSubmit(),
error=function(e) sendSweetAlert(messageId="ErrorMasque",
title = "Oops",
text=paste("Something wrong when submitting.\n \n",e),type ="error"))
},priority = 1) },priority = 1)
## FastQ list ## FastQ list
output$FastQList_out <- renderUI({ output$FastQList_out <- renderUI({
res = NULL res = NULL
...@@ -800,26 +818,7 @@ shinyServer(function(input, output,session) { ...@@ -800,26 +818,7 @@ shinyServer(function(input, output,session) {
return(res) return(res)
}) })
#
# FastqLoad <- reactive({
# input$LoadFiles
# ## Reinitializing
# if(!is.null(isolate(values$fastq_names_only))) values$fastq_names_only = NULL
#
#
# ## Get the fastq names
# home <- normalizePath("~")
# home <- ""
# # path_glob = file.path(home, paste(unlist(isolate(dir()$path[-1])), collapse = .Platform$file.sep))
#
# fastq_names = Sys.glob(isolate(path()))
#
# if(length(fastq_names)>0 && isolate(input$LoadFiles>0))
# {
# if(is.null(isolate(values$fastq_names_only)) || length(isolate(values$fastq_names_only))==0) values$fastq_names_only = gsub(pattern = path_glob,x = fastq_names,replacement = "")
# }
#
# })
## Remove FastQ function ## Remove FastQ function
......
...@@ -367,6 +367,7 @@ body <- dashboardBody( ...@@ -367,6 +367,7 @@ body <- dashboardBody(
), ),
div(style = "text-align:center;", div(style = "text-align:center;",
actionButton("submit", strong("Check and submit"), icon("chevron-circle-right"),class="btn-primary",style = "color: #fff"), actionButton("submit", strong("Check and submit"), icon("chevron-circle-right"),class="btn-primary",style = "color: #fff"),
receiveSweetAlert(messageId = "ErrorMasque"),
tags$style(type='text/css', "#submit { width:50%; margin-top: 5px;}"), tags$style(type='text/css', "#submit { width:50%; margin-top: 5px;}"),
receiveSweetAlert(messageId = "SuccessMasque") receiveSweetAlert(messageId = "SuccessMasque")
) )
...@@ -449,7 +450,7 @@ body <- dashboardBody( ...@@ -449,7 +450,7 @@ body <- dashboardBody(
column(width=6,radioButtons("TypeTable",h6(strong("Type:")),c("OTU/Gene table"="OTU","MGS table"="MGS"))), column(width=6,radioButtons("TypeTable",h6(strong("Type:")),c("OTU/Gene table"="OTU","MGS table"="MGS"))),
column(width=6,selectInput("sepcount", h6(strong("Separator:")),c("Tab" = "\t", "Comma" = ",","Semi-colon" = ";"))) column(width=6,selectInput("sepcount", h6(strong("Separator:")),c("Tab" = "\t", "Comma" = ",","Semi-colon" = ";")))
), ),
fileInput('fileCounts', h6(strong('Select your file')),width="100%"), fileInput('fileCounts', h6(strong('Select your file')),width="100%",accept = c(".csv",".tsv",'.xls','.xlsx','.txt')),
tags$script('$( "#fileCounts" ).on( "click", function() { this.value = null; });') tags$script('$( "#fileCounts" ).on( "click", function() { this.value = null; });')
), ),
conditionalPanel(condition="!input.NoTaxoFile", conditionalPanel(condition="!input.NoTaxoFile",
...@@ -464,7 +465,7 @@ body <- dashboardBody( ...@@ -464,7 +465,7 @@ body <- dashboardBody(
c("Tab" = "\t", "Comma" = ",", "Semicolon" = ";"))) c("Tab" = "\t", "Comma" = ",", "Semicolon" = ";")))
) )
), ),
fileInput('fileTaxo', h6(strong('Select your file')),width="100%"), fileInput('fileTaxo', h6(strong('Select your file')),width="100%",accept = c(".csv",".tsv",'.xls','.xlsx','.txt')),
tags$script('$( "#fileTaxo" ).on( "click", function() { this.value = null; });') tags$script('$( "#fileTaxo" ).on( "click", function() { this.value = null; });')
) )
) )
...@@ -472,7 +473,7 @@ body <- dashboardBody( ...@@ -472,7 +473,7 @@ body <- dashboardBody(
conditionalPanel(condition="input.FileFormat=='fileBiom'", conditionalPanel(condition="input.FileFormat=='fileBiom'",
box(title="Load the BIOM file",width = 3, status = "primary", solidHeader = TRUE,collapsible = FALSE, box(title="Load the BIOM file",width = 3, status = "primary", solidHeader = TRUE,collapsible = FALSE,
fileInput('fileBiom', h5(strong('Select your file')),width="100%"), fileInput('fileBiom', h5(strong('Select your file')),width="100%",accept = c(".biom")),
tags$script('$( "#fileBiom" ).on( "click", function() { this.value = null; });') tags$script('$( "#fileBiom" ).on( "click", function() { this.value = null; });')
) )
), ),
...@@ -491,7 +492,13 @@ body <- dashboardBody( ...@@ -491,7 +492,13 @@ body <- dashboardBody(
), ),
column(12,uiOutput("TabBoxData")) column(id="tabboxdata_col",width=12,uiOutput("TabBoxData")),
receiveSweetAlert(messageId = "ErrorTaxo"),
receiveSweetAlert(messageId = "ErrorBiom1"),
receiveSweetAlert(messageId = "ErrorBiom2"),
receiveSweetAlert(messageId = "ErrorSizeFactor"),
receiveSweetAlert(messageId = "ErrorCounts"),
receiveSweetAlert(messageId = "ErrorRDP")
), ),
#### Statistical analysis #### Statistical analysis
......
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