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Commit 2ce7f0ec authored by Amine GHOZLANE's avatar Amine GHOZLANE
Browse files

Add support of masque

parent 4f3f6d79
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.gitignore
View file @ 2ce7f0ec
......@@ -4,3 +4,8 @@
.Rproj.user
*.Rproj
*.json
www/masque/doing/*
www/masque/todo/*
www/masque/done/*
www/masque/error/*
www/masque.png
\ No newline at end of file
LoadPackages.R
View file @ 2ce7f0ec
options(download.file.method = 'wget')
if (!require("Rcpp")){
install.packages("Rcpp")
install.packages("Rcpp", repos="http://cran.univ-paris1.fr/")
}
if(!require(shiny)){
install.packages("shiny")
install.packages("shiny", repos="http://cran.univ-paris1.fr/")
library(shiny)
}
if(!require(shinydashboard)){
......@@ -13,52 +13,52 @@ if(!require(shinydashboard)){
}
if(!require(rjson)){
install.packages('rjson')
install.packages('rjson', repos="http://cran.univ-paris1.fr/")
library(rjson)
}
if(!require(ape)){
install.packages('ape')
install.packages('ape', repos="http://cran.univ-paris1.fr/")
library(ape)
}
if(!require(GUniFrac)){
install.packages('GUniFrac')
install.packages('GUniFrac', repos="http://cran.univ-paris1.fr/")
library(GUniFrac)
}
if(!require(devtools)){
install.packages('devtools')
install.packages('devtools', repos="http://cran.univ-paris1.fr/")
library(devtools)
}
if (!require(psych)) {
install.packages('psych')
install.packages('psych', repos="http://cran.univ-paris1.fr/")
library(psych)
}
if (!require(ggplot2)) {
install.packages('ggplot2')
install.packages('ggplot2', repos="http://cran.univ-paris1.fr/")
library(ggplot2)
}
if (!require(vegan)) {
install.packages('vegan')
install.packages('vegan', repos="http://cran.univ-paris1.fr/")
library(vegan)
}
if (!require(dendextend)) {
install.packages('dendextend')
install.packages('dendextend', repos="http://cran.univ-paris1.fr/")
library(dendextend)
}
if (!require(circlize)) {
install.packages('circlize')
install.packages('circlize', repos="http://cran.univ-paris1.fr/")
library(circlize)
}
if (!require(devtools)) {
install.packages('devtools')
install.packages('devtools', repos="http://cran.univ-paris1.fr/")
library(devtools)
}
if(!require(treeWeightD3)){
......@@ -99,12 +99,12 @@ if (!require(genefilter)) {
}
if (!require(googleVis)) {
install.packages('googleVis')
install.packages('googleVis', repos="http://cran.univ-paris1.fr/")
suppressPackageStartupMessages(library(googleVis))
}
if (!require(shinyjs)) {
install.packages('shinyjs')
install.packages('shinyjs', repos="http://cran.univ-paris1.fr/")
library(shinyjs)
}
......@@ -114,17 +114,17 @@ if(!require(d3vennR)){
}
if (!require(DT)) {
install.packages('DT')
install.packages('DT', repos="http://cran.univ-paris1.fr/")
library(DT)
}
if (!require(RColorBrewer)) {
install.packages('RColorBrewer')
install.packages('RColorBrewer', repos="http://cran.univ-paris1.fr/")
library(RColorBrewer)
}
if (!require(gplots)) {
install.packages('gplots')
install.packages('gplots', repos="http://cran.univ-paris1.fr/")
library(gplots)
}
......@@ -135,22 +135,22 @@ if (!require(DESeq2)) {
}
if (!require(ade4)) {
install.packages('ade4')
install.packages('ade4', repos="http://cran.univ-paris1.fr/")
library(ade4)
}
if (!require(scales)) {
install.packages('scales')
install.packages('scales', repos="http://cran.univ-paris1.fr/")
library(scales)
}
if (!require(phytools)) {
install.packages('phytools')
install.packages('phytools', repos="http://cran.univ-paris1.fr/")
library(phytools)
}
if(!require(philentropy)){
install.packages("philentropy")
install.packages("philentropy", repos="http://cran.univ-paris1.fr/")
library(philentropy)
}
......@@ -170,44 +170,53 @@ if (!require("shinyWidgets")){
}
if (!require("sendmailR")){
install.packages("sendmailR")
install.packages("sendmailR", repos="http://cran.univ-paris1.fr/")
library(sendmailR)
}
if (!require("shinyBS")){
install.packages("shinyBS")
install.packages("shinyBS", repos="http://cran.univ-paris1.fr/")
library(shinyBS)
}
library(tools)
if (!require("flexdashboard")){
install.packages("flexdashboard")
install.packages("flexdashboard", repos="http://cran.univ-paris1.fr/")
library(flexdashboard)
}
if (!require("backports")){
install.packages("backports")
install.packages("backports", repos="http://cran.univ-paris1.fr/")
library(backports)
}
if (!require("readr")){
install.packages("readr")
install.packages("readr", repos="http://cran.univ-paris1.fr/")
library(readr)
}
if (!require("jsonlite")){
install.packages("jsonlite")
install.packages("jsonlite", repos="http://cran.univ-paris1.fr/")
library(jsonlite)
}
if (!require("shinyFiles")){
install.packages("shinyFiles")
install.packages("shinyFiles", repos="http://cran.univ-paris1.fr/")
library(shinyFiles)
}
if (!require("htmltools")){
install.packages("htmltools", repos="http://cran.univ-paris1.fr/")
library(htmltools)
}
# if (!require("V8")){
# install.packages("V8", repos="http://cran.univ-paris1.fr/")
# library(htmltools)
# }
# if(!require(plotly)){
# install.packages("plotly")
......
Rfunctions/Data_Management.R
View file @ 2ce7f0ec
......@@ -294,7 +294,7 @@ CheckTreeFile <- function(tree)
## Check Masque Input
CheckMasque <- function(input,values)
CheckMasque <- function(input, values, check_mail=FALSE)
{
Error = NULL
HowTo = NULL
......@@ -306,8 +306,9 @@ CheckMasque <- function(input,values)
# HowTo = "<h6><strong>Make sure that you have click the &laquo Get key &raquo button and that you have pasted the key sent by mail </strong></h6>"
# }
#
if(is.null(Error) && is.null(values$login_email)){
print(check_mail)
if(is.null(Error) && is.null(values$login_email) && check_mail){
print("fuck")
Error = "<h6><strong>Invalid key </strong></h6>";
HowTo = "<h6><strong>Make sure that you have click the &laquo Get key &raquo button </strong></h6>"
}
......@@ -352,10 +353,17 @@ CheckMasque <- function(input,values)
res = SamplesMasque(input,values)
if(length(res$samples)==0) {
Error = "<h6><strong>0 sample detected</strong></h6>"
if(input$PairedOrNot=='y') HowTo = '<h6><strong>Make sur that you click the &laquo Load &raquo button. <br /> Change the working directory and/or verify the pairs matching.</strong></h6>'
if(input$PairedOrNot=='n') HowTo = '<h6><strong>Make sur that you click the &laquo Load &raquo button. <br /> Change the working directory.</strong></h6>'
if(input$PairedOrNot=='y') HowTo = '<h6><strong>Make sure that you click the &laquo Match &raquo button. <br /> Change the working directory and/or verify the pairs matching.</strong></h6>'
if(input$PairedOrNot=='n') HowTo = '<h6><strong>Make sure that your samples have the correct extension (.fastq, .fq, .fastq.gz or .fq.gz). <br /> Change the working directory.</strong></h6>'
}
}
if(is.null(Error)) {
error_file = paste(values$curdir,"www","masque","error",paste('file',values$masque_key,"_error.txt",sep=""),sep= .Platform$file.sep)
if(file.exists(error_file)){
Error = "<h6><strong>An error happened during the workflow progress. Please check your email.</strong></h6>"
}
}
return(list(Error=Error,HowTo=HowTo))
......@@ -425,7 +433,8 @@ CreateJSON <- function(input,values){
"host"=input$HostName,
"type"=input$DataTypeMasque,
"mail"=values$login_email,
"contaminant"= path_fasta
"contaminant"= path_fasta,
"pattern_R1"= input$R1files
)
df %>% jsonlite::toJSON() %>% write_lines(values$json_name)
}
......
Rfunctions/internal_masque.R
View file @ 2ce7f0ec
Project_status <- function(masque_key,curdir){
passOK = FALSE;status = NULL;file = NULL
json_files = list.files(paste(curdir,"www","masque",sep= .Platform$file.sep),pattern = "json",recursive = TRUE)
json_files = list.files(paste(curdir,"www","masque",sep= .Platform$file.sep),pattern = paste("file", masque_key, ".json", sep=""),recursive = TRUE)
allpass = gsub(gsub(json_files,pattern = ".*file",replacement = ""),pattern = ".json",replacement = "")
if(length(allpass)>0){
passOK = any(masque_key==allpass)
if(passOK){
......@@ -15,6 +13,7 @@ Project_status <- function(masque_key,curdir){
}
}
# return(list(status=status,file=json_file,passOK=passOK))
return(list(status=status,file=file,passOK=passOK))
}
......@@ -22,6 +21,7 @@ Project_status <- function(masque_key,curdir){
Project_box_result <- function(masque_key,curdir){
res = NULL
PS = Project_status(masque_key,curdir)
......@@ -31,15 +31,16 @@ Project_box_result <- function(masque_key,curdir){
res = list()
json_file = PS$file
folder_name = paste('file',masque_key,sep="")
json_file = paste(curdir,"www","masque","done",paste(folder_name, ".json", sep=""),sep= .Platform$file.sep)
json_data = rjson::fromJSON(file=json_file)
### Paste file name as folder
annot_process = paste(curdir,"www","masque","done",folder_name,"shaman_annotation_process.tsv",sep= .Platform$file.sep)
annot_process = paste(curdir,"www","masque","done",folder_name,"shaman_process_annotation.tsv",sep= .Platform$file.sep)
## Waiting for file creation (max 3min)
start = Sys.time(); diff = 0
while(!file.exists(annot_process) && diff<180){
annot_process = paste(curdir,"www","masque","done",folder_name,"shaman_annotation_process.tsv",sep= .Platform$file.sep)
annot_process = paste(curdir,"www","masque","done",folder_name,"shaman_process_annotation.tsv",sep= .Platform$file.sep)
tmp = Sys.time()
diff = tmp-start
}
......@@ -47,45 +48,79 @@ Project_box_result <- function(masque_key,curdir){
if(file.exists(annot_process))
{
ap = read.csv(annot_process,sep="\t")
build_process = paste(curdir,"www","masque","done",folder_name,"shaman_annotation_process.tsv",sep= .Platform$file.sep)
if(json_data[[1]]$type == "16S_18S") db_choices = c("Silva" = "silva","Greengenes" = "greengenes", "RDP"= "rdp")
else if(json_data[[1]]$type == "23S_28S") db_choices = c("Silva" = "silva","RDP"= "rdp")
else db_choices = c("Findley" = "findley", "Underhill"= "underhill", "Unite"= "unite", "RDP"= "rdp")
#build_process = paste(curdir,"www","masque","done",folder_name,"shaman_process_annotation.tsv",sep= .Platform$file.sep)
res[[1]] = fluidRow(
HTML('<center><h1><strong>Your project is done !</strong></h1> <br/> <em><h4> Hereafter is a summary of the building and annotation processes</h4> </em><br/> </center>'),
#HTML('<center><h1><strong>Your project is done !</strong></h1> <br/> <em><h4> Hereafter is a summary of the building and annotation processes</h4> </em><br/> </center>'),
HTML('<center><h1><strong>Your project is done !</strong></h1></center>'),
br(),
column(width=5,
valueBox(ap$Count[1],tags$strong(tags$h5("Number of amplicons", style = "width: 70%;")), color = "light-blue",width=NULL,icon = uiOutput("amplicon_icon")),
valueBox(ap$Count[2],tags$strong(tags$h5("Remaining amplicons after dereplication", style = "width: 70%;")), color = "light-blue",width=NULL,icon = uiOutput("dereplication_icon")),
valueBox(ap$Count[3],tags$strong(tags$h5("Remaining amplicons after removing singletons", style = "width: 70%;")), color = "light-blue",width=NULL,icon = uiOutput("singleton_icon")),
valueBox(ap$Count[4],tags$strong(tags$h5("Remaining amplicons after removing chimera", style = "width: 70%;")), color = "light-blue",width=NULL,icon = uiOutput("chimera_icon"))
column(width=4,
h3("OTU building process"),
shinydashboard::valueBox(ap$Count[1],tags$strong(tags$h5("Number of amplicons", style = "width: 70%;")), color = "light-blue", width = NULL, icon = uiOutput("amplicon_icon")),
shinydashboard::valueBox(ap$Count[2],tags$strong(tags$h5("Remaining amplicons after dereplication", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("dereplication_icon")),
shinydashboard::valueBox(ap$Count[3],tags$strong(tags$h5("Remaining amplicons after removing singletons", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("singleton_icon")),
shinydashboard::valueBox(ap$Count[4],tags$strong(tags$h5("Remaining amplicons after removing chimera", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("chimera_icon")),
shinydashboard::valueBox(ap$Count[5],tags$strong(tags$h5("Number of OTU", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("otu_icon"))
),
column(width=5,offset = 2,
box(title="Upload the results",width = NULL, background = "light-blue",
selectInput("masque_database","Select the database",choices=c("Silva" = "silva","Greengenes" = "greengenes")),
tags$style(type='text/css', "#masque-database { width:100%; margin-top: 5px;}"),
actionButton("RunResMasque",label = "Upload the results",icon=icon('upload')),
tags$style(type='text/css', "#RunResMasque { width:100%; margin-top: 15px;}")
#column(width=5, div(img(src = "masque.png",width = "50%",height = "20%"))),
if(json_data[[1]]$type == "16S_18S"){
column(width=5,
strong(h3("16S/18S annotation process")),
shinydashboard::valueBox(ap$Count[6],tags$strong(tags$h5("Number of OTU annotated by SILVA", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("silva_icon")),
shinydashboard::valueBox(ap$Count[7],tags$strong(tags$h5("Number of OTU annotated by Greengenes", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("greengenes_icon")),
shinydashboard::valueBox(ap$Count[8],tags$strong(tags$h5("Number of OTU annotated by RDP", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("rdp_icon"))
)
}
else if(json_data[[1]]$type == "23S_28S"){
column(width=5,
strong(h3("23S/28S annotation process")),
shinydashboard::valueBox(ap$Count[6],tags$strong(tags$h5("Number of OTU annotated by SILVA", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("silva_icon")),
shinydashboard::valueBox(ap$Count[7],tags$strong(tags$h5("Number of OTU annotated by RDP", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("rdp_icon"))
)
}
else{
column(width=5,
strong(h3("ITS annotation process")),
shinydashboard::valueBox(ap$Count[6],tags$strong(tags$h5("Number of OTU annotated by Unite", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("unite_icon")),
shinydashboard::valueBox(ap$Count[7],tags$strong(tags$h5("Number of OTU annotated by Findley", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("findley_icon")),
shinydashboard::valueBox(ap$Count[8],tags$strong(tags$h5("Number of OTU annotated by Underhill", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("underhill_icon")),
shinydashboard::valueBox(ap$Count[9],tags$strong(tags$h5("Number of OTU annotated by RDP", style = "width: 70%;")), color = "light-blue", width = NULL,icon = uiOutput("rdp_icon"))
)
},
#offset = 4,
column(width=3,
strong(h3("Start statistical analysis")),
box(title="Load the results",width = NULL, background = "light-blue",
selectInput("masque_db","Select the database",choices=db_choices),
conditionalPanel(condition="input.masque_db=='rdp'",numericInput("rdp_thres",h6(strong("Threshold:")),0.5,step=0.01,min=0.01,max=1)),
actionButton("LoadResMasque", "Upload the results",icon=icon('upload')),
tags$style(type='text/css', "#LoadResMasque { width:100%; }"),
receiveSweetAlert(messageId = "LoadResMasque")
),
#shinydashboard::box(title="Upload the results",width = NULL, background = "light-blue",
#selectInput("masque_database","Select the database",choices=c("Silva" = "silva","Greengenes" = "greengenes", "MARDE"="merde")),
#tags$style(type='text/css', "#masque_database { width:100%; margin-top: 5px;}"),
#actionButton("RunResMasque",label = "Upload the results",icon=icon('upload')),
#tags$style(type='text/css', "#RunResMasque { width:100%; margin-top: 15px;}")
#),
#receiveSweetAlert(messageId = "WTF2"),
box(id="box-zip",title="Download .zip file",width = NULL, status = "success",
downloadButton('Download_masque_zip', 'Download the results'),
tags$style(type='text/css', "#Download_masque_zip { width:100%; margin-top: 15px;}")
tags$style(type='text/css', "#Download_masque_zip { width:100%;}")
)
)
)
} else{res =HTML('<center><h1><strong>Your project is done !</strong></h1> <br/> <em><h4>Result can not be shown...</h4> </em> </center>')}
} else{res =HTML('<center><h1><strong>Your project is done !</strong></h1> <br/> <em><h4> Hereafter is a summary of the building and annotation processes</h4> </em> </center>')}
build_process = paste(curdir,"www","masque","done",folder_name,"shaman_build_process.tsv",sep= .Platform$file.sep)
build_process = paste(curdir,"www","masque","done",folder_name,"shaman_process_build.tsv",sep= .Platform$file.sep)
if(file.exists(build_process))
{
ap = read.csv(build_process,sep="\t")
res[[2]] = fluidRow(column(width=12,strong(h3("Building process table")),DT::dataTableOutput("build_process_table")))
res[[2]] = fluidRow(column(width=12,strong(h3("Detailed process table")),DT::dataTableOutput("build_process_table")))
}
......@@ -96,23 +131,26 @@ Project_box_result <- function(masque_key,curdir){
HTML('<center><h1><strong>Your project is currently running !</strong></h1> <br/> <br/> </center>'),
inlineCSS(gaugeCSS),
gaugeOutput("gaugeMasque_progress", width = "100%", height = "100%")
#jscode <- "shinyjs.refresh = function() { history.go(0); }",
#useShinyjs(),
#extendShinyjs(text = jscode),
)
}
if(PS$status=="error"){
error_message = "Failed"
json_file = PS$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)
if(file.exists(error_file)){error_message = read_lines(error_file)}
res = fluidRow(
HTML('<center><h1><strong>Sorry, the workflow failed during progression</strong></h1> <br/> <em><h4> Hereafter is the message error.</h4> </em> <br/> </center>'),
HTML('<center><h1><strong>The workflow failed during progression</strong></h1> <br/> </center>'),
column(width = 12,
div(style = "background-color: white; margin: 0 auto;width: 50%; text-align:center;border:1px solid red",
h4(strong("Error message")),
hr(style = "width: 70%;"),
h4(strong("Workflow error message")),
hr(style = "width: 70%;text-align:left;"),
HTML(paste(error_message,collapse = " <br/> ")),
br()
)
......
server.R
View file @ 2ce7f0ec
......@@ -30,28 +30,38 @@ 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,curdir=curdir)
biom_masque = NULL,tree_masque=NULL, masque_key = NULL, count_table_masque = NULL,
rdp_annot_masque = NULL, rdp_thres_masque = NULL,
paths_fastq_tmp=NULL,curdir=curdir, error_progress=FALSE)
## Counts file
dataInputCounts <-reactive({
data = NULL
inFile <- input$fileCounts
if (is.null(inFile) && is.null(values$count_table_masque)) return(NULL)
#if (is.null(inFile)) return(NULL)
if (is.null(inFile)) return(NULL)
if (!is.null(values$count_table_masque) && file.exists(values$count_table_masque)){
tryCatch(read.csv(values$count_table_masque,sep="\t",header=TRUE,check.names=FALSE)->data,
error=function(e) sendSweetAlert(messageId="ErrorCounts",
title = "Oops",
text=paste("The count file can not be read in SHAMAN.\n \n",e),type ="error"))
}
else{
tryCatch(read.csv(inFile$datapath,sep=input$sepcount,header=TRUE,check.names=FALSE)->data,
error=function(e) sendSweetAlert(messageId="ErrorCounts",
title = "Oops",
text=paste("Your file can not be read in SHAMAN.\n \n",e),type ="error"))
}
#print(data)
if(!is.null(data)){
colnames(data) = gsub("-",".",colnames(data))
## Rownames
if(!TRUE%in%duplicated(data[,1])) rownames(data)=data[,1];data=data[,-1]
try(round(data, 0)->data, silent=T)
}
return(as.data.frame(data))
})
......@@ -62,9 +72,10 @@ shinyServer(function(input, output,session) {
inFile <- input$fileTaxo
if (is.null(inFile)) return(NULL)
if (is.null(inFile) && is.null(values$rdp_annot_masque)) return(NULL)
#if (is.null(inFile)) return(NULL)
if(input$TypeTaxo=="Table")
if(input$TypeTaxo=="Table" && !is.null(inFile))
{
tryCatch(read.csv(inFile$datapath,sep=input$septaxo,header=TRUE)->data,
error=function(e) sendSweetAlert(messageId="ErrorTaxo",
......@@ -84,12 +95,20 @@ shinyServer(function(input, output,session) {
}
}
if(input$TypeTaxo=="RDP")
if(input$TypeTaxo=="RDP" && !is.null(inFile) || !is.null(values$rdp_annot_masque))
{
if (!is.null(values$rdp_annot_masque) && file.exists(values$rdp_annot_masque)){
tryCatch(read_rdp(values$rdp_annot_masque,values$rdp_thres_masque)->data,
error=function(e) sendSweetAlert(messageId="ErrorRDP",
title = "Oops",
text=paste("The annotation file can not be read in SHAMAN.\n \n",e),type ="error"))
}
else{
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"))
}
}
......@@ -108,7 +127,7 @@ shinyServer(function(input, output,session) {
data = NULL
inFile <- input$fileBiom
if (!is.null(inFile) && is.null(values$biom_masque)) {
if (!is.null(inFile) && is.null(values$biom_masque)){
tryCatch(read_biom(inFile$datapath)->data,
error=function(e) sendSweetAlert(messageId="ErrorBiom1",
title = "Oops",
......@@ -124,7 +143,13 @@ shinyServer(function(input, output,session) {
return(data)
})
observeEvent(input$fileCounts,{
values$count_table_masque=NULL;
})
observeEvent(input$fileTaxo,{
values$rdp_annot_masque=NULL;
values$rdp_thres_masque=NULL;
})
observeEvent(input$fileBiom,{
values$biom_masque=NULL;
})
......@@ -588,9 +613,12 @@ shinyServer(function(input, output,session) {
df <- data.frame(Label = colnames(taxo),Value = tmpPercent)
# res = gvisGauge(df,options=list(min=0, max=100, greenFrom=80,
# greenTo=100, yellowFrom=60, yellowTo=80,
# redFrom=0, redTo=60, width=1200, height=300))
res = gvisGauge(df,options=list(min=0, max=100, greenFrom=80,
greenTo=100, yellowFrom=60, yellowTo=80,
redFrom=0, redTo=60, width=1200, height=300))
redFrom=0, redTo=60, width=800, height=200))
}
return(res)
})
......@@ -724,7 +752,8 @@ shinyServer(function(input, output,session) {
## Action with submit button
MasqueSubmit <- eventReactive(input$submit,{
CMP = CheckMasque(input, values)
#activate check_mail
CMP = CheckMasque(input, values,check_mail = TRUE)
Error = CMP$Error
isJSONalreadyExist = file.exists(paste(values$curdir,"www","masque","doing",basename(json_name),sep= .Platform$file.sep))
......@@ -953,7 +982,7 @@ shinyServer(function(input, output,session) {
output$InfoMasque<- renderUI({
input$submit
CMP = isolate(CheckMasque(input, values))
CMP = isolate(CheckMasque(input, values, check_mail = FALSE))
if(!is.null(CMP$Error) && input$submit>0) {
toastr_error(title="Error",message=HTML(CMP$Error),closeButton = TRUE,position ="bottom-right",preventDuplicates = TRUE,newestOnTop = TRUE,
......@@ -966,7 +995,7 @@ shinyServer(function(input, output,session) {
output$InfoMasqueHowTo<- renderUI({
input$submit
CMP = isolate(CheckMasque(input, values))
CMP = isolate(CheckMasque(input, values, check_mail = FALSE))
if(!is.null(CMP$HowTo) && input$submit>0) {
toastr_success(title="How to",message=HTML(CMP$HowTo),closeButton = TRUE,position ="bottom-right",preventDuplicates = TRUE,newestOnTop = TRUE,
......@@ -1040,7 +1069,27 @@ shinyServer(function(input, output,session) {
output$chimera_icon <- renderUI(
htmltools::HTML('<img src="icons/chimera.png" alt="dna" style="width:80px;height:80px;">')
)
output$otu_icon <- renderUI(