add internal_masque + icons

Rfunctions/internal_masque.R

+Project_status <- function(masque_key,curdir){
+
+  passOK = FALSE;status = NULL;file = NULL
+  
+  json_files = list.files(paste(curdir,"www","masque",sep= .Platform$file.sep),pattern = "json",recursive = TRUE)
+  allpass = gsub(gsub(json_files,pattern = ".*file",replacement = ""),pattern = ".json",replacement = "")
+  
+  
+  if(length(allpass)>0){
+    passOK = any(masque_key==allpass)
+    if(passOK){
+      ind = which(masque_key==allpass)[1]
+      file = paste(curdir,"www","masque",json_files[ind],sep= .Platform$file.sep)
+      status = gsub(json_files[ind],pattern = "/.*",replacement = "")
+    }
+  }
+  
+  return(list(status=status,file=file,passOK=passOK))
+}
+
+
+
+
+Project_box_result <- function(masque_key,curdir){
+  res = NULL
+  PS = Project_status(masque_key,curdir)
+  
+  
+  if(PS$status=="done")
+  {
+    res = list()
+    json_file = PS$file
+    folder_name = paste('file',masque_key,sep="")
+    
+    ### Paste file name as folder
+    annot_process = paste(curdir,"www","masque","done",folder_name,"shaman_annotation_process.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)
+      tmp = Sys.time()
+      diff = tmp-start
+    }
+    
+    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$file.sep)
+      
+      res[[1]] = fluidRow(
+        HTML('<center><h1><strong>Your project is done !</strong></h1> <br/> <em><h4> Hereafter is a summary of the building and annotation processes</h4> </em><br/> </center>'),
+        br(),
+        column(width=5,
+               valueBox(ap$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$h5("Remaining amplicons after removing chimera", style = "width: 70%;")), color = "light-blue",width=NULL,icon = uiOutput("chimera_icon"))
+        ),
+        column(width=5,offset = 2,
+        box(title="Upload the results",width = NULL, background = "light-blue",
+            selectInput("masque_database","Select the database",choices=c("Silva" = "silva","Greengenes" = "greengenes")),
+            tags$style(type='text/css', "#masque-database { width:100%; margin-top: 5px;}"),
+            actionButton("RunResMasque",label = "Upload the results",icon=icon('upload')),
+            tags$style(type='text/css', "#RunResMasque { width:100%; margin-top: 15px;}")
+        ),
+        
+        box(id="box-zip",title="Download .zip file",width = NULL, status = "success",
+            downloadButton('Download_masque_zip', 'Download the results'),
+            tags$style(type='text/css', "#Download_masque_zip { width:100%; margin-top: 15px;}")
+        )
+        
+        
+        )
+        
+        )
+      
+      
+    } 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$file.sep)
+    if(file.exists(build_process))
+    {
+      ap = read.csv(build_process,sep="\t")
+    
+      res[[2]] = fluidRow(column(width=12,strong(h3("Building process table")),DT::dataTableOutput("build_process_table")))
+    }
+    
+    
+  }
+  
+  if(PS$status=="doing"){
+    res = fluidRow(
+      HTML('<center><h1><strong>Your project is currently running !</strong></h1> <br/> <br/> </center>'),
+      inlineCSS(gaugeCSS),
+      gaugeOutput("gaugeMasque_progress", width = "100%", height = "100%")
+    )
+  }
+  
+  if(PS$status=="error"){
+    
+    json_file = PS$file
+    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>'),
+      
+              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%;"),
+                         HTML(paste(error_message,collapse = " <br/> ")),
+                         br()
+                     )
+              )
+        )
+  }
+  
+  return(list(box=res,PS=PS))
+  
+}
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