modif project status

Rfunctions/internal_masque.R

@@ -25,99 +25,100 @@ 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))
+  if(PS$passOK){
+    if(PS$status=="done")
     {
-      ap = read.csv(annot_process,sep="\t")
-      build_process = paste(curdir,"www","masque","done",folder_name,"shaman_annotation_process.tsv",sep= .Platform$file.sep)
+      res = list()
+      json_file = PS$file
+      folder_name = paste('file',masque_key,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$style(type='text/css', "#Download_masque_zip { width:100%; margin-top: 15px;}")
-        )
+      ### Paste file name as folder
+      annot_process = paste(curdir,"www","masque","done",folder_name,"shaman_annotation_process.tsv",sep= .Platform$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")))
+      }
       
       
-    } 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$status=="error"){
+      error_message = "Failed"
+      json_file = PS$file
+      error_file = paste(curdir,"www","masque","error",paste('file',masque_key,"_error",".txt",sep=""),sep= .Platform$file.sep)
   
-  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"){
-    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)
-
-    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>'),
+      if(file.exists(error_file)){error_message = read_lines(error_file)}
       
-              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()
-                     )
-              )
-        )
+      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))

server.R

@@ -1441,19 +1441,21 @@ shinyServer(function(input, output,session) {
   
   
   output$gaugeMasque_progress <- renderGauge({
-    PS = Project_status()
     res = NULL
-    if(PS$status=="doing"){
-      json_file = PS$file
-      progress_file = paste(values$curdir,"www","masque","doing",paste(basename(file_path_sans_ext(json_file)),"_progress",".txt",sep=""),sep= .Platform$file.sep)
-      if(file.exists(progress_file))
-      {
-        pf = read_lines(progress_file)
-        pf = round(as.numeric(pf),1)
-        if(!is.na(pf)){
-          pf = min(pf,100); pf = max(pf,0)
+    PS = Project_status(values$masque_key,values$curdir)
+    if(PS$passOK){
+      if(PS$status=="doing"){
+        json_file = PS$file
+        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)
+          pf = round(as.numeric(pf),1)
+          if(!is.na(pf)){
+            pf = min(pf,100); pf = max(pf,0)
+          }
+          res = gauge(min(pf,100), 0,100,symbol = '%',label= "Progress...")
         }
-        res = gauge(min(pf,100), 0,100,symbol = '%',label= "Progress...")
       }
     }
     return(res)