internal_masque.R 5.31 KB
Newer Older
svolant's avatar
svolant committed
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
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)
  
svolant's avatar
svolant committed
28
29
  if(PS$passOK){
    if(PS$status=="done")
svolant's avatar
svolant committed
30
    {
svolant's avatar
svolant committed
31
32
33
      res = list()
      json_file = PS$file
      folder_name = paste('file',masque_key,sep="")
svolant's avatar
svolant committed
34
      
svolant's avatar
svolant committed
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
      ### 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)
svolant's avatar
svolant committed
51
        
svolant's avatar
svolant committed
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
        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;}")
          )
          
          
          )
          
          )
svolant's avatar
svolant committed
78
79
        
        
svolant's avatar
svolant committed
80
81
82
83
84
85
86
87
88
89
      } 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")))
      }
svolant's avatar
svolant committed
90
91
92
93
      
      
    }
    
svolant's avatar
svolant committed
94
95
96
97
98
99
100
    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%")
      )
    }
svolant's avatar
svolant committed
101
    
svolant's avatar
svolant committed
102
103
104
105
    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)
svolant's avatar
svolant committed
106
  
svolant's avatar
svolant committed
107
      if(file.exists(error_file)){error_message = read_lines(error_file)}
svolant's avatar
svolant committed
108
      
svolant's avatar
svolant committed
109
110
111
112
113
114
115
116
117
118
119
120
121
      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()
                       )
                )
          )
    }
svolant's avatar
svolant committed
122
123
124
125
126
  }
  
  return(list(box=res,PS=PS))
  
}