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shaman
Commit c1430724 authored by Amine GHOZLANE's avatar Amine GHOZLANE
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Add save experiment and check for galaxy issue

parent a2cb61f7
Pipeline #14049 passed with stage
    in 46 minutes and 24 seconds
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    Showing with 138 additions and 39 deletions
    server.R
    View file @ c1430724
    ......@@ -31,7 +31,7 @@ shinyServer(function(input, output,session) {
    json_name=json_name,num=0,pass=pass,login_email = NULL,is.valid =NULL,
    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)
    paths_fastq_tmp=NULL,curdir=curdir, error_progress=FALSE, visTarget=FALSE)
    ## Counts file
    dataInputCounts <-reactive({
    ......@@ -776,9 +776,9 @@ shinyServer(function(input, output,session) {
    ## Load target file
    observe({
    inFile <- input$fileTarget
    #values$TargetWorking = NULL
    counts = dataInput()$data$counts
    labeled = 0
    data = NULL
    ......@@ -814,6 +814,7 @@ shinyServer(function(input, output,session) {
    if(length(ind_num)==0){data = as.data.frame(apply(data,2,gsub,pattern = "-",replacement = "."))}
    }
    values$TargetWorking = as.data.frame(data)
    values$visTarget = FALSE
    # ind_sel = Target_selection()
    # if(length(ind))
    # target = as.data.frame(apply(target,2,gsub,pattern = "-",replacement = "."))
    ......@@ -873,6 +874,8 @@ shinyServer(function(input, output,session) {
    ## Action with submit button
    MasqueSubmit <- eventReactive(input$submit,{
    galaxyAlertfile=paste(values$curdir,"www","galaxy_pasteur_alert.txt",sep= .Platform$file.sep)
    galaxyAlert = NULL
    #activate check_mail
    CMP = CheckMasque(input, values,check_mail = TRUE)
    Error = CMP$Error
    ......@@ -935,16 +938,24 @@ shinyServer(function(input, output,session) {
    withProgress(message = 'Creating JSON file...',{CreateJSON(input,values)})
    if(file.exists(values$json_name)) values$num = 1
    #messageId="SuccessMasque",
    sendSweetAlert(session,
    title = "Success",
    text = paste("Your data have been submitted. You will receive an e-mail once the computation over. <br /> This can take few hours.
    <br />
    <br />
    <br />
    <em> Remind: You can close shaman and use your key to check the progression and get your results: </em>",values$pass),
    type = "success",
    html=TRUE
    )
    if(file.exists(galaxyAlertfile)){
    suppressWarnings(try(readLines(galaxyAlertfile,warn=FALSE) ->galaxyAlert,silent=TRUE))
    if(!is.null(galaxyAlert)){
    sendSweetAlert(session, title = "Warning",text = HTML(paste(galaxyAlert,values$pass)), type = "warning",html=TRUE)
    }
    }
    else{
    sendSweetAlert(session,
    title = "Success",
    text = HTML(paste("Your data have been submitted. You will receive an e-mail once the computation over. <br /> This can take few hours.
    <br />
    <br />
    <br />
    <em> Remind: You can close SHAMAN and use your key to check the progression and get your results: </em>",values$pass)),
    type = "success",
    html=TRUE
    )
    }
    }
    })
    ......@@ -2026,12 +2037,16 @@ shinyServer(function(input, output,session) {
    output$SelectInterestVar <- renderUI({
    target=values$TargetWorking
    if(!is.null(target))
    if(!is.null(target) && !values$visTarget )
    {
    namesTarget = colnames(target)[2:ncol(target)]
    selectInput("InterestVar",h6(strong("Select the variables")),namesTarget,selected=namesTarget,multiple=TRUE)
    }
    else if(!is.null(target) && values$visTarget )
    {
    namesTarget = colnames(target)[2:ncol(target)]
    selectInput("InterestVar",h6(strong("Select the variables")), namesTarget,selected=namesTarget[2],multiple=TRUE)
    }
    })
    ## Interactions
    ......@@ -2050,6 +2065,27 @@ shinyServer(function(input, output,session) {
    return(res)
    })
    ## Box for merged counts
    output$BoxCountsMerge <- renderUI({
    # input$RunDESeq
    # #counts = isolate(dataMergeCounts()$counts)
    counts = isolate(dataMergeCounts()$CT_Norm)
    taxo = input$TaxoSelect
    #
    # if(!is.null(counts) && taxo != "...")
    # {
    resDiff = ResDiffAnal()
    int = input$Interaction2
    if(!is.null(resDiff)){
    box(title=paste("Count table (",taxo,")",sep=""),width = NULL, status = "primary", solidHeader = TRUE,collapsible = TRUE,collapsed = TRUE,
    DT::dataTableOutput("CountsMerge"),
    downloadButton('ExportCounts', 'Export normalized counts'),
    downloadButton('ExportRelative', 'Export relative abundance')
    )
    }
    })
    ## Run button
    output$RunButton <- renderUI({
    ......@@ -2069,24 +2105,41 @@ shinyServer(function(input, output,session) {
    return(res)
    })
    # ## Vis button
    # output$VisButton <- renderUI({
    #
    # res = NULL
    # ChTM = "Error"
    # target = values$TargetWorking
    # labeled = values$labeled
    # CT = dataInput()$data$counts
    # taxo = input$TaxoSelect
    # VarInt = input$InterestVar
    #
    # ## Return NULL if there is no error
    # if(!is.null(CT) && length(VarInt)>=1) ChTM = CheckTargetModel(input,target,labeled,CT)$Error
    #
    # if(!is.null(target) && taxo!="..." && is.null(ChTM) && length(VarInt)>=1) res = actionButton("RunDESeq",strong("Run analysis"),icon = icon("caret-right"))
    #
    # return(res)
    # })
    SetUpVis <-eventReactive(input$RunVis,{
    target = NULL
    CT = dataInput()$data$counts
    fakeCondition = c("Samples", "Samples", "fakeCondition")
    samples = colnames(CT)
    samples = gsub(pattern = "-",replacement = ".",as.character(samples))
    condition = sample(c("A", "B"), length(samples), replace =T)
    target = data.frame(samples,samples,condition, row.names = samples)
    colnames(target) = fakeCondition
    values$TargetWorking = target
    values$labeled = 100.0
    values$visTarget = TRUE
    sendSweetAlert(session, title = "Success", text = "A fake condition was as assigned to samples. Now you select the taxonomy level and run analysis.", type = "success", html=TRUE)
    })
    ## Add contrast
    observeEvent(input$RunVis,{
    SetUpVis()
    },priority=1)
    ## Vis button
    output$VisButton <- renderUI({
    res = NULL
    target = values$TargetWorking
    VarInt = input$InterestVar
    if(is.null(target) && length(VarInt) == 0) {
    res = actionButton("RunVis",strong("Setup visualization"),icon = icon("caret-right"))
    }
    return(res)
    })
    ## Var for normalization
    output$SelectVarNorm <- renderUI({
    ......@@ -2193,13 +2246,60 @@ shinyServer(function(input, output,session) {
    }
    })
    output$ButtonBiom <- renderUI({
    observeEvent(input$confirmTarget,{
    target = NULL
    values$biom_masque = paste(values$curdir,"www","masque","done",paste("file",values$masque_key,sep=""),paste("shaman_silva.biom",sep=""),sep= .Platform$file.sep)
    # Get the old biom
    if (!is.null(values$biom_masque) && file.exists(values$biom_masque)){
    tryCatch(read_biom(values$biom_masque)->data,
    error=function(e) sendSweetAlert(session,
    title = "Oops",
    text=paste("Your file can not be read in SHAMAN.\n \n",e),type ="error"))
    }
    if(!is.null(data)){
    if(is.null(sample_metadata(data))){
    tryCatch(write_biom(make_biom(dataMergeCounts()$CT_noNorm, sample_metadata=values$TargetWorking[,-1],
    observation_metadata=dataInput()$data$taxo_biom), values$biom_masque),
    error=function(e) sendSweetAlert(session,
    title = "Oops",
    text=paste("The new experiment data cannot be saved in SHAMAN.\n \n",e),type ="error"),
    finally = sendSweetAlert(session, title = "Success", text = HTML(paste("The target file was successfully saved in the project ", values$masque_key,".
    <br />
    <br />
    <br />
    <em> Remind: We recommand to perform this association for every annotation database.</em>")), type = "success", html=TRUE))
    }
    else{
    sendSweetAlert(session,
    title = "Oops",
    text=paste("There is alread some metadata saved for this experiment.\n Contact shaman@pasteur.fr to reset modification."),type ="error")
    }
    }
    })
    ## Add contrast
    observeEvent(input$SaveTarget,{
    confirmSweetAlert(session = session, inputId = "confirmTarget", type = "warning",
    title = "The target file can be saved only once.\n Do you confirm the modification ?",
    danger_mode = TRUE)
    #SetNewTarget()
    },priority=1)
    output$SaveExperiment <- renderUI({
    res = NULL
    resDiff = ResDiffAnal()
    int = input$Interaction2
    if(!is.null(resDiff)) downloadButton('ExportBiom', 'Export BIOM')
    if(!is.null(resDiff) && !is.null(values$masque_key)) res = list(downloadButton('ExportBiom', 'Export BIOM'), actionButton("SaveTarget", "Save target",icon = icon("caret-right")))
    else if(!is.null(resDiff)) res = downloadButton('ExportBiom', 'Export BIOM')
    return(res)
    })
    # output$SaveExperiment <- renderUI({
    # resDiff = ResDiffAnal()
    # int = input$Interaction2
    # if(!is.null(resDiff) && !is.null(values$masque_key)) actionButton("SaveTarget", "Save target",icon = icon("caret-right"))
    # })
    output$ExportBiom <- downloadHandler(
    filename = function() { 'SHAMAN_data.biom' },
    content = function(file){
    ......
    ui.R
    View file @ c1430724
    ......@@ -630,10 +630,8 @@ function(request) {
    column(width=6,uiOutput("SelectInteraction2"))
    ),
    fluidRow(
    column(width=6,uiOutput('ButtonBiom')),
    #column(width=6,downloadButton('ExportBiom', 'Export BIOM')),
    #uiOutput("VisButton"),
    column(width=6,uiOutput("RunButton"))
    column(width=6,uiOutput('SaveExperiment')),
    column(width=6,uiOutput("VisButton"),uiOutput("RunButton"))
    )
    ),
    fluidRow(uiOutput("InfoModel"),uiOutput("InfoModelHowTo")),
    ......
    www/galaxy_pasteur_alert_template.txt 0 → 100644
    View file @ c1430724
    Your data have been submitted, but the galaxy server is under maintenance. SHAMAN will keep trying to submit the data until the server is turned on again.<br />You will receive an e-mail once the computation over, otherwise submit your data after the XXX<br /><br /> <br /> <br /> <em> Remind: You can close SHAMAN and use your key to check the progression and get your results: </em>
    \ No newline at end of file
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