R/tab_wf_wf_bk.R

In systemPipeR/systemPipeS: systemPipeShiny: An Interactive Framework for Workflow Management and Visualization

# ## UI
# #' @noRd
# wf_wfUI <- function(id){
#     ns <- NS(id)
#     tagList(
#         div(
#             id = "wf_wf_displayed",
#             style = "display:none",
#             tabTitle("Workflow"),
#             renderDesc(id = ns("desc"),
#             '
#
#
#             #### Workflow files
#             In SPR, workflows are defined as Rmarkdown files,
#             you can read details and obtain them
#             [here{blk}](https://systempipe.org/sp/spr/templates/). This step can
#             help you choose/ skip some steps. Make a workflow diagram to see how
#             the order SPR execute the workflow and take a preview of the
#             final report. If you just want to use the defaults, simply clicking
#             the "Add to task". SPS has already selected all steps for you.
#             ***
#             #### Workflow steps
#             Loading the default with pre-configed workflows or upload a
#             Rmd file on "Existing" option. The workflow file will be display on
#             "*Display workflow file*" box below. Workflow
#             steps are defined by "#" hashtag levels, similar to the title level in
#             markdown files. For example, text and code under the single "#" belongs
#             to the heighest level step; code under double "##" is a sub-step under the
#             nearest single "#" step from the top, *etc*.
#             ***
#             #### Add to task
#             Clicking this button will add the workflow file to the running task, will
#             be used in **step 5**. You need to select at least one step to enable
#             this button. A new R markdown file will **REPLACE** the old one. The old
#             file is backed up in the **backup** folder.
#
#             This is the last workflow preparation step (step 4 is optional). If you
#             have followed the order so far, after this step, you should see all status
#             indicators become green and you are go to lunch a workflow running session
#             at step 5.
#             ***
#             #### Select workflow steps
#             This box allows you to select workflow steps. You need to choose at lest
#             one step to enable other buttons in this box.
#
#             Clicking "Report preview" generates a preview of what the final report
#             will look like based on your step selection, but in the preview,
#             no code is evaluated. The report is displayed in the bottom of this tab.
#
#             Clicking on the "Plot steps" will show a flow chart on the right side
#             of what the step execution orders are when you run the actual workflow
#             in SPR.
#             ***
#             #### Download
#             After step selection, you can download the new Rmarkdown file by
#             "Save New Rmd".
#
#             #### more detailed manual
#             A manual with screenshots and details is on [our website{blk}](https://systempipe.org/sps/modules/workflow/)
#             '),
#             spsHr(),
#             box(
#                 title = "Confirm to use this workflow file",
#                 closable = FALSE, collapsible = TRUE,
#                 width = 12,
#                 class = "center-block",
#                 HTML(
#                     "
#                 <ul>
#                   <li>
#                     When you have finished choosing workflow steps,
#                     clicking on the <b>Add to task</b>.
#                   </li>
#                   <li>
#                     You can also <b>Save</b> it as
#                     an individual file from the browser.</p>
#                   </li>
#                 </ul>
#                 "),
#                 div(class = "text-danger",
#                     tags$ul(
#                         id = ns("warn_other"),
#                         HTML(
#                             "<li>Upon passing 'Add to task' checks, the original workflow file
#                             in the workflow folder will be overwritten. A backup of the old Rmd
#                             can be found in the <b>'backup'</b> folder.</li>"
#                         ))
#                 ),
#                 fluidRow(
#                     style = "padding-left: 40%",
#                     actionButton(ns("to_task_wf"),
#                                  label = "Add to task",
#                                  icon("paper-plane")) %>%
#                         bsHoverPopover(
#                             "Add workflow and add to workflow task",
#                             "You should choose some
#                             steps before adding it to task.",
#                             "bottom"
#                         ),
#                     downloadButton(ns("down_rmd"), "Save") %>%
#                         bsHoverPopover(
#                             "Download current workflow file",
#                             "You can download current workflow file from the
#                             browser.",
#                             "bottom"
#                         )
#                 )
#             ),
#             fluidRow(
#                 box(title = "Display workflow file", width = 12,
#                         closable = FALSE,
#                         shinyWidgets::radioGroupButtons(
#                             inputId = ns("wf_source"),
#                             label = "Choose workflow file source:",
#                             selected = "default",
#                             choiceNames = c("Default", "Upload"),
#                             choiceValues = c("default", "upload"),
#                             justified = TRUE, status = "primary",
#                             checkIcon = list(yes = icon("ok", lib = "glyphicon"),
#                                              no = "")
#                         ),
#                         fileInput(ns("rmd_file"), "Choose R markdown File",
#                                   multiple = FALSE,
#                                   accept = "Rmd"),
#                         tags$div(
#                             style = 'overflow:auto; height: 500px',
#                             networkD3::diagonalNetworkOutput(ns("wf_D3"))
#                         )
#                 )
#             ),
#             fluidRow(
#                 column(5,
#                        box(
#                            title = "Select workflow steps",
#                            width = 12,
#                            closable = FALSE,
#                            collapsible = TRUE,
#                            column(width = 12, style = "padding-left: 0;",
#                                   actionButton(ns("wf_plot_step"),
#                                                label = "Plot steps",
#                                                icon("redo-alt")),
#                                   actionButton(ns("wf_render_md"),
#                                                label = "Report preview",
#                                                icon("redo-alt"))
#                            ),
#                            hr(),
#                            p("When steps are chosen, you can plot steps and preview
#                              report document."),
#                            shinyTree::shinyTree(ns("rmd_tree"), checkbox = TRUE)
#
#                        )
#                 ),
#                 column(7,
#                        box(title = "Workflow steps selected",
#                                width = 12,
#                                closable  = FALSE,
#                                sidebar_title = "Workflow diagram legend",
#                                sidebar_background = "#337ab7",
#                                collapsible = TRUE,
#                                sidebar =  shinydashboardPlus::boxSidebar(
#                                    width = 25, background = "#337ab7",
#                                    startOpen = TRUE, icon = icon("sliders-h"),
#                                    h3("Diagram Legend"),
#                                    p("This part uses systemPipeR::plotWF function"),
#                                    tags$ul(
#                                        tags$li("Gray colored steps are steps without any code chunks, only text"),
#                                        tags$li("steps with 'NA' means unknown number of samples in this step.
#                                                If it is a real case in SPR, you should see something like
#                                                '10/10' all samples passed this step or '10/20' only half passed.")
#                                     )
#                                ),
#                                uiOutput(ns("wf_plot_ui"))
#                        )
#                 )
#             ),
#             fluidRow(
#                 box(
#                     title = "Preview of the workflow report", width = 12,
#                     closable = FALSE,
#                     uiOutput(ns("wf_md_ui"))
#                 )
#             )
#         ),
#         div(
#             id = "wf_wf_disable",
#             h3("Generate a workflow environment at Step 1 first",
#                style = "text-center text-warning")
#         )
#     )
# }
#
# ## server
# #' @importFrom shinyWidgets sendSweetAlert
# #' @importFrom shinyjs runjs enable disable
# #' @noRd
# wf_wfServer <- function(id, shared){
#     if (!eval(parse(text = 'require("shinyTree")'))) {
#         spserror('Tried to load the required package "shinyTree" but failed')
#     }
#     module <- function(input, output, session){
#         ns <- session$ns
#         rmd_file_temp <-  reactiveVal(NULL)
#         observeEvent(input$wf_source, {
#             shinyjs::toggleElement("rmd_file", anim = TRUE, condition = input$wf_source == "upload")
#         })
#         # resolve path
#         rmd_file_path <- reactive({
#             req(input$wf_source)
#             if (input$wf_source == "default") shared$wf$wf_path
#             else input$rmd_file$datapath
#         })
#         # read Rmd
#         rmd <- reactive({
#             if (!is.null(rmd_file_path())) {
#                 quiet(.subsetRmd(p = rmd_file_path()))
#             } else {
#                 NULL
#             }
#         })
#         # get selected steps
#         rmd_tree_selected <- reactive({
#             req(input$wf_source)
#             if (input$wf_source == "upload" & is.null(rmd_file_path())) {
#                 NULL
#             } else {
#                 shinyTree::get_selected(input$rmd_tree, format = "names") %>%
#                     unlist() %>%
#                     str_remove_all(" .*$") %>%
#                     findTreeParent()
#             }
#
#         })
#         # disable all on start
#         observeEvent(input$wf_source, {
#             disable("down_rmd"); disable("wf_render_md"); disable("to_task_wf")
#             disable("wf_plot_step")
#         })
#         # disable all if no step been chosen
#         observeEvent(input$rmd_tree, {
#             if (length(rmd_tree_selected()) < 1 ) {
#                 disable("down_rmd"); disable("wf_render_md"); disable("to_task_wf")
#                 disable("wf_plot_step")
#             } else {
#                 enable("down_rmd"); enable("wf_render_md"); enable("to_task_wf")
#                 enable("wf_plot_step")
#             }
#         })
#         observeEvent(c(input$wf_source, rmd_tree_selected(), rmd_file_path()), {
#             if (input$wf_source == "upload" & is.null(rmd_file_path())) {
#                 # hide tree if nothing is there
#                 runjs('document.querySelectorAll("[id*=rmd_tree]")[0].style.visibility = "hidden"')
#                shinyTree::updateTree(session = session,
#                                       treeId = "rmd_tree",
#                                       data = list(""))
#             } else {
#                 runjs('document.querySelectorAll("[id*=rmd_tree]")[0].style.visibility = ""')
#             }
#
#         })
#
#         output$wf_D3 <- networkD3::renderDiagonalNetwork({
#             networkD3::diagonalNetwork(
#                 step2listD3(rmd()$t_lvl, paste(rmd()$t_number, rmd()$t_text)),
#                 fontSize = 15)
#         })
#         output$rmd_tree <- shinyTree::renderTree({
#             # on.exit(runjs('setTimeout(function(){$("[id*=rmd_tree]").jstree("select_all");}, 100)'))
#             step2listTree(rmd()$t_lvl, paste(rmd()$t_number, rmd()$t_text))
#
#         })
#
#         # bottom right
#         observeEvent(input$wf_plot_step, {
#             rmd_tree_df <- rmd()[rmd()$t_number %in% rmd_tree_selected(), ]
#             if (length(rmd_tree_selected()) > 0) rmd_tree_df$selected <- TRUE
#             output$wf_plot_ui <- renderUI({
#                 tags$div(style = 'overflow:auto; height: 500px',
#                          HTML(.plotWF(df_wf = rmd_tree_df,
#                                      plot_style = "linear",
#                                      out_type = "shiny"))
#                 )
#             })
#         })
#
#         observeEvent(input$wf_render_md, ignoreInit = TRUE, {
#             output$wf_md_ui <- renderUI({
#                 includeMarkdown(isolate(rmd_file_temp()))
#             })
#         })
#         output$down_rmd <- downloadHandler(
#             filename <- function(){
#                 "workflow.Rmd"
#             },
#             content <- function(file){
#                 file.copy(from = rmd_file_temp(), to = file)
#             }
#         )
#         # listen to download button so it can be trigger in next observe
#         observeEvent(1, {
#             shinyjs::runjs("
#                 var click = 0;
#                 var dwnldBtn = document.getElementById('wf-wf_wf-down_rmd');
#                 dwnldBtn.onclick = function() {click += 1; Shiny.setInputValue('wf-wf_wf-saveRmd', click);}
#             ")
#         }, once = TRUE)
#         observeEvent(c(input$wf_render_md, input$to_task_wf, input$saveRmd),
#                      ignoreInit = TRUE, {
#             rmd_file_temp(tempfile(pattern = "wf", fileext = ".Rmd"))
#             shinyCatch({
#                 quiet(.subsetRmd(p = rmd_file_path(),
#                                  p_out = rmd_file_temp(),
#                                  input_steps = paste(rmd_tree_selected(),
#                                                      collapse = ","),
#                                  save_rmd = TRUE
#                 ))
#             }, blocking_level = "error")
#         })
#
#         observeEvent(input$to_task_wf, {
#             req(file.exists(rmd_file_temp()))
#             shinyCatch({
#                 # create back up folder
#                 dir.create(file.path(shared$wf$env_path, "backup"), recursive = TRUE, showWarnings = FALSE)
#                 # if wf file exists, back it up
#                 if(file.exists(shared$wf$wf_path))
#                     file.copy(
#                         shared$wf$wf_path,
#                         file.path(
#                             shared$wf$env_path,
#                             "backup",
#                             paste0(
#                                 glue("bk{Sys.time() %>% format('%Y%m%d%H%M%S')}"),
#                                 basename(shared$wf$wf_path))
#                         ),
#                         overwrite = TRUE
#                     )
#                 # overwrite wf file
#                 if(!file.copy(rmd_file_temp(), shared$wf$wf_path, overwrite = TRUE))
#                     stop("File ", shared$wf$wf_path, " can not be created or not modified")
#             }, blocking_level = "error")
#             shared$wf$flags$wf_ready = isolate(shared$wf$flags$wf_ready) + 1
#             # jump to next step
#             shinyWidgets::confirmSweetAlert(
#                 session = session,
#                 inputId = ns("confirm_next"),
#                 title = "Workflow file setup done!",
#                 closeOnClickOutside = TRUE,
#                 btn_labels = c("Step 4", "Step 5"),
#                 html = TRUE,
#                 type = "success",
#                 text = HTML(glue(
#                     "
#                     <button class='btn btn-box-tool'
#                         data-widget='chat-pane-toggle'
#                         data-toggle='tooltip'
#                         data-original-title='More'
#                         type='button' title='Workflow diagram legend'
#                         style='padding-left: 90%; padding-bottom: 0;'>
#                         <i class='fa fa-minus'></i>
#                     </button>
#                     <h4>Do you want to proceed to the step 4 or step 5?</h4>
#                     <ul class='text-left'>
#                       <li>Step 4 is <b>optional</b>, can be skipped</li>
#                       <li>If all steps' status are green, you can to go step 5 to run the workflow.</li>
#                       <li>Click outside this box to dismiss if you want to stay here.</li>
#                     </ul>
#                     "
#                 ))
#             )
#         })
#         observeEvent(input$confirm_next, {
#             if(emptyIsFalse(input$confirm_next)){
#                 shinyjs::runjs("$('#wf-wf_panel-4-heading > h4').trigger('click');")
#             } else {
#                 shinyjs::runjs("$('#wf-wf_panel-3-heading > h4').trigger('click');")
#             }
#         })
#     }
#     moduleServer(id, module)
# }
#