marton-balazs-kovacs · marton-balazs-kovacs · Nov 4, 2023 · Oct 17, 2023 · Nov 3, 2023 · Nov 4, 2023
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -52,7 +52,8 @@ Imports:
     markdown,
     lifecycle,
     rlang,
-    stats
+    stats,
+    fontawesome
 RoxygenNote: 7.2.3
 Suggests: 
     testthat,

diff --git a/NAMESPACE b/NAMESPACE
@@ -18,6 +18,7 @@ export(mod_title_page_server)
 export(mod_title_page_ui)
 export(mod_xml_report_server)
 export(mod_xml_report_ui)
+export(print_conflict_statement)
 export(print_contrib_affil)
 export(print_credit_roles)
 export(print_funding)

diff --git a/R/app_server.R b/R/app_server.R
@@ -45,6 +45,9 @@ app_server <- function(input, output,session) {
   # Show funding information in viewer window
   mod_funding_information_server("funding_information", input_data = read_out$data)
 
+  # Show conflict of interest statement
+  mod_conflict_statement_server("conflict_statement", input_data = read_out$data)
+
   # Hide on launch waiter screen
   waiter::waiter_hide()
 }
diff --git a/R/app_ui.R b/R/app_ui.R
@@ -5,6 +5,17 @@ app_ui <- function() {
     golem_add_external_resources(),
 
     navbarPage(
+      # Header
+      header = tagList(
+          div(id = "support-div",
+              a(id = "support-btn",
+                class = "btn",
+                href = "https://opencollective.com/tenzing",
+                target = "_blank",
+                "Support us",
+                )
+              )
+      ),
       # Title
       title = list(
         div(
@@ -30,7 +41,7 @@ app_ui <- function() {
                    div(
                      class = "help-icon-container",
                      title = "Copy the contributors table template in Google Drive. Go to File -> Make a copy",
-                     icon("far fa-question-circle", lib = "font-awesome", class = "help-icon")
+                     fontawesome::fa_i(name = "fas fa-circle-question", style = "color: #D45F68; font-size: 2em;")
                      )
                    ),
                  wellPanel(
@@ -40,7 +51,8 @@ app_ui <- function() {
                    tags$a(href = "https://docs.google.com/spreadsheets/d/1Gl0cwqN_nTsdFH9yhSvi9NypBfDCEhViGq4A3MnBrG8/edit?usp=sharing",
                           "contributors table template",
                           target="_blank",
-                          style = "display: inline; color: #ffdf57; text-decoration: underline;")
+                          style = "display: inline; color: #ffdf57; text-decoration: underline;",
+                          class = "link")
                    )
                  ),
                # Second step
@@ -55,7 +67,7 @@ app_ui <- function() {
                    div(
                      class = "help-icon-container",
                      title = "Use the share URL of the filled out contributors table and click on the upload button. OR upload your contributors table in a .csv, .tsv or .xlsx format.",
-                     icon("far fa-question-circle", lib = "font-awesome", class = "help-icon")
+                     fontawesome::fa_i(name = "fas fa-circle-question", style = "color: #D45F68; font-size: 2em;")
                      )
                    ),
                  wellPanel(
@@ -76,7 +88,7 @@ app_ui <- function() {
                    div(
                      class = "help-icon-container",
                      title = "You need a valid contributors table to generate the outputs. Once you have it, click on one of the output buttons to preview and download the output.",
-                     icon("far fa-question-circle", lib = "font-awesome", class = "help-icon")
+                     fontawesome::fa_i(name = "fas fa-circle-question", style = "color: #D45F68; font-size: 2em;")
                      )
                    ),
                  wellPanel(
@@ -85,21 +97,17 @@ app_ui <- function() {
                    mod_title_page_ui("title_page"),
                    mod_xml_report_ui("xml_report"),
                    mod_show_yaml_ui("show_yaml"),
-                   mod_funding_information_ui("funding_information")
+                   mod_funding_information_ui("funding_information"),
+                   mod_conflict_statement_ui("conflict_statement")
                    )
                  ),
                # Citation
                HTML(
                "<p><b>Citation:</b></br>
-              Kovacs, M., Holcombe, A., Aust, F., & Aczel, B. (2021). <a href='https://doi.org/10.3233/ISU-210109'; target='_blank'>Tenzing and the importance of tool development for research efficiency.</a> <i>Information Services & Use, 41</i>, 123-130.
-                <BR>
-                Holcombe, A. O., Kovacs, M., Aust, F., & Aczel, B. (2020). <a href='https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0244611'; target='_blank'>Documenting contributions to scholarly articles using CRediT and tenzing.</a> <i>PLOS ONE, 15</i>(12), e0244611.</p>"
+               Kovacs, M., Holcombe, A., Aust, F., & Aczel, B. (2021). <a href='https://doi.org/10.3233/ISU-210109'; target='_blank'>Tenzing and the importance of tool development for research efficiency.</a> <i>Information Services & Use, 41</i>, 123-130.
+               <BR>
+               Holcombe, A. O., Kovacs, M., Aust, F., & Aczel, B. (2020). <a href='https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0244611'; target='_blank'>Documenting contributions to scholarly articles using CRediT and tenzing.</a> <i>PLOS ONE, 15</i>(12), e0244611.</p>"
                     ),
-               # Donation
-               HTML(
-                 "<p><b>Donation:</b></br>
-                 <a href='https://opencollective.com/tenzing'; target='_blank'>Open Collective</a></p>"
-                 ),
                # Privacy notice
                HTML("<p><b>Privacy:</b><BR>
                     To get a sense of how many users we have, we log a masked version of IP addresses. You are not identifiable by the logged information.</p>")

diff --git a/R/mod_conflict_statement.R b/R/mod_conflict_statement.R
@@ -0,0 +1,154 @@
+#' conflict_statement UI Function
+#'
+#' @description A shiny Module.
+#'
+#' @param id,input,output,session Internal parameters for {shiny}.
+#'
+#' @noRd 
+#'
+#' @importFrom shiny NS tagList 
+mod_conflict_statement_ui <- function(id){
+
+  tagList(
+    div(class = "out-btn",
+        actionButton(
+          NS(id, "show_report"),
+          label = "Show conflict of interest statement",
+          class = "btn btn-primary btn-validate")
+        ) %>% 
+      tagAppendAttributes(
+        # Track click event with Matomo
+        onclick = "_paq.push(['trackEvent', 'Output', 'Click show', 'Conflict information'])"
+        )
+  )
+}
+
+#' conflict_statement Server Function
+#'
+#' @noRd 
+mod_conflict_statement_server <- function(id, input_data){
+
+  moduleServer(id, function(input, output, session) {
+    ns <- session$ns
+    # Preview ---------------------------
+    ## Render preview
+    output$preview <- renderUI({
+      if(all(is.na(input_data()[["Conflict of interest"]]))) {
+        "There are no conflict of interest statements provided for any of the contributors."
+        } else {
+          HTML(print_conflict_statement(contributors_table = input_data(), initials = input$initials))
+          }
+    })
+
+    ## Build modal
+    modal <- function() {
+      modalDialog(
+        rclipboard::rclipboardSetup(),
+        h3("Conflict of interest statement"),
+        # Toggle between initials and full names
+        div(
+          shinyWidgets::materialSwitch(
+            NS(id, "initials"),
+            label = "Full names",
+            inline = TRUE),
+          span("Initials")
+        ),
+        hr(),
+        uiOutput(NS(id, "preview")),
+        easyClose = TRUE,
+        footer = tagList(
+          div(
+            style = "display: inline-block",
+            uiOutput(session$ns("clip"))
+          ) %>% 
+            tagAppendAttributes(
+              # Track click event with Matomo
+              onclick = "_paq.push(['trackEvent', 'Output', 'Click clip', 'Conflict information'])"
+            ),
+          div(
+            style = "display: inline-block",
+            downloadButton(
+              NS(id, "report"),
+              label = "Download file",
+              class = "download-report"
+              )
+          ) %>% 
+            tagAppendAttributes(
+              # Track click event with Matomo
+              onclick = "_paq.push(['trackEvent', 'Output', 'Click download', 'Conflict information'])"
+            ),
+          modalButton("Close")
+        )
+      )
+    }
+
+    ## Show preview modal
+    observeEvent(input$show_report, {
+      showModal(modal())
+    })
+
+    # Download ---------------------------
+    ## Set up loading bar
+    waitress <- waiter::Waitress$new(theme = "overlay", infinite = TRUE)
+
+    ## Restructure dataframe for the output
+    to_download_and_clip <- reactive({
+      if(all(is.na(input_data()[["Funding"]]))) {
+        "There are no conflict of interest statements provided for any of the contributors."
+      } else {
+        print_conflict_statement(contributors_table = input_data(), initials = input$initials)
+      }
+    })
+
+    ## Set up parameters to pass to Rmd document
+    params <- reactive({
+      list(conflict_statement = to_download_and_clip())
+    })
+
+    ## Render output Rmd
+    output$report <- downloadHandler(
+      # Set filename
+      filename = function() {
+        paste0("conflict_statement_", Sys.Date(), ".doc")
+      },
+      # Set content of the file
+      content = function(file) {
+        # Start progress bar
+        waitress$notify()
+        # Copy the report file to a temporary directory before processing it
+        file_path <- file.path("inst/app/www/", "conflict_statement.Rmd")
+        file.copy("conflict_statement.Rmd", file_path, overwrite = TRUE)
+
+        # Knit the document
+        callr::r(
+          render_report,
+          list(input = file_path, output = file, format = "word_document", params = params())
+        )
+        # Stop progress bar
+        waitress$close()
+      }
+    )
+
+    # Clip ---------------------------
+    ## Add clipboard buttons
+    output$clip <- renderUI({
+      rclipboard::rclipButton(
+        inputId = "clip_btn", 
+        label = "Copy output to clipboard", 
+        clipText =  to_download_and_clip(), 
+        icon = icon("clipboard"),
+        modal = TRUE)
+    })
+
+    ## Workaround for execution within RStudio version < 1.2
+    observeEvent(input$clip_btn, clipr::write_clip(to_download_and_clip()))
+  })
+
+}
+
+## To be copied in the UI
+# mod_conflict_statement_ui("conflict_statement")
+
+## To be copied in the server
+# mod_conflict_statement_server("conflict_statement")
+
diff --git a/R/mod_credit_roles.R b/R/mod_credit_roles.R
@@ -25,7 +25,7 @@ mod_credit_roles_ui <- function(id){
       tagAppendAttributes(
         # Track click event with Matomo
         onclick = "_paq.push(['trackEvent', 'Output', 'Click show', 'Author information'])"
-      )
+        )
     )
   }
 
@@ -80,12 +80,23 @@ mod_credit_roles_server <- function(id, input_data){
           div(
             style = "display: inline-block",
             uiOutput(session$ns("clip"))
-          ),
-          downloadButton(
-            NS(id, "report"),
-            label = "Download file",
-            class = "download-report"
-          ),
+          ) %>% 
+            tagAppendAttributes(
+              # Track click event with Matomo
+              onclick = "_paq.push(['trackEvent', 'Output', 'Click clip', 'Author information'])"
+            ),
+          div(
+            style = "display: inline-block",
+            downloadButton(
+              NS(id, "report"),
+              label = "Download file",
+              class = "download-report"
+              )
+            ) %>% 
+            tagAppendAttributes(
+              # Track click event with Matomo
+              onclick = "_paq.push(['trackEvent', 'Output', 'Click download', 'Author information'])"
+            ),
           modalButton("Close")
         )
       )
@@ -154,7 +165,12 @@ mod_credit_roles_server <- function(id, input_data){
 
     ## Add clipboard buttons
     output$clip <- renderUI({
-      rclipboard::rclipButton("clip_btn", "Copy output to clipboard", to_clip(), icon("clipboard"), modal = TRUE)
+      rclipboard::rclipButton(
+        inputId = "clip_btn", 
+        label = "Copy output to clipboard",
+        clipText = to_clip(), 
+        icon = icon("clipboard"),
+        modal = TRUE)
     })
 
     ## Workaround for execution within RStudio version < 1.2

diff --git a/R/mod_funding_information.R b/R/mod_funding_information.R
@@ -15,6 +15,10 @@ mod_funding_information_ui <- function(id){
           NS(id, "show_report"),
           label = "Show funding information",
           class = "btn btn-primary btn-validate")
+        ) %>% 
+      tagAppendAttributes(
+        # Track click event with Matomo
+        onclick = "_paq.push(['trackEvent', 'Output', 'Click show', 'Funding information'])"
         )
   )
 }
@@ -56,12 +60,23 @@ mod_funding_information_server <- function(id, input_data){
           div(
             style = "display: inline-block",
             uiOutput(session$ns("clip"))
-          ),
-          downloadButton(
-            NS(id, "report"),
-            label = "Download file",
-            class = "download-report"
-          ),
+          ) %>% 
+            tagAppendAttributes(
+              # Track click event with Matomo
+              onclick = "_paq.push(['trackEvent', 'Output', 'Click clip', 'Funding information'])"
+            ),
+          div(
+            style = "display: inline-block",
+            downloadButton(
+              NS(id, "report"),
+              label = "Download file",
+              class = "download-report"
+              )
+          ) %>% 
+            tagAppendAttributes(
+              # Track click event with Matomo
+              onclick = "_paq.push(['trackEvent', 'Output', 'Click download', 'Funding information'])"
+            ),
           modalButton("Close")
         )
       )
@@ -117,7 +132,12 @@ mod_funding_information_server <- function(id, input_data){
     # Clip ---------------------------
     ## Add clipboard buttons
     output$clip <- renderUI({
-      rclipboard::rclipButton("clip_btn", "Copy output to clipboard", to_download_and_clip(), icon("clipboard"), modal = TRUE)
+      rclipboard::rclipButton(
+        inputId = "clip_btn", 
+        label = "Copy output to clipboard", 
+        clipText =  to_download_and_clip(), 
+        icon = icon("clipboard"),
+        modal = TRUE)
     })
 
     ## Workaround for execution within RStudio version < 1.2