Tillat tomme rader i csv-fil

NAMESPACE

@@ -101,6 +101,7 @@ export(publish_app)
 export(publish_server)
 export(publish_ui)
 export(registry_status_report)
+export(remove_empty_rows)
 export(report_app)
 export(report_server)
 export(report_ui)

R/checks.R

@@ -51,7 +51,7 @@
 #' is displayed.
 #'
 #' @rdname checks
-#' @internal
+#' @noRd
 #' @param input Shiny input object
 #' @param conf get_config() output
 levels_consistent_check <- function(input, conf) {
@@ -59,31 +59,31 @@
     if (input$level_direction) {
       if (input$level_green >= input$level_yellow) {
         shinyjs::html("message", "")
         return(TRUE)
       } else {
         shinyjs::html("message", "")
         shinyjs::html(
           "message",
           conf$indicator$level_inconsistent_message
         )
         return(FALSE)
       }
     } else {
       if (input$level_yellow >= input$level_green) {
         shinyjs::html("message", "")
         return(TRUE)
       } else {
         shinyjs::html("message", "")
         shinyjs::html(
           "message",
           conf$indicator$level_inconsistent_message
         )
         return(FALSE)
       }
     }
   } else {
     shinyjs::html("message", "")
     return(TRUE)
   }
 }
 
@@ -94,7 +94,7 @@
 #' @param rv A shiny::reactiveValues object
 #'
 #' @rdname checks
-#' @internal
+#' @noRd
 update_check <- function(input, conf, ns, rv, level_consistent) {
   if (any(c(
     is.null(input$indicator),
@@ -131,10 +131,10 @@
       )
     )
     if (all(no_new_values)) {
       return(NULL)
     } else {
       if (level_consistent()) {
         return(
           shiny::actionButton(
             ns("update_val"),
             "Oppdat\u00e9r verdier",
@@ -142,7 +142,7 @@
           )
         )
       } else {
         return(NULL)
       }
     }
   }
@@ -156,7 +156,7 @@
 #' @param rv A shiny::reactiveValues object
 #'
 #' @rdname checks
-#' @internal
+#' @noRd
 update_indicator_txt_check <- function(input, conf, ns, rv) {
   if (any(c(rv$title_oversize, rv$short_oversize, rv$long_oversize))) {
     NULL
@@ -167,7 +167,7 @@
       identical(input$ind_long, rv$ind_data$long_description)
     )
     if (all(no_new_text)) {
       return(NULL)
     } else if (nrow(rv$ind_data != 0)) {
       shiny::actionButton(
         ns("update_txt"),

R/misc.R

@@ -30,7 +30,6 @@ natural <- function(vals, tolerance = .Machine$double.eps^0.5) {
   abs(vals - round(vals)) < tolerance
 }
 
-
 #' @rdname misc
 #' @export
 md5_checksum <- function(df, ind = "") {
@@ -52,6 +51,18 @@ md5_checksum <- function(df, ind = "") {
   digest::digest(t, algo = "md5", serialize = FALSE)
 }
 
+#' Function for removing empty rows in csv input.
+#' In a row ";;;;;" the values will translate to
+#' NA or an empty string depending on whether the columns
+#' are numeric or strings.
+#'
+#' @rdname misc
+#' @export
+remove_empty_rows <- function(df) {
+  return(
+    df[rowSums(is.na(df) | df == "") != ncol(df), ]
+  )
+}
 
 #' @rdname misc
 #' @export
@@ -188,7 +199,7 @@ invalidate_cache <- function() {
 }
 
 #' @rdname misc
-#' @internal
+#' @noRd
 validateName <- function(x, existing_names) {
   if (is.null(x)) {
     return(NULL)

R/mod_status.R

@@ -6,7 +6,7 @@
 #'
 #' @return Shiny objects for the imongr app
 #'
-#' #' @name mod_status
+#' @name mod_status
 #' @aliases status_ui status_server status_app
 NULL
 

R/mod_upload.R

@@ -94,7 +94,6 @@ upload_ui <- function(id) {
   )
 }
 
-
 #' @rdname mod_upload
 #' @export
 upload_server <- function(id, registry_tracker, pool_verify) {
@@ -109,21 +108,23 @@ upload_server <- function(id, registry_tracker, pool_verify) {
 
     rv_return <- shiny::reactiveValues()
 
-    ## observers
+    # When you choose a registry
     shiny::observeEvent(input$registry, {
       rv_return$registry_id <- input$registry
       if (!is.null(input$upload_file)) {
         rv$inv_data <- rv$inv_data + 1
       }
     })
+
+    # When you click on the submit button
     shiny::observeEvent(input$submit, {
       insert_data_verify(
         pool = pool_verify,
-        df = df(),
+        df = input_data(),
         update = input$latest_update,
         affirm = input$latest_affirm
       )
-      insert_agg_data(pool_verify, df())
+      insert_agg_data(pool_verify, input_data())
       rv$inv_data <- rv$inv_data + 1
       shinyalert::shinyalert(conf$upload$reciept$title,
         conf$upload$reciept$body,
@@ -133,15 +134,17 @@ upload_server <- function(id, registry_tracker, pool_verify) {
       )
     })
 
-    ## reactives
-    df <- shiny::reactive({
+    # The indicator data
+    input_data <- shiny::reactive({
       if (is.null(input$upload_file)) {
         data.frame()
       } else {
-        csv_to_df(input$upload_file$datapath, input$sep, input$dec_sep)
+        csv_to_df(input$upload_file$datapath, input$sep, input$dec_sep) |>
+          remove_empty_rows()
       }
     })
 
+    # Indicator parameters and descriptions
     ind <- shiny::reactive({
       if (is.null(input$registry)) {
         data.frame()
@@ -150,7 +153,11 @@ upload_server <- function(id, registry_tracker, pool_verify) {
       }
     })
 
-    ## ui sidebar panel
+    ###########################
+    ##### On the side bar #####
+    ###########################
+
+    # The registry drop down menu
     output$select_registry <- shiny::renderUI({
       select_registry_ui(pool_verify, conf,
         input_id = ns("registry"),
@@ -159,6 +166,7 @@ upload_server <- function(id, registry_tracker, pool_verify) {
       )
     })
 
+    # The file upload menu
     output$upload_file <- shiny::renderUI({
       shiny::fileInput(
         ns("upload_file"),
@@ -174,60 +182,70 @@ upload_server <- function(id, registry_tracker, pool_verify) {
       )
     })
 
+    # The submit button
     output$submit <- shiny::renderUI({
       rv$inv_data
       submit_ui(
         ns("submit"), conf, pool_verify, input$upload_file,
-        input$registry, df(), ind(), "verify"
+        input$registry, input_data(), ind(), "verify"
       )
     })
 
+    # The wait spinner
     output$spinner <- shiny::renderText({
       input$submit
       paste("")
     })
 
+    #############################
+    ##### On the main panel #####
+    #############################
 
-    ## ui main panel
+    # The error and warning messages
     output$error_report <- shiny::renderText({
       rv$inv_data
       error_report_ui(
-        pool_verify, df(), ind(),
+        pool_verify, input_data(), ind(),
         input$upload_file, input$registry
       )
     })
 
     output$warning_report <- shiny::renderText({
       rv$inv_data
-      warning_report_ui(pool_verify, df(), input$upload_file, input$registry)
+      warning_report_ui(pool_verify, input_data(), input$upload_file, input$registry)
     })
 
+    # The instructions
     output$upload_sample_text <- shiny::renderText({
       shiny::req(input$registry)
       if (input$registry == "") {
         NULL
       } else {
         upload_sample_text_ui(pool_verify, conf, input$upload_file,
           input$registry,
-          indicators = unique(df()$ind_id)
+          indicators = unique(input_data()$ind_id)
         )
       }
     })
 
+    # A sample of the selected data file
     output$upload_sample <- shiny::renderTable({
       rv$inv_data
       upload_sample_ui(
-        df(), input$upload_file, input$registry,
+        input_data(), input$upload_file, input$registry,
         input$sample_size, input$sample_type
       )
     })
 
+    # More instructions
     output$main_doc <- shiny::renderText(conf$upload$doc$main)
 
+    # Bullet points with valid column names
     output$var_doc <- shiny::renderText({
       var_doc_ui(conf)
     })
 
+    # Numbered list with valid indicator ids
     output$valid_ind <- shiny::renderText({
       paste0(
         "<h4>", conf$upload$doc$valid_ind, " <i>",
@@ -244,6 +262,7 @@ upload_server <- function(id, registry_tracker, pool_verify) {
       colnames = FALSE
     )
 
+    # A table with example data
     output$sample_data <- shiny::renderTable(
       get_table(pool_verify, "data",
         sample = 0.00001

_pkgdown.yml

@@ -143,6 +143,7 @@ reference:
     - mod_upload
     - mod_download
     - mod_review
+    - mod_status
 
   - title: Data
     desc: >

tests/testthat/test-misc.R

@@ -49,6 +49,18 @@ test_that("a consistent md5 checksum of a data frame can be provided", {
   )
 })
 
+test_that("empty rows are removed from a data frame", {
+  test_data <- data.frame(
+    x = c(1, 2, 3, NA, 5, NA, 6, NA, NA),
+    y = c("a", "b", "c", "", "e", "f", "g", "", ""),
+    z = c(1, 2, 3, NA, 5, 6, 7, NA, NA)
+  )
+
+  expected_output <- test_data[c(-4, -8, -9), ]
+
+  expect_equal(remove_empty_rows(test_data), expected_output)
+})
+
 # For the remianing tests we need a test database
 ## first off with no data
 if (is.null(check_db(is_test_that = FALSE))) {