codebase polishing: formatter, beter naming etc

BioDT · Oct 22, 2024 · ff2f5b2 · ff2f5b2
1 parent d8c589a
commit ff2f5b2
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Showing 4 changed files with 36 additions and 38 deletions.
diff --git a/app/logic/disease_outbreaks/disease_leaflet_map.R b/app/logic/disease_outbreaks/disease_leaflet_map.R
@@ -1,6 +1,6 @@
 box::use(
   terra[rast, project],
-  leaflet[tileOptions, leaflet, addTiles, addRasterImage, setView, leafletProxy, removeImage, addRasterLegend, addLegend, addLayersControl],
+  leaflet[tileOptions, leaflet, addTiles, addRasterImage, setView, addLayersControl, layersControlOptions],
 )
 
 #' @export
@@ -17,7 +17,7 @@ disease_leaflet_map <- function(map_raster,
     setView(
       lng = 12.3601,
       lat = 51.3402,
-      zoom = 4
+      zoom = 5
     ) |>
     addRasterImage(
       map_raster,
@@ -27,7 +27,8 @@ disease_leaflet_map <- function(map_raster,
       group = "Input layer"
     ) |>
     addLayersControl(
-      overlayGroups = c("Input layer")
+      overlayGroups = c("Input layer"),
+      options = layersControlOptions(collapsed = FALSE)
     )
 
   return(leaflet_map)

diff --git a/app/view/disease_outbreaks/disease_app/disease_app.R b/app/view/disease_outbreaks/disease_app/disease_app.R
@@ -1,15 +1,15 @@
 box::use(
-  shiny[NS, tagList, moduleServer, tags, reactiveVal, reactive, observeEvent, req],
+  shiny[NS, tagList, moduleServer, tags, reactiveVal, observeEvent],
   bslib[layout_column_wrap],
   htmltools[css],
   waiter[Waiter],
-  app/logic/waiter[waiter_text],
 )
 
 box::use(
-  app/view/disease_outbreaks/disease_app/disease_map[disease_map_ui, disease_map_server],
-  app/view/disease_outbreaks/disease_app/disease_select[disease_select_ui, disease_select_server],
-  app/logic/disease_outbreaks/disease_leaflet_map[read_and_project_raster, disease_leaflet_map]
+  app / view / disease_outbreaks / disease_app / disease_map[disease_map_ui, disease_map_server],
+  app / view / disease_outbreaks / disease_app / disease_choose_file[disease_choose_file_ui, disease_choose_file_server],
+  app / logic / disease_outbreaks / disease_leaflet_map[read_and_project_raster, disease_leaflet_map],
+  app / logic / waiter[waiter_text],
 )
 
 
@@ -24,7 +24,7 @@ disease_app_ui <- function(id, i18n) {
       disease_map_ui(
         ns("disease_map"), i18n
       ),
-      disease_select_ui(
+      disease_choose_file_ui(
         ns("disease_select"), i18n
       ),
     ),
@@ -35,26 +35,25 @@ disease_app_ui <- function(id, i18n) {
 #' @export
 disease_app_server <- function(id, tab_disease_selected) {
   moduleServer(id, function(input, output, session) {
-
     # Define waiter ----
     msg <- waiter_text(message = tags$h3("Loading data...",
       style = "color: #414f2f;"
     ))
     w <- Waiter$new(
       html = msg,
       color = "rgba(256,256,256,0.9)"
-    )  
+    )
 
     ns <- session$ns
     # Variables ----
     map <- reactiveVal()
     leaflet_map <- reactiveVal()
 
-    new_tif_upload <- disease_select_server("disease_select", tab_disease_selected())
-    
+    new_tif_upload <- disease_choose_file_server("disease_select", tab_disease_selected())
+
     observeEvent(tab_disease_selected(),
       ignoreInit = TRUE,
-      {        
+      {
         w$show()
 
         "app/data/disease_outbreak/Mosaic_final.tif" |>
@@ -65,19 +64,18 @@ disease_app_server <- function(id, tab_disease_selected) {
           disease_leaflet_map(
             add_control = TRUE,
             main_map_features = TRUE
-          )  |>
+          ) |>
           leaflet_map()
 
         w$hide()
-        
+
         # MAP itself ----
         disease_map_server(
           "disease_map",
           leaflet_map = leaflet_map,
           new_tif_upload
-        ) 
+        )
       }
     )
-
   })
 }
diff --git a/...se_outbreaks/disease_app/disease_select.R → ...tbreaks/disease_app/disease_choose_file.R b/...se_outbreaks/disease_app/disease_select.R → ...tbreaks/disease_app/disease_choose_file.R
@@ -1,11 +1,10 @@
 box::use(
-  shiny[moduleServer, NS, tagList, checkboxInput, bootstrapPage, tags, observeEvent, reactiveVal, reactive, actionButton, fileInput, req, validate, need],
+  shiny[moduleServer, NS, bootstrapPage, tags, observeEvent, reactiveVal, reactive, fileInput],
   bslib[card, card_header, card_body],
-  leaflet[clearImages, leafletProxy],
 )
 
 #' @export
-disease_select_ui <- function(id, theme, i18n) {
+disease_choose_file_ui <- function(id, theme, i18n) {
   ns <- NS(id)
   bootstrapPage(
     theme = theme,
@@ -27,7 +26,7 @@ disease_select_ui <- function(id, theme, i18n) {
 }
 
 #' @export
-disease_select_server <- function(id, tab_disease_selected) {
+disease_choose_file_server <- function(id, tab_disease_selected) {
   moduleServer(id, function(input, output, session) {
     ns <- session$ns
     out <- reactiveVal(NULL)
@@ -36,9 +35,10 @@ disease_select_server <- function(id, tab_disease_selected) {
       input$tif_file,
       ignoreInit = TRUE,
       ignoreNULL = TRUE,
-    {
-      out(input$tif_file$datapath)      
-    })
+      {
+        out(input$tif_file$datapath)
+      }
+    )
 
     reactive(out())
   })

diff --git a/app/view/disease_outbreaks/disease_app/disease_map.R b/app/view/disease_outbreaks/disease_app/disease_map.R
@@ -1,12 +1,11 @@
 box::use(
-  shiny[NS, moduleServer, tags, observeEvent, reactive, actionButton, reactiveVal, checkboxInput, updateCheckboxInput, req],
+  shiny[NS, moduleServer, tags, observeEvent, req],
   bslib[card, card_header, card_body],
-  leaflet[setView, leaflet, leafletOptions, leafletOutput, renderLeaflet, addTiles, leafletProxy, addRasterImage, clearImages],
-  terra[rast, project],
+  leaflet[leafletOutput, renderLeaflet, leafletProxy, addRasterImage],
 )
 
 box::use(
-  app/logic/disease_outbreaks/disease_leaflet_map[read_and_project_raster, disease_leaflet_map]
+  app / logic / disease_outbreaks / disease_leaflet_map[read_and_project_raster]
 )
 
 #' @export
@@ -36,23 +35,23 @@ disease_map_server <- function(id, leaflet_map, new_tif_upload) {
     ns <- session$ns
 
     observeEvent(leaflet_map(), {
-      req(leaflet_map())      
+      req(leaflet_map())
       output_map <- leaflet_map()
       output$map_output <- renderLeaflet(output_map)
     })
 
     observeEvent(new_tif_upload(), {
       new_tif_rast <- new_tif_upload() |>
-                        read_and_project_raster()
-      
+        read_and_project_raster()
+
       req(new_tif_rast)
-      leafletProxy("map_output") |>
+      leafletProxy("map_output") |> # hint: leafletProxy, removeImage, addRasterLegend, addLegend,
         addRasterImage(
-        new_tif_rast,
-        opacity = 1,
-        project = FALSE,
-        group = "File upload"
-      )
+          new_tif_rast,
+          opacity = 1,
+          project = FALSE,
+          group = "File upload"
+        )
     })
   })
 }