openpharma · aclark02-arcus · Nov 11, 2024 · Oct 29, 2024 · Nov 4, 2024 · Nov 4, 2024
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: clinsight
 Title: ClinSight
-Version: 0.1.0.9008
+Version: 0.1.0.9009
 Authors@R: c(
     person("Leonard Daniël", "Samson", , "[email protected]", role = c("cre", "aut"),
            comment = c(ORCID = "0000-0002-6252-7639")),

diff --git a/NEWS.md b/NEWS.md
@@ -8,11 +8,14 @@
 - Fixed warnings in `apply_edc_specific_changes` due to the use of a vector within `dplyr::select`.
 - Gave users ability to re-organized the column order in any table.
 - Added form type as a class to be used in `create_table()` to display tables.
+- Added `Excel` download button to Queries table & patient listings that need review.
+- Added helper function to automatically determine when adding said excel button is appropriate.
 
 ## Bug fixes
 
 - When using the `shinyproxy` deployment configuration, the user name is now expected to be base64 encoded, and will now be base64 encoded by `clinsight` by default, so that the app can also handle non-ASCII signs in user names that are stored in HTTP headers. To display the user name correctly, use base64 encoding in the `application.yml` in ShinyProxy settings (for example: `http-headers.X_SP_USERNAME: "#{T(java.util.Base64).getEncoder().encodeToString(oidcUser.getFullName().getBytes())}"`).
 
+
 # clinsight 0.1.0
 
 ## Changed

diff --git a/R/fct_data_helpers.R b/R/fct_data_helpers.R
@@ -505,6 +505,35 @@ add_missing_columns <- function(
   data
 }
 
+#' Configure DT helper
+#'
+#' Small wrapper that helps handle some messiness preparing the correct `DT`
+#' dom, extensions, & options when needed. Specifically, when & how to add an
+#' Excel download button.
+#'
+#' @param data A data frame used for display in a DT table. Number of rows will
+#'   be assessed
+#' @param table_name character string, usually the form name
+#'
+#' @keywords internal
+#' @return list with three named objects: `dom`, `exts`, and `opts`
+dt_config <- function(data, table_name = "form") {
+  default_args<- formals(datatable_custom)
+  if(nrow(data) > 0 & isTRUE(get_golem_config("allow_listing_download"))) {
+    dt_dom <- 'Bfti'
+    dt_exts <- c("Buttons", eval(default_args$extensions))
+    dt_opts <- list(buttons=list(list(extend = 'excel',
+        text = '<i class="fa-solid fa-download"></i>',
+        filename = paste("clinsight", gsub(" ", "-", table_name), sep = ".")
+        )))
+  } else {
+    dt_dom <- default_args$dom |> eval()
+    dt_exts <- default_args$extensions |> eval()
+    dt_opts <- default_args$options |> eval()
+  }
+  return(list(dom = dt_dom, exts = dt_exts, opts = dt_opts))
+}
+
 #' Custom interactive datatable
 #'
 #' Small wrapper around [DT::datatable()]. Will be used to create tables in a

diff --git a/R/mod_common_forms.R b/R/mod_common_forms.R
@@ -132,8 +132,16 @@ mod_common_forms_server <- function(
         )) |> 
         adjust_colnames("^SAE ")
       if(!input$show_all_data) SAE_data$subject_id <- NULL
-      datatable_custom(SAE_data, rename_vars = table_names, rownames= FALSE,
-                       title = "Serious Adverse Events", escape = FALSE)
+
+      # determine DT dom / exts / opts
+      DT <- dt_config(SAE_data,
+        table_name = paste("SAE", ifelse(input$show_all_data,
+        "all_patients", r$subject_id), sep = ".")) 
+      datatable_custom(
+        SAE_data, rename_vars = table_names, rownames= FALSE,
+        title = "Serious Adverse Events", escape = FALSE,
+        dom = DT$dom, extensions = DT$exts, options = DT$opts
+      )
     })
 
     output[["common_form_table"]] <- DT::renderDT({
@@ -145,8 +153,14 @@ mod_common_forms_server <- function(
           dplyr::select(-dplyr::starts_with("SAE"))
       }
       if(!input$show_all_data) df$subject_id <- NULL
-      datatable_custom(df, rename_vars = table_names, rownames= FALSE,
-                       title = form, escape = FALSE)
+
+      # determine DT dom / exts / opts
+      DT <- dt_config(df,
+         table_name = paste(form, ifelse(input$show_all_data,
+         "all_patients", r$subject_id), sep = ".")) 
+      datatable_custom(
+        df, rename_vars = table_names, rownames= FALSE,title = form,
+        escape = FALSE, dom = DT$dom, extensions = DT$exts, options = DT$opts)
     })
 
   })

diff --git a/R/mod_queries.R b/R/mod_queries.R
@@ -144,11 +144,17 @@ mod_queries_server <- function(id, r, navinfo, all_forms, db_path, table_names){
         query_cols <- c("resolved", query_cols)
         table_title <- "All queries"
       }
+
+      # determine DT dom / exts / opts
+      DT <- dt_config(initial_queries()[query_cols],
+              table_name = paste(ifelse(input$show_resolved, "all", "open"),
+                           "queries", sep = ".")) 
       datatable_custom(
         initial_queries()[query_cols], 
         table_names, 
         title = table_title,
-        callback = dblclick_to_form(ns("go_to_form"))
+        callback = dblclick_to_form(ns("go_to_form")),
+        dom = DT$dom, extensions = DT$exts, options = DT$opts
       )
     })
 

diff --git a/R/mod_study_forms.R b/R/mod_study_forms.R
@@ -223,7 +223,12 @@ mod_study_forms_server <- function(
 
     output[["table"]] <- DT::renderDT({
       req(table_data_active())
-      datatable_custom(table_data_active(), table_names, escape = FALSE)
+      # determine DT dom / exts / opts
+      DT <- dt_config(table_data_active(),
+        table_name = paste(form, ifelse(input$show_all, 
+                     "all_patients", r$subject_id), sep = ".")) 
+      datatable_custom(table_data_active(), table_names, escape = FALSE,
+                       dom = DT$dom, extensions = DT$exts, options = DT$opts)
     })
 
     if(form %in% c("Vital signs", "Vitals adjusted")){

diff --git a/inst/app/www/custom.css b/inst/app/www/custom.css
@@ -1,4 +1,9 @@
 
+.dataTables_wrapper .dt-buttons {
+  padding-left: 0.75em;
+  float: right;  
+}
+
 .bslib-value-box .value-box-area {
   padding: 0.1rem 0rem 0.1rem 1rem;
 }

diff --git a/inst/golem-config.yml b/inst/golem-config.yml
@@ -1,6 +1,6 @@
 default:
   golem_name: clinsight
-  golem_version: 0.1.0.9008
+  golem_version: 0.1.0.9009
   app_prod: no
   user_identification: test_user
   study_data: !expr clinsight::clinsightful_data
@@ -11,6 +11,7 @@ default:
     Medical Monitor: medical_monitor
     Data Manager: data_manager
   allow_to_review: [admin, medical_monitor]
+  allow_listing_download: TRUE
 dev:
   golem_wd: !expr golem::pkg_path()
 test:

diff --git a/man/dt_config.Rd b/man/dt_config.Rd
diff --git a/tests/testthat/_snaps/app_feature_01/app-feature-1-002.json b/tests/testthat/_snaps/app_feature_01/app-feature-1-002.json
@@ -239,6 +239,7 @@
         "filter": "none",
         "vertical": false,
         "extensions": [
+          "Buttons",
           "Scroller",
           "ColReorder"
         ],
@@ -251,8 +252,15 @@
           "scrollResize": true,
           "scrollCollapse": true,
           "colReorder": true,
+          "buttons": [
+            {
+              "extend": "excel",
+              "text": "<i class=\"fa-solid fa-download\"><\/i>",
+              "filename": "clinsight.Adverse-events.BEL_04_772"
+            }
+          ],
           "initComplete": "function() {\n$(this.api().table().container()).find('.header').html(\"Adverse events\")\n}",
-          "dom": "f<\"header h5\">ti",
+          "dom": "Bf<\"header h5\">ti",
           "columnDefs": [
             {
               "className": "dt-right",
@@ -389,6 +397,40 @@
           "attachment": null,
           "all_files": true
         },
+        {
+          "name": "jszip",
+          "version": "1.13.6",
+          "src": {
+            "href": "jszip-1.13.6"
+          },
+          "meta": null,
+          "script": "jszip.min.js",
+          "stylesheet": null,
+          "head": null,
+          "attachment": null,
+          "package": null,
+          "all_files": false
+        },
+        {
+          "name": "dt-ext-buttons-bootstrap5",
+          "version": "1.13.6",
+          "src": {
+            "href": "dt-ext-buttons-bootstrap5-1.13.6"
+          },
+          "meta": null,
+          "script": [
+            "js/dataTables.buttons.min.js",
+            "js/buttons.html5.min.js",
+            "js/buttons.colVis.min.js",
+            "js/buttons.print.min.js",
+            "js/buttons.bootstrap5.min.js"
+          ],
+          "stylesheet": "css/buttons.bootstrap5.min.css",
+          "head": null,
+          "attachment": null,
+          "package": null,
+          "all_files": false
+        },
         {
           "name": "dt-ext-scroller-bootstrap5",
           "version": "1.13.6",

diff --git a/tests/testthat/_snaps/app_feature_01/app-feature-1-003.json b/tests/testthat/_snaps/app_feature_01/app-feature-1-003.json
@@ -239,6 +239,7 @@
         "filter": "none",
         "vertical": false,
         "extensions": [
+          "Buttons",
           "Scroller",
           "ColReorder"
         ],
@@ -251,8 +252,15 @@
           "scrollResize": true,
           "scrollCollapse": true,
           "colReorder": true,
+          "buttons": [
+            {
+              "extend": "excel",
+              "text": "<i class=\"fa-solid fa-download\"><\/i>",
+              "filename": "clinsight.Adverse-events.BEL_04_772"
+            }
+          ],
           "initComplete": "function() {\n$(this.api().table().container()).find('.header').html(\"Adverse events\")\n}",
-          "dom": "f<\"header h5\">ti",
+          "dom": "Bf<\"header h5\">ti",
           "columnDefs": [
             {
               "className": "dt-right",
@@ -389,6 +397,40 @@
           "attachment": null,
           "all_files": true
         },
+        {
+          "name": "jszip",
+          "version": "1.13.6",
+          "src": {
+            "href": "jszip-1.13.6"
+          },
+          "meta": null,
+          "script": "jszip.min.js",
+          "stylesheet": null,
+          "head": null,
+          "attachment": null,
+          "package": null,
+          "all_files": false
+        },
+        {
+          "name": "dt-ext-buttons-bootstrap5",
+          "version": "1.13.6",
+          "src": {
+            "href": "dt-ext-buttons-bootstrap5-1.13.6"
+          },
+          "meta": null,
+          "script": [
+            "js/dataTables.buttons.min.js",
+            "js/buttons.html5.min.js",
+            "js/buttons.colVis.min.js",
+            "js/buttons.print.min.js",
+            "js/buttons.bootstrap5.min.js"
+          ],
+          "stylesheet": "css/buttons.bootstrap5.min.css",
+          "head": null,
+          "attachment": null,
+          "package": null,
+          "all_files": false
+        },
         {
           "name": "dt-ext-scroller-bootstrap5",
           "version": "1.13.6",