Resolve merge conflicts with dev

Merge branch 'dev' into jt-99-review_by_row_for_reals # Conflicts: # R/mod_common_forms.R # R/mod_study_forms.R # tests/testthat/_snaps/app_feature_01/app-feature-1-002.json # tests/testthat/_snaps/app_feature_01/app-feature-1-002_.png # tests/testthat/_snaps/app_feature_01/app-feature-1-003.json # tests/testthat/_snaps/app_feature_01/app-feature-1-004.json # tests/testthat/_snaps/app_feature_01/app-feature-1-004_.png # tests/testthat/_snaps/app_feature_01/app-feature-1-005.json # tests/testthat/_snaps/app_feature_01/app-feature-1-005_.png # tests/testthat/_snaps/app_feature_03/app-feature-3-002.json # tests/testthat/_snaps/mod_study_forms/study_forms-001.json # tests/testthat/_snaps/mod_study_forms/study_forms-002.json
openpharma · Jan 15, 2025 · 4fbccfd · 4fbccfd
2 parents be53eab + ec9bebb
commit 4fbccfd
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: clinsight
 Title: ClinSight
-Version: 0.1.1.9015
+Version: 0.1.1.9016
 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
@@ -12,6 +12,7 @@
 - Review data by records IDs instead of subject & form
 - Make query handling a configurable option
 - Changed the legend to display 'significance pending' instead of 'significance unknown'.
+- Added `Excel` download button to Queries table & patient listings that need review.
 
 ## Bug fixes
 

diff --git a/R/fct_data_helpers.R b/R/fct_data_helpers.R
@@ -514,7 +514,7 @@ add_missing_columns <- function(
 #' @param rename_vars An optional named character vector. If provided, it will
 #'   rename any column names found in this vector to the provided name.
 #' @param title Optional. Character string with the title of the table.
-#' @param selection See [DT::datatable()]. Default set to 'single'. 
+#' @param selection See [DT::datatable()]. Default set to 'single'.
 #' @param extensions See [DT::datatable()]. Default set to 'Scroller'.
 #' @param dom See \url{https://datatables.net/reference/option/dom}. A div
 #'   element will be inserted before the table for the table title. Default set
@@ -531,6 +531,12 @@ add_missing_columns <- function(
 #'   * Non-modifiable defaults:
 #'     * `dom`: Defined by the `dom` parameter.
 #'     * `initComplete`: Defaults to a function to insert table title into dataTable container.
+#' @param allow_listing_download Logical, whether to allow the user to download
+#'   the table as an Excel file. Defaults to the `allow_listing_download`
+#'   configuration option in `golem-config.yml`, but can be overwritten here if
+#'   needed.
+#' @param export_label Character string with the table export label. Only used
+#'   for downloadable tables (if `allow_listing_download` is `TRUE`).
 #' @param ... Other optional arguments that will be passed to [DT::datatable()].
 #'
 #' @return A `DT::datatable` object.
@@ -545,6 +551,8 @@ datatable_custom <- function(
     extensions = c("Scroller", "ColReorder"),
     dom = "fti",
     options = list(),
+    allow_listing_download = NULL,
+    export_label = NULL,
     ...
     ){
   stopifnot(is.data.frame(data))
@@ -557,6 +565,10 @@ datatable_custom <- function(
   stopifnot(is.null(title) | is.character(title))
   stopifnot(grepl("t", dom, fixed = TRUE))
   stopifnot(is.list(options))
+  allow_listing_download <- allow_listing_download %||% 
+    get_golem_config("allow_listing_download")
+  stopifnot(is.null(allow_listing_download) | is.logical(allow_listing_download))
+  stopifnot(is.null(export_label) | is.character(export_label))
 
   default_opts <- list(
     scrollY = 400,
@@ -582,6 +594,20 @@ datatable_custom <- function(
       ),
     dom = gsub(pattern = "(t)", replacement = '<"header h5">\\1', dom)
   )
+
+  # This will conditionally add a download button to the table
+  if(nrow(data) > 0 & isTRUE(allow_listing_download)) {
+    export_label <- export_label %||% "_label.missing_"
+    extensions <- c("Buttons", extensions)
+    fixed_opts[["buttons"]] <- list(list(
+      extend = 'excel',
+      text = '<i class="fa-solid fa-download"></i>',
+      filename = paste("clinsight", export_label, sep = "."),
+      title = paste0(export_label, " | extracted from ClinSight")
+    ))
+    fixed_opts[["dom"]] <- paste0('B', fixed_opts[["dom"]])
+  }
+
   opts <- default_opts |>
     modifyList(options) |>
     modifyList(fixed_opts)

diff --git a/R/mod_navigate_review.R b/R/mod_navigate_review.R
@@ -130,7 +130,8 @@ mod_navigate_review_server <- function(
       df[["reviewed"]] <- NULL 
       if(!input$show_all_data) df$subject_id <- NULL
       datatable_custom(df, table_names,
-                       callback = dblclick_to_form(ns("go_to_form")))
+                       callback = dblclick_to_form(ns("go_to_form")), 
+                       allow_listing_download = FALSE)
     }) 
 
     queries_table_data <- reactive({
@@ -158,7 +159,8 @@ mod_navigate_review_server <- function(
           pageLength = -1
           ),
         rownames = FALSE,
-        selection = "none"
+        selection = "none",
+        allow_listing_download = FALSE
         )
     })
 

diff --git a/R/mod_queries.R b/R/mod_queries.R
@@ -149,11 +149,17 @@ 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
+
+
       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")),
+        export_label = paste(ifelse(input$show_resolved, "all", "open"),
+                           "queries", sep = ".")
       )
     })
 
@@ -184,7 +190,8 @@ mod_queries_server <- function(id, r, navinfo, all_forms, db_path, table_names){
         ),
         class = "row-border hover",
         rownames = FALSE,
-        selection = "none"
+        selection = "none",
+        allow_listing_download = FALSE
       )
     })
   })

diff --git a/R/mod_report.R b/R/mod_report.R
@@ -187,12 +187,14 @@ mod_report_server <- function(id, r, rev_data, db_path, table_names){
     })
 
     output[["review_completed_table"]] <- DT::renderDT({
-      datatable_custom(selected_review_data(), table_names, rownames = FALSE)
+      datatable_custom(selected_review_data(), table_names, rownames = FALSE, 
+                       allow_listing_download = FALSE)
     })
 
     output[["queries_raised_table"]] <- DT::renderDT({
       req(query_data())
-      datatable_custom(selected_query_data()[, -1], table_names, rownames = FALSE)
+      datatable_custom(selected_query_data()[, -1], table_names, rownames = FALSE, 
+                       allow_listing_download = FALSE)
     })
 
     output[["report"]] <- downloadHandler(

diff --git a/R/mod_review_form_tbl.R b/R/mod_review_form_tbl.R
@@ -146,6 +146,11 @@ mod_review_form_tbl_server <- function(
         rename_vars = c("Review Status" = "o_reviewed", table_names), 
         rownames= FALSE,
         title = title,
+        export_label = paste(
+          simplify_string(form), 
+          ifelse(show_all(), "all_patients", r$subject_id), 
+          sep = "."
+        ),
         escape = FALSE,
         selection = "none",
         callback = checkbox_callback,

diff --git a/R/mod_start_page.R b/R/mod_start_page.R
@@ -87,7 +87,8 @@ mod_start_page_server <- function(id, r, rev_data, navinfo, all_forms, table_nam
       tab <- datatable_custom(
         dplyr::select(rev_data$overview(), -needs_review), 
         rename_vars = table_names,
-        callback = dblclick_to_form(ns("go_to_patient"))
+        callback = dblclick_to_form(ns("go_to_patient")), 
+        allow_listing_download = FALSE
       )
       if(length(bold_rows) == 0) return(tab)
       DT::formatStyle(

diff --git a/inst/app/www/custom.css b/inst/app/www/custom.css
@@ -4,6 +4,11 @@
  --cs-marking: #97b0f8;
 }
 
+.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: 0.1.1.9015
+  golem_version: 0.1.1.9016
   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
   allow_query_inputs: TRUE
 dev:
   golem_wd: !expr golem::pkg_path()

diff --git a/man/datatable_custom.Rd b/man/datatable_custom.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
@@ -248,6 +248,7 @@
         "filter": "none",
         "vertical": false,
         "extensions": [
+          "Buttons",
           "Scroller",
           "ColReorder"
         ],
@@ -328,7 +329,15 @@
           ],
           "rowCallback": "rowCallback",
           "initComplete": "function() {\n$(this.api().table().container()).find('.header').html(\"Adverse events\")\n}",
-          "dom": "f<\"header h5\">ti",
+          "dom": "Bf<\"header h5\">ti",
+          "buttons": [
+            {
+              "extend": "excel",
+              "text": "<i class=\"fa-solid fa-download\"><\/i>",
+              "filename": "clinsight.adverse_events.BEL_04_772",
+              "title": "adverse_events.BEL_04_772 | extracted from ClinSight"
+            }
+          ],
           "order": [
 
           ],
@@ -423,6 +432,40 @@
           "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-1-002_.png b/tests/testthat/_snaps/app_feature_01/app-feature-1-002_.png
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
@@ -248,6 +248,7 @@
         "filter": "none",
         "vertical": false,
         "extensions": [
+          "Buttons",
           "Scroller",
           "ColReorder"
         ],
@@ -328,7 +329,15 @@
           ],
           "rowCallback": "rowCallback",
           "initComplete": "function() {\n$(this.api().table().container()).find('.header').html(\"Adverse events\")\n}",
-          "dom": "f<\"header h5\">ti",
+          "dom": "Bf<\"header h5\">ti",
+          "buttons": [
+            {
+              "extend": "excel",
+              "text": "<i class=\"fa-solid fa-download\"><\/i>",
+              "filename": "clinsight.adverse_events.BEL_04_772",
+              "title": "adverse_events.BEL_04_772 | extracted from ClinSight"
+            }
+          ],
           "order": [
 
           ],
@@ -423,6 +432,40 @@
           "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",