Merge pull request #142 from openpharma/jt-resolve_merge_conflicts_main

Resolve merge conflicts `main`

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: clinsight
 Title: ClinSight
-Version: 0.1.0.9008
+Version: 0.1.1.9008
 Authors@R: c(
     person("Leonard Daniël", "Samson", , "[email protected]", role = c("cre", "aut"),
            comment = c(ORCID = "0000-0002-6252-7639")),

NEWS.md

@@ -2,7 +2,6 @@
 
 ## Changed 
 
-- Added `pkgdown` GHA workflow to automatically update documentation site with PRs & pushes to `main` and `dev`
 - Generalized `merge_meta_with_data()` to allow user-defined processing functions.
 - Added a feature where, in applicable tables, a user can navigate to a form by double-clicking a table row.
 - Fixed warnings in `apply_edc_specific_changes` due to the use of a vector within `dplyr::select`.
@@ -12,7 +11,17 @@
 
 ## 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 0.1.1
+
+## Changed 
+
+- Added `pkgdown` GHA workflow to automatically update documentation site with pushes to `main`
+
+## Bug fixes
+
+- Fixed inconsistencies in app messages when saving a review for a form with items with different review states (with some items reviewed previously by a different reviewer, and some items being completely new).
+- Fixed a bug where clinsight deployed with `shinyproxy` would crash when a user with non-ASCII letters in their name would attempt to login. In this new version, 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
 

R/app_server.R

@@ -9,7 +9,7 @@
 #' the `header widgets` ([mod_header_widgets_server()]), and the `query page`
 #' ([mod_queries_server()])
 #'
-#' @param input,output,session Internal parameters for {shiny}.
+#' @param input,output,session Internal parameters for `shiny`.
 #' @seealso [app_ui()], [run_app()]
 #' 
 app_server <- function(

R/fct_data_helpers.R

@@ -391,7 +391,7 @@ get_form_level_data <- function(
 #' @param value_column A string containing the column name with the item values.
 #' @param id_column The columns identifying a unique participant (subject_id).
 #'
-#' @return as data frame with an additional column named "base_{varname}". 
+#' @return as data frame with an additional column named "base_`varname`". 
 #' @export
 #' @examples
 #'  library(dplyr)

R/fct_utils.R

@@ -755,4 +755,3 @@ decode_base64 <- function(
   }
   rawToChar(decoded)
 }
-

R/mod_query_add.R

@@ -179,6 +179,8 @@ mod_query_add_server <- function(
         db_path, query_id = new_query$query_id, n = new_query$n
       )
       query_in_db <- unique(query_in_db[names(new_query)])
+      query_in_db <- query_in_db[query_in_db$timestamp == new_query$timestamp[1], ]
+
       if(identical(new_query, query_in_db)){
         r$query_data <- dplyr::bind_rows(r$query_data, new_query)
       }

R/mod_review_forms.R

@@ -253,23 +253,34 @@ mod_review_forms_server <- function(
         tables = "all_review_data" 
       )
 
-      review_row_db <- db_get_review(
+      # Contains multiple rows, one for each item.
+      updated_rows_db <- db_get_review(
         db_path, subject = review_row$subject_id, form = review_row$item_group
-        )
-      review_row_db <- unique(review_row_db[names(review_row)])
+        )[c(names(review_row), "event_name", "item_name", "form_repeat")]
+      # Within a form, only items with a changed review state are updated and 
+      # contain the new (current) time stamp. 
+      updated_rows_db <- updated_rows_db[
+        updated_rows_db$timestamp == review_row$timestamp[1], 
+        ]
+
+      review_row_db <- unique(updated_rows_db[names(review_row)])
       if(identical(review_row_db, review_row)){
         cat("Update review data and status in app\n")
         r$review_data <- r$review_data |> 
-          dplyr::rows_update(review_row, by = c("subject_id", "item_group"))
+          dplyr::rows_update(
+            updated_rows_db, 
+            by = c("subject_id", "item_group", "event_name", "item_name", "form_repeat")
+          )
       }
 
-      review_row_memory <- review_row |> 
-        dplyr::left_join(r$review_data, by = names(review_row)) 
-      review_row_memory <- unique(review_row_memory[names(review_row)])
+      updated_items_memory <- sort(with(r$review_data, item_name[
+        reviewer == review_row$reviewer[1] & timestamp == review_row$timestamp[1]
+      ]))
+      updated_items_db <- sort(updated_rows_db$item_name)
 
       review_save_error(any(
         !identical(review_row_db, review_row),
-        !identical(review_row_memory, review_row_db)
+        !identical(updated_items_db, updated_items_memory)
       ))
 
       if(review_save_error()){

inst/golem-config.yml

@@ -1,6 +1,6 @@
 default:
   golem_name: clinsight
-  golem_version: 0.1.0.9008
+  golem_version: 0.1.1.9008
   app_prod: no
   user_identification: test_user
   study_data: !expr clinsight::clinsightful_data

tests/testthat/_snaps/mod_review_forms.md

@@ -3,36 +3,48 @@
     Code
       print(dplyr::select(r$review_data, -timestamp), width = Inf)
     Output
-      # A tibble: 2 x 12
+      # A tibble: 4 x 12
            id subject_id event_name item_group     form_repeat item_name              
         <int> <chr>      <chr>      <chr>                <dbl> <chr>                  
-      1     2 361        Visit 5    Vital signs              4 Systolic blood pressure
-      2     1 885        Any visit  Adverse events           1 AE Number              
-        event_date edit_date_time      reviewed comment reviewer                     
-        <chr>      <chr>               <chr>    <chr>   <chr>                        
-      1 2023-07-01 2023-08-30 01:01:01 No       ""      ""                           
-      2 2023-08-15 2023-09-30 01:01:01 Yes      ""      "test_name (Medical Monitor)"
-        status
-        <chr> 
-      1 new   
-      2 old   
+      1     3 361        Visit 5    Vital signs              4 Systolic blood pressure
+      2     4 361        Visit 6    Vital signs              5 Systolic blood pressure
+      3     1 885        Any visit  Adverse events           1 Atrial Fibrillation    
+      4     2 885        Any visit  Adverse events           2 Cystitis               
+        event_date edit_date_time      reviewed comment          
+        <chr>      <chr>               <chr>    <chr>            
+      1 2023-07-01 2023-08-30 01:01:01 Yes      "another comment"
+      2 2023-08-01 2023-08-02 01:01:01 No       ""               
+      3 2023-08-15 2023-09-30 01:01:01 Yes      "test comment"   
+      4 2023-09-01 2023-10-01 01:01:01 Yes      ""               
+        reviewer                      status
+        <chr>                         <chr> 
+      1 "Reviewer 2"                  old   
+      2 ""                            new   
+      3 "Reviewer 1"                  old   
+      4 "test_name (Medical Monitor)" old   
 
 ---
 
     Code
       print(dplyr::select(r$review_data, -timestamp), width = Inf)
     Output
-      # A tibble: 2 x 12
+      # A tibble: 4 x 12
            id subject_id event_name item_group     form_repeat item_name              
         <int> <chr>      <chr>      <chr>                <dbl> <chr>                  
-      1     2 361        Visit 5    Vital signs              4 Systolic blood pressure
-      2     1 885        Any visit  Adverse events           1 AE Number              
-        event_date edit_date_time      reviewed comment      
-        <chr>      <chr>               <chr>    <chr>        
-      1 2023-07-01 2023-08-30 01:01:01 No       ""           
-      2 2023-08-15 2023-09-30 01:01:01 No       "test review"
+      1     3 361        Visit 5    Vital signs              4 Systolic blood pressure
+      2     4 361        Visit 6    Vital signs              5 Systolic blood pressure
+      3     1 885        Any visit  Adverse events           1 Atrial Fibrillation    
+      4     2 885        Any visit  Adverse events           2 Cystitis               
+        event_date edit_date_time      reviewed comment          
+        <chr>      <chr>               <chr>    <chr>            
+      1 2023-07-01 2023-08-30 01:01:01 Yes      "another comment"
+      2 2023-08-01 2023-08-02 01:01:01 No       ""               
+      3 2023-08-15 2023-09-30 01:01:01 No       "test review"    
+      4 2023-09-01 2023-10-01 01:01:01 No       "test review"    
         reviewer                      status
         <chr>                         <chr> 
-      1 ""                            new   
-      2 "test_name (Medical Monitor)" new   
+      1 "Reviewer 2"                  old   
+      2 ""                            new   
+      3 "test_name (Medical Monitor)" new   
+      4 "test_name (Medical Monitor)" new   
 

tests/testthat/fixtures/make_review_testdb.R

@@ -4,27 +4,26 @@
 
 make_review_testdata <- function(){
   data.frame(
-    subject_id = c("885", "361"),
-    event_name = c("Any visit", "Visit 5"),
-    item_group = c("Adverse events", "Vital signs"),
-    form_repeat = c(1, 4),
-    item_name = c("AE Number", "Systolic blood pressure"),
-    event_date = c("2023-08-15", "2023-07-01"),
-    edit_date_time = c("2023-09-30 01:01:01", "2023-08-30 01:01:01")
+    subject_id = c("885", "885", "361", "361"),
+    event_name = c("Any visit", "Any visit", "Visit 5", "Visit 6"),
+    item_group = c("Adverse events", "Adverse events", "Vital signs", "Vital signs"),
+    form_repeat = c(1, 2, 4, 5),
+    item_name = c("Atrial Fibrillation", "Cystitis",  "Systolic blood pressure", "Systolic blood pressure"),
+    event_date = c("2023-08-15", "2023-09-01", "2023-07-01", "2023-08-01"),
+    edit_date_time = c("2023-09-30 01:01:01", "2023-10-01 01:01:01", "2023-08-30 01:01:01", "2023-08-02 01:01:01")
   ) |> 
     dplyr::mutate(
-      reviewed = "No", 
-      comment = "", 
-      reviewer = "", 
-      timestamp = "2000-01-01 01:01:01",
-      status = "new"
+      reviewed = c("Yes", "No", "Yes", "No"), 
+      comment = c("test comment", "", "another comment", ""), 
+      reviewer = c("Reviewer 1", "", "Reviewer 2", ""), 
+      timestamp = c("2000-01-01 01:01:01", "", "2023-09-01 01:01:01", ""),
+      status = c("old", "new", "old", "new")
     )
 }
 
 fixture_path <- system.file("tests/testthat/fixtures", package = "clinsight")
-db_temp_connect(paste0(fixture_path, "/review_testdb.sqlite"), {
-  if ("all_review_data" %in% DBI::dbListTables(con)) 
-    DBI::dbRemoveTable(con, "all_review_data")
+unlink(file.path(fixture_path, "review_testdb.sqlite"))
+db_temp_connect(file.path(fixture_path, "review_testdb.sqlite"), {
   db_add_primary_key(con, "all_review_data", make_review_testdata())
   db_add_log(con)
 })

tests/testthat/test-mod_report.R

@@ -279,7 +279,7 @@ describe(
         app$click("test-report-create_report")
         app$wait_for_idle(800)
         app$set_inputs("test-report-include_from_date" = "2023-01-01")
-        app$wait_for_idle()
+        app$wait_for_idle(800)
         app$expect_values()
 
         pdf_report_path <- app$get_download("test-report-report")