Update tests and global vars

RE-QDA · May 18, 2024 · a9ca8ae · a9ca8ae
1 parent 84e005c
commit a9ca8ae
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Showing 14 changed files with 37 additions and 12 deletions.
diff --git a/R/mod_about.R b/R/mod_about.R
@@ -10,7 +10,7 @@
 mod_about_ui <- function(id) {
   ns <- NS(id)
   # Citation info ----
-  rql_citation <- citation("requal")
+  rql_citation <- utils::citation("requal")
   # Extract authors
   authors <- sapply(as.character(rql_citation$author), function(x) strsplit(x, " ")) # Split the author names into first and last names
   # Format the authors as "Last name, Initial."
@@ -68,7 +68,7 @@ mod_about_ui <- function(id) {
     p("To cite package", tags$code("requal"), "in publications use:"),
     HTML(apa_citation), p(),
     p("A BibTeX entry for LaTeX users:"),
-    tags$pre(paste(toBibtex(citation("requal")), collapse = "\n"))
+    tags$pre(paste(utils::toBibtex(utils::citation("requal")), collapse = "\n"))
   )
 }
 

diff --git a/R/mod_codebook.R b/R/mod_codebook.R
@@ -198,11 +198,11 @@ mod_codebook_server <- function(id, glob) {
 
    output$export_codebook <- downloadHandler(
      filename = function() {
-       "requal_codebook_export.csv"
+       "requal_codebook.csv"
      },
      content = function(file) {
        codebook <- get_codebook_export_table(glob)
-       write.csv(codebook, file)
+       utils::write.csv(codebook, file)
      }
    )
 

diff --git a/R/mod_memo.R b/R/mod_memo.R
@@ -185,7 +185,7 @@ mod_memo_server <- function(id, glob) {
         },
         content = function(file) {
             memos <- export_memos(glob$pool, glob$active_project)
-            write.csv(memos, file)
+            utils::write.csv(memos, file)
         }
     )
 

diff --git a/R/mod_memo_utils_memo.R b/R/mod_memo_utils_memo.R
@@ -1,3 +1,5 @@
+utils::globalVariables(c("memo_title"))
+
 # list existing memos ------
 list_memo_records <- function(pool, project) {
     dplyr::tbl(pool, "memos") %>%

diff --git a/R/mod_project.R b/R/mod_project.R
@@ -1,3 +1,5 @@
+utils::globalVariables(c("project_description"))
+
 #' project UI Function
 #'
 #' @description A shiny Module.

diff --git a/R/mod_user_manager.R b/R/mod_user_manager.R
@@ -97,10 +97,10 @@ mod_user_manager_server <- function(id, glob) {
 
       modified_permissions_df <- loc$users_permissions_df %>%
       dplyr::filter(user_id %in% input$members_permissions) %>%
-      dplyr::mutate(across(matches("modify|view"), .fns = function(x) {
+      dplyr::mutate(dplyr::across(dplyr::matches("modify|view"), .fns = function(x) {
         x  <- 0 # reset permissions
       })) %>%
-      dplyr::mutate(across(all_of(input$permissions_list), .fns = function(x) {
+      dplyr::mutate(dplyr::across(dplyr::all_of(input$permissions_list), .fns = function(x) {
         x  <- 1 # apply new permissions
       }))
 

diff --git a/R/mod_user_manager_utils_user_manager.R b/R/mod_user_manager_utils_user_manager.R
@@ -1,4 +1,4 @@
-utils::globalVariables(c("user", "user_mail", "value_old"))
+utils::globalVariables(c("user", "user_mail", "value_old", "user_login"))
 
 # disabled_checkbox <- function(inputId, label, value = FALSE, width = NULL){
 #   value <- shiny::restoreInput(id = inputId, default = value)

diff --git a/R/mod_user_utils_user.R b/R/mod_user_utils_user.R
@@ -128,7 +128,7 @@ permission_button <- function(class, color, title) {
 
 transform_user_table <- function(user_table) {
   user_table %>%
-    dplyr::mutate(across(-c(user_id, created_at, user_mail, user_name, user_login),
+    dplyr::mutate(dplyr::across(-c(user_id, created_at, user_mail, user_name, user_login),
       .fn = function(x) {
         dplyr::case_when(
           x == 1 & stringr::str_detect(dplyr::cur_column(), "other_modify") ~ permission_button("fas fa-users", "black", "Can modify others"),

diff --git a/README.md b/README.md
@@ -106,7 +106,7 @@ website](https://requal.fsv.cuni.cz/).
 > de-identification. This will allow you to perform de-identification
 > locally and collaboratively analyze the de-identified dataset online.
 
-## Acknowledgement
+## Acknowledgment
 
 The application development has been supported by The Technology Agency
 of the Czech Republic, project n. TL05000054, and CLS INFRA Fellowship

diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -1,6 +1,26 @@
+Acknowledgement
+CLS
 CMD
+Coelostegus
 DESC
+DEV
+GDPR
 Lifecycle
-Reproducibility
+Programme
+RQDA
+TLS
+Thuringothyris
+UI
+caselinkage
+codebook
+codebooks
+codecat
+colours
+de
+freecode
 golem
+magrittr
+md
 reproducibility
+shinymanager
+shinytest
diff --git a/inst/test_app/tests/testthat/_snaps/app-create-codes.md b/inst/test_app/tests/testthat/_snaps/app-create-codes.md
@@ -1,4 +1,4 @@
 # {shinytest2} testing create codebook
 
-    "requal_codebook_export.csv"
+    "requal_codebook.csv"
 
diff --git a/...createcode-003-requal_codebook_export.csv → ...-codes/createcode-003-requal_codebook.csv b/...createcode-003-requal_codebook_export.csv → ...-codes/createcode-003-requal_codebook.csv
diff --git a/tests/test_basic.requal b/tests/test_basic.requal
diff --git a/tests/testthat/test-inst-app.R b/tests/testthat/test-inst-app.R
@@ -4,6 +4,7 @@ test_that("test_app works", {
     # Don't run these tests on the CRAN build servers
     skip_on_cran()
     skip_on_ci()
+    # skip_if_not(interactive())
 
     appdir <- system.file("test_app", package = "requal")
     test_app(appdir, check_setup = FALSE)