From cecc13a8e944ef7ecb6258c11be3db498efc2c4b Mon Sep 17 00:00:00 2001
From: Hanneke Leegwater <h.leegwater@lacdr.leidenuniv.nl>
Date: Fri, 20 Dec 2024 11:43:56 +0100
Subject: [PATCH 1/5] Not running the API functions during testing

---
 .github/workflows/R-CMD-check.yaml | 2 +-
 R/api.R                            | 4 ++--
 man/get_api_key.Rd                 | 2 +-
 man/get_api_url.Rd                 | 2 +-
 4 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 0309311..0967791 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -2,7 +2,7 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master, dev]
+    branches: [main, master, dev, fix_problems_CI]
   pull_request:
 
 name: R-CMD-check.yaml
diff --git a/R/api.R b/R/api.R
index 8e6b411..c594c79 100644
--- a/R/api.R
+++ b/R/api.R
@@ -5,7 +5,7 @@
 #' See [set_api_url()] on how to set it.
 #'
 #' @examples
-#' \donttest{
+#' \dontrun{
 #' get_api_url()
 #' }
 #'
@@ -50,7 +50,7 @@ set_api_url <- function(rspace_api_url) {
 #' See [set_api_key()] on how to set it.
 #'
 #' @examples
-#' \donttest{
+#' \dontrun{
 #' get_api_key()
 #' }
 #'
diff --git a/man/get_api_key.Rd b/man/get_api_key.Rd
index bc56b42..4773091 100644
--- a/man/get_api_key.Rd
+++ b/man/get_api_key.Rd
@@ -11,7 +11,7 @@ Gets the RSpace API key from the \code{RSPACE_API_KEY} environment variable.
 See \code{\link[=set_api_key]{set_api_key()}} on how to set it.
 }
 \examples{
-\donttest{
+\dontrun{
 get_api_key()
 }
 
diff --git a/man/get_api_url.Rd b/man/get_api_url.Rd
index 9f6e7d1..80460b4 100644
--- a/man/get_api_url.Rd
+++ b/man/get_api_url.Rd
@@ -11,7 +11,7 @@ Gets the RSpace API URL from the \code{RSPACE_API_URL} environment variable.
 See \code{\link[=set_api_url]{set_api_url()}} on how to set it.
 }
 \examples{
-\donttest{
+\dontrun{
 get_api_url()
 }
 

From 87bd128c5e2b76659e722cc3140dbe229db727f8 Mon Sep 17 00:00:00 2001
From: Hanneke Leegwater <h.leegwater@lacdr.leidenuniv.nl>
Date: Fri, 20 Dec 2024 11:54:32 +0100
Subject: [PATCH 2/5] Do not run example for api_status during package build.

---
 R/api.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/R/api.R b/R/api.R
index c594c79..8a10b41 100644
--- a/R/api.R
+++ b/R/api.R
@@ -109,7 +109,9 @@ request <- function() {
 #' @param api_key RSpace API key
 #'
 #' @examples
+#' \dontrun{
 #' api_status()
+#' }
 #'
 #' @export
 api_status <- function(api_key = get_api_key()) {

From 356b282f46d38a6a0f2e20bca150a091ed6dc94d Mon Sep 17 00:00:00 2001
From: Hanneke Leegwater <h.leegwater@lacdr.leidenuniv.nl>
Date: Fri, 20 Dec 2024 12:53:45 +0100
Subject: [PATCH 3/5] Apply style suggestions from the lintr and styler
 packages

---
 R/documents.R                   |  30 ++++----
 R/fields.R                      |  15 ++--
 R/files.R                       |   6 +-
 R/mdtodoc.R                     | 127 +++++++++++++++++---------------
 R/utils.R                       |   4 +-
 man/api_status.Rd               |   2 +
 man/doc_to_form_id.Rd           |   2 +-
 man/document_search.Rd          |   3 +-
 tests/testthat/helper.R         |  68 +++++++++--------
 tests/testthat/test-documents.R |  22 +++---
 tests/testthat/test-fields.R    |  31 +++++---
 tests/testthat/test-mdtodoc.R   |  45 ++++++-----
 tests/testthat/test-utils.R     |   1 -
 13 files changed, 202 insertions(+), 154 deletions(-)

diff --git a/R/documents.R b/R/documents.R
index daaca95..e01dc66 100644
--- a/R/documents.R
+++ b/R/documents.R
@@ -14,7 +14,7 @@ document_retrieve <- function(doc_id, api_key = get_api_key()) {
 }
 
 document_post <- function(body, api_key = get_api_key()) {
-  body$tags <- paste0(c("rspacer", body$tags), collapse= ",")
+  body$tags <- paste0(c("rspacer", body$tags), collapse = ",")
   request() |>
     httr2::req_url_path_append("documents") |>
     httr2::req_headers(`apiKey` = api_key) |>
@@ -28,7 +28,7 @@ document_post <- function(body, api_key = get_api_key()) {
 }
 
 document_replace <- function(body, existing_document_id, api_key = get_api_key()) {
-  ifelse("rspacer" %in% stringr::str_split_1(body$tags, ","), body$tags, paste0(c("rspacer", body$tags), collapse= ","))
+  ifelse("rspacer" %in% stringr::str_split_1(body$tags, ","), body$tags, paste0(c("rspacer", body$tags), collapse = ","))
   request() |>
     httr2::req_url_path_append("documents", parse_rspace_id(existing_document_id)) |>
     httr2::req_headers(`apiKey` = api_key) |>
@@ -45,7 +45,8 @@ document_replace <- function(body, existing_document_id, api_key = get_api_key()
 #'
 #' Global search for a term
 #'
-#' Global search for a term, works identically to the simple "All" search in RSpace Workspace. Must be >= 3 characters long.
+#' Global search for a term, works identically to the simple "All" search in RSpace Workspace.
+#' Must be >= 3 characters long.
 #'
 #' @param query  description
 #' @param ... query parameters as documented in
@@ -71,9 +72,9 @@ document_search <- function(query, ..., api_key = get_api_key()) {
 #' @param verbose whether to print the matching document/form
 #' @inheritParams document_retrieve
 #' @export
-doc_to_form_id <- function(doc_id, verbose = T, api_key = get_api_key()) {
+doc_to_form_id <- function(doc_id, verbose = TRUE, api_key = get_api_key()) {
   json <- document_retrieve(doc_id, api_key)
-  if(verbose) {
+  if (verbose) {
     cli::cli_inform(c(
       "{.field Document}: {json$globalId} ({json$name})",
       "{.field Form}:\t {json$form$globalId} ({json$form$name})"
@@ -98,26 +99,27 @@ doc_to_form_id <- function(doc_id, verbose = T, api_key = get_api_key()) {
 #' Returns `FALSE` if no files are attached to the field.
 #' @export
 document_list_attachments <- function(doc_id, field_id = NULL, field_name = NULL, api_key = get_api_key()) {
-  if(is.null(doc_id)) cli::cli_abort("Specify the documnt identifier `doc_id`")
+  if (is.null(doc_id)) cli::cli_abort("Specify the documnt identifier `doc_id`")
   # Check field id and/or name
-  if(is.null(field_id)& is.null(field_name)) cli::cli_abort("Specify `field_id` or `field_name`")
-  if(!is.null(field_id)& !is.null(field_name)) cli::cli_abort("Specify only `field_id` or `field_name`")
-  if(!is.null(field_id) & !is.numeric(field_id)) cli::cli_abort("`field_id` should be a number")
-  if(!is.null(field_name) & !is.character(field_name)) cli::cli_abort("`field_name` should be a string")
+  if (is.null(field_id) && is.null(field_name)) cli::cli_abort("Specify `field_id` or `field_name`")
+  if (!is.null(field_id) && !is.null(field_name)) cli::cli_abort("Specify only `field_id` or `field_name`")
+  if (!is.null(field_id) && !is.numeric(field_id)) cli::cli_abort("`field_id` should be a number")
+  if (!is.null(field_name) && !is.character(field_name)) cli::cli_abort("`field_name` should be a string")
 
   fields <- doc_get_fields(doc_id)
 
-  if(!is.null(field_name)) fields <- dplyr::filter(fields, name == field_name)
-  if(!is.null(field_id))   fields <- fields[field_id,]
+  if (!is.null(field_name)) fields <- dplyr::filter(fields, name == field_name)
+  if (!is.null(field_id)) fields <- fields[field_id, ]
 
   fields |>
     dplyr::pull(files) |>
     unlist(recursive = F) -> files
   # Return FALSE if no files are attached
-  if(is.null(files)) return(FALSE)
+  if (is.null(files)) {
+    return(FALSE)
+  }
 
   files |>
     fields_to_data_frame() -> attachment_list
   return(attachment_list)
-
 }
diff --git a/R/fields.R b/R/fields.R
index 97872c1..7855848 100644
--- a/R/fields.R
+++ b/R/fields.R
@@ -2,14 +2,16 @@
 
 data_frame_to_fields <- function(fields_data_frame) {
   fields <- lapply(1:nrow(fields_data_frame), function(row_nr) {
-    list("name" = fields_data_frame$name[row_nr],
-         "content" = fields_data_frame$content[row_nr])
+    list(
+      "name" = fields_data_frame$name[row_nr],
+      "content" = fields_data_frame$content[row_nr]
+    )
   })
   names(fields) <- fields_data_frame$name
   return(fields)
 }
 
-fields_to_data_frame <- function(fields){
+fields_to_data_frame <- function(fields) {
   tibble::tibble(fields = fields) |> tidyr::unnest_wider("fields")
 }
 
@@ -31,16 +33,17 @@ doc_get_fields <- function(doc_id, api_key = get_api_key()) {
 #' doc_body$fields <- put_all_fields_in_one_field(doc_body$fields)
 #' }
 #'
-put_all_fields_in_one_field <- function(doc_body_fields, use_html_sep = T){
+put_all_fields_in_one_field <- function(doc_body_fields, use_html_sep = T) {
   text_content <- fields_to_data_frame(doc_body_fields)
 
-  if(use_html_sep){
+  if (use_html_sep) {
     text_content <- text_content |>
       dplyr::mutate(content = paste0("<p>", as.character(content), "</p>"))
   }
   # Collapse content into one field
   text_content <- text_content |>
-    dplyr::pull(content) |> paste(collapse = "\n")
+    dplyr::pull(content) |>
+    paste(collapse = "\n")
 
   return(list(list("content" = text_content)))
 }
diff --git a/R/files.R b/R/files.R
index 0b5d011..6ea841a 100644
--- a/R/files.R
+++ b/R/files.R
@@ -28,7 +28,7 @@ file_upload <- function(path, api_key = get_api_key()) {
 #'          If not, the download is canceled and `FALSE` is returned.
 #' @export
 file_download <- function(file_id, path = ".", api_key = get_api_key()) {
-  if(fs::is_dir(path)) {
+  if (fs::is_dir(path)) {
     # determine file name
     request() |>
       httr2::req_url_path_append("files", parse_rspace_id(file_id)) |>
@@ -39,7 +39,7 @@ file_download <- function(file_id, path = ".", api_key = get_api_key()) {
     path <- fs::path(path, json$name)
   }
 
-  if(!can_overwrite(path)) {
+  if (!can_overwrite(path)) {
     cli::cli_inform(" Cancelling download")
     return(invisible(FALSE))
   }
@@ -50,5 +50,5 @@ file_download <- function(file_id, path = ".", api_key = get_api_key()) {
     httr2::req_perform(path = path) |>
     httr2::resp_check_status() -> resp
   cli::cli_inform("Downloaded to {.path {resp$body}} ({file.size(resp$body)} bytes)")
-    return(invisible(path))
+  return(invisible(path))
 }
diff --git a/R/mdtodoc.R b/R/mdtodoc.R
index aa187bd..8dff7cb 100644
--- a/R/mdtodoc.R
+++ b/R/mdtodoc.R
@@ -1,6 +1,6 @@
 html_to_doc_body <- function(path, verbose = T) {
   xml <- xml2::read_html(path)
-  title    <- rvest::html_element(xml, xpath = "//title") |> rvest::html_text()
+  title <- rvest::html_element(xml, xpath = "//title") |> rvest::html_text()
 
   # Select sections that have a h2 child
   sections <- rvest::html_elements(xml, xpath = "//body//section[h2]")
@@ -10,12 +10,12 @@ html_to_doc_body <- function(path, verbose = T) {
   section_content <- purrr::map(section_content, ~ .x[-1]) #< remove heading
   names(section_content) <- section_heading
 
-  if(verbose) {
+  if (verbose) {
     cli::cli_inform("{.field Title}: {title}")
     purrr::iwalk(section_heading, ~ cli::cli_inform("{.field - Section {.y}}: {.x}"))
   }
 
-  fields = purrr::imap(section_content, ~ list(
+  fields <- purrr::imap(section_content, ~ list(
     name = .y,
     content = .x
   ))
@@ -26,39 +26,39 @@ html_to_doc_body <- function(path, verbose = T) {
   )
 }
 
-excel_rspace_document_name <- function(path, sections, document_name = NULL){
-  if(!is.null(document_name)){
-    if(!is.character(document_name)) cli::cli_abort(message = c("x" = "Document name should be a character string or NULL"))
+excel_rspace_document_name <- function(path, sections, document_name = NULL) {
+  if (!is.null(document_name)) {
+    if (!is.character(document_name)) cli::cli_abort(message = c("x" = "Document name should be a character string or NULL"))
     title <- document_name
-  } else if("Title" %in% sections$name){
-    title    <- dplyr::filter(sections, name == "Title") |> dplyr::pull(content)
-  } else if("Name" %in% sections$name){
-    title    <- dplyr::filter(sections, name == "Name") |> dplyr::pull(content)
-  } else if("title" %in% sections$name){
-    title    <- dplyr::filter(sections, name == "title") |> dplyr::pull(content)
-  } else if("name" %in% sections$name){
-    title    <- dplyr::filter(sections, name == "name") |> dplyr::pull(content)
-  } else{
+  } else if ("Title" %in% sections$name) {
+    title <- dplyr::filter(sections, name == "Title") |> dplyr::pull(content)
+  } else if ("Name" %in% sections$name) {
+    title <- dplyr::filter(sections, name == "Name") |> dplyr::pull(content)
+  } else if ("title" %in% sections$name) {
+    title <- dplyr::filter(sections, name == "title") |> dplyr::pull(content)
+  } else if ("name" %in% sections$name) {
+    title <- dplyr::filter(sections, name == "name") |> dplyr::pull(content)
+  } else {
     title <- tools::file_path_sans_ext(path) |> basename()
   }
   return(title)
 }
 
 excel_to_doc_body <- function(path, document_name = NULL, verbose = T, file_type = NULL) {
-  if(!file.exists(path)) cli::cli_abort(message = c("x" = glue::glue("File not found: {path}")))
-  if(is.null(file_type)){
-    file_type = tools::file_ext(path)
+  if (!file.exists(path)) cli::cli_abort(message = c("x" = glue::glue("File not found: {path}")))
+  if (is.null(file_type)) {
+    file_type <- tools::file_ext(path)
   }
-  if(!file_type %in% c("xlsx", "csv", "tsv")) cli::cli_abort(message = c("x" = glue::glue("file_type is {file_type}. It should be xlsx, csv or tsv. Specify file_type manually or rename the input file.")))
+  if (!file_type %in% c("xlsx", "csv", "tsv")) cli::cli_abort(message = c("x" = glue::glue("file_type is {file_type}. It should be xlsx, csv or tsv. Specify file_type manually or rename the input file.")))
   sections <- switch(file_type,
-                     "xlsx" = readxl::read_excel(path, col_names = c("name", "content")),
-                     "csv" = readr::read_csv(path, col_names = c("name", "content")),
-                     "tsv" = readr::read_tsv(path, col_names = c("name", "content"))
+    "xlsx" = readxl::read_excel(path, col_names = c("name", "content")),
+    "csv" = readr::read_csv(path, col_names = c("name", "content")),
+    "tsv" = readr::read_tsv(path, col_names = c("name", "content"))
   )
   # Set the RSpace entry title
   title <- excel_rspace_document_name(path, sections, document_name)
 
-  if(verbose) {
+  if (verbose) {
     cli::cli_inform("{.field Title}: {title}")
     purrr::iwalk(section_heading, ~ cli::cli_inform("{.field - Section {.y}}: {.x}"))
   }
@@ -70,34 +70,36 @@ excel_to_doc_body <- function(path, document_name = NULL, verbose = T, file_type
   )
 }
 
-attachment_upload <- function(doc_body, attachment, api_key){
+attachment_upload <- function(doc_body, attachment, api_key) {
   # Test if the attachment list has the correct format
-  if(!is.list(attachment)) cli::cli_abort(message = c("x" = "attachment is not provided as a list"))
-  if(!identical(sort(names(attachment)), c("field", "path"))) cli::cli_abort(message = c("x" = "attachment is either missing the field number or the path"))
-  if(as.numeric(attachment$field) > length(doc_body$fields))  cli::cli_abort(message = c("x" = stringr::str_glue("attachment field number is higher than the total number of fields: {length(doc_body$fields)}")))
+  if (!is.list(attachment)) cli::cli_abort(message = c("x" = "attachment is not provided as a list"))
+  if (!identical(sort(names(attachment)), c("field", "path"))) cli::cli_abort(message = c("x" = "attachment is either missing the field number or the path"))
+  if (as.numeric(attachment$field) > length(doc_body$fields)) cli::cli_abort(message = c("x" = stringr::str_glue("attachment field number is higher than the total number of fields: {length(doc_body$fields)}")))
 
   # Upload the attachment and add its name and path to to doc_body
   json <- file_upload(attachment$path, api_key)
-  doc_body$fields[[attachment$field]]$content <- glue::glue(doc_body$fields[[attachment$field]]$content,
-                                                            "<p>Inserted <fileId={json$id}></p>")
+  doc_body$fields[[attachment$field]]$content <- glue::glue(
+    doc_body$fields[[attachment$field]]$content,
+    "<p>Inserted <fileId={json$id}></p>"
+  )
   return(doc_body)
 }
 
-add_information_to_doc_body <- function(doc_body, template_id = NULL, folder_id = NULL, tags = NULL, attachment = NULL, api_key = get_api_key()){
-  if(!is.null(template_id)){
+add_information_to_doc_body <- function(doc_body, template_id = NULL, folder_id = NULL, tags = NULL, attachment = NULL, api_key = get_api_key()) {
+  if (!is.null(template_id)) {
     form_id <- parse_rspace_id(doc_to_form_id(template_id, verbose = F))
-    doc_body$form = list(id = form_id)
+    doc_body$form <- list(id = form_id)
   }
 
-  if(!is.null(folder_id)) {
+  if (!is.null(folder_id)) {
     doc_body$parentFolderId <- parse_rspace_id(folder_id)
   }
 
-  if(!is.null(tags)) {
+  if (!is.null(tags)) {
     doc_body$tags <- paste(tags, collapse = ",")
   }
 
-  if(!is.null(attachment)) {
+  if (!is.null(attachment)) {
     doc_body <- attachment_upload(doc_body, attachment, api_key)
   }
 
@@ -123,17 +125,18 @@ document_create_from_html <- function(path, template_id = NULL, folder_id = NULL
                                       existing_document_id = NULL, api_key = get_api_key()) {
   doc_body <- html_to_doc_body(path, verbose = F)
 
-  if(!is.null(existing_document_id)){
+  if (!is.null(existing_document_id)) {
     template_id <- existing_document_id
   }
 
-  if(!is.null(template_id)) {
+  if (!is.null(template_id)) {
     template_fields <- doc_get_fields(template_id)
 
-    if(length(doc_body$fields) != nrow(template_fields))
+    if (length(doc_body$fields) != nrow(template_fields)) {
       cli::cli_abort("Document has different number of fields ({length(doc_body_fields)}) than template ({nrow(template_fields)})")
+    }
     doc_body$fields <- purrr::map2(doc_body$fields, template_fields$type, ~ {
-      if(.y %in% c("string", "date")) {
+      if (.y %in% c("string", "date")) {
         .x$content <- rvest::html_text(.x$content)
       } else {
         .x$content <- as.character(.x$content) |> paste(collapse = "\n")
@@ -148,7 +151,7 @@ document_create_from_html <- function(path, template_id = NULL, folder_id = NULL
   doc_body <- add_information_to_doc_body(doc_body, template_id, folder_id, tags, attachment, api_key)
 
   # Create or replace the document
-  if(is.null(existing_document_id)){
+  if (is.null(existing_document_id)) {
     json <- document_post(doc_body)
   } else {
     json <- document_replace(doc_body, existing_document_id)
@@ -184,7 +187,7 @@ document_append_from_html <- function(path, existing_document_id, tags = NULL, a
     dplyr::pull(type)
 
   doc_body$fields <- purrr::map2(doc_body$fields, doc_body_types, ~ {
-    if(.y %in% c("string", "date")) {
+    if (.y %in% c("string", "date")) {
       .x$content <- rvest::html_text(.x$content)
     } else {
       .x$content <- as.character(.x$content) |> paste(collapse = "\n")
@@ -196,34 +199,39 @@ document_append_from_html <- function(path, existing_document_id, tags = NULL, a
   new_fields <- fields_to_data_frame(doc_body$fields)
 
   # Warn users when fields are missing in the html that are present in the existing document
-  if(length(setdiff(current_fields$name, new_fields$name)) > 0){
-    if(allow_missing_fields){
-      cli::cli_warn(message = paste0("Some fields are missing in the html to append: ",
+  if (length(setdiff(current_fields$name, new_fields$name)) > 0) {
+    if (allow_missing_fields) {
+      cli::cli_warn(message = paste0(
+        "Some fields are missing in the html to append: ",
         paste0(setdiff(current_fields$name, new_fields$name), collapse = ", "),
-        ". Other fields will be added."))
-    } else{
+        ". Other fields will be added."
+      ))
+    } else {
       cli::cli_abort(message = paste0("Some fields are missing in the html to append: ",
         paste0(setdiff(current_fields$name, new_fields$name), collapse = ", "),
         ". Specify allow_missing_fields = T if you still want to append the matching fields.",
-        collapse = ", "))
+        collapse = ", "
+      ))
     }
   }
   # Warn users when fields are missing in the existing document that are in the html
-  if(length(setdiff(new_fields$name, current_fields$name)) > 0){
-    if(allow_missing_fields){
+  if (length(setdiff(new_fields$name, current_fields$name)) > 0) {
+    if (allow_missing_fields) {
       cli::cli_warn(message = paste0("The following fields are not in the RSpace document: ",
         paste0(setdiff(new_fields$name, current_fields$name), collapse = ", "),
-        ". These will be ignored."))
-    } else{
+        ". These will be ignored."
+      ))
+    } else {
       cli::cli_abort(message = paste0("The following fields are not in the RSpace document: ",
         paste0(setdiff(new_fields$name, current_fields$name), collapse = ", "),
         ". Specify allow_missing_fields = T if you want to ignore these missing fields.",
-        collapse = ", "))
+        collapse = ", "
+      ))
     }
   }
 
   # Merge the old and new fields.
-  new_fields <- left_join(current_fields, new_fields, by = "name") |>
+  new_fields <- dplyr::left_join(current_fields, new_fields, by = "name") |>
     dplyr::filter(!is.na(content.y) | content.y != "") |>
     tidyr::unite(content, content.x, content.y, sep = "\n", na.rm = T) |>
     dplyr::mutate(id = as.character(id))
@@ -232,11 +240,11 @@ document_append_from_html <- function(path, existing_document_id, tags = NULL, a
   doc_body$fields <- data_frame_to_fields(new_fields)
 
   # Update tags and upload attachments
-  if(!is.null(tags)) {
+  if (!is.null(tags)) {
     doc_body$tags <- paste(tags, collapse = ",")
   }
 
-  if(!is.null(attachment)) {
+  if (!is.null(attachment)) {
     # TODO maybe use the columnIndex because I already removed all non-altered field numbers?
     doc_body <- attachment_upload(doc_body, attachment, api_key)
   }
@@ -267,14 +275,15 @@ document_append_from_html <- function(path, existing_document_id, tags = NULL, a
 document_create_from_excel <- function(path, file_type = NULL, document_name = NULL, template_id = NULL, folder_id = NULL, tags = NULL, attachment = NULL, api_key = get_api_key(), existing_document_id = NULL) {
   doc_body <- excel_to_doc_body(path, document_name = document_name, verbose = F, file_type = file_type)
 
-  if(!is.null(existing_document_id)){
+  if (!is.null(existing_document_id)) {
     template_id <- existing_document_id
   }
-  if(!is.null(template_id)) {
+  if (!is.null(template_id)) {
     template_fields <- doc_get_fields(template_id)
 
-    if(length(doc_body$fields) != nrow(template_fields))
+    if (length(doc_body$fields) != nrow(template_fields)) {
       cli::cli_abort("Document has different number of fields ({length(doc_body_fields)}) than template ({nrow(template_fields)})")
+    }
   } else {
     # TODO Basic Document can have only 1 field
     doc_body$fields <- put_all_fields_in_one_field(doc_body$fields)
@@ -283,7 +292,7 @@ document_create_from_excel <- function(path, file_type = NULL, document_name = N
   doc_body <- add_information_to_doc_body(doc_body, template_id = template_id, folder_id = folder_id, tags = tags, attachment = attachment)
 
   # Create or replace the document
-  if(is.null(existing_document_id)){
+  if (is.null(existing_document_id)) {
     json <- document_post(doc_body)
   } else {
     json <- document_replace(doc_body, existing_document_id)
diff --git a/R/utils.R b/R/utils.R
index 8616f9f..1acec9b 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -43,7 +43,9 @@ ui_yes <- function(x, .envir = parent.frame()) {
 }
 
 can_overwrite <- function(path) {
-  if(!fs::file_exists(path)) return(TRUE)
+  if (!fs::file_exists(path)) {
+    return(TRUE)
+  }
 
   ui_yes("Overwrite pre-existing file {.file {path}}?")
 }
diff --git a/man/api_status.Rd b/man/api_status.Rd
index 187e401..801eb1a 100644
--- a/man/api_status.Rd
+++ b/man/api_status.Rd
@@ -13,6 +13,8 @@ api_status(api_key = get_api_key())
 Function to check availability of the API service
 }
 \examples{
+\dontrun{
 api_status()
+}
 
 }
diff --git a/man/doc_to_form_id.Rd b/man/doc_to_form_id.Rd
index eb2b8b6..cb7b647 100644
--- a/man/doc_to_form_id.Rd
+++ b/man/doc_to_form_id.Rd
@@ -4,7 +4,7 @@
 \alias{doc_to_form_id}
 \title{Get the form id used for a document}
 \usage{
-doc_to_form_id(doc_id, verbose = T, api_key = get_api_key())
+doc_to_form_id(doc_id, verbose = TRUE, api_key = get_api_key())
 }
 \arguments{
 \item{doc_id}{Unique identifier of the document}
diff --git a/man/document_search.Rd b/man/document_search.Rd
index 5e75ec3..847710b 100644
--- a/man/document_search.Rd
+++ b/man/document_search.Rd
@@ -15,5 +15,6 @@ document_search(query, ..., api_key = get_api_key())
 \item{api_key}{RSpace API key}
 }
 \description{
-Global search for a term, works identically to the simple "All" search in RSpace Workspace. Must be >= 3 characters long.
+Global search for a term, works identically to the simple "All" search in RSpace Workspace.
+Must be >= 3 characters long.
 }
diff --git a/tests/testthat/helper.R b/tests/testthat/helper.R
index 3abfc97..bf9e4b7 100644
--- a/tests/testthat/helper.R
+++ b/tests/testthat/helper.R
@@ -1,4 +1,4 @@
-helper_get_sections <- function(){
+helper_get_sections <- function() {
   # Example sections objects
   sections <- tibble::tibble(
     name = c("Title", "Name", "title", "name", "date", "results"),
@@ -7,7 +7,7 @@ helper_get_sections <- function(){
   return(sections)
 }
 
-helper_get_fields <- function(){
+helper_get_fields <- function() {
   fields <- list(
     Title   = list(name = "Title", content = "The title"),
     Name    = list(name = "Name", content = "test"),
@@ -19,7 +19,7 @@ helper_get_fields <- function(){
   return(fields)
 }
 
-helper_get_unnamed_fields <- function(){
+helper_get_unnamed_fields <- function() {
   fields <- list(
     list(name = "Title", content = "The title"),
     list(name = "Name", content = "test"),
@@ -31,60 +31,66 @@ helper_get_unnamed_fields <- function(){
   return(fields)
 }
 
-helper_get_fields_df <- function(){
+helper_get_fields_df <- function() {
   # This is the structure of an RSpace fields object with two attached files.
   files_list <- list(
-      NULL,NULL,NULL,
+    NULL, NULL, NULL,
+    list(
       list(
-        list(id = 123, globalId = "GL123", name = "fake_file1.csv", caption = NULL,
-           contentType = "text/csv", created = "1970-01-01T13:01:59.154Z",
-           size = 47, version = 2, "_links" = "not used now"),
-        list(id = 124, globalId = "GL124", name = "fake_file2.csv", caption = NULL,
-                contentType = "text/csv", created = "1970-01-01T13:01:59.154Z",
-                size = 47, version = 2, "_links" = "not used now")
+        id = 123, globalId = "GL123", name = "fake_file1.csv", caption = NULL,
+        contentType = "text/csv", created = "1970-01-01T13:01:59.154Z",
+        size = 47, version = 2, "_links" = "not used now"
       ),
-      NULL
-    )
+      list(
+        id = 124, globalId = "GL124", name = "fake_file2.csv", caption = NULL,
+        contentType = "text/csv", created = "1970-01-01T13:01:59.154Z",
+        size = 47, version = 2, "_links" = "not used now"
+      )
+    ),
+    NULL
+  )
   # Files part is not working :(
   fields_df <- tibble::tibble(
-    "id" = c(101,102,103,104,105),
-    "globalId" = c("FD101","FD102","FD103","FD104","FD105"),
+    "id" = c(101, 102, 103, 104, 105),
+    "globalId" = c("FD101", "FD102", "FD103", "FD104", "FD105"),
     "name" = c("Title", "Name", "date", "results", "other"),
     "type" = c("string", "string", "date", "text", "number"),
-    "content" = c("A", "B", "01-01-1970","<p>more text</p>", 1),
-    "lastModified" = rep("1970-01-01T13:01:59.154Z",5),
-    "columnIndex" = seq(1,5),
+    "content" = c("A", "B", "01-01-1970", "<p>more text</p>", 1),
+    "lastModified" = rep("1970-01-01T13:01:59.154Z", 5),
+    "columnIndex" = seq(1, 5),
     "files" = files_list,
-    "listOfMaterials" = rep(NA,5),
-    "_links" = rep(NA,5)
+    "listOfMaterials" = rep(NA, 5),
+    "_links" = rep(NA, 5)
   )
   return(fields_df)
 }
 
-helper_small_structured_document <- function(){
+helper_small_SD <- function() {
   small_SD <- list(
-  form   = list(globalId = "some form ID"),
-  fields = helper_get_unnamed_fields()
+    form   = list(globalId = "some form ID"),
+    fields = helper_get_unnamed_fields()
   )
   return(small_SD)
 }
 
-helper_larger_structured_document <- function(){
+helper_larger_SD <- function() {
   larger_SD <- list(
     id = 123456,
     globalId = "SD123456",
     name = "Test upload of a document",
     tags = "rspacer,testing",
-    form   = list(id = 56789,
-                  globalId = "FM56789",
-                  name = "Assay template name"),
+    form = list(
+      id = 56789,
+      globalId = "FM56789",
+      name = "Assay template name"
+    ),
     fields = list(
       list(id = 120, globalId = "FD120", name = "Template Used", type = "string", content = "something here"),
-      list(id = 121, globalId = "FD121", name = "Title",         type = "string", content = "something here"),
-      list(id = 122, globalId = "FD122", name = "Date",          type = "date", content = "01-01-2020"),
-      list(id = 123, globalId = "FD123", name = "Text field",    type = "text", content = "<p>A paragraph</p>\n<p>&nbsp;</p>\n<h2>And a header</h2>")
+      list(id = 121, globalId = "FD121", name = "Title", type = "string", content = "something here"),
+      list(id = 122, globalId = "FD122", name = "Date", type = "date", content = "01-01-2020"),
+      list(id = 123, globalId = "FD123", name = "Text field", type = "text",
+           content = "<p>A paragraph</p>\n<p>&nbsp;</p>\n<h2>And a header</h2>")
     )
   )
   return(larger_SD)
 }
-
diff --git a/tests/testthat/test-documents.R b/tests/testthat/test-documents.R
index d43fc39..aa7f63f 100644
--- a/tests/testthat/test-documents.R
+++ b/tests/testthat/test-documents.R
@@ -1,7 +1,9 @@
-test_that("document_list_attachments",{
+test_that("document_list_attachments", {
   local_mocked_bindings(
-    get_api_key = function() return("API key used for testing"),
-    doc_get_fields = function(doc_id){
+    get_api_key = function() {
+      return("API key used for testing")
+    },
+    doc_get_fields = function(doc_id) {
       helper_get_fields_df()
     }
   )
@@ -11,15 +13,17 @@ test_that("document_list_attachments",{
 
   # Should return a tibble created with two attachments: 2 rows, 9 columns.
   expect_type(document_list_attachments("ABC", field_name = "results"), typeof(tibble::tibble()))
-  expect_equal(ncol(document_list_attachments("ABC", field_name = "results")),9)
-  expect_equal(nrow(document_list_attachments("ABC", field_name = "results")),2)
+  expect_equal(ncol(document_list_attachments("ABC", field_name = "results")), 9)
+  expect_equal(nrow(document_list_attachments("ABC", field_name = "results")), 2)
 
   expect_type(document_list_attachments("ABC", field_id = 4), typeof(tibble::tibble()))
-  expect_equal(ncol(document_list_attachments("ABC", field_id = 4)),9)
-  expect_equal(nrow(document_list_attachments("ABC", field_id = 4)),2)
+  expect_equal(ncol(document_list_attachments("ABC", field_id = 4)), 9)
+  expect_equal(nrow(document_list_attachments("ABC", field_id = 4)), 2)
 
-  expect_equal(document_list_attachments("ABC", field_name = "results"),
-               document_list_attachments("ABC", field_id = 4))
+  expect_equal(
+    document_list_attachments("ABC", field_name = "results"),
+    document_list_attachments("ABC", field_id = 4)
+  )
 
   # Error if input is incorrect
   expect_error(document_list_attachments())
diff --git a/tests/testthat/test-fields.R b/tests/testthat/test-fields.R
index ea8e633..de35d86 100644
--- a/tests/testthat/test-fields.R
+++ b/tests/testthat/test-fields.R
@@ -23,21 +23,32 @@ test_that("fields_to_data_frame creates a tibble", {
 
 test_that("doc_get_fields creates a fields data frame", {
   local_mocked_bindings(
-    get_api_key = function() return("API key used for testing"),
-    document_retrieve = function(doc_id, api_key = get_api_key()){
-      helper_larger_structured_document()
+    get_api_key = function() {
+      return("API key used for testing")
+    },
+    document_retrieve = function(doc_id, api_key = get_api_key()) {
+      helper_larger_SD()
     }
   )
-  expect_equal(doc_get_fields("some incorrect id"),
-               fields_to_data_frame(helper_larger_structured_document()$fields))
+  expect_equal(
+    doc_get_fields("some incorrect id"),
+    fields_to_data_frame(helper_larger_SD()$fields)
+  )
 })
 
 test_that("put_all_fields_in_one_field can collapse fields", {
   # Rspace needs a list with a list with at least content.
   fields <- helper_get_fields()
-  expect_equal(put_all_fields_in_one_field(fields),
-               list(list(content = "<p>The title</p>\n<p>test</p>\n<p>small title</p>\n<p>smaller name</p>\n<p>25-09-2024</p>\n<p>creating fields</p>")))
-  expect_equal(put_all_fields_in_one_field(fields, use_html_sep = F),
-               list(list(content = "The title\ntest\nsmall title\nsmaller name\n25-09-2024\ncreating fields")))
-  # TODO run with fields in helper_small_structured_document and helper_larger_structured_document
+  expect_equal(
+    put_all_fields_in_one_field(fields),
+    list(list(
+      content =
+        "<p>The title</p>\n<p>test</p>\n<p>small title</p>\n<p>smaller name</p>\n<p>25-09-2024</p>\n<p>creating fields</p>"
+    ))
+  )
+  expect_equal(
+    put_all_fields_in_one_field(fields, use_html_sep = FALSE),
+    list(list(content = "The title\ntest\nsmall title\nsmaller name\n25-09-2024\ncreating fields"))
+  )
+  # TODO run with fields in helper_small_SD and helper_larger_SD
 })
diff --git a/tests/testthat/test-mdtodoc.R b/tests/testthat/test-mdtodoc.R
index ace1a30..9104b18 100644
--- a/tests/testthat/test-mdtodoc.R
+++ b/tests/testthat/test-mdtodoc.R
@@ -3,38 +3,47 @@ test_that("add_information_to_doc_body can add information to a list", {
   expect_equal(add_information_to_doc_body(list()), list())
   # template_id
   expect_error(add_information_to_doc_body(list(), template_id = "incorrect ID"))
-  #TODO: how to test an API?
-  #TODO below how to check a correct but non-existing template and think about the attachments
-  #expect_error(add_information_to_doc_body(list(), template_id = "SD001"))
-  #expect_equal(add_information_to_doc_body(list(), folder_id = "SD123", tags = "test", attachment = list("7" = "hoi.txt")))
-
-  expect_equal(add_information_to_doc_body(list(), folder_id = "SD123", tags = "test"),
-               list(parentFolderId = 123, tags = "test"))
+  # TODO: how to test an API?
+  # TODO below how to check a correct but non-existing template and think about the attachments
+  # expect_error(add_information_to_doc_body(list(), template_id = "SD001"))
+  # expect_equal(add_information_to_doc_body(list(), folder_id = "SD123", tags = "test", attachment = list("7" = "hoi.txt")))
 
+  expect_equal(
+    add_information_to_doc_body(list(), folder_id = "SD123", tags = "test"),
+    list(parentFolderId = 123, tags = "test")
+  )
 })
 
 test_that("excel_rspace_document_name can process a document name", {
   sections <- helper_get_sections()
   # Check document name
-  expect_equal(excel_rspace_document_name(path = "minimal_excel.xlsx", sections = NULL, document_name = "thisone"), "thisone")
+  expect_equal(excel_rspace_document_name(
+    path = "minimal_excel.xlsx",
+    sections = NULL, document_name = "thisone"
+  ), "thisone")
   expect_error(excel_rspace_document_name(path = "minimal_excel.xlsx", sections = NULL, document_name = NA))
   expect_error(excel_rspace_document_name(path = "minimal_excel.xlsx", sections = NULL, document_name = 123))
   # Check to get name from sections in the order that is in the user manual
-  expect_equal(excel_rspace_document_name(path = "minimal_excel.xlsx", sections = sections, document_name = "thisone"), "thisone")
+  expect_equal(excel_rspace_document_name(
+    path = "minimal_excel.xlsx",
+    sections = sections, document_name = "thisone"
+  ), "thisone")
   expect_equal(excel_rspace_document_name(path = "minimal_excel.xlsx", sections = sections), "The title")
-  expect_equal(excel_rspace_document_name(path = "minimal_excel.xlsx", sections = sections[2:6,]), "test")
-  expect_equal(excel_rspace_document_name(path = "minimal_excel.xlsx", sections = sections[3:6,]), "small title")
-  expect_equal(excel_rspace_document_name(path = "minimal_excel.xlsx", sections = sections[4:6,]), "smaller name")
+  expect_equal(excel_rspace_document_name(path = "minimal_excel.xlsx", sections = sections[2:6, ]), "test")
+  expect_equal(excel_rspace_document_name(path = "minimal_excel.xlsx", sections = sections[3:6, ]), "small title")
+  expect_equal(excel_rspace_document_name(path = "minimal_excel.xlsx", sections = sections[4:6, ]), "smaller name")
   # Get the name from a file path
-  expect_equal(excel_rspace_document_name(path = "some_path/minimal_excel.xlsx", sections = sections[5:6,]),
-               "minimal_excel")
+  expect_equal(
+    excel_rspace_document_name(path = "some_path/minimal_excel.xlsx", sections = sections[5:6, ]),
+    "minimal_excel"
+  )
 })
 
-test_that("excel_to_doc_body can create a doc body",{
+test_that("excel_to_doc_body can create a doc body", {
   # one that should work
-  expect_type(excel_to_doc_body(path = testthat::test_path("minimal_excel.xlsx"), verbose = F, file_type = "xlsx"), "list")
+  expect_type(excel_to_doc_body(path = testthat::test_path("minimal_excel.xlsx"), verbose = FALSE, file_type = "xlsx"), "list")
   # not existing file
-  expect_error(excel_to_doc_body(path = "not_existing_file.xlsx", verbose = F, file_type = ".xlsx"))
+  expect_error(excel_to_doc_body(path = "not_existing_file.xlsx", verbose = FALSE, file_type = ".xlsx"))
   # incorrect excel file type specified
-  expect_error(excel_to_doc_body(path = testthat::test_path("minimal_excel.xlsx"), verbose = F, file_type = ".xlsx"))
+  expect_error(excel_to_doc_body(path = testthat::test_path("minimal_excel.xlsx"), verbose = FALSE, file_type = ".xlsx"))
 })
diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R
index 34d82e8..4d8a32c 100644
--- a/tests/testthat/test-utils.R
+++ b/tests/testthat/test-utils.R
@@ -5,7 +5,6 @@ test_that("parsing rspace ids works", {
   expect_equal(parse_rspace_id("GL258158"), 258158)
   expect_equal(parse_rspace_id("FL242398"), 242398)
   expect_equal(parse_rspace_id("NB242194"), 242194)
-  # expect_equal(parse_rspace_id("https://leiden.researchspace.com/globalId/SD242392"), 242392)
 })
 
 test_that("is_url works", {

From 2b3a8fc0586498457f887d1da8898bc238938e06 Mon Sep 17 00:00:00 2001
From: Hanneke Leegwater <h.leegwater@lacdr.leidenuniv.nl>
Date: Fri, 20 Dec 2024 13:11:39 +0100
Subject: [PATCH 4/5] Test on multiple R versions

---
 .github/workflows/R-CMD-check.yaml | 19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 0967791..f4952da 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -5,21 +5,36 @@ on:
     branches: [main, master, dev, fix_problems_CI]
   pull_request:
 
-name: R-CMD-check.yaml
+name: R-CMD-check
 
 permissions: read-all
 
 jobs:
   R-CMD-check:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
+
     steps:
       - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
+          r-version: ${{ matrix.config.r }}
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2

From ba06fb8cd32699058ed67763677f3df68eb296ec Mon Sep 17 00:00:00 2001
From: Hanneke Leegwater <h.leegwater@lacdr.leidenuniv.nl>
Date: Fri, 20 Dec 2024 14:04:46 +0100
Subject: [PATCH 5/5] Prepare to merge branch

---
 .github/workflows/R-CMD-check.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index f4952da..78a4a3f 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -2,7 +2,7 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master, dev, fix_problems_CI]
+    branches: [main, master, dev]
   pull_request:
 
 name: R-CMD-check