Improve indentation, integrate catAndRun() msgs

and use kwb.utils::createFunctionExtdataFile()

Author: hsonne

DESCRIPTION

@@ -49,5 +49,5 @@ Remotes:
     github::kwb-r/kwb.utils
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 VignetteBuilder: knitr

R/check_for_differences.R

@@ -38,8 +38,8 @@
 #' head(diffs_df)
 #'
 #' }
-check_for_differences <- function(
-                                  df_x, df_y, dbg = TRUE) {
+check_for_differences <- function(df_x, df_y, dbg = TRUE)
+{
   name_df_x <- deparse(substitute(df_x))
   name_df_y <- deparse(substitute(df_y))
 
@@ -49,9 +49,9 @@ check_for_differences <- function(
   tidy_name <- function(name) paste0(name, "_tidy")
 
   get_text <- function(name_df, name_value) sprintf(
-      "Tidying data.frame '%s' and rename 'value' to '%s'. Saving to %s",
-      name_df, name_value, tidy_name(name_df)
-    )
+    "Tidying data.frame '%s' and rename 'value' to '%s'. Saving to %s",
+    name_df, name_value, tidy_name(name_df)
+  )
 
   df_x_tidy <- kwb.utils::catAndRun(
     messageText = get_text(name_df_x, name_value_x), dbg = dbg,
@@ -84,10 +84,12 @@ check_for_differences <- function(
 
   diffs_idx <- kwb.utils::catAndRun(
     messageText = messageText, dbg = dbg,
-    expr = which(!sapply(seq_len(nrow(df_xy_tidy)), function(row) identical(
+    expr = which(
+      !sapply(seq_len(nrow(df_xy_tidy)), function(row) identical(
         df_xy_tidy[[name_value_x]][row],
         df_xy_tidy[[name_value_y]][row]
-      )))
+      ))
+    )
   )
 
   kwb.utils::catIf(dbg, sprintf(

R/create_endnote_list.R

@@ -10,9 +10,9 @@
 #' str(endnote_list[1]$record)
 #' attr(endnote_list, "xml_file_info")
 #' attr(endnote_list, "xml_filename_without_extension")
-create_endnote_list <- function(endnote_xml = default_xml()) {
+create_endnote_list <- function(endnote_xml = default_xml())
+{
   endnote_list <- xml2::as_list(xml2::read_xml(endnote_xml))$xml$records
 
-
   add_file_info_attributes(endnote_list, endnote_xml)
 }

R/create_list_by_pubtype_from_df.R

@@ -12,7 +12,8 @@
 #' refs_list_by_pubtype <- create_list_by_pubtype_from_df(refs_df)
 #' str(refs_list_by_pubtype, 1)
 #' }
-create_list_by_pubtype_from_df <- function(refs_df) {
+create_list_by_pubtype_from_df <- function(refs_df)
+{
   refs_df <- refs_df %>%
     dplyr::arrange(dplyr::desc(.data$rec_number))
 

R/create_list_with_unique_entries.R

@@ -12,7 +12,8 @@
 #' unique_entries_list <- create_list_with_unique_entries(refs_df)
 #' str(unique_entries_list, 1)
 #' }
-create_list_with_unique_entries <- function(refs_df) {
+create_list_with_unique_entries <- function(refs_df)
+{
   select_columns <- function(pattern) {
     columns <- unique(stringr::str_extract(names(refs_df), pattern))
     columns[!is.na(columns)]

R/create_references_df_from_list.R

@@ -1,20 +1,25 @@
 # colbind: Wrapper around dplyr::bind_cols(). Makes sure that no rows get lost
 # if the data frame to add has no rows.
-colbind <- function(df, df_2) {
+colbind <- function(df, df_2)
+{
   if (nrow(df_2) == 0L) {
+
     # Return the original data frame if the data frame to add has no columns
     if (ncol(df_2) == 0L) {
       return(df)
     }
+
     # Give the data frame to add one empty row (full of NA)
     df_2 <- df_2[1L, ]
   }
+
   dplyr::bind_cols(df, df_2)
 }
 
 #' @noRd
 #' @keywords internal
-null_to_na <- function(x, na_fill = NA_character_) {
+null_to_na <- function(x, na_fill = NA_character_)
+{
   if (is.null(x[[1]])) na_fill else x[[1]]
 }
 
@@ -26,14 +31,15 @@ null_to_na <- function(x, na_fill = NA_character_) {
 #' @return one row abstract data frame
 #' @export
 #' @importFrom dplyr bind_cols
-get_abstract <- function(record_list, collapse = FALSE) {
+get_abstract <- function(record_list, collapse = FALSE)
+{
   abstract <- record_list$record$abstract
 
   if (is.null(abstract)) {
     return(NA_character_)
   }
 
-  collapse_fields(abstract, collapse, collapse_val = " ", element = 1)
+  collapse_fields(abstract, collapse, collapse_val = " ", element = 1L)
 }
 
 #' Helper function: get keywords from list for a reference
@@ -47,8 +53,12 @@ get_abstract <- function(record_list, collapse = FALSE) {
 #' @export
 #' @importFrom dplyr bind_cols
 get_keywords <- function(
-                         record_list, col_name = "keyword", extract_value = "keywords",
-                         collapse = FALSE) {
+  record_list,
+  col_name = "keyword",
+  extract_value = "keywords",
+  collapse = FALSE
+)
+{
   get_multi_entry(
     entries = record_list$record[[extract_value]],
     col_name = col_name,
@@ -68,7 +78,12 @@ get_keywords <- function(
 #' @export
 #' @importFrom dplyr bind_cols
 get_authors <- function(
-                        record_list, col_name = "author", extract_value = "authors", collapse = FALSE) {
+  record_list,
+  col_name = "author",
+  extract_value = "authors",
+  collapse = FALSE
+)
+{
   get_multi_entry(
     entries = record_list$record$contributors[[extract_value]],
     col_name = col_name,
@@ -78,8 +93,8 @@ get_authors <- function(
 }
 
 # get_multi_entry --------------------------------------------------------------
-get_multi_entry <- function(
-                            entries, col_name, element = NULL, collapse = FALSE) {
+get_multi_entry <- function(entries, col_name, element = NULL, collapse = FALSE)
+{
   if (is.null(entries)) {
     return(stats::setNames(nm = colname_i(col_name, 1), tibble::tibble(
       value = NA_character_
@@ -100,15 +115,21 @@ get_multi_entry <- function(
 }
 
 # collapse_fields --------------------------------------------------------------
-collapse_fields <- function(entries,
-                            collapse = TRUE,
-                            collapse_val = "",
-                            element) {
+collapse_fields <- function(
+  entries,
+  collapse = TRUE,
+  collapse_val = "",
+  element
+)
+{
   if (is.list(entries) && collapse) {
+
     paste(collapse = collapse_val, lapply(seq_along(entries), function(i) {
       null_to_na(entries[[i]][[element]])
     }))
+
   } else {
+
     null_to_na(entries[[element]])
   }
 }
@@ -119,8 +140,11 @@ collapse_fields <- function(entries,
 #' @return one row authors data frame
 #' @export
 #' @inheritParams get_authors
-get_secondary_authors <- function(record_list, collapse = FALSE) {
-  get_authors(record_list, "author_secondary", "secondary-authors", collapse)
+get_secondary_authors <- function(record_list, collapse = FALSE)
+{
+  get_authors(
+    record_list, "author_secondary", "secondary-authors", collapse
+  )
 }
 
 #' Helper function: get tertiary authors from list for a reference
@@ -129,8 +153,11 @@ get_secondary_authors <- function(record_list, collapse = FALSE) {
 #' @return one row authors data frame
 #' @export
 #' @inheritParams get_authors
-get_tertiary_authors <- function(record_list, collapse = FALSE) {
-  get_authors(record_list, "author_tertiary", "tertiary-authors", collapse)
+get_tertiary_authors <- function(record_list, collapse = FALSE)
+{
+  get_authors(
+    record_list, "author_tertiary", "tertiary-authors", collapse
+  )
 }
 
 #' Helper function: get pdfurls from list for a reference
@@ -143,7 +170,8 @@ get_tertiary_authors <- function(record_list, collapse = FALSE) {
 #' @export
 #' @importFrom dplyr bind_cols
 #' @importFrom tibble tibble
-get_pdfurls <- function(record_list, col_name = "urls_pdf", collapse = FALSE) {
+get_pdfurls <- function(record_list, col_name = "urls_pdf", collapse = FALSE)
+{
   get_multi_entry(
     entries = record_list$record$urls$`pdf-urls`,
     col_name = col_name,
@@ -160,13 +188,17 @@ get_pdfurls <- function(record_list, col_name = "urls_pdf", collapse = FALSE) {
 #' @export
 #' @importFrom dplyr bind_cols
 #' @importFrom tibble tibble
-record_list_to_df <- function(record_list, collapse = FALSE) {
+record_list_to_df <- function(record_list, collapse = FALSE)
+{
   get_record_entry <- function(path) get_list_entry(record_list$record, path)
+
   get_style <- function(path) {
-    collapse_fields(get_record_entry(path),
-                    collapse = collapse,
-                    collapse_val = "",
-                    element = 1)
+    collapse_fields(
+      get_record_entry(path),
+      collapse = collapse,
+      collapse_val = "",
+      element = 1L
+    )
   }
 
   replace_newline_with_semicolon <- function(text) {
@@ -239,7 +271,8 @@ record_list_to_df <- function(record_list, collapse = FALSE) {
 #' refs_df <- create_references_df(endnote_list)
 #' head(refs_df)
 #'
-create_references_df <- function(endnote_list, collapse = FALSE) {
+create_references_df <- function(endnote_list, collapse = FALSE)
+{
   extract_values_from_list <- lapply(seq_along(endnote_list), function(rec_id) {
     record_list_to_df(record_list = endnote_list[rec_id], collapse)
   })

R/give_hints.R

@@ -6,32 +6,37 @@
 #' @return vector with project_names with hints how to improve data quality (in
 #' case give_hints = TRUE)
 #' @export
-give_hints_project_names <- function(project_names, dbg = TRUE) {
+give_hints_project_names <- function(project_names, dbg = TRUE)
+{
   kwb.utils::catAndRun(
     "Generate hints for 'Project Names'",
-    expr = {
-      replace_na_with_value(project_names, "add_project_name")
-    }
+    replace_na_with_value(project_names, "add_project_name")
   )
 }
 
+get_indices_multiple_authors <- function(author_names)
+{
+  n_names <- unlist(lapply(author_names, function(x) {
+    length(stringr::str_split(x, pattern = ",")[[1L]])
+  }))
 
-get_indices_multiple_authors <- function(author_names) {
-  which(unlist(lapply(author_names, function(x)
-    length(stringr::str_split(x, pattern = ",")[[1]]))) > 2)
+  which(n_names > 2L)
 }
 
-get_indices_firstname_lastname <-  function(author_names) {
+get_indices_firstname_lastname <-  function(author_names)
+{
   which(
-  stringr::str_detect(author_names, "^\\s?\\w+\\.?\\s+\\w+") &
-    !stringr::str_detect(author_names, ",")
-)}
-
+    stringr::str_detect(author_names, "^\\s?\\w+\\.?\\s+\\w+") &
+      !stringr::str_detect(author_names, ",")
+  )
+}
 
-get_indices_ends_with_semicolon <- function(author_names) {
-  which(author_names %>%
-  stringr::str_trim() %>%
-  stringr::str_detect(".*,$"))
+get_indices_ends_with_semicolon <- function(author_names)
+{
+  author_names %>%
+    stringr::str_trim() %>%
+    stringr::str_detect(".*,$") %>%
+    which()
 }
 
 #' Helper Function: Give Hints For Author Names
@@ -43,29 +48,35 @@ get_indices_ends_with_semicolon <- function(author_names) {
 #' @return vector with author_names with hints how to improve data quality (in
 #' case give_hints = TRUE)
 #' @export
-give_hints_author_names <- function(author_names, dbg = TRUE) {
+give_hints_author_names <- function(author_names, dbg = TRUE)
+{
   kwb.utils::catAndRun(
     "Generate hints for 'Author Names'",
     dbg = dbg,
     expr = {
       multiple_authors_idx <- get_indices_multiple_authors(author_names)
       firstname_lastname_idx <- get_indices_firstname_lastname(author_names)
       ends_with_semicolon_idx <- get_indices_ends_with_semicolon(author_names)
-
-
       author_names %>%
-      replace_indices_with_value(multiple_authors_idx,
-                                 "fix_multiple_authors_per_line",
-                                 dbg) %>%
-      replace_indices_with_value(firstname_lastname_idx,
-                                 paste0("fix_firstname_lastname_with_",
-                                 "lastname_semicolon_firstname"),
-                                 dbg) %>%
-      replace_indices_with_value(ends_with_semicolon_idx,
-                                 "fix_author_name_by_deleting_last_semicolon",
-                                 dbg) %>%
-      replace_na_with_value("add_author_lastname_semicolon_firstname",
-                            dbg)
+        replace_indices_with_value(
+          multiple_authors_idx,
+          "fix_multiple_authors_per_line",
+          dbg
+        ) %>%
+        replace_indices_with_value(
+          firstname_lastname_idx,
+          "fix_firstname_lastname_with_lastname_semicolon_firstname",
+          dbg
+        ) %>%
+        replace_indices_with_value(
+          ends_with_semicolon_idx,
+          "fix_author_name_by_deleting_last_semicolon",
+          dbg
+        ) %>%
+        replace_na_with_value(
+          "add_author_lastname_semicolon_firstname",
+          dbg
+        )
     }
   )
 }
@@ -82,8 +93,6 @@ give_hints_author_names <- function(author_names, dbg = TRUE) {
 give_hints_accessiblity <- function(access, dbg = TRUE) {
   kwb.utils::catAndRun(
     "Generate hints for 'Accessiblity'",
-    expr = {
-      replace_na_with_value(access, "add_public_or_confidential")
-    }
+    expr = replace_na_with_value(access, "add_public_or_confidential")
   )
 }