error free

DESCRIPTION

@@ -32,7 +32,8 @@ Imports:
     rorcid,
     osfr,
     httr,
-    zen4R
+    zen4R,
+    whisker
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.3.1

NAMESPACE

@@ -40,3 +40,4 @@ importFrom(xtable,xtable)
 importFrom(yaml,read_yaml)
 importFrom(yaml,yaml.load)
 importFrom(zen4R,ZenodoRecord)
+importFrom(whisker, whisker.render)

R/register.R

@@ -1,3 +1,9 @@
+CONFIG <- new.env()
+CONFIG$FILTER_SUB_GROUPS <- list(
+  venues = list("community", "journal", "conference", "codecheck_nl")
+)
+CONFIG$MD_COLUMNS_WIDTHS <- "|:-------|:--------------------------------|:------------------|:---|:--------------------------|:----------|"
+
 #' Function for rendering the register into different view
 #'
 #' NOTE: You should put a GitHub API token inth the environment variable `GITHUB_PAT` to fix rate limits. Acquire one at see https://github.com/settings/tokens.
@@ -19,13 +25,10 @@
 #'
 #' @export
 register_render <- function(register = read.csv("register.csv", as.is = TRUE),
-                            filter_by = c("venue"),
+                            filter_by = c("venues"),
                             outputs = c("html", "md", "json")) {
+  CONFIG$MD_TEMPLATE <- system.file("extdata", "templates/template_register.md", package = "codecheck")
 
-  list_venue_categories <- c("community", "journal", "conference")
-  md_template <- system.file("extdata", "templates/template_register.md", package = "codecheck")
-  md_columns_widths <- "|:-------|:--------------------------------|:------------------|:---|:--------------------------|:----------|"
-
   register_table <- preprocess_register(register)
 
   # Creating list of of register tables with indices being the filter types
@@ -40,8 +43,8 @@ register_render <- function(register = read.csv("register.csv", as.is = TRUE),
   }
 
   # Rendering files
-  if ("md" %in% outputs) render_register_mds(list_register_tables, md_template, md_columns_widths)
-  if ("html" %in% outputs) render_register_htmls(list_register_tables, md_template, md_columns_widths)
+  if ("md" %in% outputs) render_register_mds(list_register_tables)
+  if ("html" %in% outputs) render_register_htmls(list_register_tables)
   if ("json" %in% outputs) render_register_jsons(list_register_tables)
 
   return(register_table)

R/utils_create_filtered_register_csvs.R

@@ -1,12 +1,12 @@
-create_filtered_register_csvs <- function(filter_by, register){
+create_filtered_register_csvs <- function(filter_by, register, FILTER_SUB_GROUPS){
 
   for (filter in filter_by){
     column_name <- determine_column_name(filter)
-    unique_values <- unique(register$column_name)
+    unique_values <- unique(register[[column_name]])
 
     for (value in unique_values) {
-      filtered_register <- register[register$column_name==value, ]
-      output_dir <- get_output_dir(filter, value)
+      filtered_register <- register[register[[column_name]]==value, ]
+      output_dir <- paste0(get_output_dir(filter, value), "register.csv")
 
       if (!dir.exists(dirname(output_dir))) {
         dir.create(dirname(output_dir), recursive = TRUE, showWarnings = TRUE)
@@ -18,27 +18,32 @@ create_filtered_register_csvs <- function(filter_by, register){
 }
 
 determine_column_name <- function(filter) {
-  result <- switch(filter,
-         "venue" = "Type",
+  column_name <- switch(filter,
+         "venues" = "Type",
          NULL # Default case is set to NULL
          )
-  if (is.null(result)) {
+  if (is.null(column_name)) {
     stop(paste("Filter", filter, "is not recognized."))
   }
 
-  return(result)
+  return(column_name)
 }
 
 get_output_dir <- function(filter, value) {
   if (filter=="none"){
     return(paste0("docs/"))
   }
 
-  else if (filter=="venue"){
+  else if (filter=="venues"){
     venue_category <- determine_venue_category(value)
-    # Removing the venue category to obtain the venue name
-    venue_name <- trimws(gsub("[()]", "", gsub(venue_category, "", venue_name)))
+    if (!(venue_category %in% CONFIG$FILTER_SUB_GROUPS[["venues"]])){
+      venue_category <- gsub(" ", "_", venue_category)
+      return(paste0("docs/", filter, "/", venue_category, "/"))
+    }
 
+    # Removing the venue category to obtain the venue name
+    venue_name <- trimws(gsub("[()]", "", gsub(venue_category, "", value)))
+    venue_name <- gsub(" ", "_", venue_name)
     return(paste0("docs/", filter, "/", venue_category, "/", venue_name, "/"))
   }
 
@@ -48,11 +53,13 @@ get_output_dir <- function(filter, value) {
 }
 
 determine_venue_category <- function(venue_name){
+  list_venue_categories <- CONFIG$FILTER_SUB_GROUPS[["venues"]]
   for (category in list_venue_categories){
     if (grepl(category, venue_name)) {
       return(category)
     }
   }
-  # The venue does not belong to the listed categories. Throwing an error
-  stop(paste("Register venue does not fall into any of the following venue categories:", toString(list_venue_categories)))
+  # The venue does not belong to the listed categories. 
+  warning(paste("Register venue does not fall into any of the following venue categories:", toString(list_venue_categories), "Setting its own name as a"))
+  return(venue_name)
 }

R/utils_register_sort.R → R/utils_filter_register_table.R

@@ -10,7 +10,8 @@ add_filtered_register_tables <- function(list_register_tables, register_table, f
     for (filter in filter_by){
         list_register_tables[[filter]] <- create_filtered_register_tables(register_table, filter)
     }
-
+
+    list_1 <- unlist(list_register_tables, recursive = TRUE)
     return(list_register_tables)
 }
 
@@ -24,13 +25,14 @@ create_filtered_register_tables <- function(register_table, filter) {
     list_filtered_register_tables <- list()
 
     column_name <- determine_column_name(filter)
-    unique_values <- unique(register_table$column_name)
-
+    unique_values <- unique(register_table[[column_name]])
     # Loop over the unique values. We create a sorted table for each value
     for (value in unique_values) {
-        filtered_table <- register_table[register_table$column_name==value, ]
+        filtered_table <- register_table[register_table[[column_name]]==value, ]
         rownames(filtered_table) <- NULL  # Reset row names to remove row numbers
         list_filtered_register_tables[[value]] <- filtered_table
     }    
+
+    print(names(list_filtered_register_tables))
     return(list_filtered_register_tables)
 }

R/utils_render_register_mds.R

@@ -18,8 +18,7 @@ load_md_template <- function(template_path){
 #'
 #' @return The modified markdown table
 adjust_markdown_title <- function(md_table, register_table_name){
-
-  if (register_table_name != "Original"){
+  if (register_table_name == "original"){
     title_addition <- ""
   }
 
@@ -71,41 +70,43 @@ add_repository_links_md <- function(register_table) {
 }
 
 # Helper function to process each table and convert it to markdown format
-render_register_md <- function(filter, register_table, register_table_name, md_table, md_columns_widths, is_temp_file=FALSE) {
+render_register_md <- function(filter, register_table, register_table_name, is_temp_file=FALSE) {
   # Fill in the content
+  md_table <- load_md_template(CONFIG$MD_TEMPLATE)
+
   markdown_content <- capture.output(kable(register_table, format = "markdown"))
-
   md_table <- adjust_markdown_title(md_table, register_table_name)
   md_table <- gsub("\\$content\\$", paste(markdown_content, collapse = "\n"), md_table)
 
   # Adjusting the column widths
   md_table <- unlist(strsplit(md_table, "\n", fixed = TRUE))
   # Determining which line to add the md column widths in
   alignment_line_index <- grep("^\\|:---", md_table)
-  md_table[alignment_line_index] <- md_columns_widths
+  md_table[alignment_line_index] <- CONFIG$MD_COLUMNS_WIDTHS
 
   # Determining the directory and saving the file
   output_dir <- get_output_dir(filter, register_table_name)
+
   if (!dir.exists(output_dir)) {
     dir.create(output_dir, recursive = TRUE, showWarnings = TRUE)
   }
 
   if (is_temp_file){
-    output_file_path <- paste0(output_dir, "temp.md")
+    output_dir <- paste0(output_dir, "temp.md")
   }
 
   else{
-    output_file_path <- paste0(output_dir, "register.md")
+    output_dir <- paste0(output_dir, "register.md")
   }
 
-  writeLines(md_table, output_file_path)
+  writeLines(md_table, output_dir)
 }
 
-render_register_mds <- function(list_register_tables, md_template){
-  md_table <- load_md_template(md_template)
+render_register_mds <- function(list_register_tables){
   for (filter in names(list_register_tables)){
-    for (register_table_name in names(list_register_tables[[filter]]))
+    for (register_table_name in names(list_register_tables[[filter]])){
       register_table <- list_register_tables[[filter]][[register_table_name]]
-      render_register_md(filter, register_table, register_table_name, md_table, md_columns_widths)
+      render_register_md(filter, register_table, register_table_name)
+    }
   }
 }

R/utils_render_reigster_html.r

@@ -34,7 +34,7 @@ add_repository_links_html <- function(register_table) {
 #' 
 #' @return None
 generate_html_document_yml <- function(filter, register_table_name) {
-  dir <- paste0(getwd(), get_output_dir(filter, register_table_name))
+  dir <- paste0(getwd(), "/", get_output_dir(filter, register_table_name))
 
   yaml_content <- sprintf(
     "# DO NOT EDIT THIS FILE MANUALLY
@@ -56,25 +56,24 @@ create_index_postfix_html <- function(filter, register_table_name){
   hrefs <- set_html_postfix_hrefs(filter, register_table_name)
 
   # Using the index_postfix_template
-  postfix_template <- readLines(paste0(getwd(), "/docs/index_postfix.html"), warn = FALSE)
-
+  postfix_template <- readLines(paste0(getwd(), "/docs/index_postfix_template.html"), warn = FALSE)
   # Render the template with the correct hrefs
   output <- whisker.render(postfix_template, hrefs)
-  writeLines(output, get_output_dir(filter, register_table_name))
+  writeLines(output, paste0(get_output_dir(filter, register_table_name), "index_postfix.html"))
 }
 
 create_index_prefix_html <- function(filter, register_table_name){
   # Using the index_prefix_template
-  prefix_template <- readLines(paste0(getwd(), "/docs/index_prefix.html"), warn = FALSE)
+  prefix_template <- readLines(paste0(getwd(), "/docs/index_prefix_template.html"), warn = FALSE)
 
-  writeLines(prefix_template, get_output_dir(filter, register_table_name))
+  writeLines(prefix_template, paste0(get_output_dir(filter, register_table_name), "index_prefix.html"))
 }
 
 create_index_header_html <- function(filter, register_table_name){
   # Using the index_header_template
-  header_template <- readLines(paste0(getwd(), "/docs/index_header.html"), warn = FALSE)
+  header_template <- readLines(paste0(getwd(), "/docs/index_header_template.html"), warn = FALSE)
 
-  writeLines(header_template, get_output_dir(filter, register_table_name))
+  writeLines(header_template, paste0(get_output_dir(filter, register_table_name), "index_header.html"))
 }
 
 set_html_postfix_hrefs <- function(filter, register_table_name) {
@@ -87,25 +86,24 @@ set_html_postfix_hrefs <- function(filter, register_table_name) {
   return(hrefs)
 }
 
-set_href <- function(filter, register_table_name, href_type) {
-  base_url <- "https://"
-
+set_href <- function(filter, register_table_name, href_type, filter_subcatetgories) {
+
   # Determine base path based on the resource type
-  switch(href_type,
-         "csv_source" = base_url <- paste0(base_url, "raw.githubusercontent.com/codecheckers/register/master/"),
-         "searchable_csv" = base_url <- paste0(base_url, "github.com/codecheckers/register/blob/master/"),
-         "json" = base_url <- paste0(base_url, "codecheck.org.uk/register/"),
-         "md" = base_url <- paste0(base_url, "codecheck.org.uk/register/")
+  result <- switch(href_type,
+         "csv_source" = list(base_url = "https://raw.githubusercontent.com/codecheckers/register/master/", ext = ".csv"),
+         "searchable_csv" = list(base_url ="https://github.com/codecheckers/register/blob/master/", ext = ".csv"),
+         "json" = base_url <- list(base_url = "https://codecheck.org.uk/register/", ext = ".json"),
+         "md" = base_url <- list(base_url = "https://codecheck.org.uk/register/", ext = ".md")
         )
 
   if (filter == "None") {
     return(paste0(base_url, "register.", href_type))
-  } else if (filter == "venue") {
+  } else if (filter == "venues") {
     venue_category <- determine_venue_category(register_table_name)
     venue_name <- trimws(gsub("[()]", "", gsub(venue_category, "", register_table_name)))
-    return(paste0(base_url, filter, "/", venue_category, "/", venue_name, "/register.", href_type))
+    return(paste0(result$base_url, filter, "/", venue_category, "/", venue_name, "/register", result$ext))
   } else {
-    return(paste0(base_url, filter, "/", register_table_name, "/register.", href_type))
+    return(paste0(result$base_url, filter, "/", register_table_name, "/register", result$ext))
   }
 }
 
@@ -115,15 +113,13 @@ create_section_htmls <- function(filter, register_table_name) {
   create_index_header_html(filter, register_table_name)
 }
 
-render_register_html <- function(filter, register_table, register_table_name, md_table, md_columns_widths){
-  generate_html_document_yml(filter, register_table_name)
-
+render_register_html <- function(filter, register_table, register_table_name){  
   # Add icons to the Repository column for HTML output, use a copy of the register.md
   register_table <- add_repository_links_html(register_table)
 
   # Dynamically create the index header, prefix and postfix files
   create_section_htmls(filter, register_table_name)
-  create_html_yaml(filter, register_table_name)
+  generate_html_document_yml(filter, register_table_name)
 
   output_dir <- get_output_dir(filter, register_table_name)
   # Capture the HTML output from a markdown file
@@ -135,12 +131,11 @@ render_register_html <- function(filter, register_table, register_table_name, md
 
   # If .md does not exist create a temp md file
   else{
-    render_register_md(filter, register_table, register_table_name, md_table, md_columns_widths, is_temp_file=TRUE)
+    render_register_md(filter, register_table, register_table_name, is_temp_file=TRUE)
     md_file_path <- paste0(output_dir, "temp.md")
     temp_md_used <- TRUE
   }
-
-  yaml_path <- normalizePath(file.path(getwd(), paste0(output_dir, "docs/html_document.yml")))
+  yaml_path <- normalizePath(file.path(getwd(), paste0(output_dir, "html_document.yml")))
 
   # Render HTML from markdown
   rmarkdown::render(
@@ -155,14 +150,12 @@ render_register_html <- function(filter, register_table, register_table_name, md
   }
 }
 
-render_register_htmls <- function(list_register_tables, md_template, md_columns_widths) {
-  md_table <- load_md_template(md_template)
-
+render_register_htmls <- function(list_register_tables) {
   # Loop over each register table
   for (filter in names(list_register_tables)){
     for (register_table_name in names(list_register_tables[[filter]])) {
       register_table <- list_register_tables[[filter]][[register_table_name]]
-      render_register_html(filter, register_table, register_table_name, md_table, md_columns_widths)
+      render_register_html(filter, register_table, register_table_name)
     }
   }
 }