Merge pull request #51 from codecheckers/revert-49-create-page-list-v…

…enues

Revert "Create page list venues"

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: codecheck
 Title: Helper Functions for CODECHECK Project
-Version: 0.5.0
+Version: 0.3.0
 Authors@R: 
     c(person(given = "Stephen",
             family = "Eglen",

R/register.R

@@ -9,18 +9,6 @@ CONFIG$MD_COLUMNS_WIDTHS <- "|:-------|:--------------------------------|:------
 CONFIG$REGISTER_COLUMNS <- list("Certificate", "Repository", "Type", "Issue", "Report", "Check date")
 CONFIG$DICT_ORCID_ID_NAME <- list()
 CONFIG$DIR_TEMP_REGISTER_CODECHECKER <- "docs/temp_register_codechecker.csv"
-CONFIG$DICT_VENUE_NAMES <- list(
-  "journal (GigaScience)" = "GigaScience",
-  "journal (J Geogr Syst)" = "Journal of Geographical Systems",
-  "journal (J Archaeol Sci)" = "Journal of Archaeological Science",
-  "journal (GigaByte)" = "GigaByte",
-  "conference (AGILEGIS)" = "AGILEGIS",
-  "community (codecheck)" = "Codecheck",
-  "community (codecheck NL)" = "Codecheck NL",
-  "community (in press)" = "In press",
-  "community (preprint)" = "Preprint"
-)
-
 
 #' Function for rendering the register into different view
 #'
@@ -45,9 +33,8 @@ CONFIG$DICT_VENUE_NAMES <- list(
 register_render <- function(register = read.csv("register.csv", as.is = TRUE),
                             filter_by = c("venues", "codecheckers"),
                             outputs = c("html", "md", "json")) {
-  CONFIG$MD_REG_TEMPLATE <- system.file("extdata", "templates/template_register.md", package = "codecheck")
-  CONFIG$MD_NON_REG_TEMPLATE <- system.file("extdata", "templates/template_non_register.md", package = "codecheck")
-
+  CONFIG$MD_TEMPLATE <- system.file("extdata", "templates/template_register.md", package = "codecheck")
+
   register_table <- preprocess_register(register, filter_by)
 
   # Creating list of of register tables with indices being the filter types
@@ -65,21 +52,9 @@ register_render <- function(register = read.csv("register.csv", as.is = TRUE),
   }
 
   # Rendering files
-  # if ("md" %in% outputs) render_register_mds(list_register_tables)
-  if ("html" %in% outputs) {
-    render_register_htmls(list_register_tables)
-
-    for (filter in filter_by){
-      render_non_register_htmls(list_register_tables[[filter]], page_type = filter)
-    }
-  }
-  if ("json" %in% outputs) {
-    # render_register_jsons(list_register_tables)
-    for (filter in filter_by){
-      render_non_register_jsons(list_register_tables[[filter]], page_type = filter)
-    }
-
-  }
+  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

@@ -95,7 +95,8 @@ get_output_dir <- function(filter, column_value) {
     }
 
     # Removing the venue category to obtain the venue name and replace the brackets
-    venue_name <- determine_venue_name(column_value, venue_category)
+    venue_name <- trimws(gsub("[()]", "", gsub(venue_category, "", column_value)))
+    venue_name <- gsub(" ", "_", venue_name)
     return(paste0("docs/", filter, "/", venue_category, "/", venue_name, "/"))  }
 
   else if (filter=="codecheckers"){
@@ -124,13 +125,3 @@ determine_venue_category <- function(venue_name){
   warning(paste("Register venue", venue_name, "does not fall into any of the following venue categories:", toString(list_venue_categories)))
   return(NULL)
 }
-
-determine_venue_name <- function(unfiltered_venue_name, venue_category){
-  if (is.null(venue_category)){
-    return(NULL)
-  }
-
-  venue_name <- trimws(gsub("[()]", "", gsub(venue_category, "", unfiltered_venue_name, ignore.case = TRUE)))
-  venue_name <- gsub(" ", "_", venue_name)
-  return(venue_name)
-}

R/utils_render_register_mds.R

@@ -90,7 +90,7 @@ render_register_md <- function(filter, register_table, register_table_name, for_
     register_table <- add_repository_links_md(register_table)
   }
   # Fill in the content
-  md_table <- load_md_template(CONFIG$MD_REG_TEMPLATE)
+  md_table <- load_md_template(CONFIG$MD_TEMPLATE)
 
   markdown_content <- capture.output(kable(register_table, format = "markdown"))
   md_table <- add_markdown_title(filter, md_table, register_table_name)

R/utils_render_reigster_html.r

@@ -32,9 +32,10 @@ add_repository_links_html <- function(register_table) {
 #' Dynamically generates a html_document.yml with the full paths to the index header, prefix 
 #' and postfix.html files. 
 #' 
-#' @param output_dir The output directory where the html_document needs to be saved.
-generate_html_document_yml <- function(output_dir) {
-  output_dir <- paste0(getwd(), "/", output_dir)
+#' @param filter The filter name
+#' @param register_table_name The register table name
+generate_html_document_yml <- function(filter, register_table_name) {
+  dir <- paste0(getwd(), "/", get_output_dir(filter, register_table_name))
 
   yaml_content <- sprintf(
     "# DO NOT EDIT THIS FILE MANUALLY
@@ -47,62 +48,54 @@ generate_html_document_yml <- function(output_dir) {
       highlight: null
       self_contained: false
       lib_dir: libs",
-    output_dir, output_dir, output_dir
+    dir, dir, dir
   )
-  writeLines(yaml_content, paste0(output_dir, "html_document.yml"))
+  writeLines(yaml_content, paste0(dir, "html_document.yml"))
 }
 
 #' Dynamically generates the index_postfix.html from a template file 
 #' 
-#' @param output_dir The output directory
 #' @param filter The filter name
-#' @param register_table_name The register table name. If this is NULL we are generating list of venues/ codecheckers
+#' @param register_table_name The register table name
 #' 
 #' @importFrom whisker whisker.render
-create_index_postfix_html <- function(output_dir, filter, register_table_name = NULL){
-  # When we have a reg table name, we adjusting the hrefs of the postfix
-  if (!is.null(register_table_name)){
-    postfix_template <- readLines(paste0(getwd(), "/docs/templates/reg_tables/index_postfix_template.html"), warn = FALSE)
-    # Render the template with the correct hrefs
-    hrefs <- generate_html_postfix_hrefs_reg(filter, register_table_name)
-  }
-
-  # Generating the postfix for non-register table pages (e.g. list of venues and codecheckers)
-  else{
-    postfix_template <- readLines(paste0(getwd(), "/docs/templates/codecheckers_venues_list/index_postfix_template.html"), warn = FALSE)
-    hrefs <- list(
-      json_href = paste0("https://codecheck.org.uk/register/", filter, "/index.json")
-    )
-  }
+create_index_postfix_html <- function(filter, register_table_name){
+  hrefs <- generate_html_postfix_hrefs(filter, register_table_name)
 
+  # Using the index_postfix_template
+  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, paste0(output_dir, "index_postfix.html"))
+  writeLines(output, paste0(get_output_dir(filter, register_table_name), "index_postfix.html"))
 }
 
 #' Dynamically generates the index_prefix.html from a template file 
 #' 
-#' @param output_dir The output directory
-create_index_prefix_html <- function(output_dir){
+#' @param filter The filter name
+#' @param register_table_name The register table name
+create_index_prefix_html <- function(filter, register_table_name){
   # Using the index_prefix_template
-  prefix_template <- readLines(paste0(getwd(), "/docs/templates/general/index_prefix_template.html"), warn = FALSE)
-  writeLines(prefix_template, paste0(output_dir, "index_prefix.html"))
+  prefix_template <- readLines(paste0(getwd(), "/docs/index_prefix_template.html"), warn = FALSE)
+
+  writeLines(prefix_template, paste0(get_output_dir(filter, register_table_name), "index_prefix.html"))
 }
 
 #' Dynamically generates the index_header.html from a template file 
 #' 
-#' @param output_dir The output directory
-create_index_header_html <- function(output_dir){
+#' @param filter The filter name
+#' @param register_table_name The register table name
+create_index_header_html <- function(filter, register_table_name){
   # Using the index_header_template
-  header_template <- readLines(paste0(getwd(), "/docs/templates/general/index_header_template.html"), warn = FALSE)
+  header_template <- readLines(paste0(getwd(), "/docs/index_header_template.html"), warn = FALSE)
 
-  writeLines(header_template, paste0(output_dir, "index_header.html"))
+  writeLines(header_template, paste0(get_output_dir(filter, register_table_name), "index_header.html"))
 }
 
-#' Generates the hrefs to set in the postfix.html file for the rendering of register tables.
+#' Generates the hrefs to set in the postfix.html file.
 #' 
 #' @param filter The filter name
 #' @param register_table_name The register table name
-generate_html_postfix_hrefs_reg <- function(filter, register_table_name) {
+generate_html_postfix_hrefs <- function(filter, register_table_name) {
   hrefs <- list(
     csv_source_href = generate_href(filter, register_table_name, "csv_source"),
     searchable_csv_href = generate_href(filter, register_table_name, "searchable_csv"),
@@ -162,15 +155,14 @@ generate_href <- function(filter, register_table_name, href_type) {
   }
 }
 
-#' Creates index postfix, prefix and the header 
+#' Creates html files for each index section- the index postfix, prefix and the header 
 #'
-#' @param output_dir The output directory of the section files
 #' @param filter The filter name 
 #' @param register_table_name The register table name
-create_index_section_files <- function(output_dir, filter, register_table_name = NULL) {
-  create_index_postfix_html(output_dir, filter, register_table_name)
-  create_index_prefix_html(output_dir)
-  create_index_header_html(output_dir)
+create_index_section_files <- function(filter, register_table_name) {
+  create_index_postfix_html(filter, register_table_name)
+  create_index_prefix_html(filter, register_table_name)
+  create_index_header_html(filter, register_table_name)
 }
 
 #' Renders register html for a single register_table
@@ -179,14 +171,14 @@ create_index_section_files <- function(output_dir, filter, register_table_name =
 #' @param register_table The register table
 #' @param register_table_name The register table name
 render_register_html <- function(filter, register_table, register_table_name){  
-
-  output_dir <- get_output_dir(filter, 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_index_section_files(output_dir, filter, register_table_name)
-  generate_html_document_yml(output_dir)
+  create_index_section_files(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
   # Note that the temp md file must be created even if a md exists because the register table
   # now has different icons under "Repository" column
@@ -222,10 +214,8 @@ render_register_html <- function(filter, register_table, register_table_name){
 render_register_htmls <- function(list_register_tables) {
   # Loop over each register table
   for (filter in names(list_register_tables)){
-    list_filtered_reg_tables <- list_register_tables[[filter]]
-
-    for (register_table_name in names(list_filtered_reg_tables)) {
-      register_table <- list_filtered_reg_tables[[register_table_name]]
+    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)
     }
   }