Merge pull request #49 from angelina-momin/create-page-list-venues

Create page list venues

Author: nuest

DESCRIPTION

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

R/register.R

@@ -9,6 +9,18 @@ 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
 #'
@@ -33,8 +45,9 @@ CONFIG$DIR_TEMP_REGISTER_CODECHECKER <- "docs/temp_register_codechecker.csv"
 register_render <- function(register = read.csv("register.csv", as.is = TRUE),
                             filter_by = c("venues", "codecheckers"),
                             outputs = c("html", "md", "json")) {
-  CONFIG$MD_TEMPLATE <- system.file("extdata", "templates/template_register.md", package = "codecheck")
-  
+  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")
+
   register_table <- preprocess_register(register, filter_by)
 
   # Creating list of of register tables with indices being the filter types
@@ -52,9 +65,21 @@ 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)
-  if ("json" %in% outputs) render_register_jsons(list_register_tables)
+  # 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)
+    }
+
+  }
 
   return(register_table)
 }

R/utils_create_filtered_register_csvs.R

@@ -95,8 +95,7 @@ get_output_dir <- function(filter, column_value) {
     }
 
     # Removing the venue category to obtain the venue name and replace the brackets
-    venue_name <- trimws(gsub("[()]", "", gsub(venue_category, "", column_value)))
-    venue_name <- gsub(" ", "_", venue_name)
+    venue_name <- determine_venue_name(column_value, venue_category)
     return(paste0("docs/", filter, "/", venue_category, "/", venue_name, "/"))  }
 
   else if (filter=="codecheckers"){
@@ -125,3 +124,13 @@ 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$MD_TEMPLATE)
+  md_table <- load_md_template(CONFIG$MD_REG_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

@@ -32,10 +32,9 @@ 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 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))
+#' @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)
 
   yaml_content <- sprintf(
     "# DO NOT EDIT THIS FILE MANUALLY
@@ -48,54 +47,62 @@ generate_html_document_yml <- function(filter, register_table_name) {
       highlight: null
       self_contained: false
       lib_dir: libs",
-    dir, dir, dir
+    output_dir, output_dir, output_dir
   )
-  writeLines(yaml_content, paste0(dir, "html_document.yml"))
+  writeLines(yaml_content, paste0(output_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
+#' @param register_table_name The register table name. If this is NULL we are generating list of venues/ codecheckers
 #' 
 #' @importFrom whisker whisker.render
-create_index_postfix_html <- function(filter, register_table_name){
-  hrefs <- generate_html_postfix_hrefs(filter, register_table_name)
+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")
+    )
+  }
 
-  # 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(get_output_dir(filter, register_table_name), "index_postfix.html"))
+  writeLines(output, paste0(output_dir, "index_postfix.html"))
 }
 
 #' Dynamically generates the index_prefix.html from a template file 
 #' 
-#' @param filter The filter name
-#' @param register_table_name The register table name
-create_index_prefix_html <- function(filter, register_table_name){
+#' @param output_dir The output directory
+create_index_prefix_html <- function(output_dir){
   # Using the index_prefix_template
-  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"))
+  prefix_template <- readLines(paste0(getwd(), "/docs/templates/general/index_prefix_template.html"), warn = FALSE)
+  writeLines(prefix_template, paste0(output_dir, "index_prefix.html"))
 }
 
 #' Dynamically generates the index_header.html from a template file 
 #' 
-#' @param filter The filter name
-#' @param register_table_name The register table name
-create_index_header_html <- function(filter, register_table_name){
+#' @param output_dir The output directory
+create_index_header_html <- function(output_dir){
   # Using the index_header_template
-  header_template <- readLines(paste0(getwd(), "/docs/index_header_template.html"), warn = FALSE)
+  header_template <- readLines(paste0(getwd(), "/docs/templates/general/index_header_template.html"), warn = FALSE)
 
-  writeLines(header_template, paste0(get_output_dir(filter, register_table_name), "index_header.html"))
+  writeLines(header_template, paste0(output_dir, "index_header.html"))
 }
 
-#' Generates the hrefs to set in the postfix.html file.
+#' Generates the hrefs to set in the postfix.html file for the rendering of register tables.
 #' 
 #' @param filter The filter name
 #' @param register_table_name The register table name
-generate_html_postfix_hrefs <- function(filter, register_table_name) {
+generate_html_postfix_hrefs_reg <- 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"),
@@ -155,14 +162,15 @@ generate_href <- function(filter, register_table_name, href_type) {
   }
 }
 
-#' Creates html files for each index section- the index postfix, prefix and the header 
+#' Creates 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(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)
+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)
 }
 
 #' Renders register html for a single register_table
@@ -171,14 +179,14 @@ create_index_section_files <- function(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){  
-  # Add icons to the Repository column for HTML output, use a copy of the register.md
+  
+  output_dir <- get_output_dir(filter, register_table_name)
   register_table <- add_repository_links_html(register_table)
 
   # Dynamically create the index header, prefix and postfix files
-  create_index_section_files(filter, register_table_name)
-  generate_html_document_yml(filter, register_table_name)
+  create_index_section_files(output_dir, filter, register_table_name)
+  generate_html_document_yml(output_dir)
 
-  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
@@ -214,8 +222,10 @@ 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)){
-    for (register_table_name in names(list_register_tables[[filter]])) {
-      register_table <- list_register_tables[[filter]][[register_table_name]]
+    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]]
       render_register_html(filter, register_table, register_table_name)
     }
   }

R/utils_render_table_codecheckers.R

@@ -0,0 +1,79 @@
+#' Renders codecheckers table in JSON format.
+#' 
+#' @param list_codechecker_reg_tables The list of codechecker register tables. The indices are the ORCID IDs.
+render_table_codecheckers_json <- function(list_codechecker_reg_tables){
+  list_orcid_ids <- names(list_codechecker_reg_tables)
+  # Check.names arg is set to FALSE so that column "ORCID ID" has the space
+  table_codecheckers <- data.frame(`ORCID ID`= list_orcid_ids, stringsAsFactors = FALSE, check.names = FALSE)
+  
+  # Column- codechecker names
+  table_codecheckers$`Codechecker name` <- sapply(
+    X = table_codecheckers$`ORCID ID`,
+    FUN = function(orcid_id) {
+      paste0(CONFIG$DICT_ORCID_ID_NAME[orcid_id])
+    }
+  )
+
+  # Column- No. of codechecks
+  table_codecheckers$`No. of codechecks` <- sapply(
+    X = table_codecheckers$`ORCID ID`,
+    FUN = function(orcid_id) {
+      paste0(nrow(list_codechecker_reg_tables[[orcid_id]]))
+    }
+  )
+
+  # Arranging the column names
+  table_codecheckers <- table_codecheckers[, c("Codechecker name", "ORCID ID", "No. of codechecks")]
+
+  return(table_codecheckers)
+}
+
+#' Renders codecheckers table in HTML format.
+#' Each codechecker name links to the register table for that specific
+#' codechecker. The ORCID IDs link to their ORCID pages.
+#' 
+#' @param list_codechecker_reg_tables The list of codechecker register tables. The indices are the ORCID IDs.
+render_table_codecheckers_html <- function(list_codechecker_reg_tables){
+
+  list_orcid_ids <- names(list_codechecker_reg_tables)
+  table_codecheckers <- data.frame(ORCID_ID = list_orcid_ids, stringsAsFactors = FALSE)
+
+  # Column- codechecker names
+  # Each codechecker name will be a hyperlink to the register table
+  # with all their codechecks
+  table_codecheckers$`Codechecker name` <- sapply(
+    X = table_codecheckers$ORCID_ID,
+    FUN = function(orcid_id) {
+      codechecker_name <- CONFIG$DICT_ORCID_ID_NAME[orcid_id]
+      paste0("[", codechecker_name, "](https://codecheck.org.uk/register/codecheckers/",
+      orcid_id, "/)")
+    }
+  )
+
+  # Column- ORCID ID link
+  table_codecheckers$ORCID_ID_Link <- sapply(
+    X = table_codecheckers$ORCID_ID,
+    FUN = function(orcid_id) {
+      paste0("[", orcid_id, "](https://orcid.org/", orcid_id, ")")
+    }
+  )
+  # Column- No. of codechecks
+  # Shown as "no_codechecks (sell all checks)" where "see all checks" links to the checks by 
+  # the codechecker
+  table_codecheckers$`No. of codechecks` <- sapply(
+    X = table_codecheckers$ORCID_ID,
+    FUN = function(orcid_id) {
+      no_codechecks <- nrow(list_codechecker_reg_tables[[orcid_id]])
+      paste0(nrow(list_codechecker_reg_tables[[orcid_id]])," [(see all checks)](https://codecheck.org.uk/register/codecheckers/",
+      orcid_id, "/)")
+    }
+  )
+
+  # Drop the original ORCID_ID column and rename ORCID_ID_Link to ORCID_ID
+  table_codecheckers <- table_codecheckers[, c("Codechecker name", "ORCID_ID_Link", "No. of codechecks")]
+  names(table_codecheckers)[names(table_codecheckers) == "ORCID_ID_Link"] <- "ORCID ID"
+
+  table_codecheckers <- kable(table_codecheckers)
+  return(table_codecheckers)
+}
+