Merge pull request #53 from angelina-momin/create-page-venues

Create page venues

.github/.gitignore

@@ -1 +1,2 @@
 *.html
+.DS_Store

.github/workflows/R-CMD-check.yaml

@@ -21,7 +21,7 @@ jobs:
       matrix:
         config:
           - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
+          # - {os: macOS-latest, r: 'release'}
           - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: codecheck
 Title: Helper Functions for CODECHECK Project
-Version: 0.4.0
+Version: 0.5.0
 Authors@R: 
     c(person(given = "Stephen",
             family = "Eglen",

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_table_codecheckers.R

@@ -5,7 +5,7 @@ render_table_codecheckers_json <- function(list_codechecker_reg_tables){
   list_orcid_ids <- names(list_codechecker_reg_tables)
   table_codecheckers <- data.frame(matrix(ncol=0, nrow = length(list_orcid_ids)), stringsAsFactors = FALSE)
 
-  col_names <- CONFIG$CODECHECKER_TABLE_COL_NAMES[["codechecker_table"]]
+  col_names <- CONFIG$NON_REG_TABLE_COL_NAMES[["codechecker_table"]]
 
   # Column- codechecker names
   table_codecheckers[[col_names[["codechecker"]]]] <- sapply(

R/utils_render_table_non_registers.R

@@ -3,10 +3,10 @@
 #' @param list_reg_tables The list of register tables to link to in this html page
 render_non_register_htmls <- function(list_reg_tables, page_type){
   output_dir <- paste0("docs/", page_type, "/")
+  extra_text <- ""
 
   if (page_type == "codecheckers"){
     table <- render_table_codecheckers_html(list_reg_tables)
-    table <- kable(table)
     # Counting number of codecheckers based of number of codechecker reg tables
     # The table is a kable table and hence we cannot count rows
     no_codecheckers <- length(list_reg_tables)
@@ -19,10 +19,15 @@ render_non_register_htmls <- function(list_reg_tables, page_type){
     This is because some codechecks involved more than one codechecker.</i>"
   }
 
-  else{
-    return()
+  else if (page_type == "venues") {
+    table <- render_table_venues_html(list_reg_tables)
+
+    no_venues <- length(list_reg_tables)
+    subtext <- paste("In total,", CONFIG$NO_CODECHECKS, "codechecks were completed for", no_venues, "venues")
   }
+
   # Creating and adjusting the markdown table
+  table <- kable(table)
   md_table <- load_md_template(CONFIG$TEMPLATE_DIR[["non_reg"]][["md_template"]])
   title <- paste0("CODECHECK List of ", page_type)
   md_table <- gsub("\\$title\\$", title, md_table)
@@ -65,13 +70,14 @@ render_non_register_htmls <- function(list_reg_tables, page_type){
 render_non_register_jsons <- function(list_reg_tables, page_type){
   output_dir <- paste0("docs/", page_type, "/")
 
-  if (page_type == "codeheckers"){
+  if (page_type == "codecheckers"){
     table <- render_table_codecheckers_json(list_reg_tables)
   }
 
-  else{
-    return()
+  else if (page_type == "venues"){
+    table <- render_table_venues_json(list_reg_tables)
   }
+
   jsonlite::write_json(
     table,
     path = paste0(output_dir, "index.json"),

R/utils_render_table_venues.R

@@ -0,0 +1,112 @@
+#' Renders venues table in JSON format.
+#' 
+#' @param list_venue_reg_tables The list of venue register tables. The indices are the venue names.
+render_table_venues_json <- function(list_venue_reg_tables){
+  col_names <- CONFIG$NON_REG_TABLE_COL_NAMES[["venues_table"]]
+  list_venue_names <- names(list_venue_reg_tables)
+
+  # Create initial data frame
+  table_venues <- data.frame(
+    matrix(ncol=0, nrow = length(list_venue_names)),
+    stringsAsFactors = FALSE, 
+    check.names = FALSE
+  )
+
+  table_venues[[col_names[["venue_name"]]]] <- list_venue_names
+
+  # Column- No. of codechecks
+  table_venues[[col_names[["no_codechecks"]]]] <- sapply(
+    X = list_venue_names,
+    FUN = function(venue_name) {
+      paste0(nrow(list_venue_reg_tables[[venue_name]]))
+    }
+  )
+
+  # Column- Venue type
+  table_venues[[col_names[["venue_type"]]]] <- sapply(
+    X = table_venues[[col_names[["venue_name"]]]],
+    FUN = function(venue_name){
+      venue_type <- determine_venue_category(venue_name)
+      stringr::str_to_title(venue_type)
+    }
+  )
+
+  # Column- venue names
+  # Using the full names of the venues
+  table_venues[[col_names[["venue_name"]]]] <- sapply(
+    X = table_venues[[col_names[["venue_name"]]]],
+    FUN = function(venue_name){
+      CONFIG$DICT_VENUE_NAMES[[venue_name]]
+    }
+  )
+
+  # Reordering the table
+  desired_order_cols <- unlist(col_names)
+  table_venues <- table_venues[, desired_order_cols]
+
+  return(table_venues)
+}
+
+#' Renders venues table in HTML format.
+#' Each venue name links to the register table for that specific
+#' venue. The ORCID IDs link to their ORCID pages.
+#' 
+#' @param list_venue_reg_tables The list of venue register tables. The indices are the ORCID IDs.
+render_table_venues_html <- function(list_venue_reg_tables){
+  col_names <- CONFIG$NON_REG_TABLE_COL_NAMES[["venues_table"]]
+
+  list_venue_names <- names(list_venue_reg_tables)
+  # Create initial data frame
+  table_venues <- data.frame(
+    matrix(ncol=0, nrow = length(list_venue_names)),
+    stringsAsFactors = FALSE, 
+    check.names = FALSE
+  )
+
+  table_venues[[col_names[["venue_name"]]]] <- list_venue_names
+
+  # Column- Venue type
+  table_venues[[col_names[["venue_type"]]]] <- sapply(
+    X = list_venue_names,
+    FUN = function(venue_name){
+      venue_type <- determine_venue_category(venue_name)
+      stringr::str_to_title(venue_type)
+    }
+  )
+
+  # Column- No. of codechecks
+  table_venues[[col_names[["no_codechecks"]]]] <- mapply(
+    FUN = function(venue_name, venue_type) {
+      no_codechecks <- nrow(list_venue_reg_tables[[venue_name]])
+      formatted_venue_type <- stringr::str_to_lower(venue_type)
+      formatted_venue_name <-  determine_venue_name(venue_name, venue_type)
+      paste0(no_codechecks," [(see all checks)](https://codecheck.org.uk/register/venues/",
+      formatted_venue_type, "/", formatted_venue_name, "/)")
+    },
+    venue_name = table_venues[[col_names[["venue_name"]]]],
+    venue_type = table_venues[[col_names[["venue_type"]]]]
+  )
+
+  # Column- venue names
+  # Each venue name will be a hyperlink to the register table
+  # with all their codechecks
+  table_venues[[col_names[["venue_name"]]]] <- mapply(
+    FUN = function(venue_name, venue_type){
+      if (is.null(CONFIG$DICT_VENUE_NAMES[[venue_name]])) {
+        return(venue_name)  # Handle cases where venue_name is not in CONFIG$DICT_VENUE_NAMES
+      }
+      formatted_venue_type <- stringr::str_to_lower(venue_type)
+      formatted_venue_name <-  determine_venue_name(venue_name, venue_type)
+      paste0("[", CONFIG$DICT_VENUE_NAMES[[venue_name]], "](https://codecheck.org.uk/register/venues/",
+            formatted_venue_type, "/", formatted_venue_name, "/)")
+    },
+    venue_name = table_venues[[col_names[["venue_name"]]]],
+    venue_type = table_venues[[col_names[["venue_type"]]]]
+  )
+
+  # Reordering the table
+  desired_order_cols <- unlist(col_names)
+  table_venues <- table_venues[, desired_order_cols]
+
+  return(table_venues)
+}

inst/extdata/config.R

@@ -6,11 +6,18 @@ CONFIG$REGISTER_COLUMNS <- list("Certificate", "Repository", "Type", "Issue", "R
 CONFIG$DIR_TEMP_REGISTER_CODECHECKER <- "docs/temp_register_codechecker.csv"
 
 # NON-REGISTER_TABLE
+# Note that the order of the names in the list will be the order of table columns in html and json
 CONFIG$NON_REG_TABLE_COL_NAMES <- list(
   "codechecker_table" = list(
     "codechecker" = "Codechecker name",
     "orcid" = "ORCID ID",
     "no_codechecks" = "No. of codechecks"
+  ),
+
+  "venues_table" = list(
+    "venue_type" = "Venue type", 
+    "venue_name" = "Venue name",
+    "no_codechecks" = "No. of codechecks"
   )
 )
 
@@ -38,3 +45,16 @@ CONFIG$TEMPLATE_DIR<- list(
     "md_template" = system.file("extdata", "templates/reg_tables/template.md", package = "codecheck")
   )
 )
+
+# DICT OF VENUE NAMES
+CONFIG$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"
+)