Add feature to filter register by venue

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

@@ -70,7 +70,7 @@ jobs:
       - name: Check
         env:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "error", check_dir = "check")
         shell: Rscript {0}
 
       - name: Upload check results

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: codecheck
 Title: Helper Functions for CODECHECK Project
-Version: 0.1.0.9006
+Version: 0.2.0
 Authors@R: 
     c(person(given = "Stephen",
             family = "Eglen",
@@ -32,10 +32,11 @@ Imports:
     rorcid,
     osfr,
     httr,
-    zen4R
+    zen4R,
+    whisker
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.1
+RoxygenNote: 7.3.1
 VignetteBuilder: knitr
 Suggests: 
     tinytest,

NAMESPACE

@@ -36,6 +36,7 @@ importFrom(stringr,str_replace_all)
 importFrom(utils,capture.output)
 importFrom(utils,read.csv)
 importFrom(utils,tail)
+importFrom(whisker,whisker.render)
 importFrom(xtable,xtable)
 importFrom(yaml,read_yaml)
 importFrom(yaml,yaml.load)

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.
@@ -19,14 +25,27 @@
 #'
 #' @export
 register_render <- function(register = read.csv("register.csv", as.is = TRUE),
+                            filter_by = c("venues"),
                             outputs = c("html", "md", "json")) {
+  CONFIG$MD_TEMPLATE <- system.file("extdata", "templates/template_register.md", package = "codecheck")
+
   register_table <- preprocess_register(register)
 
-  md_columns_widths <- "|:-------|:--------------------------------|:------------------|:---|:--------------------------|:----------|"
+  # Creating list of of register tables with indices being the filter types
+  list_register_tables <- c()
+  list_register_tables[["none"]] <- list("original"= register_table)
+
+  if (length(filter_by)!=0){
+    # Creating filtered register csvs
+    create_filtered_register_csvs(filter_by, register)
+    # Creating and adding filtered registered tables to list of tables
+    list_register_tables <- add_filtered_register_tables(list_register_tables, register_table, filter_by)
+  }
 
-  if ("md" %in% outputs) render_register_md(register_table, md_columns_widths)
-  if ("html" %in% outputs) render_register_html(register_table, register, md_columns_widths)
-  if ("json" %in% outputs) render_register_json(register_table, register)
+  # 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)
 
   return(register_table)
 }
@@ -57,7 +76,7 @@ register_check <- function(register = read.csv("register.csv", as.is = TRUE),
 
     # check certificate IDs if there is a codecheck.yml
     codecheck_yaml <- get_codecheck_yml(entry$Repository)
-    check_certificate_id(codecheck_yaml)
+    check_certificate_id(entry, codecheck_yaml)
     check_issue_status(entry)
     cat("Completed checking registry entry", toString(register[i, "Certificate"]), "\n")
   }

R/utils_create_filtered_register_csvs.R

@@ -0,0 +1,82 @@
+#' Creates filtered register csv files
+#'
+#' Each csv file is saved in the appropriate output_dir.
+#'
+#' @param filter_by A vector of strings specifying the names of the columns to filter by.
+#' @param register A dataframe representing the register data to be filtered.
+create_filtered_register_csvs <- function(filter_by, register){
+
+  for (filter in filter_by){
+    column_name <- determine_filter_column_name(filter)
+    unique_values <- unique(register[[column_name]])
+
+    for (value in unique_values) {
+      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)
+      }
+
+      write.csv(filtered_register, output_dir, row.names=FALSE)
+    }    
+  }
+}
+
+#' Determines the register table's column name to filter the data by.
+#'
+#' @param filter The filter name
+#' @return The column name to filter by
+determine_filter_column_name <- function(filter) {
+  filter_column_name <- switch(filter,
+         "venues" = "Type",
+         NULL # Default case is set to NULL
+         )
+  if (is.null(filter_column_name)) {
+    stop(paste("Filter", filter, "is not recognized."))
+  }
+
+  return(filter_column_name)
+}
+
+#' Gets the output dir depending on the filter name and the value of the filtered column
+#'
+#' @param filter The filter name
+#' @param column_value The value of the column the filter applies to
+#' @return The directory to save files to
+get_output_dir <- function(filter, column_value) {
+  if (filter=="none"){
+    return(paste0("docs/"))
+  }
+
+  else if (filter=="venues"){
+    venue_category <- determine_venue_category(column_value)
+    # In case the venue_category itself has no further subgroups we do not need subgroups
+    if (venue_category==tolower(column_value)){
+      return(paste0("docs/", filter, "/", gsub(" ", "_", venue_category), "/"))
+    }
+
+    # 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)
+    return(paste0("docs/", filter, "/", venue_category, "/", venue_name, "/"))  }
+
+  else{
+    return(paste0("docs/", filter, "/", gsub(" ", "_", tolower(column_value)), "/"))
+  }
+}
+
+#' Determines the venue category based on the venue_name
+#'
+#' @param venue_name The venue_name obtained from the "Type" column of the register
+#' @return The venue category. If the venue does not belong to any category the venue_name is returned
+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, ignore.case=TRUE)) {
+      return(category)
+    }
+  }
+  warning(paste("Register venue", venue_name, "does not fall into any of the following venue categories:", toString(list_venue_categories)))
+  return(venue_name)
+}

R/utils_filter_register_table.R

@@ -0,0 +1,36 @@
+#' Function for adding filtered register tables to a list based on specified filters.
+#' Each entry in the resulting list is a filtered register table by the filter type provided.
+#'
+#' @param list_register_tables A list to store the filtered tables
+#' @param register_table The register table to filter
+#' @param filter_by A vector of strings specifying the filter types
+#' @return A list of filtered register tables
+add_filtered_register_tables <- function(list_register_tables, register_table, filter_by) {
+
+    for (filter in filter_by){
+        list_register_tables[[filter]] <- create_filtered_register_tables(register_table, filter)
+    }
+
+    return(list_register_tables)
+}
+
+#' Function for creating a list of register tables that is filtered based on the filter type.
+#' Each entry in the resulting list is the filtered register table with index corresponding to unique values in that column.
+#'
+#' @param register_table The register table
+#' @param filter The filter name
+#' @return A list of filtered register tables
+create_filtered_register_tables <- function(register_table, filter) {
+    list_filtered_register_tables <- list()
+
+    filter_column_name <- determine_filter_column_name(filter)
+    unique_values <- unique(register_table[[filter_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[[filter_column_name]]==value, ]
+        rownames(filtered_table) <- NULL  # Reset row names to remove row numbers
+        list_filtered_register_tables[[value]] <- filtered_table
+    }    
+
+    return(list_filtered_register_tables)
+}

R/utils_preprocess_register.R

@@ -11,12 +11,11 @@ register_clear_cache <- function() {
   unlink(path, recursive = TRUE)
 }
 
-#' Function for adding clickable links to the repor for each entry in the register table.
+#' Function for adding clickable links to the report for each entry in the register table.
 #' 
 #' @param register_table The register table
 #' @param register The register from the register.csv file
-#' @return register_table
-
+#' @return The adjusted register table
 add_report_links <- function(register_table, register) {
 
   reports <- c()
@@ -39,8 +38,7 @@ add_report_links <- function(register_table, register) {
 #' 
 #' @param register_table The register table
 #' @param register The register from the register.csv file
-#' @return register_table
-
+#' @return The adjusted register table
 add_issue_number_links <- function(register_table, register) {
   register_table$Issue <- sapply(
     X = register$Issue,
@@ -60,53 +58,11 @@ add_issue_number_links <- function(register_table, register) {
   return(register_table)
 }
 
-#' Function for adding repository links to each report in the register table.
-#' 
-#' @param register_table The register table
-#' @param register The register from the register.csv file
-#' @return register_table
-
-add_repository_links <- function(register_table, register) {
-  register_table$Repository <- sapply(
-    X = register$Repository,
-    FUN = function(repository) {
-      spec <- parse_repository_spec(repository)
-      if (!any(is.na(spec))) {
-        urrl <- "#"
-
-        switch(spec["type"],
-          "github" = {
-            urrl <- paste0("https://github.com/", spec[["repo"]])
-            paste0("[", spec[["repo"]], "](", urrl, ")")
-          },
-          "osf" = {
-            urrl <- paste0("https://osf.io/", spec[["repo"]])
-            paste0("[", spec[["repo"]], "](", urrl, ")")
-          },
-          "gitlab" = {
-            urrl <- paste0("https://gitlab.com/", spec[["repo"]])
-            paste0("[", spec[["repo"]], "](", urrl, ")")
-          },
-
-          # Type is none of the above
-          {
-            repository
-          }
-        )
-      } else {
-        repository
-      }
-    }
-  )
-  return(register_table)
-}
-
 #' Function for adding check time to each report in the register table.
 #' 
 #' @param register_table The register table
 #' @param register The register from the register.csv file
-#' @return register_table
-
+#' @return The adjusted register table
 add_check_time <- function(register_table, register) {
   check_times <- c()
 
@@ -127,16 +83,13 @@ add_check_time <- function(register_table, register) {
   return(register_table)
 }
 
-#' Function for preprocessing the register to create and return the register_table.
-#' 
-#' @param register_table The register table
-#' @return register_table
-
+#' Function for preprocessing the register to create and return the preprocessed register table.
+#' @param register The register
+#' @return The preprocessed register table
 preprocess_register <- function(register) {
     register_table <- register
     register_table <- add_report_links(register_table, register)
     register_table <- add_issue_number_links(register_table, register)
-    register_table <- add_repository_links(register_table, register)
     register_table <- add_check_time(register_table, register)
     return(register_table)
 }

R/utils_register_check.R

@@ -2,9 +2,9 @@
 #' If there is a mismatch a stop is sent. Else a warning is thrown.
 #' 
 #' @param codecheck_yaml The codecheck yaml file
+#' @param entry The registry entry
 #' @return None
-
-check_certificate_id <- function(codecheck_yaml) {
+check_certificate_id <- function(entry, codecheck_yaml) {
   # Codecheck.yml found, proceeding to check certificate id
   if (!is.null(codecheck_yaml)) {
     # validate config file
@@ -30,7 +30,6 @@ check_certificate_id <- function(codecheck_yaml) {
 #' 
 #' @param entry The codecheck entry
 #' @return None
-
 check_issue_status <- function(entry) {
   if (!is.na(entry$Issue)) {
     # get the status and labels from an issue