Replace registry repository column (#66)

* Add preprocessing fn add-paper-links

* Remove add repository link function

* Update register columns and filter column function

* Add check for url in paper reference

* Change stop to warning in codecheck validation

* Remove extra lines in paper titles and links

* Fix render_register_md

* Removed add_repository_links_md

* Updating documentation with Roxygen

* align list entries for readability

* Remove loading config in register_check

* Replace preprocess next with if else

* Add render_register output_type default

* Add config$register_columns for html and md

* increase "check date" column width

* Adjust register paper title column width

* Update function documentation

* test github job run without cache

* Revert changes to workflow file

* Fix failing tests

* Bump version

---------

Co-authored-by: Daniel Nüst <[email protected]>

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: codecheck
 Title: Helper Functions for CODECHECK Project
-Version: 0.8.0
+Version: 0.9.0
 Authors@R: 
     c(person(given = "Stephen",
             family = "Eglen",

R/configuration.R

@@ -78,10 +78,7 @@ get_codecheck_yml_osf <- function(x) {
 #' @importFrom httr GET content
 #' @importFrom yaml yaml.load
 get_codecheck_yml_gitlab <- function(x) {
-  # Loading config.R file which is needed for the hyperlink
-  source(system.file("extdata", "config.R", package = "codecheck"))
-
-  link <- paste0(CONFIG$HYPERLINKS[["gitlab"]], x, "/-/raw/main/codecheck.yml?inline=false")
+  link <- paste0("https://gitlab.com/", x, "/-/raw/main/codecheck.yml?inline=false")
   response <- httr::GET(link)
 
   if (response$status == 200) {
@@ -189,6 +186,12 @@ validate_codecheck_yml <- function(configuration) {
   # the report MUST be a valid DOI
   assertthat::assert_that(codecheck_yml$report %in% rorcid::check_dois(codecheck_yml$report)$good,
                           msg = paste0(codecheck_yml$report, " is not a valid DOI"))
+
+  # Check if the paper_link contains a valid URL. We only check that it starts with https?://
+  url_regex <- "^https?://"
+  if (!grepl(url_regex, codecheck_yml$paper$reference)) {
+    warning("The paper reference in the codecheck.yml is not a valid URL")
+  } 
 
   # if ORCID are used, they must be without URL prefix and valid form, actual checking requires login, see #11
   orcid_regex <- "^(\\d{4}\\-\\d{4}\\-\\d{4}\\-\\d{3}(\\d|X))$"

R/register.R

@@ -59,6 +59,9 @@ register_render <- function(register = read.csv("register.csv", as.is = TRUE),
 register_check <- function(register = read.csv("register.csv", as.is = TRUE),
                            from = 1,
                            to = nrow(register)) {
+  # Loading config.R file
+  source(system.file("extdata", "config.R", package = "codecheck"))
+
   for (i in seq(from = from, to = to)) {
     cat("Checking", toString(register[i, ]), "\n")
     entry <- register[i, ]

R/utils_create_filtered_register_csvs.R

@@ -43,7 +43,7 @@ create_filtered_reg_csvs <- function(register, filter_by){
       register_key <- register_keys[[filter_col_name]][i]
       filtered_register <- filtered_register_list[[i]]
       table_details <- generate_table_details(register_key, filtered_register, filter)
-      filtered_register <- filter_and_drop_register_columns(filtered_register, filter)
+      filtered_register <- filter_and_drop_register_columns(filtered_register, filter, file_type = "csv")
       output_dir <- paste0(table_details[["output_dir"]], "register.csv")
       write.csv(filtered_register, output_dir, row.names=FALSE)
     }

R/utils_preprocess_register.R

@@ -11,6 +11,51 @@ register_clear_cache <- function() {
   unlink(path, recursive = TRUE)
 }
 
+#' Function for adding clickable links to the paper for each entry in the register table.
+#' 
+#' @param register_table The register table
+#' @param register The register from the register.csv file
+#' @return The adjusted register table
+add_paper_links <- function(register_table, register){
+  list_hyperlinks <- c()
+
+  # Looping over the entries in the register
+  for (i in seq_len(nrow(register))) {
+    # Retrieving the link to the paper 
+    config_yml <- get_codecheck_yml(register[i, ]$Repo)
+    paper_link <- config_yml[["paper"]][["reference"]]
+    paper_title <- config_yml[["paper"]][["title"]]
+
+    # Removing new lines from paper title and link
+    paper_title <- gsub("\n", " ", paper_title)
+    paper_link <- gsub("\n$", "", paper_link)
+
+    # Checking if there is a valid url for the paper. If not we just add the title as it is
+    url_regex <- "^https?://"
+    if (!grepl(url_regex, paper_link)){
+      warning("The codecheck_yml's paper reference is not a valid url.")
+      list_hyperlinks <- c(list_hyperlinks, paper_title)
+    }
+
+    # If we have a valid url we add hyperlink
+    else{
+      paper_hyperlink <- paste0(
+        "[",
+        paper_title,
+        "](",
+        paper_link,
+        ")"
+      )
+      list_hyperlinks <- c(list_hyperlinks, paper_hyperlink)
+    }
+  }
+  # Creating a new "Paper Title" column and moving it next to the "Repository" column
+  register_table <- register_table %>% 
+    mutate(`Paper Title` = list_hyperlinks) %>%
+    relocate(`Paper Title`, .after = Repository)
+  return(register_table)
+}
+
 #' Function for adding clickable links to the report for each entry in the register table.
 #' 
 #' @param register_table The register table
@@ -144,5 +189,6 @@ preprocess_register <- function(register, filter_by) {
     register_table <- add_report_links(register_table, register)
     register_table <- add_issue_number_links(register_table, register)
     register_table <- add_check_time(register_table, register)
+    register_table <- add_paper_links(register_table, register)
     return(register_table)
 }

R/utils_render_register_general.r

@@ -10,7 +10,6 @@ create_original_register_files <- function(register_table, outputs){
   for (output_type in outputs){
     table_details <- list(is_reg_table = TRUE)
     table_details[["output_dir"]] <- generate_output_dir(filter, table_details)
-    register_table <- filter_and_drop_register_columns(register_table, filter)
     render_register(register_table, table_details, filter, output_type)
   }
 }
@@ -30,7 +29,6 @@ create_register_files <- function(register_table, filter_by, outputs){
 
   # Creating the original register file
   create_original_register_files(register_table, outputs)
-
   # Generating filtered register table files
   # For each filter type we created the nested register tables first
   for (filter in filter_by){
@@ -58,7 +56,6 @@ create_register_files <- function(register_table, filter_by, outputs){
 
     # Get the group names (keys) based on the filter names
     register_keys <- grouped_registers %>% group_keys()
-
     # Looping over each of the output types
     for (output_type in outputs){
       for (i in seq_along(filtered_register_list)) {
@@ -68,8 +65,6 @@ create_register_files <- function(register_table, filter_by, outputs){
 
         table_details <- generate_table_details(register_key, filtered_table, filter)
 
-        # Dropping columns that are redundant
-        filtered_table <- filter_and_drop_register_columns(filtered_table, filter)
         render_register(filtered_table, table_details, filter, output_type)
       }
     }
@@ -84,12 +79,14 @@ create_register_files <- function(register_table, filter_by, outputs){
 #'
 #' @param register_table The register table
 #' @param filter A string specifying the filter to apply (e.g., "venues", "codecheckers").
+#' @param file_type The type of file we need to render the register for. 
+#'        The columns to keep depend on the file type
 #'
 #' @return The filtered register table with only the necessary columns retained.
-filter_and_drop_register_columns <- function(register_table, filter) {
+filter_and_drop_register_columns <- function(register_table, filter, file_type) {
 
   # Step 1: Columns that we want to keep
-  columns_to_keep <- CONFIG$REGISTER_COLUMNS
+  columns_to_keep <- CONFIG$REGISTER_COLUMNS[[file_type]]
 
   # Initialize final columns to columns_to_keep in case no filter is applied
   final_columns <- intersect(columns_to_keep, names(register_table))
@@ -149,10 +146,13 @@ generate_table_details <- function(table_key, table, filter, is_reg_table = TRUE
 #' @param register_table The register table that needs to be rendered into different files.
 #' @param table_details A list of details related to the table (e.g., output directory, metadata).
 #' @param filter A string specifying the filter applied to the register data.
-#' @param output_type A string specifying the desired output format ("md" for Markdown, "html" for HTML, "json" for JSON).
+#' @param output_type A string specifying the desired output format "json" for JSON, 
+#'        "csv" for CSVs, "md" for MD and "html" for HTMLs.
 #'
 #' @return None. The function generates a file in the specified format.
 render_register <- function(register_table, table_details, filter, output_type){
+  register_table <- filter_and_drop_register_columns(register_table, filter, output_type)
+
   switch(output_type,
     "md" = render_register_md(register_table, table_details, filter),
     "html" = render_html(register_table, table_details, filter),

R/utils_render_register_htmls.R

@@ -1,35 +1,3 @@
-#' Function for adding repository links in the register table for the creation of the html file.
-#' 
-#' @param register_table The register table
-#' @return Register table with adjusted repository links
-add_repository_links_html <- function(register_table) {
-  register_table$Repository <- sapply(
-    X = register_table$Repository,
-    FUN = function(repository) {
-      spec <- parse_repository_spec(repository)
-      # ! Needs refactoring
-      if (!any(is.na(spec))) {
-        urrl <- "#"
-        if (spec[["type"]] == "github") {
-          urrl <- paste0(CONFIG$HYPERLINKS[["github"]], spec[["repo"]])
-          paste0("<i class='fa fa-github'></i>&nbsp;[", spec[["repo"]], "](", urrl, ")")
-        } else if (spec[["type"]] == "osf") {
-          urrl <- paste0(CONFIG$HYPERLINKS[["osf"]], spec[["repo"]])
-          paste0("<i class='ai ai-osf'></i>&nbsp;[", spec[["repo"]], "](", urrl, ")")
-        } else if (spec[["type"]] == "gitlab") {
-          urrl <- paste0(CONFIG$HYPERLINKS[["gitlab"]], spec[["repo"]])
-          paste0("<i class='fa fa-gitlab'></i>&nbsp;[", spec[["repo"]], "](", urrl, ")")
-        } else {
-          repository
-        }
-      } else {
-        repository
-      }
-    }
-  )
-  return(register_table)
-}
-
 #' Dynamically generates a html_document.yml with the full paths to the index header, prefix 
 #' and postfix.html files. 
 #' 
@@ -164,7 +132,8 @@ render_html <- function(table, table_details, filter){
 
   # Creating md file from which HTML file is made
   if (table_details[["is_reg_table"]]){
-    render_register_md(table, table_details, filter, for_html_file = TRUE)
+    table_details[["for_html_file"]] <- TRUE
+    render_register_md(table, table_details, filter)
   }
 
   else{

R/utils_render_register_mds.R

@@ -23,79 +23,19 @@ add_markdown_title <- function(table_details, md_table, filter){
   return(md_table)
 }
 
-#' Function for adding repository links in the register table for the creation of the markdown file.
-#' 
-#' @param register_table The register table
-#' @return Register table with adjusted repository links
-add_repository_links_md <- function(register_table) {
-  register_table$Repository <- sapply(
-    X = register_table$Repository,
-    FUN = function(repository) {
-      spec <- parse_repository_spec(repository)
-      if (!any(is.na(spec))) {
-        urrl <- "#"
-        # ! Needs refactoring
-        switch(spec["type"],
-          "github" = {
-            urrl <- paste0(CONFIG$HYPERLINKS[["github"]], spec[["repo"]])
-            paste0("[", spec[["repo"]], "](", urrl, ")")
-          },
-          "osf" = {
-            urrl <- paste0(CONFIG$HYPERLINKS[["osf"]], spec[["repo"]])
-            paste0("[", spec[["repo"]], "](", urrl, ")")
-          },
-          "gitlab" = {
-            urrl <- paste0(CONFIG$HYPERLINKS[["gitlab"]], spec[["repo"]])
-            paste0("[", spec[["repo"]], "](", urrl, ")")
-          },
-
-          # Type is none of the above
-          {
-            repository
-          }
-        )
-      } else {
-        repository
-      }
-    }
-  )
-  return(register_table)
-}
-
 #' Renders register md for a single register_table
 #' 
 #' @param register_table The register table
 #' @param table_details List containing details such as the table name, subcat name.
 #' @param filter The filter
-#' @param for_html_file Flag for whether we are rendering register md for html file.
-#' Set to FALSE by default. If TRUE, no repo links are added to the repository table.
-render_register_md <- function(register_table, table_details, filter, for_html_file=FALSE) {
-
-  # If rendering md for html file, we add repo links of the appropriate format
-  register_table <- if (for_html_file) {
-    add_repository_links_html(register_table)
-  } else {
-    add_repository_links_md(register_table)
-  }
+render_register_md <- function(register_table, table_details, filter) {
 
   # Fill in the content
   md_table <- create_md_table(register_table, table_details, filter)
   output_dir <- table_details[["output_dir"]]
-  save_md_table(output_dir, md_table, for_html_file)
-}
 
-#' Save markdown table to a file
-#'
-#' The file is saved as either a temporary file (`temp.md`) or as `register.md` depending on 
-#' whether it is being rendered for an HTML file.
-#'
-#' @param output_dir The output_dir
-#' @param md_table The markdown table to be saved.
-#' @param for_html_file A logical flag indicating whether the markdown is being rendered for an HTML file. 
-#'        If TRUE, the file is saved as `temp.md`. Default is FALSE.
-save_md_table <- function(output_dir, md_table, for_html_file){
-  # If rendering md for html file we create a temp file
-  if (for_html_file){
+  # Saving the md file
+  if ("for_html_file" %in% names(table_details)){
     output_dir <- paste0(output_dir, "temp.md")
   }
 

R/utils_render_table_non_registers.R

@@ -80,7 +80,7 @@ generate_table_details_non_reg <- function(table, filter, subcat = NULL){
 #' Generates postfix hrefs for the venues/ codecheckers list pages
 #' 
 #' @param filter The filter being used such as "venues" or "codecheckers"
-#' @param table_details
+#' @param table_details A list of metadata about the table (e.g., title, subtext, extra text).
 #' @return A list of the hrefs.
 generate_html_postfix_hrefs_non_reg <- function(filter, table_details){  
   # Case we do not have subcat

inst/extdata/config.R

@@ -7,7 +7,7 @@ CONFIG <- new.env()
 # For filters other than venues we use the general column widths
 CONFIG$MD_TABLE_COLUMN_WIDTHS <- list(
   reg = list(
-    general = "|:-------|:--------------------------------|:------------------|:------------------|:---|:--------------------------|:----------|",
+    general = "|:-------|:---------------------------------------------|:------------------|:------------------|:---|:--------------------------|:------------------|",
     venues = "|:-------|:--------------------------------|:---|:--------------------------|:----------|"
   ),
 
@@ -18,7 +18,14 @@ CONFIG$MD_TABLE_COLUMN_WIDTHS <- list(
   )
 )
 
-CONFIG$REGISTER_COLUMNS <- list("Certificate", "Repository", "Type", "Venue", "Issue", "Report", "Check date")
+# These are the columns to keep in the register table
+CONFIG$REGISTER_COLUMNS <- list(
+  html = c("Certificate", "Paper Title", "Type", "Venue", "Issue", "Report", "Check date"),
+  md = c("Certificate", "Paper Title", "Type", "Venue", "Issue", "Report", "Check date"),
+  csv =   c("Certificate", "Repository", "Type", "Venue", "Issue", "Report", "Check date"),
+  json =  c("Certificate", "Repository", "Type", "Venue", "Issue", "Report", "Check date")
+)
+
 CONFIG$DIR_TEMP_REGISTER_CODECHECKER <- "docs/temp_register_codechecker.csv"
 CONFIG$FILTER_COLUMN_NAMES <- list(
   "venues" = "Venue",

inst/extdata/templates/codecheck.yml

@@ -9,9 +9,7 @@ paper:
     - name: Roland J. Baddeley
     - name: Leslie S. Smith
       ORCID: 0000-0002-3716-8013
-  reference: >
-    Network (1992) 3:61-70
-    http://pdfs.semanticscholar.org/7dcf/a42cfe3b59becb441844b72558b361693608.pdf
+  reference: http://pdfs.semanticscholar.org/7dcf/a42cfe3b59becb441844b72558b361693608.pdf
 
 manifest:
   - file: Figure2.png

inst/tinytest/yaml/author_name_missing/codecheck.yml

@@ -9,9 +9,7 @@ paper:
     - name: Roland J. Baddeley
     - n: Leslie S. Smith
       ORCID: 0000-0002-3716-8013
-  reference: >
-    Network (1992) 3:61-70
-    http://pdfs.semanticscholar.org/7dcf/a42cfe3b59becb441844b72558b361693608.pdf
+  reference: http://pdfs.semanticscholar.org/7dcf/a42cfe3b59becb441844b72558b361693608.pdf
 
 manifest:
   - file: Figure2.png

inst/tinytest/yaml/codecheck.yml

@@ -9,9 +9,7 @@ paper:
     - name: Roland J. Baddeley
     - name: Leslie S. Smith
       ORCID: 0000-0002-3716-8013
-  reference: >
-    Network (1992) 3:61-70
-    http://pdfs.semanticscholar.org/7dcf/a42cfe3b59becb441844b72558b361693608.pdf
+  reference: http://pdfs.semanticscholar.org/7dcf/a42cfe3b59becb441844b72558b361693608.pdf
 
 manifest:
   - file: Figure2.png

inst/tinytest/yaml/codechecker_name_missing/codecheck.yml

@@ -9,9 +9,7 @@ paper:
     - name: Roland J. Baddeley
     - name: Leslie S. Smith
       ORCID: 0000-0002-3716-8013
-  reference: >
-    Network (1992) 3:61-70
-    http://pdfs.semanticscholar.org/7dcf/a42cfe3b59becb441844b72558b361693608.pdf
+  reference: http://pdfs.semanticscholar.org/7dcf/a42cfe3b59becb441844b72558b361693608.pdf
 
 manifest:
   - file: Figure2.png

inst/tinytest/yaml/repository_url_invalid/codecheck-valid.yml

@@ -9,9 +9,7 @@ paper:
     - name: Roland J. Baddeley
     - name: Leslie S. Smith
       ORCID: 0000-0002-3716-8013
-  reference: >
-    Network (1992) 3:61-70
-    http://pdfs.semanticscholar.org/7dcf/a42cfe3b59becb441844b72558b361693608.pdf
+  reference: http://pdfs.semanticscholar.org/7dcf/a42cfe3b59becb441844b72558b361693608.pdf
 
 manifest:
   - file: Figure2.png