R/citation_quarto.R

In inbo/checklist: A Thorough and Strict Set of Checks for R Packages and Source Code

#' @importFrom assertthat assert_that is.string
#' @importFrom fs path
#' @importFrom yaml read_yaml
citation_quarto <- function(meta) {
  assert_that(inherits(meta, "citation_meta"))
  assert_that(meta$get_type == "quarto")
  index_file <- path(meta$get_path, "_quarto.yml")
  if (!is_file(index_file)) {
    return(
      list(
        errors = paste(index_file, "not found"), warnings = character(0),
        notes = character(0)
      )
    )
  }
  yaml <- read_yaml(index_file)
  language <- yaml$lang
  if (has_name(yaml, "flandersqmd")) {
    yaml <- yaml$flandersqmd
  } else if (has_name(yaml, "book")) {
    yaml <- yaml$book
  }
  yaml$lang <- coalesce(yaml$lang, language)
  read_organisation(meta$get_path) |>
    yaml_author(yaml = yaml) -> cit_meta
  description <- quarto_description(meta$get_path)
  cit_meta$meta$description <- description$description
  cit_meta$errors <- c(cit_meta$errors, description$errors)
  cit_meta$meta$title <- paste0(
    yaml$title,
    ifelse(has_name(yaml, "subtitle"), paste0(". ", yaml$subtitle, "."), ".")
  )
  if (has_name(yaml, "shorttitle")) {
    cit_meta$meta$shorttitle <- yaml$shorttitle
  }
  cit_meta$meta$upload_type <- "publication"
  if (has_name(yaml, "publication_date")) {
    cit_meta$meta$publication_date <- string2date(yaml$publication_date) |>
      format("%Y-%m-%d")
  }
  if (has_name(yaml, "embargo")) {
    cit_meta$meta$embargo_date <- string2date(yaml$embargo) |>
      format("%Y-%m-%d")
    cit_meta$meta$access_right <- "embargoed"
    if (!has_name(yaml, "publication_date")) {
      cit_meta$meta$publication_date <- cit_meta$meta$embargo_date
    }
  } else {
    cit_meta$meta$access_right <- "open"
  }
  license_file <- path(meta$get_path, "LICENSE.md")
  if (!is_file(license_file)) {
    cit_meta$errors <- c(cit_meta$errors, "No LICENSE.md file found")
  } else {
    license <- readLines(license_file)
    path("generic_template", "cc_by_4_0.md") |>
      system.file(package = "checklist") |>
      readLines() |>
      identical(license) -> license_ok
    if (license_ok) {
      cit_meta$meta$license <- "CC-BY-4.0"
    } else {
      cit_meta$errors <- c(
        cit_meta$errors, "LICENSE.md doesn't match with CC-BY-4.0 license"
      )
    }
  }
  if (has_name(yaml, "lang")) {
    cit_meta$meta$language <- yaml$lang
  }
  extra <- c(
    "community", "doi", "keywords", "publication_type", "publisher"
  )
  extra <- extra[extra %in% names(yaml)]
  cit_meta$meta <- c(cit_meta$meta, yaml[extra])
  publication_type <- c(
    "publication", "publication-annotationcollection", "publication-article",
    "publication-book", "publication-conferencepaper",
    "publication-conferenceproceeding", "publication-datamanagementplan",
    "publication-datapaper", "publication-deliverable",
    "publication-dissertation", "publication-journal", "publication-milestone",
    "publication-other", "publication-patent", "publication-peerreview",
    "publication-preprint", "publication-proposal", "publication-report",
    "publication-section", "publication-softwaredocumentation",
    "publication-standard", "publication-taxonomictreatment",
    "publication-technicalnote", "publication-thesis",
    "publication-workingpaper"
  )
  c(
    "No `keywords` element found"[!has_name(yaml, "keywords")],
    "No `publisher` element found"[!has_name(yaml, "publisher")],
    paste(
      "`publication_type` must be one of following:",
      paste(publication_type, collapse = ", "),
      sep = "\n"
    )[
      has_name(yaml, "publication_type") && is.string(yaml$publication_type) &&
        !yaml$publication_type %in% publication_type
    ]
  ) |>
    c(cit_meta$errors) -> cit_meta$errors
  c(
    "No `community` element found"[!has_name(yaml, "community")],
    "No `publication_type` element found"[!has_name(yaml, "publication_type")]
  ) |>
    c(cit_meta$notes) -> cit_meta$notes
  cit_meta$meta$community <- split_community(cit_meta$meta$community)
  return(cit_meta)
}


quarto_description <- function(path) {
  for (i in dir_ls(path, regexp = "\\.q?md$", recurse = TRUE)) {
    readLines(i) |>
      list() |>
      setNames("text") |>
      readme_description() -> description
    if (has_name(description, "meta") || length(description$errors) > 0) {
      break
    }
  }
  if (!has_name(description, "meta")) {
    description$errors <- c(
      description$errors,
      paste(
        "No description found.",
        "Use `<!-- description: start -->` and `<!-- description: end -->`.",
        "Place these tags around the abstract."
      )
    )
  }
  return(
    list(
      description = description$meta$description, errors = description$errors
    )
  )
}