feat: add report list generation

Refs #4

DESCRIPTION

@@ -11,6 +11,7 @@ RoxygenNote: 7.3.1
 Imports:
     bookdown,
     config,
+    dplyr,
     gert,
     httr,
     jsonlite,

NAMESPACE

@@ -8,6 +8,7 @@ export(create_fairify)
 export(create_reports)
 export(getDataPath)
 export(iconv_filename)
+export(list_reports)
 export(loadConfig)
 export(mermaid)
 export(mermaid_gen_link)
@@ -19,3 +20,4 @@ export(updateMermaid)
 export(update_fairify)
 import(utils)
 importFrom(magrittr,"%>%")
+importFrom(stats,setNames)

R/list_reports.R

+#' List reports with headers
+#'
+#' @param reports_dir [character] path for the reports
+#' @param reports [character] subfolders containing each report. By default,
+#' reports are folders in `reports_dir` that match `pattern`
+#' @param pattern [character] regex pattern for filtering report directories in
+#' `reports_dir` folder (ignored if `reports` is provided)
+#' @param index [character] name of the report index file
+#'
+#' @return A [data.frame] containing one row by report found. Each row contain the following columns:
+#'
+#'  - `report`: the folder name of the report
+#'  - `path`: the full path of the report folder
+#'  - and all the metadata located in the header of the report index file: `title`, `author`, ...
+#'
+#' @importFrom stats setNames
+#' @export
+#'
+list_reports <- function(reports_dir = file.path(pkgload::pkg_path(), "reports"),
+                         reports = list.dirs(reports_dir, full.names = FALSE, recursive = FALSE),
+                         index = "index.Rmd") {
+
+  paths <- setNames(file.path(reports_dir, reports), reports)
+  l <- lapply(paths, get_report_header)
+  df <- do.call(dplyr::bind_rows, l)
+  df <- cbind(report = reports, path = paths, df)
+  return(df)
+}
+
+
+#' Get report header
+#'
+#' @param path path of the report
+#' @inheritParams list_reports
+#'
+#' @return A [list] with header of the report index file
+#' @noRd
+#'
+get_report_header <- function(path, index = "index.Rmd") {
+  l <- read_rmd(file.path(path, index))
+  return(l$header)
+}
+
+
+#' @noRd
+#'
+#' @title Read R-markdown Documents
+#'
+#' @description
+#' Import Rmd files into objects of class [rmd_doc-class].
+#'
+#' The function `txt_body()` add a line break at the end of each element of a
+#' character vector considering them as single lines.
+#'
+#' Note that comments will be deleted in the input file.
+#'
+#' @param file Character value indicating the path and the name to the Rmd file.
+#' @param ... Arguments passed by `read_rmd()` to [readLines()].
+#'     In `txt_body()` they are character values passed to `c()`.
+#' @param skip_head Logical value indicating whether the yaml head should be
+#'     skip or not (this argument is not used at the moment).
+#'
+#' @return
+#' The function `read_rmd()` returns a [rmd_doc-class] object.
+#' The function `txt_body()`, a character vector suitable for the parameter
+#' `body` in the function [write_rmd()].
+#'
+#' @examples
+#' \dontrun{
+#' ## Read pre-installed example
+#' ex_document <- read_rmd(file.path(
+#'   path.package("yamlme"),
+#'   "taxlistjourney.Rmd"
+#' ))
+#' }
+#' @source https://github.com/kamapu/yamlme/blob/master/R/read_rmd.R
+read_rmd <- function(file, ..., skip_head = FALSE) {
+  file <- txt_body(readLines(file, ...))
+  if (substr(file[1], 1, 3) != "---") {
+    message("Rmd file seems to be headless")
+    yaml_head <- list(body = file)
+  } else {
+    idx <- cumsum(grepl("---", file, fixed = TRUE))
+    yaml_head <- list(header = yaml::yaml.load(paste0(file[idx == 1], collapse = "")))
+    yaml_head$body <- file[idx > 1][-1]
+  }
+  if (skip_head) {
+    yaml_head$header <- NULL
+  }
+  class(yaml_head) <- c("rmd_doc", "list")
+  return(yaml_head)
+}
+
+#' @noRd
+txt_body <- function(...) {
+  return(paste0(c(...), "\n"))
+}

R/render_reports.R

@@ -15,7 +15,7 @@
 #'
 #' @example man-examples/render_reports.R
 #'
-render_reports <- function(reports_dir = "./reports",
+render_reports <- function(reports_dir = file.path(pkgload::pkg_path(), "reports"),
                            reports = list.dirs(reports_dir, full.names = FALSE, recursive = FALSE),
                            publish_dir = "../../public/reports",
                            ...) {

man/list_reports.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/list_reports.R
+\name{list_reports}
+\alias{list_reports}
+\title{List reports with headers}
+\usage{
+list_reports(
+  reports_dir = file.path(pkgload::pkg_path(), "reports"),
+  reports = list.dirs(reports_dir, full.names = FALSE, recursive = FALSE),
+  index = "index.Rmd"
+)
+}
+\arguments{
+\item{reports_dir}{\link{character} path for the reports}
+
+\item{reports}{\link{character} subfolders containing each report. By default,
+reports are folders in \code{reports_dir} that match \code{pattern}}
+
+\item{index}{\link{character} name of the report index file}
+
+\item{pattern}{\link{character} regex pattern for filtering report directories in
+\code{reports_dir} folder (ignored if \code{reports} is provided)}
+}
+\value{
+A \link{data.frame} containing one row by report found. Each row contain the following columns:
+\itemize{
+\item \code{report}: the folder name of the report
+\item \code{path}: the full path of the report folder
+\item and all the metadata located in the header of the report index file: \code{title}, \code{author}, ...
+}
+}
+\description{
+List reports with headers
+}

man/render_reports.Rd

@@ -14,7 +14,7 @@ render_report(
 )
 
 render_reports(
-  reports_dir = "./reports",
+  reports_dir = file.path(pkgload::pkg_path(), "reports"),
   reports = list.dirs(reports_dir, full.names = FALSE, recursive = FALSE),
   publish_dir = "../../public/reports",
   ...