R/utils-zip-cleanup.R

In eyeris: Flexible, Extensible, & Reproducible Pupillometry Preprocessing

#' Zip and cleanup source figure files
#'
#' Creates zip files for all PNG and JPG files in each run directory under
#' source/figures/, then deletes the individual image files. This reduces
#' file count while preserving all figure data in compressed format.
#'
#' @param report_path Path to the report directory containing source/figures/
#' @param eye_suffix Optional eye suffix for binocular data
#' @param verbose Whether to print verbose output
#'
#' @return List of created zip file paths
#'
#' @keywords internal
zip_and_cleanup_source_figures <- function(
  report_path,
  eye_suffix = NULL,
  verbose = FALSE
) {
  figures_dir <- file.path(report_path, "source", "figures")

  if (!dir.exists(figures_dir)) {
    log_warn(
      "Source figures directory not found: {figures_dir}",
      verbose = verbose
    )
    return(NULL)
  }

  # find all run dirs (run-01, run-02, task-study_run-01, etc.)
  run_dirs <- list.dirs(figures_dir, full.names = TRUE, recursive = FALSE)
  run_dirs <- run_dirs[grepl(run_dir_pattern(), basename(run_dirs))]

  if (length(run_dirs) == 0) {
    log_info("No run directories found in: {figures_dir}", verbose = verbose)
    return(NULL)
  }

  created_zips <- c()

  for (run_dir in run_dirs) {
    run_name <- basename(run_dir)

    # remove existing zip files if they exist (for reprocessing)
    zip_filename <- run_name
    if (!is.null(eye_suffix)) {
      zip_filename <- paste0(zip_filename, "_", eye_suffix)
    }
    zip_filename <- paste0(zip_filename, ".zip")
    existing_zip_path <- file.path(figures_dir, zip_filename)
    if (file.exists(existing_zip_path)) {
      unlink(existing_zip_path)
      log_info("Removed existing zip file: {zip_filename}", verbose = verbose)
    }

    image_files <- list.files(
      run_dir,
      pattern = "\\.(png|jpg|jpeg)$",
      ignore.case = TRUE,
      full.names = TRUE,
      recursive = FALSE
    )

    # filter by eye_suffix if provided
    if (!is.null(eye_suffix)) {
      image_files <- image_files[grepl(eye_suffix, image_files)]
    }

    if (length(image_files) == 0) {
      log_info("No image files found in: {run_dir}", verbose = verbose)
      next
    }

    zip_filename <- run_name
    if (!is.null(eye_suffix)) {
      zip_filename <- paste0(zip_filename, "_", eye_suffix)
    }
    zip_filename <- paste0(zip_filename, ".zip")
    zip_path <- file.path(figures_dir, zip_filename)

    tryCatch(
      {
        # change to run dir to create relative paths in zip
        current_dir <- getwd()
        setwd(run_dir)

        relative_files <- c()
        for (file in image_files) {
          rel_path <- gsub(paste0("^", run_dir, "/"), "", file)
          if (file.exists(rel_path)) {
            relative_files <- c(relative_files, rel_path)
          }
        }

        if (length(relative_files) > 0) {
          utils::zip(zip_filename, files = relative_files, flags = "-r9X")

          if (file.exists(zip_filename)) {
            # move zip file to parent figures directory
            final_zip_path <- file.path(figures_dir, zip_filename)
            file.rename(zip_filename, final_zip_path)
            created_zips <- c(created_zips, final_zip_path)

            log_success(
              "Created {zip_filename} with {length(relative_files)} images",
              verbose = verbose
            )
          }
        }

        setwd(current_dir)
        # remove the entire run directory after successful zip creation
        if (!is.null(final_zip_path) && file.exists(final_zip_path)) {
          unlink(run_dir, recursive = TRUE)
          log_success("Removed run directory: {run_name}", verbose = verbose)
        }
      },
      error = function(e) {
        tryCatch(
          setwd(current_dir), # finally return to original directory
          error = function(setwd_error) {
            log_warn(
              "Failed to return to original directory: {setwd_error$message}",
              verbose = verbose
            )
          }
        )
        log_warn(
          "Failed to create zip for {run_name}: {e$message}",
          verbose = verbose
        )
      }
    )
  }

  return(created_zips)
}

#' Clean up source figures after report generation
#'
#' Removes the entire source/figures directory after the main HTML report has
#' been generated since all images are now embedded in the HTML as data URLs.
#'
#' @param report_path Path to the report directory
#' @param eye_suffix Optional eye suffix for binocular data (unused but kept for compatibility)
#' @param verbose Whether to print verbose output
#'
#' @return Invisibly returns TRUE if cleanup was successful, FALSE otherwise
#'
#' @keywords internal
cleanup_source_figures_post_render <- function(
  report_path,
  eye_suffix = NULL,
  verbose = FALSE
) {
  log_info(
    "Starting post-render cleanup of source figure files...",
    verbose = verbose
  )

  figures_dir <- file.path(report_path, "source", "figures")

  if (!dir.exists(figures_dir)) {
    log_info(
      "Source figures directory not found: {figures_dir}",
      verbose = verbose
    )
    return(invisible(FALSE))
  }

  # first clean up individual JPG/PNG files in run directories
  cleanup_run_dir_images(report_path, eye_suffix, verbose)

  tryCatch(
    {
      unlink(figures_dir, recursive = TRUE)
      log_success(
        "Removed entire source/figures directory (images embedded in HTML)",
        verbose = verbose
      )
      return(invisible(TRUE))
    },
    error = function(e) {
      log_warn(
        "Failed to remove source/figures directory: {e$message}",
        verbose = verbose
      )
      return(invisible(FALSE))
    }
  )
}

#' Clean up individual image files in run directories after HTML generation
#'
#' Removes PNG and JPG files from the root of source/figures/run-xx directories
#' after all HTML reports have been generated. This cleans up loose image files
#' that may have been created during report generation.
#'
#' @param report_path Path to the report directory containing source/figures/
#' @param eye_suffix Optional eye suffix for binocular data
#' @param verbose Whether to print verbose output
#'
#' @return Invisibly returns TRUE if cleanup was successful, FALSE otherwise
#'
#' @keywords internal
cleanup_run_dir_images <- function(
  report_path,
  eye_suffix = NULL,
  verbose = FALSE
) {
  log_info(
    "Cleaning up individual image files in run directories...",
    verbose = verbose
  )

  figures_dir <- file.path(report_path, "source", "figures")

  if (!dir.exists(figures_dir)) {
    log_info(
      "Source figures directory not found: {figures_dir}",
      verbose = verbose
    )
    return(invisible(FALSE))
  }

  # find all run dirs (run-01, run-02, task-study_run-01, etc.)
  run_dirs <- list.dirs(figures_dir, full.names = TRUE, recursive = FALSE)
  run_dirs <- run_dirs[grepl(run_dir_pattern(), basename(run_dirs))]

  if (length(run_dirs) == 0) {
    log_info("No run directories found in: {figures_dir}", verbose = verbose)
    return(invisible(TRUE))
  }

  total_files_removed <- 0

  for (run_dir in run_dirs) {
    run_name <- basename(run_dir)

    # find image files in the root of the run directory (not in subdirectories)
    image_files <- list.files(
      run_dir,
      pattern = "\\.(png|jpg|jpeg)$",
      ignore.case = TRUE,
      full.names = TRUE,
      recursive = FALSE
    )

    # optionally filter by eye_suffix
    if (!is.null(eye_suffix)) {
      image_files <- image_files[grepl(eye_suffix, image_files)]
    }

    if (length(image_files) > 0) {
      tryCatch(
        {
          unlink(image_files)
          total_files_removed <- total_files_removed + length(image_files)
          log_success(
            "Removed {length(image_files)} image files from {run_name}",
            verbose = verbose
          )
        },
        error = function(e) {
          log_warn(
            "Failed to remove image files from {run_name}: {e$message}",
            verbose = verbose
          )
        }
      )
    } else {
      log_info("No image files found in root of: {run_name}", verbose = verbose)
    }
  }

  if (total_files_removed > 0) {
    log_success(
      "Total image files removed: {total_files_removed}",
      verbose = verbose
    )
  }

  return(invisible(TRUE))
}