globals.R

# globals.R
# ::rtemisseq::
# EDG rtemis.org

# rtemis ----
msg2start <- getFromNamespace("msg2start", "rtemis")
msg2done <- getFromNamespace("msg2done", "rtemis")

# rtemislive ----
rthelp <- function(..., title = NULL, class = "rthelp") {
  div(
    div(HTML(paste0(title, " Instructions")),
      style = "color: #808080; font-weight: 300; padding-bottom:.5em;"
    ),
    HTML(paste0("<i>", paste(..., sep = "<br>")), "</i>"),
    class = class
  )
} # rtemislive::rthelp

rthelp_inline <- function(..., title = NULL, class = "rthelp-inline") {
  rthelp(..., title = title, class = class)
} # rtemislive::rthelp_inline

#' Create bulleted list
#' 
#' @return div
rthelplist <- function(x, bullet = bsicons::bs_icon("arrow-right-short"), class = "rthelplist") {
  div(
    htmltools::HTML(
      paste0(
        bullet, "<i>", x, "</i>", "<br>"
      )
    ),
    class = class
  )
} # rtemisseq::rthelplist

bold <- function(x) {
  paste0("<b>", x, "</b>")
}

hilite <- function(x) {
  paste0("<span style='color: var(--bs-primary);font-weight: bold;'>", x, "</span>")
}

nannot <- function(n) {
  ngettext(n, "annotation", "annotations")
}

#' Summarize a3 object in HTML
#'
#' @param x a3 object
#'
#' @return HTML string
#' @author EDG
summarize_a3 <- function(x) {
  n_site <- length(x$Annotations$Site)
  n_region <- length(x$Annotations$Region)
  n_ptm <- length(x$Annotations$PTM)
  n_cleavage <- length(x$Annotations$Cleavage_site)
  n_variant <- length(x$Annotations$Variant)
  htmltools::HTML(
    paste0(
      if (!is.null(x$Description)) paste0("Description: ", hilite(x$Description), "<br>"),
      if (!is.null(x$UniprotID)) paste0("Uniprot ID: ", hilite(x$UniprotID), "<br>"),
      paste0("Sequence length: ", hilite(length(x$Sequence)), "<br>"),
      "<ul>",
      if (n_site > 0) paste("<li>", hilite(n_site), "site", nannot(n_site), "<br>"),
      if (n_region > 0) paste("<li>", hilite(n_region), "region", nannot(n_region), "<br>"),
      if (n_ptm > 0) paste("<li>", hilite(n_ptm), "PTM", nannot(n_ptm), "<br>"),
      if (n_cleavage > 0) paste("<li>", hilite(n_cleavage), " cleavage site", nannot(n_cleavage), "<br>"),
      if (n_variant > 0) paste("<li>", hilite(n_variant), "variant", nannot(n_variant), "<br>"),
      "</ul>",
      if (!is.null(x$Reference)) a("Reference", href = x$Reference, target = "_blank")
    )
  )
} # rtemisseq::summarize_a3

#' Get file names and download URLs from a GitHub repository
#'
#' @param repo_owner The owner of the GitHub repository
#' @param repo_name The name of the GitHub repository
#' 
#' @return A data frame with file names and download URLs
#' 
#' @examples
#' files <- get_github_files("rtemis-org", "seq-data")
#' @export
#' @author EDG

get_github_files <- function(repo_owner, repo_name, verbosity = 1) {
  if (verbosity > 0) {
    msg2start("Getting file information from", paste0(repo_owner, "/", repo_name))
  }
  # Construct the API URL
  api_url <- paste0("https://api.github.com/repos/", repo_owner, "/", repo_name, "/contents/data")

  # Make the API request
  response <- httr::GET(api_url)

  # Check if the request was successful
  if (response[["status_code"]] == 200) {
    # Extract the file information
    files_data <- httr::content(response, as = "text", encoding = "UTF-8") |> jsonlite::fromJSON()

    # Create a data frame with file names and download URLs
    files_df <- data.frame(
      file_name = files_data[["name"]],
      download_url = files_data[["download_url"]]
    )
    if (verbosity > 0) {
      msg2done()
    }
    return(files_df)
  } else {
    print("Error: Could not retrieve file information.")
    return(NULL)
  }
} # rtemis::get_github_files