R/createMonitorISArtifacts.R

In RGLab/ImmuneSpaceCronjobs: ImmuneSpace Cronjob Tools

#' Create artifacts for MonitorIS module report using parsed logs
#'
#' @import data.table stringr
#' @param subdir sub-directory
#' @export
#'
createMonitorISArtifacts <- function(subdir) {
  if (!exists("logs_dt")) {
    logs_dt <- getCurrentRDS(subdir, "_logs.rds")
  }

  ######################################
  ###                                ###
  ######################################

  logs.study <- getCurrentRDS(subdir, "studyViewsInUI")
  logs.study <- parseLogs.study(logs.study)
  saveAndCleanUp(logs.study, subdir, "log_study")

  #######################################
  ###           log_module            ###
  #######################################
  logs.modules <- parseLogs.modules(logs_dt, searchStrings$modules)
  saveAndCleanUp(logs.modules, subdir, "log_module")

  #######################################
  ###           log_reports           ###
  #######################################
  logs.reports <- parseLogs.reports(logs_dt, searchStrings$reports)
  saveAndCleanUp(logs.reports, subdir, "log_reports")

  #######################################
  ###           log_rstudio           ###
  #######################################
  logs.rstudio <- parseLogs.rstudio(logs_dt, searchStrings$rstudio)
  saveAndCleanUp(logs.rstudio, subdir, "log_rstudio")
}

# ----------------------------------------------------------------------
parseLogs.study <- function(logs.study) {
  logs.study <- logs.study[, list(count = .N), by = c("study", "date2")]
  setorder(logs.study, date2)
  return(logs.study)
}


parseLogs.modules <- function(logs, searchString) {
  logs.modules <- logs[, module := stringr::str_extract(X5, searchString)]
  logs.modules <- logs.modules[!is.na(module)]
  logs.modules <- logs.modules[, list(count = .N), by = c("module", "date2")]
  setorder(logs.modules, date2)
  return(logs.modules)
}

parseLogs.reports <- function(logs, searchString) {
  # First half of searchString is pre-2019, second half is post
  logs.reports <- logs[, report := X5]
  logs.reports <- logs.reports[grepl(searchString, report)]
  logs.reports$report <- sapply(logs.reports$report, function(x) {
    return(regmatches(x, regexpr("SDY\\d{3}|IS\\d{1}", x)))
  })
  logs.reports <- logs.reports[, list(count = .N), by = c("report", "date2")]
  setorder(logs.reports, date2)
  return(logs.reports)
}

parseLogs.rstudio <- function(logs, searchString) {
  logs.rstudio <- logs[(grepl(searchString, X5))]
  logs.rstudio <- logs.rstudio[, list(count = .N), by = date2]
  logs.rstudio <- logs.rstudio[, Date := as.Date(cut(date2, breaks = "days"))]
  logs.rstudio <- logs.rstudio[, list(Sessions = sum(count)), by = Date]
}