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Merge pull request #166 from parmsam-pfizer/162_parse_log
Add function to parse previous text log file
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,297 @@ | ||
| #' Reformat subsections in log lines | ||
| #' | ||
| #' @param log_txt String vector. Object with log text lines | ||
| #' | ||
| #' @importFrom stringr str_detect | ||
| #' @importFrom stringr str_count | ||
| #' @importFrom stringr str_remove | ||
| #' | ||
| #' @return tibble that ensures formatted subsections | ||
| #' | ||
| #' @examples | ||
| #' \dontrun{ | ||
| #' reformat_subsections(readlines(log_file_path)) | ||
| #' } | ||
| #' | ||
| #' @noRd | ||
| #' | ||
| reformat_subsections <- function(log_txt) { | ||
| adj_log_txt <- c() | ||
| for (i in log_txt) { | ||
| adj_tf <- stringr::str_detect( | ||
| i, | ||
| "Errors:|Warnings:|Messages:|Output:|Result:" | ||
| ) | ||
| if (adj_tf) { | ||
| nrem <- stringr::str_count(i) | ||
| i <- stringr::str_remove(i, ":") | ||
| i <- | ||
| paste("-", i, paste(rep("-", 54 - nrem), collapse = ""), | ||
| collapse = "" | ||
| ) | ||
| } | ||
| adj_log_txt <- c(adj_log_txt, i) | ||
| } | ||
| return(adj_log_txt) | ||
| } | ||
|
|
||
| #' Nest sections in log lines vector | ||
| #' | ||
| #' @param adj_log_txt String vector. Object with formatted log text lines | ||
| #' | ||
| #' @importFrom stringr str_remove_all | ||
| #' | ||
| #' @return list that includes nested log sections | ||
| #' | ||
| #' @noRd | ||
| #' | ||
| nest_sections <- function(adj_log_txt) { | ||
| sect_headers <- c() | ||
| sect_status <- FALSE | ||
| sect_info <- list() | ||
| for (i in adj_log_txt) { | ||
| if (i == paste(rep("-", 80), collapse = "")) { | ||
| sect_status <- !sect_status | ||
| } else if (sect_status == TRUE) { | ||
| sect_headers <- c(sect_headers, i) | ||
| } else { | ||
| cur_pos <- length(sect_headers) | ||
| if (length(sect_info) == cur_pos) { | ||
| sect_info[[cur_pos]] <- c(sect_info[[cur_pos]], i) | ||
| } else { | ||
| sect_info[[cur_pos]] <- i | ||
| } | ||
| } | ||
| } | ||
| sect_headers <- | ||
| stringr::str_remove_all(sect_headers, "-?\\s{3,}-?") | ||
| names(sect_info) <- sect_headers | ||
|
|
||
| return(sect_info) | ||
| } | ||
|
|
||
| #' Nest subsections in log lines vector | ||
| #' | ||
| #' @param adj_log_txt String vector. Object with formatted log text lines | ||
| #' @param sect_info String vector. Object with nested sections | ||
| #' | ||
| #' @importFrom stringr str_extract | ||
| #' @importFrom stringr str_trim | ||
| #' @importFrom stringr str_remove_all | ||
| #' | ||
| #' @return list that includes nested log subsections | ||
| #' | ||
| #' @noRd | ||
| #' | ||
| nest_subsections <- function(adj_log_txt, sect_info) { | ||
| subsect_headers <- stats::na.omit( | ||
| stringr::str_extract(adj_log_txt, "\\-\\s\\w+\\s(\\w+\\s)?\\-{3,70}") | ||
| ) | ||
| subset_sections <- function(section) { | ||
| subsect_status <- FALSE | ||
| subsect_info <- list() | ||
| for (i in section) { | ||
| if (i %in% subsect_headers) { | ||
| latest_subsect <- stringr::str_trim( | ||
| stringr::str_remove_all(i, "\\-") | ||
| ) | ||
| subsect_status <- TRUE | ||
| } else if (subsect_status) { | ||
| subsect_info[[latest_subsect]] <- | ||
| c(subsect_info[[latest_subsect]], i) | ||
| } else { | ||
| subsect_info <- c(subsect_info, i) | ||
| } | ||
| } | ||
| subsect_info | ||
| } | ||
| nested_log <- lapply(sect_info, subset_sections) | ||
| return(nested_log) | ||
| } | ||
|
|
||
| #' Nest sections and subsections in log lines vector | ||
| #' | ||
| #' @param adj_log_txt String vector. Object with formatted log text lines | ||
| #' | ||
| #' @return list that includes nested log sections and subsections | ||
| #' | ||
| #' @noRd | ||
| #' | ||
| nest_log <- function(adj_log_txt) { | ||
| nest_subsections( | ||
| adj_log_txt, | ||
| nest_sections(adj_log_txt) | ||
| ) | ||
| } | ||
|
|
||
| #' Parse nested log list to tibbles for object where appropriate | ||
| #' | ||
| #' @param nested_log String vector. | ||
| #' Object with nested log output (from `nest_log()`) | ||
| #' | ||
| #' @importFrom tibble tibble | ||
| #' @importFrom tidyr separate | ||
| #' @importFrom stringr str_replace_all | ||
| #' @importFrom dplyr rename_with | ||
| #' @importFrom dplyr mutate | ||
| #' | ||
| #' @return list with objects coerced as tibbles | ||
| #' | ||
| #' @noRd | ||
| #' | ||
| parse_log <- function(nested_log) { | ||
| if (!requireNamespace("readr", quietly = TRUE)) { | ||
| warning(strwrap("Install the readr package to use log parsing feature.", | ||
| prefix = " ", initial = "")) | ||
| return(list()) | ||
| } | ||
|
|
||
| parsed_log <- nested_log | ||
|
|
||
| if ("logrx Metadata" %in% names(nested_log)) { | ||
| parsed_log$`logrx Metadata` <- | ||
| nested_log$`logrx Metadata` %>% | ||
| unlist() %>% | ||
| tibble::tibble() %>% | ||
| tidyr::separate(".", | ||
| sep = "\\: ", | ||
| into = c("Variable", "Value"), | ||
| extra = "merge" | ||
| ) | ||
| } | ||
|
|
||
| if ("User and File Information" %in% names(nested_log)) { | ||
| parsed_log$`User and File Information` <- | ||
| nested_log$`User and File Information` %>% | ||
| unlist() %>% | ||
| stringr::str_trim() %>% | ||
| tibble::tibble() %>% | ||
| tidyr::separate(".", | ||
| sep = "\\: ", | ||
| into = c("Variable", "Value") | ||
| ) | ||
| } | ||
|
|
||
| if ("Session Information" %in% names(nested_log)) { | ||
| parsed_log$`Session Information`$`Session info` <- | ||
| nested_log$`Session Information`$`Session info` %>% | ||
| unlist() %>% | ||
| stringr::str_trim() %>% | ||
| tibble::tibble() %>% | ||
| tidyr::separate(".", | ||
| sep = "\\s", | ||
| into = c("setting", "value"), | ||
| extra = "merge", | ||
| ) %>% | ||
| dplyr::mutate(dplyr::across(dplyr::where(is.character), stringr::str_trim)) | ||
|
|
||
| parsed_log$`Session Information`$`Packages` <- | ||
| nested_log$`Session Information`$`Packages` %>% | ||
| # remove indicator whether the package is attached to the search path | ||
| stringr::str_replace_all("\\*", " ") %>% | ||
| # account for loaded packages due to load_all() | ||
| stringr::str_replace_all(" P ", " ") %>% | ||
| readr::read_table(skip = 1, col_names = FALSE) %>% | ||
| dplyr::rename_with(~ c( | ||
| "package", | ||
| "version", | ||
| "date", | ||
| "lib", | ||
| "source", | ||
| "lang", | ||
| "r_version" | ||
| )) %>% | ||
| dplyr::mutate( | ||
| lang = stringr::str_remove(lang, "\\("), | ||
| r_version = stringr::str_remove(r_version, "\\)") | ||
| ) | ||
|
|
||
| parsed_log$`Session Information`$`External software` <- | ||
| nested_log$`Session Information`$`External software` %>% | ||
| stringr::str_trim() %>% | ||
| tibble::tibble() %>% | ||
| tidyr::separate(".", | ||
| sep = "\\s", | ||
| into = c("setting", "value"), | ||
| extra = "merge", | ||
| ) %>% | ||
| dplyr::mutate(dplyr::across(dplyr::where(is.character), stringr::str_trim)) | ||
| } | ||
|
|
||
| if ("Masked Functions" %in% names(nested_log)) { | ||
| parsed_log$`Masked Functions` <- | ||
| nested_log$`Masked Functions` %>% | ||
| unlist() %>% | ||
| tibble::tibble("Masked Functions" = .) | ||
| } | ||
|
|
||
| if ("Used Package and Functions" %in% names(nested_log)) { | ||
| parsed_log$`Used Package and Functions` <- | ||
| nested_log$`Used Package and Functions` %>% | ||
| unlist() %>% | ||
| tibble::tibble() %>% | ||
| tidyr::separate(".", | ||
| sep = "\\} ", | ||
| into = c("library", "function_names") | ||
| ) %>% | ||
| dplyr::mutate(library = stringr::str_remove(library, "\\{")) | ||
| } | ||
|
|
||
| if ("Program Run Time Information" %in% names(nested_log)) { | ||
| parsed_log$`Program Run Time Information` <- | ||
| nested_log$`Program Run Time Information` %>% | ||
| unlist() %>% | ||
| tibble::tibble() %>% | ||
| tidyr::separate(".", | ||
| sep = "\\: ", | ||
| into = c("Variable", "Value") | ||
| ) | ||
| } | ||
|
|
||
| if ("Log Output File" %in% names(nested_log)) { | ||
| parsed_log$`Log Output File` <- | ||
| nested_log$`Log Output File` %>% | ||
| unlist() %>% | ||
| tibble::tibble() %>% | ||
| tidyr::separate(".", | ||
| sep = "\\: ", | ||
| into = c("Variable", "Value") | ||
| ) | ||
| } | ||
|
|
||
| return(parsed_log) | ||
| } | ||
|
|
||
| #' Read and parse logrx file | ||
| #' | ||
| #' @param file String. Path to a logrx log file | ||
| #' | ||
| #' @return Tibble. Object that includes nested and parsed content | ||
| #' | ||
| #' @examples | ||
| #' \dontrun{ | ||
| #' read_log_file(previous_log_filepath) | ||
| #' } | ||
| #' | ||
| read_log_file <- function(file) { | ||
| if (!file.exists(file)) { | ||
| stop("Path does not exist:", sQuote(file)) | ||
| } | ||
|
|
||
| if (!requireNamespace("readr", quietly = TRUE)) { | ||
| warning(strwrap("Install the readr package to use log parsing feature.", | ||
| prefix = " ", initial = "")) | ||
| return(list()) | ||
| } | ||
|
|
||
| con <- file(file.path(file), "r") | ||
| flines <- readLines(con) | ||
| close(con) | ||
|
|
||
| parsed_log <- flines %>% | ||
| reformat_subsections() %>% | ||
| nest_log() %>% | ||
| parse_log() | ||
|
|
||
| return(parsed_log) | ||
| } |
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