Add function to parse previous text log file

DESCRIPTION

@@ -51,7 +51,9 @@ Imports:
     tibble,
     digest,
     lintr,
-    lifecycle
+    readr,
+    lifecycle,
+    methods
 Suggests: 
     testthat (>= 3.0.0),
     knitr,

NAMESPACE

@@ -15,6 +15,7 @@ importFrom(dplyr,distinct)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
 importFrom(dplyr,mutate)
+importFrom(dplyr,rename_with)
 importFrom(dplyr,select)
 importFrom(dplyr,ungroup)
 importFrom(lintr,lint)
@@ -31,6 +32,7 @@ importFrom(purrr,map2_dfr)
 importFrom(purrr,map_chr)
 importFrom(purrr,safely)
 importFrom(purrr,set_names)
+importFrom(readr,read_table)
 importFrom(rlang,.data)
 importFrom(rstudioapi,selectDirectory)
 importFrom(rstudioapi,selectFile)
@@ -51,14 +53,20 @@ importFrom(shiny,uiOutput)
 importFrom(stats,aggregate)
 importFrom(stringi,stri_wrap)
 importFrom(stringr,str_c)
+importFrom(stringr,str_count)
+importFrom(stringr,str_detect)
+importFrom(stringr,str_extract)
+importFrom(stringr,str_remove)
 importFrom(stringr,str_remove_all)
 importFrom(stringr,str_replace)
 importFrom(stringr,str_replace_all)
 importFrom(stringr,str_starts)
+importFrom(stringr,str_trim)
 importFrom(tibble,tibble)
 importFrom(tidyr,all_of)
 importFrom(tidyr,complete)
 importFrom(tidyr,pivot_wider)
+importFrom(tidyr,separate)
 importFrom(utils,capture.output)
 importFrom(utils,getParseData)
 importFrom(utils,lsf.str)

NEWS.md

@@ -1,8 +1,10 @@
+
 # logrx 0.3.0
 
 - Add `show_repo_url` option in `axecute()` to capture repo URL(s) into log file (#167)
 - Moved website theme to bootstarp 5, enabled search (#179)
 - Add `include_rds` argument to `axecute()` to export log as rds file
+- Add `read_log_file()` to read previous logrx log file
 - Remove argument for remove_log_object from `axecute()` still accessible via `log_write()` (#182)
 
 # logrx 0.2.2

R/axecute.R

@@ -42,7 +42,7 @@ axecute <- function(file, log_name = NA,
                     show_repo_url = FALSE,
                     ...){
    # deprecations
-   if (hasArg(remove_log_object)) {
+   if (methods::hasArg(remove_log_object)) {
       lifecycle::deprecate_stop("0.3.0", "axecute(remove_log_object = )", "axecute(include_rds = )")
    }
 

R/read_log_file.R

@@ -0,0 +1,284 @@
+#' 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 readr read_table
+#' @importFrom dplyr mutate
+#'
+#' @return list with objects coerced as tibbles
+#'
+#' @noRd
+#'
+parse_log <- function(nested_log) {
+  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 previous 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))
+  }
+  con <- file(file.path(file), "r")
+  flines <- readLines(con)
+  close(con)
+
+  parsed_log <- flines %>%
+    reformat_subsections() %>%
+    nest_log() %>%
+    parse_log()
+  return(parsed_log)
+}

_pkgdown.yml

@@ -35,6 +35,10 @@ reference:
    - write_log_header
    - write_unapproved_functions
    - write_used_functions
+- title: Read Previous Log
+  desc: Functionality to Read Previous Log Files
+- contents:
+   - read_log_file
 - title: Utilities
   desc: Utility functions
 - contents: