From 2bdfdae761ea245b55b03252970b06d95a7238d5 Mon Sep 17 00:00:00 2001
From: Sam Parmar <107635309+parmsam-pfizer@users.noreply.github.com>
Date: Tue, 14 Feb 2023 14:06:42 -0600
Subject: [PATCH 01/12] add rds saving option

---
 R/log.R | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/R/log.R b/R/log.R
index 7e10223..2c6fb58 100644
--- a/R/log.R
+++ b/R/log.R
@@ -284,9 +284,16 @@ log_write <- function(file = NA,
                         write_log_element("log_name", "Log name: "),
                         write_log_element("log_path", "Log path: "))
 
-   writeLines(cleaned_log_vec,
-              con = file.path(get_log_element("log_path"),
-                              get_log_element("log_name")))
+   if (tools::file_ext(get_log_element("log_name")) %in% c("log", "txt")){
+      writeLines(cleaned_log_vec,
+                 con = file.path(get_log_element("log_path"),
+                                 get_log_element("log_name")))
+   } else if ( tolower(tools::file_ext(get_log_element("log_name"))) == "rds") {
+      saveRDS(cleaned_log_vec,
+              file = file.path(get_log_element("log_path"),
+                               get_log_element("log_name")))
+   }
+
    if (remove_log_object) {
       log_remove()
    }

From 055c7413b04cf4b4f33dda0649e11d32dfe453b2 Mon Sep 17 00:00:00 2001
From: Sam Parmar <107635309+parmsam-pfizer@users.noreply.github.com>
Date: Tue, 14 Feb 2023 16:37:42 -0600
Subject: [PATCH 02/12] add arg to include nested Rds export

---
 R/log.R | 21 +++++++++++++++------
 1 file changed, 15 insertions(+), 6 deletions(-)

diff --git a/R/log.R b/R/log.R
index 2c6fb58..5e0b194 100644
--- a/R/log.R
+++ b/R/log.R
@@ -177,6 +177,7 @@ log_cleanup <- function() {
 #' log_write(file)
 log_write <- function(file = NA,
                       remove_log_object = TRUE,
+                      include_rds = TRUE,
                       to_report = c("messages", "output", "result")){
    # Set end time and run time
    set_log_element("end_time", strftime(Sys.time(), usetz = TRUE))
@@ -284,14 +285,22 @@ log_write <- function(file = NA,
                         write_log_element("log_name", "Log name: "),
                         write_log_element("log_path", "Log path: "))
 
-   if (tools::file_ext(get_log_element("log_name")) %in% c("log", "txt")){
-      writeLines(cleaned_log_vec,
+   writeLines(cleaned_log_vec,
                  con = file.path(get_log_element("log_path"),
                                  get_log_element("log_name")))
-   } else if ( tolower(tools::file_ext(get_log_element("log_name"))) == "rds") {
-      saveRDS(cleaned_log_vec,
-              file = file.path(get_log_element("log_path"),
-                               get_log_element("log_name")))
+   if (include_rds) {
+      cleaned_log_list <- lapply(
+         getOption('log.rx'),
+         function(i) i
+      )
+      saveRDS(cleaned_log_list,
+              file = file.path(
+                 get_log_element("log_path"),
+                 paste0(tools::file_path_sans_ext(
+                    get_log_element("log_name")
+                    ),".Rds")
+                 )
+              )
    }
 
    if (remove_log_object) {

From 29867bb7cd3446e04510ad9087522421ad1ec80a Mon Sep 17 00:00:00 2001
From: Sam Parmar <107635309+parmsam-pfizer@users.noreply.github.com>
Date: Tue, 14 Feb 2023 16:46:38 -0600
Subject: [PATCH 03/12] update session_info element in log_list to original
 output

---
 R/log.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/log.R b/R/log.R
index 5e0b194..44f60e9 100644
--- a/R/log.R
+++ b/R/log.R
@@ -293,6 +293,7 @@ log_write <- function(file = NA,
          getOption('log.rx'),
          function(i) i
       )
+      cleaned_log_list$session_info <- session_info(info = "all")
       saveRDS(cleaned_log_list,
               file = file.path(
                  get_log_element("log_path"),

From fe6c61cd857610d1ed8286d88f7873a1dc2c691b Mon Sep 17 00:00:00 2001
From: Sam Parmar <107635309+parmsam-pfizer@users.noreply.github.com>
Date: Tue, 14 Feb 2023 16:55:18 -0600
Subject: [PATCH 04/12] fix roxygen and update documentation

---
 R/log.R          | 3 ++-
 man/log_write.Rd | 3 +++
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/R/log.R b/R/log.R
index 44f60e9..4d80fd2 100644
--- a/R/log.R
+++ b/R/log.R
@@ -150,6 +150,7 @@ log_cleanup <- function() {
 #' to a log file
 #'
 #' @param file String. Path to file executed
+#' @param include_rds Boolean. Option to export log object as Rds file
 #' @param remove_log_object Boolean. Should the log object be removed after
 #' writing the log file? Defaults to TRUE
 #' @param to_report String vector. Objects to optionally report; additional
@@ -177,7 +178,7 @@ log_cleanup <- function() {
 #' log_write(file)
 log_write <- function(file = NA,
                       remove_log_object = TRUE,
-                      include_rds = TRUE,
+                      include_rds = FALSE,
                       to_report = c("messages", "output", "result")){
    # Set end time and run time
    set_log_element("end_time", strftime(Sys.time(), usetz = TRUE))
diff --git a/man/log_write.Rd b/man/log_write.Rd
index d269420..b535c8f 100644
--- a/man/log_write.Rd
+++ b/man/log_write.Rd
@@ -7,6 +7,7 @@
 log_write(
   file = NA,
   remove_log_object = TRUE,
+  include_rds = FALSE,
   to_report = c("messages", "output", "result")
 )
 }
@@ -16,6 +17,8 @@ log_write(
 \item{remove_log_object}{Boolean. Should the log object be removed after
 writing the log file? Defaults to TRUE}
 
+\item{include_rds}{Boolean. Option to export log object as Rds file}
+
 \item{to_report}{String vector. Objects to optionally report; additional
 information in \code{\link{axecute}}}
 }

From 8ac8cb4044a055f0721e6a1ec73731dbebc7d419 Mon Sep 17 00:00:00 2001
From: Sam Parmar <107635309+parmsam-pfizer@users.noreply.github.com>
Date: Wed, 15 Feb 2023 10:41:29 -0600
Subject: [PATCH 05/12] filter rds fields based on log_cleanup() and to_report

---
 R/log.R | 23 +++++++++++++++++++----
 1 file changed, 19 insertions(+), 4 deletions(-)

diff --git a/R/log.R b/R/log.R
index 4d80fd2..3b6b7f1 100644
--- a/R/log.R
+++ b/R/log.R
@@ -289,10 +289,25 @@ log_write <- function(file = NA,
    writeLines(cleaned_log_vec,
                  con = file.path(get_log_element("log_path"),
                                  get_log_element("log_name")))
-   if (include_rds) {
-      cleaned_log_list <- lapply(
-         getOption('log.rx'),
-         function(i) i
+   if (include_rds){
+      rds_fields <- c(
+         "end_time", "start_time", "run_time", "user", "hash_sum",
+         "log_path", "log_name", "file_path", "file_name",
+         "unapproved_packages_functions", "errors", "warnings"
+      )
+      log_options <- as.list(getOption('log.rx'))
+      cleaned_log_list <- Map(
+         function(i, x){
+            if(x %in% c("messages", "output", "result")){
+               if(x %in% to_report){
+                  return(i)
+               }
+            } else if(x %in% c(names(log_cleanup()), rds_fields)){
+               return(i)
+            }
+         },
+         log_options,
+         names(log_options)
       )
       cleaned_log_list$session_info <- session_info(info = "all")
       saveRDS(cleaned_log_list,

From 8f7f9bc40ce6ca1380e83a3b8642e76f8df52e9e Mon Sep 17 00:00:00 2001
From: Sam Parmar <107635309+parmsam-pfizer@users.noreply.github.com>
Date: Wed, 15 Feb 2023 12:34:44 -0600
Subject: [PATCH 06/12] add unit test for include_rds

---
 tests/testthat/test-axecute.R | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/tests/testthat/test-axecute.R b/tests/testthat/test-axecute.R
index 8f2dca2..60a6016 100644
--- a/tests/testthat/test-axecute.R
+++ b/tests/testthat/test-axecute.R
@@ -66,3 +66,35 @@ test_that("to_report works to control log output elements", {
    rm(flines, con, scriptPath, logDir)
    log_remove()
 })
+
+test_that("include_rds works to output log as rds", {
+   options("log.rx" = NULL)
+   scriptPath <- tempfile()
+   logDir <- tempdir()
+   writeLines(
+      c("message('hello logrx')",
+        "cat('this is output')",
+        "data.frame(c(8, 6, 7, 5, 3, 0, 9))"),
+      con = scriptPath)
+
+   # check no log is currently written out
+   expect_warning(expect_error(file(file.path(logDir, "log_out_nested"), "r"), "cannot open the connection"))
+
+   axecute(scriptPath,
+           log_name = "log_out_nested",
+           log_path = logDir,
+           remove_log_object = FALSE,
+           include_rds = TRUE,
+           to_report = c("messages", "result"))
+   con <- file(file.path(logDir, "log_out_nested.Rds"), "r")
+   logRDS <- readRDS(file.path(logDir, "log_out_nested.Rds"))
+
+   expect_type(logRDS, "list")
+   expect_true("messages" %in% names(logRDS))
+   expect_true(all(is.na(logRDS$output)))
+   expect_true("result" %in% names(logRDS))
+   expect_true("start_time" %in% names(logRDS))
+
+   rm(con, scriptPath, logDir, logRDS)
+   log_remove()
+})

From 2bf9ed8fdf6a459594938d960b678a29afc6548b Mon Sep 17 00:00:00 2001
From: Sam Parmar <107635309+parmsam-pfizer@users.noreply.github.com>
Date: Wed, 15 Feb 2023 12:42:56 -0600
Subject: [PATCH 07/12] add include_rds arg to axecute and update doc

---
 R/axecute.R      | 8 +++++++-
 R/log.R          | 3 ++-
 man/axecute.Rd   | 4 ++++
 man/log_write.Rd | 3 ++-
 4 files changed, 15 insertions(+), 3 deletions(-)

diff --git a/R/axecute.R b/R/axecute.R
index 7af7930..9b52e75 100644
--- a/R/axecute.R
+++ b/R/axecute.R
@@ -10,6 +10,8 @@
 #' @param log_path String. Path to log file
 #' @param remove_log_object Boolean. Should the log object be removed after
 #' writing the log file? Defaults to TRUE
+#' @param include_rds Boolean. Option to export log object as Rds file.
+#' Defaults to FALSE
 #' @param quit_on_error Boolean. Should the session quit with status 1 on error?
 #' Defaults to TRUE
 #' @param to_report String vector. Objects to optionally report, may include as
@@ -34,6 +36,7 @@
 axecute <- function(file, log_name = NA,
                     log_path = NA,
                     remove_log_object = TRUE,
+                    include_rds = FALSE,
                     quit_on_error = TRUE,
                     to_report = c("messages", "output", "result")){
 
@@ -51,7 +54,10 @@ axecute <- function(file, log_name = NA,
    any_errors <- get_log_element("errors")
 
    # write log
-   log_write(file = file, remove_log_object = remove_log_object, to_report = to_report)
+   log_write(file = file,
+             remove_log_object = remove_log_object,
+             include_rds = include_rds,
+             to_report = to_report)
 
    # if error, quit with status = 1 if not interactive
    if(!interactive() & !is.null(any_errors) & quit_on_error) {
diff --git a/R/log.R b/R/log.R
index 3b6b7f1..25bf1d5 100644
--- a/R/log.R
+++ b/R/log.R
@@ -150,7 +150,8 @@ log_cleanup <- function() {
 #' to a log file
 #'
 #' @param file String. Path to file executed
-#' @param include_rds Boolean. Option to export log object as Rds file
+#' @param include_rds Boolean. Option to export log object as Rds file.
+#' Defaults to TRUE
 #' @param remove_log_object Boolean. Should the log object be removed after
 #' writing the log file? Defaults to TRUE
 #' @param to_report String vector. Objects to optionally report; additional
diff --git a/man/axecute.Rd b/man/axecute.Rd
index 89e8e67..9784fd5 100644
--- a/man/axecute.Rd
+++ b/man/axecute.Rd
@@ -9,6 +9,7 @@ axecute(
   log_name = NA,
   log_path = NA,
   remove_log_object = TRUE,
+  include_rds = FALSE,
   quit_on_error = TRUE,
   to_report = c("messages", "output", "result")
 )
@@ -23,6 +24,9 @@ axecute(
 \item{remove_log_object}{Boolean. Should the log object be removed after
 writing the log file? Defaults to TRUE}
 
+\item{include_rds}{Boolean. Option to export log object as Rds file.
+Defaults to FALSE}
+
 \item{quit_on_error}{Boolean. Should the session quit with status 1 on error?
 Defaults to TRUE}
 
diff --git a/man/log_write.Rd b/man/log_write.Rd
index b535c8f..db67039 100644
--- a/man/log_write.Rd
+++ b/man/log_write.Rd
@@ -17,7 +17,8 @@ log_write(
 \item{remove_log_object}{Boolean. Should the log object be removed after
 writing the log file? Defaults to TRUE}
 
-\item{include_rds}{Boolean. Option to export log object as Rds file}
+\item{include_rds}{Boolean. Option to export log object as Rds file.
+Defaults to TRUE}
 
 \item{to_report}{String vector. Objects to optionally report; additional
 information in \code{\link{axecute}}}

From 317f9ce347c5590707e746e45f4e2efe88901879 Mon Sep 17 00:00:00 2001
From: Sam Parmar <107635309+parmsam-pfizer@users.noreply.github.com>
Date: Wed, 15 Feb 2023 12:58:28 -0600
Subject: [PATCH 08/12] update newsmd

---
 NEWS.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index 46a8d26..c116ddf 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,7 @@
+# logrx 0.2.2
+
+- Add `include_rds` argument to `axecute()` to export log as rds file
+
 # logrx 0.2.1
 
  - non-function objects are no longer returned as functions by `get_used_functions` (#154)

From 5fa319fc8575d115d2bb8df9b52cf381099709d9 Mon Sep 17 00:00:00 2001
From: Sam Parmar <107635309+parmsam-pfizer@users.noreply.github.com>
Date: Tue, 21 Feb 2023 15:48:28 -0600
Subject: [PATCH 09/12] update include_rds roxygen2 default

---
 R/log.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/log.R b/R/log.R
index 25bf1d5..89b5d84 100644
--- a/R/log.R
+++ b/R/log.R
@@ -151,7 +151,7 @@ log_cleanup <- function() {
 #'
 #' @param file String. Path to file executed
 #' @param include_rds Boolean. Option to export log object as Rds file.
-#' Defaults to TRUE
+#' Defaults to FALSE
 #' @param remove_log_object Boolean. Should the log object be removed after
 #' writing the log file? Defaults to TRUE
 #' @param to_report String vector. Objects to optionally report; additional

From 80152b4806bef80e380ca0d67b408c2758fff372 Mon Sep 17 00:00:00 2001
From: Sam Parmar <107635309+parmsam-pfizer@users.noreply.github.com>
Date: Tue, 21 Feb 2023 15:59:56 -0600
Subject: [PATCH 10/12] use purrr::map2 instead of Map

---
 R/log.R          | 8 ++++----
 man/log_write.Rd | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/R/log.R b/R/log.R
index 89b5d84..863d500 100644
--- a/R/log.R
+++ b/R/log.R
@@ -297,7 +297,9 @@ log_write <- function(file = NA,
          "unapproved_packages_functions", "errors", "warnings"
       )
       log_options <- as.list(getOption('log.rx'))
-      cleaned_log_list <- Map(
+      cleaned_log_list <- purrr::map2(
+         log_options,
+         names(log_options),
          function(i, x){
             if(x %in% c("messages", "output", "result")){
                if(x %in% to_report){
@@ -306,9 +308,7 @@ log_write <- function(file = NA,
             } else if(x %in% c(names(log_cleanup()), rds_fields)){
                return(i)
             }
-         },
-         log_options,
-         names(log_options)
+         }
       )
       cleaned_log_list$session_info <- session_info(info = "all")
       saveRDS(cleaned_log_list,
diff --git a/man/log_write.Rd b/man/log_write.Rd
index db67039..aa4f657 100644
--- a/man/log_write.Rd
+++ b/man/log_write.Rd
@@ -18,7 +18,7 @@ log_write(
 writing the log file? Defaults to TRUE}
 
 \item{include_rds}{Boolean. Option to export log object as Rds file.
-Defaults to TRUE}
+Defaults to FALSE}
 
 \item{to_report}{String vector. Objects to optionally report; additional
 information in \code{\link{axecute}}}

From 8dccc88caee2bb2f943dfaf19d04f44c346c05f3 Mon Sep 17 00:00:00 2001
From: Sam Parmar <107635309+parmsam-pfizer@users.noreply.github.com>
Date: Mon, 27 Feb 2023 14:56:25 -0600
Subject: [PATCH 11/12] Move the capture output to the write function

---
 R/get.R    | 2 +-
 R/log.R    | 4 ++--
 R/writer.R | 1 +
 3 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/R/get.R b/R/get.R
index 9870557..728fc52 100644
--- a/R/get.R
+++ b/R/get.R
@@ -96,7 +96,7 @@ get_file_path <- function(file = NA, normalize = TRUE){
 #' @noRd
 #'
 get_session_info <- function(){
-   return(capture.output(session_info(info = "all")))
+   return(session_info(info = "all"))
 }
 
 
diff --git a/R/log.R b/R/log.R
index 863d500..ff80c3f 100644
--- a/R/log.R
+++ b/R/log.R
@@ -294,7 +294,8 @@ log_write <- function(file = NA,
       rds_fields <- c(
          "end_time", "start_time", "run_time", "user", "hash_sum",
          "log_path", "log_name", "file_path", "file_name",
-         "unapproved_packages_functions", "errors", "warnings"
+         "unapproved_packages_functions", "errors", "warnings",
+         "session_info"
       )
       log_options <- as.list(getOption('log.rx'))
       cleaned_log_list <- purrr::map2(
@@ -310,7 +311,6 @@ log_write <- function(file = NA,
             }
          }
       )
-      cleaned_log_list$session_info <- session_info(info = "all")
       saveRDS(cleaned_log_list,
               file = file.path(
                  get_log_element("log_path"),
diff --git a/R/writer.R b/R/writer.R
index f10ac82..b114546 100644
--- a/R/writer.R
+++ b/R/writer.R
@@ -50,6 +50,7 @@ write_metadata <- function(){
 #'
 write_session_info <- function(){
    session_info <- get_log_element("session_info") %>%
+      capture.output() %>%
       # remove extra dashes on title lines
       map_chr(~ ifelse(nchar(.x) > 80 & grepl("\u2500\u2500\u2500\u2500", .x),
                    substring(.x, 1, 80),

From 03a516218fefe72564aa4a658db9695e5d7cdf07 Mon Sep 17 00:00:00 2001
From: Sam Parmar <107635309+parmsam-pfizer@users.noreply.github.com>
Date: Mon, 27 Feb 2023 14:58:12 -0600
Subject: [PATCH 12/12] update session info capture test to capture.output of
 session info obj

---
 tests/testthat/test-get.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-get.R b/tests/testthat/test-get.R
index b477174..ac09c5f 100644
--- a/tests/testthat/test-get.R
+++ b/tests/testthat/test-get.R
@@ -22,7 +22,7 @@ test_that("when given a file as an argument a non-normalized file path to that f
 })
 
 test_that("session info is captured", {
-   expect_identical(get_session_info(), capture.output(session_info(info = "all")))
+   expect_identical(capture.output(get_session_info()), capture.output(session_info(info = "all")))
 })
 
 test_that("all functions that are masked are found and returned", {