From 4115c0d554e8201ca2e6462c20e6cd5583209c13 Mon Sep 17 00:00:00 2001
From: Sam Parmar <107635309+parmsam-pfizer@users.noreply.github.com>
Date: Tue, 7 Mar 2023 14:25:44 -0500
Subject: [PATCH 1/6] add arg to capture repo urls and ensure unit tests

---
 R/axecute.R                   | 10 +++++++--
 R/get.R                       | 12 ++++++++++
 R/log.R                       | 16 +++++++++++--
 R/writer.R                    | 22 ++++++++++++++++++
 man/axecute.Rd                |  6 ++++-
 man/log_write.Rd              |  6 ++++-
 tests/testthat/test-axecute.R | 42 +++++++++++++++++++++++++++++++++++
 tests/testthat/test-log.R     |  2 +-
 8 files changed, 109 insertions(+), 7 deletions(-)

diff --git a/R/axecute.R b/R/axecute.R
index 7af7930..3dd30cf 100644
--- a/R/axecute.R
+++ b/R/axecute.R
@@ -17,6 +17,8 @@
 #' * messages: any messages generated by program execution
 #' * output: any output generated by program execution
 #' * result: any result generated by program execution
+#' @param show_repo_url Boolean. Should the repo URLs be reported
+#' Defaults to FALSE
 #'
 #' @importFrom purrr map_chr
 #'
@@ -35,7 +37,8 @@ axecute <- function(file, log_name = NA,
                     log_path = NA,
                     remove_log_object = TRUE,
                     quit_on_error = TRUE,
-                    to_report = c("messages", "output", "result")){
+                    to_report = c("messages", "output", "result"),
+                    show_repo_url = FALSE){
 
    # lower everything for consistency and check values
    to_report <- map_chr(to_report, tolower)
@@ -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,
+             to_report = to_report,
+             show_repo_url = show_repo_url)
 
    # if error, quit with status = 1 if not interactive
    if(!interactive() & !is.null(any_errors) & quit_on_error) {
diff --git a/R/get.R b/R/get.R
index 9870557..442ba0e 100644
--- a/R/get.R
+++ b/R/get.R
@@ -289,3 +289,15 @@ get_lint_results <- function(file) {
       lint(file, getOption('log.rx.lint'))
    }
 }
+
+#' Get repository URLs
+#'
+#' Obtain repository URLs possibly used to install packages in session
+#'
+#' @return results from `getOption("repos")` as list
+#'
+#' @noRd
+#'
+get_repo_urls <- function() {
+   as.list(getOption("repos"))
+}
diff --git a/R/log.R b/R/log.R
index 7e10223..5322618 100644
--- a/R/log.R
+++ b/R/log.R
@@ -83,7 +83,8 @@ log_config <- function(file = NA, log_name = NA, log_path = NA){
       "unapproved_packages_functions",
       "lint_results",
       "log_name",
-      "log_path")
+      "log_path",
+      "repo_urls")
 
    # Add attributes to the log.rx environment, and set them to NA
    for (key in 1:length(keys)){
@@ -108,6 +109,8 @@ log_config <- function(file = NA, log_name = NA, log_path = NA){
    set_log_name_path(log_name, log_path)
    # lint results
    set_log_element("lint_results", get_lint_results(file))
+   # repo urls
+   set_log_element("repo_urls", get_repo_urls())
 }
 
 #' Cleaning-up of log.rx object
@@ -154,6 +157,8 @@ log_cleanup <- function() {
 #' writing the log file? Defaults to TRUE
 #' @param to_report String vector. Objects to optionally report; additional
 #' information in \code{\link{axecute}}
+#' @param show_repo_url Boolean. Should the repo URLs be reported
+#' Defaults to FALSE
 #'
 #' @return Nothing
 #' @export
@@ -177,7 +182,8 @@ log_cleanup <- function() {
 #' log_write(file)
 log_write <- function(file = NA,
                       remove_log_object = TRUE,
-                      to_report = c("messages", "output", "result")){
+                      to_report = c("messages", "output", "result"),
+                      show_repo_url = FALSE){
    # Set end time and run time
    set_log_element("end_time", strftime(Sys.time(), usetz = TRUE))
    set_log_element("run_time",
@@ -210,6 +216,12 @@ log_write <- function(file = NA,
                         write_log_header("Session Information"),
                         write_session_info())
 
+   if (show_repo_url) {
+      cleaned_log_vec <- c(cleaned_log_vec,
+                           write_log_header("Repo URLs"),
+                           write_repo_urls())
+   }
+
    if ("masked_functions" %in% names(log_cleanup())) {
       cleaned_log_vec <- c(cleaned_log_vec,
                            write_log_header("Masked Functions"),
diff --git a/R/writer.R b/R/writer.R
index f10ac82..4bde2f2 100644
--- a/R/writer.R
+++ b/R/writer.R
@@ -62,6 +62,28 @@ write_session_info <- function(){
    return(session_info)
 }
 
+#' Format repo URLs for writing
+#'
+#' @return A vector of file name and path prefixed
+#'
+#' @noRd
+#'
+write_repo_urls <- function(){
+   repo_urls <- ifelse(is.na(get_log_element("repo_urls")),
+                       "Repo URLs not able to be determined",
+                       map2(
+                          names(get_log_element("repo_urls")),
+                          get_log_element("repo_urls"),
+                          ~paste(paste0(.x, ": "),
+                                 paste0(.y, collapse = ", "))
+                       ) %>%
+                          unname() %>%
+                          unlist()
+   )
+
+   return(repo_urls)
+}
+
 #' Format file name and path for writing
 #'
 #' @return A vector of file name and path prefixed
diff --git a/man/axecute.Rd b/man/axecute.Rd
index 89e8e67..8a385c5 100644
--- a/man/axecute.Rd
+++ b/man/axecute.Rd
@@ -10,7 +10,8 @@ axecute(
   log_path = NA,
   remove_log_object = TRUE,
   quit_on_error = TRUE,
-  to_report = c("messages", "output", "result")
+  to_report = c("messages", "output", "result"),
+  show_repo_url = FALSE
 )
 }
 \arguments{
@@ -33,6 +34,9 @@ many as necessary:
 \item output: any output generated by program execution
 \item result: any result generated by program execution
 }}
+
+\item{show_repo_url}{Boolean. Should the repo URLs be reported
+Defaults to FALSE}
 }
 \value{
 0 if there are no errors or 1 if there are any errors
diff --git a/man/log_write.Rd b/man/log_write.Rd
index d269420..4ea1713 100644
--- a/man/log_write.Rd
+++ b/man/log_write.Rd
@@ -7,7 +7,8 @@
 log_write(
   file = NA,
   remove_log_object = TRUE,
-  to_report = c("messages", "output", "result")
+  to_report = c("messages", "output", "result"),
+  show_repo_url = FALSE
 )
 }
 \arguments{
@@ -18,6 +19,9 @@ writing the log file? Defaults to TRUE}
 
 \item{to_report}{String vector. Objects to optionally report; additional
 information in \code{\link{axecute}}}
+
+\item{show_repo_url}{Boolean. Should the repo URLs be reported
+Defaults to FALSE}
 }
 \value{
 Nothing
diff --git a/tests/testthat/test-axecute.R b/tests/testthat/test-axecute.R
index 8f2dca2..932e01e 100644
--- a/tests/testthat/test-axecute.R
+++ b/tests/testthat/test-axecute.R
@@ -66,3 +66,45 @@ test_that("to_report works to control log output elements", {
    rm(flines, con, scriptPath, logDir)
    log_remove()
 })
+
+test_that("show_repo_url works to show repo url elements", {
+   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_repo_url"), "r"), "cannot open the connection"))
+
+   axecute(scriptPath, log_name = "log_out_repo_url",
+           log_path = logDir,
+           remove_log_object = FALSE,
+           show_repo_url = TRUE
+   )
+   con <- file(file.path(logDir, "log_out_repo_url"), "r")
+   flines <- readLines(con)
+   close(con)
+
+   expect_true(grepl(paste(write_log_header("Repo URLs"), collapse = ','),
+                     paste(flines,collapse = ',')))
+   rm(flines, con)
+   log_remove()
+
+   axecute(scriptPath, log_name = "log_out_repo_url2",
+           log_path = logDir,
+           remove_log_object = FALSE,
+           show_repo_url = FALSE
+   )
+   con <- file(file.path(logDir, "log_out_repo_url2"), "r")
+   flines <- readLines(con)
+   close(con)
+
+   expect_false(grepl(paste(write_log_header("Repo URLs"), collapse = ','),
+                      paste(flines,collapse = ',')))
+   rm(flines, con, scriptPath, logDir)
+   log_remove()
+})
diff --git a/tests/testthat/test-log.R b/tests/testthat/test-log.R
index d8ab347..e26338e 100644
--- a/tests/testthat/test-log.R
+++ b/tests/testthat/test-log.R
@@ -13,7 +13,7 @@ test_that("log_config configures the log and all the necessary elements", {
                      "result","output","start_time", "end_time", "run_time",
                      "file_name","file_path","user", "hash_sum", "masked_functions",
                      "used_packages_functions", "unapproved_packages_functions",
-                     "lint_results", "log_name","log_path"))
+                     "lint_results", "log_name","log_path", "repo_urls"))
 
    expect_identical(getOption("log.rx")[['file_path']], dirname(get_file_path('./test-get.R')))
    expect_identical(getOption("log.rx")[['file_name']], basename(get_file_path('./test-get.R')))

From 7c4785a336c401f9f462d36784d4af4a90a6f96d Mon Sep 17 00:00:00 2001
From: Sam Parmar <107635309+parmsam-pfizer@users.noreply.github.com>
Date: Tue, 7 Mar 2023 14:35:41 -0500
Subject: [PATCH 2/6] update news md

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

diff --git a/NEWS.md b/NEWS.md
index 46a8d26..745b583 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,7 @@
+# logrx 0.2.2
+
+- Add `show_repo_url` option in `axecute()` to capture repo URL(s) into log file
+
 # logrx 0.2.1
 
  - non-function objects are no longer returned as functions by `get_used_functions` (#154)

From 7cdac300793573a8ad9bad2469fd4126d68e86e5 Mon Sep 17 00:00:00 2001
From: Sam Parmar <107635309+parmsam-pfizer@users.noreply.github.com>
Date: Mon, 10 Jul 2023 13:46:59 -0400
Subject: [PATCH 3/6] fix unit tests

---
 tests/testthat/test-axecute.R | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-axecute.R b/tests/testthat/test-axecute.R
index 99807fd..ac45188 100644
--- a/tests/testthat/test-axecute.R
+++ b/tests/testthat/test-axecute.R
@@ -68,7 +68,17 @@ test_that("to_report works to control log output elements", {
 })
 
 test_that("show_repo_url works to show repo url elements", {
-  expect_warning(expect_error(file(file.path(logDir, "log_out_repo_url"), "r"), "cannot open the connection"))
+   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_repo_url"), "r"), "cannot open the connection"))
 
    axecute(scriptPath, log_name = "log_out_repo_url",
            log_path = logDir,
@@ -99,7 +109,6 @@ test_that("show_repo_url works to show repo url elements", {
 })
 
 test_that("include_rds works to output log as rds", {
-
    options("log.rx" = NULL)
    scriptPath <- tempfile()
    logDir <- tempdir()

From 3e0257f2127ec780bdac15b4628e901ca3eda43f Mon Sep 17 00:00:00 2001
From: Sam Parmar <107635309+parmsam-pfizer@users.noreply.github.com>
Date: Mon, 10 Jul 2023 13:47:07 -0400
Subject: [PATCH 4/6] update doc

---
 man/log_write.Rd | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/man/log_write.Rd b/man/log_write.Rd
index bff8a7b..906dc09 100644
--- a/man/log_write.Rd
+++ b/man/log_write.Rd
@@ -7,7 +7,7 @@
 log_write(
   file = NA,
   remove_log_object = TRUE,
-  show_repo_url = FALSE
+  show_repo_url = FALSE,
   include_rds = FALSE,
   to_report = c("messages", "output", "result")
 )
@@ -18,14 +18,14 @@ log_write(
 \item{remove_log_object}{Boolean. Should the log object be removed after
 writing the log file? Defaults to TRUE}
 
+\item{show_repo_url}{Boolean. Should the repo URLs be reported
+Defaults to FALSE}
+
 \item{include_rds}{Boolean. Option to export log object as Rds file.
 Defaults to FALSE}
 
 \item{to_report}{String vector. Objects to optionally report; additional
 information in \code{\link{axecute}}}
-
-\item{show_repo_url}{Boolean. Should the repo URLs be reported
-Defaults to FALSE}
 }
 \value{
 Nothing

From 3c3d70103edb7ab28b65f7da8a71e984b645140d Mon Sep 17 00:00:00 2001
From: Sam Parmar <107635309+parmsam-pfizer@users.noreply.github.com>
Date: Thu, 27 Jul 2023 09:33:45 -0500
Subject: [PATCH 5/6] Update NEWS.md

Co-authored-by: Nicholas Masel <61123199+nicholas-masel@users.noreply.github.com>
---
 NEWS.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/NEWS.md b/NEWS.md
index ad63559..58a8c7e 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,6 +1,6 @@
 # logrx 0.3.0
 
-- Add `show_repo_url` option in `axecute()` to capture repo URL(s) into log file
+- 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
 

From c5809caa254bf99f91dd4abbf758370c36c84713 Mon Sep 17 00:00:00 2001
From: Sam Parmar <107635309+parmsam-pfizer@users.noreply.github.com>
Date: Thu, 27 Jul 2023 09:33:55 -0500
Subject: [PATCH 6/6] Update R/axecute.R

Co-authored-by: Nicholas Masel <61123199+nicholas-masel@users.noreply.github.com>
---
 R/axecute.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/axecute.R b/R/axecute.R
index aa45f84..48efd02 100644
--- a/R/axecute.R
+++ b/R/axecute.R
@@ -19,7 +19,7 @@
 #' * messages: any messages generated by program execution
 #' * output: any output generated by program execution
 #' * result: any result generated by program execution
-#' @param show_repo_url Boolean. Should the repo URLs be reported
+#' @param show_repo_url Boolean. Should the repository URLs be reported
 #' Defaults to FALSE
 #'
 #' @importFrom purrr map_chr