Merge branch '140-feature-request-create-unit-test-for-rmd-files' int…

…o dev
pharmaverse · Jul 3, 2023 · df6eb4d · df6eb4d
2 parents 9ae9814 + ce6a9d0
commit df6eb4d
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Showing 5 changed files with 30 additions and 5 deletions.
diff --git a/R/get.R b/R/get.R
@@ -155,6 +155,13 @@ get_masked_functions <- function(){
 #'
 get_used_functions <- function(file){
 
+   if (grepl("*.Rmd$", file, ignore.case = TRUE)){
+      tmpfile <- tempfile(fileext = ".R")
+      on.exit(unlink(tmpfile))
+      knitr::purl(file, tmpfile)
+      file <- tmpfile
+   }
+
    # catch error
    retfun <- safely(parse,
                     quiet = FALSE,

diff --git a/R/interact.R b/R/interact.R
@@ -110,6 +110,13 @@ set_log_name_path <- function(log_name = NA, log_path = NA) {
 #' @noRd
 run_safely <- function(file) "dummy"
 
+#' Is this a R Markdown file#'
+#' @param file String. Path to file to execute
+#' @noRd
+is_rmarkdown <- function(file) {
+   grepl("*.Rmd$", file, ignore.case = TRUE)
+}
+
 #' Dummy function for running a file
 #' @noRd
 run_file <- function(file){
@@ -118,7 +125,13 @@ run_file <- function(file){
    } else{
       exec_env <- getOption("log.rx.exec.env")
    }
-   source(file, local = exec_env)
+
+   if (is_rmarkdown(file)) {
+      rmarkdown::render(file, envir = exec_env)
+   } else (
+      source(file, local = exec_env)
+   )
+
 }
 
 #' Safely run an R script and record results, outputs, messages, errors, warnings

diff --git a/R/log.R b/R/log.R
@@ -276,7 +276,7 @@ log_write <- function(file = NA,
    }
    if ("result" %in% to_report){
       cleaned_log_vec <- c(cleaned_log_vec,
-                           write_result())
+                           write_result(file))
    }
 
    cleaned_log_vec <- c(cleaned_log_vec,

diff --git a/R/writer.R b/R/writer.R
@@ -255,14 +255,19 @@ write_output <- function() {
 
 #' Format result attribute for writing
 #'
+#' @param file String. Path to file to execute
 #' @return A formatted vector of results
 #'
 #' @noRd
 #'
-write_result <- function() {
+write_result <- function(file) {
    result <- get_log_element("result")
 
-   c("\nResult:", paste0("\t", capture.output(result$value)))
+   if (is_rmarkdown(file)) {
+      c("\nResult:", paste0("\t", capture.output(result)))
+   } else {
+      c("\nResult:", paste0("\t", capture.output(result$value)))
+   }
 }
 
 #' Format lint results for writing

diff --git a/tests/testthat/test-writer.R b/tests/testthat/test-writer.R
@@ -176,7 +176,7 @@ test_that("write_result will return a formatted log result element", {
 
    run_safely_loudly(fp)
 
-   expect_identical(write_result(),
+   expect_identical(write_result(fp),
                     c("\nResult:", paste0("\t", capture.output(data.frame(test = c(8, 6, 7, 5, 3, 0, 9))))))
 
    log_remove()