ignore log and output folders ad add timestamp to logfile

.gitignore

@@ -10,8 +10,8 @@
 *.zip
 site
 !inst/testdata/*.csv
-report/*log.txt
-report/*.html
+report/output/*
+report/log/*
 
 # env file
 *.env

R/reporting.R

@@ -34,7 +34,8 @@ render_report <- function(script_path) {
 
   script_path_without_extension <- tools::file_path_sans_ext(script_path)
   base_script_name <- basename(script_path_without_extension)
-  logfile <- paste0(script_path_without_extension, "_log.txt")
+  run_time <- format(redcapcustodian::get_script_run_time(), "%Y-%m-%d_%H%M%S")
+  logfile <- here::here("report", "log", paste0(base_script_name, "_", run_time, ".txt"))
 
   result <- tryCatch({
     capture.output(quarto::quarto_render(script_path), file = logfile)
@@ -57,7 +58,7 @@ render_report <- function(script_path) {
       report_name <- paste0(
         base_script_name,
         "_",
-        format(redcapcustodian::get_script_run_time(), "%Y-%m-%d_%H%M%S"),
+        run_time,
         ".",
         file_extension
       )

report/log/.gitignore

@@ -0,0 +1,2 @@
+*
+!.gitignore

report/output/.gitignore

@@ -1,4 +1,2 @@
-*.csv
-*.xlsx
-*.html
-*.pdf
+*
+!.gitignore

report/render_report.R

@@ -7,19 +7,17 @@ library(argparse)
 init_etl("render_report")
 
 parser <- ArgumentParser()
-parser$add_argument("script_path", nargs=1, help="The full path of the script to be run")
+parser$add_argument("script_path", nargs=1, help="The path of the script to be run")
 
 if (!interactive()) {
   args <- parser$parse_args()
   script_path <- args$script_path
-  if(!fs::file_exists(script_path)) {
-    stop(sprintf("Specified file, %s, does not exist", script_path))
-  }
 } else {
-  script_path <- "study_template/report/quarto_html_example.qmd"
-  if(!fs::file_exists(script_path)) {
-    stop(sprintf("Specified file, %s, does not exist", script_path))
-  }
+  script_path <- here::here("report", "sample_report.Rmd")
+}
+
+if(!fs::file_exists(script_path)) {
+  stop(sprintf("Specified file, %s, does not exist", script_path))
 }
 
 render_results <- render_report(script_path)

study_template/.gitignore

@@ -6,4 +6,5 @@
 *.env
 !examples/testing.env
 output/
-report/*log.txt
+report/output/*
+report/log/*

study_template/report/log/.gitignore

@@ -0,0 +1,2 @@
+*
+!.gitignore

study_template/report/render_report.R

@@ -7,19 +7,17 @@ library(argparse)
 init_etl("render_report")
 
 parser <- ArgumentParser()
-parser$add_argument("script_path", nargs=1, help="The full path of the script to be run")
+parser$add_argument("script_path", nargs=1, help="The path of the script to be run")
 
 if (!interactive()) {
   args <- parser$parse_args()
   script_path <- args$script_path
-  if(!fs::file_exists(script_path)) {
-    stop(sprintf("Specified file, %s, does not exist", script_path))
-  }
 } else {
-  script_path <- "study_template/report/quarto_html_example.qmd"
-  if(!fs::file_exists(script_path)) {
-    stop(sprintf("Specified file, %s, does not exist", script_path))
-  }
+  script_path <- here::here("report", "quarto_html_example.qmd")
+}
+
+if(!fs::file_exists(script_path)) {
+  stop(sprintf("Specified file, %s, does not exist", script_path))
 }
 
 render_results <- render_report(script_path)