Merge pull request #118 from pbchase/update_render_report

Update render_report.R to support quarto files

Dockerfile

@@ -11,6 +11,7 @@ RUN R -e "install.packages(c( \
   'RCurl', \
   'REDCapR', \
   'RMariaDB', \
+  'argparse', \
   'checkmate', \
   'dbx', \
   'digest', \

report/render_report.R

@@ -5,38 +5,49 @@ library(lubridate)
 library(rmarkdown)
 library(sendmailR)
 library(redcapcustodian)
+library(argparse)
 
 init_etl("render_report")
 
-if (!dir.exists("output")){
-  dir.create("output")
-}
-
+parser <- ArgumentParser()
+parser$add_argument("script_name", nargs=1, help="Script to be run")
 if (!interactive()) {
-  args <- commandArgs(trailingOnly = T)
-  script_name <- word(args, 2, sep = "=")
+  args <- parser$parse_args()
+  script_name <- args$script_name
+  if(!fs::file_exists(script_name)) {
+    stop(sprintf("Specified file, %s, does not exist", script_name))
+  }
 } else {
-  script_name <- "sample_report.Rmd"
+  script_name <- "dummy.qmd"
+  stop(sprintf("Specified file, %s, does not exist", script_name))
 }
 
 report_name <- word(script_name, 1, sep = "\\.")
+report_type <- word(script_name, 2, sep = "\\.")
 
 script_run_time <- set_script_run_time()
+output_file <-
+  paste0(str_replace(report_name, ".*/", ""),
+         "_",
+         format(script_run_time, "%Y%m%d%H%M%S"),
+         if_else(report_type == "qmd", ".pdf", "")
+         )
+
+if (report_type == "qmd") {
+  quarto::quarto_render(
+    script_name,
+    output_file = output_file,
+    output_format = "pdf"
+  )
+} else {
+  render(
+    script_name,
+    output_file = output_file
+  )
+}
 
-output_file <- here::here(
-  "output",
-  paste0(report_name,
-  "_",
-  format(script_run_time, "%Y%m%d%H%M%S"))
-)
-
-full_path_to_output_file <- render(
-  here::here("report", script_name),
-  output_file = output_file
-)
-
-output_file_extension <- word(full_path_to_output_file, 2 , sep = "\\.")
-attachment_object <- mime_part(full_path_to_output_file, basename(full_path_to_output_file))
+output_file_extension <- word(output_file, 2 , sep = "\\.")
+attachment_object <- mime_part(output_file, output_file)
 
 email_subject <- paste(report_name, "|", script_run_time)
 body <- "Please see the attached report."

study_template/cron/quarto_html_example

@@ -0,0 +1,2 @@
+# Run the example Quarto report
+17 8-17 * * * root /usr/bin/docker run --rm --env-file /rcc/study_template/.env rcc.site Rscript report/render_report.R report/quarto_html_example.qmd

study_template/cron/sample_report

@@ -1,2 +1,2 @@
 # Run the sample Rmd report
-05 8-17 * * * root /usr/bin/docker run --rm --env-file /rcc/study_template/.env rcc.site Rscript report/render_report.R script_name=sample_report.Rmd
+05 8-17 * * * root /usr/bin/docker run --rm --env-file /rcc/study_template/.env rcc.site Rscript report/render_report.R report/sample_report.Rmd

study_template/report/quarto_html_example.qmd

@@ -0,0 +1,27 @@
+---
+title: "Quarto HTML example"
+author: "John Doe"
+format: html
+editor: visual
+---
+
+## Quarto
+
+Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>.
+
+## Running Code
+
+When you click the **Render** button a document will be generated that includes both content and the output of embedded code. You can embed code like this:
+
+```{r}
+1 + 1
+```
+
+You can add options to executable code like this
+
+```{r}
+#| echo: false
+2 * 2
+```
+
+The `echo: false` option disables the printing of code (only output is displayed).

study_template/report/quarto_pdf_example.qmd

@@ -0,0 +1,26 @@
+---
+title: "Quarto PDF example"
+format: pdf
+editor: visual
+---
+
+## Quarto
+
+Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>.
+
+## Running Code
+
+When you click the **Render** button a document will be generated that includes both content and the output of embedded code. You can embed code like this:
+
+```{r}
+1 + 1
+```
+
+You can add options to executable code like this
+
+```{r}
+#| echo: false
+2 * 2
+```
+
+The `echo: false` option disables the printing of code (only output is displayed).

study_template/report/render_report.R

@@ -5,31 +5,49 @@ library(lubridate)
 library(rmarkdown)
 library(sendmailR)
 library(redcapcustodian)
+library(argparse)
 
 init_etl("render_report")
 
+parser <- ArgumentParser()
+parser$add_argument("script_name", nargs=1, help="Script to be run")
 if (!interactive()) {
-  args <- commandArgs(trailingOnly = T)
-  script_name <- word(args, 2, sep = "=")
+  args <- parser$parse_args()
+  script_name <- args$script_name
+  if(!fs::file_exists(script_name)) {
+    stop(sprintf("Specified file, %s, does not exist", script_name))
+  }
 } else {
-  script_name <- "sample_report.Rmd"
+  script_name <- "dummy.qmd"
+  stop(sprintf("Specified file, %s, does not exist", script_name))
 }
 
 report_name <- word(script_name, 1, sep = "\\.")
+report_type <- word(script_name, 2, sep = "\\.")
 
 script_run_time <- set_script_run_time()
+output_file <-
+  paste0(str_replace(report_name, ".*/", ""),
+         "_",
+         format(script_run_time, "%Y%m%d%H%M%S"),
+         if_else(report_type == "qmd", ".pdf", "")
+         )
+
+if (report_type == "qmd") {
+  quarto::quarto_render(
+    script_name,
+    output_file = output_file,
+    output_format = "pdf"
+  )
+} else {
+  render(
+    script_name,
+    output_file = output_file
+  )
+}
 
-output_file = paste0(report_name,
-                     "_",
-                     format(script_run_time, "%Y%m%d%H%M%S"))
-
-full_path_to_output_file <- render(
-  paste0("report/", script_name),
-  output_file = output_file
-)
-
-output_file_extension <- word(full_path_to_output_file, 2 , sep = "\\.")
-attachment_object <- mime_part(full_path_to_output_file, paste0(output_file, ".", output_file_extension))
+output_file_extension <- word(output_file, 2 , sep = "\\.")
+attachment_object <- mime_part(output_file, output_file)
 
 email_subject <- paste(report_name, "|", script_run_time)
 body <- "Please see the attached report."

vignettes/custom_rscript.Rmd

@@ -194,7 +194,7 @@ Stop and think about architecture and study lifecycle.
 If you need something to run periodically, you need to make it easy to run with all of its dependencies packaged up and you need to schedule it. The modern way to package dependencies is to put them all into a container, add your application and run the container. REDCap Custodian supports containerization with Docker. The [`./study_template/Dockerfile`](https://github.com/ctsit/redcapcustodian/tree/master/study_template/Dockerfile) is template you can use to containerize your RScript and RMarkdown. Adapt it to your needs and build the container with [./build.sh](https://github.com/ctsit/redcapcustodian/tree/master/build.sh). If you have good container infrastructure, use it to build and deploy your containers. 
 
 Running automated R Markdown reports from docker requires the use of an Rmd renderer.
-[render_report.R](https://github.com/ctsit/redcapcustodian/tree/master/study_template/report/render_report.R) contains functionality to knit an Rmd, email it and then log the job run. The Rmd script name is passed as a command line argument to [render_report.R](https://github.com/ctsit/redcapcustodian/tree/master/study_template/report/render_report.R) via cron. Refer to [sample_report](https://github.com/ctsit/redcapcustodian/tree/master/study_template/cron/sample_report) for an example cron job.
+[render_report.R](https://github.com/ctsit/redcapcustodian/tree/master/study_template/report/render_report.R) contains functionality to knit an Rmd or a Qmd, email it and then log the job run. The Rmd/Qmd script name is passed as a command line argument to [render_report.R](https://github.com/ctsit/redcapcustodian/tree/master/study_template/report/render_report.R) via cron. Refer to [sample_report](https://github.com/ctsit/redcapcustodian/tree/master/study_template/cron/sample_report) for an example cron job.
 
 ## Automation with Linux and cron