Merge branch 'release/1.4.0'

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: redcapcustodian
 Type: Package
 Title: System data cleaning for REDCap
-Version: 1.3.2
+Version: 1.4.0
 Authors@R: c(
   person("Philip", "Chase",
         email = "[email protected]",

Dockerfile

@@ -1,4 +1,4 @@
-FROM rocker/tidyverse:4.2.1
+FROM rocker/verse:4.2.1
 
 WORKDIR /home/rocker
 
@@ -20,10 +20,12 @@ RUN R -e "install.packages(c( \
   'rjson', \
   'sendmailR', \
   'sqldf', \
-  'writexl' \
+  'writexl', \
+  'kableExtra' \
 ))"
 
 RUN R -e "devtools::install_github('allanvc/mRpostman')"
+RUN wget -qO- "https://yihui.org/tinytex/install-bin-unix.sh" | sh
 
 # build and install this package
 ADD . /home/rocker/redcapcustodian

NEWS.md

@@ -3,6 +3,12 @@ All notable changes to the redcapcustodian package and its contained scripts wil
 This project adheres to [Semantic Versioning](http://semver.org/).
 
 
+## [1.4.0] - 2022-12-13
+### Added
+- Switch Dockerfile from tidyverse to verse (Laurence James-Woodley)
+- Add render_report.R to render Rmds (Laurence James-Woodley)
+
+
 ## [1.3.2] - 2022-09-14
 ### Changed
 - Specify package for na.exclude() (Philip Chase)

VERSION

@@ -1 +1 @@
-1.3.2
+1.4.0

docs/custom_rscript.md

@@ -174,7 +174,9 @@ 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`](./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](./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](../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](../study_template/report/render_report.R) via cron. Refer to [sample_report](../study_template/cron/sample_report) for an example cron job.
+
 ## Automation with Linux and cron
 
 If you have no container management infrastructure available to you, but your IT support provides Linux hosts, have them build one for you, install Docker on it, and give you `sudo su` access. That will allow you to build and run docker images on the host. 

study_template/cron/sample_report

@@ -0,0 +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

study_template/report/render_report.R

@@ -0,0 +1,42 @@
+library(tidyverse)
+library(dotenv)
+library(REDCapR)
+library(lubridate)
+library(rmarkdown)
+library(sendmailR)
+library(redcapcustodian)
+
+init_etl("render_report")
+
+if (!interactive()) {
+  args <- commandArgs(trailingOnly = T)
+  script_name <- word(args, 2, sep = "=")
+} else {
+  script_name <- "sample_report.Rmd"
+}
+
+report_name <- word(script_name, 1, sep = "\\.")
+
+script_run_time <- set_script_run_time()
+
+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))
+
+email_subject <- paste(report_name, "|", script_run_time)
+body <- "Please see the attached report."
+
+email_body <- list(body, attachment_object)
+
+# send the email with the attached output file
+send_email(email_body, email_subject)
+
+log_job_success(jsonlite::toJSON(script_name))

study_template/report/sample_report.Rmd

@@ -0,0 +1,28 @@
+---
+title: "Sample Report"
+output: pdf_document
+---
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+```
+
+## R Markdown
+
+This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
+
+When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
+
+```{r cars}
+summary(cars)
+```
+
+## Including Plots
+
+You can also embed plots, for example:
+
+```{r pressure, echo=FALSE}
+plot(pressure)
+```
+
+Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.