init() function added, and record_sdd() now records date with higher precision.

Author: phgrosjean

.Rbuildignore

@@ -14,4 +14,6 @@ Makefile
 ^.*\.Rproj$
 LICENSE
 data-raw
-data-raw/*
+data-raw/*
+Untitled
+Untitled/*

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: BioDataScience
 Type: Package
-Version: 2019.6.0
+Version: 2020.0.9000
 Title: A Series of Learnr Documents for Biological Data Science
 Description: Interactive documents using learnr for studying biological data science.
 Authors@R: c(
@@ -18,5 +18,5 @@ LazyData: true
 URL: https://github.com/BioDataScience-Course/BioDataScience
 BugReports: https://github.com/BioDataScience-Course/BioDataScience/issues
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 6.1.0
+RoxygenNote: 7.1.0
 VignetteBuilder: knitr

NAMESPACE

@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(checker_sdd)
+export(init)
 export(record_sdd)
 export(run)
 export(send_mail_sdd)

NEWS.md

@@ -1,5 +1,11 @@
 # BioDataScience News
 
+## Changes in version 2020.0.9000
+
+- In `record_sdd()`, date is now recorded in GMT timezone and with microseconds.
+- An `init()` function is added to set globally `MONGO_URL` and `MONGO_BASE`
+  environment variables for lerarndown Shiny and learnr applications.
+
 ## Changes in version 2019.6.0
 
 - correction tutorial 06b_recombinaison 

R/init.R

@@ -0,0 +1,19 @@
+#' Initialize the environment for our BioDataScience courses
+#'
+#' @return Nothing, the function is used for its side-effect of creating global
+#' variables.
+#' @export
+#'
+#' @examples
+#' # Use this at the beginning of your learndown Shiny or learnr applications
+#' BioDataScience::init()
+#' # Now, you have access to MONGO_URL and MONGO_BASE
+#' Sys.getenv("MONGO_URL")
+#' Sys.getenv("MONGO_BASE")
+init <- function() {
+  # Set variable environment required to locate our sdd MongoDB database
+  Sys.setenv(MONGO_URL = "mongodb://sdd:sdd@sdd-umons-shard-00-00-umnnw.mongodb.net:27017,sdd-umons-shard-00-01-umnnw.mongodb.net:27017,sdd-umons-shard-00-02-umnnw.mongodb.net:27017/test?ssl=true&replicaSet=sdd-umons-shard-0&authSource=admin")
+  Sys.setenv(MONGO_BASE = "sdd")
+  # ... other global stuff to do here...
+  return()
+}

R/record_sdd.R

@@ -34,10 +34,11 @@ record_sdd <- function(tutorial_id, tutorial_version, user_id, event, data) {
       correct <- ""
   }
   data$correct <- NULL
-  entry <- data.frame(date = Sys.time(), tutorial = tutorial_id,
-    version = tutorial_version, user = user_id, user_name = user_name(),
-    user_email = user_email(), label = label, correct = correct, event = event,
-    data = list_to_json(data))
+  entry <- data.frame(
+    date = format(Sys.time(), format = "%Y-%m-%d %H:%M:%OS6", tz = "GMT"),
+    tutorial = tutorial_id, version = tutorial_version, user = user_id,
+    user_name = user_name(), user_email = user_email(), label = label,
+    correct = correct, event = event, data = list_to_json(data))
   # Not a good idea: if user never clicks "Submit", nothing is fed to database
   #if (correct == "") {
   #  add_file_base64(entry, file = bds_file)