MONGO_USER and MONGO_PASSWORD added

Author: phgrosjean

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: BioDataScience
 Type: Package
-Version: 2020.0.9000
+Version: 2020.0.9001
 Title: A Series of Learnr Documents for Biological Data Science
 Description: Interactive documents using learnr for studying biological data science.
 Authors@R: c(

NEWS.md

@@ -1,6 +1,8 @@
-# BioDataScience News
+# BioDataScience 2020.0.9001
 
-## Changes in version 2020.0.9000
+- Separate `MONGO_SER` and `MONGO_PASSWORD` variables in `init()` and do not set them if already there.
+
+# BioDataScience 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`

R/init.R

@@ -1,5 +1,10 @@
 #' Initialize the environment for our BioDataScience courses
 #'
+#' This function creates several environment variables that are widely used by
+#' other packages and applications. Currently, `MONGO_URL`, `MONGO_BASE`,
+#' `MONGO_USER` and `MONGO_PASSWORD` are set to default values if not already
+#' there.
+#'
 #' @return Nothing, the function is used for its side-effect of creating global
 #' variables.
 #' @export
@@ -12,8 +17,14 @@
 #' 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")
+  if (Sys.getenv("MONGO_URL") == "")
+    Sys.setenv(MONGO_URL = "mongodb://{user}:{password}@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")
+  if (Sys.getenv("MONGO_BASE") == "")
+    Sys.setenv(MONGO_BASE = "sdd")
+  if (Sys.getenv("MONGO_USER") == "")
+    Sys.setenv(MONGO_USER = "sdd")
+  if (Sys.getenv("MONGO_PASSWORD") == "")
+    Sys.setenv(MONGO_PASSWORD = "sdd")
   # ... other global stuff to do here...
   return()
 }