Merge branch 'master' into add_app_files

.Renviron.d/rstudio=FALSE/.Renviron

@@ -0,0 +1 @@
+ENV=prod

.Renviron.d/rstudio=TRUE/.Renviron

@@ -0,0 +1 @@
+ENV=dev

.Rprofile

@@ -1 +1,22 @@
-source("renv/activate.R")
+try(source("renv/activate.R"))
+
+cat("
+--------------------------------------------------------------------------------
+Welcome to the iAtlas Shiny App
+--------------------------------------------------------------------------------
+\n")
+
+if (Sys.getenv("DOCKERBUILD") == "1") {
+  try(renv::restore())
+  try(startup::startup())
+  local({
+   options(shiny.port = 3838, shiny.host = "0.0.0.0")
+  })
+} else if (length(find.package("devtools", quiet=T)) == 0 || length(find.package("renv", quiet=T)) == 0) {
+  # prompt instead since RStudio won't show progress for slow .RProfile scripts...
+  cat("TODO: Install package requirements. This may take up to an hour the first time.\n")
+  cat("RUN: source('./install.R')\n")
+} else {
+  # auto-run since it should be quick, but makes sure any new requirements are installed.
+  source('./install.R')
+}

.Rprofile.d/ENV=dev.R

@@ -0,0 +1,5 @@
+DB_NAME <- Sys.getenv("DB_NAME", unset = "iatlas_shiny_dev")
+DB_HOST <- Sys.getenv("DB_HOST", unset = "localhost")
+DB_PORT <- Sys.getenv("DB_PORT", unset = "5432")
+DB_USER <- Sys.getenv("DB_USER", unset = "postgres")
+DB_PW <- Sys.getenv("DB_PW", unset = "docker")

.Rprofile.d/ENV=prod.R

@@ -0,0 +1,5 @@
+DB_NAME <- Sys.getenv("DB_NAME", unset = "")
+DB_HOST <- Sys.getenv("DB_HOST", unset = "")
+DB_PORT <- Sys.getenv("DB_PORT", unset = "")
+DB_USER <- Sys.getenv("DB_USER", unset = "")
+DB_PW <- Sys.getenv("DB_PW", unset = "")

.Rprofile.d/ENV=test.R

@@ -0,0 +1,5 @@
+DB_NAME <- Sys.getenv("DB_NAME", unset = "iatlas_shiny_test")
+DB_HOST <- Sys.getenv("DB_HOST", unset = "localhost")
+DB_PORT <- Sys.getenv("DB_PORT", unset = "5432")
+DB_USER <- Sys.getenv("DB_USER", unset = "postgres")
+DB_PW <- Sys.getenv("DB_PW", unset = "docker")

init.R

@@ -0,0 +1,3 @@
+try(startup::startup())
+cat(crayon::blue("SUCCESS: iatlas.app is ready to go.\n"))
+cat(crayon::blue(paste0("RUN: ",crayon::bold("shiny::runApp()\n"))))

install.R

@@ -0,0 +1,2 @@
+renv::restore(confirm=FALSE)
+source('./init.R')

renv.lock

@@ -623,6 +623,13 @@
       "Repository": "CRAN",
       "Hash": "f27a078d834614513608da2c08031130"
     },
+    "startup": {
+      "Package": "startup",
+      "Version": "0.14.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "17a4b68eeeef4ab9f521caf9f16d1e86"
+    },
     "stringi": {
       "Package": "stringi",
       "Version": "1.4.5",