Updates for Easier Connect Deployments

.Rbuildignore

@@ -14,4 +14,7 @@
 ^CRAN-RELEASE$
 ^customSettings$
 ^\.github$
+^app\.R$
+^rsconnect$
 ^LICENSE\.md$
+

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: safetyGraphics
 Title: Interactive Graphics for Monitoring Clinical Trial Safety
-Version: 2.0.1
+Version: 2.1.0
 Authors@R: c(
 	person("Jeremy", "Wildfire", email = "jwildfire@gmail.com", role = c("cre","aut")),
 	person("Becca", "Krouse", role="aut"),

R/_disable_autoload.R

@@ -0,0 +1,3 @@
+# Disabling shiny autoload
+
+# See ?shiny::loadSupport for more information

R/makeChartConfig.R

@@ -34,17 +34,14 @@ makeChartConfig <- function(dirs, packages="safetyCharts", packageLocation="conf
     if(!is.null(packages)){
         for(package in packages){
             packageFound<-FALSE
-            for(lib in .libPaths()){
-
-                packageDir<-paste(lib,package,packageLocation, sep="/")               
-                if(file.exists(packageDir)) {
-                    loaded <- do.call(require,list(package))
-                    if(!loaded) do.call(library,list(package)) #Attach the library to the search list if it is installed
-                    message("- Found the {",package,"} package and added ", packageDir," to list of chart locations.")
-                    packageFound<-TRUE   
-                    dirs<-c(dirs, packageDir)
-                    break               
-                }
+            packageDir <- system.file(packageLocation, package = package)
+            if(file.exists(packageDir)) {
+                loaded <- do.call(require,list(package))
+                if(!loaded) do.call(library,list(package)) #Attach the library to the search list if it is installed
+                message("- Found the {",package,"} package and added ", packageDir," to list of chart locations.")
+                packageFound<-TRUE   
+                dirs<-c(dirs, packageDir)
+                break               
             }
             if(!packageFound){
                 message("{",package, "} package not found or '",packageLocation,"' folder does not exist, please install package and confirm that specified folder is found.")

R/mod_safetyGraphicsUI.R

@@ -12,16 +12,12 @@
 #' @export
 
 safetyGraphicsUI <- function(id, meta, domainData, mapping, standards){
-    #read css from pacakge
     ns<-NS(id)
-    app_css <- NULL
-    for(lib in .libPaths()){
-        if(is.null(app_css)){
-            css_path <- paste(lib,'safetyGraphics', 'www','index.css', sep="/")
-            if(file.exists(css_path)) app_css <-  HTML(readLines(css_path))
-        }
-    }
-
+
+    #read css from package
+    css_path <- system.file("www","index.css", package = "safetyGraphics")
+    app_css <-  HTML(readLines(css_path))
+
     #script to append population badge nav bar
     participant_badge<-tags$script(
         HTML(

R/safetyGraphicsApp.R

@@ -7,6 +7,7 @@
 #' @param autoMapping boolean indicating whether the app should attempt to automatically detect data standards and generate mappings for the data provided. Values specified in the `mapping` parameter overwrite automatically generated mappings when both are found. Defaults to true.
 #' @param filterDomain domain used for the data/filter tab. Demographics ("`dm`") is used by default. Using a domain that is not one record per participant is not recommended. 
 #' @param chartSettingsPaths path(s) where customization functions are saved relative to your working directory. All charts can have initialization (e.g. myChart_Init.R) and static charts can have charting functions (e.g. myGraphic_Chart.R).   All R files in this folder are sourced and files with the correct naming convention are linked to the chart. See the Custom Charts vignette for more details. 
+#' @param runNow Should the shiny app object created be run directly? Helpful when writing  functions to dispatch to shinyapps, rsconnect, or shinyproxy.
 #'
 #' @import shiny
 #' @import safetyData
@@ -24,7 +25,8 @@ safetyGraphicsApp <- function(
   mapping=NULL,
   autoMapping=TRUE,
   filterDomain="dm",
-  chartSettingsPaths = NULL
+  chartSettingsPaths = NULL,
+  runNow = TRUE
 ){
   message("Initializing safetyGraphicsApp")
   config <- app_startup(domainData, meta, charts, mapping, autoMapping, filterDomain, chartSettingsPaths)
@@ -43,5 +45,9 @@ safetyGraphicsApp <- function(
       )
     }
   )
-  runApp(app, launch.browser = TRUE)
+
+  if(runNow)
+    runApp(app)
+  else
+    app
 }

R/safetyGraphicsInit.R

@@ -21,14 +21,8 @@ safetyGraphicsInit <- function(charts=makeChartConfig(), delayTime=1000, maxFile
     }
   }
 
-
-  app_css <- NULL
-  for(lib in .libPaths()){
-    if(is.null(app_css)){
-      css_path <- paste(lib,'safetyGraphics', 'www','index.css', sep="/")
-      if(file.exists(css_path)) app_css <-  HTML(readLines(css_path))
-    }
-  }
+    css_path <- system.file("www","index.css", package = "safetyGraphics")
+    app_css <-  HTML(readLines(css_path))
 
   ui<-fluidPage(
     useShinyjs(),

inst/deploy/app.R

@@ -0,0 +1,5 @@
+# Launch the ShinyApp (Do not remove this comment)
+# To deploy, run: rsconnect::deployApp()
+# Or use the blue button on top of this file
+library(safetyGraphics) # or use devtools::install_github() to load dev version
+safetyGraphics::safetyGraphicsApp(runNow = FALSE) # add parameters here (if any)