Support multiple libPaths

R/app_ui.R

@@ -11,7 +11,13 @@
 
 app_ui <- function(meta, domainData, mapping, standards){
     #read css from pacakge
-    app_css <-  HTML(readLines( paste(.libPaths(),'safetyGraphics','safetyGraphics_app', 'www','index.css', sep="/")))
+    app_css <- NULL
+    for(lib in .libPaths()){
+        if(is.null(app_css)){
+            css_path <- paste(lib,'safetyGraphics','safetyGraphics_app', 'www','index.css', sep="/")
+            if(file.exists(css_path)) app_css <-  HTML(readLines(css_path))
+        }
+    }
 
     #script to append population badge nav bar
     participant_badge<-tags$script(

R/makeChartConfig.R

@@ -23,8 +23,21 @@
 makeChartConfig <- function(dirs, sourceFiles=TRUE){
     # Use the charts settings saved in safetycharts if no path is provided. 
     if(missing(dirs) || is.null(dirs)){
-        #dirs<-paste(.libPaths(),'safetycharts','chartSettings', sep="/")
-        dirs<-paste(.libPaths(),'safetycharts','config', sep="/")
+        safetyChartsFound<-FALSE
+        for(lib in .libPaths()){
+            print(lib)
+            dirs<-paste(lib,'safetyCharts','config', sep="/")               
+            if(file.exists(dirs)) {
+                print("found configs")
+                print(dirs)
+                safetyChartsFound<-TRUE   
+                break               
+            }
+        }
+
+        if(!safetyChartsFound){
+            message("safetyCharts library not found, please install safetyCharts or provide a path to custom chart configuration files. See safetyGraphics vignettes for details.")
+        }
     }
 
     if(sourceFiles){
@@ -54,12 +67,17 @@ makeChartConfig <- function(dirs, sourceFiles=TRUE){
         chart <- read_yaml(path)
         chart$path <- path
         chart$name <- path %>% file_path_sans_ext %>% basename
+        chart$order <- ifelse(
+            is.null(chart$order),
+            length(yaml_files) + 1,
+            chart$order
+        ) %>% as.numeric
+
         return(chart)
     })
 
-
-
     names(charts) <- yaml_files %>% file_path_sans_ext %>% basename
+    charts <- charts[order(purrr::map_dbl(charts, function(chart) chart$order))]
 
     message("Found ", length(yaml_files), " config files: ",paste(names(charts),collapse=", "))
 
@@ -96,6 +114,5 @@ makeChartConfig <- function(dirs, sourceFiles=TRUE){
             return(chart)
         }
     )
-
     return(charts) 
 }

R/mod_chartsTab.R

@@ -57,7 +57,6 @@ chartsTab <- function(input, output, session, chart, data, mapping){
                 message(chart$name, " has an init.")
                 print(chart$functions[chart$workflow$init])
                 params <- do.call(chart$functions[[chart$workflow$init]], params)
-                print(params)
             }
         }
         return(params)
@@ -94,4 +93,4 @@ chartsTab <- function(input, output, session, chart, data, mapping){
             type=chart$type
         )
     }
-}
+}

R/mod_filterTab.R

@@ -26,7 +26,7 @@ filterTabUI <- function(id, filterDomain = "dm"){
                     id = ns("pbar"), value = 100, 
                     total = 100, display_pct = TRUE
                 ),
-                shiny::dataTableOutput(outputId = ns("table")),
+                DT::dataTableOutput(outputId = ns("table")),
                 tags$p("Code dplyr:"),
                 verbatimTextOutput(outputId = ns("code_dplyr")),
                 tags$p("Expression:"),
@@ -80,7 +80,7 @@ filterTab <- function(input, output, session, domainData, filterDomain, id_col){
       )
     })
 
-    output$table <- shiny::renderDataTable({
+    output$table <- DT::renderDataTable({
       res_filter$data_filtered()
     }, options = list(pageLength = 5))
 

R/mod_mappingColumn.R

@@ -109,7 +109,7 @@ mappingColumn <- function(input, output, session, meta, data){
 
   # return the values for all fields as a data.frame   
   meta <- reactive({
-    col_meta <- data.frame(text_key = col_meta$text_key, current=col_val())
+    col_meta <- data.frame(text_key = col_meta$text_key, current=col_val(), stringsAsFactors = FALSE)
     if(nrow(field_meta)>0){
       for(field_id in field_ids){
         field_meta <- data.frame(text_key = field_id,  current=field_vals[[field_id]]())