v2.2

DESCRIPTION

@@ -16,11 +16,12 @@ Depends: R (>= 4.0)
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 Suggests:
     ggplot2 (>= 3.3.0),
     knitr (>= 1.34),
     rmarkdown (>= 2.10),
+    safetyProfile, 
     shinydashboard (>= 0.7.1),
     shinytest (>= 1.5.0),
     testthat (>= 3.0.4),

NAMESPACE

@@ -3,6 +3,7 @@
 export("%>%")
 export(app_startup)
 export(chartsNav)
+export(chartsNavUI)
 export(chartsTab)
 export(chartsTabUI)
 export(detectStandard)
@@ -32,6 +33,8 @@ export(mappingSelectUI)
 export(mappingTab)
 export(mappingTabUI)
 export(prepareChart)
+export(profileTab)
+export(profileTabUI)
 export(safetyGraphicsApp)
 export(safetyGraphicsInit)
 export(safetyGraphicsServer)
@@ -59,6 +62,8 @@ importFrom(magrittr,"%>%")
 importFrom(purrr,keep)
 importFrom(purrr,map)
 importFrom(purrr,map2)
+importFrom(purrr,map_lgl)
+importFrom(purrr,set_names)
 importFrom(rlang,.data)
 importFrom(shiny,dataTableOutput)
 importFrom(shiny,renderDataTable)
@@ -72,6 +77,7 @@ importFrom(shinyjs,hide)
 importFrom(shinyjs,html)
 importFrom(shinyjs,removeClass)
 importFrom(shinyjs,show)
+importFrom(shinyjs,toggleClass)
 importFrom(shinyjs,useShinyjs)
 importFrom(sortable,add_rank_list)
 importFrom(sortable,bucket_list)

R/app_startup.R

@@ -9,7 +9,9 @@
 #' @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 appName character string defining the name of the app (default = "safetyGraphics")
+#' @param hexPath path to image file with a hex or other logo. safetyGraphics hex used by default.
+#' @param homeTabPath path to html content to be used on the home page. default is a summary of the safetyGraphics framework.
 #' 
 #' @return List of elements for used to initialize the shiny app with the following parameters
 #'  \itemize{
@@ -21,7 +23,13 @@
 #' }
 #' 
 #' @export
-app_startup<-function(domainData=NULL, meta=NULL, charts=NULL, mapping=NULL, autoMapping=NULL, filterDomain=NULL, chartSettingsPaths=NULL){
+app_startup<-function(domainData=NULL, meta=NULL, charts=NULL, mapping=NULL, autoMapping=NULL, filterDomain=NULL, chartSettingsPaths=NULL, appName=NULL, hexPath=NULL, homeTabPath=NULL){
+
+    # Set defaults for app name, hex and home page content. 
+    if (!is.character(appName)) appName <- 'safetyGraphics'
+    if (!is.character(hexPath) || !file.exists(hexPath)) hexPath <- system.file("resources/safetyGraphicsHex.png", package = "safetyGraphics")
+    if (!is.character(homeTabPath) || !file.exists(homeTabPath)) homeTabPath <- system.file('resources/safetyGraphicsHomeTab.html', package = 'safetyGraphics')
+
     # If charts are not provided, load them from chartSettingsPath or the safetyCharts package
     if(is.null(charts)){
         if(is.null(chartSettingsPaths)){
@@ -47,18 +55,18 @@ app_startup<-function(domainData=NULL, meta=NULL, charts=NULL, mapping=NULL, aut
         message("- Dropped ", length(envDrops), " chart(s) with `env` paramter missing or not set to 'safetyGraphics': ",paste(names(envDrops), collapse=", "))
     }
     charts <- charts %>% purrr::keep(~.x$envValid)
-    
+
     #Drop charts if data for required domain(s) is not found
     domainDrops <- charts %>% purrr::keep(~(!all(.x$domain %in% names(domainData))))
     if(length(domainDrops)>0){
         message("- Dropped ", length(domainDrops), " chart(s) with missing data domains: ", paste(names(domainDrops), collapse=", "))
     }
     charts <- charts %>% purrr::keep(~all(.x$domain %in% names(domainData)))
-    
+
     # sort charts based on order  
     chartOrder <- order(charts %>% map_dbl(~.x$order) %>% unlist())
     charts <- charts[chartOrder]
-    
+
     message("- Initializing app with ",length(charts), " chart(s).")
 
     # Set filterDomain to NULL if specified domain doesn't exist
@@ -81,8 +89,11 @@ app_startup<-function(domainData=NULL, meta=NULL, charts=NULL, mapping=NULL, aut
         domainData=domainData,
         mapping=mappingObj$mapping,
         standards=mappingObj$standard,
-        filterDomain=filterDomain
+        filterDomain=filterDomain, 
+        appName=appName,
+        hexPath=hexPath,
+        homeTabPath = homeTabPath
     ) 
 
     return(config)
-}
+}

R/getChartStatus.R

@@ -0,0 +1,120 @@
+#' Check the status of a chart based on the current mapping
+#'
+#' Checks a chart's status when column-level chart specifications are provided in chart$dataSpec.
+#' Note that safetyGraphicsApp() does not allow a `mapping` value that is not found in `domainData`,
+#' so this function only needs to check that an expected parameter exists in `mapping` (not that the
+#' specified column is found in the loaded data). 
+#' 
+#' @param chart `list` chart object
+#' @param mapping `data.frame` current mapping
+#' 
+#' @return `list` Named list with properties:
+#' - status `logical`
+#' - domains `list` list specifying whether all columns are specified in each domain
+#' - columns `list`  list that matches the structure of chart$dataSpec and indicates which variables are available. 
+#'
+#' @examples
+#' sample_chart <- list(
+#'     domains=c("aes","dm"),
+#'     dataSpec=list(
+#'         aes=c("id_col","custom_col"),
+#'         dm=c("id_col","test_col")
+#'     )
+#' )
+#' 
+#' sample_mapping <- data.frame(
+#'     domain=c("aes","aes","dm","dm"),
+#'     text_key=c("id_col","custom_col","id_col","test_col"),
+#'     current=c("myID","AEcol","myID","dmCol")
+#' )
+#' 
+#' check <- safetyGraphics:::getChartStatus(chart=sample_chart, mapping=sample_mapping) 
+#' # check$status=TRUE
+#'
+#' # Add data spec to each chart.
+#' charts <- makeChartConfig() %>%
+#'     map(function(chart) {
+#'         chart$mapping <- chart$domain %>%
+#'             map_dfr(function(domain) {
+#'                 do.call(
+#'                     `::`,
+#'                     list(
+#'                         'safetyCharts',
+#'                         paste0('meta_', domain)
+#'                     )
+#'                 )
+#'             }) %>%
+#'             distinct(domain, col_key, current = standard_adam) %>%
+#'             filter(!is.na(current)) %>%
+#'             select(domain, text_key = col_key, current)
+#' 
+#'         chart$dataSpec <- chart$domain %>%
+#'             map(function(domain) {
+#'                 chart$mapping %>%
+#'                     filter(.data$domain == !!domain) %>%
+#'                     pull(text_key) %>%
+#'                     unique()
+#'             }) %>%
+#'             set_names(chart$domain)
+#' 
+#'         chart
+#'     })
+#'
+#' checks <- map(charts, ~getChartStatus(.x, .x$mapping))
+#' 
+#' @importFrom purrr imap map
+#' @importFrom rlang set_names
+#'
+#' @keywords internal
+getChartStatus <- function(chart, mapping){
+    stopifnot(
+        "Can't get status since chart does not have dataSpec associated."=hasName(chart, 'dataSpec')
+    )
+
+    # check to see whether each individual column has a mapping defined
+    missingCols<-c()
+    colStatus <- names(chart$dataSpec) %>% map(function(domain){
+        domainMapping <- generateMappingList(settingsDF=mapping, domain=domain)
+        requiredCols <- chart$dataSpec[[domain]]
+        colStatus <- requiredCols %>% map(function(col){
+            if(hasName(domainMapping,col)){
+                status<-case_when(
+                    domainMapping[[col]]=='' ~ FALSE,
+                    is.na(domainMapping[[col]]) ~ FALSE,
+                    is.character(domainMapping[[col]]) ~ TRUE
+                )
+            } else{
+                status<-FALSE
+            }            
+            return(status)
+        }) %>% set_names(requiredCols)
+        return(colStatus)    
+    })%>% set_names(names(chart$dataSpec))
+
+    # check to see whether all columns in a domain were valid
+    domainStatus <- colStatus %>%
+        map(~all(unlist(.x))) %>%
+        set_names(names(colStatus))
+
+    # check to see whether all columns in all domains were valid
+    status <- ifelse(all(unlist(domainStatus)),TRUE, FALSE)
+
+    # make a text summary
+    if(status){
+        summary <- "All required mappings found"
+    }else{
+        missingCols <- colStatus %>% imap(function(cols,domain){
+            missingDomainCols <- cols %>% imap(function(status, col){
+                if(status){
+                    return(NULL)
+                }else{
+                    return(paste0(domain,"$",col))
+                }
+            })
+            return(missingDomainCols)
+        })
+        summary<- paste0("Missing Mappings: ",paste(unlist(missingCols),collapse=","))
+    }
+
+    return(list(chart=chart$name, columns=colStatus, domains=domainStatus, status=status, summary=summary))
+}

R/makeChartSummary.R

@@ -2,12 +2,24 @@
 #' @description  makes a nicely formatted html summary for a chart object
 #'
 #' @param chart list containing chart specifications
+#' @param status (optional) chart status from `getChartStatus`. Default is NULL. 
 #' @param showLinks boolean indicating whether to include links
 #' @param class character to include as class
 #' 
 #' @export
 
-makeChartSummary<- function(chart, showLinks=TRUE, class="chart-header"){
+makeChartSummary<- function(chart, status=NULL, showLinks=TRUE, class="chart-header"){
+
+    if(!is.null(status)){
+        if(status$status){
+            status <- div(class="status", tags$small("Status"), tags$i(class="fa fa-check-circle", style="color: green"),title=status$summary)
+        }else{
+            status <- div(class="status", tags$small("Status"), tags$i(class="fa fa-times-circle", style="color: red"),title=status$summary)
+        }
+    }else{
+        status <- NULL
+    }
+
     if(utils::hasName(chart,"links")){
         links<-purrr::map2(
             chart$links, 
@@ -23,24 +35,28 @@ makeChartSummary<- function(chart, showLinks=TRUE, class="chart-header"){
     }else{
         links<-NULL
     }
-
-    labelDiv<-div(tags$small("Chart"),chart$label)
-    typeDiv<-div(tags$small("Type"), chart$type)
-    dataDiv<-div(tags$small("Data Domain"), paste(chart$domain,collapse=" "))
 
+    labelDiv<-div(class="name", tags$small("Chart"),chart$label)
+    typeDiv<-div(class="type", tags$small("Type"), chart$type)
+    dataDiv<-div(class="domain", tags$small("Data Domain"), paste(chart$domain,collapse=" "))
+
+    class <- c('chart-summary',class)
+
     if(showLinks){
         summary<-div(
             labelDiv,
             typeDiv,
             dataDiv, 
             links,
+            status,
             class=class
         )
     } else {
         summary<-div(
             labelDiv,
             typeDiv,
             dataDiv, 
+            status,
             class=class
         )
     }

R/mod_chartsNav.R

@@ -1,22 +1,65 @@
 #' Adds a navbar tab that initializes the Chart Module UI
 #'
-#' @param chart  chart metadata 
-#' @param ns namespace
+#' @param id module id
+#' @param chart chart metadata 
 #' 
 #' @export 
 #' 
 
-chartsNav <- function(chart,ns){
-    appendTab(
-        inputId = "safetyGraphicsApp",
-        menuName = "Charts",
-        tab = tabPanel(
-            title = makeChartSummary(chart, showLinks=FALSE, class="chart-nav"), 
-            value = chart$name, 
-            chartsTabUI(
-                id=ns(chart$name),
-                chart=chart
-            )
+chartsNavUI <- function(id, chart) {
+    ns <- NS(id)
+
+    panel<-tabPanel(
+        title = uiOutput(ns("tabTitle")), 
+        value = chart$name, 
+        chartsTabUI(
+            id=ns("chart"),
+            chart=chart
         )
     )
-}
+
+    return(panel)
+}
+
+#' Server for  a navbar tab 
+#'
+#' @param input Input objects from module namespace
+#' @param output Output objects from module namespace
+#' @param session An environment that can be used to access information and functionality relating to the session
+#' @param chart list containing a safetyGraphics chart object like those returned by \link{makeChartConfig}.
+#' @param data named list of current data sets (Reactive).
+#' @param mapping tibble capturing the current data mappings (Reactive).
+#' 
+#' @export 
+#' 
+
+chartsNav<-function(input, output, session, chart, data, mapping){
+    ns <- session$ns
+
+    chartStatus <- reactive({
+        if(hasName(chart, 'dataSpec')){
+            status<-getChartStatus(chart, mapping())
+        }else{
+            status<-NULL
+        }
+        return(status)
+    })    
+
+    output$tabTitle <- renderUI({
+        makeChartSummary(
+            chart,
+            status=chartStatus(),
+            showLinks=FALSE,
+            class="chart-nav"
+        )
+    })
+
+    callModule(
+        module=chartsTab,
+        id='chart',
+        chart=chart,
+        data=data,
+        mapping=mapping,
+        status=chartStatus
+    )
+}