Safety data migration

DESCRIPTION

@@ -42,10 +42,13 @@ Imports:
     magrittr,
     purrr,
     rlang,
+    safetyData,
+    safetyCharts,
     shiny,
     shinyjs,
     shinyWidgets,
     stringr,
     yaml
+Remotes: safetyGraphics/safetyCharts
 VignetteBuilder: knitr
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -43,6 +43,7 @@ export(settingsMappingUI)
 import(datamods)
 import(dplyr)
 import(listviewer)
+import(safetyData)
 import(shiny)
 import(yaml)
 importFrom(DT,renderDT)

R/app_init_addin.R

@@ -124,9 +124,9 @@ app_init_addin <- function(){
 
     safetyGraphicsApp1 <- function(
       domainData=list(
-        labs=safetyGraphics::labs, 
-        aes=safetyGraphics::aes, 
-        dm=safetyGraphics::dm
+        labs=safetyData::adam_adlbc, 
+        aes=safetyData::adam_adae, 
+        dm=safetyData::adam_adsl
       ),
       meta = safetyGraphics::meta, 
       charts=NULL,

R/detectStandard.R

@@ -10,8 +10,8 @@
 #'
 #' @return A data frame describing the detected standard for each \code{"text_key"} in the provided metadata. Columns are \code{"domain"}, \code{"text_key"}, \code{"column"} and \code{"standard"}.
 #' @examples 
-#' detectStandard(data=safetyGraphics::aes)  #aes domain evaluated by default
-#' detectStandard(data=safetyGraphics::labs,domain="labs" ) 
+#' detectStandard(data=safetyData::adam_adae)  #aes domain evaluated by default
+#' detectStandard(data=safetyData::adam_adlbc,domain="labs" ) 
 #'
 #' @importFrom stringr str_detect 
 #' 

R/evaluateStandard.R

@@ -10,8 +10,21 @@
 #' @return a list describing to what degree the data set matches the data standard. The "match" property describes compliance with the standard as "full", "partial" or "none". The "checks" property is a list of the data elements expected for the standard and whether they are "valid" in the given data set. "total_checks", "valid_checks" and "invalid_checks" provide counts of the specified checks. "match_percent" is calculated as valid_checks/total_checks.  "mapping" is a data frame describing the detected standard for each \code{"text_key"} in the provided metadata. Columns are \code{"text_key"}, \code{"current"} containing the name of the matched column or field value in the data and \code{"match"} a boolean indicating whether the data matches the standard. 
 #'  
 #' @examples
-#' evaluateStandard(data=labs, meta=meta, domain="labs", standard="adam") # Match is TRUE
-#' evaluateStandard(data=labs, meta=meta, domain="labs", standard="sdtm") # Match is FALSE
+#' # Match is TRUE
+#' evaluateStandard(
+#'  data=safetyData::adam_adlbc, 
+#'  meta=meta, 
+#'  domain="labs", 
+#'  standard="adam"
+#' ) 
+#' 
+#' # Match is FALSE
+#' evaluateStandard(
+#'  data=safetyData::adam_adlbc, 
+#'  meta=meta, 
+#'  domain="labs", 
+#'  standard="sdtm"
+#' ) 
 #'
 #' @import dplyr
 #' @importFrom purrr map 

R/hasColumn.R

@@ -7,8 +7,8 @@
 #' @return logical scalar. TRUE if the column is found. FALSE otherwise
 #'
 #' @examples
-#' safetyGraphics:::hasColumn(columnName="PARAM",data=labs) #TRUE
-#' safetyGraphics:::hasColumn(columnName="Not_a_column",data=labs) #FALSE
+#' safetyGraphics:::hasColumn(columnName="PARAM",data=safetyData::adam_adlbc) #TRUE
+#' safetyGraphics:::hasColumn(columnName="Not_a_column",data=safetyData::adam_adlbc) #FALSE
 #'
 #' @keywords internal
 

R/hasField.R

@@ -8,8 +8,19 @@
 #' @return logical scalar. TRUE if field_value is found. FALSE otherwise
 #'
 #' @examples
-#' safetyGraphics:::hasField(fieldValue="Bilirubin (umol/L)",columnName="PARAM",data=labs) #TRUE
-#' safetyGraphics:::hasField(fieldValue="Not_a_real_value",columnName="",data=labs) #FALSE
+#' #TRUE
+#' safetyGraphics:::hasField(
+#'  fieldValue="Bilirubin (umol/L)",
+#'  columnName="PARAM",
+#'  data=safetyData::adam_adlbc
+#' )
+#' 
+#' #FALSE
+#' safetyGraphics:::hasField(
+#'  fieldValue="Not_a_real_value",
+#'  columnName="",
+#'  data=safetyData::adam_adlbc
+#' )
 #'
 #' @keywords internal
 

R/makeChartConfig.R

@@ -73,13 +73,28 @@ makeChartConfig <- function(dirs, sourceFiles=TRUE){
             chart$order
         ) %>% as.numeric
 
+        #charts should be available to export unless the are modules or chart$export is set to false
+        chart$export <- ifelse(
+            is.null(chart$export),
+            TRUE,
+            chart$export
+        )
+
         return(chart)
     })
-
+    
     names(charts) <- yaml_files %>% file_path_sans_ext %>% basename
-    charts <- charts[order(purrr::map_dbl(charts, function(chart) chart$order))]
+    charts <- charts[order(purrr::map_dbl(charts, function(chart) chart$order))] 
+
+    # Drop charts where order is negative
+    drops <- charts[purrr::map_lgl(charts, function(chart) chart$order < 0)]
+    if(length(drops)>0){
+        message("Dropped ", length(drops), " charts: ",paste(names(drops),collapse=", "))
+        message("To display these charts, set the `order` parameter in the chart object or yaml file to a positive number.")
+        charts <- charts[purrr::map_lgl(charts, function(chart) chart$order >= 0)]
+    }
 
-    message("Found ", length(yaml_files), " config files: ",paste(names(charts),collapse=", "))
+    message("Loaded ", length(charts), " charts: ",paste(names(charts),collapse=", "))
 
     # Bind workflow functions to chart object
     all_functions <- as.character(utils::lsf.str(".GlobalEnv"))

R/mod_reportsTab.R

@@ -47,10 +47,9 @@ reportsTab <- function(input, output, session, charts, data, mapping){
   # create checkbox for selecting charts of interest
   output$checkboxes <- renderUI({
     # no support for modules or broken widgets yet
-    noExport <- c("aeTimelines","hepexplorer","safetyShiftPlot","tplyr_shift")
     chart_type <- charts %>% map(., ~.$type) %>% unlist 
-    chart_name <- charts %>% map(., ~.$name) %>% unlist 
-    charts_keep <- ((! chart_type == "module") & (! chart_name %in% noExport))
+    chart_export <- charts %>% map(., ~.$export) %>% unlist 
+    charts_keep <- ((! chart_type == "module") & (chart_export))
 
     charts_labels <- charts %>% map(., ~ .$label) %>% unlist
     charts_vec <- names(charts)[charts_keep]

R/safetyGraphicsApp.R

@@ -1,20 +1,21 @@
 #' Run the interactive safety graphics app
 #'
 #' @param meta data frame containing the metadata for use in the app. See the preloaded file (\code{?safetyGraphics::meta}) for more data specifications and details. Defaults to \code{safetyGraphics::meta}. 
-#' @param domainData named list of data.frames to be loaded in to the app.
+#' @param domainData named list of data.frames to be loaded in to the app. Sample AdAM data from the safetyData package used by default
 #' @param charts data.frame of charts to be used in the app
 #' @param mapping data.frame specifying the initial values for each data mapping. If no mapping is provided, the app will attempt to generate one via \code{detectStandard()}
 #' @param chartSettingsPaths path(s) where customization functions are saved relative to your working directory. All charts can have itialization (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. 
 #'
 #' @import shiny
+#' @import safetyData
 #' 
 #' @export
 
 safetyGraphicsApp <- function(
   domainData=list(
-    labs=safetyGraphics::labs, 
-    aes=safetyGraphics::aes, 
-    dm=safetyGraphics::dm
+    labs=safetyData::adam_adlbc, 
+    aes=safetyData::adam_adae, 
+    dm=safetyData::adam_adsl
   ),
   meta = safetyGraphics::meta, 
   charts=NULL,