change example json & update README

Author: RayStick

R/data-json_metadata.R

@@ -3,10 +3,10 @@
 #' Example metadata for a health dataset, to demo the function domain_mapping.R \cr \cr
 #' This data was created with these five steps:
 #' \enumerate{
-#'   \item Go to https://modelcatalogue.cs.ox.ac.uk/hdruk_live/#/catalogue/dataModel/17e86f3f-ec29-4c8e-9efc-8793a74b107d
+#'   \item Go to https://modelcatalogue.cs.ox.ac.uk/hdruk_live/#/catalogue/dataModel/16920b16-e24c-49f9-b4df-3dc85779822b/dataClasses
 #'   \item Download json metadata file by selecting the 'Export as JSON' option on the download button
 #'   \item \code{install.packages("rjson")}
-#'   \item \code{json_metadata <- rjson::fromJSON(file = '/browseMetadata/data-raw/maternity_indicators_dataset_(mids)_20240105T132210.json')}
+#'   \item \code{json_metadata <- rjson::fromJSON(file = '/browseMetadata/data-raw/national_community_child_health_database_(ncchd)_20240405T130125.json')}
 #'   \item \code{usethis::use_data(json_metadata)}
 #' }
 #'
@@ -16,5 +16,5 @@
 #'
 #' @format Nested lists
 #'
-#' @source https://modelcatalogue.cs.ox.ac.uk/hdruk_live/#/catalogue/dataModel/17e86f3f-ec29-4c8e-9efc-8793a74b107d
+#' @source https://modelcatalogue.cs.ox.ac.uk/hdruk_live/#/catalogue/dataModel/16920b16-e24c-49f9-b4df-3dc85779822b/dataClasses
 "json_metadata"

R/domain_mapping.R

@@ -181,16 +181,14 @@ domain_mapping <- function(json_file = NULL, domain_file = NULL, look_up_file =
         } else {
         # collect user responses
         decision_output <- user_categorisation(selectTable_df$Label[datavar],selectTable_df$Description[datavar],selectTable_df$Type[datavar])
-        for (d in 1:length(decision_output$decision)) {
-          # input user responses into output
-          this_Output <- row_Output
-          this_Output[nrow(this_Output) + 1 , ] <- NA
-          this_Output$DataElement[1] <- selectTable_df$Label[datavar]
-          this_Output$Domain_code[1] <- decision_output$decision[d]
-          this_Output$Note[1] <- decision_output$decision_note[1]
-          Output <- rbind(Output,this_Output)
-          utils::write.csv(Output, output_fname, row.names = FALSE) # save as we go in case session terminates prematurely
-          }
+        # input user responses into output
+        this_Output <- row_Output
+        this_Output[nrow(this_Output) + 1 , ] <- NA
+        this_Output$DataElement[1] <- selectTable_df$Label[datavar]
+        this_Output$Domain_code[1] <- decision_output$decision[1]
+        this_Output$Note[1] <- decision_output$decision_note[1]
+        Output <- rbind(Output,this_Output)
+        utils::write.csv(Output, output_fname, row.names = FALSE) # save as we go in case session terminates prematurely
         }
     } # end of loop for DataElement
 

R/user_categorisation.R

@@ -19,24 +19,24 @@ user_categorisation <- function(data_element,data_desc,data_type) {
     "\n\nDATA TYPE -----> ", data_type, "\n"
   ))
 
-    # ask user for categorisation
-    decision <- numeric(0)
-    cat("\n \n")
-    cli_alert_info("Categorise this data element (one or multiple domains):")
-    cat("\n")
-    while (length(decision) == 0) {
-      decision <- scan(file="",what=0)
+  # ask user for categorisation
+  decision <- character(0)
+  cat("\n \n")
+  cli_alert_info("Categorise this data element into one or more domains, e.g. 5 or 5,8:")
+  cat("\n")
+  while (length(decision) == 0) {
+    decision <- scan(file="",what="",n=1)
     }
 
-    # ask user for note on categorisation
-    decision_note <- character(0)
-    cat("\n \n")
-    cli_alert_info("Write a note to go with this decision (or 'None'):")
-    cat("\n")
-    while (length(decision_note) == 0) {
-      decision_note <- scan(file="",what="",n=1)
-      }
+  # ask user for note on categorisation
+  decision_note <- character(0)
+  cat("\n \n")
+  cli_alert_info("Write a note to go with this decision (or 'N'):")
+  cat("\n")
+  while (length(decision_note) == 0) {
+    decision_note <- scan(file="",what="",n=1)
+    }
 
-return(list(decision = decision,decision_note = decision_note))
+  return(list(decision = decision,decision_note = decision_note))
 
-}
+  }