define2validate.R

## This gist is obsoleted. Refer https://github.com/mokjpn/Define2Validate/ for the new version.

library(R4DSXML)
library(testthat)
library(validate)

define2validate <- function(domain, file="exampleRules.yaml", definexml="Odm_Define.xml") {
  varmd <- subset(getVarMD(definexml), IGD_Name == domain)
  cat(file=file, append=FALSE, "")
  out <- function(...) cat(file=file, append=TRUE, paste(...,"\n",sep=""))
  out("rules:")
  expect_gt(nrow(varmd), 0)
  for(row in 1:nrow(varmd)) {
    varname <- varmd[row, "ID_Name"]    
    
    varLength <- varmd[row, "ID_Length"]
    if(!is.na(varLength)) {
      out("-")
      out("  expr: nchar(as.character(", varname, ")) <= ", varLength)
      out("  name: Length of ", varname)
    }
    varMandatory <- varmd[row, "IR_Mandatory"]
    expect_false(is.na(varMandatory))
    if(varMandatory == "Yes") {
      out("-")
      out("  expr: '!is.na(", varname, ")'")
      out("  name: ",varname, " is mandatory")
    }
  
    varDataType <- varmd[row, "ID_DataType"]
    expect_false(is.na(varDataType))
    if(varDataType == "integer") {
      out("-")
      out("  expr: regexpr(\"^[0-9-]+$\",as.character(", varname,")) == 1") 
      out("  name: ",varname, " should be integer") 
      }
    if(varDataType == "date") {
      out("-")
      out("  expr: regexpr(\"^([0-9]{4})-([0-9]{2})-([0-9]{2})T([0-9]{2}):([0-9]{2}):([0-9]{2})$\",as.character(", varname,")) == 1") 
      out("  name: ", varname, " should be Date")
    }

    varCodeList <- varmd[row, "ID_CodeListOID"]
    if(!is.na(varCodeList)) {
      out("-")
      out("  expr: as.character(", varname, ") %in% CT[CT$OID == \"", varCodeList, "\", \"CodedValue\"]" )
      out("  name: ", varname, " should follow codelist " , varCodeList)
    }
  }
  out("---")
}