Validate CDISC Dataset-XML with corresponding Define-XML metadata, using R and R4DSXML. Currently only a few rules are implemented, but this supports variable-level metadata, value-level metadata, and controlled terminology defined in your Define-XML.
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Install the required package. testthat, validate from CRAN, R4DSXML from GitHub.
install.packages(c("testthat","validate","devtools")) library(devtools) install_github("DataDrivenInc/R4DSXML/R4DSXML") -
Load the script.
source("https://raw.githubusercontent.com/mokjpn/Define2Validate/master/define2validate.R")
Assume you have your Define-XML file(Odm_Define.xml) for your LB domain dataset(Odm_LB.xml).
- Load the required package.
library(R4DSXML)
library(testthat)
library(validate)
- Specify domain of your Dataset-XML
Domain="LB"
- Call
define2validate()to make validation rule file for validate package. Validation rules will be stored inexampleRules.yamlfile.
define2validate(Domain, file="exampleRules.yaml", definexml="Odm_Define.xml")
- Create
validatorobject.
v <- validator(.file="exampleRules.yaml")
- Read your dataset.
x <- read.dataset.xml(paste("Odm_", Domain, ".xml", sep=""), "Odm_Define.xml")
- Read Controlled Terminology.
CT <- getCT("Odm_Define.xml")
Note: variable name for controlled terminology is fixed to "CT".
- Define
%notin%operator if you use it in your Define-XML's RangeCheck element.
"%notin%" <- function(x, table) !match(x, table, nomatch = 0) > 0
- Do validation and get the summarized result.
cf <- confront(x,v)
summary(cf)
Poster presentation at CDISC Europe Interchange 2017
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Currently, inside definition of "Where Clauses" in Define-XML, referred variables must be from the same domain of value lists that uses the where clauses.
For example, value-level metadata for VS domain variable sometimes refers to variables of DM domain. It will give a error on define2validate.
This limitation is proposed as Issue #1.
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External definition of controlled terminology is not supported yet.
Only controlled terminologies defined inside Define-XML are supported now.
| rule | items | passes | fails | nNA | error | warning | expression |
|---|---|---|---|---|---|---|---|
| Length of DOMAIN | 6 | 6 | 0 | 0 | FALSE | FALSE | nchar(as.character(DOMAIN)) <= 2 |
| DOMAIN is mandatory | 6 | 6 | 0 | 0 | FALSE | FALSE | !is.na(DOMAIN) |
| DOMAIN should follow codelist CL.DOMAIN | 6 | 6 | 0 | 0 | FALSE | FALSE | as.character(DOMAIN) %in% CT[CT[, "OID"] == "CL.DOMAIN", "CodedValue"] |
| Length of LBSEQ | 6 | 6 | 0 | 0 | FALSE | FALSE | nchar(as.character(LBSEQ)) <= 2 |
| LBSEQ is mandatory | 6 | 6 | 0 | 0 | FALSE | FALSE | !is.na(LBSEQ) |
| LBSEQ should be integer | 6 | 6 | 0 | 0 | FALSE | FALSE | regexpr("^[0-9-]+$", as.character(LBSEQ)) == 1 |
| Length of LBREFID | 6 | 6 | 0 | 0 | FALSE | FALSE | nchar(as.character(LBREFID)) <= 7 |
| Length of LBTESTCD | 6 | 6 | 0 | 0 | FALSE | FALSE | nchar(as.character(LBTESTCD)) <= 7 |
| LBTESTCD is mandatory | 6 | 6 | 0 | 0 | FALSE | FALSE | !is.na(LBTESTCD) |
| LBTESTCD should follow codelist CL.LBTESTCD | 6 | 6 | 0 | 0 | FALSE | FALSE | as.character(LBTESTCD) %in% CT[CT[, "OID"] == "CL.LBTESTCD", "CodedValue"] |
| Length of LBTEST | 6 | 6 | 0 | 0 | FALSE | FALSE | nchar(as.character(LBTEST)) <= 22 |
| LBTEST is mandatory | 6 | 6 | 0 | 0 | FALSE | FALSE | !is.na(LBTEST) |
| LBTEST should follow codelist CL.LBTEST | 6 | 6 | 0 | 0 | FALSE | FALSE | as.character(LBTEST) %in% CT[CT[, "OID"] == "CL.LBTEST", "CodedValue"] |
| Length of LBCAT | 6 | 6 | 0 | 0 | FALSE | FALSE | nchar(as.character(LBCAT)) <= 10 |
| Length of LBORRES | 6 | 5 | 1 | 0 | FALSE | FALSE | nchar(as.character(LBORRES)) <= 8 |
| Length of LBORRESU | 6 | 6 | 0 | 0 | FALSE | FALSE | nchar(as.character(LBORRESU)) <= 7 |
| LBORRESU should follow codelist CL.LBRESU | 6 | 6 | 0 | 0 | FALSE | FALSE | as.character(LBORRESU) %in% CT[CT[, "OID"] == "CL.LBRESU", "CodedValue"] |
| Length of LBORNRLO | 6 | 6 | 0 | 0 | FALSE | FALSE | nchar(as.character(LBORNRLO)) <= 8 |
| Length of LBORNRHI | 6 | 6 | 0 | 0 | FALSE | FALSE | nchar(as.character(LBORNRHI)) <= 8 |
| Length of LBSTRESC | 6 | 6 | 0 | 0 | FALSE | FALSE | nchar(as.character(LBSTRESC)) <= 8 |
| Length of LBSTRESN | 6 | 6 | 0 | 0 | FALSE | FALSE | nchar(as.character(LBSTRESN)) <= 5 |
| LBSTRESN should be float | 6 | 6 | 0 | 0 | FALSE | FALSE | (regexpr("^[0-9.+-eE]+$", as.character(LBSTRESN)) == 1) & !is.na(as.numeric(LBSTRESN)) |
| Length of LBSTRESU | 6 | 6 | 0 | 0 | FALSE | FALSE | nchar(as.character(LBSTRESU)) <= 7 |
| Length of LBSTNRLO | 6 | 6 | 0 | 0 | FALSE | FALSE | nchar(as.character(LBSTNRLO)) <= 4 |
| LBSTNRLO should be float | 6 | 6 | 0 | 0 | FALSE | FALSE | (regexpr("^[0-9.+-eE]+$", as.character(LBSTNRLO)) == 1) & !is.na(as.numeric(LBSTNRLO)) |
| Length of LBSTNRHI | 6 | 6 | 0 | 0 | FALSE | FALSE | nchar(as.character(LBSTNRHI)) <= 4 |
| LBSTNRHI should be float | 6 | 6 | 0 | 0 | FALSE | FALSE | (regexpr("^[0-9.+-eE]+$", as.character(LBSTNRHI)) == 1) & !is.na(as.numeric(LBSTNRHI)) |
| Length of LBSTNRC | 0 | 0 | 0 | 0 | TRUE | FALSE | nchar(as.character(LBSTNRC)) <= 19 |
| Length of LBNRIND | 6 | 6 | 0 | 0 | FALSE | FALSE | nchar(as.character(LBNRIND)) <= 20 |
| LBNRIND should follow codelist CL.NRIND | 6 | 0 | 6 | 0 | FALSE | FALSE | as.character(LBNRIND) %in% CT[CT[, "OID"] == "CL.NRIND", "CodedValue"] |
| Length of LBSPEC | 6 | 6 | 0 | 0 | FALSE | FALSE | nchar(as.character(LBSPEC)) <= 5 |
| LBSPEC should follow codelist CL.SPECTYPE | 6 | 0 | 6 | 0 | FALSE | FALSE | as.character(LBSPEC) %in% CT[CT[, "OID"] == "CL.SPECTYPE", "CodedValue"] |
| Length of LBMETHOD | 0 | 0 | 0 | 0 | TRUE | FALSE | nchar(as.character(LBMETHOD)) <= 8 |
| LBMETHOD should follow codelist CL.METHOD | 0 | 0 | 0 | 0 | TRUE | FALSE | as.character(LBMETHOD) %in% CT[CT[, "OID"] == "CL.METHOD", "CodedValue"] |
| Length of LBBLFL | 6 | 3 | 0 | 3 | FALSE | FALSE | nchar(as.character(LBBLFL)) <= 1 |
| LBBLFL should follow codelist CL.NY | 6 | 0 | 6 | 0 | FALSE | FALSE | as.character(LBBLFL) %in% CT[CT[, "OID"] == "CL.NY", "CodedValue"] |
| Length of LBFAST | 6 | 6 | 0 | 0 | FALSE | FALSE | nchar(as.character(LBFAST)) <= 1 |
| LBFAST should follow codelist CL.NY | 6 | 0 | 6 | 0 | FALSE | FALSE | as.character(LBFAST) %in% CT[CT[, "OID"] == "CL.NY", "CodedValue"] |
| Length of VISITNUM | 6 | 6 | 0 | 0 | FALSE | FALSE | nchar(as.character(VISITNUM)) <= 2 |
| VISITNUM should be integer | 6 | 6 | 0 | 0 | FALSE | FALSE | regexpr("^[0-9-]+$", as.character(VISITNUM)) == 1 |
| Length of VISIT | 6 | 6 | 0 | 0 | FALSE | FALSE | nchar(as.character(VISIT)) <= 7 |
| Length of VISITDY | 6 | 6 | 0 | 0 | FALSE | FALSE | nchar(as.character(VISITDY)) <= 3 |
| VISITDY should be integer | 6 | 6 | 0 | 0 | FALSE | FALSE | regexpr("^[0-9-]+$", as.character(VISITDY)) == 1 |
| Length of LBDY | 6 | 6 | 0 | 0 | FALSE | FALSE | nchar(as.character(LBDY)) <= 3 |
| LBDY should be integer | 6 | 6 | 0 | 0 | FALSE | FALSE | regexpr("^[0-9-]+$", as.character(LBDY)) == 1 |
| Length of BILI(LBORRES) | 6 | 5 | 1 | 0 | FALSE | FALSE | (!(LBTESTCD == "BILI" & LBCAT == "CHEMISTRY" & LBSPEC == "BLOOD")) | nchar(as.character(LBORRES)) <= 3 |
| BILI(LBORRES) should be float | 6 | 5 | 1 | 0 | FALSE | TRUE | (!(LBTESTCD == "BILI" & LBCAT == "CHEMISTRY" & LBSPEC == "BLOOD")) | (regexpr("^[0-9.+-eE]+$", as.character(LBORRES)) == 1) & !is.na(as.numeric(LBORRES)) |
| Length of BUN(LBORRES) | 6 | 6 | 0 | 0 | FALSE | FALSE | (!(LBTESTCD == "BUN" & LBCAT == "CHEMISTRY" & LBSPEC == "BLOOD")) | nchar(as.character(LBORRES)) <= 4 |
| BUN(LBORRES) should be float | 6 | 6 | 0 | 0 | FALSE | TRUE | (!(LBTESTCD == "BUN" & LBCAT == "CHEMISTRY" & LBSPEC == "BLOOD")) | (regexpr("^[0-9.+-eE]+$", as.character(LBORRES)) == 1) & !is.na(as.numeric(LBORRES)) |
| Length of GLUC(LBORRES) | 6 | 6 | 0 | 0 | FALSE | FALSE | (!(LBTESTCD == "GLUC" & LBCAT == "CHEMISTRY" & LBSPEC == "BLOOD")) | nchar(as.character(LBORRES)) <= 3 |
| GLUC(LBORRES) should be float | 6 | 6 | 0 | 0 | FALSE | TRUE | (!(LBTESTCD == "GLUC" & LBCAT == "CHEMISTRY" & LBSPEC == "BLOOD")) | (regexpr("^[0-9.+-eE]+$", as.character(LBORRES)) == 1) & !is.na(as.numeric(LBORRES)) |
| Length of GLUC(LBORRES) | 0 | 0 | 0 | 0 | TRUE | FALSE | (!(LBTESTCD == "GLUC" & LBCAT == "URINALYSIS" & LBSPEC == "URINE" & LBMETHOD == "DIPSTICK")) | nchar(as.character(LBORRES)) <= 8 |
| Length of GLUC(LBORRES) | 0 | 0 | 0 | 0 | TRUE | FALSE | (!(LBTESTCD == "GLUC" & LBCAT == "URINALYSIS" & LBSPEC == "URINE" & LBMETHOD == "QUANT")) | nchar(as.character(LBORRES)) <= 8 |
| Length of HCT(LBORRES) | 6 | 6 | 0 | 0 | FALSE | FALSE | (!(LBTESTCD == "HCT" & LBCAT == "HEMATOLOGY" & LBSPEC == "BLOOD")) | nchar(as.character(LBORRES)) <= 4 |
| HCT(LBORRES) should be float | 6 | 6 | 0 | 0 | FALSE | TRUE | (!(LBTESTCD == "HCT" & LBCAT == "HEMATOLOGY" & LBSPEC == "BLOOD")) | (regexpr("^[0-9.+-eE]+$", as.character(LBORRES)) == 1) & !is.na(as.numeric(LBORRES)) |
| Length of HGB(LBORRES) | 6 | 6 | 0 | 0 | FALSE | FALSE | (!(LBTESTCD == "HGB" & LBCAT == "HEMATOLOGY" & LBSPEC == "BLOOD")) | nchar(as.character(LBORRES)) <= 4 |
| HGB(LBORRES) should be float | 6 | 6 | 0 | 0 | FALSE | TRUE | (!(LBTESTCD == "HGB" & LBCAT == "HEMATOLOGY" & LBSPEC == "BLOOD")) | (regexpr("^[0-9.+-eE]+$", as.character(LBORRES)) == 1) & !is.na(as.numeric(LBORRES)) |
| Length of LYM(LBORRES) | 6 | 6 | 0 | 0 | FALSE | FALSE | (!(LBTESTCD == "LYM" & LBCAT == "HEMATOLOGY" & LBSPEC == "BLOOD")) | nchar(as.character(LBORRES)) <= 4 |
| LYM(LBORRES) should be float | 6 | 6 | 0 | 0 | FALSE | TRUE | (!(LBTESTCD == "LYM" & LBCAT == "HEMATOLOGY" & LBSPEC == "BLOOD")) | (regexpr("^[0-9.+-eE]+$", as.character(LBORRES)) == 1) & !is.na(as.numeric(LBORRES)) |
| Length of OCCBLD(LBORRES) | 6 | 6 | 0 | 0 | FALSE | FALSE | (!(LBTESTCD == "OCCBLD" & LBCAT == "URINALYSIS" & LBSPEC == "URINE")) | nchar(as.character(LBORRES)) <= 8 |
| Length of PH(LBORRES) | 6 | 6 | 0 | 0 | FALSE | FALSE | (!(LBTESTCD == "PH" & LBCAT == "URINALYSIS" & LBSPEC == "URINE")) | nchar(as.character(LBORRES)) <= 3 |
| PH(LBORRES) should be float | 6 | 6 | 0 | 0 | FALSE | TRUE | (!(LBTESTCD == "PH" & LBCAT == "URINALYSIS" & LBSPEC == "URINE")) | (regexpr("^[0-9.+-eE]+$", as.character(LBORRES)) == 1) & !is.na(as.numeric(LBORRES)) |
| Length of VITB12(LBORRES) | 6 | 6 | 0 | 0 | FALSE | FALSE | (!(LBTESTCD == "VITB12" & LBCAT == "CHEMISTRY" & LBSPEC == "SERUM")) | nchar(as.character(LBORRES)) <= 3 |
| VITB12(LBORRES) should be integer | 6 | 6 | 0 | 0 | FALSE | FALSE | (!(LBTESTCD == "VITB12" & LBCAT == "CHEMISTRY" & LBSPEC == "SERUM")) | regexpr("^[0-9-]+$", as.character(LBORRES)) == 1 |
| Length of VITB9(LBORRES) | 6 | 6 | 0 | 0 | FALSE | FALSE | (!(LBTESTCD == "VITB9" & LBCAT == "CHEMISTRY" & LBSPEC == "BLOOD")) | nchar(as.character(LBORRES)) <= 5 |
| VITB9(LBORRES) should be float | 6 | 6 | 0 | 0 | FALSE | TRUE | (!(LBTESTCD == "VITB9" & LBCAT == "CHEMISTRY" & LBSPEC == "BLOOD")) | (regexpr("^[0-9.+-eE]+$", as.character(LBORRES)) == 1) & !is.na(as.numeric(LBORRES)) |