Add 3tr_validate_filename.R

Author: mrueda

docs/content/3tr-specific/3tr_validate_filename.R

@@ -0,0 +1,32 @@
+#!/usr/bin/env Rscript
+# Author: Manuel Rueda ([email protected])
+# Date: Oct-17-2025
+#
+# Minimal filename validator for the 3TR clinical naming convention.
+# Usage: Rscript validate_filename_simple.R <filename>
+# Exits 0 if valid, 1 if invalid.
+
+pattern <- paste0(
+  "^[A-Z0-9]+_[A-Z0-9]+_[A-Za-z0-9-]+_",
+  "(?:REDCAP-(?:RAW|LABEL|DICT)|CSV-RAW)_",
+  "\\d{8}_",
+  "(?:PASS|FAIL|PARTIAL|NA)-[A-Z0-9]+",
+  "(?:_CONV-(?:OMOP|PXF|BFF)(?:-[0-9]+(?:[._][0-9]+)*)?)?",
+  "\\.(?:csv|json)$"
+)
+
+args <- commandArgs(trailingOnly = TRUE)
+
+if (length(args) != 1) {
+  cat("Usage: Rscript validate_filename_simple.R <filename>\n")
+  quit(status = 1)
+}
+
+name <- args[[1]]
+if (grepl(pattern, name, perl = TRUE)) {
+  cat("OK", name, "\n")
+  quit(status = 0)
+} else {
+  cat("INVALID", name, "\n")
+  quit(status = 1)
+}

docs/content/3tr-specific/pheno-clinical-data-nomenclature.md

@@ -78,7 +78,7 @@ Use this to lint filenames. Adjust only if you extend vocabularies.
 
 ## CLI Linter Scripts
 
-Use the accompanying [Python](https://github.com/CNAG-Biomedical-Informatics/omicsdm-documentation/blob/main/docs/content/3tr-specific/3tr_validate_filename.py)  or [Perl](https://github.com/CNAG-Biomedical-Informatics/omicsdm-documentation/blob/main/docs/content/3tr-specific/3tr_validate_filename.pl) scripts to validate names locally.
+Use the accompanying [Python](https://github.com/CNAG-Biomedical-Informatics/omicsdm-documentation/blob/main/docs/content/3tr-specific/3tr_validate_filename.py), [Perl](https://github.com/CNAG-Biomedical-Informatics/omicsdm-documentation/blob/main/docs/content/3tr-specific/3tr_validate_filename.pl) or [R](https://github.com/CNAG-Biomedical-Informatics/omicsdm-documentation/blob/main/docs/content/3tr-specific/3tr_validate_filename.R) scripts to validate names locally.
 
 **Example**
 
@@ -88,4 +88,7 @@ python3 3tr_validate_filename.py 3TR_MS_Study123_REDCAP-RAW_20231204_NA-CNAG.csv
 
 # Perl 5
 perl 3tr_validate_filename.pl 3TR_MS_Study123_REDCAP-RAW_20231204_NA-CNAG.csv
+
+# R
+Rscript 3tr_validate_filename.R 3TR_MS_Study123_REDCAP-RAW_20231204_NA-CNAG.csv
 ```