From 087b6a295cd1771061fefafcddbb775749637c5a Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 25 Apr 2024 21:11:40 -0400
Subject: [PATCH] feat: Accept phenotype as a pseudo-datatype

---
 .../src/validators/filenameIdentify.ts        | 23 ++++++-------------
 1 file changed, 7 insertions(+), 16 deletions(-)

diff --git a/bids-validator/src/validators/filenameIdentify.ts b/bids-validator/src/validators/filenameIdentify.ts
index c3a0ac060..e19754205 100644
--- a/bids-validator/src/validators/filenameIdentify.ts
+++ b/bids-validator/src/validators/filenameIdentify.ts
@@ -74,27 +74,18 @@ export function _findRuleMatches(node, path, context) {
 
 export async function datatypeFromDirectory(schema, context) {
   const subEntity = schema.objects.entities.subject.name
-  const subFormat = schema.objects.formats[subEntity.format]
   const sesEntity = schema.objects.entities.session.name
-  const sesFormat = schema.objects.formats[sesEntity.format]
   const parts = context.file.path.split(SEPARATOR)
-  let datatypeIndex = 2
-  if (parts[0] !== '') {
-    // we assume paths have leading '/'
-  }
-  // Ignoring associated data for now
-  const subParts = parts[1].split('-')
-  if (!(subParts.length === 2 && subParts[0] === subEntity)) {
-    // first directory must be subject
-  }
-  if (parts.length < 3) {
+  let datatypeIndex = parts.length - 2
+  if (datatypeIndex < 1) {
     return Promise.resolve()
   }
-  const sesParts = parts[2].split('-')
-  if (sesParts.length === 2 && sesParts[0] === sesEntity) {
-    datatypeIndex = 3
-  }
   const dirDatatype = parts[datatypeIndex]
+  if (dirDatatype === 'phenotype') {
+    // Phenotype is a pseudo-datatype for now.
+    context.datatype = dirDatatype
+    return Promise.resolve()
+  }
   for (let key in schema.rules.modalities) {
     if (schema.rules.modalities[key].datatypes.includes(dirDatatype)) {
       context.modality = key