From 722ecadb1a03ceeb27145fbfb120f2d1ecf72849 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 25 Apr 2024 16:59:50 -0400
Subject: [PATCH 1/3] Enable stems to be globs

---
 bids-validator/src/deps/path.ts                   | 3 +++
 bids-validator/src/validators/filenameIdentify.ts | 4 ++--
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/bids-validator/src/deps/path.ts b/bids-validator/src/deps/path.ts
index a19d88058..de21eb5e6 100644
--- a/bids-validator/src/deps/path.ts
+++ b/bids-validator/src/deps/path.ts
@@ -9,3 +9,6 @@ export {
   parse,
   SEPARATOR,
 } from 'https://deno.land/std@0.217.0/path/mod.ts'
+export {
+  globToRegExp,
+} from 'https://deno.land/std@0.217.0/path/glob_to_regexp.ts'
diff --git a/bids-validator/src/validators/filenameIdentify.ts b/bids-validator/src/validators/filenameIdentify.ts
index 5cfbdc6cc..c3a0ac060 100644
--- a/bids-validator/src/validators/filenameIdentify.ts
+++ b/bids-validator/src/validators/filenameIdentify.ts
@@ -12,7 +12,7 @@
  * object in the schema for reference.
  */
 // @ts-nocheck
-import { SEPARATOR } from '../deps/path.ts'
+import { SEPARATOR, globToRegExp } from '../deps/path.ts'
 import { GenericSchema, Schema } from '../types/schema.ts'
 import { BIDSContext } from '../schema/context.ts'
 import { lookupModality } from '../schema/modalities.ts'
@@ -56,7 +56,7 @@ function findRuleMatches(schema, context) {
 export function _findRuleMatches(node, path, context) {
   if (
     ('path' in node && context.file.name.endsWith(node.path)) ||
-    ('stem' in node && context.file.name.startsWith(node.stem)) ||
+    ('stem' in node && context.file.name.match(globToRegExp(node.stem + '*'))) ||
     ('suffixes' in node && node.suffixes.includes(context.suffix))
   ) {
     context.filenameRules.push(path)

From 2e84f817fa89aba6c951e9296cdd862f85ccbf4a Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 25 Apr 2024 21:11:40 -0400
Subject: [PATCH 2/3] 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

From 9822199eecfb85cd9751d9cfa373a6e14c524752 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 25 Apr 2024 21:46:50 -0400
Subject: [PATCH 3/3] fix: Check if rule.entities exists before accessing keys

---
 bids-validator/src/validators/filenameIdentify.ts | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bids-validator/src/validators/filenameIdentify.ts b/bids-validator/src/validators/filenameIdentify.ts
index e19754205..0816cf638 100644
--- a/bids-validator/src/validators/filenameIdentify.ts
+++ b/bids-validator/src/validators/filenameIdentify.ts
@@ -145,9 +145,9 @@ function entitiesExtensionsInRule(
 ): boolean {
   const rule = schema[path]
   const fileEntities = Object.keys(context.entities)
-  const ruleEntities = Object.keys(rule.entities).map((key) =>
+  const ruleEntities = rule.entities ? Object.keys(rule.entities).map((key) =>
     lookupEntityLiteral(key, schema),
-  )
+  ) : []
   const extInRule =
     !rule.extensions ||
     (rule.extensions && rule.extensions.includes(context.extension))