From beb0101485562e46eebf57d25d86d37893b6040c Mon Sep 17 00:00:00 2001
From: Alexander Jones <happy5214@gmail.com>
Date: Fri, 25 Oct 2024 09:00:52 -0500
Subject: [PATCH 1/2] Fix legacy HED tests (which had several pieces of
 actually invalid data)

---
 bids-validator/tests/hed.spec.js | 28 ++++++++++------------------
 1 file changed, 10 insertions(+), 18 deletions(-)

diff --git a/bids-validator/tests/hed.spec.js b/bids-validator/tests/hed.spec.js
index 11ea1c5a5..cf5fe8f13 100644
--- a/bids-validator/tests/hed.spec.js
+++ b/bids-validator/tests/hed.spec.js
@@ -27,7 +27,7 @@ describe('HED', function () {
     ]
     const jsonDictionary = {
       '/sub01/sub01_task-test_events.json': {
-        myCodes: {
+        test: {
           HED: {
             one: 'Duration/5 s',
           },
@@ -55,12 +55,8 @@ describe('HED', function () {
     ]
     const jsonDictionary = {
       '/sub01/sub01_task-test_events.json': {
-        myCodes: {
-          test: {
-            HED: {
-              one: 'Label/#',
-            },
-          },
+        test: {
+          HED: 'Label/#',
         },
       },
       '/dataset_description.json': { HEDVersion: '8.0.0' },
@@ -86,11 +82,9 @@ describe('HED', function () {
 
     const jsonDictionary = {
       '/sub01/sub01_task-test_events.json': {
-        myCodes: {
-          test: {
-            HED: {
-              one: 'ts:Sensory-presentation, Label/#',
-            },
+        test: {
+          HED: {
+            one: 'ts:Sensory-presentation, Train',
           },
         },
       },
@@ -148,11 +142,9 @@ describe('HED', function () {
 
     const jsonDictionary = {
       '/sub01/sub01_task-test_events.json': {
-        myCodes: {
-          test: {
-            HED: {
-              one: 'ts:Sensory-presentation, Label/#, sc:Sleep-deprivation',
-            },
+        test: {
+          HED: {
+            one: 'ts:Sensory-presentation, Walk, sc:Sleep-deprivation',
           },
         },
       },
@@ -260,7 +252,7 @@ describe('HED', function () {
     ]
     const jsonDictionary = {
       '/sub01/sub01_task-test_events.json': {
-        myCodes: {
+        test: {
           HED: {
             one: 'Duration/5 s',
           },

From a656a9c619e25ef5a2c51aeb0a9e7514d1e17e9c Mon Sep 17 00:00:00 2001
From: Alexander Jones <happy5214@gmail.com>
Date: Wed, 30 Oct 2024 20:54:27 -0500
Subject: [PATCH 2/2] Fix handling of IssueErrors thrown from hed-validator
 (second attempt)

This does not issue warnings for missing HEDVersion fields for every dataset.
---
 bids-validator/validators/hed.js | 60 ++++++++++++++++++--------------
 1 file changed, 33 insertions(+), 27 deletions(-)

diff --git a/bids-validator/validators/hed.js b/bids-validator/validators/hed.js
index 4dde02b48..59ea86c55 100644
--- a/bids-validator/validators/hed.js
+++ b/bids-validator/validators/hed.js
@@ -29,32 +29,24 @@ async function checkHedStrings(tsvs, jsonContents, jsonFiles) {
     )
   }
 
-  const issues = []
-  for (const [sidecarName, sidecarContents] of Object.entries(jsonContents)) {
-    try {
-      const sidecarFile = buildSidecar(sidecarName, sidecarContents, jsonFiles)
-      issues.push(...validateFile(sidecarFile, hedSchemas))
-    } catch (e) {
-      issues.push(new Issue({ code: 109 }))
-      return issues
-    }
-  }
+  const sidecarIssues = validateFiles(
+    buildSidecars(jsonContents, jsonFiles),
+    hedSchemas,
+  )
 
-  if (issues.some((issue) => issue.isError())) {
-    return issues
+  if (sidecarIssues.some((issue) => issue.isError() || issue.code === 109)) {
+    return sidecarIssues
   }
 
-  for (const tsv of tsvs) {
-    try {
-      const tsvFile = buildTsv(tsv, jsonContents)
-      issues.push(...validateFile(tsvFile, hedSchemas))
-    } catch (e) {
-      issues.push(new Issue({ code: 109 }))
-      return issues
-    }
-  }
+  const tsvIssues = validateFiles(buildTsvs(tsvs, jsonContents), hedSchemas)
 
-  return issues
+  return [...sidecarIssues, ...tsvIssues]
+}
+
+function* buildSidecars(jsonContents, jsonFiles) {
+  for (const [sidecarName, sidecarContents] of Object.entries(jsonContents)) {
+    yield buildSidecar(sidecarName, sidecarContents, jsonFiles)
+  }
 }
 
 function buildSidecar(sidecarName, sidecarContents, jsonFiles) {
@@ -63,6 +55,12 @@ function buildSidecar(sidecarName, sidecarContents, jsonFiles) {
   return new hedValidator.bids.BidsSidecar(sidecarName, sidecarContents, file)
 }
 
+function* buildTsvs(tsvs, jsonContents) {
+  for (const tsv of tsvs) {
+    yield buildTsv(tsv, jsonContents)
+  }
+}
+
 function buildTsv(tsv, jsonContents) {
   const potentialSidecars = utils.files.potentialLocations(
     tsv.file.relativePath.replace('.tsv', '.json'),
@@ -81,12 +79,20 @@ function buildTsv(tsv, jsonContents) {
   )
 }
 
-function validateFile(file, hedSchemas) {
-  const issues = file.validate(hedSchemas)
-  if (issues === null) {
-    throw new Error()
+function validateFiles(fileGenerator, hedSchemas) {
+  const issues = []
+  for (const file of fileGenerator) {
+    try {
+      const fileIssues = file.validate(hedSchemas)
+      if (fileIssues === null) {
+        return [new hedValidator.bids.BidsIssue(109)]
+      }
+      issues.push(fileIssues)
+    } catch (issueError) {
+      return hedValidator.bids.BidsHedIssue.fromHedIssues(issueError, file.file)
+    }
   }
-  return issues
+  return issues.flat()
 }
 
 function getSidecarFileObject(sidecarName, jsonFiles) {