From 1606d7f379307d739ffd9510d1ad01e894ed34f2 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Fri, 12 Jul 2024 09:47:38 -0500
Subject: [PATCH 01/13] Add jsonschema based type checking for sidecar entry
 values.

---
 bids-validator/src/deps/ajv.ts                |  4 ++
 bids-validator/src/issues/list.ts             |  4 ++
 bids-validator/src/schema/applyRules.ts       | 27 +++++++++++++
 bids-validator/src/schema/context.ts          | 39 ++++++++++++++++++-
 bids-validator/src/types/schema.ts            |  4 ++
 bids-validator/src/utils/objectPathHandler.ts |  3 ++
 bids-validator/src/validators/bids.ts         |  4 +-
 7 files changed, 82 insertions(+), 3 deletions(-)
 create mode 100644 bids-validator/src/deps/ajv.ts

diff --git a/bids-validator/src/deps/ajv.ts b/bids-validator/src/deps/ajv.ts
new file mode 100644
index 000000000..e8ae699ac
--- /dev/null
+++ b/bids-validator/src/deps/ajv.ts
@@ -0,0 +1,4 @@
+export {Ajv} from 'https://esm.sh/ajv@8.16.0';
+import ValidateFunction from 'https://esm.sh/ajv@8.16.0';
+import JSONSchemaType from 'https://esm.sh/ajv@8.16.0';
+export { ValidateFunction, JSONSchemaType }
diff --git a/bids-validator/src/issues/list.ts b/bids-validator/src/issues/list.ts
index 6310d51aa..fc8ddae1a 100644
--- a/bids-validator/src/issues/list.ts
+++ b/bids-validator/src/issues/list.ts
@@ -47,6 +47,10 @@ export const filenameIssues: IssueDefinitionRecord = {
     severity: "warning",
     reason: "A data files JSON sidecar is missing a key listed as recommended.",
   },
+  JSON_SCHEMA_VALIDATION_ERROR: {
+    severity: "error",
+    reason: "Invalid JSON sidecar file. The sidecar is not formatted according the schema.",
+  },
   TSV_ERROR: {
     severity: "error",
     reason: "generic place holder for errors from tsv files",
diff --git a/bids-validator/src/schema/applyRules.ts b/bids-validator/src/schema/applyRules.ts
index 5bd2ce47f..253404e46 100644
--- a/bids-validator/src/schema/applyRules.ts
+++ b/bids-validator/src/schema/applyRules.ts
@@ -171,6 +171,7 @@ function schemaObjectTypeCheck(
   if (value === "n/a") {
     return true;
   }
+
   if ("anyOf" in schemaObject) {
     return schemaObject.anyOf.some((x) =>
       schemaObjectTypeCheck(x, value, schema)
@@ -179,6 +180,7 @@ function schemaObjectTypeCheck(
   if ("enum" in schemaObject && schemaObject.enum) {
     return schemaObject.enum.some((x) => x === value);
   }
+
   // @ts-expect-error
   const format = schema.objects.formats[schemaObject.type];
   const re = new RegExp(`^${format.pattern}$`);
@@ -442,6 +444,31 @@ function evalJsonCheck(
         ]);
       }
     }
+    let originFileKey = ''
+    if (keyName in context.sidecarKeyOrigin) {
+      originFileKey = `${context.sidecarKeyOrigin[keyName]}.${keyName}`
+    }
+    if (context.dataset.sidecarKeyValidated.has(originFileKey)) {
+      return
+    }
+    if (keyName in context.sidecar) {
+      const validate = context.dataset.ajv.compile(schema.objects.metadata[key])
+      const result = validate(context.sidecar[keyName])
+      if (result === false) {
+        for (let error of validate.errors) {
+          const message = 'message' in error ? `message: ${error['message']}` : ''
+          context.issues.addNonSchemaIssue("JSON_SCHEMA_VALIDATION_ERROR", [
+            {
+              ...context.file,
+              evidence: `Failed for this file.key: ${originFileKey} ${message}`
+            }
+          ])
+        }
+      }
+      if (originFileKey) {
+        context.dataset.sidecarKeyValidated.add(originFileKey)
+      }
+    }
   }
 }
 
diff --git a/bids-validator/src/schema/context.ts b/bids-validator/src/schema/context.ts
index 094e3e277..19839717a 100644
--- a/bids-validator/src/schema/context.ts
+++ b/bids-validator/src/schema/context.ts
@@ -16,6 +16,11 @@ import { loadHeader } from '../files/nifti.ts'
 import { buildAssociations } from './associations.ts'
 import { ValidatorOptions } from '../setup/options.ts'
 import { logger } from '../utils/logger.ts'
+import {Ajv, ValidateFunction, JSONSchemaType} from "../deps/ajv.ts";
+import { memoize } from "../utils/memoize.ts";
+import {
+  GenericSchema,
+} from "../types/schema.ts";
 
 export class BIDSContextDataset implements ContextDataset {
   dataset_description: Record<string, unknown>
@@ -25,13 +30,21 @@ export class BIDSContextDataset implements ContextDataset {
   ignored: any[]
   modalities: any[]
   subjects?: ContextDatasetSubjects
+  ajv: Ajv
+  sidecarKeyValidated: Set<string>
 
-  constructor(options?: ValidatorOptions, description = {}) {
+  constructor(options?: ValidatorOptions, schema?: GenericSchema, description = {}) {
     this.dataset_description = description
     this.files = []
     this.tree = {}
     this.ignored = []
     this.modalities = []
+    this.ajv = new Ajv({strictSchema: false})
+    this.ajv.compile = memoize(this.ajv.compile)
+    this.sidecarKeyValidated = new Set<string>()
+    if (schema) {
+      this.setCustomAjvFormats(schema)
+    }
     if (options) {
       this.options = options
     }
@@ -44,6 +57,27 @@ export class BIDSContextDataset implements ContextDataset {
       this.dataset_description.DatasetType = 'raw'
     }
   }
+
+  setCustomAjvFormats(schema: GenericSchema): void {
+    if (typeof schema['objects.formats'] !== "object") {
+        // logger.warning(
+        console.log(
+          `schema.objects.formats missing from schema, format validation disabled.`,
+        )
+        return
+    }
+    const schemaFormats = schema['objects.formats']
+    for (let key of Object.keys(schemaFormats)) {
+      if (typeof schemaFormats[key]['pattern'] !== 'string') {
+        // logger.warning(
+        console.log(
+          `schema.objects.formats.${key} pattern missing or invalid. Skipping this format for addition to context json validator`,
+        )
+        continue
+      }
+      this.ajv.addFormat(key, schemaFormats[key]['pattern'])
+    }
+  }
 }
 
 export class BIDSContextDatasetSubjects implements ContextDatasetSubjects {
@@ -78,6 +112,7 @@ export class BIDSContext implements Context {
   datatype: string
   modality: string
   sidecar: Record<string, any>
+  sidecarKeyOrigin: Record<string, string>
   json: object
   columns: ColumnsMap
   associations: ContextAssociations
@@ -102,6 +137,7 @@ export class BIDSContext implements Context {
     this.datatype = ''
     this.modality = ''
     this.sidecar = {}
+    this.sidecarKeyOrigin = {}
     this.columns = new ColumnsMap()
     this.json = {}
     this.associations = {} as ContextAssociations
@@ -163,6 +199,7 @@ export class BIDSContext implements Context {
         .then((text) => JSON.parse(text))
         .catch((error) => {})
       this.sidecar = { ...this.sidecar, ...json }
+      Object.keys(json).map(x => this.sidecarKeyOrigin[x] = validSidecars[0].path)
     }
     const nextDir = fileTree.directories.find((directory) => {
       return this.file.path.startsWith(directory.path)
diff --git a/bids-validator/src/types/schema.ts b/bids-validator/src/types/schema.ts
index 6862cd527..424751deb 100644
--- a/bids-validator/src/types/schema.ts
+++ b/bids-validator/src/types/schema.ts
@@ -81,7 +81,11 @@ export interface SchemaFields {
 
 interface SchemaType {
   type: string
+  format?: string
   enum?: string[]
+  items?: SchemaType[]
+  minItems?: number
+  maxItems?: number
 }
 
 interface AnyOf {
diff --git a/bids-validator/src/utils/objectPathHandler.ts b/bids-validator/src/utils/objectPathHandler.ts
index 91736280a..f98f59c42 100644
--- a/bids-validator/src/utils/objectPathHandler.ts
+++ b/bids-validator/src/utils/objectPathHandler.ts
@@ -9,6 +9,9 @@ export const hasProp = <K extends PropertyKey, T>(
 export const objectPathHandler = {
   get(target: unknown, property: string) {
     let res = target
+    if (typeof property === "symbol") {
+      return res
+    }
     for (const prop of property.split('.')) {
       if (hasProp(res, prop)) {
         res = res[prop]
diff --git a/bids-validator/src/validators/bids.ts b/bids-validator/src/validators/bids.ts
index 395784e5e..356e63d91 100644
--- a/bids-validator/src/validators/bids.ts
+++ b/bids-validator/src/validators/bids.ts
@@ -49,9 +49,9 @@ export async function validate(
   if (ddFile) {
     const description = await ddFile.text().then((text) => JSON.parse(text));
     summary.dataProcessed = description.DatasetType === "derivative";
-    dsContext = new BIDSContextDataset(options, description);
+    dsContext = new BIDSContextDataset(options, schema, description);
   } else {
-    dsContext = new BIDSContextDataset(options);
+    dsContext = new BIDSContextDataset(options, schema);
     issues.addNonSchemaIssue('MISSING_DATASET_DESCRIPTION', [] as IssueFile[]);
   }
 

From 27a4c45ed548dabcf0c27c95fd2449d06425ca57 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Fri, 12 Jul 2024 10:20:16 -0500
Subject: [PATCH 02/13] fix some ts errors, ignore some to get tests going

---
 bids-validator/src/schema/applyRules.ts | 32 +++++++++++++++++--------
 bids-validator/src/schema/context.ts    | 11 +++++----
 bids-validator/src/types/context.ts     |  4 ++++
 bids-validator/src/types/schema.ts      |  1 +
 4 files changed, 33 insertions(+), 15 deletions(-)

diff --git a/bids-validator/src/schema/applyRules.ts b/bids-validator/src/schema/applyRules.ts
index 253404e46..574d871a8 100644
--- a/bids-validator/src/schema/applyRules.ts
+++ b/bids-validator/src/schema/applyRules.ts
@@ -426,7 +426,7 @@ function evalJsonCheck(
   for (const [key, requirement] of Object.entries(rule.fields)) {
     const severity = getFieldSeverity(requirement, context);
     // @ts-expect-error
-    const keyName = schema.objects.metadata[key].name;
+    const keyName: string = schema.objects.metadata[key].name;
     if (severity && severity !== "ignore" && !(keyName in context.sidecar)) {
       if (requirement.issue?.code && requirement.issue?.message) {
         context.issues.add({
@@ -451,18 +451,30 @@ function evalJsonCheck(
     if (context.dataset.sidecarKeyValidated.has(originFileKey)) {
       return
     }
-    if (keyName in context.sidecar) {
-      const validate = context.dataset.ajv.compile(schema.objects.metadata[key])
+
+    if (keyName in context.sidecar && schema.objects.metadata && keyName in schema.objects.metadata) {
+      // @ts-expect-error
+      const validate = context.dataset.ajv.compile(schema.objects.metadata[keyName])
       const result = validate(context.sidecar[keyName])
       if (result === false) {
-        for (let error of validate.errors) {
-          const message = 'message' in error ? `message: ${error['message']}` : ''
-          context.issues.addNonSchemaIssue("JSON_SCHEMA_VALIDATION_ERROR", [
-            {
-              ...context.file,
-              evidence: `Failed for this file.key: ${originFileKey} ${message}`
-            }
+        let messages = []
+        if (!validate.errors) {
+            context.issues.addNonSchemaIssue("JSON_SCHEMA_VALIDATION_ERROR", [
+              {
+                ...context.file,
+                evidence: `Failed for this file.key: ${originFileKey}`
+              }
           ])
+        } else {
+          for (let error of validate.errors) {
+            const message = 'message' in error ? `message: ${error['message']}` : ''
+            context.issues.addNonSchemaIssue("JSON_SCHEMA_VALIDATION_ERROR", [
+              {
+                ...context.file,
+                evidence: `Failed for this file.key: ${originFileKey} ${message}`
+              }
+            ])
+          }
         }
       }
       if (originFileKey) {
diff --git a/bids-validator/src/schema/context.ts b/bids-validator/src/schema/context.ts
index 19839717a..aec6a3cb9 100644
--- a/bids-validator/src/schema/context.ts
+++ b/bids-validator/src/schema/context.ts
@@ -19,7 +19,7 @@ import { logger } from '../utils/logger.ts'
 import {Ajv, ValidateFunction, JSONSchemaType} from "../deps/ajv.ts";
 import { memoize } from "../utils/memoize.ts";
 import {
-  GenericSchema,
+  Schema
 } from "../types/schema.ts";
 
 export class BIDSContextDataset implements ContextDataset {
@@ -33,13 +33,14 @@ export class BIDSContextDataset implements ContextDataset {
   ajv: Ajv
   sidecarKeyValidated: Set<string>
 
-  constructor(options?: ValidatorOptions, schema?: GenericSchema, description = {}) {
+  constructor(options?: ValidatorOptions, schema?: Schema, description = {}) {
     this.dataset_description = description
     this.files = []
     this.tree = {}
     this.ignored = []
     this.modalities = []
     this.ajv = new Ajv({strictSchema: false})
+    // @ts-expect-error
     this.ajv.compile = memoize(this.ajv.compile)
     this.sidecarKeyValidated = new Set<string>()
     if (schema) {
@@ -58,15 +59,15 @@ export class BIDSContextDataset implements ContextDataset {
     }
   }
 
-  setCustomAjvFormats(schema: GenericSchema): void {
-    if (typeof schema['objects.formats'] !== "object") {
+  setCustomAjvFormats(schema: Schema): void {
+    if (typeof schema.objects.formats !== "object") {
         // logger.warning(
         console.log(
           `schema.objects.formats missing from schema, format validation disabled.`,
         )
         return
     }
-    const schemaFormats = schema['objects.formats']
+    const schemaFormats = schema.objects.formats
     for (let key of Object.keys(schemaFormats)) {
       if (typeof schemaFormats[key]['pattern'] !== 'string') {
         // logger.warning(
diff --git a/bids-validator/src/types/context.ts b/bids-validator/src/types/context.ts
index 4b47ef0cf..cbc2e2e84 100644
--- a/bids-validator/src/types/context.ts
+++ b/bids-validator/src/types/context.ts
@@ -1,4 +1,5 @@
 import { ValidatorOptions } from '../setup/options.ts'
+import { Ajv } from "../deps/ajv.ts";
 
 export interface ContextDatasetSubjects {
   sub_dirs: string[]
@@ -13,6 +14,8 @@ export interface ContextDataset {
   modalities: any[]
   subjects?: ContextDatasetSubjects
   options?: ValidatorOptions
+  ajv: Ajv
+  sidecarKeyValidated: Set<string>
 }
 export interface ContextSubjectSessions {
   ses_dirs: string[]
@@ -97,6 +100,7 @@ export interface Context {
   extension: string
   modality: string
   sidecar: Record<string, any>
+  sidecarKeyOrigin: Record<string, string>
   associations: ContextAssociations
   columns: object
   json: object
diff --git a/bids-validator/src/types/schema.ts b/bids-validator/src/types/schema.ts
index 424751deb..b8a4f86f1 100644
--- a/bids-validator/src/types/schema.ts
+++ b/bids-validator/src/types/schema.ts
@@ -71,6 +71,7 @@ export interface GenericRule {
   format?: string
   required?: string
   index_columns?: string[]
+  metadata?: Record<string, string>
 }
 
 export interface SchemaFields {

From 9231f97ccbbbfc6430d086ad26a43fc746dae632 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Fri, 12 Jul 2024 10:42:52 -0500
Subject: [PATCH 03/13] add schemapath to json validation error message

---
 bids-validator/src/schema/applyRules.ts | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/bids-validator/src/schema/applyRules.ts b/bids-validator/src/schema/applyRules.ts
index 574d871a8..6ff0eadac 100644
--- a/bids-validator/src/schema/applyRules.ts
+++ b/bids-validator/src/schema/applyRules.ts
@@ -457,12 +457,13 @@ function evalJsonCheck(
       const validate = context.dataset.ajv.compile(schema.objects.metadata[keyName])
       const result = validate(context.sidecar[keyName])
       if (result === false) {
+        const evidenceBase = `Failed for this file.key: ${originFileKey} Schema path: ${schemaPath}`
         let messages = []
         if (!validate.errors) {
             context.issues.addNonSchemaIssue("JSON_SCHEMA_VALIDATION_ERROR", [
               {
                 ...context.file,
-                evidence: `Failed for this file.key: ${originFileKey}`
+                evidence: evidenceBase
               }
           ])
         } else {
@@ -471,7 +472,7 @@ function evalJsonCheck(
             context.issues.addNonSchemaIssue("JSON_SCHEMA_VALIDATION_ERROR", [
               {
                 ...context.file,
-                evidence: `Failed for this file.key: ${originFileKey} ${message}`
+                evidence: `${evidenceBase} ${message}`
               }
             ])
           }

From 90032c4a3897c3e4130f6e2f71c71ecaa1db33e0 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Fri, 12 Jul 2024 10:45:40 -0500
Subject: [PATCH 04/13] Update bids-validator/src/schema/applyRules.ts

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 bids-validator/src/schema/applyRules.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bids-validator/src/schema/applyRules.ts b/bids-validator/src/schema/applyRules.ts
index 6ff0eadac..fdbad4757 100644
--- a/bids-validator/src/schema/applyRules.ts
+++ b/bids-validator/src/schema/applyRules.ts
@@ -446,7 +446,7 @@ function evalJsonCheck(
     }
     let originFileKey = ''
     if (keyName in context.sidecarKeyOrigin) {
-      originFileKey = `${context.sidecarKeyOrigin[keyName]}.${keyName}`
+      originFileKey = `${context.sidecarKeyOrigin[keyName]}:${keyName}`
     }
     if (context.dataset.sidecarKeyValidated.has(originFileKey)) {
       return

From 5b00b5fa1344636177aeb90b8e86654f09e98d7b Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Mon, 15 Jul 2024 14:16:37 -0500
Subject: [PATCH 05/13] put all ajv exports in a single line with import type
 modifier as needed

---
 bids-validator/src/deps/ajv.ts | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/bids-validator/src/deps/ajv.ts b/bids-validator/src/deps/ajv.ts
index e8ae699ac..fc6116de2 100644
--- a/bids-validator/src/deps/ajv.ts
+++ b/bids-validator/src/deps/ajv.ts
@@ -1,4 +1 @@
-export {Ajv} from 'https://esm.sh/ajv@8.16.0';
-import ValidateFunction from 'https://esm.sh/ajv@8.16.0';
-import JSONSchemaType from 'https://esm.sh/ajv@8.16.0';
-export { ValidateFunction, JSONSchemaType }
+export {Ajv, type ValidateFunction, type JSONSchemaType } from 'https://esm.sh/ajv@8.16.0';

From 13e666c145fb0a7fca465f4488c7cc97e27fd196 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Mon, 15 Jul 2024 14:39:39 -0500
Subject: [PATCH 06/13] Update bids-validator/src/schema/applyRules.ts

Co-authored-by: Nell Hardcastle <nell@dev-nell.com>
---
 bids-validator/src/schema/applyRules.ts | 1 -
 1 file changed, 1 deletion(-)

diff --git a/bids-validator/src/schema/applyRules.ts b/bids-validator/src/schema/applyRules.ts
index fdbad4757..d8b3c2c6c 100644
--- a/bids-validator/src/schema/applyRules.ts
+++ b/bids-validator/src/schema/applyRules.ts
@@ -458,7 +458,6 @@ function evalJsonCheck(
       const result = validate(context.sidecar[keyName])
       if (result === false) {
         const evidenceBase = `Failed for this file.key: ${originFileKey} Schema path: ${schemaPath}`
-        let messages = []
         if (!validate.errors) {
             context.issues.addNonSchemaIssue("JSON_SCHEMA_VALIDATION_ERROR", [
               {

From 52e1a74bb3ded06ae567eccbe88bf0502bb32d95 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Mon, 15 Jul 2024 14:41:13 -0500
Subject: [PATCH 07/13] add logger warning if filekey origin map not populated
 in context. Bail out of json validation earlier if key not in sidecar

---
 bids-validator/src/schema/applyRules.ts | 60 ++++++++++++++-----------
 1 file changed, 34 insertions(+), 26 deletions(-)

diff --git a/bids-validator/src/schema/applyRules.ts b/bids-validator/src/schema/applyRules.ts
index fdbad4757..f2a8ecb10 100644
--- a/bids-validator/src/schema/applyRules.ts
+++ b/bids-validator/src/schema/applyRules.ts
@@ -444,43 +444,51 @@ function evalJsonCheck(
         ]);
       }
     }
+
+    /* Regardless of if key is required/recommended/optional, we do no
+     * further valdiation if it is not present in sidecar.
+     */
+    if (!(keyName in context.sidecar)) {
+      return
+    }
+
     let originFileKey = ''
     if (keyName in context.sidecarKeyOrigin) {
       originFileKey = `${context.sidecarKeyOrigin[keyName]}:${keyName}`
+    } else {
+      logger.warning(`sidecarKeyOrigin map failed to initialize for ${context.file.path} on key ${keyName}. Validation caching not active for this key.`)
     }
+
     if (context.dataset.sidecarKeyValidated.has(originFileKey)) {
       return
     }
 
-    if (keyName in context.sidecar && schema.objects.metadata && keyName in schema.objects.metadata) {
-      // @ts-expect-error
-      const validate = context.dataset.ajv.compile(schema.objects.metadata[keyName])
-      const result = validate(context.sidecar[keyName])
-      if (result === false) {
-        const evidenceBase = `Failed for this file.key: ${originFileKey} Schema path: ${schemaPath}`
-        let messages = []
-        if (!validate.errors) {
-            context.issues.addNonSchemaIssue("JSON_SCHEMA_VALIDATION_ERROR", [
-              {
-                ...context.file,
-                evidence: evidenceBase
-              }
+    // @ts-expect-error
+    const validate = context.dataset.ajv.compile(schema.objects.metadata[keyName])
+    const result = validate(context.sidecar[keyName])
+    if (result === false) {
+      const evidenceBase = `Failed for this file.key: ${originFileKey} Schema path: ${schemaPath}`
+      if (!validate.errors) {
+          context.issues.addNonSchemaIssue("JSON_SCHEMA_VALIDATION_ERROR", [
+            {
+              ...context.file,
+              evidence: evidenceBase
+            }
+        ])
+      } else {
+        for (let error of validate.errors) {
+          const message = 'message' in error ? `message: ${error['message']}` : ''
+          context.issues.addNonSchemaIssue("JSON_SCHEMA_VALIDATION_ERROR", [
+            {
+              ...context.file,
+              evidence: `${evidenceBase} ${message}`
+            }
           ])
-        } else {
-          for (let error of validate.errors) {
-            const message = 'message' in error ? `message: ${error['message']}` : ''
-            context.issues.addNonSchemaIssue("JSON_SCHEMA_VALIDATION_ERROR", [
-              {
-                ...context.file,
-                evidence: `${evidenceBase} ${message}`
-              }
-            ])
-          }
         }
       }
-      if (originFileKey) {
-        context.dataset.sidecarKeyValidated.add(originFileKey)
-      }
+    }
+    if (originFileKey) {
+      context.dataset.sidecarKeyValidated.add(originFileKey)
     }
   }
 }

From 9ed3e6eba57ab268d04822643670fc5c8d003226 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Thu, 18 Jul 2024 14:32:40 -0500
Subject: [PATCH 08/13] bump bids-examples

---
 bids-validator/tests/data/bids-examples | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bids-validator/tests/data/bids-examples b/bids-validator/tests/data/bids-examples
index 6470461ce..ea3f7f65d 160000
--- a/bids-validator/tests/data/bids-examples
+++ b/bids-validator/tests/data/bids-examples
@@ -1 +1 @@
-Subproject commit 6470461ce3c357080e39a11d7d7b1c4cde9f567b
+Subproject commit ea3f7f65d68850630ab7c550cbe62aac9fceec47

From fd1575a96159882db899053ad84261266b4572b9 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Thu, 18 Jul 2024 16:27:37 -0500
Subject: [PATCH 09/13] bump examples

---
 bids-validator/tests/data/bids-examples | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bids-validator/tests/data/bids-examples b/bids-validator/tests/data/bids-examples
index ea3f7f65d..401f4cfc0 160000
--- a/bids-validator/tests/data/bids-examples
+++ b/bids-validator/tests/data/bids-examples
@@ -1 +1 @@
-Subproject commit ea3f7f65d68850630ab7c550cbe62aac9fceec47
+Subproject commit 401f4cfc0709be0e39c32766b79894160a8a3e45

From 6b61737431e9d781fb905e205e28a9ddc12fc523 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Mon, 29 Jul 2024 18:43:10 -0400
Subject: [PATCH 10/13] FIX: Compile correct metadata definition

---
 bids-validator/src/schema/applyRules.ts | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/bids-validator/src/schema/applyRules.ts b/bids-validator/src/schema/applyRules.ts
index 950f83c55..3417f2fa6 100644
--- a/bids-validator/src/schema/applyRules.ts
+++ b/bids-validator/src/schema/applyRules.ts
@@ -415,7 +415,8 @@ function evalJsonCheck(
   for (const [key, requirement] of Object.entries(rule.fields)) {
     const severity = getFieldSeverity(requirement, context)
     // @ts-expect-error
-    const keyName: string = schema.objects.metadata[key].name;
+    const metadataDef = schema.objects.metadata[key];
+    const keyName: string = metadataDef.name;
     if (severity && severity !== "ignore" && !(keyName in context.sidecar)) {
       if (requirement.issue?.code && requirement.issue?.message) {
         context.issues.add({
@@ -452,8 +453,7 @@ function evalJsonCheck(
       return
     }
 
-    // @ts-expect-error
-    const validate = context.dataset.ajv.compile(schema.objects.metadata[keyName])
+    const validate = context.dataset.ajv.compile(metadataDef)
     const result = validate(context.sidecar[keyName])
     if (result === false) {
       const evidenceBase = `Failed for this file.key: ${originFileKey} Schema path: ${schemaPath}`

From 8b5ec124d0f9dd77cac27245577b50927a2542f4 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Mon, 29 Jul 2024 19:04:25 -0400
Subject: [PATCH 11/13] Remove unused ts-expect-error

---
 bids-validator/src/schema/applyRules.ts | 1 -
 1 file changed, 1 deletion(-)

diff --git a/bids-validator/src/schema/applyRules.ts b/bids-validator/src/schema/applyRules.ts
index 0a3e493aa..16bc07fcc 100644
--- a/bids-validator/src/schema/applyRules.ts
+++ b/bids-validator/src/schema/applyRules.ts
@@ -175,7 +175,6 @@ function schemaObjectTypeCheck(
     return schemaObject.enum.some((x) => x === value)
   }
 
-  // @ts-expect-error
   const format = schemaObject.format
     // @ts-expect-error
     ? schema.objects.formats[schemaObject.format]

From 92cbef9624663b719b7b4c22b6104669eb518f09 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Mon, 29 Jul 2024 19:08:32 -0400
Subject: [PATCH 12/13] chore(fmt): deno fmt [ignore-rev]

---
 bids-validator/src/deps/ajv.ts                |  2 +-
 bids-validator/src/issues/list.ts             |  4 +--
 bids-validator/src/schema/applyRules.ts       | 32 +++++++++----------
 bids-validator/src/schema/context.ts          | 24 +++++++-------
 bids-validator/src/types/context.ts           |  2 +-
 bids-validator/src/utils/objectPathHandler.ts |  2 +-
 bids-validator/src/validators/bids.ts         | 10 +++---
 7 files changed, 37 insertions(+), 39 deletions(-)

diff --git a/bids-validator/src/deps/ajv.ts b/bids-validator/src/deps/ajv.ts
index fc6116de2..d42c5ad69 100644
--- a/bids-validator/src/deps/ajv.ts
+++ b/bids-validator/src/deps/ajv.ts
@@ -1 +1 @@
-export {Ajv, type ValidateFunction, type JSONSchemaType } from 'https://esm.sh/ajv@8.16.0';
+export { Ajv, type JSONSchemaType, type ValidateFunction } from 'https://esm.sh/ajv@8.16.0'
diff --git a/bids-validator/src/issues/list.ts b/bids-validator/src/issues/list.ts
index eacc89001..8af740533 100644
--- a/bids-validator/src/issues/list.ts
+++ b/bids-validator/src/issues/list.ts
@@ -43,8 +43,8 @@ export const filenameIssues: IssueDefinitionRecord = {
     reason: 'A data files JSON sidecar is missing a key listed as recommended.',
   },
   JSON_SCHEMA_VALIDATION_ERROR: {
-    severity: "error",
-    reason: "Invalid JSON sidecar file. The sidecar is not formatted according the schema.",
+    severity: 'error',
+    reason: 'Invalid JSON sidecar file. The sidecar is not formatted according the schema.',
   },
   TSV_ERROR: {
     severity: 'error',
diff --git a/bids-validator/src/schema/applyRules.ts b/bids-validator/src/schema/applyRules.ts
index 16bc07fcc..27593b39e 100644
--- a/bids-validator/src/schema/applyRules.ts
+++ b/bids-validator/src/schema/applyRules.ts
@@ -166,10 +166,8 @@ function schemaObjectTypeCheck(
     return true
   }
 
-  if ("anyOf" in schemaObject) {
-    return schemaObject.anyOf.some((x) =>
-      schemaObjectTypeCheck(x, value, schema)
-    );
+  if ('anyOf' in schemaObject) {
+    return schemaObject.anyOf.some((x) => schemaObjectTypeCheck(x, value, schema))
   }
   if ('enum' in schemaObject && schemaObject.enum) {
     return schemaObject.enum.some((x) => x === value)
@@ -418,9 +416,9 @@ function evalJsonCheck(
   for (const [key, requirement] of Object.entries(rule.fields)) {
     const severity = getFieldSeverity(requirement, context)
     // @ts-expect-error
-    const metadataDef = schema.objects.metadata[key];
-    const keyName: string = metadataDef.name;
-    if (severity && severity !== "ignore" && !(keyName in context.sidecar)) {
+    const metadataDef = schema.objects.metadata[key]
+    const keyName: string = metadataDef.name
+    if (severity && severity !== 'ignore' && !(keyName in context.sidecar)) {
       if (requirement.issue?.code && requirement.issue?.message) {
         context.issues.add({
           key: requirement.issue.code,
@@ -456,7 +454,9 @@ function evalJsonCheck(
     if (keyName in context.sidecarKeyOrigin) {
       originFileKey = `${context.sidecarKeyOrigin[keyName]}:${keyName}`
     } else {
-      logger.warning(`sidecarKeyOrigin map failed to initialize for ${context.file.path} on key ${keyName}. Validation caching not active for this key.`)
+      logger.warning(
+        `sidecarKeyOrigin map failed to initialize for ${context.file.path} on key ${keyName}. Validation caching not active for this key.`,
+      )
     }
 
     if (context.dataset.sidecarKeyValidated.has(originFileKey)) {
@@ -468,20 +468,20 @@ function evalJsonCheck(
     if (result === false) {
       const evidenceBase = `Failed for this file.key: ${originFileKey} Schema path: ${schemaPath}`
       if (!validate.errors) {
-          context.issues.addNonSchemaIssue("JSON_SCHEMA_VALIDATION_ERROR", [
-            {
-              ...context.file,
-              evidence: evidenceBase
-            }
+        context.issues.addNonSchemaIssue('JSON_SCHEMA_VALIDATION_ERROR', [
+          {
+            ...context.file,
+            evidence: evidenceBase,
+          },
         ])
       } else {
         for (let error of validate.errors) {
           const message = 'message' in error ? `message: ${error['message']}` : ''
-          context.issues.addNonSchemaIssue("JSON_SCHEMA_VALIDATION_ERROR", [
+          context.issues.addNonSchemaIssue('JSON_SCHEMA_VALIDATION_ERROR', [
             {
               ...context.file,
-              evidence: `${evidenceBase} ${message}`
-            }
+              evidence: `${evidenceBase} ${message}`,
+            },
           ])
         }
       }
diff --git a/bids-validator/src/schema/context.ts b/bids-validator/src/schema/context.ts
index 51bfdeb33..70031ce26 100644
--- a/bids-validator/src/schema/context.ts
+++ b/bids-validator/src/schema/context.ts
@@ -16,11 +16,9 @@ import { loadHeader } from '../files/nifti.ts'
 import { buildAssociations } from './associations.ts'
 import { ValidatorOptions } from '../setup/options.ts'
 import { logger } from '../utils/logger.ts'
-import {Ajv, ValidateFunction, JSONSchemaType} from "../deps/ajv.ts";
-import { memoize } from "../utils/memoize.ts";
-import {
-  Schema
-} from "../types/schema.ts";
+import { Ajv, JSONSchemaType, ValidateFunction } from '../deps/ajv.ts'
+import { memoize } from '../utils/memoize.ts'
+import { Schema } from '../types/schema.ts'
 
 export class BIDSContextDataset implements ContextDataset {
   dataset_description: Record<string, unknown>
@@ -39,7 +37,7 @@ export class BIDSContextDataset implements ContextDataset {
     this.tree = {}
     this.ignored = []
     this.modalities = []
-    this.ajv = new Ajv({strictSchema: false})
+    this.ajv = new Ajv({ strictSchema: false })
     // @ts-expect-error
     this.ajv.compile = memoize(this.ajv.compile)
     this.sidecarKeyValidated = new Set<string>()
@@ -60,12 +58,12 @@ export class BIDSContextDataset implements ContextDataset {
   }
 
   setCustomAjvFormats(schema: Schema): void {
-    if (typeof schema.objects.formats !== "object") {
-        // logger.warning(
-        console.log(
-          `schema.objects.formats missing from schema, format validation disabled.`,
-        )
-        return
+    if (typeof schema.objects.formats !== 'object') {
+      // logger.warning(
+      console.log(
+        `schema.objects.formats missing from schema, format validation disabled.`,
+      )
+      return
     }
     const schemaFormats = schema.objects.formats
     for (let key of Object.keys(schemaFormats)) {
@@ -199,7 +197,7 @@ export class BIDSContext implements Context {
         .then((text) => JSON.parse(text))
         .catch((error) => {})
       this.sidecar = { ...this.sidecar, ...json }
-      Object.keys(json).map(x => this.sidecarKeyOrigin[x] = validSidecars[0].path)
+      Object.keys(json).map((x) => this.sidecarKeyOrigin[x] = validSidecars[0].path)
     }
     const nextDir = fileTree.directories.find((directory) => {
       return this.file.path.startsWith(directory.path)
diff --git a/bids-validator/src/types/context.ts b/bids-validator/src/types/context.ts
index cbc2e2e84..86f182d98 100644
--- a/bids-validator/src/types/context.ts
+++ b/bids-validator/src/types/context.ts
@@ -1,5 +1,5 @@
 import { ValidatorOptions } from '../setup/options.ts'
-import { Ajv } from "../deps/ajv.ts";
+import { Ajv } from '../deps/ajv.ts'
 
 export interface ContextDatasetSubjects {
   sub_dirs: string[]
diff --git a/bids-validator/src/utils/objectPathHandler.ts b/bids-validator/src/utils/objectPathHandler.ts
index f98f59c42..8abaa525e 100644
--- a/bids-validator/src/utils/objectPathHandler.ts
+++ b/bids-validator/src/utils/objectPathHandler.ts
@@ -9,7 +9,7 @@ export const hasProp = <K extends PropertyKey, T>(
 export const objectPathHandler = {
   get(target: unknown, property: string) {
     let res = target
-    if (typeof property === "symbol") {
+    if (typeof property === 'symbol') {
       return res
     }
     for (const prop of property.split('.')) {
diff --git a/bids-validator/src/validators/bids.ts b/bids-validator/src/validators/bids.ts
index e0fd862cc..ca448c99b 100644
--- a/bids-validator/src/validators/bids.ts
+++ b/bids-validator/src/validators/bids.ts
@@ -47,12 +47,12 @@ export async function validate(
 
   let dsContext
   if (ddFile) {
-    const description = await ddFile.text().then((text) => JSON.parse(text));
-    summary.dataProcessed = description.DatasetType === "derivative";
-    dsContext = new BIDSContextDataset(options, schema, description);
+    const description = await ddFile.text().then((text) => JSON.parse(text))
+    summary.dataProcessed = description.DatasetType === 'derivative'
+    dsContext = new BIDSContextDataset(options, schema, description)
   } else {
-    dsContext = new BIDSContextDataset(options, schema);
-    issues.addNonSchemaIssue('MISSING_DATASET_DESCRIPTION', [] as IssueFile[]);
+    dsContext = new BIDSContextDataset(options, schema)
+    issues.addNonSchemaIssue('MISSING_DATASET_DESCRIPTION', [] as IssueFile[])
   }
 
   let derivatives: FileTree[] = []

From 1945f1e23b719d2a2edb73ef3b1e6d8036a0cb3e Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Mon, 29 Jul 2024 19:10:52 -0400
Subject: [PATCH 13/13] git log --grep "\[ignore-rev\]" --pretty=format:"# %ad
 - %ae - %s%n%H" > .git-blame-ignore-revs

---
 .git-blame-ignore-revs | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index 7059d6f23..dc71356bb 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -1,2 +1,4 @@
+# Mon Jul 29 19:08:32 2024 -0400 - effigies@gmail.com - chore(fmt): deno fmt [ignore-rev]
+92cbef9624663b719b7b4c22b6104669eb518f09
 # Sun Jul 28 22:01:32 2024 -0400 - effigies@gmail.com - chore(fmt): deno fmt [ignore-rev]
 1bccd0a2d09f1b7ff6a26d99c7845bf59908c421
\ No newline at end of file