Generate JSON schema's from spec schema to validate values in sidecars.

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 }

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",

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(`^${format.pattern}$`);
@@ -424,7 +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({
@@ -442,6 +444,44 @@ 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 && 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
+              }
+          ])
+        } 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)
+      }
+    }
   }
 }
 

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 {
+  Schema
+} from "../types/schema.ts";
 
 export class BIDSContextDataset implements ContextDataset {
   dataset_description: Record<string, unknown>
@@ -25,13 +30,22 @@ export class BIDSContextDataset implements ContextDataset {
   ignored: any[]
   modalities: any[]
   subjects?: ContextDatasetSubjects
+  ajv: Ajv
+  sidecarKeyValidated: Set<string>
 
-  constructor(options?: ValidatorOptions, 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) {
+      this.setCustomAjvFormats(schema)
+    }
     if (options) {
       this.options = options
     }
@@ -44,6 +58,27 @@ export class BIDSContextDataset implements ContextDataset {
       this.dataset_description.DatasetType = 'raw'
     }
   }
+
+  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
+    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 +113,7 @@ 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 +138,7 @@ 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 +200,7 @@ 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)

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

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 {
@@ -81,7 +82,11 @@ export interface SchemaFields {
 
 interface SchemaType {
   type: string
+  format?: string
   enum?: string[]
+  items?: SchemaType[]
+  minItems?: number
+  maxItems?: number
 }
 
 interface AnyOf {

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]

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[]);
   }