@openneuro/server 4.20.0-alpha.1 → 4.20.0-alpha.4

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@openneuro/server",
-  "version": "4.20.0-alpha.1",
+  "version": "4.20.0-alpha.4",
   "description": "Core service for the OpenNeuro platform.",
   "license": "MIT",
   "main": "src/server.js",
@@ -21,7 +21,7 @@
     "@elastic/elasticsearch": "7.15.0",
     "@graphql-tools/schema": "^10.0.0",
     "@keyv/redis": "^2.7.0",
-    "@openneuro/search": "^4.20.0-alpha.1",
+    "@openneuro/search": "^4.20.0-alpha.4",
     "@passport-next/passport-google-oauth2": "^1.0.0",
     "@sentry/node": "^4.5.3",
     "base64url": "^3.0.0",
@@ -80,14 +80,13 @@
     "core-js": "^3.10.1",
     "ioredis-mock": "^8.8.1",
     "nodemon": "^2.0.7",
-    "supertest": "^3.0.0",
     "ts-node-dev": "1.1.6",
     "tsc-watch": "^4.2.9",
-    "vitest": "0.33.0",
-    "vitest-fetch-mock": "^0.2.1"
+    "vitest": "0.34.4",
+    "vitest-fetch-mock": "0.2.2"
   },
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "60ca7376fddf72b9516b582ee46c585ef526a39f"
+  "gitHead": "b658c22b75a090a38bdfc3aab081304f5d43c9c8"
 }

package/src/graphql/resolvers/datasetType.ts

@@ -0,0 +1,6 @@
+import { description } from './description.js'
+
+export async function datasetType(dsOrSnapshot): Promise<'schema' | 'legacy'> {
+  const dsDescription = await description(dsOrSnapshot)
+  return dsDescription.DatasetType === 'derivative' ? 'schema' : 'legacy'
+}

package/src/graphql/resolvers/issues.js

@@ -1,13 +1,19 @@
 import Issue from '../../models/issue'
+import { datasetType } from './datasetType'
 import { revalidate } from './validation.js'
 
 /**
  * Issues resolver
  */
-export const issues = (dataset, _, { userInfo }) => {
+export const issues = async (dataset, _, { userInfo }) => {
   return Issue.findOne({
     id: dataset.revision,
     datasetId: dataset.id,
+    // Match if we have no validatorMetadata or the correct 'legacy' / 'schema' value if we do
+    $or: [
+      { 'validatorMetadata.validator': await datasetType(dataset) },
+      { validatorMetadata: { $exists: false } },
+    ],
   })
     .exec()
     .then(data => {
@@ -26,11 +32,16 @@ export const issues = (dataset, _, { userInfo }) => {
 /**
  * Snapshot issues resolver
  */
-export const snapshotIssues = snapshot => {
+export const snapshotIssues = async snapshot => {
   const datasetId = snapshot.id.split(':')[0]
   return Issue.findOne({
     id: snapshot.hexsha,
     datasetId,
+    // Match if we have no validatorMetadata or the correct 'legacy' / 'schema' value if we do
+    $or: [
+      { 'validatorMetadata.validator': await datasetType(snapshot) },
+      { validatorMetadata: { $exists: false } },
+    ],
   })
     .exec()
     .then(data => (data ? data.issues : null))

package/src/graphql/resolvers/summary.ts

@@ -1,4 +1,5 @@
 import Summary, { SummaryDocument } from '../../models/summary'
+import { datasetType } from './datasetType'
 
 /**
  * Summary resolver
@@ -8,6 +9,11 @@ export async function summary(dataset): Promise<Partial<SummaryDocument>> {
     await Summary.findOne({
       id: dataset.revision,
       datasetId: dataset.id,
+      // Match if we have no validatorMetadata or the correct 'legacy' / 'schema' value if we do
+      $or: [
+        { 'validatorMetadata.validator': await datasetType(dataset) },
+        { validatorMetadata: { $exists: false } },
+      ],
     }).exec()
   )?.toObject()
   if (datasetSummary) {
@@ -27,7 +33,11 @@ export async function summary(dataset): Promise<Partial<SummaryDocument>> {
  */
 export const updateSummary = (obj, args) => {
   return Summary.updateOne(
-    { id: args.summary.id, datasetId: args.summary.datasetId },
+    {
+      id: args.summary.id,
+      datasetId: args.summary.datasetId,
+      validatorMetadata: args.summary.validatorMetadata,
+    },
     args.summary,
     {
       upsert: true,

package/src/graphql/resolvers/validation.js

@@ -12,7 +12,11 @@ import { redlock } from '../../libs/redis.js'
  */
 export const updateValidation = (obj, args) => {
   return Issue.updateOne(
-    { id: args.validation.id, datasetId: args.validation.datasetId },
+    {
+      id: args.validation.id,
+      datasetId: args.validation.datasetId,
+      validatorMetadata: args.validation.validatorMetadata,
+    },
     args.validation,
     {
       upsert: true,

package/src/graphql/schema.js

@@ -219,6 +219,14 @@ export const typeDefs = `
     TracerRadionuclide: [String]
   }
 
+  # BIDS Validator metadata
+  input ValidatorMetadata {
+    # Unique string identifying the type of BIDS validator software
+    validator: String
+    # Semantic versioning string for the version of the validation software
+    version: String
+  }
+
   input SummaryInput {
     id: ID! # Git reference for this summary
     datasetId: ID!
@@ -233,6 +241,10 @@ export const typeDefs = `
     totalFiles: Int!
     dataProcessed: Boolean
     pet: SummaryPetInput
+    # Metadata for validation software used
+    validatorMetadata: ValidatorMetadata
+    # BIDS Specification schema version
+    schemaVersion: String
   }
 
   input SubjectMetadataInput {
@@ -246,6 +258,7 @@ export const typeDefs = `
     id: ID! # Git reference for this validation
     datasetId: ID!
     issues: [ValidationIssueInput]!
+    validatorMetadata: ValidatorMetadata
   }
 
   # Dataset Metadata
@@ -598,6 +611,8 @@ export const typeDefs = `
     totalFiles: Int!
     dataProcessed: Boolean
     pet: SummaryPetFields
+    # BIDS Specification schema version
+    schemaVersion: String
   }
 
   type SummaryPetFields {
@@ -645,7 +660,7 @@ export const typeDefs = `
   type ValidationIssue {
     severity: Severity!
     key: String!
-    code: Int!
+    code: Int
     reason: String!
     files: [ValidationIssueFile]
     additionalFileCount: Int
@@ -655,7 +670,7 @@ export const typeDefs = `
   input ValidationIssueInput {
     severity: Severity!
     key: String!
-    code: Int!
+    code: Int
     reason: String!
     files: [ValidationIssueFileInput]
     additionalFileCount: Int
@@ -663,8 +678,10 @@ export const typeDefs = `
   }
 
   type ValidationIssueFile {
+    name: String
+    path: String
     key: String!
-    code: Int!
+    code: Int
     file: ValidationIssueFileDetail
     evidence: String
     line: Int
@@ -675,15 +692,19 @@ export const typeDefs = `
   }
 
   input ValidationIssueFileInput {
-    key: String!
-    code: Int!
+    name: String
+    path: String
+    key: String
+    code: Int
     file: ValidationIssueFileDetailInput
     evidence: String
     line: Int
     character: Int
-    severity: Severity!
+    severity: Severity
     reason: String
     helpUrl: String
+    # Temporary field for compatibility (remove after bids-validator@1.13.0)
+    _datasetAbsPath: String
   }
 
   type ValidationIssueFileDetail {

package/src/models/issue.ts

@@ -5,12 +5,20 @@ export interface IssueDocument extends Document {
   id: string
   datasetId: string
   issues: object
+  validatorMetadata: {
+    validator: string
+    version: string
+  }
 }
 
 const issueSchema = new Schema({
   id: { type: String, required: true },
   datasetId: { type: String, required: true },
   issues: Object,
+  validatorMetadata: {
+    validator: String,
+    version: String,
+  },
 })
 
 const Issue = model<IssueDocument>('Issue', issueSchema)

package/src/models/summary.ts

@@ -24,6 +24,10 @@ export interface SummaryDocument extends Document {
   size: number
   dataProcessed: boolean
   pet: SummaryPetField
+  validatorMetadata: {
+    validator: string
+    version: string
+  }
 }
 
 const summarySchema = new Schema({
@@ -47,6 +51,10 @@ const summarySchema = new Schema({
     TracerName: [String],
     TracerRadionuclide: [String],
   },
+  validatorMetadata: {
+    validator: String,
+    version: String,
+  },
 })
 
 summarySchema.index({ id: 1 })