@openneuro/server 4.31.2 → 4.32.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@openneuro/server",
-  "version": "4.31.2",
+  "version": "4.32.0",
   "description": "Core service for the OpenNeuro platform.",
   "license": "MIT",
   "main": "src/server.js",
@@ -21,7 +21,7 @@
     "@elastic/elasticsearch": "8.13.1",
     "@graphql-tools/schema": "^10.0.0",
     "@keyv/redis": "^2.7.0",
-    "@openneuro/search": "^4.31.2",
+    "@openneuro/search": "^4.32.0",
     "@sentry/node": "^8.25.0",
     "@sentry/profiling-node": "^8.25.0",
     "base64url": "^3.0.0",
@@ -85,5 +85,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "d2665a438f56c1b2400f33073a43f2e996c286d1"
+  "gitHead": "3dd549a9ec43bbbf00a295a35b30f43cb7c29ffd"
 }

package/src/graphql/resolvers/dataset-search.ts

@@ -181,8 +181,10 @@ const parseQuery = async (query, datasetType, datasetStatus, userId) => {
       })
     } else if (datasetStatus === "Invalid") {
       addClause(query, "filter", {
-        term: {
-          ["draft.issues.severity"]: "error",
+        range: {
+          "latestSnapshot.validation.errors": {
+            gt: 0,
+          },
         },
       })
     }

package/src/graphql/resolvers/draft.ts

@@ -1,6 +1,6 @@
 import Summary from "../../models/summary"
 import { summary } from "./summary"
-import { issues } from "./issues.js"
+import { issues, issuesDraftStatus } from "./issues.js"
 import { description } from "./description.js"
 import { readme } from "./readme.js"
 import { getDraftRevision } from "../../datalad/draft.js"
@@ -37,6 +37,7 @@ const draft = {
   size: draftSize,
   summary,
   issues,
+  issuesStatus: issuesDraftStatus,
   validation,
   modified: (obj) => obj.modified,
   description,

package/src/graphql/resolvers/issues.ts

@@ -46,3 +46,42 @@ export const snapshotIssues = async (snapshot) => {
     .exec()
     .then((data) => (data ? data.issues : null))
 }
+
+/**
+ * Resolver implementation for legacy validator status summary
+ */
+export async function issuesStatus(datasetId, version) {
+  const data = await Issue.findOne({
+    id: version,
+    datasetId,
+  }).exec()
+  if (data) {
+    const warnings = data.issues.filter((issue) =>
+      issue.severity === "warning"
+    ).length
+    const errors = data.issues.filter((issue) =>
+      issue.severity === "error"
+    ).length
+    return {
+      errors,
+      warnings,
+    }
+  } else {
+    return null
+  }
+}
+
+/**
+ * Draft specific issues status resolver
+ */
+export function issuesDraftStatus(dataset) {
+  return issuesStatus(dataset.id, dataset.revision)
+}
+
+/**
+ * Draft specific issues status resolver
+ */
+export function issuesSnapshotStatus(snapshot) {
+  const datasetId = snapshot.id.split(":")[0]
+  return issuesStatus(datasetId, snapshot.hexsha)
+}

package/src/graphql/resolvers/snapshots.ts

@@ -5,7 +5,7 @@ import { checkDatasetRead, checkDatasetWrite } from "../permissions"
 import { readme } from "./readme.js"
 import { description } from "./description.js"
 import { summary } from "./summary"
-import { snapshotIssues } from "./issues.js"
+import { issuesSnapshotStatus, snapshotIssues } from "./issues.js"
 import { getFiles } from "../../datalad/files"
 import Summary from "../../models/summary"
 import DatasetModel from "../../models/dataset"
@@ -259,6 +259,7 @@ export const deleteSnapshot = (obj, { datasetId, tag }, { user, userInfo }) => {
 const Snapshot = {
   analytics: (snapshot) => analytics(snapshot),
   issues: (snapshot) => snapshotIssues(snapshot),
+  issuesStatus: (snapshot) => issuesSnapshotStatus(snapshot),
   validation: (snapshot) => snapshotValidation(snapshot),
 }
 

package/src/graphql/schema.ts

@@ -497,6 +497,8 @@ export const typeDefs = `
     summary: Summary
     # Validator issues (legacy validator)
     issues: [ValidationIssue]
+    # Validator issues status (legacy validator)
+    issuesStatus: ValidationIssueStatus
     # Validator issues (schema validator)
     validation: DatasetValidation
     # Committed files in the working tree
@@ -526,6 +528,8 @@ export const typeDefs = `
     summary: Summary
     # Validator issues (legacy validator)
     issues: [ValidationIssue]
+    # Validator issues status (legacy validator)
+    issuesStatus: ValidationIssueStatus
     # Validator issues (schema validator)
     validation: DatasetValidation
     # Snapshot files
@@ -710,6 +714,12 @@ export const typeDefs = `
     helpUrl: String
   }
 
+  # Legacy validator count of errors and warnings
+  type ValidationIssueStatus {
+    errors: Int
+    warnings: Int
+  }
+
   input ValidatorIssueInput {
     code: String!
     subCode: String

package/src/handlers/sitemap.ts

@@ -5,12 +5,19 @@ import Dataset from "../models/dataset"
 // Static URLs - manual for now, could be generated from routes
 export const sitemapStaticUrls = () => [
   { url: "/", priority: 0.9, changefreq: "weekly" },
-  { url: "/public/datasets", priority: 1.0, changefreq: "daily" },
+  { url: "/search", priority: 0.8, changefreq: "daily" },
+  { url: "/search/modality/mri", priority: 0.7, changefreq: "daily" },
+  { url: "/search/modality/pet", priority: 0.7, changefreq: "daily" },
+  { url: "/search/modality/meg", priority: 0.7, changefreq: "daily" },
+  { url: "/search/modality/eeg", priority: 0.7, changefreq: "daily" },
+  { url: "/search/modality/ieeg", priority: 0.7, changefreq: "daily" },
+  { url: "/search/modality/nirs", priority: 0.7, changefreq: "daily" },
+  { url: "/search/nih", priority: 0.7, changefreq: "daily" },
   { url: "/faq", priority: 0.6, changefreq: "monthly" },
   { url: "/pet", priority: 0.5, changefreq: "monthly" },
   { url: "/terms", priority: 0.5, changefreq: "monthly" },
   { url: "/cite", priority: 0.4, changefreq: "monthly" },
-  { url: "/public/jobs", priority: 0.5, changefreq: "monthly" },
+  { url: "/image-attribution", priority: 0.4, changefreq: "monthly" },
   { url: "/crn/graphql", priority: 0.3 },
 ]
 

package/src/libs/authentication/migration.ts

@@ -1,22 +1,16 @@
-/** 
+/**
  * Migration of accounts from previous providers (Google) to ORCID as primary authentication
- * 
+ *
  * Runs on successful oauth linking these accounts
- * 
- * Either Google -> ORCID (creates / updates ORCID account with the Google account and merges any data) 
+ *
+ * Either Google -> ORCID (creates / updates ORCID account with the Google account and merges any data)
  * or ORCID + Google (merges Google account data into existing account)
  */
 
-/**
- * 
- */
+/** */
 function migrationOrcidToGoogle() {
-
 }
 
-/**
- * 
- */
+/** */
 function migrationGoogleToOrcid() {
-
-}
+}

package/src/models/issue.ts

@@ -2,10 +2,14 @@ import mongoose from "mongoose"
 import type { Document } from "mongoose"
 const { Schema, model } = mongoose
 
+export interface LegacyValidatorIssue {
+  severity: "error" | "warning"
+}
+
 export interface IssueDocument extends Document {
   id: string
   datasetId: string
-  issues: object
+  issues: LegacyValidatorIssue[]
   validatorMetadata: {
     validator: string
     version: string
@@ -15,7 +19,7 @@ export interface IssueDocument extends Document {
 const issueSchema = new Schema({
   id: { type: String, required: true },
   datasetId: { type: String, required: true },
-  issues: Object,
+  issues: [Object],
   validatorMetadata: {
     validator: String,
     version: String,