@openneuro/server 4.2.5-alpha.0 → 4.3.0-alpha.3

package/Dockerfile

@@ -11,7 +11,8 @@ WORKDIR /srv
 COPY --from=build /srv/packages/openneuro-server/package.json /srv/package.json
 COPY --from=build /srv/.yarnrc.yml /srv/.yarnrc.yml
 COPY --from=build /srv/.yarn /srv/.yarn
-COPY --from=build /srv/.pnp.js /srv/.pnp.js
+COPY --from=build /srv/.pnp.cjs /srv/.pnp.cjs
+COPY --from=build /srv/.pnp.loader.mjs /srv/.pnp.loader.mjs
 COPY --from=build /srv/packages/openneuro-server/dist /srv/packages/openneuro-server/dist
 
 HEALTHCHECK --interval=10s --retries=10 CMD curl -f 'http://localhost:8111' || exit 1

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@openneuro/server",
-  "version": "4.2.5-alpha.0",
+  "version": "4.3.0-alpha.3",
   "description": "Core service for the OpenNeuro platform.",
   "license": "MIT",
   "main": "src/server.js",
@@ -89,7 +89,6 @@
     "ioredis-mock": "^3.8.1",
     "jest": "^26.6.3",
     "mockingoose": "2.11.0",
-    "mongo-mock": "3.7.1",
     "nodemon": "^2.0.7",
     "supertest": "^3.0.0",
     "ts-node-dev": "1.1.6",
@@ -104,5 +103,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "d72d3bbe43716e22497d07621736302c2330749f"
+  "gitHead": "28a399f30997634ecd417539006c188f4249c9a6"
 }

package/src/__mocks__/mongoose.js

@@ -1,4 +1,3 @@
-jest.unmock('mongodb')
 import mongoose from 'mongoose'
 
 export default mongoose

package/src/graphql/resolvers/__tests__/user.spec.js

@@ -3,24 +3,13 @@ import { users } from '../user.js'
 describe('user resolvers', () => {
   describe('users()', () => {
     it('throws an error for non-admins', () => {
-      expect(() =>
+      expect(
         users(
           null,
           { id: '3311cfe8-9764-434d-b80e-1b1ee72c686d' },
           { userInfo: {} },
         ),
-      ).toThrowError()
-    })
-    it('admins should be able to override restrictions', () => {
-      expect(() =>
-        users(
-          null,
-          { id: '3311cfe8-9764-434d-b80e-1b1ee72c686d' },
-          {
-            userInfo: { admin: true },
-          },
-        ),
-      ).not.toThrowError()
+      ).rejects.toEqual(new Error('You must be a site admin to retrieve users'))
     })
   })
 })

package/src/graphql/resolvers/mutation.js

@@ -15,6 +15,7 @@ import {
   createSnapshot,
   deleteSnapshot,
   deprecateSnapshot,
+  undoDeprecateSnapshot,
 } from './snapshots.js'
 import { removeUser, setAdmin, setBlocked } from './user.js'
 import { updateSummary } from './summary.js'
@@ -44,6 +45,7 @@ const Mutation = {
   flagAnnexObject,
   createSnapshot,
   deprecateSnapshot,
+  undoDeprecateSnapshot,
   deleteSnapshot,
   updateSummary,
   updateValidation,

package/src/graphql/resolvers/snapshots.js

@@ -9,10 +9,6 @@ import { getFiles, filterFiles } from '../../datalad/files.js'
 import DatasetModel from '../../models/dataset'
 import { filterRemovedAnnexObjects } from '../utils/file.js'
 import DeprecatedSnapshot from '../../models/deprecatedSnapshot'
-import { checkDatasetAdmin } from '../permissions.js'
-import SnapshotModel from '../../models/snapshot'
-import User from '../../models/user'
-import * as Sentry from '@sentry/node'
 import { redis } from '../../libs/redis'
 import CacheItem, { CacheType } from '../../cache/item'
 import { normalizeDOI } from '../../libs/doi/normalize'
@@ -34,15 +30,16 @@ export const snapshot = (obj, { datasetId, tag }, context) => {
           getFiles(datasetId, snapshot.hexsha)
             .then(filterFiles(prefix))
             .then(filterRemovedAnnexObjects(datasetId, context.userInfo)),
-        deprecated: () => deprecated(snapshot),
+        deprecated: () => deprecated({ datasetId, tag }),
         related: () => related(datasetId),
       }))
     },
   )
 }
 
-export const deprecated = snapshot => {
-  return DeprecatedSnapshot.findOne({ id: snapshot.hexsha }).populate('user')
+export const deprecated = ({ datasetId, tag }) => {
+  const id = `${datasetId}:${tag}`
+  return DeprecatedSnapshot.findOne({ id }).lean().exec()
 }
 
 /**
@@ -89,22 +86,41 @@ export const deprecateSnapshot = async (
   { datasetId, tag, reason },
   { user, userInfo },
 ) => {
-  try {
-    await checkDatasetAdmin(datasetId, user, userInfo)
-    const [snapshot, userDoc] = await Promise.all([
-      SnapshotModel.findOne({ datasetId, tag }),
-      User.findOne({ id: user }),
-    ])
-    await DeprecatedSnapshot.create({
-      id: snapshot.hexsha,
-      user: userDoc._id,
-      cause: reason,
-      timestamp: new Date(),
-    })
-    return true
-  } catch (err) {
-    Sentry.captureException(err)
-    throw err
+  const id = `${datasetId}:${tag}`
+  await checkDatasetWrite(datasetId, user, userInfo)
+  const timestamp = new Date()
+  await DeprecatedSnapshot.updateOne(
+    { id },
+    {
+      id,
+      user,
+      reason,
+      timestamp,
+    },
+    { upsert: true },
+  )
+  return {
+    id,
+    deprecated: {
+      id,
+      user,
+      reason,
+      timestamp,
+    },
+  }
+}
+
+export const undoDeprecateSnapshot = async (
+  obj,
+  { datasetId, tag },
+  { user, userInfo },
+) => {
+  const id = `${datasetId}:${tag}`
+  await checkDatasetWrite(datasetId, user, userInfo)
+  await DeprecatedSnapshot.findOneAndDelete({ id })
+  return {
+    id,
+    deprecated: null,
   }
 }
 

package/src/graphql/resolvers/user.js

@@ -13,7 +13,9 @@ export const users = (obj, args, { userInfo }) => {
   if (userInfo.admin) {
     return User.find().exec()
   } else {
-    throw new Error('You must be a site admin to retrieve users')
+    return Promise.reject(
+      new Error('You must be a site admin to retrieve users'),
+    )
   }
 }
 
@@ -21,7 +23,7 @@ export const removeUser = (obj, { id }, { userInfo }) => {
   if (userInfo.admin) {
     return User.findByIdAndRemove(id).exec()
   } else {
-    throw new Error('You must be a site admin to remove users')
+    return Promise.reject(new Error('You must be a site admin to remove users'))
   }
 }
 
@@ -29,7 +31,9 @@ export const setAdmin = (obj, { id, admin }, { userInfo }) => {
   if (userInfo.admin) {
     return User.findOneAndUpdate({ id }, { admin }).exec()
   } else {
-    throw new Error('You must be a site admin to modify this value')
+    return Promise.reject(
+      new Error('You must be a site admin to modify this value'),
+    )
   }
 }
 
@@ -37,7 +41,7 @@ export const setBlocked = (obj, { id, blocked }, { userInfo }) => {
   if (userInfo.admin) {
     return User.findOneAndUpdate({ id }, { blocked }).exec()
   } else {
-    throw new Error('You must be a site admin to block a user')
+    return Promise.reject(new Error('You must be a site admin to block a user'))
   }
 }
 

package/src/graphql/schema.js

@@ -176,7 +176,9 @@ export const typeDefs = `
     # Reset draft commit
     resetDraft(datasetId: ID!, ref: String!): Boolean
     # Flag snapshot as deprecated
-    deprecateSnapshot(datasetId: ID!, tag: String!, reason: String!): Boolean
+    deprecateSnapshot(datasetId: ID!, tag: String!, reason: String!): Snapshot
+    # Unflag snapshot as deprecated
+    undoDeprecateSnapshot(datasetId: ID!, tag: String!): Snapshot
     # Create anonymous read only reviewer
     createReviewer(datasetId: ID!): DatasetReviewer
     # Remove reviewer
@@ -485,9 +487,9 @@ export const typeDefs = `
     # hexsha of deprecated snapshots
     id: ID!
     # ID of user who flagged snapshot as deprecated
-    user: User
+    user: String
     # Reason for deprecating snaphot
-    cause: String
+    reason: String
     # Timestamp of snapshot deprecation
     timestamp: Date
   }

package/src/models/deprecatedSnapshot.ts

@@ -4,7 +4,7 @@ const { Schema, model } = mongoose
 export interface DeprecatedSnapshotDocument extends Document {
   id: string // snapshot hexsha
   user: string
-  cause: string
+  reason: string
   timestamp: Date
 }
 
@@ -13,9 +13,8 @@ const deprecatedSnapshotSchema = new Schema({
   user: {
     type: String,
     required: true,
-    ref: 'User',
   },
-  cause: {
+  reason: {
     type: String,
     required: true,
   },

package/src/__mocks__/mongodb.js

@@ -1,5 +0,0 @@
-import mongodb from 'mongo-mock'
-
-mongodb.max_delay = 0
-
-module.exports = mongodb