@openneuro/server 4.4.5 → 4.4.9

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@openneuro/server",
-  "version": "4.4.5",
+  "version": "4.4.9",
   "description": "Core service for the OpenNeuro platform.",
   "license": "MIT",
   "main": "src/server.js",
@@ -31,7 +31,7 @@
     "date-fns": "^2.16.1",
     "draft-js": "^0.11.7",
     "draft-js-export-html": "^1.4.1",
-    "elastic-apm-node": "3.12.1",
+    "elastic-apm-node": "^3.28.0",
     "express": "^4.17.1",
     "graphql": "14.7.0",
     "graphql-bigint": "^1.0.0",
@@ -47,7 +47,7 @@
     "jsonwebtoken": "^8.3.0",
     "mime-types": "^2.1.19",
     "moment": "^2.14.1",
-    "mongoose": "5.12.3",
+    "mongoose": "6.2.0",
     "morgan": "^1.6.1",
     "node-fetch": "^2.6.0",
     "node-mailjet": "^3.3.5",
@@ -104,5 +104,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "4b32c902a55ea3fc31648e11ecc5b8da94b7555d"
+  "gitHead": "af313c7d80f6aade5786075853d00023c52db60e"
 }

package/src/datalad/__tests__/dataset.spec.js

@@ -16,7 +16,7 @@ describe('dataset model operations', () => {
       // Setup a default sequence value to return for each test
       mockingoose.Counter.toReturn(
         { _id: 'dataset', sequence_value: 1 },
-        'findOneAndUpdate',
+        'findOne',
       )
     })
     it('resolves to dataset id string', async done => {

package/src/datalad/__tests__/snapshots.spec.js

@@ -28,7 +28,7 @@ describe('snapshot model operations', () => {
       // Setup a default sequence value to return for each test
       mockingoose.Counter.toReturn(
         { _id: 'dataset', sequence_value: 1 },
-        'findOneAndUpdate',
+        'findOne',
       )
     })
     it('posts to the DataLad /datasets/{dsId}/snapshots/{snapshot} endpoint', async done => {

package/src/datalad/description.js

@@ -9,7 +9,7 @@ import { fileUrl, getFiles } from './files.js'
 import { generateDataladCookie } from '../libs/authentication/jwt'
 import { getDatasetWorker } from '../libs/datalad-service'
 import CacheItem, { CacheType } from '../cache/item'
-import { datasetOrSnapshot } from './utils.js'
+import { datasetOrSnapshot } from '../utils/datasetOrSnapshot'
 
 export const defaultDescription = {
   Name: 'Unnamed Dataset',

package/src/datalad/readme.js

@@ -3,7 +3,7 @@ import { addFileString, commitFiles } from './dataset'
 import { redis } from '../libs/redis'
 import CacheItem, { CacheType } from '../cache/item'
 import { getDatasetWorker } from '../libs/datalad-service'
-import { datasetOrSnapshot } from './utils.js'
+import { datasetOrSnapshot } from '../utils/datasetOrSnapshot'
 
 export const readmeUrl = (datasetId, revision) => {
   return `http://${getDatasetWorker(

package/src/datalad/utils.js

@@ -23,15 +23,3 @@ export const addFileUrl = (datasetId, tag) => file => {
     }
   }
 }
-
-/**
- * Helper for resolvers with dataset and snapshot parents
- * @param {object} obj A snapshot or dataset parent object
- */
-export function datasetOrSnapshot(obj) {
-  if ('tag' in obj) {
-    return { datasetId: obj.id.split(':')[0], revision: obj.hexsha || obj.tag }
-  } else {
-    return { datasetId: obj.id, revision: obj.revision }
-  }
-}

package/src/graphql/resolvers/__tests__/brainlife.spec.ts

@@ -0,0 +1,17 @@
+import { HasId } from '../../../utils/datasetOrSnapshot'
+import { brainlifeQuery } from '../brainlife'
+
+describe('brainlife resolvers', () => {
+  it('correctly queries drafts', () => {
+    expect(brainlifeQuery({ id: 'ds000001' } as HasId).toString()).toEqual(
+      'https://brainlife.io/api/warehouse/datalad/datasets?find=%7B%22removed%22%3Afalse%2C%22path%22%3A%7B%22%24regex%22%3A%22%5EOpenNeuro%2Fds000001%22%7D%7D',
+    )
+  })
+  it('correctly queries versioned datasets', () => {
+    expect(
+      brainlifeQuery({ id: 'ds000001:1.0.0', tag: '1.0.0' }).toString(),
+    ).toEqual(
+      'https://brainlife.io/api/warehouse/datalad/datasets?find=%7B%22removed%22%3Afalse%2C%22path%22%3A%7B%22%24regex%22%3A%22%5EOpenNeuro%2Fds000001%22%7D%2C%22version%22%3A%221.0.0%22%7D',
+    )
+  })
+})

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

@@ -12,7 +12,7 @@ describe('dataset resolvers', () => {
     mockingoose.resetAll()
     mockingoose.Counter.toReturn(
       { _id: 'dataset', sequence_value: 1 },
-      'findOneAndUpdate',
+      'findOne',
     )
   })
   describe('createDataset()', () => {

package/src/graphql/resolvers/brainlife.ts

@@ -0,0 +1,55 @@
+import {
+  DatasetOrSnapshot,
+  getDatasetFromSnapshotId,
+} from '../../utils/datasetOrSnapshot'
+
+interface BrainlifeFindQuery {
+  removed: boolean
+  path?: {
+    $regex: string
+  }
+  version?: string
+}
+
+/**
+ * Construct a query to check if a dataset or snapshot exists on Brainlife
+ */
+export function brainlifeQuery(dataset: DatasetOrSnapshot): URL {
+  const find: BrainlifeFindQuery = {
+    removed: false,
+  }
+
+  if ('tag' in dataset) {
+    find.path = {
+      $regex: `^OpenNeuro/${getDatasetFromSnapshotId(dataset.id)}`,
+    }
+    find.version = dataset.tag
+  } else {
+    find.path = { $regex: `^OpenNeuro/${dataset.id}` }
+  }
+
+  const url = new URL('https://brainlife.io/api/warehouse/datalad/datasets')
+  url.searchParams.append('find', JSON.stringify(find))
+
+  return url
+}
+
+/**
+ * Make a request to Brainlife to check if a dataset exists
+ */
+export const onBrainlife = async (
+  dataset: DatasetOrSnapshot,
+): Promise<boolean> => {
+  try {
+    const url = brainlifeQuery(dataset)
+    const res = await fetch(url.toString())
+    const body = await res.json()
+    if (Array.isArray(body) && body.length) {
+      return true
+    } else {
+      return false
+    }
+  } catch (err) {
+    return false
+  }
+}

package/src/graphql/resolvers/dataset.js

@@ -22,6 +22,7 @@ import { UpdatedFile } from '../utils/file.js'
 import { getDatasetWorker } from '../../libs/datalad-service.js'
 import { getDraftHead } from '../../datalad/dataset.js'
 import { getFileName } from '../../datalad/files.js'
+import { onBrainlife } from './brainlife'
 import semver from 'semver'
 
 export const dataset = async (obj, { id }, { user, userInfo }) => {
@@ -284,24 +285,6 @@ export const starred = (obj, _, { user }) =>
     ? datalad.getUserStarred(obj.id, user).then(res => (res ? true : false))
     : null
 
-/**
- * Is this dataset available on brainlife?
- */
-export const onBrainlife = async dataset => {
-  try {
-    const url = `https://brainlife.io/api/warehouse/datalad/datasets?find={"path":{"$regex":"${dataset.id}$"}}`
-    const res = await fetch(url)
-    const body = await res.json()
-    if (Array.isArray(body) && body.length) {
-      return body[0].path === `OpenNeuroDatasets/${dataset.id}`
-    } else {
-      return false
-    }
-  } catch (err) {
-    return false
-  }
-}
-
 const worker = obj => getDatasetWorker(obj.id)
 
 /**

package/src/graphql/resolvers/snapshots.js

@@ -1,5 +1,6 @@
 import * as datalad from '../../datalad/snapshots.js'
 import { dataset, analytics, snapshotCreationComparison } from './dataset.js'
+import { onBrainlife } from './brainlife'
 import { checkDatasetRead, checkDatasetWrite } from '../permissions.js'
 import { readme } from './readme.js'
 import { description } from './description.js'
@@ -32,6 +33,7 @@ export const snapshot = (obj, { datasetId, tag }, context) => {
             .then(filterRemovedAnnexObjects(datasetId, context.userInfo)),
         deprecated: () => deprecated({ datasetId, tag }),
         related: () => related(datasetId),
+        onBrainlife: () => onBrainlife(snapshot),
       }))
     },
   )

package/src/graphql/schema.js

@@ -459,6 +459,8 @@ export const typeDefs = `
     deprecated: DeprecatedSnapshot
     # Related DOI references
     related: [RelatedObject]
+    # Is the snapshot available for analysis on Brainlife?
+    onBrainlife: Boolean @cacheControl(maxAge: 10080, scope: PUBLIC)
   }
 
   # RelatedObject nature of relationship

package/src/libs/email/index.ts

@@ -36,11 +36,12 @@ export const mailjetFormat = (email: Record<string, string>) => ({
  * @param email Nodemailer style email record
  */
 export const send = (email: Record<string, string>): Promise<Response> => {
-  // Mailjet is not configured, instead log emails
-  if (!perform_api_call) {
+  if (perform_api_call) {
+    return transport
+      .post('send', { version: 'v3.1', perform_api_call })
+      .request(mailjetFormat(email))
+  } else {
+    // Mailjet is not configured, instead log emails
     console.dir(email)
   }
-  return transport
-    .post('send', { version: 'v3.1', perform_api_call })
-    .request(mailjetFormat(email))
 }

package/src/models/__tests__/ingestDataset.spec.ts

@@ -30,7 +30,7 @@ describe('IngestDataset model', () => {
       notified: false,
     })
     goodUrlModel.validate(result => {
-      expect(result).toBe(null)
+      expect(result).toBe(undefined)
       done()
     })
   })

package/src/models/comment.ts

@@ -2,6 +2,7 @@ import mongoose, { Document } from 'mongoose'
 const { Schema, model } = mongoose
 
 export interface CommentDocument extends Document {
+  _id: string
   createDate: Date
   datasetId: string
   datasetLabel: string

package/src/models/snapshot.ts

@@ -2,6 +2,7 @@ import mongoose, { Document } from 'mongoose'
 const { Schema, model } = mongoose
 
 export interface SnapshotDocument extends Document {
+  id: string
   datasetId: string
   tag: string
   created: Date

package/src/server.js

@@ -23,12 +23,8 @@ const redisConnectionSetup = async () => {
 }
 
 mongoose.connect(config.mongo.url, {
-  useNewUrlParser: true,
   dbName: config.mongo.dbName,
   connectTimeoutMS: config.mongo.connectTimeoutMS,
-  useFindAndModify: false,
-  useUnifiedTopology: true,
-  useCreateIndex: true,
 })
 
 redisConnectionSetup().then(() => {

package/src/{datalad/__tests__/utils.spec.js → utils/__tests__/datasetOrSnapshot.spec.ts}

@@ -1,4 +1,7 @@
-import { datasetOrSnapshot } from '../utils.js'
+import {
+  datasetOrSnapshot,
+  getDatasetFromSnapshotId,
+} from '../datasetOrSnapshot'
 
 describe('datasetOrSnapshot()', () => {
   it('resolves a dataset object correctly', () => {
@@ -39,4 +42,9 @@ describe('datasetOrSnapshot()', () => {
       revision: '1.0.1',
     })
   })
+  describe('getDatasetFromSnapshotId', () => {
+    it('extracts the datasetId correctly', () => {
+      expect(getDatasetFromSnapshotId('ds000001:1.0.0')).toBe('ds000001')
+    })
+  })
 })

package/src/utils/datasetOrSnapshot.ts

@@ -0,0 +1,42 @@
+export interface HasId {
+  id: string
+  revision: string
+}
+
+export interface HasSnapshotId {
+  id: string
+  tag: string
+  hexsha?: string
+}
+
+export interface DatasetRevisionReference {
+  datasetId: string
+  revision: string
+}
+
+export type DatasetOrSnapshot = HasId | HasSnapshotId
+
+/**
+ * Helper for resolvers with dataset and snapshot parents
+ * @param {object} obj A snapshot or dataset parent object
+ */
+export function datasetOrSnapshot(
+  obj: DatasetOrSnapshot,
+): DatasetRevisionReference {
+  if ('tag' in obj) {
+    return {
+      datasetId: getDatasetFromSnapshotId(obj.id),
+      revision: obj.hexsha || obj.tag,
+    }
+  } else {
+    return { datasetId: obj.id, revision: obj.revision }
+  }
+}
+
+/**
+ * @param snapshotId 'ds000001:1.0.0' style snapshot ID
+ * @returns {string} Dataset id portion 'ds000001'
+ */
+export function getDatasetFromSnapshotId(snapshotId: string): string {
+  return snapshotId.split(':')[0]
+}