@openneuro/server 4.4.3 → 4.4.7

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@openneuro/server",
-  "version": "4.4.3",
+  "version": "4.4.7",
   "description": "Core service for the OpenNeuro platform.",
   "license": "MIT",
   "main": "src/server.js",
@@ -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": "1f7523d0925047a02597242f68efd9c1c42cc695"
+  "gitHead": "4373b377ffa4f0bcd71a7abaf07235c262f6cdb2"
 }

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/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/dataset.js

@@ -287,13 +287,24 @@ export const starred = (obj, _, { user }) =>
 /**
  * Is this dataset available on brainlife?
  */
-export const onBrainlife = async dataset => {
+export const onBrainlife = async datasetOrSnapshot => {
   try {
-    const url = `https://brainlife.io/api/warehouse/datalad/datasets?find={"path":{"$regex":"${dataset.id}$"}}`
+    const find = {
+      removed: false,
+    }
+    if (datasetOrSnapshot.tag) {
+      find.path = { $regex: '^OpenNeuro/' + datasetOrSnapshot.id.split(':')[0] }
+      find.version = datasetOrSnapshot.tag
+    } else {
+      find.path = { $regex: '^OpenNeuro/' + datasetOrSnapshot.id }
+    }
+    const url = `https://brainlife.io/api/warehouse/datalad/datasets?find=${JSON.stringify(
+      find,
+    )}`
     const res = await fetch(url)
     const body = await res.json()
     if (Array.isArray(body) && body.length) {
-      return body[0].path === `OpenNeuroDatasets/${dataset.id}`
+      return true
     } else {
       return false
     }

package/src/graphql/resolvers/snapshots.js

@@ -1,5 +1,10 @@
 import * as datalad from '../../datalad/snapshots.js'
-import { dataset, analytics, snapshotCreationComparison } from './dataset.js'
+import {
+  dataset,
+  analytics,
+  snapshotCreationComparison,
+  onBrainlife,
+} from './dataset.js'
 import { checkDatasetRead, checkDatasetWrite } from '../permissions.js'
 import { readme } from './readme.js'
 import { description } from './description.js'
@@ -32,6 +37,7 @@ export const snapshot = (obj, { datasetId, tag }, context) => {
             .then(filterRemovedAnnexObjects(datasetId, context.userInfo)),
         deprecated: () => deprecated({ datasetId, tag }),
         related: () => related(datasetId),
+        onBrainlife,
       }))
     },
   )

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/libs/email/templates/__tests__/__snapshots__/comment-created.spec.ts.snap

@@ -57,7 +57,7 @@ exports[`email template -> comment created renders with expected arguments 1`] =
 </head>
 <body>
 	<div class=\\"top-bar\\">
-		<img src=\\"https://openneuro.org/assets/CRN-Logo-Placeholder.png\\" />
+		<img src=\\"https://openneuro.org/assets/email-header.1cb8bf76.png\\" />
 	</div>
 	<div class=\\"content\\">
 		<h2>Hi, J. Doe</h2>

package/src/libs/email/templates/__tests__/__snapshots__/dataset-deleted.spec.ts.snap

@@ -39,7 +39,7 @@ exports[`email template -> comment created renders with expected arguments 1`] =
 </head>
 <body>
 	<div class=\\"top-bar\\">
-		<img src=\\"https://openneuro.org/assets/CRN-Logo-Placeholder.png\\" />
+		<img src=\\"https://openneuro.org/assets/email-header.1cb8bf76.png\\" />
 	</div>
 	<div class=\\"content\\">
 		<h2>Hi, J. Doe</h2>

package/src/libs/email/templates/__tests__/__snapshots__/owner-unsubscribed.spec.ts.snap

@@ -39,7 +39,7 @@ exports[`email template -> comment created renders with expected arguments 1`] =
 </head>
 <body>
 	<div class=\\"top-bar\\">
-		<img src=\\"https://openneuro.org/assets/CRN-Logo-Placeholder.png\\" />
+		<img src=\\"https://openneuro.org/assets/email-header.1cb8bf76.png\\" />
 	</div>
 	<div class=\\"content\\">
 		<h2>Hi, J. Doe</h2>

package/src/libs/email/templates/__tests__/__snapshots__/snapshot-created.spec.ts.snap

@@ -57,7 +57,7 @@ exports[`email template -> comment created renders with expected arguments 1`] =
 </head>
 <body>
 	<div class=\\"top-bar\\">
-		<img src=\\"https://openneuro.org/assets/CRN-Logo-Placeholder.png\\" />
+		<img src=\\"https://openneuro.org/assets/email-header.1cb8bf76.png\\" />
 	</div>
 	<div class=\\"content\\">
 		<h2>Hi, J. Doe</h2>

package/src/libs/email/templates/__tests__/__snapshots__/snapshot-reminder.spec.ts.snap

@@ -39,7 +39,7 @@ exports[`email template -> comment created renders with expected arguments 1`] =
 </head>
 <body>
 	<div class=\\"top-bar\\">
-		<img src=\\"https://openneuro.org/assets/CRN-Logo-Placeholder.png\\" />
+		<img src=\\"https://openneuro.org/assets/email-header.1cb8bf76.png\\" />
 	</div>
 	<div class=\\"content\\">
 		<h2>Hi, J. Doe</h2>

package/src/libs/email/templates/comment-created.ts

@@ -74,7 +74,7 @@ export const commentCreated = ({
 </head>
 <body>
 	<div class="top-bar">
-		<img src="${siteUrl}/assets/CRN-Logo-Placeholder.png" />
+		<img src="${siteUrl}/assets/email-header.1cb8bf76.png" />
 	</div>
 	<div class="content">
 		<h2>Hi, ${name}</h2>

package/src/libs/email/templates/dataset-deleted.ts

@@ -44,7 +44,7 @@ export const datasetDeleted = ({
 </head>
 <body>
 	<div class="top-bar">
-		<img src="${siteUrl}/assets/CRN-Logo-Placeholder.png" />
+		<img src="${siteUrl}/assets/email-header.1cb8bf76.png" />
 	</div>
 	<div class="content">
 		<h2>Hi, ${name}</h2>

package/src/libs/email/templates/dataset-import-failed.ts

@@ -66,13 +66,13 @@ export const datasetImportFailed = ({
 </head>
 <body>
 	<div class="top-bar">
-		<img src="${siteUrl}/assets/CRN-Logo-Placeholder.png" />
+		<img src="${siteUrl}/assets/email-header.1cb8bf76.png" />
 	</div>
 	<div class="content">
 		<h2>Hi, ${name}</h2>
 
 		<p>
-			A dataset imported you requested failed. It was imported as <b>${datasetId}</b>. 
+			A dataset import you requested failed. It was imported as <b>${datasetId}</b>. 
 		</p>
 
 		<div>

package/src/libs/email/templates/dataset-imported.ts

@@ -62,13 +62,13 @@ export const datasetImportEmail = ({
 </head>
 <body>
 	<div class="top-bar">
-		<img src="${siteUrl}/assets/CRN-Logo-Placeholder.png" />
+		<img src="${siteUrl}/assets/email-header.1cb8bf76.png" />
 	</div>
 	<div class="content">
 		<h2>Hi, ${name}</h2>
 
 		<p>
-			A dataset imported you requested has finished. It was imported as <b>${datasetId}</b>. 
+			A dataset import you requested has finished. It was imported as <b>${datasetId}</b>. 
 		</p>
 
 		<div>

package/src/libs/email/templates/owner-unsubscribed.ts

@@ -44,7 +44,7 @@ export const ownerUnsubscribed = ({
 </head>
 <body>
 	<div class="top-bar">
-		<img src="${siteUrl}/assets/CRN-Logo-Placeholder.png" />
+		<img src="${siteUrl}/assets/email-header.1cb8bf76.png" />
 	</div>
 	<div class="content">
 		<h2>Hi, ${name}</h2>

package/src/libs/email/templates/snapshot-created.ts

@@ -68,7 +68,7 @@ export const snapshotCreated = ({
 </head>
 <body>
 	<div class="top-bar">
-		<img src="${siteUrl}/assets/CRN-Logo-Placeholder.png" />
+		<img src="${siteUrl}/assets/email-header.1cb8bf76.png" />
 	</div>
 	<div class="content">
 		<h2>Hi, ${name}</h2>

package/src/libs/email/templates/snapshot-reminder.ts

@@ -46,7 +46,7 @@ export const snapshotReminder = ({
 </head>
 <body>
 	<div class="top-bar">
-		<img src="${siteUrl}/assets/CRN-Logo-Placeholder.png" />
+		<img src="${siteUrl}/assets/email-header.1cb8bf76.png" />
 	</div>
 	<div class="content">
 		<h2>Hi, ${name}</h2>

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/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(() => {