@openneuro/server 4.20.5 → 4.20.6-alpha.3

package/src/libs/{notifications.js → notifications.ts}

@@ -1,22 +1,21 @@
 /*eslint no-console: ["error", { allow: ["log"] }] */
-import config from '../config'
-import { send as emailSend } from './email'
-import request from 'superagent'
-import User from '../models/user'
-import Subscription from '../models/subscription'
-import { format } from 'date-fns'
-import url from 'url'
-import bidsId from './bidsId'
-import { convertFromRaw, EditorState } from 'draft-js'
-import { stateToHTML } from 'draft-js-export-html'
-import { getDatasetWorker } from '../libs/datalad-service'
-import { commentCreated } from '../libs/email/templates/comment-created'
-import { datasetDeleted } from '../libs/email/templates/dataset-deleted'
-import { ownerUnsubscribed } from '../libs/email/templates/owner-unsubscribed'
-import { snapshotCreated } from '../libs/email/templates/snapshot-created'
-import { snapshotReminder } from '../libs/email/templates/snapshot-reminder'
-import { datasetImportEmail } from '../libs/email/templates/dataset-imported'
-import { datasetImportFailed } from '../libs/email/templates/dataset-import-failed'
+import config from "../config"
+import { send as emailSend } from "./email"
+import request from "superagent"
+import User from "../models/user"
+import Subscription from "../models/subscription"
+import { format } from "date-fns"
+import url from "url"
+import { convertFromRaw, EditorState } from "draft-js"
+import { stateToHTML } from "draft-js-export-html"
+import { getDatasetWorker } from "./datalad-service"
+import { commentCreated } from "./email/templates/comment-created"
+import { datasetDeleted } from "./email/templates/dataset-deleted"
+import { ownerUnsubscribed } from "./email/templates/owner-unsubscribed"
+import { snapshotCreated } from "./email/templates/snapshot-created"
+import { snapshotReminder } from "./email/templates/snapshot-reminder"
+import { datasetImportEmail } from "./email/templates/dataset-imported"
+import { datasetImportFailed } from "./email/templates/dataset-import-failed"
 
 // public api ---------------------------------------------
 
@@ -25,7 +24,7 @@ const notifications = {
    * Send
    */
   send(notification) {
-    if (notification.type === 'email') {
+    if (notification.type === "email") {
       emailSend(notification.email)
     }
   },
@@ -42,18 +41,20 @@ const notifications = {
     const tag = body.tag
     const uploaderId = uploader ? uploader.id : null
     const URI = getDatasetWorker(datasetId)
-    const datasetDescriptionUrl = `${URI}/datasets/${datasetId}/snapshots/${tag}/files/dataset_description.json`
-    const changesUrl = `${URI}/datasets/${datasetId}/snapshots/${tag}/files/CHANGES`
+    const datasetDescriptionUrl =
+      `${URI}/datasets/${datasetId}/snapshots/${tag}/files/dataset_description.json`
+    const changesUrl =
+      `${URI}/datasets/${datasetId}/snapshots/${tag}/files/CHANGES`
 
     // get the dataset description
     const descriptionResponse = await request.get(datasetDescriptionUrl)
     const description = descriptionResponse.body
-    const datasetLabel = description.Name ? description.Name : 'Unnamed Dataset'
+    const datasetLabel = description.Name ? description.Name : "Unnamed Dataset"
 
     // get the snapshot changelog
     const changesResponse = await request
       .get(changesUrl)
-      .responseType('application/octet-stream')
+      .responseType("application/octet-stream")
     const changelog = changesResponse.body
       ? changesResponse.body.toString()
       : null
@@ -62,25 +63,24 @@ const notifications = {
       datasetId: datasetId,
     }).exec()
     // create the email object for each user
-    subscriptions.forEach(async subscription => {
+    subscriptions.forEach(async (subscription) => {
       const user = await User.findOne({ id: subscription.userId }).exec()
       if (user && user.id !== uploaderId) {
         const emailContent = {
-          _id: datasetId + '_' + user._id + '_' + 'snapshot_created',
-          type: 'email',
+          _id: datasetId + "_" + user._id + "_" + "snapshot_created",
+          type: "email",
           email: {
             to: user.email,
             name: user.name,
-            subject: 'Snapshot Created',
+            subject: "Snapshot Created",
             html: snapshotCreated({
               name: user.name,
               datasetLabel: datasetLabel,
-              datasetId: bidsId.decodeId(datasetId),
+              datasetId: datasetId,
               versionNumber: tag,
               changelog: changelog,
-              siteUrl:
-                url.parse(config.url).protocol +
-                '//' +
+              siteUrl: url.parse(config.url).protocol +
+                "//" +
                 url.parse(config.url).hostname,
             }),
           },
@@ -103,12 +103,13 @@ const notifications = {
     const datasetLabel = comment.datasetLabel
       ? comment.datasetLabel
       : comment.datasetId
-    const userId =
-      comment.user && comment.user.email ? comment.user.email : null
+    const userId = comment.user && comment.user.email
+      ? comment.user.email
+      : null
     const content = comment.text
     const commentId = comment._id ? comment._id : null
     const isReply = comment.parentId ? comment.parentId : null
-    const commentStatus = isReply ? 'reply to a comment' : 'comment'
+    const commentStatus = isReply ? "reply to a comment" : "comment"
     const editorState = EditorState.createWithContent(
       convertFromRaw(JSON.parse(content)),
     )
@@ -118,44 +119,41 @@ const notifications = {
     // get all users that are subscribed to the dataset
     Subscription.find({ datasetId: datasetId })
       .exec()
-      .then(subscriptions => {
+      .then((subscriptions) => {
         // create the email object for each user, using subscription userid and scitran
-        subscriptions.forEach(subscription => {
+        subscriptions.forEach((subscription) => {
           User.findOne({ id: subscription.userId })
             .exec()
-            .then(user => {
+            .then((user) => {
               if (user && user.email !== userId) {
                 const emailContent = {
-                  _id:
-                    datasetId +
-                    '_' +
+                  _id: datasetId +
+                    "_" +
                     subscription._id +
-                    '_' +
+                    "_" +
                     comment._id +
-                    '_' +
-                    'comment_created',
-                  type: 'email',
+                    "_" +
+                    "comment_created",
+                  type: "email",
                   email: {
                     to: user.email,
                     name: user.name,
-                    from:
-                      'reply-' +
+                    from: "reply-" +
                       encodeURIComponent(comment._id) +
-                      '-' +
+                      "-" +
                       encodeURIComponent(user._id),
-                    subject: 'Comment Created',
+                    subject: "Comment Created",
                     html: commentCreated({
                       name: user.name,
-                      datasetName: bidsId.decodeId(datasetId),
+                      datasetName: datasetId,
                       datasetLabel: datasetLabel,
                       commentUserId: userId,
                       commentId: commentId,
-                      dateCreated: format(comment.createDate, 'MMMM Do'),
+                      dateCreated: format(comment.createDate, "MMMM Do"),
                       commentContent: htmlContent,
                       commentStatus: commentStatus,
-                      siteUrl:
-                        url.parse(config.url).protocol +
-                        '//' +
+                      siteUrl: url.parse(config.url).protocol +
+                        "//" +
                         url.parse(config.url).hostname,
                     }),
                   },
@@ -176,39 +174,34 @@ const notifications = {
    * them that a the dataset has been deleted.
    */
   datasetDeleted(datasetId) {
-    console.log(
-      'datasetDeleted notification sent with datasetName:',
-      bidsId.decodeId(datasetId),
-    )
+    console.log("datasetDeleted notification sent with datasetName:", datasetId)
 
     // get all users that are subscribed to the dataset
     Subscription.find({ datasetId: datasetId })
       .exec()
-      .then(subscriptions => {
+      .then((subscriptions) => {
         // create the email object for each user, using subscription userid and scitran
-        subscriptions.forEach(subscription => {
+        subscriptions.forEach((subscription) => {
           User.findOne({ id: subscription.userId })
             .exec()
-            .then(user => {
+            .then((user) => {
               if (user) {
                 const emailContent = {
-                  _id:
-                    datasetId +
-                    '_' +
+                  _id: datasetId +
+                    "_" +
                     subscription._id +
-                    '_' +
-                    'dataset_deleted',
-                  type: 'email',
+                    "_" +
+                    "dataset_deleted",
+                  type: "email",
                   email: {
                     to: user.email,
                     name: user.name,
-                    subject: 'Dataset Deleted',
+                    subject: "Dataset Deleted",
                     html: datasetDeleted({
                       name: user.name,
-                      datasetName: bidsId.decodeId(datasetId),
-                      siteUrl:
-                        url.parse(config.url).protocol +
-                        '//' +
+                      datasetName: datasetId,
+                      siteUrl: url.parse(config.url).protocol +
+                        "//" +
                         url.parse(config.url).hostname,
                     }),
                   },
@@ -229,38 +222,36 @@ const notifications = {
    */
   ownerUnsubscribed(datasetId) {
     console.log(
-      'ownerUnsubscribed notification sent with datasetName:',
-      bidsId.decodeId(datasetId),
+      "ownerUnsubscribed notification sent with datasetName:",
+      datasetId,
     )
 
     // get all users that are subscribed to the dataset
     Subscription.find({ datasetId: datasetId })
       .exec()
-      .then(subscriptions => {
+      .then((subscriptions) => {
         // create the email object for each user, using subscription userid and scitran
-        subscriptions.forEach(subscription => {
+        subscriptions.forEach((subscription) => {
           User.findOne({ id: subscription.userId })
             .exec()
-            .then(user => {
+            .then((user) => {
               if (user) {
                 const emailContent = {
-                  _id:
-                    datasetId +
-                    '_' +
+                  _id: datasetId +
+                    "_" +
                     subscription._id +
-                    '_' +
-                    'owner_unsubscribed',
-                  type: 'email',
+                    "_" +
+                    "owner_unsubscribed",
+                  type: "email",
                   email: {
                     to: user.email,
                     name: user.name,
-                    subject: 'Owner Unsubscribed',
+                    subject: "Owner Unsubscribed",
                     html: ownerUnsubscribed({
                       name: user.name,
-                      datasetName: bidsId.decodeId(datasetId),
-                      siteUrl:
-                        url.parse(config.url).protocol +
-                        '//' +
+                      datasetName: datasetId,
+                      siteUrl: url.parse(config.url).protocol +
+                        "//" +
                         url.parse(config.url).hostname,
                     }),
                   },
@@ -281,38 +272,36 @@ const notifications = {
    */
   async snapshotReminder(datasetId) {
     console.log(
-      'snapshotReminder notification sent with datasetName:',
-      bidsId.decodeId(datasetId),
+      "snapshotReminder notification sent with datasetName:",
+      datasetId,
     )
 
     // get all users that are subscribed to the dataset
     await Subscription.find({ datasetId: datasetId })
       .exec()
-      .then(subscriptions => {
+      .then((subscriptions) => {
         // create the email object for each user, using subscription userid and scitran
-        subscriptions.forEach(subscription => {
+        subscriptions.forEach((subscription) => {
           User.findOne({ id: subscription.userId })
             .exec()
-            .then(user => {
+            .then((user) => {
               if (user) {
                 const emailContent = {
-                  _id:
-                    datasetId +
-                    '_' +
+                  _id: datasetId +
+                    "_" +
                     subscription._id +
-                    '_' +
-                    'snapshot_reminder',
-                  type: 'email',
+                    "_" +
+                    "snapshot_reminder",
+                  type: "email",
                   email: {
                     to: user.email,
                     name: user.name,
-                    subject: 'Snapshot Reminder',
+                    subject: "Snapshot Reminder",
                     html: snapshotReminder({
                       name: user.name,
-                      datasetName: bidsId.decodeId(datasetId),
-                      siteUrl:
-                        url.parse(config.url).protocol +
-                        '//' +
+                      datasetName: datasetId,
+                      siteUrl: url.parse(config.url).protocol +
+                        "//" +
                         url.parse(config.url).hostname,
                       datasetId,
                     }),
@@ -340,30 +329,28 @@ const notifications = {
       html = datasetImportEmail({
         name: user.name,
         datasetId: datasetId,
-        siteUrl:
-          url.parse(config.url).protocol +
-          '//' +
+        siteUrl: url.parse(config.url).protocol +
+          "//" +
           url.parse(config.url).hostname,
       })
     } else {
       html = datasetImportFailed({
         name: user.name,
         datasetId: datasetId,
-        message: success ? '' : message,
-        siteUrl:
-          url.parse(config.url).protocol +
-          '//' +
+        message: success ? "" : message,
+        siteUrl: url.parse(config.url).protocol +
+          "//" +
           url.parse(config.url).hostname,
         retryUrl: retryUrl,
       })
     }
     const emailContent = {
-      _id: datasetId + '_' + user._id + '_' + 'dataset_imported',
-      type: 'email',
+      _id: datasetId + "_" + user._id + "_" + "dataset_imported",
+      type: "email",
       email: {
         to: user.email,
         name: user.name,
-        subject: `Dataset Import ${success ? 'Success' : 'Failed'}`,
+        subject: `Dataset Import ${success ? "Success" : "Failed"}`,
         html: html,
       },
     }

package/src/libs/{orcid.js → orcid.ts}

@@ -1,14 +1,14 @@
 // Camel case rule is disabled since ORCID API uses snake case variables
-import request from 'request'
-import xmldoc from 'xmldoc'
-import config from '../config'
+import request from "request"
+import xmldoc from "xmldoc"
+import config from "../config"
 
 export default {
   getProfile(token) {
     return new Promise((resolve, reject) => {
-      const data = token.split(':')
+      const data = token.split(":")
       if (data.length != 2) {
-        reject('Invalid token')
+        reject("Invalid token")
       }
       const orcid = data[0]
       const accessToken = data[1]
@@ -22,7 +22,7 @@ export default {
           if (err) {
             return reject({
               message:
-                'An unexpected ORCID login failure occurred, please try again later.',
+                "An unexpected ORCID login failure occurred, please try again later.",
             })
           }
           let doc
@@ -31,36 +31,36 @@ export default {
             doc = new xmldoc.XmlDocument(res.body)
           } catch (err) {
             return reject({
-              type: 'config',
+              type: "config",
               message:
-                'ORCID auth response invalid, most likely this is a misconfigured ORCID_API_ENDPOINT value',
+                "ORCID auth response invalid, most likely this is a misconfigured ORCID_API_ENDPOINT value",
             })
           }
           let name = doc.valueWithPath(
-            'person:person.person:name.personal-details:credit-name',
+            "person:person.person:name.personal-details:credit-name",
           )
           const firstname = doc.valueWithPath(
-            'person:person.person:name.personal-details:given-names',
+            "person:person.person:name.personal-details:given-names",
           )
           const lastname = doc.valueWithPath(
-            'person:person.person:name.personal-details:family-name',
+            "person:person.person:name.personal-details:family-name",
           )
           const email = doc.valueWithPath(
-            'person:person.email:emails.email:email.email:email',
+            "person:person.email:emails.email:email.email:email",
           )
 
           if (!name) {
             if (!firstname) {
               return reject({
-                type: 'given',
+                type: "given",
                 message:
-                  'Your ORCID account does not have a given name, or it is not public. Please fix your account before continuing.',
+                  "Your ORCID account does not have a given name, or it is not public. Please fix your account before continuing.",
               })
             } else if (!lastname) {
               return reject({
-                type: 'family',
+                type: "family",
                 message:
-                  'Your ORCID account does not have a family name, or it is not public. Please fix your account before continuing.',
+                  "Your ORCID account does not have a family name, or it is not public. Please fix your account before continuing.",
               })
             } else {
               name = `${firstname} ${lastname}`
@@ -69,9 +69,9 @@ export default {
 
           if (!email) {
             return reject({
-              type: 'email',
+              type: "email",
               message:
-                'Your ORCID account does not have an e-mail, or your e-mail is not public. Please fix your account before continuing.',
+                "Your ORCID account does not have an e-mail, or your e-mail is not public. Please fix your account before continuing.",
             })
           }
 
@@ -92,7 +92,7 @@ export default {
           client_id: config.auth.orcid.clientID,
           client_secret: config.auth.orcid.clientSecret,
           redirect_uri: config.auth.orcid.redirectURI,
-          grant_type: 'refresh_token',
+          grant_type: "refresh_token",
           refresh_token: refreshToken,
         },
         json: true,
@@ -115,7 +115,7 @@ export default {
           client_id: config.auth.orcid.clientID,
           client_secret: config.auth.orcid.clientSecret,
           redirect_uri: config.auth.orcid.redirectURI,
-          grant_type: 'authorization_code',
+          grant_type: "authorization_code",
           code,
         },
         json: true,

package/src/libs/{redis.js → redis.ts}

@@ -1,14 +1,14 @@
 /*eslint no-console: ["error", { allow: ["log"] }] */
 
 // dependencies --------------------------------------------------
-import Redis from 'ioredis'
-import Redlock from 'redlock'
+import Redis from "ioredis"
+import Redlock from "redlock"
 
 let redis = null
 let redlock = null
 
-const connect = async config => {
-  return new Promise(resolve => {
+const connect = async (config) => {
+  return new Promise((resolve) => {
     if (!redis) {
       console.log(
         'Connecting to Redis "redis://%s:%d/0"',
@@ -17,7 +17,7 @@ const connect = async config => {
       )
       redis = new Redis(config)
       redlock = new Redlock([redis])
-      redis.on('connect', () => {
+      redis.on("connect", () => {
         resolve(redis)
       })
     } else {
@@ -27,4 +27,4 @@ const connect = async config => {
 }
 
 export default { connect }
-export { redis, redlock, connect }
+export { connect, redis, redlock }

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

@@ -1,30 +1,30 @@
-import { vi } from 'vitest'
-import IngestDataset from '../ingestDataset'
+import { vi } from "vitest"
+import IngestDataset from "../ingestDataset"
 
-vi.mock('ioredis')
+vi.mock("ioredis")
 
-describe('IngestDataset model', () => {
-  it('IngestDataset model fails if required fields are missing', () => {
+describe("IngestDataset model", () => {
+  it("IngestDataset model fails if required fields are missing", () => {
     const model = new IngestDataset()
     const result = model.validateSync()
-    expect(result.name).toEqual('ValidationError')
+    expect(result.name).toEqual("ValidationError")
   })
-  it('IngestDataset model URL validation fails with a bad URL', async () => {
+  it("IngestDataset model URL validation fails with a bad URL", async () => {
     const badUrlModel = new IngestDataset({
-      datasetId: 'ds00000',
-      userId: 'b3df6399-d1be-4e07-b997-9f7aa3ed1f8e',
-      url: 'this is not a valid URL',
+      datasetId: "ds00000",
+      userId: "b3df6399-d1be-4e07-b997-9f7aa3ed1f8e",
+      url: "this is not a valid URL",
       imported: false,
       notified: false,
     })
     const result = badUrlModel.validateSync()
-    expect(result.name).toEqual('ValidationError')
+    expect(result.name).toEqual("ValidationError")
   })
-  it('IngestDataset model URL validation succeeds with a good URL', async () => {
+  it("IngestDataset model URL validation succeeds with a good URL", async () => {
     const goodUrlModel = new IngestDataset({
-      datasetId: 'ds00000',
-      userId: 'b3df6399-d1be-4e07-b997-9f7aa3ed1f8e',
-      url: 'https://example.com',
+      datasetId: "ds00000",
+      userId: "b3df6399-d1be-4e07-b997-9f7aa3ed1f8e",
+      url: "https://example.com",
       imported: false,
       notified: false,
     })

package/src/models/analytics.ts

@@ -1,4 +1,4 @@
-import mongoose, { Document } from 'mongoose'
+import mongoose, { Document } from "mongoose"
 const { Schema, model } = mongoose
 
 export interface AnalyticsDocument extends Document {
@@ -17,6 +17,6 @@ const analyticsSchema = new Schema({
   views: { type: Number, required: false },
 })
 
-const Analytics = model<AnalyticsDocument>('Analytics', analyticsSchema)
+const Analytics = model<AnalyticsDocument>("Analytics", analyticsSchema)
 
 export default Analytics

package/src/models/badAnnexObject.ts

@@ -1,5 +1,5 @@
-import mongoose, { Document } from 'mongoose'
-import { UserDocument } from './user'
+import mongoose, { Document } from "mongoose"
+import { UserDocument } from "./user"
 const ObjectId = mongoose.Schema.Types.ObjectId
 
 export interface BadAnnexObject extends Document {
@@ -24,17 +24,17 @@ const badAnnexObject = new mongoose.Schema(
     filepath: String,
     annexKey: String,
     removed: { type: Boolean, default: false },
-    remover: { type: ObjectId, ref: 'User' },
+    remover: { type: ObjectId, ref: "User" },
     flagged: { type: Boolean, default: false },
-    flagger: { type: ObjectId, ref: 'User' },
+    flagger: { type: ObjectId, ref: "User" },
   },
-  { timestamps: { createdAt: 'created_at' } },
+  { timestamps: { createdAt: "created_at" } },
 )
 
 badAnnexObject.index({ datasetId: 1, annexKey: 1 }, { unique: true })
 
 const BadAnnexObject = mongoose.model<BadAnnexObject>(
-  'BadAnnexObject',
+  "BadAnnexObject",
   badAnnexObject,
 )
 

package/src/models/comment.ts

@@ -1,4 +1,4 @@
-import mongoose, { Document } from 'mongoose'
+import mongoose, { Document } from "mongoose"
 const { Schema, model } = mongoose
 
 export interface CommentDocument extends Document {
@@ -26,21 +26,21 @@ const commentSchema = new Schema(
 )
 
 // Foreign key virtuals
-commentSchema.virtual('poster', {
-  ref: 'User',
-  localField: 'user._id',
-  foreignField: 'id',
+commentSchema.virtual("poster", {
+  ref: "User",
+  localField: "user._id",
+  foreignField: "id",
   justOne: true,
 })
 
 // Foreign key virtuals
-commentSchema.virtual('parent', {
-  ref: 'Comment',
-  localField: 'parentId',
-  foreignField: '_id',
+commentSchema.virtual("parent", {
+  ref: "Comment",
+  localField: "parentId",
+  foreignField: "_id",
   justOne: true,
 })
 
-const Comment = model<CommentDocument>('Comment', commentSchema)
+const Comment = model<CommentDocument>("Comment", commentSchema)
 
 export default Comment