@openneuro/server 4.28.3 → 4.29.0-alpha.1

package/src/graphql/resolvers/mutation.ts

@@ -10,7 +10,6 @@ import {
   trackAnalytics,
   updatePublic,
 } from "./dataset.js"
-import { updateRef } from "./draft.js"
 import {
   createSnapshot,
   deleteSnapshot,
@@ -20,7 +19,11 @@ import {
 import { removeUser, setAdmin, setBlocked } from "./user.js"
 import { updateSummary } from "./summary"
 import { revalidate, updateValidation } from "./validation.js"
-import { removePermissions, updatePermissions } from "./permissions"
+import {
+  removePermissions,
+  updateOrcidPermissions,
+  updatePermissions,
+} from "./permissions"
 import { followDataset } from "./follow.js"
 import { starDataset } from "./stars.js"
 import { publishDataset } from "./publish.js"
@@ -55,6 +58,7 @@ const Mutation = {
   updateValidation,
   updatePublic,
   updatePermissions,
+  updateOrcidPermissions,
   removePermissions,
   removeUser,
   setAdmin,
@@ -71,7 +75,6 @@ const Mutation = {
   deleteComment,
   subscribeToNewsletter,
   addMetadata,
-  updateRef,
   prepareUpload,
   finishUpload,
   cacheClear,

package/src/graphql/resolvers/permissions.ts

@@ -1,5 +1,7 @@
-import User, { UserDocument } from "../../models/user"
-import Permission, { PermissionDocument } from "../../models/permission"
+import User from "../../models/user"
+import type { UserDocument } from "../../models/user"
+import Permission from "../../models/permission"
+import type { PermissionDocument } from "../../models/permission"
 import { checkDatasetAdmin } from "../permissions"
 import { user } from "./user"
 
@@ -27,17 +29,33 @@ const publishPermissions = async (datasetId) => {
   const ds = { id: datasetId }
   const { id, userPermissions } = await permissions(ds)
   const permissionsUpdated = {
-    id: datasetId,
-    permissions: {
-      id,
-      userPermissions: await Promise.all(
-        userPermissions.map(async (userPermission) => ({
-          ...userPermission,
-          user: await user(ds, { id: userPermission.userId }),
-        })),
-      ),
-    },
+    id,
+    userPermissions: await Promise.all(
+      userPermissions.map(async (userPermission) => ({
+        ...userPermission,
+        user: await user(ds, { id: userPermission.userId }),
+      })),
+    ),
+  }
+  return permissionsUpdated
+}
+
+async function updateUsers(datasetId: string, level: string, users) {
+  for (const user of users) {
+    await Permission.updateOne(
+      {
+        datasetId: datasetId,
+        userId: user.id,
+      },
+      {
+        datasetId: datasetId,
+        userId: user.id,
+        level: level,
+      },
+      { upsert: true },
+    ).exec()
   }
+  return publishPermissions(datasetId)
 }
 
 /**
@@ -54,28 +72,29 @@ export const updatePermissions = async (obj, args, { user, userInfo }) => {
     throw new Error("A user with that email address does not exist")
   }
 
-  const userPromises = users.map((user) => {
-    return new Promise<void>((resolve, reject) => {
-      Permission.updateOne(
-        {
-          datasetId: args.datasetId,
-          userId: user.id,
-        },
-        {
-          datasetId: args.datasetId,
-          userId: user.id,
-          level: args.level,
-        },
-        { upsert: true },
-      )
-        .exec()
-        .then(() => resolve())
-        .catch((err) => reject(err))
-    })
+  return updateUsers(args.datasetId, args.level, users)
+}
+
+/**
+ * ORCID variant of updatePermissions
+ */
+export const updateOrcidPermissions = async (obj, args, { user, userInfo }) => {
+  await checkDatasetAdmin(args.datasetId, user, userInfo)
+  // Get all users associated with the ORCID provided
+  const users = await User.find({
+    "$or": [{ "orcid": args.userOrcid }, {
+      "providerId": args.userOrcid,
+      "provider": "orcid",
+    }],
   })
-  return Promise.all(userPromises).then(() =>
-    publishPermissions(args.datasetId)
-  )
+    .collation({ locale: "en", strength: 2 })
+    .exec()
+
+  if (!users.length) {
+    throw new Error("A user with that ORCID does not exist")
+  }
+
+  return updateUsers(args.datasetId, args.level, users)
 }
 
 /**

package/src/graphql/resolvers/reset.ts

@@ -13,7 +13,7 @@ export const resetDraft = async (
   try {
     await resetDraftTask(datasetId, ref)
     return true
-  } catch (err) {
+  } catch (_err) {
     return false
   }
 }

package/src/graphql/resolvers/reviewer.ts

@@ -37,6 +37,7 @@ export async function deleteReviewer(
 /**
  * Resolver for dataset reviewers
  */
+/* eslint-disable-next-line @typescript-eslint/no-unused-vars */
 export function reviewers(obj, _, { user, userInfo }) {
   return Reviewer.find({ datasetId: obj.id }).lean().exec()
 }

package/src/graphql/resolvers/snapshots.ts

@@ -16,6 +16,7 @@ import CacheItem, { CacheType } from "../../cache/item"
 import { normalizeDOI } from "../../libs/doi/normalize"
 import { getDraftHead } from "../../datalad/dataset"
 import { downloadFiles } from "../../datalad/snapshots"
+import { snapshotValidation } from "./validation"
 
 export const snapshots = (obj) => {
   return datalad.getSnapshots(obj.id)
@@ -77,7 +78,7 @@ export const matchKnownObjects = (desc) => {
         } else {
           objects.push({ id: rawDOI })
         }
-      } catch (err) {
+      } catch (_err) {
         continue
       }
     }
@@ -227,7 +228,7 @@ export const latestSnapshot = async (obj, _, context) => {
     // In the case where there are no real snapshots, return most recent commit as snapshot
     return await snapshot(
       obj,
-      { datasetId: obj.id, tag: await getDraftHead(obj.id) },
+      { datasetId: obj.id, tag: (await getDraftHead(obj.id)).ref },
       context,
     )
   }
@@ -258,6 +259,7 @@ export const deleteSnapshot = (obj, { datasetId, tag }, { user, userInfo }) => {
 const Snapshot = {
   analytics: (snapshot) => analytics(snapshot),
   issues: (snapshot) => snapshotIssues(snapshot),
+  validation: (snapshot) => snapshotValidation(snapshot),
 }
 
 export default Snapshot

package/src/graphql/resolvers/summary.ts

@@ -1,5 +1,5 @@
-import Summary, { SummaryDocument } from "../../models/summary"
-import { datasetType } from "./datasetType"
+import Summary from "../../models/summary"
+import type { SummaryDocument } from "../../models/summary"
 
 /**
  * Summary resolver
@@ -9,9 +9,9 @@ export async function summary(dataset): Promise<Partial<SummaryDocument>> {
     await Summary.findOne({
       id: dataset.revision,
       datasetId: dataset.id,
-      // Match if we have no validatorMetadata or the correct 'legacy' / 'schema' value if we do
       $or: [
-        { "validatorMetadata.validator": await datasetType(dataset) },
+        { "validatorMetadata.validator": "schema" },
+        { "validatorMetadata.validator": "legacy" },
         { validatorMetadata: { $exists: false } },
       ],
     }).exec()

package/src/graphql/resolvers/validation.ts

@@ -1,16 +1,51 @@
 import config from "../../config"
 import { generateDataladCookie } from "../../libs/authentication/jwt"
 import { getDatasetWorker } from "../../libs/datalad-service"
-import Issue from "../../models/issue"
+import Validation from "../../models/validation"
 import { redlock } from "../../libs/redis"
 
+/**
+ * Issues resolver for schema validator
+ */
+export const validation = async (dataset, _, { userInfo }) => {
+  return Validation.findOne({
+    id: dataset.revision,
+    datasetId: dataset.id,
+  })
+    .exec()
+    .then((data) => {
+      if (!data && userInfo) {
+        // If no results were found, acquire a lock and run validation
+        revalidate(
+          null,
+          { datasetId: dataset.id, ref: dataset.revision },
+          { userInfo },
+        )
+      }
+      return data
+    })
+}
+
+/**
+ * Snapshot issues resolver for schema validator
+ */
+export const snapshotValidation = async (snapshot) => {
+  const datasetId = snapshot.id.split(":")[0]
+  return Validation.findOne({
+    id: snapshot.hexsha,
+    datasetId,
+  })
+    .exec()
+    .then((data) => (data ? data.issues : null))
+}
+
 /**
  * Save issues data returned by the datalad service
  *
  * Returns only a boolean if successful or not
  */
 export const updateValidation = (obj, args) => {
-  return Issue.updateOne(
+  return Validation.updateOne(
     {
       id: args.validation.id,
       datasetId: args.validation.datasetId,

package/src/graphql/schema.ts

@@ -1,4 +1,3 @@
-// @ts-nocheck
 import { schemaComposer } from "graphql-compose"
 import resolvers from "./resolvers"
 import {
@@ -120,9 +119,11 @@ export const typeDefs = `
     # Update a draft summary
     updateSummary(summary: SummaryInput!): Summary
     # Update a draft with validation results
-    updateValidation(validation: ValidationInput!): Boolean
+    updateValidation(validation: ValidatorInput!): Boolean
     # Update a users's permissions on a dataset
-    updatePermissions(datasetId: ID!, userEmail: String!, level: String): User
+    updatePermissions(datasetId: ID!, userEmail: String!, level: String!): DatasetPermissions
+    # Update a users's permissions for a given ORCID
+    updateOrcidPermissions(datasetId: ID!, userOrcid: String!, level: String!): DatasetPermissions
     # Remove a users's permissions on a dataset
     removePermissions(datasetId: ID!, userId: String!): Boolean
     # Remove a user
@@ -155,8 +156,6 @@ export const typeDefs = `
     subscribeToNewsletter(email: String!): Boolean
     # Upserts dataset metadata
     addMetadata(datasetId: ID!, metadata: MetadataInput!): Metadata
-    # Update draft reference pointer
-    updateRef(datasetId: ID!, ref: String!): Boolean
     # Start an upload
     prepareUpload(datasetId: ID!, uploadId: ID!): UploadMetadata
     # Add files from a completed upload to the dataset draft
@@ -219,7 +218,15 @@ export const typeDefs = `
   }
 
   # BIDS Validator metadata
-  input ValidatorMetadata {
+  type ValidatorMetadata {
+    # Unique string identifying the type of BIDS validator software
+    validator: String
+    # Semantic versioning string for the version of the validation software
+    version: String
+  }
+
+  # BIDS Validator metadata
+  input ValidatorMetadataInput {
     # Unique string identifying the type of BIDS validator software
     validator: String
     # Semantic versioning string for the version of the validation software
@@ -241,7 +248,7 @@ export const typeDefs = `
     dataProcessed: Boolean
     pet: SummaryPetInput
     # Metadata for validation software used
-    validatorMetadata: ValidatorMetadata
+    validatorMetadata: ValidatorMetadataInput
     # BIDS Specification schema version
     schemaVersion: String
   }
@@ -253,11 +260,12 @@ export const typeDefs = `
     group: String
   }
 
-  input ValidationInput {
+  input ValidatorInput {
     id: ID! # Git reference for this validation
     datasetId: ID!
-    issues: [ValidationIssueInput]!
-    validatorMetadata: ValidatorMetadata
+    issues: [ValidatorIssueInput]!
+    codeMessages: [ValidatorCodeMessageInput]!
+    validatorMetadata: ValidatorMetadataInput!
   }
 
   # Dataset Metadata
@@ -287,13 +295,6 @@ export const typeDefs = `
     affirmedConsent: Boolean
   }
 
-  # Validation updated message
-  type ValidationUpdate {
-    id: ID!
-    datasetId: ID!
-    issues: [ValidationIssue]
-  }
-
   # Information for pagination in a connection.
   type PageInfo {
     # When paginating forwards, are there more items?
@@ -450,6 +451,28 @@ export const typeDefs = `
     binary: Boolean
   }
 
+  type ValidatorCodeMessage {
+    code: String!
+    message: String!
+  }
+
+  # BIDS Validator (schema) issues
+  type ValidatorIssue {
+    code: String!
+    subCode: String
+    location: String
+    severity: Severity
+    rule: String
+  }
+
+  type DatasetValidation {
+    # Hash of the data validated
+    id: String
+    datasetId: String
+    issues: [ValidatorIssue]
+    codeMessages: [ValidatorCodeMessage]
+  }
+
   # Ephemeral draft or working tree for a dataset
   type Draft {
     id: ID
@@ -459,8 +482,10 @@ export const typeDefs = `
     modified: DateTime
     # Validator summary
     summary: Summary
-    # Validator issues
+    # Validator issues (legacy validator)
     issues: [ValidationIssue]
+    # Validator issues (schema validator)
+    validation: DatasetValidation
     # Committed files in the working tree
     files(tree: String): [DatasetFile]
     # dataset_description.json fields
@@ -486,8 +511,10 @@ export const typeDefs = `
     created: DateTime
     # bids-validator summary of this snapshot
     summary: Summary
-    # bids-validator issues for this snapshot
+    # Validator issues (legacy validator)
     issues: [ValidationIssue]
+    # Validator issues (schema validator)
+    validation: DatasetValidation
     # Snapshot files
     files(tree: String): [DatasetFile]
     # dataset_description.json fields
@@ -614,6 +641,8 @@ export const typeDefs = `
     pet: SummaryPetFields
     # BIDS Specification schema version
     schemaVersion: String
+    # Validator metadata
+    validatorMetadata: ValidatorMetadata
   }
 
   type SummaryPetFields {
@@ -668,14 +697,17 @@ export const typeDefs = `
     helpUrl: String
   }
 
-  input ValidationIssueInput {
-    severity: Severity!
-    key: String!
-    code: Int
-    reason: String!
-    files: [ValidationIssueFileInput]
-    additionalFileCount: Int
-    helpUrl: String
+  input ValidatorIssueInput {
+    code: String!
+    subCode: String
+    location: String
+    severity: Severity
+    rule: String
+  }
+
+  input ValidatorCodeMessageInput {
+    code: String!
+    message: String!
   }
 
   type ValidationIssueFile {
@@ -692,35 +724,12 @@ export const typeDefs = `
     helpUrl: String
   }
 
-  input ValidationIssueFileInput {
-    name: String
-    path: String
-    key: String
-    code: Int
-    file: ValidationIssueFileDetailInput
-    evidence: String
-    line: Int
-    character: Int
-    severity: Severity
-    reason: String
-    helpUrl: String
-    # Temporary field for compatibility (remove after bids-validator@1.13.0)
-    _datasetAbsPath: String
-  }
-
   type ValidationIssueFileDetail {
     name: String
     path: String
     relativePath: String
   }
 
-  input ValidationIssueFileDetailInput {
-    name: String
-    path: String
-    relativePath: String
-    webkitRelativePath: String
-  }
-
   # File metadata and link to contents
   type DatasetFile {
     id: ID!

package/src/handlers/comments.ts

@@ -1,6 +1,5 @@
-// @ts-nocheck
 import notifications from "../libs/notifications.js"
-import { format } from "date-fns/format"
+import formatISO from "date-fns/formatISO"
 import User from "../models/user"
 import Comment from "../models/comment"
 import MailgunIdentifier from "../models/mailgunIdentifier"
@@ -15,9 +14,11 @@ const ObjectID = mongoose.Schema.Types.ObjectId
  * item that can be stored as if it came from
  * a client-side draft.js editor
  */
-const textToDraft = (text) => {
+const textToDraft = (text: string) => {
   return JSON.stringify(
-    convertToRaw(ContentState.createFromBlockArray(convertFromHTML(text))),
+    convertToRaw(
+      ContentState.createFromBlockArray(convertFromHTML(text).contentBlocks),
+    ),
   )
 }
 
@@ -28,7 +29,6 @@ const textToDraft = (text) => {
  * ** maybe returns the newly created comment id
  */
 export async function reply(req, res, next) {
-  /* eslint-disable no-console */
   let comment
   const parentId = req.params.commentId
     ? decodeURIComponent(req.params.commentId)
@@ -49,6 +49,7 @@ export async function reply(req, res, next) {
   }
   const user = await User.findOne({ id: userId }).exec()
   const originalComment = await Comment.findOne({
+    // @ts-expect-error This is needed as an object and also a type
     _id: ObjectID(parentId),
   }).exec()
   if (user && originalComment) {
@@ -63,7 +64,7 @@ export async function reply(req, res, next) {
       parentId: parentId,
       text: text,
       user: flattenedUser,
-      createDate: format(new Date()),
+      createDate: formatISO(new Date()),
     }
     Comment.create(comment, (err, response) => {
       if (err) {

package/src/handlers/datalad.ts

@@ -71,12 +71,11 @@ export const getFile = async (req, res) => {
         if (r.status === 404) {
           res.status(404).send("Requested dataset or file cannot be found")
         } else {
-          // @ts-expect-error
+          // @ts-expect-error https://github.com/denoland/deno/issues/19620
           Readable.fromWeb(r.body, { highWaterMark: 4194304 }).pipe(res)
         }
       })
-      .catch((err) => {
-        console.error(err)
+      .catch((_err) => {
         res.status(500).send("Internal error transferring requested file")
       })
   }

package/src/libs/__tests__/dataset.spec.ts

@@ -1,6 +1,6 @@
 import { vi } from "vitest"
 import { MongoMemoryServer } from "mongodb-memory-server"
-import { connect, disconnect } from "mongoose"
+import { connect } from "mongoose"
 import { getAccessionNumber } from "../dataset"
 
 vi.mock("ioredis")

package/src/libs/email/index.ts

@@ -1,14 +1,14 @@
 import config from "../../config"
+import mailjet from "node-mailjet"
 
 let transport
 let perform_api_call = true
 try {
-  const mailjet = require("node-mailjet")
   transport = mailjet.connect(
     config.notifications.email.apiKey,
     config.notifications.email.secret,
   )
-} catch (err) {
+} catch (_err) {
   perform_api_call = false
 }
 
@@ -42,6 +42,7 @@ export const send = (email: Record<string, string>): Promise<Response> => {
       .request(mailjetFormat(email))
   } else {
     // Mailjet is not configured, instead log emails
+    /* eslint-disable no-console */
     console.dir(email)
   }
 }

package/src/models/analytics.ts

@@ -1,4 +1,5 @@
-import mongoose, { Document } from "mongoose"
+import mongoose from "mongoose"
+import type { Document } from "mongoose"
 const { Schema, model } = mongoose
 
 export interface AnalyticsDocument extends Document {

package/src/models/badAnnexObject.ts

@@ -1,5 +1,6 @@
-import mongoose, { Document } from "mongoose"
-import { UserDocument } from "./user"
+import mongoose from "mongoose"
+import type { Document } from "mongoose"
+import type { UserDocument } from "./user"
 const ObjectId = mongoose.Schema.Types.ObjectId
 
 export interface BadAnnexObject extends Document {

package/src/models/comment.ts

@@ -1,4 +1,5 @@
-import mongoose, { Document } from "mongoose"
+import mongoose from "mongoose"
+import type { Document } from "mongoose"
 const { Schema, model } = mongoose
 
 export interface CommentDocument extends Document {

package/src/models/counter.ts

@@ -1,4 +1,5 @@
-import mongoose, { Document } from "mongoose"
+import mongoose from "mongoose"
+import type { Document } from "mongoose"
 const { Schema, model } = mongoose
 
 export interface CounterDocument extends Document {

package/src/models/dataset.ts

@@ -1,4 +1,5 @@
-import mongoose, { Document } from "mongoose"
+import mongoose from "mongoose"
+import type { Document } from "mongoose"
 const { Schema, model } = mongoose
 
 // External relations annotating the whole dataset
@@ -28,7 +29,7 @@ export interface DatasetDocument extends Document {
   views: number
   related: [DatasetRelationDocument]
   schemaValidator: boolean
-  _conditions: any
+  _conditions: object
 }
 
 const datasetSchema = new Schema<DatasetDocument>(

package/src/models/deletion.ts

@@ -1,4 +1,5 @@
-import mongoose, { Document } from "mongoose"
+import mongoose from "mongoose"
+import type { Document } from "mongoose"
 const { Schema, model } = mongoose
 
 export interface DeletionDocument extends Document {

package/src/models/deprecatedSnapshot.ts

@@ -1,4 +1,5 @@
-import mongoose, { Document } from "mongoose"
+import mongoose from "mongoose"
+import type { Document } from "mongoose"
 const { Schema, model } = mongoose
 
 export interface DeprecatedSnapshotDocument extends Document {

package/src/models/doi.ts

@@ -1,4 +1,5 @@
-import mongoose, { Document } from "mongoose"
+import mongoose from "mongoose"
+import type { Document } from "mongoose"
 const { Schema, model } = mongoose
 
 export interface DoiDocument extends Document {

package/src/models/file.ts

@@ -1,10 +1,11 @@
-import mongoose, { Document } from "mongoose"
+import mongoose from "mongoose"
+import type { Document } from "mongoose"
 const { Schema, model } = mongoose
 
 export interface FileDocument extends Document {
   datasetId: string
   tag: string
-  files: any[]
+  files: object[]
 }
 
 const fileSchema = new Schema({

package/src/models/ingestDataset.ts

@@ -1,7 +1,8 @@
 /**
  * Model for ingest of new datasets from a remote URL (zip/tarball)
  */
-import mongoose, { Document, ObjectId } from "mongoose"
+import mongoose from "mongoose"
+import type { Document, ObjectId } from "mongoose"
 const { Schema, model } = mongoose
 import { validateUrl } from "../utils/validateUrl"
 

package/src/models/issue.ts

@@ -1,4 +1,5 @@
-import mongoose, { Document } from "mongoose"
+import mongoose from "mongoose"
+import type { Document } from "mongoose"
 const { Schema, model } = mongoose
 
 export interface IssueDocument extends Document {