Merge pull request #531 from desci-labs/highlight-adaptation

Add support for Comments on Nodes

desci-server/prisma/migrations/20240925135142_add_uuid_and_visible_and_make_nodeattestation_id_optional/migration.sql

@@ -0,0 +1,14 @@
+-- DropForeignKey
+ALTER TABLE "Annotation" DROP CONSTRAINT "Annotation_nodeAttestationId_fkey";
+
+-- AlterTable
+ALTER TABLE "Annotation" ADD COLUMN     "nodeId" INTEGER,
+ADD COLUMN     "uuid" TEXT,
+ADD COLUMN     "visible" BOOLEAN NOT NULL DEFAULT true,
+ALTER COLUMN "nodeAttestationId" DROP NOT NULL;
+
+-- AddForeignKey
+ALTER TABLE "Annotation" ADD CONSTRAINT "Annotation_nodeAttestationId_fkey" FOREIGN KEY ("nodeAttestationId") REFERENCES "NodeAttestation"("id") ON DELETE SET NULL ON UPDATE CASCADE;
+
+-- AddForeignKey
+ALTER TABLE "Annotation" ADD CONSTRAINT "Annotation_uuid_fkey" FOREIGN KEY ("uuid") REFERENCES "Node"("uuid") ON DELETE SET NULL ON UPDATE CASCADE;

desci-server/prisma/migrations/20240926094958_remove_nodeid_column_from_annotation/migration.sql

@@ -0,0 +1,8 @@
+/*
+  Warnings:
+
+  - You are about to drop the column `nodeId` on the `Annotation` table. All the data in the column will be lost.
+
+*/
+-- AlterTable
+ALTER TABLE "Annotation" DROP COLUMN "nodeId";

desci-server/prisma/schema.prisma

@@ -51,6 +51,7 @@ model Node {
   DoiSubmissionQueue  DoiSubmissionQueue[]
   BookmarkedNode      BookmarkedNode[]
   DeferredEmails      DeferredEmails[]
+  Annotation          Annotation[]
 
   @@index([ownerId])
   @@index([uuid])
@@ -811,16 +812,19 @@ enum EmailType {
 
 //Comments on attestations
 model Annotation {
-  id                Int             @id @default(autoincrement())
+  id                Int              @id @default(autoincrement())
   type              AnnotationType
   body              String
-  highlights        Json[]          @default([])
-  links             String[]        @default([])
+  highlights        Json[]           @default([])
+  links             String[]         @default([])
   authorId          Int
-  author            User            @relation(fields: [authorId], references: [id])
-  nodeAttestationId Int
-  attestation       NodeAttestation @relation(fields: [nodeAttestationId], references: [id])
+  author            User             @relation(fields: [authorId], references: [id])
+  nodeAttestationId Int?
+  attestation       NodeAttestation? @relation(fields: [nodeAttestationId], references: [id])
   deferredEmailsId  Int?
+  uuid              String?
+  node              Node?            @relation(fields: [uuid], references: [uuid])
+  visible           Boolean          @default(true)
 }
 
 //An emoji reaction to a node

desci-server/src/controllers/attestations/comments.ts

@@ -1,5 +1,5 @@
 import { HighlightBlock } from '@desci-labs/desci-models';
-import { ActionType, Annotation } from '@prisma/client';
+import { ActionType, Annotation, AnnotationType } from '@prisma/client';
 import { NextFunction, Request, Response } from 'express';
 import _ from 'lodash';
 import zod from 'zod';
@@ -13,7 +13,9 @@ import {
   asyncMap,
   attestationService,
   createCommentSchema,
+  ensureUuidEndsWithDot,
   logger as parentLogger,
+  prisma,
 } from '../../internal.js';
 import { saveInteraction } from '../../services/interactionLog.js';
 import { client } from '../../services/ipfs.js';
@@ -78,7 +80,7 @@ export const removeComment = async (req: Request<RemoveCommentBody, any, any>, r
 type AddCommentBody = zod.infer<typeof createCommentSchema>;
 
 export const addComment = async (req: Request<any, any, AddCommentBody['body']>, res: Response<AddCommentResponse>) => {
-  const { authorId, claimId, body, highlights, links } = req.body;
+  const { authorId, claimId, body, highlights, links, uuid, visible } = req.body;
   const user = (req as any).user;
 
   if (parseInt(authorId.toString()) !== user.id) throw new ForbiddenError();
@@ -89,6 +91,11 @@ export const addComment = async (req: Request<any, any, AddCommentBody['body']>,
     user: (req as any).user,
     body: req.body,
   });
+
+  if (uuid) {
+    const node = await prisma.node.findFirst({ where: { uuid: ensureUuidEndsWithDot(uuid) } });
+    if (!node) throw new NotFoundError('Node with uuid ${uuid} not found');
+  }
   logger.trace(`addComment`);
 
   let annotation: Annotation;
@@ -102,19 +109,23 @@ export const addComment = async (req: Request<any, any, AddCommentBody['body']>,
     });
     logger.info({ processedHighlights }, 'processedHighlights');
     annotation = await attestationService.createHighlight({
-      claimId: parseInt(claimId.toString()),
+      claimId: claimId && parseInt(claimId.toString()),
       authorId: user.id,
       comment: body,
       links,
       highlights: processedHighlights as unknown as HighlightBlock[],
+      visible,
+      ...(uuid && { uuid: ensureUuidEndsWithDot(uuid) }),
     });
     await saveInteraction(req, ActionType.ADD_COMMENT, { annotationId: annotation.id, claimId, authorId });
   } else {
     annotation = await attestationService.createComment({
-      claimId: parseInt(claimId.toString()),
+      claimId: claimId && parseInt(claimId.toString()),
       authorId: user.id,
       comment: body,
       links,
+      visible,
+      ...(uuid && { uuid: ensureUuidEndsWithDot(uuid) }),
     });
   }
   await saveInteraction(req, ActionType.ADD_COMMENT, { annotationId: annotation.id, claimId, authorId });

desci-server/src/controllers/attestations/recommendations.ts

@@ -60,7 +60,6 @@ export const getValidatedAttestations = async (req: Request, res: Response, _nex
   logger.info({ communityName });
   const community = await communityService.findCommunityByNameOrSlug(communityName);
   if (!community) throw new NotFoundError('Community not found');
-  logger.info({ community });
 
   const attestations = await attestationService.getCommunityAttestations({
     communityId: community.id,
@@ -83,6 +82,6 @@ export const getValidatedRecommendations = async (req: Request, res: Response, _
     communityName: attestation.community.name,
     AttestationVersion: attestation.AttestationVersion[0],
   }));
-  logger.info({ attestations }, 'getValidatedRecommendations');
+  logger.info({ recommendations: attestations.length }, 'getValidatedRecommendations');
   return new SuccessResponse(response).send(res);
 };

desci-server/src/controllers/nodes/comments.ts

@@ -0,0 +1,35 @@
+import { Response, NextFunction } from 'express';
+import _ from 'lodash';
+import z from 'zod';
+
+import {
+  NotFoundError,
+  RequestWithNode,
+  SuccessResponse,
+  attestationService,
+  ensureUuidEndsWithDot,
+  getCommentsSchema,
+  logger,
+  prisma,
+} from '../../internal.js';
+
+export const getGeneralComments = async (req: RequestWithNode, res: Response, _next: NextFunction) => {
+  const { uuid } = req.params as z.infer<typeof getCommentsSchema>['params'];
+  const node = await prisma.node.findFirst({ where: { uuid: ensureUuidEndsWithDot(uuid) } });
+  if (!node) throw new NotFoundError("Can't comment on unknown research object");
+
+  const restrictVisibility = node.ownerId !== req?.user?.id;
+
+  logger.info({ restrictVisibility }, 'Query Comments');
+  const comments = await attestationService.getComments({
+    uuid: ensureUuidEndsWithDot(uuid),
+    ...(restrictVisibility && { visible: true }),
+  });
+
+  const data = comments.map((comment) => {
+    const author = _.pick(comment.author, ['id', 'name', 'orcid']);
+    return { ...comment, author, highlights: comment.highlights.map((h) => JSON.parse(h as string)) };
+  });
+
+  return new SuccessResponse(data).send(res);
+};

desci-server/src/controllers/nodes/createDpid.ts

@@ -7,11 +7,11 @@ import { ethers } from 'ethers';
 import { Response } from 'express';
 import { Logger } from 'pino';
 
+import { CERAMIC_API_URL } from '../../config/index.js';
 import { logger as parentLogger } from '../../logger.js';
 import { RequestWithNode } from '../../middleware/authorisation.js';
-import { setDpidAlias } from '../../services/nodeManager.js';
-import { CERAMIC_API_URL } from '../../config/index.js';
 import { getAliasRegistry, getHotWallet, getRegistryOwnerWallet } from '../../services/chain.js';
+import { setDpidAlias } from '../../services/nodeManager.js';
 
 type DpidResponse = DpidSuccessResponse | DpidErrorResponse;
 export type DpidSuccessResponse = {
@@ -56,9 +56,7 @@ export const createDpid = async (req: RequestWithNode, res: Response<DpidRespons
   }
 };
 
-export const getOrCreateDpid = async (
-  streamId: string,
-): Promise<number> => {
+export const getOrCreateDpid = async (streamId: string): Promise<number> => {
   const logger = parentLogger.child({
     module: 'NODE::mintDpid',
     ceramicStream: streamId,
@@ -97,10 +95,7 @@ export const getOrCreateDpid = async (
  * Note: this method in the registry contract is only callable by contract
  * owner, so this is not generally available.
  */
-export const upgradeDpid = async (
-  dpid: number,
-  ceramicStream: string
-): Promise<number> => {
+export const upgradeDpid = async (dpid: number, ceramicStream: string): Promise<number> => {
   const logger = parentLogger.child({
     module: 'NODE::upgradeDpid',
     ceramicStream,
@@ -130,12 +125,7 @@ export const upgradeDpid = async (
  * This should be checked before upgrading a dPID, to make sure
  * the new stream accurately represents the publish history.
  */
-const validateHistory = async (
-  dpid: number,
-  ceramicStream: string,
-  registry: DpidAliasRegistry,
-  logger: Logger
-) => {
+const validateHistory = async (dpid: number, ceramicStream: string, registry: DpidAliasRegistry, logger: Logger) => {
   const client = newCeramicClient(CERAMIC_API_URL);
   const legacyEntry = await registry.legacyLookup(dpid);
 

desci-server/src/controllers/nodes/index.ts

@@ -13,3 +13,8 @@ export * from './nodesCover.js';
 export * from './manager.js';
 export * from './metadata.js';
 export * from './doi.js';
+export * from './comments.js';
+export * from './sharedNodes.js';
+export * from './searchNodes.js';
+export * from './versionDetails.js';
+export * from './thumbnails.js';

desci-server/src/controllers/nodes/prepublish.ts

@@ -82,6 +82,7 @@ export const prepublish = async (req: RequestWithNode, res: Response<PrepublishR
       skipDuplicates: true,
     });
 
+    logger.info({ nodeFileTreeDagCid }, 'publishDraftComments::Root');
     logger.info(
       `[Prepublish DAG Skeleton Refs] Created ${createdPublicRefs.count} public data refs for node ${node.id}`,
     );

desci-server/src/controllers/nodes/publish.ts

@@ -3,6 +3,7 @@ import { ActionType, Node, Prisma, PublishTaskQueue, PublishTaskQueueStatus, Use
 import { Request, Response, NextFunction } from 'express';
 
 import { prisma } from '../../client.js';
+import { attestationService } from '../../internal.js';
 import { logger as parentLogger } from '../../logger.js';
 import { getManifestByCid } from '../../services/data/processing.js';
 import { getTargetDpidUrl } from '../../services/fixDpid.js';
@@ -15,6 +16,7 @@ import {
   setDpidAlias,
 } from '../../services/nodeManager.js';
 import { publishServices } from '../../services/PublishServices.js';
+import { getIndexedResearchObjects } from '../../theGraph.js';
 import { discordNotify } from '../../utils/discordUtils.js';
 import { ensureUuidEndsWithDot } from '../../utils.js';
 
@@ -69,7 +71,6 @@ export const publish = async (req: PublishRequest, res: Response<PublishResBody>
     body: req.body,
     uuid,
     cid,
-    manifest,
     transactionId,
     ceramicStream,
     commitId,
@@ -160,6 +161,24 @@ export const publish = async (req: PublishRequest, res: Response<PublishResBody>
 
     updateAssociatedAttestations(node.uuid, dpidAlias ? dpidAlias.toString() : manifest.dpid?.id);
 
+    const root = await prisma.publicDataReference.findFirst({
+      where: { nodeId: node.id, root: true, userId: owner.id },
+      orderBy: { updatedAt: 'desc' },
+    });
+    const result = await getIndexedResearchObjects([ensureUuidEndsWithDot(uuid)]);
+    // if node is being published for the first time default to 1
+    const version = result ? result.researchObjects?.[0]?.versions.length : 1;
+    logger.info({ root, result, version }, 'publishDraftComments::Root');
+
+    // publish draft comments
+    await attestationService.publishDraftComments({
+      node,
+      userId: owner.id,
+      dpidAlias: dpidAlias ?? parseInt(manifest.dpid?.id),
+      rootCid: root.rootCid,
+      version,
+    });
+
     return res.send({
       ok: true,
       dpid: dpidAlias ?? parseInt(manifest.dpid?.id),

desci-server/src/controllers/raw/versions.ts

@@ -5,7 +5,7 @@ import { getIndexedResearchObjects, IndexedResearchObject } from '../../theGraph
 import { ensureUuidEndsWithDot } from '../../utils.js';
 
 const logger = parentLogger.child({
-  module: "RAW::versionsController"
+  module: 'RAW::versionsController',
 });
 
 /**
@@ -19,12 +19,10 @@ export const versions = async (req: Request, res: Response, next: NextFunction)
     const { researchObjects } = await getIndexedResearchObjects([uuid]);
     result = researchObjects[0];
   } catch (err) {
-    logger.error(
-      { result, err }, `[ERROR] graph lookup fail ${err.message}`,
-    );
+    logger.error({ result, err }, `[ERROR] graph lookup fail ${err.message}`);
   }
   if (!result) {
-    logger.warn({ uuid, result }, "could not find indexed versions");
+    logger.warn({ uuid, result }, 'could not find indexed versions');
     res.status(404).send({ ok: false, msg: `could not locate uuid ${uuid}` });
     return;
   }

desci-server/src/routes/v1/attestations/index.ts

@@ -62,7 +62,7 @@ router.post('/claim', [ensureUser, validate(claimAttestationSchema)], asyncHandl
 router.post('/unclaim', [ensureUser, validate(removeClaimSchema)], asyncHandler(removeClaim));
 router.post('/claimAll', [ensureUser, validate(claimEntryAttestationsSchema)], asyncHandler(claimEntryRequirements));
 
-router.post('/comment', [ensureUser, validate(createCommentSchema)], asyncHandler(addComment));
+router.post('/comments', [ensureUser, validate(createCommentSchema)], asyncHandler(addComment));
 router.post('/reaction', [ensureUser, validate(addReactionSchema)], asyncHandler(addReaction));
 router.post('/verification', [ensureUser, validate(addVerificationSchema)], asyncHandler(addVerification));