Merge branch 'develop' into cover-page-api

.env.example

@@ -123,3 +123,10 @@ DPID_URL_OVERRIDE=https://dev-beta.dpid.org
 MUTE_PUBLISH_WORKER=false
 # SingleNodeLockServce
 MAX_LOCK_TIME=3600 # 1 hour
+
+DOI_PREFIX=https://doi.org/10.62891
+
+# Cross ref api 
+CROSSREF_API=https://api.crossref.org
+CROSSREF_API_KEY=
+CROSSREF_EMAIL=

.env.test

@@ -72,4 +72,11 @@ VSCODE_ACCESS_TOKEN=
 NODES_MEDIA_SERVER_URL=http://host.docker.internal:5454
 
 REPO_SERVICE_SECRET_KEY="m8sIy5BPygBcX3+ZmMVuAA10k6w59BSCZd+Z5+VLYm4="
-REPO_SERVER_URL=http://host.docker.internal:5485
+REPO_SERVER_URL=http://host.docker.internal:5485
+
+DOI_PREFIX=https://doi.org/10.62891
+
+# Cross ref api 
+CROSSREF_API=https://api.crossref.org
+CROSSREF_API_KEY=
+CROSSREF_EMAIL=

.github/workflows/deploy-staging-services.yaml

@@ -13,6 +13,7 @@ env:
   CONTAINER_IMAGE_REPO: desci-repo-server
   CONTAINER_IMAGE_MEDIA: nodes-media-server
   CONTAINER_IMAGE_ISOLATED: desci-media-isolated
+  CONTAINER_IMAGE_PROXY: "reverse-proxy"
   DOCKER_BUILDKIT: 1
 
 jobs:
@@ -294,23 +295,23 @@ jobs:
         run: |
           # Build and tag the image
           docker build \
-            -t $CONTAINER_IMAGE-staging:latest \
-            -t $AWS_ACCOUNT_ID.dkr.ecr.$AWS_DEFAULT_REGION.amazonaws.com/$CONTAINER_IMAGE-staging \
-             ./$CONTAINER_IMAGE
+            -t $CONTAINER_IMAGE_PROXY-staging:latest \
+            -t $AWS_ACCOUNT_ID.dkr.ecr.$AWS_DEFAULT_REGION.amazonaws.com/$CONTAINER_IMAGE_PROXY-staging \
+             ./$CONTAINER_IMAGE_PROXY
 
       - name: Push (STAGING)
         run: |
           # Push image to AWS ECR
           aws ecr get-login-password --region $AWS_DEFAULT_REGION | docker login --username AWS --password-stdin $AWS_ACCOUNT_ID.dkr.ecr.$AWS_DEFAULT_REGION.amazonaws.com
-          docker tag $CONTAINER_IMAGE-staging:latest $AWS_ACCOUNT_ID.dkr.ecr.$AWS_DEFAULT_REGION.amazonaws.com/$CONTAINER_IMAGE-staging:${{ github.sha }}
-          docker tag $CONTAINER_IMAGE-staging:latest $AWS_ACCOUNT_ID.dkr.ecr.$AWS_DEFAULT_REGION.amazonaws.com/$CONTAINER_IMAGE-staging:latest
-          docker push $AWS_ACCOUNT_ID.dkr.ecr.$AWS_DEFAULT_REGION.amazonaws.com/$CONTAINER_IMAGE-staging:${{ github.sha }}
-          docker push $AWS_ACCOUNT_ID.dkr.ecr.$AWS_DEFAULT_REGION.amazonaws.com/$CONTAINER_IMAGE-staging:latest
+          docker tag $CONTAINER_IMAGE_PROXY-staging:latest $AWS_ACCOUNT_ID.dkr.ecr.$AWS_DEFAULT_REGION.amazonaws.com/$CONTAINER_IMAGE_PROXY-staging:${{ github.sha }}
+          docker tag $CONTAINER_IMAGE_PROXY-staging:latest $AWS_ACCOUNT_ID.dkr.ecr.$AWS_DEFAULT_REGION.amazonaws.com/$CONTAINER_IMAGE_PROXY-staging:latest
+          docker push $AWS_ACCOUNT_ID.dkr.ecr.$AWS_DEFAULT_REGION.amazonaws.com/$CONTAINER_IMAGE_PROXY-staging:${{ github.sha }}
+          docker push $AWS_ACCOUNT_ID.dkr.ecr.$AWS_DEFAULT_REGION.amazonaws.com/$CONTAINER_IMAGE_PROXY-staging:latest
       
       - name: Deploy to EKS (STAGING)
         run: | # defaults to latest kubectl binary version
-          kubectl apply -f $CONTAINER_IMAGE/deployment.yaml
-          kubectl set image deployment/reverse-proxy-staging reverse-proxy-staging=$AWS_ACCOUNT_ID.dkr.ecr.$AWS_DEFAULT_REGION.amazonaws.com/$CONTAINER_IMAGE-staging:${{ github.sha }} --record
+          kubectl apply -f $CONTAINER_IMAGE_PROXY/deployment.yaml
+          kubectl set image deployment/reverse-proxy-staging reverse-proxy-staging=$AWS_ACCOUNT_ID.dkr.ecr.$AWS_DEFAULT_REGION.amazonaws.com/$CONTAINER_IMAGE_PROXY-staging:${{ github.sha }} --record
 
       - name: Verify EKS Deployment (STAGING)
         run: |

.vscode/settings.json

@@ -1,7 +1,7 @@
 {
   "explorer.compactFolders": false,
   "files.exclude": {
-    "**/node_modules/**": true
+    "**/node_modules/**": false
   },
   "editor.formatOnSave": true, // Tell VSCode to format files on save
   "editor.defaultFormatter": "esbenp.prettier-vscode",

desci-server/kubernetes/deployment_dev.yaml

@@ -41,6 +41,7 @@ spec:
           export SESSION_KEY={{ .Data.SESSION_KEY }}
           export COOKIE_DOMAIN={{ .Data.COOKIE_DOMAIN }}
           export ORCID_API_DOMAIN={{ .Data.ORCID_API_DOMAIN }}
+          export DPID_URL_OVERRIDE={{ .Data.DPID_URL_OVERRIDE }}
           export ORCID_CLIENT_ID={{ .Data.ORCID_CLIENT_ID }}
           export ORCID_CLIENT_SECRET={{ .Data.ORCID_CLIENT_SECRET }}
           export ARWEAVE_ENABLED=0
@@ -78,6 +79,10 @@ spec:
           export IPFS_READ_ONLY_GATEWAY_SERVER_URL={{ .Data.IPFS_READ_ONLY_GATEWAY_SERVER_URL }}
           export ETHEREUM_RPC_URL={{ .Data.ETHEREUM_RPC_URL }}
           export GOOGLE_CLIENT_ID={{ .Data.GOOGLE_CLIENT_ID }}
+          export DOI_PREFIX={{ .Data.DOI_PREFIX }}
+          export CROSSREF_API={{ .Data.CROSSREF_API }}
+          export CROSSREF_API_KEY={{ .Data.CROSSREF_API_KEY }}
+          export CROSSREF_EMAIL={{ .Data.CROSSREF_EMAIL }}
           export DEBUG_TEST=0;
           echo "appfinish";
           {{- end -}}

desci-server/kubernetes/deployment_prod.yaml

@@ -43,6 +43,7 @@ spec:
           export ORCID_API_DOMAIN={{ .Data.ORCID_API_DOMAIN }}
           export ORCID_CLIENT_ID={{ .Data.ORCID_CLIENT_ID }}
           export ORCID_CLIENT_SECRET={{ .Data.ORCID_CLIENT_SECRET }}
+          export DPID_URL_OVERRIDE={{ .Data.DPID_URL_OVERRIDE }}
           export ARWEAVE_ENABLED=0
           export ARWEAVE_HOST=
           export ARWEAVE_PORT=1984
@@ -78,6 +79,10 @@ spec:
           export IPFS_READ_ONLY_GATEWAY_SERVER_URL={{ .Data.IPFS_READ_ONLY_GATEWAY_SERVER_URL }}
           export ETHEREUM_RPC_URL={{ .Data.ETHEREUM_RPC_URL }}
           export GOOGLE_CLIENT_ID={{ .Data.GOOGLE_CLIENT_ID }}
+          export DOI_PREFIX={{ .Data.DOI_PREFIX }}
+          export CROSSREF_API={{ .Data.CROSSREF_API }}
+          export CROSSREF_API_KEY={{ .Data.CROSSREF_API_KEY }}
+          export CROSSREF_EMAIL={{ .Data.CROSSREF_EMAIL }}
           export IGNORE_LINE=0;
           export DEBUG_TEST=0;
           echo "appfinish";

desci-server/kubernetes/deployment_staging.yaml

@@ -55,6 +55,7 @@ spec:
           export ORCID_API_DOMAIN={{ .Data.ORCID_API_DOMAIN }}
           export ORCID_CLIENT_ID={{ .Data.ORCID_CLIENT_ID }}
           export ORCID_CLIENT_SECRET={{ .Data.ORCID_CLIENT_SECRET }}
+          export DPID_URL_OVERRIDE={{ .Data.DPID_URL_OVERRIDE }}
           export ARWEAVE_ENABLED=0
           export ARWEAVE_HOST=
           export ARWEAVE_PORT=1984
@@ -90,6 +91,10 @@ spec:
           export IPFS_READ_ONLY_GATEWAY_SERVER_URL={{ .Data.IPFS_READ_ONLY_GATEWAY_SERVER_URL }}
           export ETHEREUM_RPC_URL={{ .Data.ETHEREUM_RPC_URL }}
           export GOOGLE_CLIENT_ID={{ .Data.GOOGLE_CLIENT_ID }}
+          export DOI_PREFIX={{ .Data.DOI_PREFIX }}
+          export CROSSREF_API={{ .Data.CROSSREF_API }}
+          export CROSSREF_API_KEY={{ .Data.CROSSREF_API_KEY }}
+          export CROSSREF_EMAIL={{ .Data.CROSSREF_EMAIL }}
           export DEBUG_TEST=0;
           echo "appfinish";
           {{- end -}}

desci-server/prisma/migrations/20240604123832_add_doi_records_table/migration.sql

@@ -0,0 +1,20 @@
+-- CreateTable
+CREATE TABLE "DoiRecord" (
+    "id" SERIAL NOT NULL,
+    "doi" TEXT NOT NULL,
+    "dpid" TEXT NOT NULL,
+    "uuid" TEXT NOT NULL,
+    "createdAt" TIMESTAMP(3) NOT NULL DEFAULT CURRENT_TIMESTAMP,
+    "updatedAt" TIMESTAMP(3) NOT NULL,
+
+    CONSTRAINT "DoiRecord_pkey" PRIMARY KEY ("id")
+);
+
+-- CreateIndex
+CREATE UNIQUE INDEX "DoiRecord_doi_key" ON "DoiRecord"("doi");
+
+-- CreateIndex
+CREATE UNIQUE INDEX "DoiRecord_dpid_key" ON "DoiRecord"("dpid");
+
+-- AddForeignKey
+ALTER TABLE "DoiRecord" ADD CONSTRAINT "DoiRecord_uuid_fkey" FOREIGN KEY ("uuid") REFERENCES "Node"("uuid") ON DELETE RESTRICT ON UPDATE CASCADE;

desci-server/prisma/schema.prisma

@@ -45,6 +45,7 @@ model Node {
   OrcidPutCodes       OrcidPutCodes[]
   DistributionPdfs    DistributionPdfs[]
   PdfPreviews         PdfPreviews[]
+  DoiRecord           DoiRecord[]
 
   @@index([ownerId])
   @@index([uuid])
@@ -833,6 +834,16 @@ model OrcidPutCodes {
   @@unique([orcid, uuid, reference])
 }
 
+model DoiRecord {
+  id        Int      @id @default(autoincrement())
+  doi       String   @unique
+  dpid      String   @unique
+  uuid      String
+  node      Node     @relation(fields: [uuid], references: [uuid])
+  createdAt DateTime @default(now())
+  updatedAt DateTime @updatedAt
+}
+
 enum ORCIDRecord {
   WORK
   QUALIFICATION

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

@@ -3,15 +3,10 @@ import { NextFunction, Request, Response } from 'express';
 import _ from 'lodash';
 
 import {
-  AuthFailureResponse,
-  BadRequestError,
   ForbiddenError,
-  NotFoundError,
-  RequestWithUser,
   SuccessMessageResponse,
   SuccessResponse,
   attestationService,
-  communityService,
   ensureUuidEndsWithDot,
   prisma,
 } from '../../internal.js';
@@ -130,18 +125,3 @@ export const getAttestationVerifications = async (req: Request, res: Response, n
 
   return new SuccessResponse(data).send(res);
 };
-
-export const canVerifyClaim = async (req: RequestWithUser, res: Response) => {
-  const logger = parentLogger.child({
-    module: 'ATTESTATIONS::canVerify',
-  });
-  const userId = req.user.id;
-  const claimId = parseInt(req.params.claimId);
-
-  const claim = await attestationService.findClaimById(claimId);
-  const isMember = await communityService.findMemberByUserId(claim.desciCommunityId, userId);
-
-  logger.info({ userId: req.user.id, claimId, community: claim.desciCommunityId }, 'Claim Verification check');
-  if (!isMember) new SuccessResponse({ ok: false }).send(res);
-  else new SuccessResponse({ ok: true }).send(res);
-};

desci-server/src/controllers/communities/feed.ts

@@ -39,11 +39,13 @@ export const getCommunityFeed = async (req: Request, res: Response, next: NextFu
   });
 
   let data = await Promise.all(nodes.map(resolveLatestNode));
-  data = data.sort((c1, c2) => {
-    const key1 = c1.engagements.verifications + c1.engagements.annotations + c1.engagements.reactions;
-    const key2 = c2.engagements.verifications + c2.engagements.annotations + c2.engagements.reactions;
-    return key2 - key1;
-  });
+  data = data
+    .sort((c1, c2) => {
+      const key1 = c1.engagements.verifications + c1.engagements.annotations + c1.engagements.reactions;
+      const key2 = c2.engagements.verifications + c2.engagements.annotations + c2.engagements.reactions;
+      return key2 - key1;
+    })
+    .reverse();
   return new SuccessResponse(data).send(res);
 };
 
@@ -85,15 +87,21 @@ export const getAllFeeds = async (req: Request, res: Response, next: NextFunctio
    * or
    * fallback to last submission/attestation claim date
    */
-  data = data.sort((entryA, entryB) => {
-    const key1 = entryA.engagements.verifications + entryA.engagements.annotations + entryA.engagements.reactions;
-    const key2 = entryB.engagements.verifications + entryB.engagements.annotations + entryB.engagements.reactions;
-    if (key1 !== key2) return key2 - key1;
+  data = data
+    .sort((entryA, entryB) => {
+      const key1 = entryA.engagements.verifications + entryA.engagements.annotations + entryA.engagements.reactions;
+      const key2 = entryB.engagements.verifications + entryB.engagements.annotations + entryB.engagements.reactions;
+      if (key1 !== key2) return key2 - key1;
 
-    const entryALastClaimedAt = new Date(entryA.NodeAttestation[entryA.NodeAttestation.length - 1].claimedAt).getTime();
-    const entryBlastClaimedAt = new Date(entryB.NodeAttestation[entryB.NodeAttestation.length - 1].claimedAt).getTime();
-    return entryBlastClaimedAt - entryALastClaimedAt;
-  });
+      const entryALastClaimedAt = new Date(
+        entryA.NodeAttestation[entryA.NodeAttestation.length - 1].claimedAt,
+      ).getTime();
+      const entryBlastClaimedAt = new Date(
+        entryB.NodeAttestation[entryB.NodeAttestation.length - 1].claimedAt,
+      ).getTime();
+      return entryBlastClaimedAt - entryALastClaimedAt;
+    })
+    .reverse();
 
   return new SuccessResponse(data).send(res);
 };

desci-server/src/controllers/communities/guard.ts

@@ -0,0 +1,18 @@
+import { Response } from 'express';
+
+import { SuccessResponse, communityService, logger } from '../../internal.js';
+import { RequestWithUser } from '../../middleware/authorisation.js';
+
+export const checkMemberGuard = async (req: RequestWithUser, res: Response) => {
+  const log = logger.child({
+    module: 'ATTESTATIONS::MemberGuard',
+  });
+  const userId = req.user.id;
+  const communityId = parseInt(req.params.communityId);
+
+  log.info({ userId: req.user.id, community: communityId }, 'Community Member Guard check');
+  const isMember = await communityService.findMemberByUserId(communityId, userId);
+
+  if (!isMember) new SuccessResponse({ ok: false }).send(res);
+  else new SuccessResponse({ ok: true }).send(res);
+};

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

@@ -3,3 +3,4 @@ export * from './radar.js';
 export * from './list.js';
 export * from './types.js';
 export * from './util.js';
+export * from './guard.js';

desci-server/src/controllers/doi/check.ts

@@ -0,0 +1,27 @@
+import { NextFunction, Request, Response } from 'express';
+
+import { DoiError } from '../../core/doi/error.js';
+import { BadRequestError, SuccessResponse, doiService, logger } from '../../internal.js';
+
+export const checkMintability = async (req: Request, res: Response, _next: NextFunction) => {
+  const { uuid } = req.params;
+  if (!uuid) throw new BadRequestError();
+  try {
+    await doiService.checkMintability(uuid);
+    new SuccessResponse(true).send(res);
+  } catch (err) {
+    logger.error(err, 'module:: checkMintability');
+    if (!(err instanceof DoiError)) {
+      // TODO: Sentry error reporting
+    }
+    new SuccessResponse(false).send(res);
+  }
+};
+
+export const getDoi = async (req: Request, res: Response, next: NextFunction) => {
+  const { identifier } = req.params;
+  if (!identifier) throw new BadRequestError();
+
+  const doi = await doiService.getDoiByDpidOrUuid(identifier);
+  new SuccessResponse(doi).send(res);
+};

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

@@ -0,0 +1,2 @@
+export * from './check.js';
+export * from './mint.js';

desci-server/src/controllers/doi/mint.ts

@@ -0,0 +1,11 @@
+import { Request, Response, NextFunction } from 'express';
+
+import { BadRequestError, SuccessResponse, doiService, ensureUuidEndsWithDot } from '../../internal.js';
+
+export const mintDoi = async (req: Request, res: Response, next: NextFunction) => {
+  const { uuid } = req.params;
+  if (!uuid) throw new BadRequestError();
+  const sanitizedUuid = ensureUuidEndsWithDot(uuid);
+  const doi = await doiService.mintDoi(sanitizedUuid);
+  new SuccessResponse(doi).send(res);
+};

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

@@ -1,6 +1,6 @@
 import { ResearchObjectV1 } from '@desci-labs/desci-models';
 import { NodeVersion } from '@prisma/client';
-import { Response } from 'express';
+import { NextFunction, Response } from 'express';
 
 import { prisma } from '../../client.js';
 import { logger as parentLogger } from '../../logger.js';
@@ -30,7 +30,7 @@ export interface PrepublishErrorResponse {
 /**
  * DAGifies the drafts current DB tree state, adds the structure to IPFS (No Files Pinned, Folders staged), and updates the manifest data bucket CID.
  */
-export const prepublish = async (req: RequestWithNode, res: Response<PrepublishResponse>) => {
+export const prepublish = async (req: RequestWithNode, res: Response, _next: NextFunction) => {
   const owner = req.user;
   const node = req.node;
   const { uuid } = req.body;

desci-server/src/core/ApiError.ts

@@ -9,6 +9,7 @@ import {
   InternalErrorResponse,
   NotFoundResponse,
 } from './ApiResponse.js';
+import { DoiError, DoiErrorType } from './doi/error.js';
 
 export enum ApiErrorType {
   BAD_REQUEST = 'BadRequestError',
@@ -46,7 +47,7 @@ export abstract class ApiError extends Error {
     }
   }
 
-  public static transform(err: Error, res): Response {
+  public static transform(err: Error, res: Response): Response {
     if (err instanceof AttestationError) {
       switch (err.type) {
         case AttestationErrorType.DUPLICATE:
@@ -60,6 +61,16 @@ export abstract class ApiError extends Error {
         default:
           return new InternalErrorResponse(err.message).send(res);
       }
+    } else if (err instanceof DoiError) {
+      switch (err.type) {
+        case DoiErrorType.BAD_METADATA:
+        case DoiErrorType.NO_MANUSCRIPT:
+        case DoiErrorType.INCOMPLETE_ATTESTATIONS:
+        case DoiErrorType.DUPLICATE_MINT:
+          return new BadRequestResponse(err.message, err).send(res);
+        default:
+          return new InternalErrorResponse(err.message).send(res);
+      }
     }
     return new InternalErrorResponse(err.message).send(res);
   }