Merge pull request #437 from desci-labs/develop

promote main
desci-labs · Jul 17, 2024 · c9b02c3 · c9b02c3
2 parents 3c9206c + ca7b456
commit c9b02c3
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Showing 23 changed files with 335 additions and 87 deletions.
diff --git a/.gitignore b/.gitignore
@@ -17,3 +17,4 @@ node-modules/
 node_modules/*
 .idea
 .composedbRuntimeDefinition.json
+openalex-importer
diff --git a/desci-contracts/subgraph/subgraph.sepoliaProd.yaml b/desci-contracts/subgraph/subgraph.sepoliaProd.yaml
@@ -8,7 +8,7 @@ dataSources:
     name: DeSciNodes
     network: sepolia
     source:
-      address: "0xB954B4F1c01DcA2508278C4426EaF895f4133aDF"
+      address: "0x1fA4c72680af35FE1eb7345509E39498be6Ce03b"
       abi: ResearchObjectMigrated
       startBlock: 5530308
     mapping:

diff --git a/desci-media-isolated/.env.example b/desci-media-isolated/.env.example
@@ -2,4 +2,6 @@ NODE_ENV=development
 
 PORT=7771
 
-IPFS_GATEWAY=http://host.docker.internal:5420/v1/ipfs
+IPFS_GATEWAY=http://host.docker.internal:5420/v1/ipfs
+
+DPID_RESOLVER_URL=https://dev-beta.dpid.org
diff --git a/desci-media-isolated/kubernetes/deployment_dev.yaml b/desci-media-isolated/kubernetes/deployment_dev.yaml
@@ -46,6 +46,8 @@ spec:
               value: '7771'
             - name: IPFS_GATEWAY
               value: 'https://ipfs.desci.com/ipfs'
+            - name: DPID_RESOLVER_URL
+              value: 'https://dev-beta.dpid.org'
           resources:
             limits:
               cpu: '4'

diff --git a/desci-media-isolated/kubernetes/deployment_prod.yaml b/desci-media-isolated/kubernetes/deployment_prod.yaml
@@ -42,15 +42,19 @@ spec:
             - containerPort: 7771
               name: api
           env:
+            - name: NODE_ENV
+              value: 'production'
             - name: PORT
               value: '7771'
             - name: IPFS_GATEWAY
-              value: 'http://host.docker.internal:5420/v1/ipfs'
+              value: 'https://ipfs.desci.com/ipfs'
+            - name: DPID_RESOLVER_URL
+              value: 'https://beta.dpid.org'
           resources:
             limits:
-              cpu: '0.5'
-              memory: 2Gi
+              cpu: '4'
+              memory: 4Gi
             requests:
-              cpu: 250m
-              memory: 1Gi
+              cpu: '1'
+              memory: 2Gi
       serviceAccountName: 'default'
diff --git a/desci-media-isolated/kubernetes/deployment_staging.yaml b/desci-media-isolated/kubernetes/deployment_staging.yaml
@@ -46,6 +46,8 @@ spec:
               value: '7771'
             - name: IPFS_GATEWAY
               value: 'http://host.docker.internal:5420/v1/ipfs'
+            - name: DPID_RESOLVER_URL
+              value: 'https://dev-beta.dpid.org'
           resources:
             limits:
               cpu: '0.5'

diff --git a/desci-media-isolated/src/services/pdf.ts b/desci-media-isolated/src/services/pdf.ts
@@ -85,8 +85,10 @@ export class PdfManipulationService {
       /*
        * Header
        */
+      const dpidResolverUrl = process.env.DPID_RESOLVER_URL ?? 'https://beta.dpid.org';
+
       const licenseStartsWithVowel = startsWithVowel(license);
-      const nodeUrl = usingDoi ? `https://doi.org/${doi}` : `https://beta.dpid.org/${dpid}`;
+      const nodeUrl = usingDoi ? `https://doi.org/${doi}` : `${dpidResolverUrl}/${dpid}`;
       const topHeader = `Research object ${nodeUrl}, this version posted ${publishDate}. The copyright holder for this research object (which was not certified by peer review) is the author/funder, who has granted DeSci Labs a non-exclsuive license to display the research object in perpetuity. It is made available under a${
         licenseStartsWithVowel ? 'n' : ''
       } ${license} license.`;

diff --git a/desci-server/kubernetes/deployment_prod.yaml b/desci-server/kubernetes/deployment_prod.yaml
@@ -88,8 +88,8 @@ spec:
           export CROSSREF_METADATA_API={{ .Data.CROSSREF_METADATA_API }}
           export CROSSREF_ADMIN_API={{ .Data.CROSSREF_ADMIN_API }}
           export CROSSREF_NOTIFY_ENDPOINT={{ .Data.CROSSREF_NOTIFY_ENDPOINT }}
-          export AUTOMATED_METADATA_API={{ .Data.AUTOMATED_METADATA_API }}
-          export AUTOMATED_METADATA_API_KEY={{ .Data.AUTOMATED_METADATA_API_KEY }}
+          export AUTOMATED_METADATA_API="{{ .Data.AUTOMATED_METADATA_API }}"
+          export AUTOMATED_METADATA_API_KEY="{{ .Data.AUTOMATED_METADATA_API_KEY }}"
           export IGNORE_LINE=0;
           export DEBUG_TEST=0;
           echo "appfinish";

diff --git a/desci-server/package.json b/desci-server/package.json
@@ -117,6 +117,7 @@
     "url-safe-base64": "1.2.0",
     "uuid": "^8.3.2",
     "ws": "^8.15.0",
+    "xml-js": "^1.6.11",
     "yauzl": "^2.10.0",
     "zod": "^3.22.4"
   },

diff --git a/desci-server/src/controllers/attestations/recommendations.ts b/desci-server/src/controllers/attestations/recommendations.ts
@@ -13,27 +13,27 @@ const logger = parentLogger.child({ module: 'Recommendations' });
 
 export const getAllRecommendations = async (_req: Request, res: Response, _next: NextFunction) => {
   const attestations = await attestationService.getRecommendedAttestations();
-  const communityEntries = _(attestations)
-    .groupBy((x) => x.desciCommunityId)
-    .map((value, key) => ({
-      community: value[0].desciCommunity.name,
-      communityId: key,
-      attestations: value.map((attestation) => ({
-        id: attestation.id,
-        communityId: value[0].attestation.community.id,
-        communityName: value[0].attestation.community.name,
-        attestationId: attestation.attestationId,
-        attestationVersionId: attestation.attestationVersionId,
-        required: attestation.required,
-        createdAt: attestation.createdAt,
-        name: attestation.attestationVersion.name,
-        description: attestation.attestationVersion.description,
-        image_url: attestation.attestationVersion.image_url,
+  const attestationEntries = _(attestations)
+    .groupBy((x) => x.attestationId)
+    .map((value, _) => ({
+      attestationId: value[0].attestationId,
+      attestationVersionId: value[0].attestationVersionId,
+      required: value[0].required,
+      createdAt: value[0].createdAt,
+      name: value[0].attestationVersion.name,
+      description: value[0].attestationVersion.description,
+      image_url: value[0].attestationVersion.image_url,
+      communities: value.map((entry) => ({
+        communityId: entry.desciCommunityId,
+        communityName: entry.desciCommunity.name,
+        image_url: entry.desciCommunity.image_url,
       })),
     }))
-    .value();
+    .value()
+    .sort((entryA, entryB) => entryB.communities.length - entryA.communities.length);
 
-  return new SuccessResponse(communityEntries).send(res);
+  logger.info({ attestationEntries }, 'getAllRecommendations');
+  return new SuccessResponse(attestationEntries).send(res);
 };
 
 export const getCommunityRecommendations = async (req: Request, res: Response, _next: NextFunction) => {

diff --git a/desci-server/src/controllers/auth/magic.ts b/desci-server/src/controllers/auth/magic.ts
@@ -5,6 +5,7 @@ import jwt from 'jsonwebtoken';
 import { prisma as prismaClient } from '../../client.js';
 import { logger } from '../../logger.js';
 import { magicLinkRedeem, sendMagicLink } from '../../services/auth.js';
+import { contributorService } from '../../services/Contributors.js';
 import { saveInteraction } from '../../services/interactionLog.js';
 import { checkIfUserAcceptedTerms, connectOrcidToUserIfPossible } from '../../services/user.js';
 import { sendCookie } from '../../utils/sendCookie.js';
@@ -52,6 +53,15 @@ export const magic = async (req: Request, res: Response, next: NextFunction) =>
           email,
         },
       });
+
+      if (user.email) {
+        // Inherits existing user contribution entries that were made with the same email
+        const inheritedContributions = await contributorService.updateContributorEntriesForNewUser({
+          email: user.email,
+          userId: user.id,
+        });
+        logger.trace({ inheritedContributions: inheritedContributions?.count, user, email });
+      }
     }
 
     try {

diff --git a/desci-server/src/controllers/doi/mint.ts b/desci-server/src/controllers/doi/mint.ts
@@ -1,4 +1,5 @@
 import { DoiStatus } from '@prisma/client';
+import sgMail from '@sendgrid/mail';
 import { Request, Response, NextFunction } from 'express';
 import _ from 'lodash';
 
@@ -14,6 +15,7 @@ import {
   logger as parentLogger,
   prisma,
 } from '../../internal.js';
+import { DoiMintedEmailHtml } from '../../templates/emails/utils/emailRenderer.js';
 
 export const mintDoi = async (req: Request, res: Response, _next: NextFunction) => {
   const { uuid } = req.params;
@@ -52,41 +54,84 @@ export const handleCrossrefNotificationCallback = async (
 
   if (!submission) {
     logger.error({ payload: req.payload }, 'Crossref Notifiication: pending submission not found');
-    throw new NotFoundError('submission not found');
+    // throw new NotFoundError('submission not found');
+    new SuccessMessageResponse().send(res);
+    return;
+  }
+
+  if (submission.status === DoiStatus.SUCCESS) {
+    new SuccessMessageResponse().send(res);
+    return;
   }
 
   await doiService.updateSubmission({ id: submission.id }, { notification: req.payload });
   logger.info('SUBMISSION UPDATED');
 
   new SuccessMessageResponse().send(res);
 
-  // check retrieve url to get submission result
-  const response = await crossRefClient.retrieveSubmission(req.payload.retrieveUrl);
+  try {
+    // check retrieve url to get submission result
+    const response = await crossRefClient.retrieveSubmission(req.payload.retrieveUrl);
 
-  logger.info({ response, submission }, 'CREATE DOI CALLBACK RESPONSE');
-  if (response.success) {
-    logger.info('CREATE DOI ');
-    const doiRecord = await prisma.doiRecord.create({
-      data: {
-        uuid: submission.uuid,
-        dpid: submission.dpid,
-        doi: submission.uniqueDoi,
-      },
-    });
-    await doiService.updateSubmission(
-      { id: submission.id },
-      {
-        status: DoiStatus.SUCCESS,
-        doiRecordId: doiRecord.id,
-      },
-    );
-  } else {
-    logger.info('ERROR CREATING DOI');
-    await doiService.updateSubmission(
-      { id: submission.id },
-      { status: response.failure ? DoiStatus.FAILED : DoiStatus.PENDING },
-    );
-  }
+    logger.info({ response, submission }, 'CREATE DOI CALLBACK RESPONSE');
+    if (response.success) {
+      logger.info({ response, submission }, 'CREATE DOI ');
 
-  // TODO: email authors about the submission status
+      const doiRecord = await prisma.doiRecord.create({
+        data: {
+          uuid: submission.uuid,
+          dpid: submission.dpid,
+          doi: submission.uniqueDoi,
+        },
+      });
+      await doiService.updateSubmission(
+        { id: submission.id },
+        {
+          status: DoiStatus.SUCCESS,
+          doiRecordId: doiRecord.id,
+        },
+      );
+
+      // Send Notification Email Node author about the submission status
+      const node = await prisma.node.findFirst({
+        where: { uuid: submission.uuid },
+        include: { owner: { select: { email: true, name: true } } },
+      });
+
+      if (!node.owner.email) return;
+      const message = {
+        to: node.owner.email,
+        from: 'no-reply@desci.com',
+        subject: 'DOI Registration successful 🎉',
+        text: `Hello ${node.owner.name}, You DOI registration for the research object ${node.title} has been completed. Here is your DOI: ${process.env.CROSSREF_DOI_URL}/${submission.uniqueDoi}`,
+        html: DoiMintedEmailHtml({
+          dpid: submission.dpid,
+          userName: node.owner.name.split(' ')?.[0] ?? '',
+          dpidPath: `${process.env.DAPP_URL}/dpid/${submission.dpid}`,
+          doi: `${process.env.CROSSREF_DOI_URL}/${submission.uniqueDoi}`,
+          nodeTitle: node.title,
+        }),
+      };
+
+      try {
+        logger.info({ members: message, NODE_ENV: process.env.NODE_ENV }, 'DOI MINTED EMAIL');
+        if (process.env.NODE_ENV === 'production') {
+          const response = await sgMail.send(message);
+          logger.info(response, '[EMAIL]:: Response');
+        } else {
+          logger.info({ nodeEnv: process.env.NODE_ENV }, message.subject);
+        }
+      } catch (err) {
+        logger.info({ err }, '[ERROR]:: DOI MINTED EMAIL');
+      }
+    } else {
+      logger.info('ERROR CREATING DOI');
+      await doiService.updateSubmission(
+        { id: submission.id },
+        { status: response.failure ? DoiStatus.FAILED : DoiStatus.PENDING },
+      );
+    }
+  } catch (error) {
+    logger.error({ error }, 'Error updating DOI submission');
+  }
 };
diff --git a/desci-server/src/controllers/nodes/checkNodeAccess.ts b/desci-server/src/controllers/nodes/checkNodeAccess.ts
@@ -1,13 +1,12 @@
+import { ResearchObjectV1, ResearchObjectV1Dpid } from '@desci-labs/desci-models';
+import { NodeCover } from '@prisma/client';
 import type { Request, Response } from 'express';
 
 import { prisma } from '../../client.js';
 import { resolveNodeManifest } from '../../internal.js';
 import { logger as parentLogger } from '../../logger.js';
-import { decodeBase64UrlSafeToHex, ensureUuidEndsWithDot, randomUUID64 } from '../../utils.js';
 import { IndexedResearchObject, getIndexedResearchObjects } from '../../theGraph.js';
-import { ResearchObjectV1, ResearchObjectV1Dpid } from '@desci-labs/desci-models';
-import { NodeCover } from '@prisma/client';
-import { PRIV_SHARE_CONTRIBUTION_PREFIX } from '../../services/Contributors.js';
+import { decodeBase64UrlSafeToHex, ensureUuidEndsWithDot, randomUUID64 } from '../../utils.js';
 
 const logger = parentLogger.child({
   module: 'NODE::checkNodeAccess',
@@ -44,19 +43,21 @@ type GetCheckNodeAccessErrorResponse = {
 };
 
 export const checkNodeAccess = async (
-  req: Request<any, any, any>,
+  req: Request<any, any, any, { g?: string; shareId?: string }>,
   res: Response<GetCheckNodeAccessResponse | GetCheckNodeAccessErrorResponse>,
 ) => {
   const owner = (req as any).user;
   const ipfsQuery = req.query.g;
+  const { shareId } = req.query;
 
   logger.info({
     body: req.body,
     user: (req as any).user,
     ipfsQuery,
+    shareId,
   });
 
-  let node = await prisma.node.findFirst({
+  const node = await prisma.node.findFirst({
     select: {
       uuid: true,
       id: true,
@@ -78,12 +79,12 @@ export const checkNodeAccess = async (
     res.status(404).send({ ok: false, message: 'Node not found' });
     return;
   }
-
-  const privSharedNode = owner
+  // debugger;
+  const privSharedNode = !!shareId
     ? await prisma.privateShare.findFirst({
         where: {
-          memo: `${PRIV_SHARE_CONTRIBUTION_PREFIX}${owner?.email}`,
           nodeUUID: node.uuid,
+          shareId: shareId,
         },
       })
     : undefined;

diff --git a/desci-server/src/services/Attestation.ts b/desci-server/src/services/Attestation.ts
@@ -744,7 +744,7 @@ export class AttestationService {
             image_url: true,
           },
         },
-        desciCommunity: { select: { name: true, hidden: true } },
+        desciCommunity: { select: { name: true, hidden: true, image_url: true } },
       },
       where: {
         desciCommunity: {
@@ -874,7 +874,7 @@ export class AttestationService {
         EXISTS
       (SELECT *
         from "CommunityEntryAttestation" c1
-        where t1."attestationId" = c1."attestationId" and t1."attestationVersionId" = c1."attestationVersionId" and c1."desciCommunityId" = ${communityId})
+        where t1."attestationId" = c1."attestationId" and t1."attestationVersionId" = c1."attestationVersionId" and c1."desciCommunityId" = ${communityId} )
         GROUP BY
   		t1.id
     `) as CommunityRadarNode[];

diff --git a/desci-server/src/services/Communities.ts b/desci-server/src/services/Communities.ts
@@ -99,7 +99,7 @@ export class CommunityService {
         EXISTS
       (SELECT *
         from "CommunityEntryAttestation" c1
-        where t1."attestationId" = c1."attestationId" and t1."attestationVersionId" = c1."attestationVersionId" and c1."desciCommunityId" = ${communityId})
+        where t1."attestationId" = c1."attestationId" and t1."attestationVersionId" = c1."attestationVersionId" and c1."desciCommunityId" = ${communityId} and c1."required" = true)
         GROUP BY
   		t1.id
     `) as CommunityRadarNode[];
@@ -180,7 +180,7 @@ export class CommunityService {
         EXISTS
       (SELECT *
         from "CommunityEntryAttestation" c1
-        where t1."attestationId" = c1."attestationId" and t1."attestationVersionId" = c1."attestationVersionId" and c1."desciCommunityId" = ${communityId})
+        where t1."attestationId" = c1."attestationId" and t1."attestationVersionId" = c1."attestationVersionId" and c1."desciCommunityId" = ${communityId} and c1."required" = true)
         GROUP BY
   		t1.id
     `) as CommunityRadarNode[];