From 790f700a9df6e98565805b79bc0abd8b11f67ea9 Mon Sep 17 00:00:00 2001
From: m0ar <edvard@hubinette.me>
Date: Tue, 21 May 2024 14:06:39 +0200
Subject: [PATCH 1/3] workflows: patch staging deployment of reverse-proxy

---
 .../workflows/deploy-staging-services.yaml    | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/deploy-staging-services.yaml b/.github/workflows/deploy-staging-services.yaml
index 5dba2ae8..c1bf2437 100644
--- a/.github/workflows/deploy-staging-services.yaml
+++ b/.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: |

From 061fae95dac0310971d4a5ab3061c0c0b6e043a9 Mon Sep 17 00:00:00 2001
From: m0ar <edvard@hubinette.me>
Date: Thu, 16 May 2024 16:27:24 +0200
Subject: [PATCH 2/3] server: fix email logos

---
 .../src/templates/emails/BaseProvider.tsx     |  4 +---
 .../src/templates/emails/MagicCode.tsx        |  6 +-----
 .../src/templates/emails/MainLayout.tsx       | 20 ++++++++-----------
 3 files changed, 10 insertions(+), 20 deletions(-)

diff --git a/desci-server/src/templates/emails/BaseProvider.tsx b/desci-server/src/templates/emails/BaseProvider.tsx
index 747bb1c6..7d515f2d 100644
--- a/desci-server/src/templates/emails/BaseProvider.tsx
+++ b/desci-server/src/templates/emails/BaseProvider.tsx
@@ -1,7 +1,7 @@
 import { Tailwind } from '@react-email/components';
 import React from 'react';
 
-const BaseProvider = ({ children }: { children: JSX.Element }) => {
+export const BaseProvider = ({ children }: { children: JSX.Element }) => {
   return (
     <Tailwind
       config={{
@@ -19,5 +19,3 @@ const BaseProvider = ({ children }: { children: JSX.Element }) => {
     </Tailwind>
   );
 };
-
-export default BaseProvider;
diff --git a/desci-server/src/templates/emails/MagicCode.tsx b/desci-server/src/templates/emails/MagicCode.tsx
index f4bf2f42..81ca2dcd 100644
--- a/desci-server/src/templates/emails/MagicCode.tsx
+++ b/desci-server/src/templates/emails/MagicCode.tsx
@@ -1,16 +1,12 @@
 import {
   Body,
   Container,
-  Column,
   Head,
   Heading,
   Html,
   Preview,
-  Row,
   Text,
-  Button,
   Section,
-  render,
 } from '@react-email/components';
 import * as React from 'react';
 
@@ -29,7 +25,7 @@ export const MagicCodeEmail = ({ magicCode, ip }: MagicCodeEmailProps) => (
   >
     <Html>
       <Head />
-      <Preview>Confirm your contribution</Preview>
+      <Preview>Confirm your identity</Preview>
       <Body style={main}>
         <Container style={container}>
           <Heading style={h1} className="text-center !text-black">
diff --git a/desci-server/src/templates/emails/MainLayout.tsx b/desci-server/src/templates/emails/MainLayout.tsx
index 3c0382ce..aa411c98 100644
--- a/desci-server/src/templates/emails/MainLayout.tsx
+++ b/desci-server/src/templates/emails/MainLayout.tsx
@@ -1,27 +1,23 @@
-import { url } from 'inspector';
 
 import {
   Body,
   Container,
   Column,
   Head,
-  Heading,
   Html,
   Img,
   Link,
-  Preview,
   Row,
   Section,
   Text,
   Font,
 } from '@react-email/components';
 import React from 'react';
+import { BaseProvider } from './BaseProvider.js';
 
-import BaseProvider from './BaseProvider.js';
-
-export const emailAssetsBaseUrl = 'https://ipfs.desci.com/ipfs';
-const cubertBkg = 'bafkreih6yx7ywj7trvpp45vergrnytad7ezsku75tefyro4qrrcfrrmrt4';
-const labsLogo = 'bafkreifvb7tleo5jaidjjf6lfjxb5bpjbs2nswp47bi7zh3hxbpc6fjyf4';
+export const emailAssetsBaseUrl = 'https://pub.desci.com/ipfs';
+// const cubertBkg = 'bafkreih6yx7ywj7trvpp45vergrnytad7ezsku75tefyro4qrrcfrrmrt4';
+const labsLogo = 'bafkreie2jto3flk2r43yt545xrasftbsc2atp5eb7qcbsmhacm26k4wiz4';
 const defaultFooterMsg = "If you didn't request this email, there's nothing to worry about, you can safely ignore it.";
 
 const MainLayout = ({ children, footerMsg = defaultFooterMsg }: { children: JSX.Element; footerMsg?: string }) => {
@@ -55,11 +51,11 @@ const MainLayout = ({ children, footerMsg = defaultFooterMsg }: { children: JSX.
             <Container className="backdrop-blur-2xl bg-opacity-50">
               <Section className="h-full backdrop-blur-lg w-full" align="center">
                 <Img
-                  src={`${emailAssetsBaseUrl}/${labsLogo}`}
+                  src={ `${emailAssetsBaseUrl}/${labsLogo}` }
                   width="193"
                   height="60"
                   alt="Desci Labs"
-                  className="m-auto invert"
+                  className="m-auto invert mix-blend-difference"
                 />
               </Section>
               <Section>{children}</Section>
@@ -70,11 +66,11 @@ const MainLayout = ({ children, footerMsg = defaultFooterMsg }: { children: JSX.
                 <Column className="">
                   <Link href="https://desci.com" target="_blank" rel="noopener noreferrer">
                     <Img
-                      src={`${emailAssetsBaseUrl}/${labsLogo}`}
+                      src={ `${emailAssetsBaseUrl}/${labsLogo}` }
                       width="135"
                       height="42"
                       alt="Desci Labs"
-                      className="invert"
+                      className="invert mix-blend-difference"
                     />
                   </Link>
                 </Column>

From 97a6f55b84dde6e9d9c78cd6354cd1c1bb6c3a6c Mon Sep 17 00:00:00 2001
From: shadrach-tayo <shadrachtemitayo@gmail.com>
Date: Wed, 22 May 2024 18:17:10 +0200
Subject: [PATCH 3/3] fix: Orcid schema and updates to OrcidApiService
 implementation

---
 desci-server/src/services/orcid.ts | 64 ++++++++++++++++++++++++------
 1 file changed, 52 insertions(+), 12 deletions(-)

diff --git a/desci-server/src/services/orcid.ts b/desci-server/src/services/orcid.ts
index 682eee87..6944393c 100644
--- a/desci-server/src/services/orcid.ts
+++ b/desci-server/src/services/orcid.ts
@@ -85,7 +85,21 @@ class OrcidApiService {
             userId: authToken.userId,
           },
         });
-        logger.info({ status: response.status, statusText: response.statusText, data }, 'REFRESH TOKEN RESPONSE');
+        logger.info(
+          {
+            status: response.status,
+            statusText: response.statusText,
+            data: {
+              name: data.name,
+              scope: data.scope,
+              token_type: data.token_type,
+              orcid: data.orcid,
+              refreshToken: !!data.refresh_token,
+              accessToken: !!data.access_token,
+            },
+          },
+          'REFRESH TOKEN RESPONSE',
+        );
       } else {
         logger.info(
           { status: response.status, statusText: response.statusText, BODY: await response.json() },
@@ -230,13 +244,15 @@ class OrcidApiService {
 
       const latestVersion = researchObject.versions[researchObject.versions.length - 1];
       const publicationDate = new Date(parseInt(latestVersion.time) * 1000).toLocaleDateString().replaceAll('/', '-');
+      const contributorsXml = generateContributors(latestManifest.authors ?? [], orcid);
       const nodeRecordPromise = this.putNodeWorkRecord({
         orcid,
         authToken,
         uuid: nodeUuid,
-        userId: user.id,
         nodeVersion,
         publicationDate,
+        contributorsXml,
+        userId: user.id,
         manifest: latestManifest,
       });
       const claimRecordPromises = claims.map((claim) => {
@@ -250,6 +266,7 @@ class OrcidApiService {
           publicationDate,
           orcid,
           authToken,
+          contributorsXml,
           uuid: nodeUuid,
           userId: user.id,
           nodeVersion: claimedVersionNumber,
@@ -283,6 +300,7 @@ class OrcidApiService {
     authToken,
     orcid,
     nodeVersion,
+    contributorsXml,
   }: {
     manifest: ResearchObjectV1;
     publicationDate: string;
@@ -291,6 +309,7 @@ class OrcidApiService {
     authToken: string;
     orcid: string;
     nodeVersion: number;
+    contributorsXml: string;
   }) {
     try {
       const orcidPutCode = await prisma.orcidPutCodes.findUnique({
@@ -298,7 +317,7 @@ class OrcidApiService {
       });
       const putCode = orcidPutCode?.putcode;
 
-      let data = generateNodeWorkRecord({ manifest, publicationDate, nodeVersion, putCode });
+      let data = generateNodeWorkRecord({ manifest, publicationDate, nodeVersion, putCode, contributorsXml });
       data = data.replace(/\\"/g, '"');
 
       const url = `${this.baseUrl}/${orcid}/work${putCode ? '/' + putCode : ''}`;
@@ -388,8 +407,10 @@ class OrcidApiService {
     orcid,
     claim,
     nodeVersion,
+    contributorsXml,
   }: {
     claim: Claim;
+    contributorsXml: string;
     manifest: ResearchObjectV1;
     nodeVersion: number;
     publicationDate: string;
@@ -410,7 +431,14 @@ class OrcidApiService {
       });
       const putCode = orcidPutCode?.putcode;
 
-      let data = generateClaimWorkRecord({ nodeVersion, manifest, publicationDate, claim, putCode });
+      let data = generateClaimWorkRecord({
+        nodeVersion,
+        manifest,
+        publicationDate,
+        claim,
+        putCode,
+        contributorsXml,
+      });
       data = data.replace(/\\"/g, '"');
 
       const url = `${this.baseUrl}/${orcid}/work${putCode ? '/' + putCode : ''}`;
@@ -500,9 +528,11 @@ const generateClaimWorkRecord = ({
   claim,
   nodeVersion,
   publicationDate,
+  contributorsXml,
 }: {
   manifest: ResearchObjectV1;
   claim: Claim;
+  contributorsXml: string;
   putCode?: string;
   nodeVersion: number;
   publicationDate: string;
@@ -514,9 +544,9 @@ const generateClaimWorkRecord = ({
       ? 'data-set'
       : 'preprint';
 
-  const description = `${claim.name} Attestation`;
+  const description = `${claim.name} availability verified`;
   const [month, day, year] = publicationDate.split('-');
-  const externalUrl = `${DPID_URL_OVERRIDE}/${manifest.dpid.id}/attestation/${claim.id}`;
+  const externalUrl = `${DPID_URL_OVERRIDE}/${manifest.dpid.id}/v${nodeVersion}/attestation/${claim.id}`;
   const dataRoot = `${DPID_URL_OVERRIDE}/${manifest.dpid.id}/v${nodeVersion}`;
   logger.info({ codeAttr, workType, publicationDate, day, month, year, externalUrl }, 'CODE ATTR');
   return (
@@ -525,7 +555,6 @@ const generateClaimWorkRecord = ({
     '> ' +
     '<work:title>' +
     ` <common:title>${manifest.title}</common:title>
-      <common:subtitle>${description}</common:subtitle>
     </work:title>
     <work:short-description>${description}</work:short-description>
     <work:type>${workType}</work:type>
@@ -548,7 +577,8 @@ const generateClaimWorkRecord = ({
             <common:external-id-relationship>part-of</common:external-id-relationship>
         </common:external-id>
     </common:external-ids>
-    ${generateContributors(manifest.authors ?? [])}
+    <common:url>${externalUrl}</common:url>
+    ${contributorsXml}
     </work:work>
     `
   );
@@ -571,11 +601,13 @@ const generateNodeWorkRecord = ({
   nodeVersion,
   putCode,
   publicationDate,
+  contributorsXml,
 }: {
   manifest: ResearchObjectV1;
   nodeVersion: number;
   putCode?: string;
   publicationDate: string;
+  contributorsXml: string;
 }): string => {
   const codeAttr = putCode ? 'put-code="' + putCode + '"' : '';
   const workType = 'preprint';
@@ -588,9 +620,7 @@ const generateNodeWorkRecord = ({
     '> ' +
     '<work:title>' +
     ` <common:title>${manifest.title}</common:title>
-      ${manifest.description.trim() ? `<common:subtitle>${manifest.description.trim()}</common:subtitle>` : ``}
     </work:title>
-    ${manifest?.description?.trim() ? `<work:short-description>${manifest.description}</work:short-description>` : ``}
     <work:type>${workType}</work:type>
     <common:publication-date>
       <common:year>${year}</common:year>
@@ -605,7 +635,8 @@ const generateNodeWorkRecord = ({
         <common:external-id-relationship>self</common:external-id-relationship>
       </common:external-id>
     </common:external-ids>
-    ${generateContributors(manifest.authors ?? [])}
+    <common:url>${dataRoot}</common:url>
+    ${contributorsXml}
     </work:work>
     `
   );
@@ -617,11 +648,20 @@ const generateNodeWorkRecord = ({
  * @param authors[] - A list of ResearchObjectV1Author entries
  * @returns {string} xml string of the constructed contributor data
  */
-const generateContributors = (authors: ResearchObjectV1Author[]): string => {
+const generateContributors = (authors: ResearchObjectV1Author[], ownerOrcid: string): string => {
+  authors.reverse();
+
+  const authorIndex = authors.findIndex((author) => author.orcid === ownerOrcid);
+  if (authorIndex !== -1 && authorIndex !== 0) {
+    const mainAuthor = authors.splice(authorIndex, 1);
+    authors.unshift(mainAuthor[0]);
+  }
+
   const contributors =
     authors?.length > 0
       ? `<work:contributors>
     ${authors
+      .filter((author) => !!author.name)
       .map((author, idx) => {
         return `<work:contributor>
             ${