From 44980f7f0a09576507195fa1de561634af18080e Mon Sep 17 00:00:00 2001
From: slugb0t <wheresdorian@gmail.com>
Date: Thu, 10 Oct 2024 19:26:46 -0700
Subject: [PATCH 01/27] test

---
 bot/utils/tools/index.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bot/utils/tools/index.js b/bot/utils/tools/index.js
index 72592412..bc41a823 100644
--- a/bot/utils/tools/index.js
+++ b/bot/utils/tools/index.js
@@ -309,7 +309,7 @@ export async function isRepoEmpty(context, owner, repoName) {
   }
 }
 
-/**
+/** *
  * * Verify the installation and analytics collections
  * @param {object} context - GitHub payload context
  * @param {object} repository - The repository object metadata

From 018b2556a51742d4ea4fab73bf692a9c173a01a8 Mon Sep 17 00:00:00 2001
From: slugb0t <wheresdorian@gmail.com>
Date: Fri, 11 Oct 2024 11:01:20 -0700
Subject: [PATCH 02/27] feat: :sparkles: update status on zenodo workflow error

---
 bot/index.js       |  8 ++++++++
 ui/components.d.ts | 20 ++++++++++++++++++++
 2 files changed, 28 insertions(+)

diff --git a/bot/index.js b/bot/index.js
index 4f88e2f9..7784c367 100644
--- a/bot/index.js
+++ b/bot/index.js
@@ -892,6 +892,14 @@ export default async (app, { getRouter }) => {
       } catch (error) {
         // Update the issue with the new body
         await createIssue(context, owner, repository, ISSUE_TITLE, quickTemplate);
+        await db.zenodoDeposition.update({
+          data: {
+            status: "error",
+          },
+          where: {
+            repository_id: repository.id,
+          }
+        });
         consola.error(`Error publishing to Zenodo: ${error}`);
       }
 
diff --git a/ui/components.d.ts b/ui/components.d.ts
index d981901c..76417937 100644
--- a/ui/components.d.ts
+++ b/ui/components.d.ts
@@ -8,7 +8,27 @@ export {}
 declare module 'vue' {
   export interface GlobalComponents {
     NAlert: typeof import('naive-ui')['NAlert']
+    NAvatar: typeof import('naive-ui')['NAvatar']
+    NBadge: typeof import('naive-ui')['NBadge']
+    NBreadcrumb: typeof import('naive-ui')['NBreadcrumb']
+    NBreadcrumbItem: typeof import('naive-ui')['NBreadcrumbItem']
+    NButton: typeof import('naive-ui')['NButton']
+    NCard: typeof import('naive-ui')['NCard']
+    NCheckbox: typeof import('naive-ui')['NCheckbox']
+    NCollapse: typeof import('naive-ui')['NCollapse']
+    NCollapseItem: typeof import('naive-ui')['NCollapseItem']
+    NDivider: typeof import('naive-ui')['NDivider']
+    NDropdown: typeof import('naive-ui')['NDropdown']
     NFlex: typeof import('naive-ui')['NFlex']
+    NForm: typeof import('naive-ui')['NForm']
+    NFormItem: typeof import('naive-ui')['NFormItem']
+    NInput: typeof import('naive-ui')['NInput']
+    NRadio: typeof import('naive-ui')['NRadio']
+    NRadioButton: typeof import('naive-ui')['NRadioButton']
+    NRadioGroup: typeof import('naive-ui')['NRadioGroup']
+    NSelect: typeof import('naive-ui')['NSelect']
+    NTag: typeof import('naive-ui')['NTag']
+    NTooltip: typeof import('naive-ui')['NTooltip']
     RouterLink: typeof import('vue-router')['RouterLink']
     RouterView: typeof import('vue-router')['RouterView']
   }

From 0d92eb83a9070b0ac0b2373cb089f560512f8a8d Mon Sep 17 00:00:00 2001
From: slugb0t <wheresdorian@gmail.com>
Date: Fri, 11 Oct 2024 12:22:21 -0700
Subject: [PATCH 03/27] feat: :sparkles: progress updates on zenodo release to
 github issue

---
 bot/archival/index.js       |  2 +-
 bot/cwl/index.js            |  7 ++--
 bot/index.js                | 77 ++++++++++++++++++-------------------
 bot/license/index.js        |  1 -
 bot/metadata/index.js       |  2 +-
 bot/utils/renderer/index.js |  1 -
 ui/components.d.ts          |  3 --
 7 files changed, 43 insertions(+), 50 deletions(-)

diff --git a/bot/archival/index.js b/bot/archival/index.js
index 23411cca..8c73acbf 100644
--- a/bot/archival/index.js
+++ b/bot/archival/index.js
@@ -175,7 +175,7 @@ export async function getZenodoDepositionInfo(
       }
 
       // Create a new version of an existing Zenodo deposition
-      consola.info(`Creating a new version of Zenodo deposition ${depositionId}...`);
+      // consola.info(`Creating a new version of Zenodo deposition ${depositionId}...`);
       const responseText = await createNewVersionOfDeposition(zenodoToken, depositionId);
       const latestDraftLink = responseText.links.latest_draft;
 
diff --git a/bot/cwl/index.js b/bot/cwl/index.js
index f6bb24bf..64493575 100644
--- a/bot/cwl/index.js
+++ b/bot/cwl/index.js
@@ -119,7 +119,6 @@ export async function applyCWLTemplate(
   const identifier = createId();
   const overallSection = `\n\n## Language Specific Standards\n\nTo make your software FAIR is it important to follow language specific standards and best practices. Codefair will check below that your code complies with applicable standards,`;
   let url = `${CODEFAIR_DOMAIN}/view/cwl-validation/${identifier}`;
-  consola.warn(subjects.cwl)
 
   // Delete file entries from db if they were removed from the repository
   if (subjects.cwl.removed_files.length > 0) {
@@ -148,7 +147,6 @@ export async function applyCWLTemplate(
   }
 
   // New/Modified CWL files were found, begin validation workflow
-  consola.start("Validating new/modified CWL files for", repository.name);
   const cwlFiles = [];
   let validOverall = true;
   let tableContent = "";
@@ -158,13 +156,14 @@ export async function applyCWLTemplate(
       repository_id: repository.id,
     },
   });
-
+  
   if (subjects.cwl.files.length === 0) {
     consola.warn(
       `No new/modified CWL files found in the repository, ${repository.name}`,
     );
   }
-
+  
+  consola.start("Validating CWL files for", repository.name);
   // Validate each CWL file from list
   for (const file of subjects.cwl.files) {
     const fileSplit = file.name.split(".");
diff --git a/bot/index.js b/bot/index.js
index 7784c367..be9920e2 100644
--- a/bot/index.js
+++ b/bot/index.js
@@ -25,7 +25,7 @@ checkEnvVariable("CODEFAIR_APP_DOMAIN");
 const CODEFAIR_DOMAIN = process.env.CODEFAIR_APP_DOMAIN;
 const ISSUE_TITLE = `FAIR Compliance Dashboard`;
 const CLOSED_ISSUE_BODY = `Codefair has been disabled for this repository. If you would like to re-enable it, please reopen this issue.`;
-const { ZENODO_ENDPOINT, ZENODO_API_ENDPOINT } = process.env;
+const { ZENODO_ENDPOINT, ZENODO_API_ENDPOINT, GITHUB_APP_NAME } = process.env;
 
 /**
  * This is the main entrypoint to your Probot app
@@ -271,12 +271,6 @@ export default async (app, { getRouter }) => {
       );
 
       if (installation?.action_count > 0) {
-        consola.warn(
-          "Action limit count down:",
-          installation.action_count,
-          "for",
-          repository.name,
-        );
         const result = await db.installation.update({
           data: {
             action_count: {
@@ -298,8 +292,7 @@ export default async (app, { getRouter }) => {
         return;
       }
 
-      if (installation?.action_count === 0) {
-        consola.warn("Removing action limit for", repository.name);
+      if (installation?.action_count === 1) {
         db.installation.update({
           data: {
             action_count: 0,
@@ -317,12 +310,11 @@ export default async (app, { getRouter }) => {
 
     // Check if the author of the commit is the bot
     const commitAuthor = context.payload.head_commit.author;
-    if (commitAuthor && commitAuthor.username === "codefair-test[bot]") {
+    if (commitAuthor?.name === `${GITHUB_APP_NAME}[bot]`) {
       const commitMessages = ["chore: 📝 Update CITATION.cff with Zenodo identifier", "chore: 📝 Update codemeta.json with Zenodo identifier"]
       // consola.info("Commit made by codefair-test, checking commit message...");
-      if (latestCommitInfo.latest_commit_message.includes(commitMessages[0]) || latestCommitInfo.latest_commit_message.includes(commitMessages[1])) {
-      // consola.info("Skipping validation as per commit message.");
-      return;
+      if (latestCommitInfo.latest_commit_message === commitMessages[0] || latestCommitInfo.latest_commit_message === commitMessages[1]) {
+        return;
       }
     }
 
@@ -558,8 +550,9 @@ export default async (app, { getRouter }) => {
     const issueTitle = context.payload.issue.title;
     const { repository } = context.payload;
     const owner = context.payload.repository.owner.login;
+    const potentialBot = context.payload.sender.login;
 
-    if (!issueTitle === ISSUE_TITLE) {
+    if (!issueTitle === ISSUE_TITLE && potentialBot === `${GITHUB_APP_NAME}[bot]`) {
       return;
     }
 
@@ -719,7 +712,20 @@ export default async (app, { getRouter }) => {
 
     if (issueBody.includes("<!-- @codefair-bot publish-zenodo")) {
       consola.log("Publishing to Zenodo...");
-      const quickTemplate = issueBody.substring(0, issueBody.indexOf("<!-- @codefair-bot publish-zenodo"));
+      const issueBodyRemovedCommand = issueBody.substring(0, issueBody.indexOf("<!-- @codefair-bot publish-zenodo"));
+      const issueBodyNoArchiveSection = issueBodyRemovedCommand.substring(0, issueBody.indexOf("## FAIR Software Release"));
+      const badgeURL = `${CODEFAIR_DOMAIN}/dashboard/${owner}/${repository.name}/release/zenodo`;
+      const releaseBadge = `[![Create Release](https://img.shields.io/badge/Create_Release-00bcd4.svg)](${badgeURL})`
+      // Gather the information for the Zenodo deposition provided in the issue body
+      const match = issueBody.match(/<!--\s*@codefair-bot\s*publish-zenodo\s*([\s\S]*?)-->/);
+      if (!match) {
+        throw new Error("Zenodo publish information not found in issue body.");
+      }
+      const [depositionId, releaseId, tagVersion, userWhoSubmitted] = match[1].trim().split(/\s+/);
+      // consola.info("Deposition ID:", depositionId);
+      // consola.info("Release ID:", releaseId);
+      // consola.info("Tag Version:", tagVersion);
+      // consola.info("User Who Submitted:", userWhoSubmitted);
       try {
         // 1. Get the metadata from the repository
         const citationCff = await getCitationContent(context, owner, repository);
@@ -738,19 +744,6 @@ export default async (app, { getRouter }) => {
           throw new Error("Error validating the codemeta:", error);
         }
 
-        // Gather the information for the Zenodo deposition provided in the issue body
-        const match = issueBody.match(/<!--\s*@codefair-bot\s*publish-zenodo\s*([\s\S]*?)-->/);
-        if (!match) {
-          throw new Error("Zenodo publish information not found in issue body.");
-        }
-
-        const [depositionId, releaseId, tagVersion, userWhoSubmitted] = match[1].trim().split(/\s+/);
-
-        consola.info("Deposition ID:", depositionId);
-        consola.info("Release ID:", releaseId);
-        consola.info("Tag Version:", tagVersion);
-        consola.info("User Who Submitted:", userWhoSubmitted);
-
         // Fetch the Zenodo token from the database
         const deposition = await db.zenodoToken.findFirst({
           where: {
@@ -782,11 +775,16 @@ export default async (app, { getRouter }) => {
 
         // 3. Create the Zenodo record or get the existing one
         let zenodoDepositionInfo = await getZenodoDepositionInfo(depositionId, zenodoToken);
-
+        
         // 4. Set the bucket URL and DOI
         const newDepositionId = zenodoDepositionInfo.id;
         const bucket_url = zenodoDepositionInfo.links.bucket;
         const zenodoDoi = zenodoDepositionInfo.metadata.prereserve_doi.doi;
+        
+        // Update the GitHub issue with a status report
+        const tempString = `${issueBodyNoArchiveSection}\n\n## FAIR Software Release 🔄\n***${tagVersion}*** of your software is being released on GitHub and archived on Zenodo. A draft deposition was created and will be adding the necessary files and metadata.`;
+        const finalTempString = await applyLastModifiedTemplate(tempString);
+        await createIssue(context, owner, repository, ISSUE_TITLE, finalTempString);
 
         // 5. Update the CITATION.cff and codemeta.json files with the DOI
         await updateMetadataIdentifier(context, owner, repository, zenodoDoi, tagVersion);
@@ -831,6 +829,11 @@ export default async (app, { getRouter }) => {
 
         await uploadReleaseAssetsToZenodo(zenodoToken, draftRelease.data.assets, repositoryArchive, owner, context, bucket_url, repository, tagVersion);
 
+        // Update the GitHub issue with a status report
+        const afterUploadString = `${issueBodyNoArchiveSection}\n\n## FAIR Software Release 🔄\n***${tagVersion}*** of your software is being released on GitHub and archived on Zenodo. All assets from the GitHub repository's draft release have been successfully uploaded to the Zenodo deposition draft.`;
+        const finalUploadString = await applyLastModifiedTemplate(afterUploadString);
+        await createIssue(context, owner, repository, ISSUE_TITLE, finalUploadString);
+
         // 8. Publish the Zenodo deposition
         consola.start("Publishing the Zenodo deposition...", newDepositionId);
         const publishDeposition = await fetch(
@@ -862,14 +865,9 @@ export default async (app, { getRouter }) => {
         consola.success("Updated release to not be a draft!");
 
         // 9. Append to the issueBody that the deposition has been published
-        // First remove everything after the ## Fair Software Release
-        // consola.warn(issueBody);
-        const updatedIssueBody = quickTemplate.substring(0, issueBody.indexOf("## FAIR Software Release"));
-        const badgeURL = `${CODEFAIR_DOMAIN}/dashboard/${owner}/${repository.name}/release/zenodo`;
-        const releaseBadge = `[![Create Release](https://img.shields.io/badge/Create_Release-00bcd4.svg)](${badgeURL})`
         const badge = `[![DOI](https://img.shields.io/badge/DOI-${zenodoDoi}-blue)](${ZENODO_ENDPOINT}/records/${newDepositionId})`;
-        const newIssueBody = `${updatedIssueBody}\n\n## FAIR Software Release ✔️\n***${tagVersion}*** of your software was successfully released on GitHub and archived on Zenodo. You can view the Zenodo archive by clicking the button below:\n\n${badge}\n\nReady to create your next FAIR release? Click the button below:\n\n${releaseBadge}`;
-        const finalTemplate = await applyLastModifiedTemplate(newIssueBody);
+        const issueBodyArchiveSection = `${issueBodyNoArchiveSection}\n\n## FAIR Software Release ✔️\n***${tagVersion}*** of your software was successfully released on GitHub and archived on Zenodo. You can view the Zenodo archive by clicking the button below:\n\n${badge}\n\nReady to create your next FAIR release? Click the button below:\n\n${releaseBadge}`;
+        const finalTemplate = await applyLastModifiedTemplate(issueBodyArchiveSection);
 
         // Update the issue with the new body
         await createIssue(context, owner, repository, ISSUE_TITLE, finalTemplate);
@@ -891,7 +889,10 @@ export default async (app, { getRouter }) => {
         consola.success("Updated the Zenodo deposition in the database!");
       } catch (error) {
         // Update the issue with the new body
-        await createIssue(context, owner, repository, ISSUE_TITLE, quickTemplate);
+        // Update the GitHub issue with a status report
+        const afterUploadString = `${issueBodyNoArchiveSection}\n\n## FAIR Software Release ❌\n***${tagVersion}*** of your software was not successfully released on GitHub and archived on Zenodo. There was an error during the publication process. Please try again later or reach out to the Codefair team for additional help.`;
+        const finalUploadString = await applyLastModifiedTemplate(afterUploadString);
+        await createIssue(context, owner, repository, ISSUE_TITLE, finalUploadString);
         await db.zenodoDeposition.update({
           data: {
             status: "error",
@@ -902,8 +903,6 @@ export default async (app, { getRouter }) => {
         });
         consola.error(`Error publishing to Zenodo: ${error}`);
       }
-
-
     }
   });
 
diff --git a/bot/license/index.js b/bot/license/index.js
index 2ea566f3..7cc4ffd0 100644
--- a/bot/license/index.js
+++ b/bot/license/index.js
@@ -16,7 +16,6 @@ const CODEFAIR_DOMAIN = process.env.CODEFAIR_APP_DOMAIN;
  * @returns {boolean} - Returns true if a license is found in the repository, false otherwise
  */
 export async function checkForLicense(context, owner, repo) {
-  consola.info("Checking for license...");
   try {
     await context.octokit.rest.licenses.getForRepo({
       owner,
diff --git a/bot/metadata/index.js b/bot/metadata/index.js
index 67217a16..e0106083 100644
--- a/bot/metadata/index.js
+++ b/bot/metadata/index.js
@@ -520,7 +520,7 @@ export async function applyMetadataTemplate(
     });
 
     if (license?.license_id) {
-      
+      metadata.license = `https://spdx.org/licenses/${license.license_id}`;
     }
 
     // License, codemeta.json and CITATION.cff files were found
diff --git a/bot/utils/renderer/index.js b/bot/utils/renderer/index.js
index 4e8a0baf..29052dc4 100644
--- a/bot/utils/renderer/index.js
+++ b/bot/utils/renderer/index.js
@@ -30,7 +30,6 @@ export async function renderIssues(
   subjects,
   prInfo = { title: "", link: "" },
 ) {
-  consola.info("Is repository empty?", emptyRepo);
   if (emptyRepo) {
     consola.success(
       "Applying empty repo template for repository:",
diff --git a/ui/components.d.ts b/ui/components.d.ts
index 76417937..58afd572 100644
--- a/ui/components.d.ts
+++ b/ui/components.d.ts
@@ -18,7 +18,6 @@ declare module 'vue' {
     NCollapse: typeof import('naive-ui')['NCollapse']
     NCollapseItem: typeof import('naive-ui')['NCollapseItem']
     NDivider: typeof import('naive-ui')['NDivider']
-    NDropdown: typeof import('naive-ui')['NDropdown']
     NFlex: typeof import('naive-ui')['NFlex']
     NForm: typeof import('naive-ui')['NForm']
     NFormItem: typeof import('naive-ui')['NFormItem']
@@ -27,8 +26,6 @@ declare module 'vue' {
     NRadioButton: typeof import('naive-ui')['NRadioButton']
     NRadioGroup: typeof import('naive-ui')['NRadioGroup']
     NSelect: typeof import('naive-ui')['NSelect']
-    NTag: typeof import('naive-ui')['NTag']
-    NTooltip: typeof import('naive-ui')['NTooltip']
     RouterLink: typeof import('vue-router')['RouterLink']
     RouterView: typeof import('vue-router')['RouterView']
   }

From d93d321f9ee627931a58ecedec342eaa73017b37 Mon Sep 17 00:00:00 2001
From: Sanjay Soundarajan <sanjay.16@live.com>
Date: Fri, 11 Oct 2024 12:50:01 -0700
Subject: [PATCH 04/27] feat: add support for zenodo progress (#80)

---
 ui/components.d.ts                            |   1 +
 ui/pages/dashboard/[owner]/[repo]/index.vue   |  57 +++++++++-
 .../[owner]/[repo]/release/zenodo.vue         | 107 +++++++++++++++++-
 ui/prisma/schema.prisma                       |   2 +-
 ui/server/api/[owner]/[repo]/dashboard.get.ts |  10 ++
 .../[repo]/release/zenodo/index.get.ts        |   4 +-
 .../[repo]/release/zenodo/index.post.ts       |  11 ++
 .../[repo]/release/zenodo/status.get.ts       |  32 ++++++
 8 files changed, 210 insertions(+), 14 deletions(-)
 create mode 100644 ui/server/api/[owner]/[repo]/release/zenodo/status.get.ts

diff --git a/ui/components.d.ts b/ui/components.d.ts
index 58afd572..e7617c99 100644
--- a/ui/components.d.ts
+++ b/ui/components.d.ts
@@ -22,6 +22,7 @@ declare module 'vue' {
     NForm: typeof import('naive-ui')['NForm']
     NFormItem: typeof import('naive-ui')['NFormItem']
     NInput: typeof import('naive-ui')['NInput']
+    NModal: typeof import('naive-ui')['NModal']
     NRadio: typeof import('naive-ui')['NRadio']
     NRadioButton: typeof import('naive-ui')['NRadioButton']
     NRadioGroup: typeof import('naive-ui')['NRadioGroup']
diff --git a/ui/pages/dashboard/[owner]/[repo]/index.vue b/ui/pages/dashboard/[owner]/[repo]/index.vue
index 135e93c6..b0800b45 100644
--- a/ui/pages/dashboard/[owner]/[repo]/index.vue
+++ b/ui/pages/dashboard/[owner]/[repo]/index.vue
@@ -223,15 +223,20 @@ const handleSettingsSelect = (key: any) => {
               Contains a valid license
             </n-tag>
 
-            <n-tag
+            <n-tooltip
               v-else-if="data?.licenseRequest?.licenseStatus === 'invalid'"
-              type="error"
+              trigger="hover"
             >
-              <template #icon>
-                <Icon name="icon-park-solid:close-one" size="16" />
+              <template #trigger>
+                <n-tag type="warning">
+                  <template #icon>
+                    <Icon name="ic:round-warning" size="16" />
+                  </template>
+                  Might not contain a valid license
+                </n-tag>
               </template>
-              Does not contain a valid license
-            </n-tag>
+              We couldn't determine if the license for this repository is valid.
+            </n-tooltip>
           </div>
         </template>
 
@@ -438,6 +443,46 @@ const handleSettingsSelect = (key: any) => {
           <Icon name="mingcute:rocket-fill" size="40" />
         </template>
 
+        <template #header-extra>
+          <n-flex>
+            <NuxtLink
+              v-if="data?.zenodoDeposition?.lastPublishedZenodoDoi"
+              :to="`https://doi.org/${data?.zenodoDeposition?.lastPublishedZenodoDoi}`"
+              target="_blank"
+              class="cursor-pointer"
+            >
+              <n-tag type="success" class="cursor-pointer">
+                <template #icon>
+                  <Icon name="simple-icons:doi" size="16" />
+                </template>
+                {{ data?.zenodoDeposition?.lastPublishedZenodoDoi }}
+              </n-tag>
+            </NuxtLink>
+
+            <div v-if="data?.zenodoDeposition?.zenodoStatus">
+              <n-tag
+                v-if="data?.zenodoDeposition?.zenodoStatus === 'inProgress'"
+                type="info"
+              >
+                <template #icon>
+                  <Icon name="icon-park-solid:loading-three" size="16" />
+                </template>
+                Publish in progress
+              </n-tag>
+
+              <n-tag
+                v-else-if="data?.zenodoDeposition?.zenodoStatus === 'error'"
+                type="error"
+              >
+                <template #icon>
+                  <Icon name="icon-park-solid:close-one" size="16" />
+                </template>
+                There was an error publishing to Zenodo
+              </n-tag>
+            </div>
+          </n-flex>
+        </template>
+
         <template #content>
           <div class="flex w-full flex-col">
             <p>
diff --git a/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue b/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue
index 469d62ae..d7bcbe14 100644
--- a/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue
+++ b/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue
@@ -110,6 +110,7 @@ if (data.value) {
   zenodoLoginUrl.value = data.value.zenodoLoginUrl;
   selectedDeposition.value = data.value.zenodoDepositionId?.toString() || null;
   haveValidZenodoToken.value = data.value.haveValidZenodoToken;
+
   license.value.id = data.value.license.id || "";
   license.value.identifier = data.value.license.identifier;
   metadataId.value = data.value.metadataId;
@@ -180,6 +181,12 @@ if (data.value) {
 
   // githubFormValue.value.release = "new";
   // githubFormValue.value.title = faker.lorem.sentence();
+
+  // slight hack but login step comes after the license and metadata checks
+  if (haveValidZenodoToken.value) {
+    licenseChecked.value = true;
+    metadataChecked.value = true;
+  }
 }
 
 const createDraftGithubReleaseSpinner = ref(false);
@@ -333,6 +340,29 @@ const handleGithubTagChange = () => {
 const zenodoPublishSpinner = ref(false);
 const zenodoDraftSpinner = ref(false);
 
+const showZenodoPublishProgressModal = ref(false);
+const zenodoPublishProgressInterval = ref<any>(null);
+
+const checkForZenodoPublishProgress = () => {
+  zenodoPublishProgressInterval.value = setInterval(async () => {
+    await $fetch(`/api/${owner}/${repo}/release/zenodo/status`, {
+      headers: useRequestHeaders(["cookie"]),
+      method: "GET",
+    })
+      .then(async (response) => {
+        if (response.zenodoWorkflowStatus !== "inProgress") {
+          showZenodoPublishProgressModal.value = false;
+          clearInterval(zenodoPublishProgressInterval.value);
+
+          await navigateTo(`/dashboard/${owner}/${repo}`);
+        }
+      })
+      .catch((error) => {
+        console.error("Error checking Zenodo publish progress:", error);
+      });
+  }, 3000);
+};
+
 const startZenodoPublishProcess = async (shouldPublish: boolean = false) => {
   if (shouldPublish) {
     zenodoPublishSpinner.value = true;
@@ -375,6 +405,7 @@ const startZenodoPublishProcess = async (shouldPublish: boolean = false) => {
           title: "Success",
           message: "Your Zenodo publish process has been started.",
         });
+        checkForZenodoPublishProgress();
       } else {
         push.success({
           title: "Success",
@@ -398,6 +429,24 @@ const startZenodoPublishProcess = async (shouldPublish: boolean = false) => {
 const validateZenodoForm = () => {
   zenodoFormRef.value?.validate((errors) => {
     if (!errors) {
+      // Check if the selected zenodo deposition is an actual option
+      if (selectedDeposition.value?.toString() !== "new") {
+        if (
+          selectableDepositions.value.find(
+            (item) => item.value === selectedDeposition.value?.toString(),
+          )
+        ) {
+          // do nothing
+        } else {
+          zenodoFormIsValid.value = false;
+          push.error({
+            title: "Error",
+            message: "Please select a valid Zenodo deposition.",
+          });
+          return;
+        }
+      }
+
       zenodoFormIsValid.value = true;
 
       push.success({
@@ -454,12 +503,13 @@ onBeforeUnmount(() => {
 
     <n-divider />
 
-    <h2 class="pb-6">Confirm required metadata files</h2>
-
-    <n-flex vertical class="mb-4">
+    <n-flex vertical>
       <n-alert
         v-if="
-          lastSelectedUser && lastSelectedGithubTag && lastSelectedGithubRelease
+          lastSelectedUser &&
+          lastSelectedGithubTag &&
+          lastSelectedGithubRelease &&
+          data?.zenodoWorkflowStatus !== 'published'
         "
         :type="user?.username === lastSelectedUser ? 'info' : 'warning'"
         class="w-full"
@@ -488,6 +538,33 @@ onBeforeUnmount(() => {
         .
       </n-alert>
 
+      <n-alert
+        v-if="data?.lastPublishedZenodoDoi"
+        type="success"
+        class="w-full"
+      >
+        This repository was last released on Zenodo at
+        <NuxtLink
+          :to="`https://doi.org/${data?.lastPublishedZenodoDoi}`"
+          target="_blank"
+          class="text-blue-500 underline transition-all hover:text-blue-700"
+          >{{ data?.lastPublishedZenodoDoi }}</NuxtLink
+        >.
+      </n-alert>
+
+      <n-alert
+        v-if="data?.lastPublishedZenodoDoi === 'inProgress'"
+        type="info"
+        class="w-full"
+      >
+        Zenodo is currently publishing this repository. You can check the status
+        of the Zenodo deposition on the dashboard.
+      </n-alert>
+    </n-flex>
+
+    <h2 class="py-6">Confirm required metadata files</h2>
+
+    <n-flex vertical class="mb-4">
       <CardDashboard
         title="License"
         subheader="A license file is required for the repository to be released on Zenodo."
@@ -498,7 +575,7 @@ onBeforeUnmount(() => {
 
         <template #content>
           <div class="flex w-full flex-col">
-            <n-flex class="mb-4 border p-2" align="center">
+            <n-flex v-if="license.id" class="mb-4 border p-2" align="center">
               <Icon name="tabler:license" size="24" />
 
               <p class="text-sm">
@@ -947,5 +1024,25 @@ onBeforeUnmount(() => {
         <pre>{{ data }}</pre>
       </n-collapse-item>
     </n-collapse>
+
+    <n-modal
+      v-model:show="showZenodoPublishProgressModal"
+      preset="card"
+      title="Zenodo publish in progress"
+      :bordered="false"
+      size="huge"
+      :mask-closable="false"
+      :close-on-esc="false"
+      style="width: 600px"
+    >
+      <n-flex vertical>
+        <p>
+          The workflow for publishing this repository to Zenodo is currently in
+          progress. You can check the status of this workflow on the dashboard.
+        </p>
+
+        <n-spin size="large" />
+      </n-flex>
+    </n-modal>
   </main>
 </template>
diff --git a/ui/prisma/schema.prisma b/ui/prisma/schema.prisma
index c7c25f2c..7bd9ddcc 100644
--- a/ui/prisma/schema.prisma
+++ b/ui/prisma/schema.prisma
@@ -147,7 +147,7 @@ model ZenodoDeposition {
   github_release_id Int?
   github_tag_name   String?
 
-  status String @default("unpublished") // unpublished or published only
+  status String @default("unpublished") // inProgress, published, error, draft
 
   user_id String
   user    User   @relation(fields: [user_id], references: [id], onDelete: Cascade)
diff --git a/ui/server/api/[owner]/[repo]/dashboard.get.ts b/ui/server/api/[owner]/[repo]/dashboard.get.ts
index fbc0dd13..2eafacae 100644
--- a/ui/server/api/[owner]/[repo]/dashboard.get.ts
+++ b/ui/server/api/[owner]/[repo]/dashboard.get.ts
@@ -17,6 +17,7 @@ export default defineEventHandler(async (event) => {
       CodeMetadata: true,
       CwlValidation: true,
       LicenseRequest: true,
+      ZenodoDeposition: true,
     },
     where: {
       owner,
@@ -34,6 +35,7 @@ export default defineEventHandler(async (event) => {
   const licenseRequest = installation.LicenseRequest;
   const codeMetadataRequest = installation.CodeMetadata;
   const cwlValidation = installation.CwlValidation;
+  const zenodoDeposition = installation.ZenodoDeposition;
 
   return {
     codeMetadataRequest: codeMetadataRequest
@@ -73,5 +75,13 @@ export default defineEventHandler(async (event) => {
           timestamp: licenseRequest.updated_at || null,
         }
       : null,
+    zenodoDeposition: zenodoDeposition
+      ? {
+          lastPublishedZenodoDoi:
+            zenodoDeposition.last_published_zenodo_doi || null,
+          zenodoId: zenodoDeposition.zenodo_id || null,
+          zenodoStatus: zenodoDeposition.status || null,
+        }
+      : null,
   };
 });
diff --git a/ui/server/api/[owner]/[repo]/release/zenodo/index.get.ts b/ui/server/api/[owner]/[repo]/release/zenodo/index.get.ts
index 0f23bfbd..1bfdc616 100644
--- a/ui/server/api/[owner]/[repo]/release/zenodo/index.get.ts
+++ b/ui/server/api/[owner]/[repo]/release/zenodo/index.get.ts
@@ -169,6 +169,7 @@ export default defineEventHandler(async (event) => {
       zenodoDeposition?.existing_zenodo_deposition_id || null,
     githubReleases,
     haveValidZenodoToken,
+    lastPublishedZenodoDoi: zenodoDeposition?.last_published_zenodo_doi || "",
     lastSelectedGithubRelease: zenodoDeposition?.github_release_id || null,
     lastSelectedGithubReleaseTitle:
       githubReleases.find(
@@ -180,13 +181,12 @@ export default defineEventHandler(async (event) => {
       id: licenseResponse.license_id || "",
       identifier: licenseResponse.identifier || "",
     },
-    // rawZenodoDepositions: rawData,
     metadataId: metadataResponse.identifier,
-    // rawReleases: githubReleasesJson,
     token: zenodoTokenInfo?.token || "",
     zenodoDepositionId: zenodoDeposition?.zenodo_id || null,
     zenodoDepositions: existingDepositions,
     zenodoLoginUrl: zenodoLoginUrl || "",
     zenodoMetadata,
+    zenodoWorkflowStatus: zenodoDeposition?.status || "",
   };
 });
diff --git a/ui/server/api/[owner]/[repo]/release/zenodo/index.post.ts b/ui/server/api/[owner]/[repo]/release/zenodo/index.post.ts
index e93dc01d..8984f1d5 100644
--- a/ui/server/api/[owner]/[repo]/release/zenodo/index.post.ts
+++ b/ui/server/api/[owner]/[repo]/release/zenodo/index.post.ts
@@ -205,6 +205,7 @@ export default defineEventHandler(async (event) => {
         github_release_id: parseInt(release) || null,
         github_tag_name: tag,
         repository_id: installation.id,
+        status: "draft",
         user_id: user?.id || "",
         zenodo_id: parseInt(zenodoDepositionId) || null,
         zenodo_metadata: metadata,
@@ -216,6 +217,7 @@ export default defineEventHandler(async (event) => {
         existing_zenodo_deposition_id: useExistingDeposition,
         github_release_id: parseInt(release) || null,
         github_tag_name: tag,
+        status: "draft",
         user_id: user?.id || "",
         zenodo_id: parseInt(zenodoDepositionId) || null,
         zenodo_metadata: metadata,
@@ -263,6 +265,15 @@ export default defineEventHandler(async (event) => {
         },
       );
 
+      await prisma.zenodoDeposition.update({
+        data: {
+          status: "inProgress",
+        },
+        where: {
+          repository_id: installation.id,
+        },
+      });
+
       return {
         message: "Zenodo publish process started",
       };
diff --git a/ui/server/api/[owner]/[repo]/release/zenodo/status.get.ts b/ui/server/api/[owner]/[repo]/release/zenodo/status.get.ts
new file mode 100644
index 00000000..a798fbf7
--- /dev/null
+++ b/ui/server/api/[owner]/[repo]/release/zenodo/status.get.ts
@@ -0,0 +1,32 @@
+export default defineEventHandler(async (event) => {
+  protectRoute(event);
+
+  const { owner, repo } = event.context.params as {
+    owner: string;
+    repo: string;
+  };
+
+  // Check if the user has write permissions to the repository
+  await repoWritePermissions(event, owner, repo);
+
+  const isOrg = await ownerIsOrganization(event, owner);
+  await isOrganizationMember(event, isOrg, owner);
+
+  const zenodoDeposition = await prisma.zenodoDeposition.findFirst({
+    where: {
+      repository: {
+        owner,
+        repo,
+      },
+    },
+  });
+
+  if (!zenodoDeposition) {
+    throw createError({
+      statusCode: 404,
+      statusMessage: "Zenodo deposition not found",
+    });
+  }
+
+  return { zenodoWorkflowStatus: zenodoDeposition.status || "" };
+});

From cf4f40cc9f0c62ca878076b207cd306592a2c8a4 Mon Sep 17 00:00:00 2001
From: Sanjay Soundarajan <sanjay.16@live.com>
Date: Fri, 11 Oct 2024 13:29:19 -0700
Subject: [PATCH 05/27] fix: invalid zenodo selector form

---
 ui/components.d.ts                                   | 4 ++++
 ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue | 4 ++--
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/ui/components.d.ts b/ui/components.d.ts
index e7617c99..6181f80b 100644
--- a/ui/components.d.ts
+++ b/ui/components.d.ts
@@ -18,6 +18,7 @@ declare module 'vue' {
     NCollapse: typeof import('naive-ui')['NCollapse']
     NCollapseItem: typeof import('naive-ui')['NCollapseItem']
     NDivider: typeof import('naive-ui')['NDivider']
+    NDropdown: typeof import('naive-ui')['NDropdown']
     NFlex: typeof import('naive-ui')['NFlex']
     NForm: typeof import('naive-ui')['NForm']
     NFormItem: typeof import('naive-ui')['NFormItem']
@@ -27,6 +28,9 @@ declare module 'vue' {
     NRadioButton: typeof import('naive-ui')['NRadioButton']
     NRadioGroup: typeof import('naive-ui')['NRadioGroup']
     NSelect: typeof import('naive-ui')['NSelect']
+    NSpin: typeof import('naive-ui')['NSpin']
+    NTag: typeof import('naive-ui')['NTag']
+    NTooltip: typeof import('naive-ui')['NTooltip']
     RouterLink: typeof import('vue-router')['RouterLink']
     RouterView: typeof import('vue-router')['RouterView']
   }
diff --git a/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue b/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue
index d7bcbe14..de1ea771 100644
--- a/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue
+++ b/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue
@@ -429,8 +429,8 @@ const startZenodoPublishProcess = async (shouldPublish: boolean = false) => {
 const validateZenodoForm = () => {
   zenodoFormRef.value?.validate((errors) => {
     if (!errors) {
-      // Check if the selected zenodo deposition is an actual option
-      if (selectedDeposition.value?.toString() !== "new") {
+      // Check if the selected zenodo deposition is an actual option'
+      if (selectedExistingDeposition.value !== "new") {
         if (
           selectableDepositions.value.find(
             (item) => item.value === selectedDeposition.value?.toString(),

From 5ecdbc192e62aaebb0b14b0913b0ab7b08f0939c Mon Sep 17 00:00:00 2001
From: slugb0t <wheresdorian@gmail.com>
Date: Fri, 11 Oct 2024 13:33:25 -0700
Subject: [PATCH 06/27] fix: :bug: patch double workflow when staging, prod,
 dev bots are installed

---
 bot/index.js | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/bot/index.js b/bot/index.js
index be9920e2..b1b8a0c7 100644
--- a/bot/index.js
+++ b/bot/index.js
@@ -552,7 +552,7 @@ export default async (app, { getRouter }) => {
     const owner = context.payload.repository.owner.login;
     const potentialBot = context.payload.sender.login;
 
-    if (!issueTitle === ISSUE_TITLE && potentialBot === `${GITHUB_APP_NAME}[bot]`) {
+    if (issueTitle != ISSUE_TITLE && potentialBot != `${GITHUB_APP_NAME}[bot]`) {
       return;
     }
 
@@ -781,7 +781,6 @@ export default async (app, { getRouter }) => {
         const bucket_url = zenodoDepositionInfo.links.bucket;
         const zenodoDoi = zenodoDepositionInfo.metadata.prereserve_doi.doi;
         
-        // Update the GitHub issue with a status report
         const tempString = `${issueBodyNoArchiveSection}\n\n## FAIR Software Release 🔄\n***${tagVersion}*** of your software is being released on GitHub and archived on Zenodo. A draft deposition was created and will be adding the necessary files and metadata.`;
         const finalTempString = await applyLastModifiedTemplate(tempString);
         await createIssue(context, owner, repository, ISSUE_TITLE, finalTempString);

From 63d885ffa202b44c28431afb0e81b1a3c24b9110 Mon Sep 17 00:00:00 2001
From: Sanjay Soundarajan <sanjay.16@live.com>
Date: Fri, 11 Oct 2024 14:14:58 -0700
Subject: [PATCH 07/27] fix: add zenodo form explanation text

---
 ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue b/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue
index de1ea771..ecff90d9 100644
--- a/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue
+++ b/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue
@@ -748,7 +748,8 @@ onBeforeUnmount(() => {
                   Your <code> codemeta.json </code> file is used to generate the
                   title, description, and metadata of your Zenodo deposition.
                   Please make sure that the content of this file is correct and
-                  up-to-date.
+                  up-to-date. Provide below metadata required by Zenodo but not
+                  available in codemeta.json.
                 </n-alert>
 
                 <n-form

From fc7bf0fd075758475c29179af42e6b37be7274ea Mon Sep 17 00:00:00 2001
From: Sanjay Soundarajan <sanjay.16@live.com>
Date: Fri, 11 Oct 2024 15:03:58 -0700
Subject: [PATCH 08/27] fix: update ui based on review comments (#81)

---
 .../[owner]/[repo]/release/zenodo.vue         | 103 ++++++++++++------
 1 file changed, 69 insertions(+), 34 deletions(-)

diff --git a/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue b/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue
index ecff90d9..bd760a9e 100644
--- a/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue
+++ b/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue
@@ -92,6 +92,8 @@ const lastSelectedGithubTag = ref<string | null>(null);
 const lastSelectedGithubRelease = ref<number | null>(null);
 const lastSelectedGithubReleaseTitle = ref<string | null>(null);
 
+const zenodoDraftIsReadyForRelease = ref(false);
+
 const { data, error } = await useFetch(`/api/${owner}/${repo}/release/zenodo`, {
   headers: useRequestHeaders(["cookie"]),
   method: "GET",
@@ -349,12 +351,13 @@ const checkForZenodoPublishProgress = () => {
       headers: useRequestHeaders(["cookie"]),
       method: "GET",
     })
-      .then(async (response) => {
+      .then((response) => {
         if (response.zenodoWorkflowStatus !== "inProgress") {
           showZenodoPublishProgressModal.value = false;
           clearInterval(zenodoPublishProgressInterval.value);
 
-          await navigateTo(`/dashboard/${owner}/${repo}`);
+          // remoad the page
+          window.location.reload();
         }
       })
       .catch((error) => {
@@ -560,13 +563,22 @@ onBeforeUnmount(() => {
         Zenodo is currently publishing this repository. You can check the status
         of the Zenodo deposition on the dashboard.
       </n-alert>
+
+      <n-alert
+        v-if="data?.lastPublishedZenodoDoi === 'error'"
+        type="error"
+        class="w-full"
+      >
+        There was an error with publishing this repository to Zenodo. Please try
+        again later or contact the Codefair team for assistance.
+      </n-alert>
     </n-flex>
 
-    <h2 class="py-6">Confirm required metadata files</h2>
+    <h2 class="py-6">Required metadata files</h2>
 
     <n-flex vertical class="mb-4">
       <CardDashboard
-        title="License"
+        title="Confirm License"
         subheader="A license file is required for the repository to be released on Zenodo."
       >
         <template #icon>
@@ -603,7 +615,7 @@ onBeforeUnmount(() => {
       </CardDashboard>
 
       <CardDashboard
-        title="Code metadata"
+        title="Confirm metadata"
         subheader="A code metadata file is required for the repository to be released on Zenodo."
       >
         <template #icon>
@@ -644,7 +656,7 @@ onBeforeUnmount(() => {
     <div v-if="allConfirmed">
       <n-divider />
 
-      <h2 class="pb-6">Select Zenodo deposition</h2>
+      <h2 class="pb-6">Zenodo deposition</h2>
 
       <CardDashboard title="Check Zenodo connection">
         <template #icon>
@@ -737,7 +749,7 @@ onBeforeUnmount(() => {
 
           <h2 class="pb-6">Zenodo metadata</h2>
 
-          <CardDashboard title="Add missing metadata">
+          <CardDashboard title="Provide repository-specific metadata">
             <template #icon>
               <Icon name="material-symbols:add-notes-outline" size="40" />
             </template>
@@ -783,7 +795,7 @@ onBeforeUnmount(() => {
                   </n-form-item>
 
                   <n-button @click="validateZenodoForm">
-                    Validate metadata
+                    Confirm metadata
                   </n-button>
                 </n-form>
               </div>
@@ -966,9 +978,9 @@ onBeforeUnmount(() => {
           <div v-if="githubFormIsValid || githubReleaseIsDraft">
             <n-divider />
 
-            <h2 class="pb-6">Publish Zenodo release</h2>
+            <h2 class="pb-6">Zenodo release</h2>
 
-            <CardDashboard title="Publish Zenodo release">
+            <CardDashboard title="Publish release on Zenodo">
               <template #icon>
                 <Icon name="simple-icons:zenodo" size="40" />
               </template>
@@ -981,31 +993,54 @@ onBeforeUnmount(() => {
                   </p>
 
                   <n-flex justify="space-between">
-                    <n-button
-                      :loading="zenodoDraftSpinner"
-                      secondary
-                      type="primary"
-                      @click="startZenodoPublishProcess(false)"
-                    >
-                      <template #icon>
-                        <Icon name="fa:save" size="16" />
-                      </template>
-
-                      Save draft
-                    </n-button>
-
-                    <n-button
-                      :loading="zenodoPublishSpinner"
-                      type="primary"
-                      color="black"
-                      @click="startZenodoPublishProcess(true)"
-                    >
-                      <template #icon>
-                        <Icon name="raphael:start" size="16" />
-                      </template>
+                    <n-flex justify="start">
+                      <n-button
+                        :loading="zenodoDraftSpinner"
+                        secondary
+                        type="primary"
+                        @click="startZenodoPublishProcess(false)"
+                      >
+                        <template #icon>
+                          <Icon name="fa:save" size="16" />
+                        </template>
+
+                        Save draft
+                      </n-button>
 
-                      Start the Zenodo publish process
-                    </n-button>
+                      <TransitionFade>
+                        <n-button
+                          v-if="!zenodoDraftIsReadyForRelease"
+                          secondary
+                          type="info"
+                          @click="zenodoDraftIsReadyForRelease = true"
+                        >
+                          <template #icon>
+                            <Icon name="basil:play-solid" size="16" />
+                          </template>
+
+                          My draft is ready for release
+                        </n-button>
+                      </TransitionFade>
+                    </n-flex>
+
+                    <TransitionFade>
+                      <n-button
+                        v-if="zenodoDraftIsReadyForRelease"
+                        :loading="zenodoPublishSpinner"
+                        type="primary"
+                        color="black"
+                        @click="startZenodoPublishProcess(true)"
+                      >
+                        <template #icon>
+                          <Icon
+                            name="material-symbols-light:play-circle"
+                            size="16"
+                          />
+                        </template>
+
+                        Start the Zenodo publish process
+                      </n-button>
+                    </TransitionFade>
                   </n-flex>
                 </div>
               </template>

From b8fbd5956a2c2eb5773b7d3b75538b3717fb0b8d Mon Sep 17 00:00:00 2001
From: Sanjay Soundarajan <sanjay.16@live.com>
Date: Fri, 11 Oct 2024 15:13:59 -0700
Subject: [PATCH 09/27] fix: show zenodo modal progress

---
 ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue b/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue
index ecff90d9..c7d2dacc 100644
--- a/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue
+++ b/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue
@@ -344,6 +344,8 @@ const showZenodoPublishProgressModal = ref(false);
 const zenodoPublishProgressInterval = ref<any>(null);
 
 const checkForZenodoPublishProgress = () => {
+  showZenodoPublishProgressModal.value = true;
+
   zenodoPublishProgressInterval.value = setInterval(async () => {
     await $fetch(`/api/${owner}/${repo}/release/zenodo/status`, {
       headers: useRequestHeaders(["cookie"]),

From ea677e63c2feff07c76b4395a9b0ad595273b0cc Mon Sep 17 00:00:00 2001
From: Sanjay Soundarajan <sanjay.16@live.com>
Date: Fri, 11 Oct 2024 15:25:22 -0700
Subject: [PATCH 10/27] fix: change zenodo redirect url

---
 ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue b/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue
index af0b1ebf..dcc598bc 100644
--- a/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue
+++ b/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue
@@ -353,13 +353,12 @@ const checkForZenodoPublishProgress = () => {
       headers: useRequestHeaders(["cookie"]),
       method: "GET",
     })
-      .then((response) => {
+      .then(async (response) => {
         if (response.zenodoWorkflowStatus !== "inProgress") {
           showZenodoPublishProgressModal.value = false;
           clearInterval(zenodoPublishProgressInterval.value);
 
-          // remoad the page
-          window.location.reload();
+          await navigateTo(`/dashboard/${owner}/${repo}/`);
         }
       })
       .catch((error) => {
@@ -491,6 +490,7 @@ onMounted(() => {
 
 onBeforeUnmount(() => {
   clearInterval(githubReleaseInterval.value);
+  clearInterval(zenodoPublishProgressInterval.value);
 });
 </script>
 

From 97ff272ed559448f3378bb0aa84230279e1f6d59 Mon Sep 17 00:00:00 2001
From: slugb0t <wheresdorian@gmail.com>
Date: Fri, 11 Oct 2024 15:36:55 -0700
Subject: [PATCH 11/27] feat: :sparkles: :card_file_box: database migrations
 for Analytics table

---
 .../20241011223412_analytics/migration.sql    |  3 +++
 bot/prisma/schema.prisma                      | 25 ++++++++++++-------
 .../20241011223412_analytics/migration.sql    |  3 +++
 ui/prisma/schema.prisma                       | 23 +++++++++++------
 4 files changed, 37 insertions(+), 17 deletions(-)
 create mode 100644 bot/prisma/migrations/20241011223412_analytics/migration.sql
 create mode 100644 ui/prisma/migrations/20241011223412_analytics/migration.sql

diff --git a/bot/prisma/migrations/20241011223412_analytics/migration.sql b/bot/prisma/migrations/20241011223412_analytics/migration.sql
new file mode 100644
index 00000000..ad1d3e13
--- /dev/null
+++ b/bot/prisma/migrations/20241011223412_analytics/migration.sql
@@ -0,0 +1,3 @@
+-- AlterTable
+ALTER TABLE "Analytics" ADD COLUMN     "create_release" INTEGER NOT NULL DEFAULT 0,
+ADD COLUMN     "zenodo_release" INTEGER NOT NULL DEFAULT 0;
diff --git a/bot/prisma/schema.prisma b/bot/prisma/schema.prisma
index c7c25f2c..a82331cd 100644
--- a/bot/prisma/schema.prisma
+++ b/bot/prisma/schema.prisma
@@ -147,19 +147,26 @@ model ZenodoDeposition {
   github_release_id Int?
   github_tag_name   String?
 
-  status String @default("unpublished") // unpublished or published only
+  status String @default("unpublished") // inProgress, published, error, draft
 
   user_id String
   user    User   @relation(fields: [user_id], references: [id], onDelete: Cascade)
 }
 
 model Analytics {
-  id                       Int      @id
-  cwl_validated_file_count Int      @default(0)
-  cwl_rerun_validation     Int      @default(0)
-  license_created          Int      @default(0)
-  update_codemeta          Int      @default(0)
-  update_citation          Int      @default(0)
-  created_at               DateTime @default(now())
-  updated_at               DateTime @updatedAt
+  id Int @id
+
+  cwl_validated_file_count Int @default(0)
+  cwl_rerun_validation     Int @default(0)
+
+  license_created Int @default(0)
+
+  update_codemeta Int @default(0)
+  update_citation Int @default(0)
+
+  create_release Int @default(0)
+  zenodo_release Int @default(0)
+
+  created_at DateTime @default(now())
+  updated_at DateTime @updatedAt
 }
diff --git a/ui/prisma/migrations/20241011223412_analytics/migration.sql b/ui/prisma/migrations/20241011223412_analytics/migration.sql
new file mode 100644
index 00000000..ad1d3e13
--- /dev/null
+++ b/ui/prisma/migrations/20241011223412_analytics/migration.sql
@@ -0,0 +1,3 @@
+-- AlterTable
+ALTER TABLE "Analytics" ADD COLUMN     "create_release" INTEGER NOT NULL DEFAULT 0,
+ADD COLUMN     "zenodo_release" INTEGER NOT NULL DEFAULT 0;
diff --git a/ui/prisma/schema.prisma b/ui/prisma/schema.prisma
index 7bd9ddcc..a82331cd 100644
--- a/ui/prisma/schema.prisma
+++ b/ui/prisma/schema.prisma
@@ -154,12 +154,19 @@ model ZenodoDeposition {
 }
 
 model Analytics {
-  id                       Int      @id
-  cwl_validated_file_count Int      @default(0)
-  cwl_rerun_validation     Int      @default(0)
-  license_created          Int      @default(0)
-  update_codemeta          Int      @default(0)
-  update_citation          Int      @default(0)
-  created_at               DateTime @default(now())
-  updated_at               DateTime @updatedAt
+  id Int @id
+
+  cwl_validated_file_count Int @default(0)
+  cwl_rerun_validation     Int @default(0)
+
+  license_created Int @default(0)
+
+  update_codemeta Int @default(0)
+  update_citation Int @default(0)
+
+  create_release Int @default(0)
+  zenodo_release Int @default(0)
+
+  created_at DateTime @default(now())
+  updated_at DateTime @updatedAt
 }

From 4da2e47f45724ba52385453fe08c733235ef0c5d Mon Sep 17 00:00:00 2001
From: slugb0t <wheresdorian@gmail.com>
Date: Fri, 11 Oct 2024 15:50:06 -0700
Subject: [PATCH 12/27] feat: :sparkles: :card_file_box: track amount of
 releases created with codefair

---
 bot/index.js | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/bot/index.js b/bot/index.js
index b1b8a0c7..99fbf395 100644
--- a/bot/index.js
+++ b/bot/index.js
@@ -885,7 +885,22 @@ export default async (app, { getRouter }) => {
             repository_id: repository.id,
           }
         });
+
         consola.success("Updated the Zenodo deposition in the database!");
+
+        await db.analytics.update({
+          data: {
+            zenodo_release: {
+              increment: 1
+            },
+            create_release: {
+              increment: 1
+            }
+          },
+          where: {
+            id: repository.id
+          }
+        });
       } catch (error) {
         // Update the issue with the new body
         // Update the GitHub issue with a status report

From 08bc09ccf39266d7b87cfc8a9abbc6cffacb24bf Mon Sep 17 00:00:00 2001
From: Sanjay Soundarajan <sanjay.16@live.com>
Date: Fri, 11 Oct 2024 15:58:37 -0700
Subject: [PATCH 13/27] chore: update version numbers

---
 bot/package.json |  4 ++--
 old-package.json | 17 -----------------
 ui/package.json  |  4 ++--
 3 files changed, 4 insertions(+), 21 deletions(-)
 delete mode 100644 old-package.json

diff --git a/bot/package.json b/bot/package.json
index 5bfae76f..275937ea 100644
--- a/bot/package.json
+++ b/bot/package.json
@@ -1,6 +1,6 @@
 {
-  "name": "codefair",
-  "version": "2.0.1",
+  "name": "codefair-bot",
+  "version": "3.0.0",
   "private": true,
   "description": "Checks for License and Citation in a Github repo",
   "author": "slugb0t",
diff --git a/old-package.json b/old-package.json
deleted file mode 100644
index 14c4eb16..00000000
--- a/old-package.json
+++ /dev/null
@@ -1,17 +0,0 @@
-{
-  "name": "codefair-monorepo",
-  "private": "true",
-  "devDependencies": {
-    "dotenv": "^16.4.5",
-    "npm-run-all": "^4.1.5",
-    "tsx": "^4.16.2"
-  },
-  "scripts": {
-    "bot:dev": "pnpm -C bot dev",
-    "bot:build": "pnpm -C bot build",
-    "ui:dev": "pnpm -C ui dev",
-    "ui:build": "pnpm -C ui build",
-    "dev": "pnpm --stream -r dev",
-    "scripts:deploy": "tsx ./scripts/deploy.ts"
-  }
-}
diff --git a/ui/package.json b/ui/package.json
index a63cb0de..786fc080 100644
--- a/ui/package.json
+++ b/ui/package.json
@@ -1,6 +1,6 @@
 {
-  "name": "codefair",
-  "version": "2.0.1",
+  "name": "codefair-app",
+  "version": "3.0.0",
   "private": true,
   "scripts": {
     "tunnel": "lt --port 3000 --subdomain codefair",

From c94b67ef66a629fb84df50f492483d30b636a625 Mon Sep 17 00:00:00 2001
From: slugb0t <wheresdorian@gmail.com>
Date: Fri, 11 Oct 2024 16:58:00 -0700
Subject: [PATCH 14/27] fix: :bug: zenodo version = github tag version

---
 bot/archival/index.js | 1 +
 1 file changed, 1 insertion(+)

diff --git a/bot/archival/index.js b/bot/archival/index.js
index 8c73acbf..579cf3c6 100644
--- a/bot/archival/index.js
+++ b/bot/archival/index.js
@@ -262,6 +262,7 @@ export async function getZenodoMetadata(codemetadata, repository) {
       access_right: "open",
       publication_date: new_date,
       license: licenseId,
+      version: codeMetaContent?.version,
     }
   }
 }

From 17ce4a094a7d99b837c50b304dc4d3ed8704e562 Mon Sep 17 00:00:00 2001
From: Sanjay Soundarajan <sanjay.16@live.com>
Date: Fri, 11 Oct 2024 17:14:04 -0700
Subject: [PATCH 15/27] feat: support zenodo version field

---
 .../dashboard/[owner]/[repo]/release/zenodo.vue | 17 +++++++++++++++++
 .../[owner]/[repo]/release/zenodo/index.get.ts  |  1 +
 .../[owner]/[repo]/release/zenodo/index.post.ts |  1 +
 ui/types/zenodo.d.ts                            |  1 +
 4 files changed, 20 insertions(+)

diff --git a/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue b/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue
index dcc598bc..868e2ed4 100644
--- a/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue
+++ b/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue
@@ -48,6 +48,7 @@ const selectableDepositions = ref<Array<SelectOption | SelectGroupOption>>([]);
 const zenodoFormIsValid = ref(false);
 const zenodoFormRef = ref<FormInst | null>(null);
 const zenodoFormValue = ref<ZenodoMetadata>({
+  version: "",
   accessRight: null,
 });
 const zenodoFormRules = ref({
@@ -56,6 +57,11 @@ const zenodoFormRules = ref({
     required: true,
     trigger: ["blur", "input"],
   },
+  version: {
+    message: "Please input a version",
+    required: true,
+    trigger: ["blur", "input"],
+  },
 });
 
 const githubFormIsValid = ref(false);
@@ -133,6 +139,7 @@ if (data.value) {
 
   zenodoFormValue.value.accessRight =
     data.value.zenodoMetadata.accessRight || null;
+  zenodoFormValue.value.version = data.value.zenodoMetadata.version || "";
 
   lastSelectedUser.value = data.value.lastSelectedUser;
   lastSelectedGithubTag.value = data.value.lastSelectedGithubTag;
@@ -773,6 +780,16 @@ onBeforeUnmount(() => {
                   :rules="zenodoFormRules"
                   size="large"
                 >
+                  <n-form-item
+                    label="Version number for this release"
+                    path="version"
+                  >
+                    <n-input
+                      v-model:value="zenodoFormValue.version"
+                      placeholder="1.0.0"
+                    />
+                  </n-form-item>
+
                   <n-form-item label="Access Right" path="accessRight">
                     <n-radio-group
                       v-model:value="zenodoFormValue.accessRight"
diff --git a/ui/server/api/[owner]/[repo]/release/zenodo/index.get.ts b/ui/server/api/[owner]/[repo]/release/zenodo/index.get.ts
index 1bfdc616..bbb9c862 100644
--- a/ui/server/api/[owner]/[repo]/release/zenodo/index.get.ts
+++ b/ui/server/api/[owner]/[repo]/release/zenodo/index.get.ts
@@ -127,6 +127,7 @@ export default defineEventHandler(async (event) => {
 
   const zenodoMetadata: ZenodoMetadata = {
     accessRight: raw?.accessRight || null,
+    version: raw?.version || "",
   };
 
   // Get a list of github releases
diff --git a/ui/server/api/[owner]/[repo]/release/zenodo/index.post.ts b/ui/server/api/[owner]/[repo]/release/zenodo/index.post.ts
index 8984f1d5..000b94c3 100644
--- a/ui/server/api/[owner]/[repo]/release/zenodo/index.post.ts
+++ b/ui/server/api/[owner]/[repo]/release/zenodo/index.post.ts
@@ -13,6 +13,7 @@ export default defineEventHandler(async (event) => {
     .object({
       metadata: z.object({
         accessRight: z.string(),
+        version: z.string(),
       }),
       publish: z.boolean(),
       release: z.string(),
diff --git a/ui/types/zenodo.d.ts b/ui/types/zenodo.d.ts
index d6ddc9fd..880814ff 100644
--- a/ui/types/zenodo.d.ts
+++ b/ui/types/zenodo.d.ts
@@ -8,4 +8,5 @@ interface ZenodoDeposition {
 
 interface ZenodoMetadata {
   accessRight: string | null;
+  version: string;
 }

From cd8fd009d5be8ca04447f59de07077df65a2e50d Mon Sep 17 00:00:00 2001
From: slugb0t <wheresdorian@gmail.com>
Date: Fri, 11 Oct 2024 17:24:54 -0700
Subject: [PATCH 16/27] feat: :sparkles: :card_file_box: extracting zenodo
 metdata from saved user inputs

---
 bot/archival/index.js | 15 +++++++++++++--
 bot/metadata/index.js | 15 +++++++++++++--
 2 files changed, 26 insertions(+), 4 deletions(-)

diff --git a/bot/archival/index.js b/bot/archival/index.js
index 579cf3c6..05de0c96 100644
--- a/bot/archival/index.js
+++ b/bot/archival/index.js
@@ -253,16 +253,27 @@ export async function getZenodoMetadata(codemetadata, repository) {
     throw new Error(`License not found for URL: ${codeMetaContent.license}`);
   }
 
+  const zenodoMetadata = await dbInstance.zenodoDeposition.findUnique({
+    where: {
+      repository_id: repository.id,
+    }
+  })
+
+  if (!zenodoMetadata) {
+    consola.error("Zenodo metadata not found in the database. Please create a new Zenodo deposition.");
+    throw new Error("Zenodo metadata not found in the database. Please create a new Zenodo deposition.");
+  } 
+
   return {
     metadata: {
       title: codeMetaContent?.name,
       description: codeMetaContent?.description,
       upload_type: "software",
       creators: zenodoCreators,
-      access_right: "open",
+      access_right: zenodoMetadata.zenodo_metadata.access_right,
       publication_date: new_date,
       license: licenseId,
-      version: codeMetaContent?.version,
+      version: zenodoMetadata.zenodo_metadata.version,
     }
   }
 }
diff --git a/bot/metadata/index.js b/bot/metadata/index.js
index e0106083..bd9cc9ee 100644
--- a/bot/metadata/index.js
+++ b/bot/metadata/index.js
@@ -350,11 +350,22 @@ export async function updateMetadataIdentifier(context, owner, repository, ident
   const citationSha = citationObj.sha;
   const updated_date = new Date().toISOString().split('T')[0];
 
+  const zenodoMetadata = await dbInstance.zenodoDeposition.findUnique({
+    where: {
+      repository_id: repository.id,
+    }
+  })
+
+  if (!zenodoMetadata) {
+    consola.error("Zenodo metadata not found in the database. Please create a new Zenodo deposition.");
+    throw new Error("Zenodo metadata not found in the database. Please create a new Zenodo deposition.");
+  } 
+
   citationFile.doi = identifier;
   citationFile["date-released"] = updated_date;
-  citationFile.version = version;
+  citationFile.version = zenodoMetadata.zenodo_metadata.version;
   codeMetaFile.identifier = identifier;
-  codeMetaFile.version = version;
+  codeMetaFile.version = zenodoMetadata.zenodo_metadata.version;
   codeMetaFile.dateModified = updated_date;
   codeMetaFile.datePublished = updated_date;
 

From d65b3a2b9a7bf1ae54cee118f47fdf9095ee8288 Mon Sep 17 00:00:00 2001
From: slugb0t <wheresdorian@gmail.com>
Date: Fri, 11 Oct 2024 17:35:57 -0700
Subject: [PATCH 17/27] refactor: :sparkles: add fallbacks for versioning
 releases on github and zenodo

---
 bot/archival/index.js | 4 ++--
 bot/metadata/index.js | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/bot/archival/index.js b/bot/archival/index.js
index 05de0c96..04e473cf 100644
--- a/bot/archival/index.js
+++ b/bot/archival/index.js
@@ -270,10 +270,10 @@ export async function getZenodoMetadata(codemetadata, repository) {
       description: codeMetaContent?.description,
       upload_type: "software",
       creators: zenodoCreators,
-      access_right: zenodoMetadata.zenodo_metadata.access_right,
+      access_right: zenodoMetadata?.zenodo_metadata?.access_right || "open access",
       publication_date: new_date,
       license: licenseId,
-      version: zenodoMetadata.zenodo_metadata.version,
+      version: zenodoMetadata?.zenodo_metadata?.version || codeMetaContent?.version,
     }
   }
 }
diff --git a/bot/metadata/index.js b/bot/metadata/index.js
index bd9cc9ee..6b1e6ef1 100644
--- a/bot/metadata/index.js
+++ b/bot/metadata/index.js
@@ -363,9 +363,9 @@ export async function updateMetadataIdentifier(context, owner, repository, ident
 
   citationFile.doi = identifier;
   citationFile["date-released"] = updated_date;
-  citationFile.version = zenodoMetadata.zenodo_metadata.version;
+  citationFile.version = zenodoMetadata?.zenodo_metadata?.version || version;
   codeMetaFile.identifier = identifier;
-  codeMetaFile.version = zenodoMetadata.zenodo_metadata.version;
+  codeMetaFile.version = zenodoMetadata?.zenodo_metadata?.version || version;
   codeMetaFile.dateModified = updated_date;
   codeMetaFile.datePublished = updated_date;
 

From 216f76606a15d00430a4710e62b2e2b3dbf6a435 Mon Sep 17 00:00:00 2001
From: Sanjay Soundarajan <sanjay.16@live.com>
Date: Fri, 11 Oct 2024 17:38:53 -0700
Subject: [PATCH 18/27] fix: update zendo publish modal (#82)

---
 .../[owner]/[repo]/release/zenodo.vue         | 150 +++++++++++-------
 .../[repo]/release/zenodo/status.get.ts       |   5 +-
 2 files changed, 100 insertions(+), 55 deletions(-)

diff --git a/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue b/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue
index 868e2ed4..edc622bf 100644
--- a/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue
+++ b/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue
@@ -48,8 +48,8 @@ const selectableDepositions = ref<Array<SelectOption | SelectGroupOption>>([]);
 const zenodoFormIsValid = ref(false);
 const zenodoFormRef = ref<FormInst | null>(null);
 const zenodoFormValue = ref<ZenodoMetadata>({
-  version: "",
   accessRight: null,
+  version: "",
 });
 const zenodoFormRules = ref({
   accessRight: {
@@ -305,6 +305,7 @@ const checkIfGithubReleaseIsDraft = async () => {
 };
 
 const handleGithubReleaseChange = () => {
+  zenodoDraftIsReadyForRelease.value = false;
   githubFormValue.value.releaseTitle = "";
   checkIfGithubReleaseIsDraft();
 };
@@ -342,6 +343,7 @@ const renderGithubReleaseLabel = (option: SelectOption): any => {
 };
 
 const handleGithubTagChange = () => {
+  zenodoDraftIsReadyForRelease.value = false;
   githubFormValue.value.tagTitle = "";
   checkIfGithubReleaseIsDraft();
 };
@@ -351,6 +353,8 @@ const zenodoDraftSpinner = ref(false);
 
 const showZenodoPublishProgressModal = ref(false);
 const zenodoPublishProgressInterval = ref<any>(null);
+const zenodoPublishStatus = ref<string>("");
+const zenodoPublishDOI = ref<string>("");
 
 const checkForZenodoPublishProgress = () => {
   showZenodoPublishProgressModal.value = true;
@@ -362,7 +366,9 @@ const checkForZenodoPublishProgress = () => {
     })
       .then(async (response) => {
         if (response.zenodoWorkflowStatus !== "inProgress") {
-          showZenodoPublishProgressModal.value = false;
+          zenodoPublishStatus.value = response.zenodoWorkflowStatus;
+          zenodoPublishDOI.value = response.zenodoDoi;
+
           clearInterval(zenodoPublishProgressInterval.value);
 
           await navigateTo(`/dashboard/${owner}/${repo}/`);
@@ -955,6 +961,19 @@ onBeforeUnmount(() => {
                         Do not publish your Github release yet. We will handle
                         this step for you.
                       </n-alert>
+
+                      <n-button
+                        v-if="!zenodoDraftIsReadyForRelease"
+                        secondary
+                        type="primary"
+                        @click="zenodoDraftIsReadyForRelease = true"
+                      >
+                        <template #icon>
+                          <Icon name="basil:play-solid" size="16" />
+                        </template>
+
+                        My draft is ready for release
+                      </n-button>
                     </div>
 
                     <div
@@ -994,7 +1013,12 @@ onBeforeUnmount(() => {
             </CardDashboard>
           </div>
 
-          <div v-if="githubFormIsValid || githubReleaseIsDraft">
+          <div
+            v-if="
+              (githubFormIsValid || githubReleaseIsDraft) &&
+              zenodoDraftIsReadyForRelease
+            "
+          >
             <n-divider />
 
             <h2 class="pb-6">Zenodo release</h2>
@@ -1012,54 +1036,34 @@ onBeforeUnmount(() => {
                   </p>
 
                   <n-flex justify="space-between">
-                    <n-flex justify="start">
-                      <n-button
-                        :loading="zenodoDraftSpinner"
-                        secondary
-                        type="primary"
-                        @click="startZenodoPublishProcess(false)"
-                      >
-                        <template #icon>
-                          <Icon name="fa:save" size="16" />
-                        </template>
-
-                        Save draft
-                      </n-button>
-
-                      <TransitionFade>
-                        <n-button
-                          v-if="!zenodoDraftIsReadyForRelease"
-                          secondary
-                          type="info"
-                          @click="zenodoDraftIsReadyForRelease = true"
-                        >
-                          <template #icon>
-                            <Icon name="basil:play-solid" size="16" />
-                          </template>
-
-                          My draft is ready for release
-                        </n-button>
-                      </TransitionFade>
-                    </n-flex>
-
-                    <TransitionFade>
-                      <n-button
-                        v-if="zenodoDraftIsReadyForRelease"
-                        :loading="zenodoPublishSpinner"
-                        type="primary"
-                        color="black"
-                        @click="startZenodoPublishProcess(true)"
-                      >
-                        <template #icon>
-                          <Icon
-                            name="material-symbols-light:play-circle"
-                            size="16"
-                          />
-                        </template>
-
-                        Start the Zenodo publish process
-                      </n-button>
-                    </TransitionFade>
+                    <n-button
+                      :loading="zenodoDraftSpinner"
+                      secondary
+                      type="primary"
+                      @click="startZenodoPublishProcess(false)"
+                    >
+                      <template #icon>
+                        <Icon name="fa:save" size="16" />
+                      </template>
+
+                      Save draft
+                    </n-button>
+
+                    <n-button
+                      :loading="zenodoPublishSpinner"
+                      type="primary"
+                      color="black"
+                      @click="startZenodoPublishProcess(true)"
+                    >
+                      <template #icon>
+                        <Icon
+                          name="material-symbols-light:play-circle"
+                          size="16"
+                        />
+                      </template>
+
+                      Start the Zenodo publish process
+                    </n-button>
                   </n-flex>
                 </div>
               </template>
@@ -1083,21 +1087,59 @@ onBeforeUnmount(() => {
     <n-modal
       v-model:show="showZenodoPublishProgressModal"
       preset="card"
-      title="Zenodo publish in progress"
+      :title="
+        zenodoPublishStatus === 'inProgress'
+          ? 'Zenodo publish in progress'
+          : 'Zenodo publish completed'
+      "
       :bordered="false"
       size="huge"
       :mask-closable="false"
       :close-on-esc="false"
       style="width: 600px"
     >
-      <n-flex vertical>
+      <n-flex v-if="zenodoPublishStatus === 'inProgress'" vertical>
         <p>
           The workflow for publishing this repository to Zenodo is currently in
-          progress. You can check the status of this workflow on the dashboard.
+          progress. You can check the status of this workflow on the dashboard
         </p>
 
         <n-spin size="large" />
       </n-flex>
+
+      <n-flex v-else-if="zenodoPublishStatus === 'error'" vertical>
+        <p>
+          There was an error with publishing this repository to Zenodo. Please
+          try again later or contact the Codefair team for assistance.
+        </p>
+      </n-flex>
+
+      <n-flex v-else-if="zenodoPublishStatus === 'published'" vertical>
+        <p>
+          Your Zenodo deposition has been published. You can view the Zenodo
+          record on the dashboard.
+        </p>
+
+        <NuxtLink :to="`https://doi.org/${zenodoPublishDOI}`" target="_blank">
+          <n-button type="primary">
+            <template #icon>
+              <Icon name="simple-icons:zenodo" size="16" />
+            </template>
+            View Zenodo record
+          </n-button>
+        </NuxtLink>
+      </n-flex>
+
+      <template #footer>
+        <n-flex justify="end">
+          <n-button
+            type="success"
+            @click="showZenodoPublishProgressModal = false"
+          >
+            Okay
+          </n-button>
+        </n-flex>
+      </template>
     </n-modal>
   </main>
 </template>
diff --git a/ui/server/api/[owner]/[repo]/release/zenodo/status.get.ts b/ui/server/api/[owner]/[repo]/release/zenodo/status.get.ts
index a798fbf7..2a8940e2 100644
--- a/ui/server/api/[owner]/[repo]/release/zenodo/status.get.ts
+++ b/ui/server/api/[owner]/[repo]/release/zenodo/status.get.ts
@@ -28,5 +28,8 @@ export default defineEventHandler(async (event) => {
     });
   }
 
-  return { zenodoWorkflowStatus: zenodoDeposition.status || "" };
+  return {
+    zenodoDoi: zenodoDeposition.last_published_zenodo_doi || "",
+    zenodoWorkflowStatus: zenodoDeposition.status || "",
+  };
 });

From 7cf1b46f182e1109b1ee06231fef0638ff427d70 Mon Sep 17 00:00:00 2001
From: slugb0t <wheresdorian@gmail.com>
Date: Fri, 11 Oct 2024 17:55:54 -0700
Subject: [PATCH 19/27] fix: :bug: correct access_right value

---
 bot/archival/index.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bot/archival/index.js b/bot/archival/index.js
index 04e473cf..0a606329 100644
--- a/bot/archival/index.js
+++ b/bot/archival/index.js
@@ -270,10 +270,10 @@ export async function getZenodoMetadata(codemetadata, repository) {
       description: codeMetaContent?.description,
       upload_type: "software",
       creators: zenodoCreators,
-      access_right: zenodoMetadata?.zenodo_metadata?.access_right || "open access",
+      access_right: zenodoMetadata.zenodo_metadata.access_right || "open",
       publication_date: new_date,
       license: licenseId,
-      version: zenodoMetadata?.zenodo_metadata?.version || codeMetaContent?.version,
+      version: zenodoMetadata.zenodo_metadata.version || codeMetaContent?.version,
     }
   }
 }

From e746628a1522bc6e51d2f6bb88c5700dbf3159f7 Mon Sep 17 00:00:00 2001
From: slugb0t <wheresdorian@gmail.com>
Date: Fri, 11 Oct 2024 17:56:18 -0700
Subject: [PATCH 20/27] fix: :bug: correct access_right value with no fallback

---
 bot/archival/index.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bot/archival/index.js b/bot/archival/index.js
index 0a606329..51a3cc20 100644
--- a/bot/archival/index.js
+++ b/bot/archival/index.js
@@ -270,7 +270,7 @@ export async function getZenodoMetadata(codemetadata, repository) {
       description: codeMetaContent?.description,
       upload_type: "software",
       creators: zenodoCreators,
-      access_right: zenodoMetadata.zenodo_metadata.access_right || "open",
+      access_right: zenodoMetadata.zenodo_metadata.access_right,
       publication_date: new_date,
       license: licenseId,
       version: zenodoMetadata.zenodo_metadata.version || codeMetaContent?.version,

From 1388a9443169b99c9d41c32fcd15e6f20a6dd029 Mon Sep 17 00:00:00 2001
From: slugb0t <wheresdorian@gmail.com>
Date: Fri, 11 Oct 2024 18:04:00 -0700
Subject: [PATCH 21/27] fix: :bug: don't modify date published on codemeta file

---
 bot/metadata/index.js | 1 -
 1 file changed, 1 deletion(-)

diff --git a/bot/metadata/index.js b/bot/metadata/index.js
index 6b1e6ef1..750ae6c4 100644
--- a/bot/metadata/index.js
+++ b/bot/metadata/index.js
@@ -367,7 +367,6 @@ export async function updateMetadataIdentifier(context, owner, repository, ident
   codeMetaFile.identifier = identifier;
   codeMetaFile.version = zenodoMetadata?.zenodo_metadata?.version || version;
   codeMetaFile.dateModified = updated_date;
-  codeMetaFile.datePublished = updated_date;
 
   if (codeMetaFile?.license) {
     const response = await dbInstance.licenseRequest.findUnique({

From 9cca1bca1868e1fb9f9bba9fad820d5c1067941c Mon Sep 17 00:00:00 2001
From: Sanjay Soundarajan <sanjay.16@live.com>
Date: Fri, 11 Oct 2024 18:21:55 -0700
Subject: [PATCH 22/27] feat: add better error messages in zenodo modal

---
 .../[owner]/[repo]/release/zenodo.vue         | 37 ++++++++++---------
 1 file changed, 20 insertions(+), 17 deletions(-)

diff --git a/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue b/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue
index edc622bf..7bb42783 100644
--- a/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue
+++ b/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue
@@ -370,8 +370,6 @@ const checkForZenodoPublishProgress = () => {
           zenodoPublishDOI.value = response.zenodoDoi;
 
           clearInterval(zenodoPublishProgressInterval.value);
-
-          await navigateTo(`/dashboard/${owner}/${repo}/`);
         }
       })
       .catch((error) => {
@@ -380,6 +378,10 @@ const checkForZenodoPublishProgress = () => {
   }, 3000);
 };
 
+const navigateToDashboard = async () => {
+  await navigateTo(`/dashboard/${owner}/${repo}/`);
+};
+
 const startZenodoPublishProcess = async (shouldPublish: boolean = false) => {
   if (shouldPublish) {
     zenodoPublishSpinner.value = true;
@@ -1090,7 +1092,11 @@ onBeforeUnmount(() => {
       :title="
         zenodoPublishStatus === 'inProgress'
           ? 'Zenodo publish in progress'
-          : 'Zenodo publish completed'
+          : zenodoPublishStatus === 'error'
+            ? 'Zenodo publish error'
+            : zenodoPublishStatus === 'published'
+              ? 'Zenodo publish success'
+              : 'Something went wrong'
       "
       :bordered="false"
       size="huge"
@@ -1119,23 +1125,20 @@ onBeforeUnmount(() => {
           Your Zenodo deposition has been published. You can view the Zenodo
           record on the dashboard.
         </p>
-
-        <NuxtLink :to="`https://doi.org/${zenodoPublishDOI}`" target="_blank">
-          <n-button type="primary">
-            <template #icon>
-              <Icon name="simple-icons:zenodo" size="16" />
-            </template>
-            View Zenodo record
-          </n-button>
-        </NuxtLink>
       </n-flex>
 
       <template #footer>
-        <n-flex justify="end">
-          <n-button
-            type="success"
-            @click="showZenodoPublishProgressModal = false"
-          >
+        <n-flex justify="space-between">
+          <NuxtLink :to="`https://doi.org/${zenodoPublishDOI}`" target="_blank">
+            <n-button type="primary" v-if="zenodoPublishStatus === 'published'">
+              <template #icon>
+                <Icon name="simple-icons:zenodo" size="16" />
+              </template>
+              View Zenodo record
+            </n-button>
+          </NuxtLink>
+
+          <n-button type="success" @click="navigateToDashboard">
             Okay
           </n-button>
         </n-flex>

From feb74964997c2792d78f36e2f409dac5f6c9225c Mon Sep 17 00:00:00 2001
From: slugb0t <wheresdorian@gmail.com>
Date: Sat, 12 Oct 2024 16:19:03 -0700
Subject: [PATCH 23/27] fix: :bug: track PR url for the code metadata PR

---
 ui/components.d.ts                                    |  5 +++++
 ui/server/api/codeMetadata/[identifier]/index.post.ts | 10 ++++++++++
 2 files changed, 15 insertions(+)

diff --git a/ui/components.d.ts b/ui/components.d.ts
index 6181f80b..c7125bed 100644
--- a/ui/components.d.ts
+++ b/ui/components.d.ts
@@ -17,17 +17,22 @@ declare module 'vue' {
     NCheckbox: typeof import('naive-ui')['NCheckbox']
     NCollapse: typeof import('naive-ui')['NCollapse']
     NCollapseItem: typeof import('naive-ui')['NCollapseItem']
+    NCollapseTransition: typeof import('naive-ui')['NCollapseTransition']
+    NDatePicker: typeof import('naive-ui')['NDatePicker']
     NDivider: typeof import('naive-ui')['NDivider']
     NDropdown: typeof import('naive-ui')['NDropdown']
+    NDynamicInput: typeof import('naive-ui')['NDynamicInput']
     NFlex: typeof import('naive-ui')['NFlex']
     NForm: typeof import('naive-ui')['NForm']
     NFormItem: typeof import('naive-ui')['NFormItem']
     NInput: typeof import('naive-ui')['NInput']
     NModal: typeof import('naive-ui')['NModal']
+    NPopconfirm: typeof import('naive-ui')['NPopconfirm']
     NRadio: typeof import('naive-ui')['NRadio']
     NRadioButton: typeof import('naive-ui')['NRadioButton']
     NRadioGroup: typeof import('naive-ui')['NRadioGroup']
     NSelect: typeof import('naive-ui')['NSelect']
+    NSpace: typeof import('naive-ui')['NSpace']
     NSpin: typeof import('naive-ui')['NSpin']
     NTag: typeof import('naive-ui')['NTag']
     NTooltip: typeof import('naive-ui')['NTooltip']
diff --git a/ui/server/api/codeMetadata/[identifier]/index.post.ts b/ui/server/api/codeMetadata/[identifier]/index.post.ts
index c16c2064..abe67d54 100644
--- a/ui/server/api/codeMetadata/[identifier]/index.post.ts
+++ b/ui/server/api/codeMetadata/[identifier]/index.post.ts
@@ -448,6 +448,16 @@ export default defineEventHandler(async (event) => {
     },
   );
 
+  // Save the PR URL to the database
+  await prisma.codeMetadata.update({
+    data: {
+      pull_request_url: pullRequestData.html_url,
+    },
+    where: {
+      id: codeMetadataRequest.id,
+    },
+  });
+
   // Update the analytics data for the repository
   const existingAnalytics = await prisma.analytics.findUnique({
     where: {

From bf9b9df45622457af9c5a394c6b8cdcec225124b Mon Sep 17 00:00:00 2001
From: slugb0t <wheresdorian@gmail.com>
Date: Sat, 12 Oct 2024 16:20:01 -0700
Subject: [PATCH 24/27] refactor: :recycle: use db when referring to pr url

---
 bot/utils/renderer/index.js | 18 ++++++++++++++----
 1 file changed, 14 insertions(+), 4 deletions(-)

diff --git a/bot/utils/renderer/index.js b/bot/utils/renderer/index.js
index 29052dc4..b60d0ba2 100644
--- a/bot/utils/renderer/index.js
+++ b/bot/utils/renderer/index.js
@@ -7,6 +7,7 @@ import { applyCWLTemplate } from "../../cwl/index.js";
 import { applyMetadataTemplate } from "../../metadata/index.js";
 import { applyLicenseTemplate } from "../../license/index.js";
 import { applyArchivalTemplate } from "../../archival/index.js";
+import dbInstance from "../../db.js";
 
 const { GITHUB_APP_NAME } = process.env;
 
@@ -52,9 +53,14 @@ export async function renderIssues(
     context,
   );
 
+  // Check if pull request url exist in db
+  const prUrl = await dbInstance.licenseRequest.findUnique({
+    where: { repository_id: repository.id },
+  });
+
   // If License PR is open, add the PR number to the dashboard
-  if (prInfo.title === "feat: ✨ LICENSE file added") {
-    baseTemplate += `\n\nA pull request for the LICENSE file is open. You can view the pull request:\n\n[![License](https://img.shields.io/badge/View_PR-6366f1.svg)](${prInfo.link})`;
+  if (prUrl?.pull_request_url) {
+    baseTemplate += `\n\nA pull request for the LICENSE file is open. You can view the pull request:\n\n[![License](https://img.shields.io/badge/View_PR-6366f1.svg)](${prUrl.pull_request_url})`;
   }
 
   baseTemplate = await applyMetadataTemplate(
@@ -65,8 +71,12 @@ export async function renderIssues(
     context,
   );
 
-  if (prInfo.title === "feat: ✨ metadata files added") {
-    baseTemplate += `\n\nA pull request for the metadata files is open. You can view the pull request:\n\n[![Metadata](https://img.shields.io/badge/View_PR-6366f1.svg)](${prInfo.link})`;
+  const metadataPrUrl = await dbInstance.codeMetadata.findUnique({
+    where: { repository_id: repository.id },
+  });
+
+  if (metadataPrUrl?.pull_request_url) {
+    baseTemplate += `\n\nA pull request for the metadata files is open. You can view the pull request:\n\n[![Metadata](https://img.shields.io/badge/View_PR-6366f1.svg)](${metadataPrUrl.pull_request_url})`;
   }
 
   baseTemplate = await applyCWLTemplate(

From fc0c53b009f2e60e25604e07d9637247a85d3f80 Mon Sep 17 00:00:00 2001
From: slugb0t <wheresdorian@gmail.com>
Date: Sat, 12 Oct 2024 16:43:40 -0700
Subject: [PATCH 25/27] fix: :bug: :card_file_box: patches for the commit
 tracking information

---
 bot/index.js         | 103 ++++++++++++++++++++++++++++---------------
 bot/license/index.js |   3 ++
 2 files changed, 71 insertions(+), 35 deletions(-)

diff --git a/bot/index.js b/bot/index.js
index 99fbf395..2ffa9f79 100644
--- a/bot/index.js
+++ b/bot/index.js
@@ -246,12 +246,15 @@ export default async (app, { getRouter }) => {
     const emptyRepo = await isRepoEmpty(context, owner, repository.name);
 
     const latestCommitInfo = {
-      latest_commit_date: context.payload.head_commit.timestamp,
-      latest_commit_message: context.payload.head_commit.message,
-      latest_commit_sha: context.payload.head_commit.id,
-      latest_commit_url: context.payload.head_commit.url,
+      latest_commit_date: context.payload.head_commit.timestamp || "",
+      latest_commit_message: context.payload.head_commit.message || "",
+      latest_commit_sha: context.payload.head_commit.id || "",
+      latest_commit_url: context.payload.head_commit.url || "",
     };
 
+    // consola.info("Latest commit info:", latestCommitInfo);
+    // consola.info("Context.payload.head_commit:", context.payload.head_commit);
+
     let fullCodefairRun = false;
 
     const installation = await db.installation.findUnique({
@@ -271,7 +274,7 @@ export default async (app, { getRouter }) => {
       );
 
       if (installation?.action_count > 0) {
-        const result = await db.installation.update({
+        const response = await db.installation.update({
           data: {
             action_count: {
               set:
@@ -287,13 +290,16 @@ export default async (app, { getRouter }) => {
           where: { id: repository.id },
         });
 
-        console.log(result);
+        if (installation?.action_count === 0) {
+          fullCodefairRun = true;
+        }
 
-        return;
-      }
+        // console.log(result);
+        console.log("Updated installation:", response);
 
-      if (installation?.action_count === 1) {
-        db.installation.update({
+        return;
+      } else {
+        const response = await db.installation.update({
           data: {
             action_count: 0,
             latest_commit_date: latestCommitInfo.latest_commit_date,
@@ -303,8 +309,7 @@ export default async (app, { getRouter }) => {
           },
           where: { id: repository.id },
         });
-
-        fullCodefairRun = true;
+        console.log("Updated installation:", response);
       }
     }
 
@@ -459,12 +464,34 @@ export default async (app, { getRouter }) => {
     const prLink = context.payload.pull_request.html_url;
     const definedPRTitles = [
       "feat: ✨ LICENSE file added",
-      "feat: ✨ metadata files added",
+      "feat: ✨ Add code metadata files",
     ];
 
     const emptyRepo = await isRepoEmpty(context, owner, repository.name);
 
-    await verifyInstallationAnalytics(context, repository);
+    // Get the latest commit information if repo is not empty
+    const latestCommitInfo = {};
+    if (!emptyRepo) {
+      // Get the name of the main branch
+      const mainBranch = await getDefaultBranch(context, owner, repository.name);
+      // Gather the latest commit to main info
+      const latestCommit = await context.octokit.repos.getCommit({
+        owner,
+        ref: mainBranch,
+        repo: repository.name,
+      });
+
+      latestCommitInfo.latest_commit_sha = latestCommit.data.sha || "";
+      latestCommitInfo.latest_commit_message =
+        latestCommit.data.commit.message || "";
+      latestCommitInfo.latest_commit_url = latestCommit.data.html_url || "";
+      latestCommitInfo.latest_commit_date =
+        latestCommit.data.commit.committer.date || "";
+    }
+
+    consola.info("Latest commit info:", latestCommitInfo);
+
+    await verifyInstallationAnalytics(context, repository, 0, latestCommitInfo);
 
     const installation = await db.installation.findUnique({
       where: {
@@ -473,30 +500,9 @@ export default async (app, { getRouter }) => {
     });
 
     if (installation?.action_count > 0) {
-      db.installation.update({
-        data: {
-          action_count: {
-            set:
-              installation.action_count - 1 < 0
-                ? 0
-                : installation.action_count - 1,
-          },
-        },
-        where: { id: repository.id },
-      });
       return;
     }
 
-    if (installation?.action_count === 0) {
-      consola.info("Removing action limit for", repository.name);
-      db.installation.update({
-        data: {
-          action_count: 0,
-        },
-        where: { id: repository.id },
-      });
-    }
-
     if (definedPRTitles.includes(prTitle)) {
       const prInfo = {
         title: prTitle,
@@ -1035,6 +1041,33 @@ export default async (app, { getRouter }) => {
     }
   });
 
+  app.on("pull_request.closed", async (context) => {
+    // Remove the PR url from the database
+    if (context.payload.pull_request.title === "feat: ✨ LICENSE file added" && context.payload.pull_request.merged) {
+      await db.licenseRequest.update({
+        data: {
+          pull_request_url: "",
+        },
+        where: {
+          repository_id: context.payload.repository.id,
+        },
+      });
+    }
+
+    if (context.payload.pull_request.title === "feat: ✨ Add code metadata files" && context.payload.pull_request.merged) {
+      await db.codeMetadata.update({
+        data: {
+          pull_request_url: "",
+        },
+        where: {
+          repository_id: context.payload.repository.id,
+        },
+      });
+    }
+  }
+);
+
+
   // When a release is published
   // app.on("release.drafted", async (context) => {
   //   // Check if the release was made using the Codefair dashboard
diff --git a/bot/license/index.js b/bot/license/index.js
index 7cc4ffd0..0522bc18 100644
--- a/bot/license/index.js
+++ b/bot/license/index.js
@@ -194,6 +194,9 @@ export async function applyLicenseTemplate(
       "base64",
     ).toString("utf-8");
 
+    // consola.info("License id:", licenseId);
+    // consola.info("License content:", licenseContent);
+
     if (
       licenseRequest.data.license.spdx_id === "no-license" ||
       licenseRequest.data.license.spdx_id === "NOASSERTION"

From 18fdc7e04d125d31bd54b4191a39e71caed84789 Mon Sep 17 00:00:00 2001
From: Sanjay Soundarajan <sanjay.16@live.com>
Date: Sat, 12 Oct 2024 17:35:04 -0700
Subject: [PATCH 26/27] fix: minor style fixes

---
 ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue b/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue
index 7bb42783..5f11cec5 100644
--- a/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue
+++ b/ui/pages/dashboard/[owner]/[repo]/release/zenodo.vue
@@ -364,7 +364,7 @@ const checkForZenodoPublishProgress = () => {
       headers: useRequestHeaders(["cookie"]),
       method: "GET",
     })
-      .then(async (response) => {
+      .then((response) => {
         if (response.zenodoWorkflowStatus !== "inProgress") {
           zenodoPublishStatus.value = response.zenodoWorkflowStatus;
           zenodoPublishDOI.value = response.zenodoDoi;
@@ -1130,7 +1130,7 @@ onBeforeUnmount(() => {
       <template #footer>
         <n-flex justify="space-between">
           <NuxtLink :to="`https://doi.org/${zenodoPublishDOI}`" target="_blank">
-            <n-button type="primary" v-if="zenodoPublishStatus === 'published'">
+            <n-button v-if="zenodoPublishStatus === 'published'" type="primary">
               <template #icon>
                 <Icon name="simple-icons:zenodo" size="16" />
               </template>

From 4f8a4a4e496a338161ea23d55887d601bbcabff5 Mon Sep 17 00:00:00 2001
From: slugb0t <wheresdorian@gmail.com>
Date: Mon, 14 Oct 2024 17:26:47 -0700
Subject: [PATCH 27/27] refactor: :recycle: two versions of release button

---
 bot/archival/index.js | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/bot/archival/index.js b/bot/archival/index.js
index 51a3cc20..964ad6e4 100644
--- a/bot/archival/index.js
+++ b/bot/archival/index.js
@@ -28,6 +28,7 @@ export async function applyArchivalTemplate(
     }
   });
   const alreadyReleaseText = ` of your software was successfully released on GitHub and archived on Zenodo. You can view the Zenodo archive by clicking the button below:`
+  const firstReleaseBadgeButton = `[![Create Release](https://img.shields.io/badge/Create_Release-dc2626.svg)](${badgeURL})`
   const releaseBadgeButton = `[![Create Release](https://img.shields.io/badge/Create_Release-00bcd4.svg)](${badgeURL})`
   const newReleaseText = `To make your software FAIR, it is necessary to archive it in an archival repository like Zenodo every time you make a release. When you are ready to make your next release, click the "Create release" button below to easily create a FAIR release where your metadata files are updated (including with a DOI) before creating a GitHub release and archiving it.\n\n`
 
@@ -44,7 +45,7 @@ export async function applyArchivalTemplate(
     //     user_id: "",
     //   }
     // });
-    baseTemplate += `${archiveTitle} ❌\n\n${newReleaseText}\n\n${releaseBadgeButton}`;
+    baseTemplate += `${archiveTitle} ❌\n\n${newReleaseText}\n\n${firstReleaseBadgeButton}`;
   } else {
     // entry does exist, update the existing one
     await dbInstance.zenodoDeposition.update({