Introduce Paper Add/Update workflows (#460)

Co-authored-by:  dvdkouril <[email protected]>

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1 @@
+blank_issues_enabled: true

.github/ISSUE_TEMPLATE/paper.yml

@@ -0,0 +1,88 @@
+name: "📚 Add or Update a Paper"
+description: "Add or update a paper from Zotero to the HIDIVE website"
+labels: ["paper-bot"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        This template is for adding or updating a paper on the HIDIVE website.
+
+        Upon submission, a **GitHub Action** will start a **pull request** to update the website with the new paper details.
+
+  - type: input
+    id: zotero_id
+    attributes:
+      label: Zotero ID
+      description: >-
+        Enter the Zotero ID from either the HIDIVE Lab [preprint collection](https://www.zotero.org/groups/5145258/hidive/collections/AJKTPNSI)
+        or [publication collection](https://www.zotero.org/groups/5145258/hidive/collections/YGTEVG73).
+        This ID will be used to automatically fetch all publication details from Zotero.
+      placeholder: "e.g., D8YCD6QT"
+    validations:
+      required: true
+
+  - type: input
+    id: preprint
+    attributes:
+      label: Preprint
+      description: >-
+        Enter a Zotero ID or URL for the preprint. **Leave blank if the Zotero ID above is for a preprint**.
+      placeholder: "e.g., A6ZAJIIA or https://arxiv.org/abs/1234.56789"
+
+  - type: markdown
+    attributes:
+      value: |
+        > [!NOTE]
+        > Prefer a preprint Zotero ID above if **updating a preprint to a publication**. It will update the existing website entry.
+
+        ### Optional Fields
+        The following fields are optional. They can be left blank and updated later if needed.
+
+  - type: textarea
+    id: members
+    attributes:
+      label: Lab Members
+      description: "Tag lab members on paper. See the [lab member](https://github.com/hms-dbmi/gehlenborglab-website/tree/main/_members) directory for available identifiers, one per line."
+      placeholder: "nils-gehlenborg\nflat-stanley\njane-doe"
+
+  - type: textarea
+    id: image
+    attributes:
+      label: Image
+      description: "Add an image related to the publication"
+      placeholder: "Drage and drop or paste an image... (ensure it uploads)"
+
+  - type: input
+    id: website
+    attributes:
+      label: Website
+      description: "A URL for a website related to the publication"
+      placeholder: "e.g., https://example.com/publication-website"
+
+  - type: input
+    id: code
+    attributes:
+      label: Code Repository
+      description: "A link for the code related to the publication"
+      placeholder: "e.g., https://github.com/username/repo"
+
+  - type: textarea
+    id: videos
+    attributes:
+      label: Video Resources
+      description: "List video resources related to the publication. Use the format 'Title | URL' for each entry, one per line."
+      placeholder: "Introduction Video | https://example.com/intro\nConference Presentation | https://example.com/presentation"
+
+  - type: textarea
+    id: other_resources
+    attributes:
+      label: Other Resources
+      description: "List other resources related to the publication. Use the format 'Title | URL' for each entry, one per line."
+      placeholder: "Data Repository | https://example.com/data\nSlides | https://example.com/slides"
+
+  - type: textarea
+    id: awards
+    attributes:
+      label: Awards
+      description: "Enter awards for the publication (one per line)"
+      placeholder: "Best Paper Award at XXX\nInnovation Prize Y\nMost Cited Paper 2054"

.github/workflows/deploy.yml

@@ -4,7 +4,7 @@ on: [push, pull_request]
 
 jobs:
   build:
-
+    if: github.repository == 'hms-dbmi/gehlenborglab-website'
     # Available versions:
     # https://docs.github.com/en/free-pro-team@latest/actions/reference/workflow-syntax-for-github-actions#jobsjob_idruns-on
     runs-on: ubuntu-20.04
@@ -57,4 +57,4 @@ jobs:
     - name: Invalidate Cache
       if: ${{ github.event_name == 'push' && github.ref  == 'refs/heads/main' }}
       run: |
-        aws cloudfront create-invalidation --distribution-id ${{secrets.CF_DISTRIBUTION_ID}} --paths "/*"
+        aws cloudfront create-invalidation --distribution-id ${{secrets.CF_DISTRIBUTION_ID}} --paths "/*"

.github/workflows/fetch-papers.yml

@@ -0,0 +1,48 @@
+name: Fetch HIDIVE Papers
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '0 0 * * 1' # Every Monday at 00:00
+
+permissions:
+  contents: write
+  issues: write
+  pull-requests: write
+
+jobs:
+  fetch-papers:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: denoland/setup-deno@v1
+        with:
+          deno-version: v1.x
+
+      - name: Fetch HIDIVE Papers
+        run: deno run -A scripts/fetch-hidive-zotero-items.ts --outdir=assets/papers --issue-file=/tmp/issue-body.md
+
+      - name: Create Pull Request
+        uses: peter-evans/create-pull-request@v7
+        with:
+          commit-message: Fetch HIDIVE Papers
+          title: "Update HIDIVE Papers"
+          branch: hidive-papers
+          body: "This is an automated pull request to update the HIDIVE papers."
+          labels: fetch-papers-bot
+
+      - name: Open or Update Missing Papers Issue
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          # Check if an issue with the label 'fetch-papers-bot' exists
+          ISSUE_NUMBER=$(gh issue list --label fetch-papers-bot --limit 1 --json number --jq '.[0].number')
+
+          if [ -n "$ISSUE_NUMBER" ]; then
+            # Update existing issue
+            gh issue edit $ISSUE_NUMBER --body-file /tmp/issue-body.md
+            echo "Updated existing issue #$ISSUE_NUMBER"
+          else
+            gh issue create --title "Missing HIDIVE Papers" --body-file /tmp/issue-body.md --label fetch-papers-bot
+            echo "Created new issue for missing papers"
+          fi

.github/workflows/update-paper.yml

@@ -0,0 +1,53 @@
+name: Update Paper
+
+on:
+  issues:
+    types: [opened, edited]
+
+permissions:
+  contents: write
+  issues: write
+  pull-requests: write
+
+jobs:
+  process-issue:
+    if: contains(github.event.issue.labels.*.name, 'paper-bot')
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Parse Issue
+        id: parse-issue
+        uses: GrantBirki/[email protected]
+        with:
+          body: ${{ github.event.issue.body }}
+          csv_to_list: false
+
+      - name: Create PR body with Fixes line
+        run: |
+          echo "Fixes #${{ github.event.issue.number }}" > /tmp/pr-body.md
+          echo "" >> /tmp/pr-body.md
+
+      - uses: denoland/setup-deno@v1
+        with:
+          deno-version: v1.x
+
+      - name: Update Paper
+        id: output-issue
+        run: echo ${{ toJson(steps.parse-issue.outputs.json) }} | deno run -A scripts/update-hidive-paper.ts - >> /tmp/pr-body.md
+
+      - name: Extract Zotero ID
+        id: extract-zotero-id
+        run: |
+          ZOTERO_ID=$(echo ${{ toJson(steps.parse-issue.outputs.json) }} | jq -r .zotero_id)
+          echo "zotero-id=$ZOTERO_ID" >> $GITHUB_OUTPUT
+
+      - name: Create Pull Request
+        uses: peter-evans/create-pull-request@v7
+        with:
+          commit-message: Update paper
+          title: "${{ github.event.issue.title }}"
+          branch: "update-paper-${{ steps.extract-zotero-id.outputs.zotero-id }}"
+          body-path: /tmp/pr-body.md
+          labels: paper-bot