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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,17 @@ | ||
| name: Deploy | ||
| on: | ||
| workflow_dispatch: | ||
| jobs: | ||
| deploy: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Run SSH command | ||
| env: | ||
| SSH_PRIVATE_KEY: ${{ secrets.AWS_PEM }} | ||
| HOST: ${{ secrets.AWS_HOST }} | ||
| run: | | ||
| echo $SSH_PRIVATE_KEY | ssh -i /dev/stdin -o StrictHostKeyChecking=no "$HOST" "sh /data/services/restart_bioregistry.sh" | ||
| mkdir -p ~/.ssh | ||
| echo "$SSH_PRIVATE_KEY" > ~/.ssh/id_rsa | ||
| chmod 600 ~/.ssh/id_rsa | ||
| ssh -i ~/.ssh/id_rsa -o StrictHostKeyChecking=no "$HOST" "sh /data/services/restart_bioregistry.sh" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,101 @@ | ||
| name: Run Paper Ranking Script and Update Issue | ||
|
|
||
| on: | ||
| schedule: | ||
| - cron: '0 0 1 * *' # runs on the first day of every month | ||
| workflow_dispatch: | ||
|
|
||
| jobs: | ||
| paper-ranking: | ||
| runs-on: ubuntu-latest | ||
|
|
||
| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v3 | ||
|
|
||
| - name: Set up Python | ||
| uses: actions/setup-python@v3 | ||
| with: | ||
| python-version: "3.12" | ||
|
|
||
| - name: Install dependencies | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| pip install -r src/bioregistry/analysis/paper_ranking_requirements.txt | ||
| - name: Set Date Variables | ||
| id: set-date-variables | ||
| run: | | ||
| end_date=$(date +'%Y-%m-%d') | ||
| start_date=$(date -d "$end_date - 30 days" +'%Y-%m-%d') | ||
| echo "START_DATE=$start_date" >> $GITHUB_ENV | ||
| echo "END_DATE=$end_date" >> $GITHUB_ENV | ||
| - name: Set PYTHONPATH | ||
| run: | | ||
| echo "PYTHONPATH=$PWD/src" >> $GITHUB_ENV | ||
| - name: Run Paper Ranking Script | ||
| id: run-ranking-script | ||
| run: | | ||
| echo "PYTHONPATH=$PYTHONPATH" # Verify PYTHONPATH | ||
| python src/bioregistry/analysis/paper_ranking.py --start-date ${{ env.START_DATE }} --end-date ${{ env.END_DATE }} | ||
| - name: Upload Full List as Artifact | ||
| uses: actions/upload-artifact@v3 | ||
| with: | ||
| name: full-predictions-list-${{ env.START_DATE }}-to-${{ env.END_DATE }} | ||
| path: exports/analyses/paper_ranking/predictions_${{ env.START_DATE }}_to_${{ env.END_DATE }}.tsv | ||
|
|
||
| - name: Find Existing Issue | ||
| id: find-issue | ||
| uses: actions/github-script@v6 | ||
| with: | ||
| github-token: ${{ secrets.GITHUB_TOKEN }} | ||
| script: | | ||
| const { data: issues } = await github.rest.issues.listForRepo({ | ||
| owner: context.repo.owner, | ||
| repo: context.repo.repo, | ||
| state: 'open', | ||
| labels: 'paper-ranking-results' | ||
| }); | ||
| const issue = issues.find(issue => issue.title === 'Potentially relevant papers ranked for curation'); | ||
| return issue ? issue.number : null; | ||
| - name: Create or Update Issue with Comment | ||
| id: create-or-update-issue | ||
| uses: actions/github-script@v6 | ||
| with: | ||
| github-token: ${{ secrets.GITHUB_TOKEN }} | ||
| script: | | ||
| const fs = require('fs'); | ||
| const issueNumber = ${{ steps.find-issue.outputs.result }}; | ||
| const startDate = process.env.START_DATE; | ||
| const endDate = process.env.END_DATE; | ||
| const content = fs.readFileSync(`exports/analyses/paper_ranking/predictions_${startDate}_to_${endDate}.tsv`, 'utf8'); | ||
| const lines = content.split('\n').slice(1, 21); | ||
| const rows = lines.map(line => { | ||
| const [pubmed, title] = line.split('\t'); | ||
| const link = `https://bioregistry.io/pubmed:${pubmed}`; | ||
| return `| [${pubmed}](${link}) | ${title} |`; | ||
| }); | ||
| const tableHeader = '| PubMed ID | Title |\n| --- | --- |\n'; | ||
| const commentBody = `This issue contains monthly updates to an automatically ranked list of PubMed papers as candidates for curation in the Bioregistry. Papers may be relevant in at least three ways: \n(1) as a new prefix for a resource that can be added to the Bioregistry,\n(2) as a provider for an existing prefix, or\n(3) as a new publication for an existing prefix already in the Bioregistry.\n\nThese curations can happen in separate issues and pull requests. The full list of ranked papers can be found [here](https://github.com/${{ github.repository }}/blob/main/exports/analyses/paper_ranking/predictions_${startDate}_to_${endDate}.tsv). If you review any of these papers for relevance, you should edit the curated papers file [here](https://github.com/${{ github.repository }}/blob/main/src/bioregistry/data/curated_papers.tsv); these curations are taken into account when retraining the ranking model.\n\n**New entries for ${startDate} to ${endDate}:**\n\n${tableHeader}${rows.join('\n')}`; | ||
| if (issueNumber) { | ||
| await github.rest.issues.createComment({ | ||
| owner: context.repo.owner, | ||
| repo: context.repo.repo, | ||
| issue_number: issueNumber, | ||
| body: commentBody, | ||
| }); | ||
| } else { | ||
| const response = await github.rest.issues.create({ | ||
| owner: context.repo.owner, | ||
| repo: context.repo.repo, | ||
| title: 'Potentially relevant papers ranked for curation', | ||
| body: `${commentBody}`, | ||
| labels: ['paper-ranking-results'], | ||
| }); | ||
| core.setOutput('issue-number', response.data.number); | ||
| } |
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