PubMed Monitor #61
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| name: PubMed Monitor | |
| on: | |
| schedule: | |
| # 每天早上 8:17 UTC 运行一次（避开整点） | |
| - cron: '17 8 * * *' | |
| workflow_dispatch: | |
| inputs: | |
| query: | |
| description: 'PubMed 检索词' | |
| required: false | |
| default: '"Speciation"[Mesh] OR "Hybridization, Genetic"[Mesh] OR "Genetic Introgression"[Mesh] OR "Reproductive Isolation"[Mesh] OR "Gene Flow"[Mesh] OR (speciation[Title/Abstract] AND species[Title/Abstract]) OR ("lineage sorting"[Title/Abstract]) OR ("adaptive radiation"[Title/Abstract]) OR ("incipient species"[Title/Abstract])' | |
| type: string | |
| days: | |
| description: '追溯天数' | |
| required: false | |
| default: '7' | |
| type: string | |
| max_papers: | |
| description: '最大文献数（分析前）' | |
| required: false | |
| default: '20' | |
| type: string | |
| concurrency: | |
| group: pubmed-monitor | |
| cancel-in-progress: true | |
| permissions: | |
| issues: write | |
| contents: read | |
| env: | |
| QUERY: ${{ github.event.inputs.query || '"Speciation"[Mesh] OR "Hybridization, Genetic"[Mesh] OR "Genetic Introgression"[Mesh] OR "Reproductive Isolation"[Mesh] OR "Gene Flow"[Mesh] OR (speciation[Title/Abstract] AND species[Title/Abstract]) OR ("lineage sorting"[Title/Abstract]) OR ("adaptive radiation"[Title/Abstract]) OR ("incipient species"[Title/Abstract])' }} | |
| DAYS: ${{ github.event.inputs.days || '7' }} | |
| MAX_PAPERS: ${{ github.event.inputs.max_papers || '20' }} | |
| GH_TOKEN: ${{ secrets.PAT_TOKEN }} | |
| LOG_LEVEL: DEBUG | |
| MCP_LOG_DETAIL: "1" | |
| PROMPT_LOG: "1" | |
| PUBMED_EMAIL: ${{ secrets.PUBMED_EMAIL }} | |
| # Anthropic API 配置 | |
| ANTHROPIC_AUTH_TOKEN: ${{ secrets.ANTHROPIC_AUTH_TOKEN }} | |
| ANTHROPIC_BASE_URL: ${{ secrets.ANTHROPIC_BASE_URL || 'https://api.minimaxi.com/anthropic' }} | |
| ANTHROPIC_MODEL: ${{ secrets.ANTHROPIC_MODEL || 'MiniMax-M2.1' }} | |
| CLAUDE_AGENT_SDK_SKIP_VERSION_CHECK: "true" | |
| jobs: | |
| monitor: | |
| if: github.repository == 'gqy20/IssueLab' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: astral-sh/setup-uv@v7 | |
| with: | |
| python-version: '3.13' | |
| enable-cache: true | |
| - run: uv sync | |
| - name: Run PubMed Monitor | |
| run: | | |
| set -euo pipefail | |
| mkdir -p artifacts/observability | |
| echo "🔍 扫描 PubMed 新文献..." | |
| echo "📊 检索词: ${{ env.QUERY }}" | |
| echo "📅 追溯天数: ${{ env.DAYS }}" | |
| echo "" | |
| uv run python scripts/monitor_pubmed.py \ | |
| --token "${{ env.GH_TOKEN }}" \ | |
| --repo "${{ github.repository }}" \ | |
| --query '${{ env.QUERY }}' \ | |
| --days ${{ env.DAYS }} \ | |
| --max-papers ${{ env.MAX_PAPERS }} \ | |
| --email "${{ env.PUBMED_EMAIL }}" \ | |
| --output artifacts/pubmed_candidates.json \ | |
| --metrics-output artifacts/observability/pubmed_metrics.json \ | |
| 2>&1 | tee artifacts/observability/pubmed_monitor.log | |
| - name: Emit observability summary | |
| if: always() | |
| env: | |
| WF_NAME: ${{ github.workflow }} | |
| JOB_NAME: monitor | |
| RUN_ID: ${{ github.run_id }} | |
| REPO_NAME: ${{ github.repository }} | |
| SHA: ${{ github.sha }} | |
| run: | | |
| set -euo pipefail | |
| mkdir -p artifacts/observability | |
| python - << 'PY' | |
| import json | |
| import os | |
| from datetime import UTC, datetime | |
| from pathlib import Path | |
| metrics_path = Path("artifacts/observability/pubmed_metrics.json") | |
| m = {} | |
| if metrics_path.exists(): | |
| try: | |
| m = json.loads(metrics_path.read_text(encoding="utf-8")) | |
| except Exception: | |
| m = {} | |
| input_count = int(m.get("fetched_count", 0) or 0) | |
| success_count = int(m.get("created_issues", 0) or 0) | |
| failed_count = 0 | |
| skipped_count = 0 | |
| status_raw = str(m.get("status", "")) | |
| failures = [] | |
| if status_raw in {"no_recommendation", "insufficient_candidates", "no_new_after_dedupe", "no_new_papers"}: | |
| skipped_count = 1 | |
| if status_raw == "started": | |
| failures.append({"code": "METRICS_MISSING", "count": 1, "samples": []}) | |
| status = "success" | |
| if failures: | |
| status = "partial" | |
| elif skipped_count > 0 and success_count == 0: | |
| status = "skipped" | |
| payload = { | |
| "schema_version": "v1", | |
| "workflow": os.getenv("WF_NAME"), | |
| "job": os.getenv("JOB_NAME"), | |
| "run_id": os.getenv("RUN_ID"), | |
| "repo": os.getenv("REPO_NAME"), | |
| "sha": os.getenv("SHA"), | |
| "finished_at": datetime.now(UTC).isoformat().replace("+00:00", "Z"), | |
| "metrics": { | |
| "input_count": input_count, | |
| "success_count": success_count, | |
| "failed_count": failed_count, | |
| "skipped_count": skipped_count, | |
| "new_papers_count": int(m.get("new_papers_count", 0) or 0), | |
| "recommended_count": int(m.get("recommended_count", 0) or 0), | |
| "created_issues": int(m.get("created_issues", 0) or 0), | |
| }, | |
| "failures_topn": failures[:5], | |
| "status": status, | |
| } | |
| Path("artifacts/observability/pubmed_monitor__monitor.json").write_text( | |
| json.dumps(payload, ensure_ascii=False, indent=2), encoding="utf-8" | |
| ) | |
| summary = [ | |
| "## Observability (pubmed monitor)", | |
| "", | |
| "| metric | value |", | |
| "|---|---:|", | |
| f"| input_count | {payload['metrics']['input_count']} |", | |
| f"| new_papers_count | {payload['metrics']['new_papers_count']} |", | |
| f"| recommended_count | {payload['metrics']['recommended_count']} |", | |
| f"| created_issues | {payload['metrics']['created_issues']} |", | |
| f"| status | {payload['status']} |", | |
| ] | |
| with open(os.environ["GITHUB_STEP_SUMMARY"], "a", encoding="utf-8") as fh: | |
| fh.write("\n".join(summary) + "\n") | |
| PY | |
| - name: Upload observability artifact | |
| if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: pubmed-monitor-observability-${{ github.run_id }} | |
| path: artifacts/observability/ | |
| retention-days: 14 |