run_analysis_once.py

#!/usr/bin/env python3
"""Initialize DeepGraph and process one paper end-to-end."""

from config import WORKSPACE_DIR, PDF_CACHE_DIR
from db.database import init_db
from db.evidence_graph import backfill_entity_resolutions
from db.taxonomy import seed_taxonomy, backfill_result_taxonomy
from orchestrator.pipeline import ingest_papers, process_single_paper
from db import database as db


def main() -> None:
    WORKSPACE_DIR.mkdir(parents=True, exist_ok=True)
    PDF_CACHE_DIR.mkdir(parents=True, exist_ok=True)

    init_db()
    seed_taxonomy()
    backfill_result_taxonomy()
    backfill_entity_resolutions()

    if db.fetchone("SELECT COUNT(*) as c FROM papers")["c"] == 0:
        ingest_papers(max_papers=1)

    paper = db.fetchone("SELECT id FROM papers ORDER BY published_date DESC LIMIT 1")
    if not paper:
        print("No papers available to process.", flush=True)
        return

    paper_id = paper["id"]
    print(f"processing {paper_id}", flush=True)
    print(process_single_paper(paper_id), flush=True)


if __name__ == "__main__":
    main()