feat: initial commit - oncology literature search platform

OncoLit: a multi-tenant oncology literature search, feed, and collaboration platform. Built with FastAPI + Vue 3 + PostgreSQL. Includes PubMed pipeline, drug approvals, AI summaries, and systematic review tools.
2026-07-27 07:59:18 +08:00
commit a6cd99a4ca
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+"""Additional integrity checks"""
+import asyncio
+from sqlalchemy import text
+from sqlalchemy.ext.asyncio import create_async_engine
+
+DATABASE_URL = 'postgresql+asyncpg://scilit:scilit_prod_2026@postgres:5432/scilit'
+
+async def main():
+    engine = create_async_engine(DATABASE_URL)
+    async with engine.connect() as conn:
+        # 1. Records where article_date has real month/day but pub_date is Jan-01
+        r = await conn.execute(text("""
+            SELECT id, pmid, pub_date, article_date FROM global_literature
+            WHERE EXTRACT(MONTH FROM pub_date)=1 AND EXTRACT(DAY FROM pub_date)=1
+            AND article_date IS NOT NULL 
+            AND NOT (EXTRACT(MONTH FROM article_date)=1 AND EXTRACT(DAY FROM article_date)=1)
+            LIMIT 20
+        """))
+        print('=== Records where article_date can fix pub_date ===')
+        for row in r:
+            print(f'  pmid={row.pmid} pub_date={row.pub_date} article_date={row.article_date}')
+
+        # 2. Check for records with NULL pub_year but valid pub_date
+        r = await conn.execute(text("""
+            SELECT COUNT(*) FROM global_literature
+            WHERE pub_date IS NOT NULL AND pub_year IS NULL
+        """))
+        print(f'\npub_date set but pub_year NULL: {r.scalar()}')
+
+        # 3. Check for records with NULL pub_date but valid pub_year
+        r = await conn.execute(text("""
+            SELECT COUNT(*) FROM global_literature
+            WHERE pub_date IS NULL AND pub_year IS NOT NULL
+        """))
+        print(f'pub_year set but pub_date NULL: {r.scalar()}')
+
+        # 4. Check if there are records WITHOUT any date info at all
+        r = await conn.execute(text("""
+            SELECT COUNT(*) FROM global_literature
+            WHERE pub_date IS NULL AND pub_year IS NULL AND article_date IS NULL
+        """))
+        print(f'No date info at all: {r.scalar()}')
+        
+        # 5. Latest literature records - sample top 10 for sanity check
+        r = await conn.execute(text("""
+            SELECT pmid, pub_date, pub_year, title FROM global_literature
+            ORDER BY pub_year DESC NULLS LAST, pmid DESC LIMIT 5
+        """))
+        print('\n=== Latest 5 records ===')
+        for row in r:
+            title_short = (row.title or '')[:60]
+            print(f'  PMID={row.pmid} date={row.pub_date} year={row.pub_year} title={title_short}...')
+        
+        # 6. Check for records that are in user_feed but patient hasn't been generated
+        r = await conn.execute(text("""
+            SELECT COUNT(*) FROM user_feed uf
+            WHERE NOT EXISTS (SELECT 1 FROM global_literature gl WHERE gl.id = uf.literature_id)
+        """))
+        print(f'\nUserFeed pointing to non-existent literature: {r.scalar()}')
+        
+    await engine.dispose()
+
+asyncio.run(main())