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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.
56 lines
2.7 KiB
Python
56 lines
2.7 KiB
Python
"""Test a batch of 2017 YYYY-01-01 records"""
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import asyncio, httpx, lxml.etree as ET
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from datetime import date
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from sqlalchemy import text
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from sqlalchemy.ext.asyncio import create_async_engine
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DATABASE_URL = 'postgresql+asyncpg://scilit:scilit_prod_2026@postgres:5432/scilit'
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MONTH_MAP = {'jan':1,'january':1,'1':1,'feb':2,'february':2,'2':2,'mar':3,'march':3,'3':3,'apr':4,'april':4,'4':4,'may':5,'5':5,'jun':6,'june':6,'6':6,'jul':7,'july':7,'7':7,'aug':8,'august':8,'8':8,'sep':9,'september':9,'9':9,'oct':10,'october':10,'10':10,'nov':11,'november':11,'11':11,'dec':12,'december':12,'12':12,}
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DAYS = [0,31,29,31,30,31,30,31,31,30,31,30,31]
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def mn(m): return MONTH_MAP.get(m.strip().lower(), 1)
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def cd(m,d,y):
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if d<1: return 1
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md=DAYS[m]
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if m==2 and d==29 and not (y%4==0 and (y%100!=0 or y%400==0)): md=28
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return min(d,md)
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def ppd(elem):
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pde=elem.find('.//PubDate')
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if pde is None: return None
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ye=pde.find('Year'); me=pde.find('Month'); de=pde.find('Day')
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if ye is not None and ye.text:
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y=int(ye.text.strip()); hm=me is not None and me.text; hd=de is not None and de.text
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if not hm and not hd: return None
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m=mn(me.text.strip()) if hm else 1; d=int(de.text.strip()) if hd else 1; d=cd(m,d,y)
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return date(y,m,d)
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return None
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async def main():
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engine = create_async_engine(DATABASE_URL)
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async with engine.connect() as conn:
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r = await conn.execute(text("""SELECT id, pmid, pub_date, pub_year FROM global_literature
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WHERE pub_date IS NOT NULL AND EXTRACT(MONTH FROM pub_date)=1 AND EXTRACT(DAY FROM pub_date)=1
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AND pmid IS NOT NULL AND pub_year = 2017
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ORDER BY pmid ASC LIMIT 200"""))
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rows = r.all()
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await engine.dispose()
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pmids = [str(r.pmid) for r in rows]
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print(f'Testing {len(rows)} 2017 PMIDs: {pmids[0]} ~ {pmids[-1]}')
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async with httpx.AsyncClient(timeout=60) as c:
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resp = await c.get('https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi',params={'db':'pubmed','id':','.join(pmids),'retmode':'xml'})
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root = ET.fromstring(resp.content)
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arts = root.findall('PubmedArticle')
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fixed=0; year_only=0; still_jan01=0
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efetch_map = {}
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for art in arts:
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pmid_e=art.find('MedlineCitation/PMID'); pmid=int(pmid_e.text) if pmid_e is not None else None
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pd=ppd(art)
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if pmid: efetch_map[pmid]=pd
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for row in rows:
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pd=efetch_map.get(row.pmid)
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if pd is None: year_only+=1
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elif pd.month==1 and pd.day==1: still_jan01+=1
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else: fixed+=1
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print(f'Can fix: {fixed}, Year-only: {year_only}, Still Jan-01: {still_jan01}')
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asyncio.run(main())
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