Connect RAG citations to extended papers and guidelines

cloudflare/src/index.js

@@ -14,7 +14,8 @@ async function hash(s){const b=await crypto.subtle.digest('SHA-256',new TextEnco
 function baseAnswer(q){q=(q||'').toLowerCase();return (KB.find(x=>q.includes(x[0]))?.[1]||'ابتدا ایمنی، شدت علائم، مصرف مواد، خواب، پایبندی و علل طبی بررسی شوند. برای پاسخ دقیق‌تر موضوع و بازه زمانی را بدون اطلاعات هویتی بنویسید.')+'\n\n⚠️ جایگزین ارزیابی پزشک نیست.'}
 function clean(s=''){return String(s).replace(/<[^>]+>/g,' ').replace(/\s+/g,' ').slice(0,4000)}
 async function scanPapers(env){const q=encodeURIComponent('dual diagnosis psychosis substance use treatment');const r=await fetch(`https://api.crossref.org/works?query=${q}&filter=from-pub-date:2023-01-01,until-pub-date:2026-08-06,type:journal-article&select=DOI,title,abstract,container-title,published,published-print,URL&sort=relevance&order=desc&rows=20`,{headers:{'user-agent':'DualDiagnosisEvidenceBot/1.0 (mailto:research@example.invalid)'}});if(!r.ok)throw Error('Crossref '+r.status);const items=(await r.json()).message.items;let n=0;for(const x of items){const doi=x.DOI||x.URL;if(!doi)continue;const title=clean(x.title?.[0]||'بدون عنوان'),abstract=clean(x.abstract||''),journal=clean(x['container-title']?.[0]||''),parts=x['published-print']?.['date-parts']?.[0]||x.published?.['date-parts']?.[0]||[],published=parts.join('-'),url=x.URL||`https://doi.org/${doi}`;await env.DB.prepare('INSERT INTO articles(doi,title,abstract,journal,published,url,source,fetched_at) VALUES(?,?,?,?,?,?,?,?) ON CONFLICT(doi) DO UPDATE SET title=excluded.title,abstract=excluded.abstract,journal=excluded.journal,published=excluded.published,url=excluded.url,fetched_at=excluded.fetched_at').bind(doi,title,abstract,journal,published,url,'Crossref',new Date().toISOString()).run();n++}return n}
-async function papersFor(env,q){const lower=(q||'').toLowerCase(),map={'روان':'psychosis','سایکوز':'psychosis','ماده':'substance','اعتیاد':'addiction','لغزش':'relapse','خودکشی':'suicide','کانابیس':'cannabis','حشیش':'cannabis','درمان':'treatment'};const expanded=lower+' '+Object.entries(map).filter(([fa])=>lower.includes(fa)).map(x=>x[1]).join(' ');const terms=expanded.split(/\s+/).filter(x=>x.length>3).slice(-6);if(!terms.length)return (await env.DB.prepare('SELECT title,abstract,journal,published,url FROM articles ORDER BY published DESC LIMIT 5').all()).results;const where=terms.map(()=>'(lower(title) LIKE ? OR lower(abstract) LIKE ?)').join(' OR '),bind=terms.flatMap(t=>[`%${t}%`,`%${t}%`]);const found=(await env.DB.prepare(`SELECT title,abstract,journal,published,url FROM articles WHERE ${where} ORDER BY published DESC LIMIT 5`).bind(...bind).all()).results;return found.length?found:(await env.DB.prepare('SELECT title,abstract,journal,published,url FROM articles ORDER BY published DESC LIMIT 5').all()).results}
+async function papersFor(env,q){const lower=(q||'').toLowerCase(),map={'روان':'psychosis','سایکوز':'psychosis','ماده':'substance','اعتیاد':'addiction','لغزش':'relapse','خودکشی':'suicide','کانابیس':'cannabis','حشیش':'cannabis','درمان':'treatment','خانواده':'family','اوردوز':'overdose'};const expanded=lower+' '+Object.entries(map).filter(([fa])=>lower.includes(fa)).map(x=>x[1]).join(' ');const terms=expanded.split(/\s+/).filter(x=>x.length>3).slice(-6);if(!terms.length)return (await env.DB.prepare('SELECT title,abstract,journal,year AS published,url,corpus,treatment_tags FROM research_papers ORDER BY cited_by_count DESC LIMIT 5').all()).results;const where=terms.map(()=>'(lower(title) LIKE ? OR lower(abstract) LIKE ? OR lower(treatment_tags) LIKE ?)').join(' OR '),bind=terms.flatMap(t=>[`%${t}%`,`%${t}%`,`%${t}%`]);const found=(await env.DB.prepare(`SELECT title,abstract,journal,year AS published,url,corpus,treatment_tags FROM research_papers WHERE ${where} ORDER BY cited_by_count DESC LIMIT 5`).bind(...bind).all()).results;return found.length?found:(await env.DB.prepare('SELECT title,abstract,journal,year AS published,url,corpus,treatment_tags FROM research_papers ORDER BY cited_by_count DESC LIMIT 5').all()).results}
+async function guidelinesFor(env,q){const lower=(q||'').toLowerCase(),keys=['opioid','methadone','stimulant','overdose','harm','psychosis','treatment','الکل','متادون','افیون','محرک','اوردوز','کاهش آسیب'];const terms=keys.filter(x=>lower.includes(x));if(!terms.length)return (await env.GUIDELINES_DB.prepare('SELECT title,organization,year,url,tags,status FROM guidelines ORDER BY year DESC LIMIT 3').all()).results;const where=terms.map(()=>'(lower(title) LIKE ? OR lower(tags) LIKE ?)').join(' OR '),bind=terms.flatMap(t=>[`%${t}%`,`%${t}%`]);return (await env.GUIDELINES_DB.prepare(`SELECT title,organization,year,url,tags,status FROM guidelines WHERE ${where} ORDER BY year DESC LIMIT 3`).bind(...bind).all()).results}
 async function handle(req,env){const u=new URL(req.url);if(req.method==='OPTIONS')return new Response(null,{headers:{'access-control-allow-origin':'*','access-control-allow-headers':'content-type'}});if(u.pathname==='/')return new Response(HTML,{headers:{'content-type':'text/html;charset=utf-8','x-content-type-options':'nosniff'}});
 if(u.pathname==='/api/dashboard'){const [a,o,h,al,ar,p]=await Promise.all([env.DB.prepare('SELECT count(*) n FROM assessments').first(),env.DB.prepare("SELECT count(*) n FROM alerts WHERE status='open'").first(),env.DB.prepare("SELECT count(*) n FROM assessments WHERE level IN ('بالا','خیلی بالا','بحرانی')").first(),env.DB.prepare('SELECT created_at,patient_id,score,level FROM assessments ORDER BY created_at DESC LIMIT 30').all(),env.DB.prepare("SELECT created_at,patient_id,level,status FROM alerts WHERE status='open' ORDER BY created_at DESC LIMIT 30").all(),env.DB.prepare('SELECT count(*) n FROM articles').first()]);return json({stats:{assessments:a.n,openAlerts:o.n,highRisk:h.n,articles:p.n},assessments:al.results,alerts:ar.results})}
 if(u.pathname==='/api/articles')return json({articles:(await env.DB.prepare('SELECT title,journal,published,url,source FROM articles ORDER BY published DESC LIMIT 50').all()).results});
@@ -27,6 +28,6 @@ if(req.method==='POST'&&u.pathname==='/api/academy/certificate'){const d=await r
 if(u.pathname.startsWith('/api/certificate/')){const code=u.pathname.split('/').pop(),c=await env.DB.prepare('SELECT audience,issued_at,modules_count,verification_code FROM certificates WHERE verification_code=?').bind(code).first();return c?json({valid:true,...c,notice:'Educational participation certificate; not a clinical license.'}):json({valid:false},404)}
 if(req.method==='POST'&&u.pathname==='/api/admin/scan'){if(req.headers.get('authorization')!==`Bearer ${env.ADMIN_TOKEN}`)return json({error:'unauthorized'},401);return json({imported:await scanPapers(env)})}
 if(req.method==='POST'&&u.pathname==='/api/risk'){const d=await req.json();let score=0;for(const k in W)score+=Math.max(0,Math.min(4,+d[k]||0))*W[k];let level=score>=45?'خیلی بالا':score>=28?'بالا':score>=14?'متوسط':'پایین';if(+d.suicide===4||+d.withdrawal===4)level='بحرانی';const actions={بحرانی:'ارزیابی فوری حضوری/اورژانس؛ بیمار تنها نماند.','خیلی بالا':'بازبینی همان‌روز توسط روان‌پزشک.',بالا:'تماس با تیم درمان طی ۲۴ ساعت.',متوسط:'بازبینی بالینی طی ۷۲ ساعت.',پایین:'ادامه پایش برنامه‌ریزی‌شده.'};const pid=await hash(env.PATIENT_SALT+':'+(d.patientRef||crypto.randomUUID())),id=crypto.randomUUID(),now=new Date().toISOString();await env.DB.prepare('INSERT INTO assessments VALUES(?,?,?,?,?,?)').bind(id,pid,now,score,level,JSON.stringify(d)).run();if(['بالا','خیلی بالا','بحرانی'].includes(level))await env.DB.prepare('INSERT INTO alerts VALUES(?,?,?,?,?,?)').bind(crypto.randomUUID(),id,pid,now,level,'open').run();return json({id,score,level,action:actions[level],storage:'Cloudflare D1',disclaimer:'جایگزین ارزیابی پزشک نیست.'})}
-if(req.method==='POST'&&u.pathname==='/api/chat'){const started=Date.now(),body=await req.json(),question=body.question,role=['admin','doctor','family','patient'].includes(body.role)?body.role:'patient';if(!question)return json({error:'لطفاً سؤال را بنویسید.'},400);const key=await hash(role+':'+question.trim().toLowerCase()),cached=await env.DB.prepare("SELECT answer,source FROM rag_cache WHERE cache_key=? AND created_at>datetime('now','-7 days')").bind(key).first();if(cached){await env.DB.prepare('INSERT INTO api_usage(endpoint,provider,latency_ms,success,created_at) VALUES(?,?,?,?,?)').bind('/api/chat','cache',Date.now()-started,1,new Date().toISOString()).run();return json({...cached,role,cached:true})}const papers=await papersFor(env,question),context=papers.map((p,i)=>`${i+1}. ${p.title} (${p.journal}, ${p.published}) ${p.abstract||''}`).join('\n').slice(0,8000),roleGuide={patient:'برای بیمار با زبان ساده، امیدبخش و بدون دوز یا جزئیات حساس پاسخ بده.',family:'برای خانواده، اقدامات حمایتی، علائم هشدار و زمان تماس با پزشک را ساده توضیح بده؛ دوز نده.',doctor:'برای پزشک با زبان فنی، محدودیت شواهد و DOIها پاسخ بده؛ دوز فقط اگر در شواهد تأییدشده حاضر است و هرگز نسخه فردی نده.',admin:'فقط درباره عملکرد سامانه، داده، منابع و پایش پاسخ بده؛ توصیه درمانی نده.'},messages=[{role:'system',content:`به فارسی و فقط بر اساس شواهد داده‌شده پاسخ بده. شماره مقاله را ذکر کن، عدم قطعیت را صریح بگو و جایگزین پزشک نشو. ${roleGuide[role]}`},{role:'user',content:`نقش مخاطب: ${role}\nپرسش: ${question}\nشواهد:\n${context}`}];let answer,provider='Cloudflare Workers AI';try{const x=await env.AI.run('@cf/meta/llama-3.1-8b-instruct-fast',{messages,max_tokens:500});answer=x.response}catch(e){provider='Hugging Face RAG';try{const r=await fetch('https://router.huggingface.co/v1/chat/completions',{method:'POST',headers:{Authorization:'Bearer '+env.HF_TOKEN,'content-type':'application/json'},body:JSON.stringify({model:env.HF_MODEL,messages,max_tokens:500})});const x=await r.json();answer=x.choices?.[0]?.message?.content}catch{}}if(!answer){answer=baseAnswer(question);provider='RAG داخلی'}await Promise.all([env.DB.prepare('INSERT OR REPLACE INTO rag_cache VALUES(?,?,?,?)').bind(key,answer,provider,new Date().toISOString()).run(),env.DB.prepare('INSERT INTO api_usage(endpoint,provider,latency_ms,success,created_at) VALUES(?,?,?,?,?)').bind('/api/chat',provider,Date.now()-started,1,new Date().toISOString()).run()]);return json({answer,role,source:provider,papers,latency_ms:Date.now()-started})}
+if(req.method==='POST'&&u.pathname==='/api/chat'){const started=Date.now(),body=await req.json(),question=body.question,role=['admin','doctor','family','patient'].includes(body.role)?body.role:'patient';if(!question)return json({error:'لطفاً سؤال را بنویسید.'},400);const key=await hash(role+':'+question.trim().toLowerCase()),cached=await env.DB.prepare("SELECT answer,source FROM rag_cache WHERE cache_key=? AND created_at>datetime('now','-7 days')").bind(key).first();const [papers,guidelines]=await Promise.all([papersFor(env,question),guidelinesFor(env,question)]),context=(papers.map((p,i)=>`مقاله ${i+1}. ${p.title} (${p.journal}, ${p.published}) ${p.abstract||''} URL:${p.url}`).join('\n')+'\n'+guidelines.map((g,i)=>`استاندارد ${i+1}. ${g.title} (${g.organization}, ${g.year}) URL:${g.url} status:${g.status}`).join('\n')).slice(0,10000),roleGuide={patient:'برای بیمار با زبان ساده، امیدبخش و بدون دوز یا جزئیات حساس پاسخ بده.',family:'برای خانواده، اقدامات حمایتی، علائم هشدار و زمان تماس با پزشک را ساده توضیح بده؛ دوز نده.',doctor:'برای پزشک با زبان فنی، محدودیت شواهد و DOIها پاسخ بده؛ دوز فقط اگر در شواهد تأییدشده حاضر است و هرگز نسخه فردی نده.',admin:'فقط درباره عملکرد سامانه، داده، منابع و پایش پاسخ بده؛ توصیه درمانی نده.'},messages=[{role:'system',content:`به فارسی و فقط بر اساس شواهد داده‌شده پاسخ بده. شماره مقاله را ذکر کن، عدم قطعیت را صریح بگو و جایگزین پزشک نشو. ${roleGuide[role]}`},{role:'user',content:`نقش مخاطب: ${role}\nپرسش: ${question}\nشواهد:\n${context}`}];let answer,provider='Cloudflare Workers AI';try{const x=await env.AI.run('@cf/meta/llama-3.1-8b-instruct-fast',{messages,max_tokens:500});answer=x.response}catch(e){provider='Hugging Face RAG';try{const r=await fetch('https://router.huggingface.co/v1/chat/completions',{method:'POST',headers:{Authorization:'Bearer '+env.HF_TOKEN,'content-type':'application/json'},body:JSON.stringify({model:env.HF_MODEL,messages,max_tokens:500})});const x=await r.json();answer=x.choices?.[0]?.message?.content}catch{}}if(!answer){answer=baseAnswer(question);provider='RAG داخلی'}await Promise.all([env.DB.prepare('INSERT OR REPLACE INTO rag_cache VALUES(?,?,?,?)').bind(key,answer,provider,new Date().toISOString()).run(),env.DB.prepare('INSERT INTO api_usage(endpoint,provider,latency_ms,success,created_at) VALUES(?,?,?,?,?)').bind('/api/chat',provider,Date.now()-started,1,new Date().toISOString()).run()]);return json({answer,role,source:provider,papers,guidelines,latency_ms:Date.now()-started})}
 return json({error:'مسیر پیدا نشد'},404)}
 export default{fetch(req,env){return handle(req,env).catch(e=>json({error:'خطای داخلی',detail:String(e)},500))},async scheduled(event,env,ctx){ctx.waitUntil(scanPapers(env))}};

data/articles/open_access_pdf_manifest.jsonl

@@ -0,0 +1,199 @@
+{"openalex_id": "https://openalex.org/W3164324796", "title": "Age at onset of mental disorders worldwide: large-scale meta-analysis of 192 epidemiological studies", "corpus": "international", "doi": "https://doi.org/10.1038/s41380-021-01161-7", "is_oa": true, "oa_status": "hybrid", "pdf_url": "https://www.nature.com/articles/s41380-021-01161-7.pdf", "landing_page_url": "https://doi.org/10.1038/s41380-021-01161-7", "content_length_bytes": 1695820}
+{"openalex_id": "https://openalex.org/W3048791385", "title": "Mental Health, Substance Use, and Suicidal Ideation During the COVID-19 Pandemic — United States, June 24–30, 2020", "corpus": "international", "doi": "https://doi.org/10.15585/mmwr.mm6932a1", "is_oa": true, "oa_status": "diamond", "pdf_url": "https://www.cdc.gov/mmwr/volumes/69/wr/pdfs/mm6932a1-H.pdf", "landing_page_url": "https://doi.org/10.15585/mmwr.mm6932a1", "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W4308369850", "title": "CDC Clinical Practice Guideline for Prescribing Opioids for Pain<b>—</b>United States, 2022", "corpus": "international", "doi": "https://doi.org/10.15585/mmwr.rr7103a1", "is_oa": true, "oa_status": "diamond", "pdf_url": "https://www.cdc.gov/mmwr/volumes/71/rr/pdfs/rr7103a1-H.pdf", "landing_page_url": "https://doi.org/10.15585/mmwr.rr7103a1", "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W3012261821", "title": "Drug and Opioid-Involved Overdose Deaths — United States, 2017–2018", "corpus": "international", "doi": "https://doi.org/10.15585/mmwr.mm6911a4", "is_oa": true, "oa_status": "diamond", "pdf_url": "https://www.cdc.gov/mmwr/volumes/69/wr/pdfs/mm6911a4-H.pdf", "landing_page_url": "https://doi.org/10.15585/mmwr.mm6911a4", "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W3087653702", "title": "A meta‐review of “lifestyle psychiatry”: the role of exercise, smoking, diet and sleep in the prevention and treatment of mental disorders", "corpus": "international", "doi": "https://doi.org/10.1002/wps.20773", "is_oa": true, "oa_status": "green", "pdf_url": null, "landing_page_url": "https://kclpure.kcl.ac.uk/portal/en/publications/6d90a68c-7ccd-442a-8f79-c74b296c12fb", "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W3127222350", "title": "Trends and Geographic Patterns in Drug and Synthetic Opioid Overdose Deaths — United States, 2013–2019", "corpus": "international", "doi": "https://doi.org/10.15585/mmwr.mm7006a4", "is_oa": true, "oa_status": "diamond", "pdf_url": "https://www.cdc.gov/mmwr/volumes/70/wr/pdfs/mm7006a4-H.pdf", "landing_page_url": "https://doi.org/10.15585/mmwr.mm7006a4", "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W3005454586", "title": "Comparative Effectiveness of Different Treatment Pathways for Opioid Use Disorder", "corpus": "international", "doi": "https://doi.org/10.1001/jamanetworkopen.2019.20622", "is_oa": true, "oa_status": "gold", "pdf_url": "https://jamanetwork.com/journals/jamanetworkopen/articlepdf/2760032/wakeman_2020_oi_190774.pdf", "landing_page_url": "https://doi.org/10.1001/jamanetworkopen.2019.20622", "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W3160915496", "title": "The rise of illicit fentanyls, stimulants and the fourth wave of the opioid overdose crisis", "corpus": "international", "doi": "https://doi.org/10.1097/yco.0000000000000717", "is_oa": true, "oa_status": "hybrid", "pdf_url": null, "landing_page_url": "https://doi.org/10.1097/yco.0000000000000717", "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W4225885267", "title": "Schizophrenia", "corpus": "international", "doi": "https://doi.org/10.1016/s0140-6736(21)01730-x", "is_oa": true, "oa_status": "bronze", "pdf_url": "http://www.thelancet.com/article/S014067362101730X/pdf", "landing_page_url": "https://doi.org/10.1016/s0140-6736(21)01730-x", "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W3082177965", "title": "The American Psychiatric Association Practice Guideline for the Treatment of Patients With Schizophrenia", "corpus": "international", "doi": "https://doi.org/10.1176/appi.ajp.2020.177901", "is_oa": true, "oa_status": "bronze", "pdf_url": "https://ajp.psychiatryonline.org/doi/pdf/10.1176/appi.ajp.2020.177901", "landing_page_url": "https://doi.org/10.1176/appi.ajp.2020.177901", "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W4317811195", "title": "Cognitive impairment in schizophrenia: aetiology, pathophysiology, and treatment", "corpus": "international", "doi": "https://doi.org/10.1038/s41380-023-01949-9", "is_oa": true, "oa_status": "hybrid", "pdf_url": "https://www.nature.com/articles/s41380-023-01949-9.pdf", "landing_page_url": "https://doi.org/10.1038/s41380-023-01949-9", "content_length_bytes": 1845018}
+{"openalex_id": "https://openalex.org/W3000475066", "title": "Opioid use disorder", "corpus": "international", "doi": "https://doi.org/10.1038/s41572-019-0137-5", "is_oa": false, "oa_status": "closed", "pdf_url": null, "landing_page_url": null, "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W2999889141", "title": "Dopamine and glutamate in schizophrenia: biology, symptoms and treatment", "corpus": "international", "doi": "https://doi.org/10.1002/wps.20693", "is_oa": true, "oa_status": "bronze", "pdf_url": "https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/wps.20693", "landing_page_url": "https://doi.org/10.1002/wps.20693", "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W3165633131", "title": "Association of Opioid Agonist Treatment With All-Cause Mortality and Specific Causes of Death Among People With Opioid Dependence", "corpus": "international", "doi": "https://doi.org/10.1001/jamapsychiatry.2021.0976", "is_oa": true, "oa_status": "bronze", "pdf_url": "https://jamanetwork.com/journals/jamapsychiatry/articlepdf/2780655/jamapsychiatry_santo_2021_oi_210027_1647372061.14743.pdf", "landing_page_url": "https://doi.org/10.1001/jamapsychiatry.2021.0976", "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W3131397527", "title": "Cannabis use and cannabis use disorder", "corpus": "international", "doi": "https://doi.org/10.1038/s41572-021-00247-4", "is_oa": true, "oa_status": "green", "pdf_url": null, "landing_page_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/8655458", "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W3005496517", "title": "The changing opioid crisis: development, challenges and opportunities", "corpus": "international", "doi": "https://doi.org/10.1038/s41380-020-0661-4", "is_oa": true, "oa_status": "green", "pdf_url": null, "landing_page_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/7398847", "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W3013064929", "title": "The transition to compulsion in addiction", "corpus": "international", "doi": "https://doi.org/10.1038/s41583-020-0289-z", "is_oa": true, "oa_status": "green", "pdf_url": null, "landing_page_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/7610550", "content_length_bytes": null}
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+{"openalex_id": "https://openalex.org/W2615519130", "title": "A Narrative Review of Acute Adult Poisoning in Iran.", "corpus": "iran_affiliated", "doi": null, "is_oa": true, "oa_status": "green", "pdf_url": null, "landing_page_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/5523040", "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W2797671008", "title": "Islam and cannabis: Legalisation and religious debate in Iran", "corpus": "iran_affiliated", "doi": "https://doi.org/10.1016/j.drugpo.2018.03.009", "is_oa": true, "oa_status": "hybrid", "pdf_url": "https://www.sciencedirect.com/science/article/pii/S0955395918300793/pdf", "landing_page_url": "https://doi.org/10.1016/j.drugpo.2018.03.009", "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W4380991962", "title": "Challenges in addiction-affected families: a systematic review of qualitative studies", "corpus": "iran_affiliated", "doi": "https://doi.org/10.1186/s12888-023-04927-1", "is_oa": true, "oa_status": "gold", "pdf_url": "https://bmcpsychiatry.biomedcentral.com/counter/pdf/10.1186/s12888-023-04927-1", "landing_page_url": "https://doi.org/10.1186/s12888-023-04927-1", "content_length_bytes": 2175437}
+{"openalex_id": "https://openalex.org/W4289745178", "title": "RETRACTED ARTICLE: Quality of life and its correlated factors among patients with substance use disorders: a systematic review and meta-analysis", "corpus": "iran_affiliated", "doi": "https://doi.org/10.1186/s13690-022-00940-0", "is_oa": true, "oa_status": "gold", "pdf_url": "https://archpublichealth.biomedcentral.com/counter/pdf/10.1186/s13690-022-00940-0", "landing_page_url": "https://doi.org/10.1186/s13690-022-00940-0", "content_length_bytes": 2343757}
+{"openalex_id": "https://openalex.org/W4294921688", "title": "Nanobiosensors for detection of opioids: A review of latest advancements", "corpus": "iran_affiliated", "doi": "https://doi.org/10.1016/j.ejpb.2022.08.017", "is_oa": true, "oa_status": "hybrid", "pdf_url": "https://www.sciencedirect.com/science/article/pii/S0939641122001825/pdf", "landing_page_url": "https://doi.org/10.1016/j.ejpb.2022.08.017", "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W3154562936", "title": "Smoking, alcohol and opioids effect on coronary microcirculation: an update overview", "corpus": "iran_affiliated", "doi": "https://doi.org/10.1186/s12872-021-01990-y", "is_oa": true, "oa_status": "gold", "pdf_url": "https://bmccardiovascdisord.biomedcentral.com/track/pdf/10.1186/s12872-021-01990-y", "landing_page_url": "https://doi.org/10.1186/s12872-021-01990-y", "content_length_bytes": 1263266}
+{"openalex_id": "https://openalex.org/W4391445622", "title": "Stigma toward substance use disorders: a multinational perspective and call for action", "corpus": "iran_affiliated", "doi": "https://doi.org/10.3389/fpsyt.2024.1295818", "is_oa": true, "oa_status": "gold", "pdf_url": "https://www.frontiersin.org/journals/psychiatry/articles/10.3389/fpsyt.2024.1295818/pdf", "landing_page_url": "https://doi.org/10.3389/fpsyt.2024.1295818", "content_length_bytes": 550414}
+{"openalex_id": "https://openalex.org/W4383710830", "title": "Suicidality risk after using cannabis and cannabinoids: An umbrella review", "corpus": "iran_affiliated", "doi": "https://doi.org/10.1080/19585969.2023.2231466", "is_oa": true, "oa_status": "diamond", "pdf_url": "https://www.tandfonline.com/doi/pdf/10.1080/19585969.2023.2231466?needAccess=true&role=button", "landing_page_url": "https://doi.org/10.1080/19585969.2023.2231466", "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W4292466668", "title": "Effects of sleep quality on the association between problematic internet use and quality of life in people with substance use disorder", "corpus": "iran_affiliated", "doi": "https://doi.org/10.1192/bjo.2022.557", "is_oa": true, "oa_status": "gold", "pdf_url": "https://www.cambridge.org/core/services/aop-cambridge-core/content/view/2E9652D7C6B8EC63A262917B08934699/S2056472422005579a.pdf/div-class-title-effects-of-sleep-quality-on-the-association-between-problematic-internet-use-and-quality-of-life-in-people-with-substance-use-disorder-div.pdf", "landing_page_url": "https://doi.org/10.1192/bjo.2022.557", "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W4407196018", "title": "Cannabis Use Disorder Emergency Department Visits and Hospitalizations and 5-Year Mortality", "corpus": "iran_affiliated", "doi": "https://doi.org/10.1001/jamanetworkopen.2024.57852", "is_oa": true, "oa_status": "gold", "pdf_url": "https://jamanetwork.com/journals/jamanetworkopen/articlepdf/2829914/myran_2025_oi_241619_1741789723.16626.pdf", "landing_page_url": "https://doi.org/10.1001/jamanetworkopen.2024.57852", "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W2411323064", "title": "Perspectives on neurocognitive rehabilitation as an adjunct treatment for addictive disorders", "corpus": "iran_affiliated", "doi": "https://doi.org/10.1016/bs.pbr.2015.07.022", "is_oa": false, "oa_status": "closed", "pdf_url": null, "landing_page_url": null, "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W2787687656", "title": "Using Metabolomics to Investigate Biomarkers of Drug Addiction", "corpus": "iran_affiliated", "doi": "https://doi.org/10.1016/j.molmed.2017.12.005", "is_oa": true, "oa_status": "bronze", "pdf_url": "http://www.cell.com/article/S1471491417302289/pdf", "landing_page_url": "https://doi.org/10.1016/j.molmed.2017.12.005", "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W2981435075", "title": "Orexin-1 Receptor Signaling in Ventral Pallidum Regulates Motivation for the Opioid Remifentanil", "corpus": "iran_affiliated", "doi": "https://doi.org/10.1523/jneurosci.0255-19.2019", "is_oa": true, "oa_status": "bronze", "pdf_url": "https://www.jneurosci.org/content/jneuro/39/49/9831.full.pdf", "landing_page_url": "https://doi.org/10.1523/jneurosci.0255-19.2019", "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W2769941763", "title": "Cognitive rehabilitation for individuals with opioid use disorder: A randomized controlled trial", "corpus": "iran_affiliated", "doi": "https://doi.org/10.1080/09602011.2017.1391103", "is_oa": false, "oa_status": "closed", "pdf_url": null, "landing_page_url": null, "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W2799355503", "title": "Opioid Use Disorder Induces Oxidative Stress and Inflammation The Attenuating Effect of Methadone Maintenance Treatment", "corpus": "iran_affiliated", "doi": "https://doi.org/10.5281/zenodo.17080915", "is_oa": true, "oa_status": "green", "pdf_url": null, "landing_page_url": "https://doaj.org/article/ff27ac1b0082474898c99945b7082869", "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W3022536673", "title": "Mathematical models of HIV/AIDS and drug addiction in prisons", "corpus": "iran_affiliated", "doi": "https://doi.org/10.1140/epjp/s13360-020-00400-0", "is_oa": false, "oa_status": "closed", "pdf_url": null, "landing_page_url": null, "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W2972570320", "title": "Persistent effects of the orexin-1 receptor antagonist SB-334867 on motivation for the fast acting opioid remifentanil", "corpus": "iran_affiliated", "doi": "https://doi.org/10.1016/j.brainres.2019.146461", "is_oa": true, "oa_status": "green", "pdf_url": null, "landing_page_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/7069781", "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W3164167749", "title": "Crystal methamphetamine use in British Columbia, Canada: A cross-sectional study of people who access harm reduction services", "corpus": "iran_affiliated", "doi": "https://doi.org/10.1371/journal.pone.0252090", "is_oa": true, "oa_status": "gold", "pdf_url": "https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0252090&type=printable", "landing_page_url": "https://doi.org/10.1371/journal.pone.0252090", "content_length_bytes": 587412}
+{"openalex_id": "https://openalex.org/W2498896755", "title": "Effectiveness of Mindfulness-Based Relapse Prevention for Co-occurring Substance Use and Depression Disorders", "corpus": "iran_affiliated", "doi": "https://doi.org/10.1007/s12671-016-0576-y", "is_oa": false, "oa_status": "closed", "pdf_url": null, "landing_page_url": null, "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W2257494416", "title": "The effect of different concentrations of TDZ and BA on in vitro regeneration of Iranian cannabis (Cannabis sativa) using cotyledon and epicotyl explants", "corpus": "iran_affiliated", "doi": "https://doi.org/10.22058/jpmb.2015.15371", "is_oa": false, "oa_status": "closed", "pdf_url": null, "landing_page_url": null, "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W2903865762", "title": "Single high-dose buprenorphine for opioid craving during withdrawal", "corpus": "iran_affiliated", "doi": "https://doi.org/10.1186/s13063-018-3055-z", "is_oa": true, "oa_status": "gold", "pdf_url": "https://trialsjournal.biomedcentral.com/counter/pdf/10.1186/s13063-018-3055-z", "landing_page_url": "https://doi.org/10.1186/s13063-018-3055-z", "content_length_bytes": 795104}
+{"openalex_id": "https://openalex.org/W3028959192", "title": "Crosstalk between Sleep Disturbance and Opioid Use Disorder: A Narrative Review.", "corpus": "iran_affiliated", "doi": "https://doi.org/10.22122/ahj.v12i2.249", "is_oa": true, "oa_status": "green", "pdf_url": null, "landing_page_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/7395935", "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W2201776622", "title": "Predictors of Continued Use of Extended-Released Naltrexone (XR-NTX) for Opioid-Dependence: An Analysis of Heroin and Non-Heroin Opioid Users in Los Angeles County", "corpus": "iran_affiliated", "doi": "https://doi.org/10.1016/j.jsat.2015.12.004", "is_oa": false, "oa_status": "closed", "pdf_url": null, "landing_page_url": null, "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W2760952519", "title": "Gender differences in substance use patterns and disorders among an Iranian patient sample receiving methadone maintenance treatment", "corpus": "iran_affiliated", "doi": "https://doi.org/10.19082/5354", "is_oa": true, "oa_status": "gold", "pdf_url": "http://www.ephysician.ir/2017/5354.pdf", "landing_page_url": "https://doi.org/10.19082/5354", "content_length_bytes": 189904}
+{"openalex_id": "https://openalex.org/W3165196861", "title": "Deep brain stimulation of the nucleus accumbens/ventral capsule for severe and intractable opioid and benzodiazepine use disorder.", "corpus": "iran_affiliated", "doi": "https://doi.org/10.1037/pha0000453", "is_oa": true, "oa_status": "hybrid", "pdf_url": null, "landing_page_url": "https://doi.org/10.1037/pha0000453", "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W3015638401", "title": "The impact of motivational interviewing on relapse to substance use among women in Iran: a randomized clinical trial", "corpus": "iran_affiliated", "doi": "https://doi.org/10.1186/s12888-020-02561-9", "is_oa": true, "oa_status": "gold", "pdf_url": "https://bmcpsychiatry.biomedcentral.com/track/pdf/10.1186/s12888-020-02561-9", "landing_page_url": "https://doi.org/10.1186/s12888-020-02561-9", "content_length_bytes": 672815}
+{"openalex_id": "https://openalex.org/W2949416517", "title": "Understanding the relapse process: exploring Iranian women’s substance use experiences", "corpus": "iran_affiliated", "doi": "https://doi.org/10.1186/s13011-019-0216-3", "is_oa": true, "oa_status": "gold", "pdf_url": "https://substanceabusepolicy.biomedcentral.com/track/pdf/10.1186/s13011-019-0216-3", "landing_page_url": "https://doi.org/10.1186/s13011-019-0216-3", "content_length_bytes": 666502}
+{"openalex_id": "https://openalex.org/W4220755145", "title": "Setting the policy agenda for the treatment of substance use disorders in Iran", "corpus": "iran_affiliated", "doi": "https://doi.org/10.1186/s12954-022-00612-w", "is_oa": true, "oa_status": "gold", "pdf_url": "https://harmreductionjournal.biomedcentral.com/track/pdf/10.1186/s12954-022-00612-w", "landing_page_url": "https://doi.org/10.1186/s12954-022-00612-w", "content_length_bytes": 1024854}
+{"openalex_id": "https://openalex.org/W3162981813", "title": "The Role of Impulsivity and Sensitivity to Reward in Dropout of Addiction Treatment in Heroin Addicts.", "corpus": "iran_affiliated", "doi": "https://doi.org/10.22122/ahj.v13i1.290", "is_oa": true, "oa_status": "green", "pdf_url": null, "landing_page_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/8080170", "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W2743169768", "title": "Association of OPRK1 gene polymorphisms with opioid dependence in addicted men undergoing methadone treatment in an Iranian population", "corpus": "iran_affiliated", "doi": "https://doi.org/10.1080/10550887.2017.1361724", "is_oa": false, "oa_status": "closed", "pdf_url": null, "landing_page_url": null, "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W2969946430", "title": "Adolescent nicotine challenge promotes the future vulnerability to opioid addiction: Involvement of lateral paragigantocellularis neurons", "corpus": "iran_affiliated", "doi": "https://doi.org/10.1016/j.lfs.2019.116784", "is_oa": false, "oa_status": "closed", "pdf_url": null, "landing_page_url": null, "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W2996338856", "title": "Effectiveness of Emotion Regulation Group Therapy on Craving, Emotion Problems, and Marital Satisfaction in Patients with Substance Use Disorders: A Randomized Clinical Trial", "corpus": "iran_affiliated", "doi": "https://doi.org/10.18502/ijps.v14i4.1978", "is_oa": true, "oa_status": "gold", "pdf_url": null, "landing_page_url": "https://doi.org/10.18502/ijps.v14i4.1978", "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W4409605265", "title": "A systematic review on the role of EEG and fMRI-Neurofeedback training in the treatment of substance use disorders and behavioral addiction", "corpus": "iran_affiliated", "doi": "https://doi.org/10.1016/j.psychres.2025.116474", "is_oa": false, "oa_status": "closed", "pdf_url": null, "landing_page_url": null, "content_length_bytes": null}
+{"openalex_id": "https://openalex.org/W3175183069", "title": "Comparison of self-reported substance use with biological testing among treatment-seeking patients with opioid use disorder", "corpus": "iran_affiliated", "doi": "https://doi.org/10.1016/j.jsat.2021.108555", "is_oa": false, "oa_status": "closed", "pdf_url": null, "landing_page_url": null, "content_length_bytes": null}

data/articles/open_access_pdf_report.json

@@ -0,0 +1,10 @@
+{
+  "records": 199,
+  "open_access_records": 167,
+  "direct_pdf_urls": 128,
+  "sizes_known": 48,
+  "known_total_bytes": 73418942,
+  "known_total_mb": 70.02,
+  "estimated_total_mb_if_avg": 186.71,
+  "notice": "Only legal OA URLs; no paywall bypass. Size is an HTTP estimate."
+}

scripts/discover_open_access_pdfs.py

@@ -0,0 +1,32 @@
+"""Discover legal Open Access PDF URLs and estimate sizes; does not bypass paywalls."""
+import concurrent.futures, json, urllib.parse, urllib.request
+from pathlib import Path
+FILES=['data/articles/international_100.jsonl','data/articles/iran_affiliated_100.jsonl']
+def api(ids):
+ f='openalex_id:'+('|'.join(x.rsplit('/',1)[-1] for x in ids));u='https://api.openalex.org/works?filter='+urllib.parse.quote(f)+'&per-page=50&mailto=research@example.invalid'
+ return json.load(urllib.request.urlopen(u,timeout=60))['results']
+def size(url):
+ if not url:return None
+ try:
+  req=urllib.request.Request(url,method='HEAD',headers={'User-Agent':'Mozilla/5.0 research metadata checker'})
+  with urllib.request.urlopen(req,timeout=12) as r:
+   n=r.headers.get('Content-Length');return int(n) if n and n.isdigit() else None
+ except:return None
+def main():
+ rows=[]
+ for f in FILES:rows += [json.loads(x) for x in open(f,encoding='utf-8') if x.strip()]
+ byid={x['openalex_id'].rsplit('/',1)[-1]:x for x in rows}; works=[]
+ ids=list(byid)
+ for i in range(0,len(ids),50):works+=api(ids[i:i+50])
+ manifest=[]
+ for w in works:
+  oid=w['id'].rsplit('/',1)[-1]; base=byid.get(oid,{}); loc=w.get('best_oa_location') or {}; pdf=loc.get('pdf_url')
+  manifest.append({'openalex_id':w['id'],'title':w.get('title'),'corpus':base.get('corpus'),'doi':w.get('doi'),'is_oa':(w.get('open_access') or {}).get('is_oa',False),'oa_status':(w.get('open_access') or {}).get('oa_status'),'pdf_url':pdf,'landing_page_url':loc.get('landing_page_url')})
+ with concurrent.futures.ThreadPoolExecutor(max_workers=12) as ex:
+  sizes=list(ex.map(lambda x:size(x['pdf_url']),manifest))
+ for x,n in zip(manifest,sizes):x['content_length_bytes']=n
+ out=Path('data/articles/open_access_pdf_manifest.jsonl');out.write_text('\n'.join(json.dumps(x,ensure_ascii=False) for x in manifest)+'\n',encoding='utf-8')
+ pdf=[x for x in manifest if x['pdf_url']]; known=[x['content_length_bytes'] for x in pdf if x['content_length_bytes']]
+ report={'records':len(manifest),'open_access_records':sum(x['is_oa'] for x in manifest),'direct_pdf_urls':len(pdf),'sizes_known':len(known),'known_total_bytes':sum(known),'known_total_mb':round(sum(known)/1024/1024,2),'estimated_total_mb_if_avg':round((sum(known)/len(known)*len(pdf))/1024/1024,2) if known else None,'notice':'Only legal OA URLs; no paywall bypass. Size is an HTTP estimate.'}
+ Path('data/articles/open_access_pdf_report.json').write_text(json.dumps(report,ensure_ascii=False,indent=2),encoding='utf-8');print(report)
+if __name__=='__main__':main()