revert to og

backend/main.py

@@ -40,98 +40,49 @@ GROQ_MODEL   = "llama-3.3-70b-versatile"
 GROQ_API_KEY = os.environ.get("GROQ_API_KEY", "")
 
 # ── Prompts ───────────────────────────────────────────────────────────────────
-EXTRACTION_SYSTEM = """
-You are an expert in bioengineering and experimental reproducibility.
-
-Extract structured protocol parameters from the Methods section of a research paper.
-
-Return ONLY valid JSON:
-
+EXTRACTION_SYSTEM = """Extract protocol parameters from this research paper. Return ONLY valid JSON:
 {
-  "title": "",
-  "authors": "",
-  "year": "",
-  "protocol_type": "",
+  "title": "paper title",
+  "authors": "first author et al.",
+  "year": "year",
+  "protocol_type": "e.g. Western blot / ELISA / PCR",
   "parameters": {
-    "reagents": [],
-    "cell_lines": [],
-    "organisms": [],
-    "temperatures": [],
-    "timings": [],
-    "concentrations": [],
-    "equipment": [],
-    "buffers": [],
-    "selection": [],
-    "analysis_pipeline": [],
-    "other": []
+    "reagents": [{"name": "...", "concentration": "...", "vendor": "..."}],
+    "cell_lines": [{"name": "...", "culture_conditions": "...", "serum": "..."}],
+    "temperatures": [{"step": "...", "value": "...", "unit": "C"}],
+    "timings": [{"step": "...", "duration": "..."}],
+    "equipment": [{"name": "...", "settings": "..."}],
+    "buffers": [{"name": "...", "composition": "...", "pH": "..."}],
+    "antibodies": [{"target": "...", "dilution": "...", "vendor": "..."}],
+    "other": [{"parameter": "...", "value": "..."}]
   }
-}
-
-Guidelines:
-
-- Extract exact numerical values with units
-- Preserve scientific names exactly as written
-- Include concentrations, temperatures, durations, and volumes
-- If a value is missing, write "Not specified"
-- Do not summarize or infer missing data
-- Focus on experimentally relevant parameters only
-"""
-
-COMPARISON_SYSTEM = """
-You are a senior scientist evaluating experimental reproducibility.
-
-Compare protocols from multiple research papers and identify methodological contradictions.
-
-Return ONLY valid JSON:
+}"""
 
+COMPARISON_SYSTEM = """You are an expert in bioengineering reproducibility and experimental methodology.
+Compare protocols from multiple research papers and identify ALL methodological contradictions.
+Return ONLY valid JSON (no markdown fences, no extra text) using this schema:
 {
-  "protocol_type": "",
+  "protocol_type": "detected protocol type",
   "contradictions": [
     {
-      "parameter": "",
-      "category": "",
+      "parameter": "parameter name",
+      "category": "reagents|cell_lines|temperatures|timings|equipment|buffers|antibodies|other",
       "severity": "high|medium|low",
-      "values": {
-        "paper_0": "",
-        "paper_1": ""
-      },
-      "explanation": ""
+      "values": {"paper_0": "value from paper 1", "paper_1": "value from paper 2"},
+      "explanation": "why this is a contradiction and its likely impact on reproducibility"
     }
   ],
-  "ranked_issues": [],
+  "ranked_issues": [
+    {"rank": 1, "parameter": "...", "severity": "high|medium|low", "brief": "one-sentence impact"}
+  ],
   "optimal_protocol": {
-    "rationale": "",
-    "parameters": []
+    "rationale": "overall recommendation rationale",
+    "parameters": [
+      {"label": "parameter name", "value": "recommended value", "reason": "why this is optimal"}
+    ]
   },
-  "summary": {
-    "total_contradictions": 0,
-    "high": 0,
-    "medium": 0,
-    "low": 0
-  }
-}
-
-Rules:
-
-1. A contradiction exists when the same parameter has different numerical values.
-2. Always report exact numbers with units.
-3. Ignore parameters that appear in only one paper.
-4. Do not compare unrelated reagents or buffers.
-5. Focus on parameters that affect reproducibility.
-
-Severity guide:
-
-HIGH:
-- affects experimental outcome
-- changes biological behavior
-- alters measurement conditions
-
-MEDIUM:
-- affects efficiency or data quality
-
-LOW:
-- minor procedural differences
-"""
+  "summary": {"total_contradictions": 0, "high": 0, "medium": 0, "low": 0}
+}"""
 
 # ── Core helpers ──────────────────────────────────────────────────────────────