cite-agent 1.3.5__py3-none-any.whl → 1.3.7__py3-none-any.whl

src/services/research_service/critical_paper_detector.py

@@ -1,577 +0,0 @@
-# src/services/research_service/critical_paper_detector.py
-
-import logging
-import re
-import math
-from typing import List, Dict, Any, Set, Optional
-from collections import Counter
-import networkx as nx  # type: ignore[import]
-from datetime import datetime, timezone
-
-# Configure structured logging
-logger = logging.getLogger(__name__)
-
-
-def _utc_timestamp() -> str:
-    return datetime.now(timezone.utc).isoformat()
-
-class CriticalPaperDetector:
-    """
-    Enhanced critical paper detector with comprehensive error handling, security, and observability.
-    
-    Features:
-    - Secure paper analysis and scoring
-    - Input validation and sanitization
-    - Comprehensive error handling and fallback logic
-    - Structured logging and monitoring
-    - Protection against injection attacks
-    - Multi-factor paper importance scoring
-    """
-    
-    def __init__(self, db_operations=None):
-        """
-        Initialize detector with enhanced security and error handling.
-        
-        Args:
-            db_operations: Optional database operations instance
-            
-        Raises:
-            ValueError: If initialization fails
-        """
-        try:
-            #logger.info("Initializing CriticalPaperDetector with enhanced security")
-            
-            self.db = db_operations
-            
-            # Define importance indicators with enhanced coverage
-            self.method_terms = {
-                "novel", "methodology", "approach", "framework", "technique", 
-                "algorithm", "protocol", "procedure", "process", "method",
-                "implementation", "design", "architecture", "strategy",
-                "paradigm", "model", "system", "mechanism", "solution"
-            }
-            
-            self.result_terms = {
-                "significant", "breakthrough", "discovery", "finding",
-                "evidence", "proves", "demonstrates", "shows", "reveals",
-                "establishes", "confirms", "validates", "supports", "indicates",
-                "suggests", "implies", "concludes", "determines", "identifies"
-            }
-            
-            self.contradiction_terms = {
-                "contrary", "opposed", "conflict", "contradiction", "inconsistent",
-                "challenge", "dispute", "unlike", "differs", "contrast",
-                "disagreement", "debate", "controversy", "question", "doubt",
-                "skepticism", "criticism", "limitation", "weakness", "flaw"
-            }
-            
-            #logger.info("CriticalPaperDetector initialized successfully")
-            
-        except Exception as e:
-            logger.error(f"Failed to initialize CriticalPaperDetector: {str(e)}")
-            raise
-    
-    def _validate_papers(self, papers: List[Dict[str, Any]]) -> None:
-        """
-        Validate papers list for security and safety.
-        
-        Args:
-            papers: Papers list to validate
-            
-        Raises:
-            ValueError: If papers list is invalid
-        """
-        if not isinstance(papers, list):
-            raise ValueError("Papers must be a list")
-        
-        if len(papers) > 1000:  # Reasonable limit
-            raise ValueError("Too many papers (max 1000)")
-        
-        for i, paper in enumerate(papers):
-            if not isinstance(paper, dict):
-                raise ValueError(f"Paper at index {i} must be a dictionary")
-            
-            # Validate required fields
-            if "id" not in paper:
-                raise ValueError(f"Paper at index {i} missing required 'id' field")
-            
-            paper_id = str(paper["id"])
-            if len(paper_id) > 100:
-                raise ValueError(f"Paper ID at index {i} too long (max 100 characters)")
-            
-            # Check for potentially dangerous content in text fields
-            text_fields = ["title", "abstract", "summary"]
-            for field in text_fields:
-                if field in paper and paper[field]:
-                    content = str(paper[field])
-                    if len(content) > 10000:  # Reasonable limit
-                        raise ValueError(f"Paper {field} at index {i} too long (max 10000 characters)")
-    
-    def _validate_threshold(self, threshold_percentage: int) -> None:
-        """
-        Validate threshold percentage.
-        
-        Args:
-            threshold_percentage: Threshold percentage to validate
-            
-        Raises:
-            ValueError: If threshold is invalid
-        """
-        if not isinstance(threshold_percentage, int):
-            raise ValueError("Threshold percentage must be an integer")
-        
-        if threshold_percentage < 1 or threshold_percentage > 50:
-            raise ValueError("Threshold percentage must be between 1 and 50")
-    
-    def _sanitize_text(self, text: str, max_length: int = 10000) -> str:
-        """
-        Sanitize text to prevent injection attacks.
-        
-        Args:
-            text: Text to sanitize
-            max_length: Maximum allowed length
-            
-        Returns:
-            Sanitized text
-        """
-        if not isinstance(text, str):
-            return ""
-        
-        if len(text) > max_length:
-            text = text[:max_length]
-        
-        # Basic XSS protection
-        sanitized = text.replace('<', '&lt;').replace('>', '&gt;')
-        
-        # Remove null bytes and other control characters
-        sanitized = ''.join(char for char in sanitized if ord(char) >= 32 or char in '\n\r\t')
-        
-        return sanitized.strip()
-    
-    async def identify_critical_papers(self, papers: List[Dict[str, Any]], 
-                                    threshold_percentage: int = 20) -> List[Dict[str, Any]]:
-        """
-        Identify critical papers with enhanced error handling and security.
-        
-        Args:
-            papers: List of paper dictionaries with metadata
-            threshold_percentage: Percentage of papers to mark as critical
-            
-        Returns:
-            List of critical papers with scores
-            
-        Raises:
-            ValueError: If inputs are invalid
-        """
-        try:
-            # Input validation
-            self._validate_papers(papers)
-            self._validate_threshold(threshold_percentage)
-            
-            if not papers:
-                #logger.info("No papers provided for critical analysis")
-                return []
-            
-            #logger.info(f"Analyzing {len(papers)} papers for critical importance (threshold: {threshold_percentage}%)")
-            
-            # Calculate scores for all papers with error handling
-            paper_scores = {}
-            for i, paper in enumerate(papers):
-                try:
-                    score = self._calculate_paper_score(paper)
-                    paper_scores[paper["id"]] = score
-                except Exception as e:
-                    logger.warning(f"Error calculating score for paper {i}: {str(e)}")
-                    paper_scores[paper["id"]] = 0.0  # Default score
-            
-            # Determine threshold based on percentage
-            num_critical = max(1, int(len(papers) * threshold_percentage / 100))
-            
-            # Get top scoring papers
-            top_papers = sorted(
-                [(paper_id, score) for paper_id, score in paper_scores.items()],
-                key=lambda x: x[1],
-                reverse=True
-            )[:num_critical]
-            
-            # Format results with error handling
-            results = []
-            for paper_id, score in top_papers:
-                try:
-                    paper_data = next((p for p in papers if p["id"] == paper_id), None)
-                    if paper_data:
-                        results.append({
-                            "paper_id": paper_id,
-                            "title": self._sanitize_text(paper_data.get("title", "Unknown"), max_length=200),
-                            "score": round(score, 2),
-                            "factors": self._get_factor_breakdown(paper_data, score),
-                            "analyzed_at": _utc_timestamp()
-                        })
-                except Exception as e:
-                    logger.warning(f"Error formatting result for paper {paper_id}: {str(e)}")
-                    continue
-            
-            #logger.info(f"Successfully identified {len(results)} critical papers")
-            return results
-            
-        except ValueError as e:
-            logger.error(f"Invalid input for critical paper identification: {str(e)}")
-            raise
-        except Exception as e:
-            logger.error(f"Error identifying critical papers: {str(e)}")
-            return []
-    
-    def _calculate_paper_score(self, paper: Dict[str, Any]) -> float:
-        """
-        Calculate importance score for a paper with enhanced error handling.
-        
-        Args:
-            paper: Paper dictionary with metadata
-            
-        Returns:
-            Numerical score (higher = more important)
-        """
-        try:
-            score = 0.0
-            
-            # Factor 1: Citation impact (if available)
-            try:
-                citation_score = self._calculate_citation_score(paper)
-                score += citation_score * 0.25  # 25% weight
-            except Exception as e:
-                logger.warning(f"Error calculating citation score: {str(e)}")
-                score += 0.0
-            
-            # Factor 2: Recency
-            try:
-                recency_score = self._calculate_recency_score(paper)
-                score += recency_score * 0.15  # 15% weight
-            except Exception as e:
-                logger.warning(f"Error calculating recency score: {str(e)}")
-                score += 5.0  # Default middle score
-            
-            # Factor 3: Title and abstract significance
-            try:
-                significance_score = self._calculate_significance_score(paper)
-                score += significance_score * 0.20  # 20% weight
-            except Exception as e:
-                logger.warning(f"Error calculating significance score: {str(e)}")
-                score += 0.0
-            
-            # Factor 4: Methodology novelty
-            try:
-                methodology_score = self._calculate_methodology_score(paper)
-                score += methodology_score * 0.20  # 20% weight
-            except Exception as e:
-                logger.warning(f"Error calculating methodology score: {str(e)}")
-                score += 0.0
-            
-            # Factor 5: Contradiction potential
-            try:
-                contradiction_score = self._calculate_contradiction_score(paper)
-                score += contradiction_score * 0.20  # 20% weight
-            except Exception as e:
-                logger.warning(f"Error calculating contradiction score: {str(e)}")
-                score += 0.0
-            
-            return max(0.0, min(10.0, score))  # Ensure score is between 0 and 10
-            
-        except Exception as e:
-            logger.error(f"Error calculating paper score: {str(e)}")
-            return 0.0
-    
-    def _calculate_citation_score(self, paper: Dict[str, Any]) -> float:
-        """
-        Calculate score based on citation count with enhanced error handling.
-        
-        Args:
-            paper: Paper dictionary
-            
-        Returns:
-            Citation score
-        """
-        try:
-            citation_count = paper.get("citation_count", 0)
-            
-            # Validate citation count
-            if not isinstance(citation_count, (int, float)):
-                return 0.0
-            
-            citation_count = max(0, int(citation_count))
-            
-            # Log-scale to prevent extremely cited papers from dominating
-            if citation_count > 0:
-                return min(10.0, 2.0 * math.log10(citation_count + 1))
-            return 0.0
-            
-        except Exception as e:
-            logger.warning(f"Error calculating citation score: {str(e)}")
-            return 0.0
-    
-    def _calculate_recency_score(self, paper: Dict[str, Any]) -> float:
-        """
-        Calculate score based on paper recency with enhanced error handling.
-        
-        Args:
-            paper: Paper dictionary
-            
-        Returns:
-            Recency score
-        """
-        try:
-            year = paper.get("year")
-            
-            # Try to extract year from various fields
-            if not year:
-                # Try published_date
-                if paper.get("published_date"):
-                    year_match = re.search(r'20\d\d', str(paper.get("published_date", "")))
-                    if year_match:
-                        year = int(year_match.group(0))
-                
-                # Try publication_date
-                if not year and paper.get("publication_date"):
-                    year_match = re.search(r'20\d\d', str(paper.get("publication_date", "")))
-                    if year_match:
-                        year = int(year_match.group(0))
-            
-            if not year:
-                return 5.0  # Middle score if unknown
-                
-            # Convert to int if it's a string
-            if isinstance(year, str):
-                try:
-                    year = int(year)
-                except ValueError:
-                    return 5.0
-            
-            # Validate year range
-            current_year = datetime.now().year
-            if year < 1900 or year > current_year + 1:
-                return 5.0  # Invalid year, use middle score
-            
-            # Scoring by recency
-            years_old = current_year - year
-            
-            if years_old <= 1:
-                return 10.0  # Very recent (0-1 years)
-            elif years_old <= 3:
-                return 8.0   # Recent (1-3 years)
-            elif years_old <= 5:
-                return 6.0   # Somewhat recent (3-5 years)
-            elif years_old <= 10:
-                return 4.0   # Older but still relevant (5-10 years)
-            else:
-                return 2.0   # Much older (>10 years)
-                
-        except Exception as e:
-            logger.warning(f"Error calculating recency score: {str(e)}")
-            return 5.0  # Default middle score
-    
-    def _calculate_significance_score(self, paper: Dict[str, Any]) -> float:
-        """
-        Calculate score based on title and abstract significance indicators with enhanced error handling.
-        
-        Args:
-            paper: Paper dictionary
-            
-        Returns:
-            Significance score
-        """
-        try:
-            title = self._sanitize_text(paper.get("title", ""), max_length=1000).lower()
-            abstract = self._sanitize_text(paper.get("abstract", ""), max_length=5000).lower()
-            
-            combined_text = title + " " + abstract
-            
-            # Check for significant result terms
-            result_count = sum(1 for term in self.result_terms if term in combined_text)
-            
-            # Score based on significance indicators
-            score = min(10.0, result_count * 2.0)
-            
-            return score
-            
-        except Exception as e:
-            logger.warning(f"Error calculating significance score: {str(e)}")
-            return 0.0
-    
-    def _calculate_methodology_score(self, paper: Dict[str, Any]) -> float:
-        """
-        Calculate score based on methodology innovation indicators with enhanced error handling.
-        
-        Args:
-            paper: Paper dictionary
-            
-        Returns:
-            Methodology score
-        """
-        try:
-            title = self._sanitize_text(paper.get("title", ""), max_length=1000).lower()
-            abstract = self._sanitize_text(paper.get("abstract", ""), max_length=5000).lower()
-            
-            combined_text = title + " " + abstract
-            
-            # Check for methodology terms
-            method_count = sum(1 for term in self.method_terms if term in combined_text)
-            
-            # Score based on methodology indicators
-            score = min(10.0, method_count * 2.0)
-            
-            return score
-            
-        except Exception as e:
-            logger.warning(f"Error calculating methodology score: {str(e)}")
-            return 0.0
-    
-    def _calculate_contradiction_score(self, paper: Dict[str, Any]) -> float:
-        """
-        Calculate score based on contradiction/challenge indicators with enhanced error handling.
-        
-        Args:
-            paper: Paper dictionary
-            
-        Returns:
-            Contradiction score
-        """
-        try:
-            title = self._sanitize_text(paper.get("title", ""), max_length=1000).lower()
-            abstract = self._sanitize_text(paper.get("abstract", ""), max_length=5000).lower()
-            
-            combined_text = title + " " + abstract
-            
-            # Check for contradiction terms
-            contradiction_count = sum(1 for term in self.contradiction_terms if term in combined_text)
-            
-            # Score based on contradiction indicators
-            score = min(10.0, contradiction_count * 2.0)
-            
-            return score
-            
-        except Exception as e:
-            logger.warning(f"Error calculating contradiction score: {str(e)}")
-            return 0.0
-    
-    def _get_factor_breakdown(self, paper: Dict[str, Any], total_score: float) -> Dict[str, Any]:
-        """
-        Get detailed breakdown of scoring factors with enhanced error handling.
-        
-        Args:
-            paper: Paper dictionary
-            total_score: Total calculated score
-            
-        Returns:
-            Factor breakdown dictionary
-        """
-        try:
-            factors = {}
-            
-            # Calculate individual factor scores
-            try:
-                factors["citation_impact"] = round(self._calculate_citation_score(paper) * 0.25, 2)
-            except Exception:
-                factors["citation_impact"] = 0.0
-            
-            try:
-                factors["recency"] = round(self._calculate_recency_score(paper) * 0.15, 2)
-            except Exception:
-                factors["recency"] = 0.0
-            
-            try:
-                factors["significance"] = round(self._calculate_significance_score(paper) * 0.20, 2)
-            except Exception:
-                factors["significance"] = 0.0
-            
-            try:
-                factors["methodology"] = round(self._calculate_methodology_score(paper) * 0.20, 2)
-            except Exception:
-                factors["methodology"] = 0.0
-            
-            try:
-                factors["contradiction_potential"] = round(self._calculate_contradiction_score(paper) * 0.20, 2)
-            except Exception:
-                factors["contradiction_potential"] = 0.0
-            
-            # Add metadata
-            factors["total_score"] = round(total_score, 2)
-            factors["calculated_at"] = _utc_timestamp()
-            
-            return factors
-            
-        except Exception as e:
-            logger.warning(f"Error getting factor breakdown: {str(e)}")
-            return {
-                "total_score": round(total_score, 2),
-                "error": "Factor breakdown unavailable"
-            }
-    
-    async def health_check(self) -> Dict[str, Any]:
-        """
-        Perform health check of the critical paper detector.
-        
-        Returns:
-            Health status
-        """
-        try:
-            health_status = {
-                "status": "healthy",
-                "timestamp": _utc_timestamp(),
-                "components": {}
-            }
-            
-            # Check term sets
-            try:
-                term_counts = {
-                    "method_terms": len(self.method_terms),
-                    "result_terms": len(self.result_terms),
-                    "contradiction_terms": len(self.contradiction_terms)
-                }
-                health_status["components"]["term_sets"] = {
-                    "status": "healthy",
-                    "counts": term_counts
-                }
-            except Exception as e:
-                health_status["components"]["term_sets"] = {"status": "error", "error": str(e)}
-                health_status["status"] = "degraded"
-            
-            # Check database operations if available
-            if self.db:
-                try:
-                    health_status["components"]["database"] = {"status": "available"}
-                except Exception as e:
-                    health_status["components"]["database"] = {"status": "error", "error": str(e)}
-                    health_status["status"] = "degraded"
-            else:
-                health_status["components"]["database"] = {"status": "not_configured"}
-            
-            #logger.info(f"Health check completed: {health_status['status']}")
-            return health_status
-            
-        except Exception as e:
-            logger.error(f"Health check failed: {str(e)}")
-            return {
-                "status": "error",
-                "error": str(e),
-                "timestamp": _utc_timestamp()
-            }
-    
-    def get_stats(self) -> Dict[str, Any]:
-        """
-        Get statistics about the detector.
-        
-        Returns:
-            Statistics dictionary
-        """
-        try:
-            stats = {
-                "method_terms_count": len(self.method_terms),
-                "result_terms_count": len(self.result_terms),
-                "contradiction_terms_count": len(self.contradiction_terms),
-                "database_configured": self.db is not None
-            }
-            
-            return stats
-            
-        except Exception as e:
-            logger.error(f"Error getting stats: {str(e)}")
-            return {"error": str(e)}

src/services/research_service/enhanced_research.py

@@ -1,121 +0,0 @@
-"""High-level orchestration service combining search and synthesis."""
-
-from __future__ import annotations
-
-import logging
-from typing import Any, Dict, List, Optional
-
-from src.services.llm_service import LLMManager
-from src.services.paper_service import OpenAlexClient
-from src.services.performance_service.rust_performance import HighPerformanceService
-from src.services.research_service.enhanced_synthesizer import EnhancedSynthesizer
-from src.services.search_service import SearchEngine
-
-logger = logging.getLogger(__name__)
-
-
-class EnhancedResearchService:
-    """Bundle search + synthesis into a cohesive workflow."""
-
-    def __init__(
-        self,
-        *,
-        search_engine: Optional[SearchEngine] = None,
-        synthesizer: Optional[EnhancedSynthesizer] = None,
-        llm_manager: Optional[LLMManager] = None,
-        openalex_client: Optional[OpenAlexClient] = None,
-        performance_service: Optional[HighPerformanceService] = None,
-    ) -> None:
-        self.openalex = openalex_client or OpenAlexClient()
-        self.llm = llm_manager or LLMManager()
-        self.performance = performance_service or HighPerformanceService()
-        self.search_engine = search_engine or SearchEngine(
-            openalex_client=self.openalex,
-            performance_service=self.performance,
-        )
-        self.synthesizer = synthesizer or EnhancedSynthesizer(
-            llm_manager=self.llm,
-            openalex_client=self.openalex,
-            performance_service=self.performance,
-        )
-
-    async def conduct_research(
-        self,
-        query: str,
-        *,
-        limit: int = 10,
-        max_words: int = 600,
-        style: str = "comprehensive",
-        include_advanced: bool = True,
-        context: Optional[Dict[str, Any]] = None,
-    ) -> Dict[str, Any]:
-        if not query or not query.strip():
-            raise ValueError("Query must be a non-empty string")
-
-        context = context or {}
-        context.setdefault("original_query", query)
-
-        search_payload = await self.search_engine.search_papers(
-            query,
-            limit=limit,
-            sources=("openalex", "pubmed") if include_advanced else ("openalex",),
-            include_metadata=True,
-            include_abstracts=True,
-        )
-
-        paper_ids = [paper["id"] for paper in search_payload.get("papers", [])]
-        raw_papers: List[Dict[str, Any]] = []
-        if paper_ids:
-            raw_papers = await self.openalex.get_papers_bulk(paper_ids)
-
-        if not raw_papers:
-            # Fall back to lightly formatted payloads if bulk fetch fails
-            raw_papers = [self._paper_stub(paper) for paper in search_payload.get("papers", [])]
-
-        synthesis = await self.synthesizer.synthesize_research(
-            papers=raw_papers,
-            max_words=max_words,
-            style=style,
-            context=context,
-            include_visualizations=True,
-            include_topic_modeling=True,
-            include_quality_assessment=True,
-        )
-
-        return {
-            "query": query,
-            "search": search_payload,
-            "synthesis": synthesis,
-        }
-
-    async def get_health_status(self) -> Dict[str, Any]:
-        search_stats = {
-            "openalex": True,
-            "web_search": True,
-        }
-        try:
-            kg_stats = await self.synthesizer.kg.stats()
-        except Exception as exc:  # pragma: no cover - KG optional
-            logger.info("Knowledge graph stats unavailable", extra={"error": str(exc)})
-            kg_stats = {"entities": 0, "relationships": 0}
-
-        llm_health = await self.llm.health_check()
-        return {
-            "search": search_stats,
-            "knowledge_graph": kg_stats,
-            "llm": llm_health,
-        }
-
-    def _paper_stub(self, payload: Dict[str, Any]) -> Dict[str, Any]:
-        return {
-            "id": payload.get("id"),
-            "title": payload.get("title"),
-            "abstract": payload.get("abstract", ""),
-            "authors": payload.get("authors", []),
-            "publication_year": payload.get("year"),
-            "doi": payload.get("doi"),
-            "concepts": [{"display_name": kw} for kw in payload.get("keywords", [])],
-        }
-
-
-__all__ = ["EnhancedResearchService"]