scitex 2.13.0__py3-none-any.whl → 2.15.1__py3-none-any.whl

scitex/scholar/storage/_LibraryManager.py

@@ -1,37 +1,110 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-# Timestamp: "2025-10-08 05:41:15 (ywatanabe)"
-# File: /home/ywatanabe/proj/scitex_repo/src/scitex/scholar/storage/_LibraryManager.py
-# ----------------------------------------
-from __future__ import annotations
-import os
-
-__FILE__ = "./src/scitex/scholar/storage/_LibraryManager.py"
-__DIR__ = os.path.dirname(__FILE__)
-# ----------------------------------------
+# Timestamp: "2026-01-24 (ywatanabe)"
+# File: /home/ywatanabe/proj/scitex-python/src/scitex/scholar/storage/_LibraryManager.py
+
+"""
+Unified manager for Scholar library structure and paper storage.
+
+This module provides a comprehensive library manager that:
+- Manages paper storage in the master library
+- Handles metadata conversion and standardization
+- Creates project symlinks for organization
+- Generates BibTeX entries and structures
+- Resolves DOIs and updates library metadata
+
+The main class inherits from multiple mixins for modular functionality:
+- StorageHelpersMixin: Storage helper methods (has_*, load, save)
+- MetadataConversionMixin: Metadata conversion utilities
+- PaperSavingMixin: Paper saving methods
+- ResolutionMixin: DOI resolution and library structure creation
+- SymlinkHandlersMixin: Symlink generation and management
+- BibtexHandlersMixin: BibTeX structure and entry generation
+- LibraryOperationsMixin: Library operations (update, validate)
+"""
 
-__FILE__ = __file__
+from __future__ import annotations
 
-import asyncio
-import copy
-import json
-import re
-from collections import OrderedDict
-from datetime import datetime
-from pathlib import Path
-from typing import Any, Dict, List, Optional
+from typing import Optional
 
 from scitex import logging
 from scitex.scholar.config import ScholarConfig
-from scitex.scholar.metadata_engines.utils import BASE_STRUCTURE, standardize_metadata
 from scitex.scholar.storage._DeduplicationManager import DeduplicationManager
-from scitex.scholar.utils import TextNormalizer
+
+from ._mixins import (
+    BibtexHandlersMixin,
+    LibraryOperationsMixin,
+    MetadataConversionMixin,
+    PaperSavingMixin,
+    ResolutionMixin,
+    StorageHelpersMixin,
+    SymlinkHandlersMixin,
+)
 
 logger = logging.getLogger(__name__)
 
 
-class LibraryManager:
-    """Unified manager for Scholar library structure and paper storage."""
+class LibraryManager(
+    StorageHelpersMixin,
+    MetadataConversionMixin,
+    PaperSavingMixin,
+    ResolutionMixin,
+    SymlinkHandlersMixin,
+    BibtexHandlersMixin,
+    LibraryOperationsMixin,
+):
+    """
+    Unified manager for Scholar library structure and paper storage.
+
+    This class provides comprehensive functionality for managing the Scholar
+    library, including:
+    - Storage helpers (check metadata, URLs, PDFs)
+    - Paper loading and incremental saving
+    - Metadata conversion to standardized format
+    - DOI resolution and library structure creation
+    - Project symlink management
+    - BibTeX entry generation
+    - Library validation and updates
+
+    Parameters
+    ----------
+    project : str, optional
+        Project name for organizing papers
+    single_doi_resolver : object, optional
+        DOI resolver instance for resolving DOIs from metadata
+    config : ScholarConfig, optional
+        Configuration object for Scholar settings
+
+    Attributes
+    ----------
+    config : ScholarConfig
+        Configuration object
+    project : str
+        Current project name
+    library_master_dir : Path
+        Path to the master library directory
+    single_doi_resolver : object
+        DOI resolver instance
+    dedup_manager : DeduplicationManager
+        Deduplication manager instance
+
+    Examples
+    --------
+    >>> # Basic usage
+    >>> manager = LibraryManager(project="my_research")
+    >>> paper_id = manager.save_resolved_paper(
+    ...     title="My Paper",
+    ...     doi="10.1234/example",
+    ...     authors=["Author One", "Author Two"],
+    ...     year=2024,
+    ... )
+
+    >>> # Check if paper exists
+    >>> has_pdf = manager.has_pdf(paper_id)
+    >>> has_meta = manager.has_metadata(paper_id)
+
+    >>> # Load paper
+    >>> paper = manager.load_paper_from_id(paper_id)
+    """
 
     def __init__(
         self,
@@ -47,1679 +120,8 @@ class LibraryManager:
         self._source_filename = "papers"
         self.dedup_manager = DeduplicationManager(config=self.config)
 
-    # =========================================================================
-    # Storage Helper Methods (Phase 1)
-    # =========================================================================
-
-    def has_metadata(self, paper_id: str) -> bool:
-        """Check if metadata.json exists for paper.
-
-        Args:
-            paper_id: 8-digit paper ID
-
-        Returns:
-            True if metadata.json exists, False otherwise
-        """
-        metadata_file = self.library_master_dir / paper_id / "metadata.json"
-        return metadata_file.exists()
-
-    def has_urls(self, paper_id: str) -> bool:
-        """Check if PDF URLs exist in metadata.
-
-        Args:
-            paper_id: 8-digit paper ID
-
-        Returns:
-            True if metadata has PDF URLs, False otherwise
-        """
-        if not self.has_metadata(paper_id):
-            return False
-
-        metadata_file = self.library_master_dir / paper_id / "metadata.json"
-        try:
-            with open(metadata_file, "r") as f:
-                data = json.load(f)
-
-            # Check nested structure: metadata.url.pdfs
-            urls = data.get("metadata", {}).get("url", {}).get("pdfs", [])
-            return len(urls) > 0
-        except Exception:
-            return False
-
-    def has_pdf(self, paper_id: str) -> bool:
-        """Check if PDF file exists in storage.
-
-        Args:
-            paper_id: 8-digit paper ID
-
-        Returns:
-            True if any PDF file exists, False otherwise
-        """
-        paper_dir = self.library_master_dir / paper_id
-        if not paper_dir.exists():
-            return False
-
-        # Check for any PDF files
-        pdf_files = list(paper_dir.glob("*.pdf"))
-        return len(pdf_files) > 0
-
-    def load_paper_from_id(self, paper_id: str) -> Optional["Paper"]:
-        """Load Paper object from storage by ID.
-
-        Args:
-            paper_id: 8-digit paper ID
-
-        Returns:
-            Paper object if found, None otherwise
-        """
-        from scitex.scholar.core.Paper import Paper
-
-        metadata_file = self.library_master_dir / paper_id / "metadata.json"
-
-        if not metadata_file.exists():
-            return None
-
-        try:
-            with open(metadata_file, "r") as f:
-                data = json.load(f)
-
-            # Use Paper.from_dict() which handles Pydantic validation
-            paper = Paper.from_dict(data)
-            return paper
-
-        except Exception as e:
-            logger.error(f"Failed to load paper {paper_id}: {e}")
-            return None
-
-    def save_paper_incremental(self, paper_id: str, paper: "Paper") -> None:
-        """Save Paper object to storage (incremental update).
-
-        This saves the complete Paper object to metadata.json,
-        preserving existing data and updating with new fields.
-
-        Args:
-            paper_id: 8-digit paper ID
-            paper: Paper object to save
-        """
-        storage_path = self.library_master_dir / paper_id
-        storage_path.mkdir(parents=True, exist_ok=True)
-
-        metadata_file = storage_path / "metadata.json"
-
-        # Load existing metadata if it exists
-        existing_data = {}
-        if metadata_file.exists():
-            try:
-                with open(metadata_file, "r") as f:
-                    existing_data = json.load(f)
-            except Exception:
-                pass
-
-        # Get new data from Paper object
-        new_data = paper.model_dump()
-
-        # Merge: new data takes precedence for non-None values
-        merged_data = self._merge_metadata(existing_data, new_data)
-
-        # Update timestamps
-        if "container" not in merged_data:
-            merged_data["container"] = {}
-        merged_data["container"]["updated_at"] = datetime.now().isoformat()
-
-        # Save to file
-        with open(metadata_file, "w") as f:
-            json.dump(merged_data, f, indent=2, ensure_ascii=False)
-
-        logger.debug(f"Saved paper {paper_id} to storage")
-
-    def _merge_metadata(self, existing: Dict, new: Dict) -> Dict:
-        """Recursively merge metadata dicts, preferring new non-None values."""
-        result = existing.copy()
-
-        for key, new_value in new.items():
-            if key not in result:
-                result[key] = new_value
-            elif new_value is None:
-                # Keep existing value if new is None
-                pass
-            elif isinstance(new_value, dict) and isinstance(result[key], dict):
-                # Recursively merge nested dicts
-                result[key] = self._merge_metadata(result[key], new_value)
-            elif isinstance(new_value, list) and len(new_value) > 0:
-                # Update lists if new list is not empty
-                result[key] = new_value
-            elif new_value:
-                # Update with new non-empty value
-                result[key] = new_value
-
-        return result
-
-    # =========================================================================
-    # Existing Methods
-    # =========================================================================
-
-    def _dotdict_to_dict(self, obj):
-        """Recursively convert DotDict to plain dict for JSON serialization."""
-        from scitex.dict import DotDict
-
-        if isinstance(obj, DotDict):
-            return {k: self._dotdict_to_dict(v) for k, v in obj._data.items()}
-        elif isinstance(obj, dict):
-            return {k: self._dotdict_to_dict(v) for k, v in obj.items()}
-        elif isinstance(obj, list):
-            return [self._dotdict_to_dict(item) for item in obj]
-        else:
-            return obj
-
-    def _add_engine_to_list(self, engines_list: list, source: str) -> None:
-        """Helper to add source to engines list if not already present."""
-        if source and source not in engines_list:
-            engines_list.append(source)
-
-    def _convert_to_standardized_metadata(self, flat_metadata: Dict) -> OrderedDict:
-        """Convert flat metadata dict to standardized nested structure with _engines tracking."""
-        standardized = copy.deepcopy(BASE_STRUCTURE)
-
-        # Map flat fields to standardized structure
-        # ID section
-        if "doi" in flat_metadata:
-            standardized["id"]["doi"] = flat_metadata["doi"]
-            self._add_engine_to_list(
-                standardized["id"]["doi_engines"],
-                flat_metadata.get("doi_source"),
-            )
-        if "scitex_id" in flat_metadata:
-            standardized["id"]["scholar_id"] = flat_metadata["scitex_id"]
-
-        # Basic section
-        if "title" in flat_metadata:
-            standardized["basic"]["title"] = flat_metadata["title"]
-            self._add_engine_to_list(
-                standardized["basic"]["title_engines"],
-                flat_metadata.get("title_source"),
-            )
-        if "authors" in flat_metadata:
-            standardized["basic"]["authors"] = flat_metadata["authors"]
-            self._add_engine_to_list(
-                standardized["basic"]["authors_engines"],
-                flat_metadata.get("authors_source"),
-            )
-        if "year" in flat_metadata:
-            standardized["basic"]["year"] = flat_metadata["year"]
-            self._add_engine_to_list(
-                standardized["basic"]["year_engines"],
-                flat_metadata.get("year_source"),
-            )
-        if "abstract" in flat_metadata:
-            standardized["basic"]["abstract"] = flat_metadata["abstract"]
-            self._add_engine_to_list(
-                standardized["basic"]["abstract_engines"],
-                flat_metadata.get("abstract_source"),
-            )
-
-        # Citation count section
-        if "citation_count" in flat_metadata:
-            cc_value = flat_metadata["citation_count"]
-            # Handle both scalar (4) and dict ({"total": 4}) formats
-            if isinstance(cc_value, dict):
-                # If it's a dict, extract the total value
-                standardized["citation_count"]["total"] = cc_value.get("total")
-                self._add_engine_to_list(
-                    standardized["citation_count"]["total_engines"],
-                    cc_value.get("total_source"),
-                )
-                # Copy yearly breakdowns if present
-                for year in [
-                    "2025",
-                    "2024",
-                    "2023",
-                    "2022",
-                    "2021",
-                    "2020",
-                    "2019",
-                    "2018",
-                    "2017",
-                    "2016",
-                    "2015",
-                ]:
-                    if year in cc_value:
-                        standardized["citation_count"][year] = cc_value[year]
-                        if f"{year}_source" in cc_value:
-                            self._add_engine_to_list(
-                                standardized["citation_count"][f"{year}_engines"],
-                                cc_value.get(f"{year}_source"),
-                            )
-            else:
-                # If it's a scalar, just assign it to total
-                standardized["citation_count"]["total"] = cc_value
-                self._add_engine_to_list(
-                    standardized["citation_count"]["total_engines"],
-                    flat_metadata.get("citation_count_source"),
-                )
-
-        # Publication section
-        if "journal" in flat_metadata:
-            standardized["publication"]["journal"] = flat_metadata["journal"]
-            self._add_engine_to_list(
-                standardized["publication"]["journal_engines"],
-                flat_metadata.get("journal_source"),
-            )
-        if "short_journal" in flat_metadata:
-            standardized["publication"]["short_journal"] = flat_metadata[
-                "short_journal"
-            ]
-        if "impact_factor" in flat_metadata:
-            standardized["publication"]["impact_factor"] = flat_metadata[
-                "impact_factor"
-            ]
-        if "issn" in flat_metadata:
-            standardized["publication"]["issn"] = flat_metadata["issn"]
-        if "volume" in flat_metadata:
-            standardized["publication"]["volume"] = flat_metadata["volume"]
-        if "issue" in flat_metadata:
-            standardized["publication"]["issue"] = flat_metadata["issue"]
-        if "pages" in flat_metadata:
-            # Split pages into first_page and last_page if needed
-            pages = flat_metadata["pages"]
-            if pages and "-" in str(pages):
-                first, last = str(pages).split("-", 1)
-                standardized["publication"]["first_page"] = first.strip()
-                standardized["publication"]["last_page"] = last.strip()
-        if "publisher" in flat_metadata:
-            standardized["publication"]["publisher"] = flat_metadata["publisher"]
-
-        # URL section
-        if "url_doi" in flat_metadata:
-            standardized["url"]["doi"] = flat_metadata["url_doi"]
-        if "url_publisher" in flat_metadata:
-            standardized["url"]["publisher"] = flat_metadata["url_publisher"]
-            self._add_engine_to_list(
-                standardized["url"]["publisher_engines"], "ScholarURLFinder"
-            )
-        if "url_openurl_query" in flat_metadata:
-            standardized["url"]["openurl_query"] = flat_metadata["url_openurl_query"]
-        if "url_openurl_resolved" in flat_metadata:
-            standardized["url"]["openurl_resolved"] = flat_metadata[
-                "url_openurl_resolved"
-            ]
-            self._add_engine_to_list(
-                standardized["url"]["openurl_resolved_engines"],
-                "ScholarURLFinder",
-            )
-        if "urls_pdf" in flat_metadata:
-            standardized["url"]["pdfs"] = flat_metadata["urls_pdf"]
-            self._add_engine_to_list(
-                standardized["url"]["pdfs_engines"], "ScholarURLFinder"
-            )
-
-        # Path section
-        if "pdf_path" in flat_metadata:
-            standardized["path"]["pdfs"] = [flat_metadata["pdf_path"]]
-            self._add_engine_to_list(
-                standardized["path"]["pdfs_engines"],
-                "ScholarPDFDownloaderWithScreenshotsParallel",
-            )
-
-        return standardized
-
-    def _call_path_manager_get_storage_paths(
-        self, paper_info: Dict, collection_name: str = "MASTER"
-    ) -> Dict[str, Any]:
-        """Helper to call PathManager's get_paper_storage_paths with proper parameters."""
-        # Extract parameters from paper_info dict
-        doi = paper_info.get("doi")
-        title = paper_info.get("title")
-        authors = paper_info.get("authors", [])
-        year = paper_info.get("year")
-        journal = paper_info.get("journal")
-
-        # Call PathManager with individual parameters
-        storage_path, readable_name, paper_id = (
-            self.config.path_manager.get_paper_storage_paths(
-                doi=doi,
-                title=title,
-                authors=authors,
-                year=year,
-                journal=journal,
-                project=collection_name,
-            )
-        )
-
-        # Return in the expected dict format
-        return {
-            "storage_path": storage_path,
-            "readable_name": readable_name,
-            "unique_id": paper_id,
-        }
-
-    def check_library_for_doi(
-        self, title: str, year: Optional[int] = None
-    ) -> Optional[str]:
-        """Check if DOI already exists in master Scholar library."""
-
-        try:
-            for paper_dir in self.library_master_dir.iterdir():
-                if not paper_dir.is_dir():
-                    continue
-
-                metadata_file = paper_dir / "metadata.json"
-                if metadata_file.exists():
-                    try:
-                        with open(metadata_file, "r") as file_:
-                            metadata = json.load(file_)
-
-                        stored_title = metadata.get("title", "")
-                        stored_year = metadata.get("year")
-                        stored_doi = metadata.get("doi")
-
-                        title_match = self._is_title_similar(title, stored_title)
-                        year_match = (
-                            not year
-                            or not stored_year
-                            or abs(int(stored_year) - int(year)) <= 1
-                            if isinstance(stored_year, (int, str))
-                            and str(stored_year).isdigit()
-                            else stored_year == year
-                        )
-
-                        if title_match and year_match and stored_doi:
-                            logger.info(
-                                f"DOI found in master Scholar library: {stored_doi} (paper_id: {paper_dir.name})"
-                            )
-                            return stored_doi
-
-                    except (
-                        json.JSONDecodeError,
-                        KeyError,
-                        ValueError,
-                    ) as exc_:
-                        logger.debug(
-                            f"Error reading metadata from {metadata_file}: {exc_}"
-                        )
-                        continue
-
-            return None
-
-        except Exception as exc_:
-            logger.debug(f"Error checking master Scholar library: {exc_}")
-            return None
-
-    def save_resolved_paper(
-        self,
-        # Can accept either a Paper object or individual fields
-        paper_data: Optional["Paper"] = None,
-        # Required bibliographic fields (if not providing paper_data)
-        title: Optional[str] = None,
-        doi: Optional[str] = None,
-        # Optional bibliographic fields
-        authors: Optional[List[str]] = None,
-        year: Optional[int] = None,
-        journal: Optional[str] = None,
-        abstract: Optional[str] = None,
-        # Additional bibliographic fields
-        volume: Optional[str] = None,
-        issue: Optional[str] = None,
-        pages: Optional[str] = None,
-        publisher: Optional[str] = None,
-        issn: Optional[str] = None,
-        short_journal: Optional[str] = None,
-        # Enrichment fields
-        citation_count: Optional[int] = None,
-        impact_factor: Optional[float] = None,
-        # Source tracking (which engine/database provided this info)
-        doi_source: Optional[str] = None,
-        title_source: Optional[str] = None,
-        abstract_source: Optional[str] = None,
-        authors_source: Optional[str] = None,
-        year_source: Optional[str] = None,
-        journal_source: Optional[str] = None,
-        # Library management
-        library_id: Optional[str] = None,
-        project: Optional[str] = None,
-        # Legacy support (will be removed)
-        metadata: Optional[Dict] = None,
-        bibtex_source: Optional[str] = None,
-        source: Optional[str] = None,  # Legacy doi_source
-        paper_id: Optional[str] = None,  # Legacy library_id
-        **kwargs,  # For backward compatibility
-    ) -> str:
-        """Save successfully resolved paper to Scholar library."""
-
-        # If paper_data is provided, extract fields from it
-        if paper_data is not None:
-            if hasattr(paper_data, "metadata"):
-                # Pydantic Paper object
-                title = title or (paper_data.metadata.basic.title or "")
-                doi = doi or (paper_data.metadata.id.doi or "")
-                authors = authors or paper_data.metadata.basic.authors
-                year = year or paper_data.metadata.basic.year
-                journal = journal or paper_data.metadata.publication.journal
-                abstract = abstract or paper_data.metadata.basic.abstract
-                publisher = publisher or paper_data.metadata.publication.publisher
-                impact_factor = (
-                    impact_factor or paper_data.metadata.publication.impact_factor
-                )
-                library_id = library_id or paper_data.container.library_id
-            elif isinstance(paper_data, dict):
-                # Dict paper object
-                title = title or paper_data.get("title", "")
-                doi = doi or paper_data.get("doi", "")
-                authors = authors or paper_data.get("authors", [])
-                year = year or paper_data.get("year")
-                journal = journal or paper_data.get("journal")
-                abstract = abstract or paper_data.get("abstract")
-                publisher = publisher or paper_data.get("publisher")
-                impact_factor = impact_factor or paper_data.get("impact_factor")
-                library_id = (
-                    library_id
-                    or paper_data.get("scitex_id")
-                    or paper_data.get("scholar_id")
-                )
-
-        # Handle legacy parameters
-        if paper_id and not library_id:
-            library_id = paper_id
-        if source and not doi_source:
-            doi_source = source
-
-        # Build paper_info with explicit parameters (not metadata dict)
-        paper_info = {
-            "title": title,
-            "year": year,
-            "authors": authors or [],
-            "doi": doi,
-            "journal": journal,
-        }
-
-        # Only use metadata dict as fallback for backward compatibility
-        if metadata:
-            if not journal:
-                journal = metadata.get("journal")
-                paper_info["journal"] = journal
-            if not year:
-                year = metadata.get("year")
-                paper_info["year"] = year
-            if not authors:
-                authors = metadata.get("authors")
-                paper_info["authors"] = authors or []
-
-        # Check for existing paper first (deduplication)
-        check_metadata = {
-            "doi": doi,
-            "title": title,
-            "authors": authors or [],
-            "year": year,
-        }
-        existing_paper_dir = self.dedup_manager.check_for_existing_paper(check_metadata)
-
-        if existing_paper_dir:
-            logger.info(f"Found existing paper: {existing_paper_dir.name}")
-            # Update existing paper instead of creating new
-            master_storage_path = existing_paper_dir
-            paper_id = existing_paper_dir.name
-            readable_name = None  # Will be determined from existing symlinks
-        else:
-            # Call PathManager with individual parameters for new paper
-            storage_path, readable_name, paper_id = (
-                self.config.path_manager.get_paper_storage_paths(
-                    doi=doi,
-                    title=title,
-                    authors=authors or [],
-                    year=year,
-                    journal=journal,
-                    project="MASTER",
-                )
-            )
-            master_storage_path = storage_path
-
-            # Use provided library_id if available, otherwise use generated paper_id
-            if library_id:
-                paper_id = library_id
-
-        master_metadata_file = master_storage_path / "metadata.json"
-
-        existing_metadata = {}
-        if master_metadata_file.exists():
-            try:
-                with open(master_metadata_file, "r") as file_:
-                    existing_metadata = json.load(file_)
-            except (json.JSONDecodeError, IOError):
-                existing_metadata = {}
-
-        # Clean text fields
-        clean_title = TextNormalizer.clean_metadata_text(
-            existing_metadata.get("title", title)
-        )
-
-        # Use explicit abstract parameter first, then metadata dict, then existing
-        clean_abstract = None
-        if abstract:
-            clean_abstract = TextNormalizer.clean_metadata_text(abstract)
-        elif metadata and metadata.get("abstract"):
-            clean_abstract = TextNormalizer.clean_metadata_text(metadata["abstract"])
-        elif existing_metadata.get("abstract"):
-            clean_abstract = TextNormalizer.clean_metadata_text(
-                existing_metadata["abstract"]
-            )
-
-        # Handle doi_source - explicit parameter takes precedence
-        doi_source_value = doi_source or existing_metadata.get("doi_source")
-        if not doi_source_value and source:
-            # Normalize legacy source parameter
-            if "crossref" in source.lower():
-                doi_source_value = "crossref"
-            elif "semantic" in source.lower():
-                doi_source_value = "semantic_scholar"
-            elif "pubmed" in source.lower():
-                doi_source_value = "pubmed"
-            elif "openalex" in source.lower():
-                doi_source_value = "openalex"
-            else:
-                doi_source_value = source
-
-        comprehensive_metadata = {
-            # Core bibliographic fields
-            "title": clean_title,
-            "title_source": title_source
-            or existing_metadata.get("title_source", "input"),
-            "doi": existing_metadata.get("doi", doi),
-            "doi_source": doi_source_value,
-            "year": existing_metadata.get("year", year),
-            "year_source": year_source
-            or existing_metadata.get("year_source", "input" if year else None),
-            "authors": existing_metadata.get("authors", authors or []),
-            "authors_source": authors_source
-            or existing_metadata.get("authors_source", "input" if authors else None),
-            "journal": existing_metadata.get("journal", journal),
-            "journal_source": journal_source
-            or existing_metadata.get("journal_source", "input" if journal else None),
-            # Additional bibliographic fields from explicit parameters
-            "volume": existing_metadata.get("volume", volume),
-            "issue": existing_metadata.get("issue", issue),
-            "pages": existing_metadata.get("pages", pages),
-            "publisher": existing_metadata.get("publisher", publisher),
-            "issn": existing_metadata.get("issn", issn),
-            "short_journal": existing_metadata.get("short_journal", short_journal),
-            # Abstract with source tracking
-            "abstract": existing_metadata.get("abstract", clean_abstract),
-            "abstract_source": abstract_source
-            or existing_metadata.get("abstract_source", "input" if abstract else None),
-            # Enrichment fields
-            "citation_count": existing_metadata.get("citation_count", citation_count),
-            "impact_factor": existing_metadata.get("impact_factor", impact_factor),
-            "scitex_id": existing_metadata.get(
-                "scitex_id", existing_metadata.get("scholar_id", paper_id)
-            ),
-            "created_at": existing_metadata.get(
-                "created_at", datetime.now().isoformat()
-            ),
-            "created_by": existing_metadata.get("created_by", "SciTeX Scholar"),
-            "updated_at": datetime.now().isoformat(),
-            "projects": existing_metadata.get(
-                "projects", [] if self.project == "master" else [self.project]
-            ),
-            "master_storage_path": str(master_storage_path),
-            "readable_name": readable_name,
-            "metadata_file": str(master_metadata_file),
-        }
-
-        # Store plain dict version for JSON serialization
-        comprehensive_metadata_plain = self._dotdict_to_dict(comprehensive_metadata)
-
-        # Convert to standardized format before saving
-        standardized_metadata = self._convert_to_standardized_metadata(
-            comprehensive_metadata_plain
-        )
-
-        # Wrap with Paper container properties
-        final_structure = OrderedDict(
-            [
-                ("metadata", standardized_metadata),
-                (
-                    "container",
-                    OrderedDict(
-                        [
-                            (
-                                "scitex_id",
-                                comprehensive_metadata_plain.get("scitex_id"),
-                            ),
-                            ("library_id", paper_id),
-                            (
-                                "created_at",
-                                comprehensive_metadata_plain.get("created_at"),
-                            ),
-                            (
-                                "created_by",
-                                comprehensive_metadata_plain.get("created_by"),
-                            ),
-                            (
-                                "updated_at",
-                                comprehensive_metadata_plain.get("updated_at"),
-                            ),
-                            (
-                                "projects",
-                                comprehensive_metadata_plain.get("projects", []),
-                            ),
-                            ("master_storage_path", str(master_storage_path)),
-                            ("readable_name", readable_name),
-                            ("metadata_file", str(master_metadata_file)),
-                            (
-                                "pdf_downloaded_at",
-                                comprehensive_metadata_plain.get("pdf_downloaded_at"),
-                            ),
-                            (
-                                "pdf_size_bytes",
-                                comprehensive_metadata_plain.get("pdf_size_bytes"),
-                            ),
-                        ]
-                    ),
-                ),
-            ]
-        )
-
-        with open(master_metadata_file, "w") as file_:
-            json.dump(final_structure, file_, indent=2, ensure_ascii=False)
-
-        logger.success(f"Saved paper to MASTER Scholar library: {paper_id}")
-
-        # Create project symlink if project is specified and not MASTER
-        if self.project and self.project not in ["master", "MASTER"]:
-            try:
-                # Use centralized naming logic - use original comprehensive_metadata (not plain)
-                readable_name = self._generate_readable_name(
-                    comprehensive_metadata=comprehensive_metadata,
-                    master_storage_path=master_storage_path,
-                    authors=authors,
-                    year=year,
-                    journal=journal,
-                )
-
-                self._create_project_symlink(
-                    master_storage_path=master_storage_path,
-                    project=self.project,
-                    readable_name=readable_name,
-                )
-            except Exception as exc_:
-                logger.error(f"Failed to create symlink for {paper_id}: {exc_}")
-
-        return paper_id
-
-    def save_unresolved_paper(
-        self,
-        title: str,
-        year: Optional[int] = None,
-        authors: Optional[List[str]] = None,
-        reason: str = "DOI not found",
-        bibtex_source: Optional[str] = None,
-    ) -> None:
-        """Save paper that couldn't be resolved to unresolved directory."""
-        clean_title = TextNormalizer.clean_metadata_text(title) if title else ""
-        unresolved_info = {
-            "title": clean_title,
-            "year": year,
-            "authors": authors or [],
-            "reason": reason,
-            "bibtex_source": bibtex_source,
-            "project": self.project,
-            "created_at": datetime.now().isoformat(),
-            "created_by": "SciTeX Scholar",
-        }
-
-        project_lib_path = (
-            self.config.path_manager.get_scholar_library_path() / self.project
-        )
-        unresolved_dir = project_lib_path / "unresolved"
-        unresolved_dir.mkdir(parents=True, exist_ok=True)
-
-        safe_title = title or "untitled"
-        safe_title = re.sub(r"[^\w\s-]", "", safe_title)[:50]
-        safe_title = re.sub(r"[-\s]+", "_", safe_title)
-        timestamp = datetime.now().strftime("%Y%m%d_%H%M%S")
-        unresolved_file = unresolved_dir / f"{safe_title}_{timestamp}.json"
-
-        with open(unresolved_file, "w") as file_:
-            json.dump(unresolved_info, file_, indent=2, ensure_ascii=False)
-
-        logger.warning(f"Saved unresolved entry: {unresolved_file.name}")
-
-    async def resolve_and_create_library_structure_async(
-        self,
-        papers: List[Dict[str, Any]],
-        project: str,
-        sources: Optional[List[str]] = None,
-    ) -> Dict[str, Dict[str, str]]:
-        """Resolve DOIs and create full Scholar library structure with proper paths."""
-        if not self.single_doi_resolver:
-            raise ValueError("SingleDOIResolver is required for resolving DOIs")
-
-        results = {}
-        for paper in papers:
-            title = paper.get("title")
-            if not title:
-                logger.warning(f"Skipping paper without title: {paper}")
-                continue
-
-            logger.info(f"Processing: {title[:50]}...")
-
-            try:
-                doi_result = await self.single_doi_resolver.metadata2doi_async(
-                    title=title,
-                    year=paper.get("year"),
-                    authors=paper.get("authors"),
-                    sources=sources,
-                )
-
-                enhanced_metadata = self._extract_enhanced_metadata(doi_result, paper)
-                paper_info = {**paper, **enhanced_metadata}
-
-                storage_paths = self._call_path_manager_get_storage_paths(
-                    paper_info=paper_info, collection_name="MASTER"
-                )
-                paper_id = storage_paths["unique_id"]
-                storage_path = storage_paths["storage_path"]
-                metadata_file = storage_path / "metadata.json"
-
-                complete_metadata = self._create_complete_metadata(
-                    paper, doi_result, paper_id, enhanced_metadata
-                )
-
-                with open(metadata_file, "w") as file_:
-                    json.dump(complete_metadata, file_, indent=2)
-
-                logger.success(
-                    f"Saved metadata.json for {paper_id} ({len(complete_metadata)} fields)"
-                )
-
-                project_symlink_path = self._create_project_symlink(
-                    master_storage_path=storage_path,
-                    project=project,
-                    readable_name=storage_paths["readable_name"],
-                )
-
-                bibtex_source_filename = getattr(self, "_source_filename", "papers")
-                info_dir = self._create_bibtex_info_structure(
-                    project=project,
-                    paper_info={**paper, **enhanced_metadata},
-                    complete_metadata=complete_metadata,
-                    bibtex_source_filename=bibtex_source_filename,
-                )
-
-                results[title] = {
-                    "scitex_id": paper_id,
-                    "scholar_id": paper_id,
-                    "doi": complete_metadata.get("doi"),
-                    "master_storage_path": str(storage_path),
-                    "project_symlink_path": (
-                        str(project_symlink_path) if project_symlink_path else None
-                    ),
-                    "readable_name": storage_paths["readable_name"],
-                    "metadata_file": str(metadata_file),
-                    "info_dir": str(info_dir) if info_dir else None,
-                }
-
-                logger.info(f"Created library entry: {paper_id}")
-                if complete_metadata.get("doi"):
-                    logger.info(f"   DOI: {complete_metadata['doi']}")
-                logger.info(f"   Storage: {storage_path}")
-
-            except Exception as exc_:
-                logger.error(f"❌ Error processing '{title[:30]}...': {exc_}")
-
-        logger.success(
-            f"Created Scholar library entries for {len(results)}/{len(papers)} papers"
-        )
-        return results
-
-    async def resolve_and_create_library_structure_with_source_async(
-        self,
-        papers: List[Dict[str, Any]],
-        project: str,
-        sources: Optional[List[str]] = None,
-        bibtex_source_filename: str = "papers",
-    ) -> Dict[str, Dict[str, str]]:
-        """Enhanced version that passes source filename for BibTeX structure."""
-        self._source_filename = bibtex_source_filename
-        return await self.resolve_and_create_library_structure_async(
-            papers=papers, project=project, sources=sources
-        )
-
-    def _extract_enhanced_metadata(
-        self, doi_result: Optional[Dict], paper: Dict
-    ) -> Dict[str, Any]:
-        """Extract enhanced metadata from DOI resolution result."""
-        enhanced = {}
-        if doi_result and isinstance(doi_result, dict):
-            metadata_source = doi_result.get("metadata", {})
-            enhanced.update(
-                {
-                    "doi": doi_result.get("doi"),
-                    "journal": metadata_source.get("journal")
-                    or doi_result.get("journal")
-                    or paper.get("journal"),
-                    "authors": metadata_source.get("authors")
-                    or doi_result.get("authors")
-                    or paper.get("authors"),
-                    "year": metadata_source.get("year")
-                    or doi_result.get("year")
-                    or paper.get("year"),
-                    "title": metadata_source.get("title")
-                    or doi_result.get("title")
-                    or paper.get("title"),
-                    "abstract": metadata_source.get("abstract")
-                    or doi_result.get("abstract"),
-                    "publisher": metadata_source.get("publisher")
-                    or doi_result.get("publisher"),
-                    "volume": metadata_source.get("volume") or doi_result.get("volume"),
-                    "issue": metadata_source.get("issue") or doi_result.get("issue"),
-                    "pages": metadata_source.get("pages") or doi_result.get("pages"),
-                    "issn": metadata_source.get("issn") or doi_result.get("issn"),
-                    "short_journal": metadata_source.get("short_journal")
-                    or doi_result.get("short_journal"),
-                }
-            )
-
-            if doi_result.get("doi"):
-                logger.success(
-                    f"Enhanced metadata from DOI source: {dict(metadata_source)}"
-                )
-
-        return enhanced
-
-    def _create_complete_metadata(
-        self,
-        paper: Dict,
-        doi_result: Optional[Dict],
-        paper_id: str,
-        enhanced_metadata: Dict,
-    ) -> Dict[str, Any]:
-        """Create complete metadata dictionary with source tracking."""
-        raw_title = enhanced_metadata.get("title") or paper.get("title")
-        clean_title = TextNormalizer.clean_metadata_text(raw_title) if raw_title else ""
-        raw_abstract = None
-        if enhanced_metadata.get("abstract"):
-            raw_abstract = TextNormalizer.clean_metadata_text(
-                enhanced_metadata["abstract"]
-            )
-
-        doi_source_value = None
-        if doi_result and doi_result.get("source"):
-            source = doi_result["source"]
-            if "crossref" in source.lower():
-                doi_source_value = "crossref"
-            elif "semantic" in source.lower():
-                doi_source_value = "semantic_scholar"
-            elif "pubmed" in source.lower():
-                doi_source_value = "pubmed"
-            elif "openalex" in source.lower():
-                doi_source_value = "openalex"
-            else:
-                doi_source_value = source
-
-        complete_metadata = {
-            "title": clean_title,
-            "title_source": (
-                doi_source_value
-                if enhanced_metadata.get("title") != paper.get("title")
-                else "manual"
-            ),
-            "authors": enhanced_metadata.get("authors") or paper.get("authors"),
-            "authors_source": (
-                doi_source_value
-                if enhanced_metadata.get("authors") != paper.get("authors")
-                else ("manual" if paper.get("authors") else None)
-            ),
-            "year": enhanced_metadata.get("year") or paper.get("year"),
-            "year_source": (
-                doi_source_value
-                if enhanced_metadata.get("year") != paper.get("year")
-                else ("manual" if paper.get("year") else None)
-            ),
-            "journal": enhanced_metadata.get("journal") or paper.get("journal"),
-            "journal_source": (
-                doi_source_value
-                if enhanced_metadata.get("journal") != paper.get("journal")
-                else ("manual" if paper.get("journal") else None)
-            ),
-            "abstract": raw_abstract,
-            "abstract_source": (
-                doi_source_value if enhanced_metadata.get("abstract") else None
-            ),
-            "scitex_id": paper_id,
-            "created_at": datetime.now().isoformat(),
-            "created_by": "SciTeX Scholar",
-        }
-
-        if doi_result and isinstance(doi_result, dict):
-            safe_fields = [
-                "publisher",
-                "volume",
-                "issue",
-                "pages",
-                "issn",
-                "short_journal",
-            ]
-            for field in safe_fields:
-                value = enhanced_metadata.get(field)
-                if value is not None:
-                    complete_metadata[field] = value
-                    complete_metadata[f"{field}_source"] = (
-                        doi_source_value or "unknown_api"
-                    )
-
-        if doi_result and doi_result.get("doi"):
-            complete_metadata.update(
-                {"doi": doi_result["doi"], "doi_source": doi_source_value}
-            )
-            logger.success(f"DOI resolved for {paper_id}: {doi_result['doi']}")
-        else:
-            complete_metadata.update(
-                {
-                    "doi": None,
-                    "doi_source": None,
-                    "doi_resolution_failed": True,
-                }
-            )
-            logger.warning(
-                f"DOI resolution failed for {paper_id}: {paper.get('title', '')[:40]}..."
-            )
-
-        standard_fields = {
-            "keywords": None,
-            "references": None,
-            "venue": None,
-            "publisher": None,
-            "volume": None,
-            "issue": None,
-            "pages": None,
-            "issn": None,
-            "short_journal": None,
-        }
-
-        missing_fields = []
-        for field, default_value in standard_fields.items():
-            if field not in complete_metadata or complete_metadata[field] is None:
-                complete_metadata[field] = default_value
-                missing_fields.append(field)
-
-        if missing_fields:
-            logger.info(
-                f"Missing fields for future enhancement: {', '.join(missing_fields)}"
-            )
-
-        storage_paths = self._call_path_manager_get_storage_paths(
-            paper_info={**paper, **enhanced_metadata}, collection_name="MASTER"
-        )
-        storage_path = storage_paths["storage_path"]
-
-        complete_metadata.update(
-            {
-                "master_storage_path": str(storage_path),
-                "readable_name": storage_paths["readable_name"],
-                "metadata_file": str(storage_path / "metadata.json"),
-            }
-        )
-
-        return complete_metadata
-
-    def _generate_readable_name(
-        self,
-        comprehensive_metadata: Dict,
-        master_storage_path: Path,
-        authors: Optional[List[str]] = None,
-        year: Optional[int] = None,
-        journal: Optional[str] = None,
-    ) -> str:
-        """Generate readable symlink name from metadata.
-
-        Single source of truth for symlink naming format.
-        """
-        # Extract author
-        first_author = "Unknown"
-        if authors and len(authors) > 0:
-            author_parts = authors[0].split()
-            first_author = (
-                author_parts[-1] if len(author_parts) > 1 else author_parts[0]
-            )
-            first_author = "".join(c for c in first_author if c.isalnum() or c == "-")[
-                :20
-            ]
-
-        # Format year (handle DotDict and other non-int types)
-        from scitex.dict import DotDict
-
-        if isinstance(year, DotDict):
-            # Extract value if it's a DotDict
-            year = None  # Can't extract year from DotDict structure, use Unknown
-
-        # Convert to int if it's a string representation
-        if isinstance(year, str) and year.isdigit():
-            year = int(year)
-
-        # Only use year if it's actually an int
-        if isinstance(year, int):
-            year_str = f"{year:04d}"
-        else:
-            year_str = "0000"
-
-        # Clean journal name using PathManager (single source of truth)
-        journal_clean = "Unknown"
-        if journal:
-            journal_clean = self.config.path_manager._sanitize_filename(journal)[:30]
-            if not journal_clean:
-                journal_clean = "Unknown"
-
-        # Get citation count and impact factor (handle both flat and nested formats)
-        # Check if this is the nested structure from file (has "metadata" key)
-        if "metadata" in comprehensive_metadata:
-            # Nested structure from file
-            metadata_section = comprehensive_metadata.get("metadata", {})
-
-            # Extract citation count from nested structure
-            cc_val = metadata_section.get("citation_count", {})
-            if isinstance(cc_val, dict):
-                cc = cc_val.get("total", 0) or 0
-            else:
-                cc = cc_val or 0
-
-            # Extract impact factor from nested structure
-            publication_section = metadata_section.get("publication", {})
-            if_val = publication_section.get("impact_factor", 0.0) or 0.0
-
-        else:
-            # Flat structure (during initial save)
-            cc_val = comprehensive_metadata.get("citation_count", 0)
-            if isinstance(cc_val, dict):
-                cc = cc_val.get("total", 0) or 0
-            else:
-                cc = cc_val or 0
-
-            # Try multiple paths for impact_factor
-            if_val = (
-                comprehensive_metadata.get("journal_impact_factor")
-                or comprehensive_metadata.get("impact_factor")
-                or comprehensive_metadata.get("publication", {}).get("impact_factor")
-            )
-            if isinstance(if_val, dict):
-                if_val = if_val.get("value", 0.0) or 0.0
-            else:
-                if_val = if_val or 0.0
-
-        # Check PDF status with more granular states
-        pdf_files = list(master_storage_path.glob("*.pdf"))
-        screenshot_dir = master_storage_path / "screenshots"
-        has_screenshots = screenshot_dir.exists() and any(screenshot_dir.iterdir())
-        downloading_marker = master_storage_path / ".downloading"
-        attempted_marker = master_storage_path / ".download_attempted"
-
-        # Extract DOI from metadata to check availability
-        doi = None
-        if "metadata" in comprehensive_metadata:
-            # Nested structure from file
-            doi = comprehensive_metadata.get("metadata", {}).get("id", {}).get("doi")
-        else:
-            # Flat structure (during initial save)
-            doi = comprehensive_metadata.get("doi")
-
-        if downloading_marker.exists():
-            # Download in progress
-            pdf_status_letter = "r"
-        elif pdf_files:
-            # Has PDF = Successful
-            pdf_status_letter = "s"
-        elif has_screenshots:
-            # Has screenshots but no PDF = Failed (attempted but failed)
-            pdf_status_letter = "f"
-        elif attempted_marker.exists():
-            # Download was attempted but failed early (before screenshots)
-            pdf_status_letter = "f"
-        elif not doi:
-            # No DOI = Failed (cannot download without identifier)
-            pdf_status_letter = "f"
-        else:
-            # No PDF, no screenshots, no attempts, has DOI = Pending (not attempted yet)
-            pdf_status_letter = "p"
-
-        pdf_status_id_map = {
-            "p": 0,
-            "r": 1,
-            "f": 2,
-            "s": 3,
-        }
-        pdf_status_str = f"{pdf_status_id_map[pdf_status_letter]}{pdf_status_letter}"
-        # Format: CC_000000-PDF_s-IF_032-2016-Author-Journal
-        # PDF status: r=running, s=successful, f=failed, p=pending
-        # readable_name = f"CC_{cc:06d}-PDF_{pdf_status_letter}-IF_{int(if_val):03d}-{year_str}-{first_author}-{journal_clean}"
-        readable_name = f"PDF-{pdf_status_str}_CC-{cc:06d}_IF-{int(if_val):03d}_{year_str}_{first_author}_{journal_clean}"
-
-        return readable_name
-
-    def update_symlink(
-        self,
-        master_storage_path: Path,
-        project: str,
-        metadata: Optional[Dict] = None,
-    ) -> Optional[Path]:
-        """Update project symlink to reflect current paper status.
-
-        This should be called whenever paper status changes (pending → running → success/failed).
-        Generates new readable name based on current state (checking .downloading marker, PDFs, etc.)
-        and updates the symlink accordingly.
-
-        Args:
-            master_storage_path: Path to paper in master library
-            project: Project name
-            metadata: Optional metadata dict (if not provided, will read from file)
-
-        Returns:
-            Path to the created symlink, or None if failed
-        """
-        try:
-            # Load metadata if not provided
-            if metadata is None:
-                metadata_file = master_storage_path / "metadata.json"
-                if metadata_file.exists():
-                    import json
-
-                    with open(metadata_file, "r") as f:
-                        metadata = json.load(f)
-                else:
-                    logger.warning(f"No metadata found for {master_storage_path.name}")
-                    return None
-
-            # Extract metadata from nested structure if needed
-            # Metadata file has structure: {"metadata": {"basic": {...}, "id": {...}, ...}, "container": {...}}
-            if "metadata" in metadata:
-                # Nested structure from file
-                meta_section = metadata.get("metadata", {})
-                basic_section = meta_section.get("basic", {})
-                pub_section = meta_section.get("publication", {})
-
-                authors = basic_section.get("authors")
-                year = basic_section.get("year")
-                journal = pub_section.get("journal")
-            else:
-                # Flat structure (should not happen when reading from file, but handle it)
-                authors = metadata.get("authors")
-                year = metadata.get("year")
-                journal = metadata.get("journal")
-
-            # Generate readable name based on current state
-            readable_name = self._generate_readable_name(
-                comprehensive_metadata=metadata,
-                master_storage_path=master_storage_path,
-                authors=authors,
-                year=year,
-                journal=journal,
-            )
-
-            # Create/update symlink
-            return self._create_project_symlink(
-                master_storage_path=master_storage_path,
-                project=project,
-                readable_name=readable_name,
-            )
-        except Exception as exc_:
-            logger.error(
-                f"Failed to update symlink for {master_storage_path.name}: {exc_}"
-            )
-            return None
-
-    def _create_project_symlink(
-        self, master_storage_path: Path, project: str, readable_name: str
-    ) -> Optional[Path]:
-        """Create symlink in project directory pointing to master storage.
-
-        Removes old symlinks for the same paper with different statuses
-        (e.g., removes PDF_p when creating PDF_s).
-        """
-
-        try:
-            project_dir = self.config.path_manager.get_library_project_dir(project)
-            symlink_path = project_dir / readable_name
-
-            # Extract the master ID from the target path to find old symlinks
-            master_id = master_storage_path.name
-
-            # Remove old symlinks pointing to the same master entry
-            # but with different statuses (PDF_p, PDF_f, PDF_s)
-            for existing_link in project_dir.iterdir():
-                if not existing_link.is_symlink():
-                    continue
-
-                # Check if this symlink points to the same master entry
-                try:
-                    target = existing_link.resolve()
-                    if target.name == master_id and existing_link.name != readable_name:
-                        # This is an old symlink for the same paper
-                        logger.debug(f"Removing old symlink: {existing_link.name}")
-                        existing_link.unlink()
-                except Exception as e:
-                    # Handle broken symlinks
-                    logger.debug(f"Skipping broken symlink {existing_link.name}: {e}")
-                    continue
-
-            # Create new symlink
-            if not symlink_path.exists():
-                relative_path = os.path.relpath(master_storage_path, project_dir)
-                symlink_path.symlink_to(relative_path)
-                logger.success(
-                    f"Created project symlink: {symlink_path} -> {relative_path}"
-                )
-            else:
-                logger.debug(f"Project symlink already exists: {symlink_path}")
-
-            return symlink_path
-
-        except Exception as exc_:
-            logger.warning(f"Failed to create project symlink: {exc_}")
-            return None
-
-    def _create_bibtex_info_structure(
-        self,
-        project: str,
-        paper_info: Dict[str, Any],
-        complete_metadata: Dict[str, Any],
-        bibtex_source_filename: str = "papers",
-    ) -> Optional[Path]:
-        """Create info/papers_bib/pac.bib structure."""
-        try:
-            project_dir = self.config.path_manager.get_library_project_dir(project)
-            info_dir = project_dir / "info" / f"{bibtex_source_filename}_bib"
-            info_dir.mkdir(parents=True, exist_ok=True)
-
-            bibtex_file = info_dir / f"{bibtex_source_filename}.bib"
-            unresolved_dir = info_dir / "unresolved"
-            unresolved_dir.mkdir(parents=True, exist_ok=True)
-
-            first_author = "unknown"
-            if complete_metadata.get("authors"):
-                authors = complete_metadata["authors"]
-                if isinstance(authors, list) and authors:
-                    first_author = str(authors[0]).split()[-1].lower()
-                elif isinstance(authors, str):
-                    first_author = authors.split()[-1].lower()
-
-            year = complete_metadata.get("year", "unknown")
-            entry_key = f"{first_author}{year}"
-
-            bibtex_entry = self._generate_bibtex_entry(complete_metadata, entry_key)
-
-            if bibtex_file.exists():
-                with open(bibtex_file, "a", encoding="utf-8") as file_:
-                    file_.write(f"\n{bibtex_entry}")
-            else:
-                with open(bibtex_file, "w", encoding="utf-8") as file_:
-                    file_.write(bibtex_entry)
-
-            if not complete_metadata.get("doi"):
-                unresolved_file = unresolved_dir / f"{entry_key}.json"
-                unresolved_data = {
-                    "title": complete_metadata.get("title", ""),
-                    "authors": complete_metadata.get("authors", []),
-                    "year": complete_metadata.get("year", ""),
-                    "journal": complete_metadata.get("journal", ""),
-                    "scholar_id": complete_metadata.get("scholar_id", ""),
-                    "resolution_failed": True,
-                    "timestamp": complete_metadata.get("created_at", ""),
-                }
-                with open(unresolved_file, "w", encoding="utf-8") as file_:
-                    json.dump(unresolved_data, file_, indent=2)
-                logger.info(f"Added unresolved entry: {unresolved_file}")
-
-            logger.success(f"Updated BibTeX info structure: {bibtex_file}")
-            return info_dir
-
-        except Exception as exc_:
-            logger.warning(f"Failed to create BibTeX info structure: {exc_}")
-            return None
-
-    def _generate_bibtex_entry(self, metadata: Dict[str, Any], entry_key: str) -> str:
-        """Generate BibTeX entry from metadata."""
-        entry_type = "article"
-        if metadata.get("journal"):
-            entry_type = "article"
-        elif metadata.get("booktitle"):
-            entry_type = "inproceedings"
-        elif metadata.get("publisher") and not metadata.get("journal"):
-            entry_type = "book"
-
-        bibtex = f"@{entry_type}{{{entry_key},\n"
-
-        field_mappings = {
-            "title": "title",
-            "authors": "author",
-            "year": "year",
-            "journal": "journal",
-            "doi": "doi",
-            "volume": "volume",
-            "issue": "number",
-            "pages": "pages",
-            "publisher": "publisher",
-            "booktitle": "booktitle",
-            "abstract": "abstract",
-        }
-
-        for meta_field, bibtex_field in field_mappings.items():
-            value = metadata.get(meta_field)
-            if value:
-                if isinstance(value, list):
-                    value = " and ".join(str(val_) for val_ in value)
-                value_escaped = str(value).replace("{", "\\{").replace("}", "\\}")
-                bibtex += f"  {bibtex_field} = {{{value_escaped}}},\n"
-
-                source_field = f"{meta_field}_source"
-                if source_field in metadata:
-                    bibtex += f"  % {bibtex_field}_source = {metadata[source_field]}\n"
-
-        bibtex += f"  % scholar_id = {metadata.get('scholar_id', 'unknown')},\n"
-        bibtex += f"  % created_at = {metadata.get('created_at', 'unknown')},\n"
-        bibtex += f"  % created_by = {metadata.get('created_by', 'unknown')},\n"
-        bibtex += "}\n"
-
-        return bibtex
-
-    # def _ensure_project_symlink(
-    #     self,
-    #     title: str,
-    #     year: Optional[int] = None,
-    #     authors: Optional[List[str]] = None,
-    #     paper_id: str = None,
-    #     master_storage_path: Path = None,
-    # ) -> None:
-    #     """Ensure project symlink exists for paper in master library."""
-    #     try:
-    #         if not paper_id or not master_storage_path:
-    #             return
-
-    #         project_lib_path = (
-    #             self.config.path_manager.get_scholar_library_path()
-    #             / self.project
-    #         )
-    #         project_lib_path.mkdir(parents=True, exist_ok=True)
-
-    #         paper_info = {
-    #             "title": title,
-    #             "year": year,
-    #             "authors": authors or [],
-    #         }
-    #         readable_paths = self.config.path_manager.get_paper_storage_paths(
-    #             paper_info=paper_info, collection_name=self.project
-    #         )
-    #         readable_name = readable_paths["readable_name"]
-    #         symlink_path = project_lib_path / readable_name
-
-    #         relative_path = f"../MASTER/{paper_id}"
-    #         if not symlink_path.exists():
-    #             symlink_path.symlink_to(relative_path)
-    #             logger.info(
-    #                 f"Created project symlink: {readable_name} -> {relative_path}"
-    #             )
-
-    #     except Exception as exc_:
-    #         logger.debug(f"Error creating project symlink: {exc_}")
-
-    def _ensure_project_symlink(
-        self,
-        title: str,
-        year: Optional[int] = None,
-        authors: Optional[List[str]] = None,
-        paper_id: str = None,
-        master_storage_path: Path = None,
-    ) -> None:
-        try:
-            if not paper_id or not master_storage_path:
-                return
-
-            project_lib_path = (
-                self.config.path_manager.get_scholar_library_path() / self.project
-            )
-            project_lib_path.mkdir(parents=True, exist_ok=True)
-
-            paper_info = {
-                "title": title,
-                "year": year,
-                "authors": authors or [],
-            }
-            readable_paths = self._call_path_manager_get_storage_paths(
-                paper_info=paper_info, collection_name=self.project
-            )
-            readable_name = readable_paths["readable_name"]
-            symlink_path = project_lib_path / readable_name
-            relative_path = f"../MASTER/{paper_id}"
-
-            if not symlink_path.exists():
-                symlink_path.symlink_to(relative_path)
-                logger.info(
-                    f"Created project symlink: {readable_name} -> {relative_path}"
-                )
-        except Exception as exc_:
-            logger.debug(f"Error creating project symlink: {exc_}")
-
-    def _is_title_similar(
-        self, title1: str, title2: str, threshold: float = 0.7
-    ) -> bool:
-        """Check if two titles are similar enough to be considered the same paper."""
-        if not title1 or not title2:
-            return False
-
-        def normalize_title(title: str) -> str:
-            title = title.lower()
-            title = re.sub(r"[^\w\s]", " ", title)
-            title = re.sub(r"\s+", " ", title)
-            return title.strip()
-
-        norm_title1 = normalize_title(title1)
-        norm_title2 = normalize_title(title2)
-
-        words1 = set(norm_title1.split())
-        words2 = set(norm_title2.split())
-
-        if not words1 or not words2:
-            return False
-
-        intersection = len(words1.intersection(words2))
-        union = len(words1.union(words2))
-        similarity = intersection / union if union > 0 else 0.0
-
-        return similarity >= threshold
-
-    def update_library_metadata(
-        self,
-        paper_id: str,
-        project: str,
-        doi: str,
-        metadata: Dict[str, Any],
-        create_structure: bool = True,
-    ) -> bool:
-        """Update Scholar library metadata.json with resolved DOI."""
-        try:
-            library_path = self.config.path_manager.library_dir
-            paper_dir = library_path / project / paper_id
-            metadata_file = paper_dir / "metadata.json"
-
-            if create_structure and not paper_dir.exists():
-                self.config.path_manager._ensure_directory(paper_dir)
-                logger.info(f"Created Scholar library structure: {paper_dir}")
-
-            existing_metadata = {}
-            if metadata_file.exists():
-                try:
-                    with open(metadata_file, "r") as file_:
-                        existing_metadata = json.load(file_)
-                except Exception as exc_:
-                    logger.warning(f"Error loading existing metadata: {exc_}")
-
-            updated_metadata = {
-                **existing_metadata,
-                **metadata,
-                "doi": doi,
-                "doi_resolved_at": datetime.now().isoformat(),
-                "doi_source": "batch_doi_resolver",
-            }
-
-            with open(metadata_file, "w") as file_:
-                json.dump(updated_metadata, file_, indent=2)
-
-            logger.success(f"Updated metadata for {paper_id}: DOI {doi}")
-            return True
-
-        except Exception as exc_:
-            logger.error(f"Error updating library metadata for {paper_id}: {exc_}")
-            return False
-
-    def create_writer_directory_structure(self, paper_id: str, project: str) -> Path:
-        """Create basic paper directory structure."""
-        library_path = self.config.path_manager.library_dir
-        paper_dir = library_path / project / paper_id
-
-        self.config.path_manager._ensure_directory(paper_dir)
-
-        for subdir in ["attachments", "screenshots"]:
-            subdir_path = paper_dir / subdir
-            self.config.path_manager._ensure_directory(subdir_path)
-
-        logger.info(f"Created Scholar library structure: {paper_dir}")
-        return paper_dir
-
-    def validate_library_structure(self, project: str) -> Dict[str, Any]:
-        """Validate existing library structure for a project."""
-        validation = {
-            "valid": True,
-            "warnings": [],
-            "errors": [],
-            "paper_count": 0,
-            "missing_metadata": [],
-        }
-
-        library_path = self.config.path_manager.library_dir
-        project_dir = library_path / project
-
-        if not project_dir.exists():
-            validation["errors"].append(
-                f"Project directory does not exist: {project_dir}"
-            )
-            validation["valid"] = False
-            return validation
-
-        for paper_dir in project_dir.iterdir():
-            if paper_dir.is_dir() and len(paper_dir.name) == 8:
-                validation["paper_count"] += 1
-
-                metadata_file = paper_dir / "metadata.json"
-                if not metadata_file.exists():
-                    validation["missing_metadata"].append(paper_dir.name)
-                    validation["warnings"].append(
-                        f"Missing metadata.json: {paper_dir.name}"
-                    )
-
-        return validation
-
-    def resolve_and_update_library(
-        self,
-        papers_with_ids: List[Dict[str, Any]],
-        project: str,
-        sources: Optional[List[str]] = None,
-    ) -> Dict[str, str]:
-        """Resolve DOIs and update Scholar library metadata.json files."""
-        if not self.single_doi_resolver:
-            raise ValueError("SingleDOIResolver is required for resolving DOIs")
-
-        results = {}
-        for paper in papers_with_ids:
-            paper_id = paper.get("paper_id")
-            if not paper_id:
-                logger.warning(
-                    f"Skipping paper without paper_id: {paper.get('title', 'Unknown')}"
-                )
-                continue
-
-            title = paper.get("title")
-            if not title:
-                logger.warning(f"Skipping paper {paper_id} without title")
-                continue
-
-            logger.info(f"Resolving DOI for {paper_id}: {title[:50]}...")
-
-            try:
-                result = asyncio.run(
-                    self.single_doi_resolver.metadata2doi_async(
-                        title=title,
-                        year=paper.get("year"),
-                        authors=paper.get("authors"),
-                        sources=sources,
-                    )
-                )
-
-                if result and isinstance(result, dict) and result.get("doi"):
-                    doi = result["doi"]
-
-                    success = self.update_library_metadata(
-                        paper_id=paper_id,
-                        project=project,
-                        doi=doi,
-                        metadata={
-                            "title": title,
-                            "title_source": "input",
-                            "year": paper.get("year"),
-                            "year_source": ("input" if paper.get("year") else None),
-                            "authors": paper.get("authors"),
-                            "authors_source": (
-                                "input" if paper.get("authors") else None
-                            ),
-                            "journal": paper.get("journal"),
-                            "journal_source": (
-                                "input" if paper.get("journal") else None
-                            ),
-                            "doi_resolution_source": result.get("source"),
-                        },
-                    )
-
-                    if success:
-                        results[paper_id] = doi
-                        logger.success(f"✅ {paper_id}: {doi}")
-                    else:
-                        logger.error(
-                            f"❌ {paper_id}: DOI resolved but metadata update failed"
-                        )
-                else:
-                    logger.warning(f"⚠️ {paper_id}: No DOI found")
-
-            except Exception as exc_:
-                logger.error(f"❌ {paper_id}: Error during resolution: {exc_}")
-
-        logger.success(
-            f"Resolved {len(results)}/{len(papers_with_ids)} DOIs and updated library metadata"
-        )
-        return results
-
-    def resolve_and_create_library_structure(
-        self,
-        papers: List[Dict[str, Any]],
-        project: str,
-        sources: Optional[List[str]] = None,
-    ) -> Dict[str, Dict[str, str]]:
-        """Synchronous wrapper for resolve_and_create_library_structure_async."""
-        try:
-            loop = asyncio.get_event_loop()
-            if loop.is_running():
-                raise RuntimeError(
-                    "Cannot run synchronous version in async context. "
-                    "Use resolve_and_create_library_structure_async() instead."
-                )
-            else:
-                return loop.run_until_complete(
-                    self.resolve_and_create_library_structure_async(
-                        papers, project, sources
-                    )
-                )
-        except RuntimeError:
-            return asyncio.run(
-                self.resolve_and_create_library_structure_async(
-                    papers, project, sources
-                )
-            )
-
 
 __all__ = ["LibraryManager"]
 
+
 # EOF