scitex 2.14.0__py3-none-any.whl

scitex/scholar/storage/_LibraryManager.py

@@ -0,0 +1,1725 @@
+#!/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__)
+# ----------------------------------------
+
+__FILE__ = __file__
+
+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 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
+
+logger = logging.getLogger(__name__)
+
+
+class LibraryManager:
+    """Unified manager for Scholar library structure and paper storage."""
+
+    def __init__(
+        self,
+        project: str = None,
+        single_doi_resolver=None,
+        config: Optional[ScholarConfig] = None,
+    ):
+        """Initialize library manager."""
+        self.config = config or ScholarConfig()
+        self.project = self.config.resolve("project", project)
+        self.library_master_dir = self.config.path_manager.get_library_master_dir()
+        self.single_doi_resolver = single_doi_resolver
+        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