#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Timestamp: 2026-01-27
# File: src/scitex_writer/_mcp/tools/bib.py
"""Bibliography MCP tools."""
import re
from typing import Optional
from fastmcp import FastMCP
from ..utils import resolve_project_path
def register_tools(mcp: FastMCP) -> None:
"""Register bibliography tools."""
@mcp.tool()
def writer_list_bibfiles(project_dir: str) -> dict:
"""[writer] List all bibliography files in the project."""
try:
project_path = resolve_project_path(project_dir)
bib_dir = project_path / "00_shared" / "bib_files"
if not bib_dir.exists():
return {"success": True, "bibfiles": [], "count": 0}
bibfiles = []
for bib_file in sorted(bib_dir.glob("*.bib")):
content = bib_file.read_text(encoding="utf-8")
entry_count = content.count("@")
bibfiles.append(
{
"name": bib_file.name,
"path": str(bib_file),
"entry_count": entry_count,
"is_merged": bib_file.name == "bibliography.bib",
}
)
return {"success": True, "bibfiles": bibfiles, "count": len(bibfiles)}
except Exception as e:
return {"success": False, "error": str(e)}
@mcp.tool()
def writer_list_bibentries(project_dir: str, bibfile: Optional[str] = None) -> dict:
"""[writer] List all BibTeX entries in the project or specific file."""
try:
project_path = resolve_project_path(project_dir)
bib_dir = project_path / "00_shared" / "bib_files"
if not bib_dir.exists():
return {"success": True, "entries": [], "count": 0}
entries = []
files_to_scan = (
[bib_dir / bibfile] if bibfile else list(bib_dir.glob("*.bib"))
)
for bib_file in files_to_scan:
if not bib_file.exists():
continue
content = bib_file.read_text(encoding="utf-8")
# Extract citation keys and types
pattern = r"@(\w+)\{([^,\s]+)"
for match in re.finditer(pattern, content):
entry_type, citation_key = match.groups()
entries.append(
{
"citation_key": citation_key,
"entry_type": entry_type,
"bibfile": bib_file.name,
}
)
return {"success": True, "entries": entries, "count": len(entries)}
except Exception as e:
return {"success": False, "error": str(e)}
@mcp.tool()
def writer_get_bibentry(project_dir: str, citation_key: str) -> dict:
"""[writer] Get a specific BibTeX entry by citation key."""
try:
project_path = resolve_project_path(project_dir)
bib_dir = project_path / "00_shared" / "bib_files"
if not bib_dir.exists():
return {"success": False, "error": "No bib_files directory found"}
for bib_file in bib_dir.glob("*.bib"):
content = bib_file.read_text(encoding="utf-8")
# Match @type{citation_key, ... }
pattern = rf"(@\w+\{{{citation_key}\s*,.*?(?=\n@|\Z))"
match = re.search(pattern, content, re.DOTALL)
if match:
return {
"success": True,
"citation_key": citation_key,
"bibfile": str(bib_file),
"entry": match.group(1).strip(),
}
return {
"success": False,
"error": f"Citation key not found: {citation_key}",
}
except Exception as e:
return {"success": False, "error": str(e)}
@mcp.tool()
def writer_add_bibentry(
project_dir: str,
bibtex_entry: str,
bibfile: str = "custom.bib",
deduplicate: bool = True,
) -> dict:
"""[writer] Add a BibTeX entry to a bibliography file.
Args:
project_dir: Path to project
bibtex_entry: The BibTeX entry to add
bibfile: Target bib file name (default: custom.bib)
deduplicate: Check for existing entry with same key (default: True)
"""
try:
project_path = resolve_project_path(project_dir)
bib_dir = project_path / "00_shared" / "bib_files"
bib_dir.mkdir(parents=True, exist_ok=True)
# Extract citation key from entry
key_match = re.search(r"@\w+\{([^,\s]+)", bibtex_entry)
if not key_match:
return {"success": False, "error": "Could not parse citation key"}
citation_key = key_match.group(1)
# Check for duplicates if requested
if deduplicate:
existing = writer_get_bibentry.__wrapped__(project_dir, citation_key)
if existing.get("success"):
return {
"success": False,
"error": f"Duplicate citation key: {citation_key}",
"existing_file": existing.get("bibfile"),
}
bib_path = bib_dir / bibfile
if bib_path.exists():
current_content = bib_path.read_text(encoding="utf-8")
if not current_content.endswith("\n"):
current_content += "\n"
new_content = current_content + "\n" + bibtex_entry.strip() + "\n"
else:
new_content = bibtex_entry.strip() + "\n"
bib_path.write_text(new_content, encoding="utf-8")
return {
"success": True,
"bibfile": str(bib_path),
"citation_key": citation_key,
"message": f"Entry '{citation_key}' added to {bibfile}",
}
except Exception as e:
return {"success": False, "error": str(e)}
@mcp.tool()
def writer_remove_bibentry(
project_dir: str,
citation_key: str,
) -> dict:
"""[writer] Remove a BibTeX entry by citation key."""
try:
project_path = resolve_project_path(project_dir)
bib_dir = project_path / "00_shared" / "bib_files"
if not bib_dir.exists():
return {"success": False, "error": "No bib_files directory found"}
for bib_file in bib_dir.glob("*.bib"):
content = bib_file.read_text(encoding="utf-8")
# Match the full entry
pattern = rf"@\w+\{{{citation_key}\s*,.*?(?=\n@|\Z)"
match = re.search(pattern, content, re.DOTALL)
if match:
new_content = content[: match.start()] + content[match.end() :]
# Clean up extra newlines
new_content = re.sub(r"\n{3,}", "\n\n", new_content).strip() + "\n"
bib_file.write_text(new_content, encoding="utf-8")
return {
"success": True,
"citation_key": citation_key,
"removed_from": str(bib_file),
}
return {
"success": False,
"error": f"Citation key not found: {citation_key}",
}
except Exception as e:
return {"success": False, "error": str(e)}
@mcp.tool()
def writer_merge_bibfiles(
project_dir: str,
output_file: str = "bibliography.bib",
deduplicate: bool = True,
) -> dict:
"""[writer] Merge all .bib files into one, with optional deduplication.
Deduplication is done by citation key (first occurrence wins).
"""
try:
project_path = resolve_project_path(project_dir)
bib_dir = project_path / "00_shared" / "bib_files"
if not bib_dir.exists():
return {"success": False, "error": "No bib_files directory found"}
output_path = bib_dir / output_file
seen_keys = set()
merged_entries = []
duplicates = []
for bib_file in sorted(bib_dir.glob("*.bib")):
if bib_file.name == output_file:
continue
content = bib_file.read_text(encoding="utf-8")
# Split into entries
entries = re.findall(r"(@\w+\{[^@]*)", content, re.DOTALL)
for entry in entries:
entry = entry.strip()
if not entry:
continue
# Extract citation key
key_match = re.search(r"@\w+\{([^,\s]+)", entry)
if not key_match:
continue
citation_key = key_match.group(1)
if deduplicate and citation_key in seen_keys:
duplicates.append({"key": citation_key, "file": bib_file.name})
continue
seen_keys.add(citation_key)
merged_entries.append(entry)
# Write merged file
output_content = "\n\n".join(merged_entries) + "\n"
output_path.write_text(output_content, encoding="utf-8")
return {
"success": True,
"output_file": str(output_path),
"entry_count": len(merged_entries),
"duplicates_skipped": len(duplicates),
"duplicates": duplicates[:10] if duplicates else [],
}
except Exception as e:
return {"success": False, "error": str(e)}
# EOF
/