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"""
BibTeX file parser.
"""
import re
from dataclasses import dataclass, field
from typing import Optional
from pathlib import Path
import bibtexparser
from bibtexparser.bparser import BibTexParser
from bibtexparser.customization import convert_to_unicode
@dataclass
class BibEntry:
"""Represents a parsed bibliography entry."""
key: str
entry_type: str
title: str = ""
author: str = ""
year: str = ""
abstract: str = ""
url: str = ""
doi: str = ""
arxiv_id: str = ""
journal: str = ""
booktitle: str = ""
publisher: str = ""
pages: str = ""
volume: str = ""
number: str = ""
raw_entry: dict = field(default_factory=dict)
@property
def has_arxiv(self) -> bool:
"""Check if entry has arXiv information."""
return bool(self.arxiv_id)
@property
def search_query(self) -> str:
"""Get search query for this entry."""
return self.title or self.key
class BibParser:
"""Parser for .bib files."""
# Patterns for extracting arXiv IDs
ARXIV_PATTERNS = [
# New format: 2301.00001 or 2301.00001v1
r'(\d{4}\.\d{4,5}(?:v\d+)?)',
# Old format: hep-th/9901001 or math.GT/0309136
r'([a-z-]+(?:\.[A-Z]{2})?/\d{7}(?:v\d+)?)',
# arXiv: prefix
r'arXiv:(\d{4}\.\d{4,5}(?:v\d+)?)',
r'arXiv:([a-z-]+(?:\.[A-Z]{2})?/\d{7}(?:v\d+)?)',
]
# URL patterns for arXiv
ARXIV_URL_PATTERNS = [
r'arxiv\.org/abs/(\d{4}\.\d{4,5}(?:v\d+)?)',
r'arxiv\.org/abs/([a-z-]+(?:\.[A-Z]{2})?/\d{7}(?:v\d+)?)',
r'arxiv\.org/pdf/(\d{4}\.\d{4,5}(?:v\d+)?)(?:\.pdf)?',
r'arxiv\.org/pdf/([a-z-]+(?:\.[A-Z]{2})?/\d{7}(?:v\d+)?)(?:\.pdf)?',
]
def __init__(self):
self.entries: list[BibEntry] = []
def parse_file(self, filepath: str) -> list[BibEntry]:
"""Parse a .bib file and return list of entries."""
path = Path(filepath)
if not path.exists():
raise FileNotFoundError(f"Bib file not found: {filepath}")
with open(path, 'r', encoding='utf-8', errors='replace') as f:
content = f.read()
return self.parse_content(content)
def parse_content(self, content: str) -> list[BibEntry]:
"""Parse bib content string."""
parser = BibTexParser(common_strings=True)
parser.customization = convert_to_unicode
try:
bib_database = bibtexparser.loads(content, parser=parser)
except Exception as e:
raise ValueError(f"Failed to parse bib content: {e}")
self.entries = []
for entry in bib_database.entries:
bib_entry = self._convert_entry(entry)
self.entries.append(bib_entry)
return self.entries
def _convert_entry(self, entry: dict) -> BibEntry:
"""Convert a bibtexparser entry to BibEntry."""
# Extract basic fields
bib_entry = BibEntry(
key=entry.get('ID', ''),
entry_type=entry.get('ENTRYTYPE', ''),
title=entry.get('title', ''),
author=entry.get('author', ''),
year=entry.get('year', ''),
abstract=entry.get('abstract', ''),
url=entry.get('url', ''),
doi=entry.get('doi', ''),
journal=entry.get('journal', ''),
booktitle=entry.get('booktitle', ''),
publisher=entry.get('publisher', ''),
pages=entry.get('pages', ''),
volume=entry.get('volume', ''),
number=entry.get('number', ''),
raw_entry=entry.copy()
)
# Extract arXiv ID
bib_entry.arxiv_id = self._extract_arxiv_id(entry)
return bib_entry
def _extract_arxiv_id(self, entry: dict) -> str:
"""Extract arXiv ID from entry."""
# Check eprint field first
eprint = entry.get('eprint', '')
if eprint:
arxiv_id = self._parse_arxiv_id(eprint)
if arxiv_id:
return arxiv_id
# Check arxiv field
arxiv = entry.get('arxiv', '')
if arxiv:
arxiv_id = self._parse_arxiv_id(arxiv)
if arxiv_id:
return arxiv_id
# Check URL field
url = entry.get('url', '')
if url:
for pattern in self.ARXIV_URL_PATTERNS:
match = re.search(pattern, url, re.IGNORECASE)
if match:
return match.group(1)
# Check journal field for "arXiv preprint arXiv:XXXX.XXXXX" format
journal = entry.get('journal', '')
if journal and 'arxiv' in journal.lower():
arxiv_id = self._parse_arxiv_id(journal)
if arxiv_id:
return arxiv_id
# Check note field
note = entry.get('note', '')
if note:
arxiv_id = self._parse_arxiv_id(note)
if arxiv_id:
return arxiv_id
return ""
def _parse_arxiv_id(self, text: str) -> str:
"""Parse arXiv ID from text."""
for pattern in self.ARXIV_PATTERNS:
match = re.search(pattern, text)
if match:
return match.group(1)
return ""
def get_entry_by_key(self, key: str) -> Optional[BibEntry]:
"""Get entry by citation key."""
for entry in self.entries:
if entry.key == key:
return entry
return None
def filter_file(self, input_path: str, output_path: str, keys_to_keep: set[str]):
"""
Create a new bib file containing only specified keys.
Preserves original formatting, comments, and strings.
"""
with open(input_path, 'r', encoding='utf-8') as f:
content = f.read()
filtered_content = self._filter_content(content, keys_to_keep)
with open(output_path, 'w', encoding='utf-8') as f:
f.write(filtered_content)
def _filter_content(self, content: str, keys_to_keep: set[str]) -> str:
"""Filter content string keeping only specified keys."""
ranges_to_remove = []
i = 0
length = len(content)
while i < length:
if content[i] == '@':
start = i
# Find opening brace
brace_open = content.find('{', i)
if brace_open == -1:
i += 1
continue
# Get entry type
entry_type = content[i+1:brace_open].strip().lower()
# Skip comments
if entry_type == 'comment':
i = brace_open + 1
continue
# Find matching closing brace to determine entry end
balance = 1
j = brace_open + 1
in_quote = False
while j < length and balance > 0:
char = content[j]
# Handle escaped characters
if char == '\\':
j += 2
continue
if char == '"':
in_quote = not in_quote
elif not in_quote:
if char == '{':
balance += 1
elif char == '}':
balance -= 1
j += 1
end = j
# Extract key (between { and ,)
# Only for standard entries, not @string or @preamble
if entry_type not in ('string', 'preamble'):
# Find comma or end of entry
# Key is usually the first token after {
key_part = content[brace_open+1:end]
comma_pos = key_part.find(',')
if comma_pos != -1:
key = key_part[:comma_pos].strip()
# If key is NOT in keep list, mark for removal
if key not in keys_to_keep:
ranges_to_remove.append((start, end))
i = end
else:
i += 1
# Reconstruct content
new_content = []
last_pos = 0
for start, end in ranges_to_remove:
new_content.append(content[last_pos:start])
# Clean up whitespace after removed entry
last_pos = end
while last_pos < length and content[last_pos] in ' \t\r':
last_pos += 1
if last_pos < length and content[last_pos] == '\n':
last_pos += 1
new_content.append(content[last_pos:])
return "".join(new_content)
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