File size: 11,061 Bytes
3d83b62 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 | """Verification service for BibTeX entries.
This service extracts the core verification logic from app.py,
making it reusable for both Gradio UI and FastAPI endpoints.
"""
import tempfile
import threading
from pathlib import Path
from concurrent.futures import ThreadPoolExecutor, as_completed
from dataclasses import dataclass
from typing import Optional
from src.parsers import BibParser
from src.fetchers import (
ArxivFetcher,
ScholarFetcher,
CrossRefFetcher,
SemanticScholarFetcher,
OpenAlexFetcher,
DBLPFetcher,
)
from src.analyzers import MetadataComparator, DuplicateDetector
from src.report.generator import EntryReport
from src.config.workflow import get_default_workflow
from src.utils.normalizer import TextNormalizer
from src.core.config import settings
from src.core.logging import get_logger
from src.core.exceptions import ParserException, FetcherException
logger = get_logger(__name__)
@dataclass
class VerificationResult:
"""Result of BibTeX verification."""
entry_reports: list[EntryReport]
duplicate_groups: list
verified_count: int
warning_count: int
error_count: int
total_count: int
@property
def success_rate(self) -> float:
"""Calculate success rate."""
if self.total_count == 0:
return 0.0
return (self.verified_count / self.total_count) * 100
class VerificationService:
"""Service for verifying BibTeX entries against academic databases."""
def __init__(self):
"""Initialize verification service."""
self.parser = BibParser()
self.arxiv_fetcher = ArxivFetcher()
self.crossref_fetcher = CrossRefFetcher()
self.scholar_fetcher = ScholarFetcher()
self.semantic_scholar_fetcher = SemanticScholarFetcher()
self.openalex_fetcher = OpenAlexFetcher()
self.dblp_fetcher = DBLPFetcher()
self.comparator = MetadataComparator()
self.duplicate_detector = DuplicateDetector()
logger.info("VerificationService initialized")
def verify_bibtex_string(
self,
bibtex_content: str,
progress_callback: Optional[callable] = None,
) -> VerificationResult:
"""Verify BibTeX content from string.
Args:
bibtex_content: BibTeX content as string
progress_callback: Optional callback for progress updates (progress, desc)
Returns:
VerificationResult with all verification data
Raises:
ParserException: If BibTeX parsing fails
FetcherException: If fetching fails
"""
if not bibtex_content.strip():
raise ParserException("Empty BibTeX content provided")
logger.info("Starting BibTeX verification")
# Parse BibTeX
try:
if progress_callback:
progress_callback(0, "Parsing BibTeX...")
# Write to temporary file
with tempfile.NamedTemporaryFile(
mode="w", suffix=".bib", delete=False, encoding="utf-8"
) as f:
f.write(bibtex_content)
temp_bib_path = f.name
entries = self.parser.parse_file(temp_bib_path)
Path(temp_bib_path).unlink() # Delete temp file
if not entries:
raise ParserException("No valid BibTeX entries found")
logger.info(f"Parsed {len(entries)} BibTeX entries")
except Exception as e:
logger.error(f"BibTeX parsing failed: {e}")
raise ParserException(f"Failed to parse BibTeX: {str(e)}")
# Detect duplicates
duplicate_groups = self.duplicate_detector.find_duplicates(entries)
if duplicate_groups:
logger.warning(f"Found {len(duplicate_groups)} duplicate groups")
# Get workflow configuration
workflow_config = get_default_workflow()
# Process entries
entry_reports = []
progress_lock = threading.Lock()
verified_count = 0
warning_count = 0
error_count = 0
if progress_callback:
progress_callback(0.1, "Initializing fetchers...")
def process_single_entry(entry, idx, total):
"""Process a single BibTeX entry."""
comparison_result = None
all_results = []
for step in workflow_config.get_enabled_steps():
result = None
try:
if step.name == "arxiv_id" and entry.has_arxiv and self.arxiv_fetcher:
arxiv_meta = self.arxiv_fetcher.fetch_by_id(entry.arxiv_id)
if arxiv_meta:
result = self.comparator.compare_with_arxiv(entry, arxiv_meta)
elif step.name == "crossref_doi" and entry.doi and self.crossref_fetcher:
crossref_result = self.crossref_fetcher.search_by_doi(entry.doi)
if crossref_result:
result = self.comparator.compare_with_crossref(entry, crossref_result)
elif step.name == "semantic_scholar" and entry.title and self.semantic_scholar_fetcher:
ss_result = (
self.semantic_scholar_fetcher.fetch_by_doi(entry.doi)
if entry.doi
else None
)
if not ss_result:
ss_result = self.semantic_scholar_fetcher.search_by_title(entry.title)
if ss_result:
result = self.comparator.compare_with_semantic_scholar(entry, ss_result)
elif step.name == "dblp" and entry.title and self.dblp_fetcher:
dblp_result = self.dblp_fetcher.search_by_title(entry.title)
if dblp_result:
result = self.comparator.compare_with_dblp(entry, dblp_result)
elif step.name == "openalex" and entry.title and self.openalex_fetcher:
oa_result = (
self.openalex_fetcher.fetch_by_doi(entry.doi)
if entry.doi
else None
)
if not oa_result:
oa_result = self.openalex_fetcher.search_by_title(entry.title)
if oa_result:
result = self.comparator.compare_with_openalex(entry, oa_result)
elif step.name == "arxiv_title" and entry.title and self.arxiv_fetcher:
results = self.arxiv_fetcher.search_by_title(entry.title, max_results=3)
if results:
best_result = None
best_sim = 0.0
norm1 = TextNormalizer.normalize_for_comparison(entry.title)
for r in results:
sim = TextNormalizer.similarity_ratio(
norm1,
TextNormalizer.normalize_for_comparison(r.title),
)
if sim > best_sim:
best_sim, best_result = sim, r
if best_result and best_sim > 0.5:
result = self.comparator.compare_with_arxiv(entry, best_result)
elif step.name == "crossref_title" and entry.title and self.crossref_fetcher:
crossref_result = self.crossref_fetcher.search_by_title(entry.title)
if crossref_result:
result = self.comparator.compare_with_crossref(entry, crossref_result)
elif step.name == "google_scholar" and entry.title and self.scholar_fetcher:
scholar_result = self.scholar_fetcher.search_by_title(entry.title)
if scholar_result:
result = self.comparator.compare_with_scholar(entry, scholar_result)
except Exception as e:
logger.warning(f"Error in step {step.name} for entry {entry.key}: {e}")
continue
if result:
all_results.append(result)
if result.is_match:
comparison_result = result
break
# Select best result if no perfect match
if not comparison_result and all_results:
all_results.sort(key=lambda r: r.confidence, reverse=True)
comparison_result = all_results[0]
elif not comparison_result:
comparison_result = self.comparator.create_unable_result(
entry, "Unable to find this paper in any data source"
)
return EntryReport(entry=entry, comparison=comparison_result)
# Process entries concurrently
max_workers = min(settings.max_workers, len(entries))
logger.info(f"Processing {len(entries)} entries with {max_workers} workers")
with ThreadPoolExecutor(max_workers=max_workers) as executor:
future_to_entry = {
executor.submit(process_single_entry, e, i, len(entries)): (e, i)
for i, e in enumerate(entries)
}
for future in as_completed(future_to_entry):
entry, idx = future_to_entry[future]
try:
entry_report = future.result()
with progress_lock:
entry_reports.append(entry_report)
if entry_report.comparison and entry_report.comparison.is_match:
verified_count += 1
elif entry_report.comparison and entry_report.comparison.has_issues:
warning_count += 1
else:
error_count += 1
if progress_callback:
progress_callback(
0.1 + (0.9 * (idx + 1) / len(entries)),
f"Verifying entries {idx + 1}/{len(entries)}...",
)
except Exception as e:
with progress_lock:
error_count += 1
logger.error(f"Error processing entry {entry.key}: {e}")
logger.info(
f"Verification complete: {verified_count} verified, "
f"{warning_count} warnings, {error_count} errors"
)
return VerificationResult(
entry_reports=entry_reports,
duplicate_groups=duplicate_groups,
verified_count=verified_count,
warning_count=warning_count,
error_count=error_count,
total_count=len(entries),
)
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