academic-refchecker 2.0.20__tar.gz → 2.0.21__tar.gz

{academic_refchecker-2.0.20/academic_refchecker.egg-info → academic_refchecker-2.0.21}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: academic-refchecker
-Version: 2.0.20
+Version: 2.0.21
 Summary: A comprehensive tool for validating reference accuracy in academic papers
 Author-email: Mark Russinovich <markrussinovich@hotmail.com>
 License-Expression: MIT
@@ -124,6 +124,7 @@ academic-refchecker --paper /path/to/paper.pdf
 - **Comprehensive checks**: Titles, authors, years, venues, DOIs, ArXiv IDs
 - **Smart matching**: Handles formatting variations (BERT vs B-ERT, pre-trained vs pretrained)
 - **Detailed reports**: Errors, warnings, corrected references
+- **Bulk web checks**: Upload multiple files or a ZIP in the Web UI to validate many papers at once
 
 ## Sample Output
 
@@ -184,6 +185,8 @@ The Web UI shows live progress, history, and export (including corrected values)
 refchecker-webui --port 8000
 ```
 
+*Tip: You can bulk-check multiple papers by selecting several files or a single ZIP; the Web UI will group them into a batch in the history sidebar.*
+
 #### Development (frontend)
 
 ```bash
@@ -331,17 +334,17 @@ LLM-powered extraction improves accuracy with complex bibliographies. Claude Son
 | Provider | Env Variable | Example Model |
 |----------|--------------|---------------|
 | Anthropic | `ANTHROPIC_API_KEY` | `claude-sonnet-4-20250514` |
-| OpenAI | `OPENAI_API_KEY` | `gpt-4o` |
-| Google | `GOOGLE_API_KEY` | `gemini-2.5-flash` |
-| Azure | `AZURE_OPENAI_API_KEY` | `gpt-4` |
-| vLLM | (local) | `meta-llama/Llama-3.1-8B-Instruct` |
+| OpenAI | `OPENAI_API_KEY` | `gpt-5.2-mini` |
+| Google | `GOOGLE_API_KEY` | `gemini-3` |
+| Azure | `AZURE_OPENAI_API_KEY` | `gpt-4o` |
+| vLLM | (local) | `meta-llama/Llama-3.3-70B-Instruct` |
 
 ```bash
 export ANTHROPIC_API_KEY=your_key
 academic-refchecker --paper 1706.03762 --llm-provider anthropic
 
-academic-refchecker --paper paper.pdf --llm-provider openai --llm-model gpt-4o
-academic-refchecker --paper paper.pdf --llm-provider vllm --llm-model meta-llama/Llama-3.1-8B-Instruct
+academic-refchecker --paper paper.pdf --llm-provider openai --llm-model gpt-5.2-mini
+academic-refchecker --paper paper.pdf --llm-provider vllm --llm-model meta-llama/Llama-3.3-70B-Instruct
 ```
 
 #### Local models (vLLM)
@@ -350,7 +353,7 @@ There is no separate “GPU Docker image”. For local inference, install the vL
 
 ```bash
 pip install "academic-refchecker[vllm]"
-python scripts/start_vllm_server.py --model meta-llama/Llama-3.1-8B-Instruct --port 8001
+python scripts/start_vllm_server.py --model meta-llama/Llama-3.3-70B-Instruct --port 8001
 academic-refchecker --paper paper.pdf --llm-provider vllm --llm-endpoint http://localhost:8001/v1
 ```
 

{academic_refchecker-2.0.20 → academic_refchecker-2.0.21}/README.md

@@ -52,6 +52,7 @@ academic-refchecker --paper /path/to/paper.pdf
 - **Comprehensive checks**: Titles, authors, years, venues, DOIs, ArXiv IDs
 - **Smart matching**: Handles formatting variations (BERT vs B-ERT, pre-trained vs pretrained)
 - **Detailed reports**: Errors, warnings, corrected references
+- **Bulk web checks**: Upload multiple files or a ZIP in the Web UI to validate many papers at once
 
 ## Sample Output
 
@@ -112,6 +113,8 @@ The Web UI shows live progress, history, and export (including corrected values)
 refchecker-webui --port 8000
 ```
 
+*Tip: You can bulk-check multiple papers by selecting several files or a single ZIP; the Web UI will group them into a batch in the history sidebar.*
+
 #### Development (frontend)
 
 ```bash
@@ -259,17 +262,17 @@ LLM-powered extraction improves accuracy with complex bibliographies. Claude Son
 | Provider | Env Variable | Example Model |
 |----------|--------------|---------------|
 | Anthropic | `ANTHROPIC_API_KEY` | `claude-sonnet-4-20250514` |
-| OpenAI | `OPENAI_API_KEY` | `gpt-4o` |
-| Google | `GOOGLE_API_KEY` | `gemini-2.5-flash` |
-| Azure | `AZURE_OPENAI_API_KEY` | `gpt-4` |
-| vLLM | (local) | `meta-llama/Llama-3.1-8B-Instruct` |
+| OpenAI | `OPENAI_API_KEY` | `gpt-5.2-mini` |
+| Google | `GOOGLE_API_KEY` | `gemini-3` |
+| Azure | `AZURE_OPENAI_API_KEY` | `gpt-4o` |
+| vLLM | (local) | `meta-llama/Llama-3.3-70B-Instruct` |
 
 ```bash
 export ANTHROPIC_API_KEY=your_key
 academic-refchecker --paper 1706.03762 --llm-provider anthropic
 
-academic-refchecker --paper paper.pdf --llm-provider openai --llm-model gpt-4o
-academic-refchecker --paper paper.pdf --llm-provider vllm --llm-model meta-llama/Llama-3.1-8B-Instruct
+academic-refchecker --paper paper.pdf --llm-provider openai --llm-model gpt-5.2-mini
+academic-refchecker --paper paper.pdf --llm-provider vllm --llm-model meta-llama/Llama-3.3-70B-Instruct
 ```
 
 #### Local models (vLLM)
@@ -278,7 +281,7 @@ There is no separate “GPU Docker image”. For local inference, install the vL
 
 ```bash
 pip install "academic-refchecker[vllm]"
-python scripts/start_vllm_server.py --model meta-llama/Llama-3.1-8B-Instruct --port 8001
+python scripts/start_vllm_server.py --model meta-llama/Llama-3.3-70B-Instruct --port 8001
 academic-refchecker --paper paper.pdf --llm-provider vllm --llm-endpoint http://localhost:8001/v1
 ```
 

{academic_refchecker-2.0.20 → academic_refchecker-2.0.21/academic_refchecker.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: academic-refchecker
-Version: 2.0.20
+Version: 2.0.21
 Summary: A comprehensive tool for validating reference accuracy in academic papers
 Author-email: Mark Russinovich <markrussinovich@hotmail.com>
 License-Expression: MIT
@@ -124,6 +124,7 @@ academic-refchecker --paper /path/to/paper.pdf
 - **Comprehensive checks**: Titles, authors, years, venues, DOIs, ArXiv IDs
 - **Smart matching**: Handles formatting variations (BERT vs B-ERT, pre-trained vs pretrained)
 - **Detailed reports**: Errors, warnings, corrected references
+- **Bulk web checks**: Upload multiple files or a ZIP in the Web UI to validate many papers at once
 
 ## Sample Output
 
@@ -184,6 +185,8 @@ The Web UI shows live progress, history, and export (including corrected values)
 refchecker-webui --port 8000
 ```
 
+*Tip: You can bulk-check multiple papers by selecting several files or a single ZIP; the Web UI will group them into a batch in the history sidebar.*
+
 #### Development (frontend)
 
 ```bash
@@ -331,17 +334,17 @@ LLM-powered extraction improves accuracy with complex bibliographies. Claude Son
 | Provider | Env Variable | Example Model |
 |----------|--------------|---------------|
 | Anthropic | `ANTHROPIC_API_KEY` | `claude-sonnet-4-20250514` |
-| OpenAI | `OPENAI_API_KEY` | `gpt-4o` |
-| Google | `GOOGLE_API_KEY` | `gemini-2.5-flash` |
-| Azure | `AZURE_OPENAI_API_KEY` | `gpt-4` |
-| vLLM | (local) | `meta-llama/Llama-3.1-8B-Instruct` |
+| OpenAI | `OPENAI_API_KEY` | `gpt-5.2-mini` |
+| Google | `GOOGLE_API_KEY` | `gemini-3` |
+| Azure | `AZURE_OPENAI_API_KEY` | `gpt-4o` |
+| vLLM | (local) | `meta-llama/Llama-3.3-70B-Instruct` |
 
 ```bash
 export ANTHROPIC_API_KEY=your_key
 academic-refchecker --paper 1706.03762 --llm-provider anthropic
 
-academic-refchecker --paper paper.pdf --llm-provider openai --llm-model gpt-4o
-academic-refchecker --paper paper.pdf --llm-provider vllm --llm-model meta-llama/Llama-3.1-8B-Instruct
+academic-refchecker --paper paper.pdf --llm-provider openai --llm-model gpt-5.2-mini
+academic-refchecker --paper paper.pdf --llm-provider vllm --llm-model meta-llama/Llama-3.3-70B-Instruct
 ```
 
 #### Local models (vLLM)
@@ -350,7 +353,7 @@ There is no separate “GPU Docker image”. For local inference, install the vL
 
 ```bash
 pip install "academic-refchecker[vllm]"
-python scripts/start_vllm_server.py --model meta-llama/Llama-3.1-8B-Instruct --port 8001
+python scripts/start_vllm_server.py --model meta-llama/Llama-3.3-70B-Instruct --port 8001
 academic-refchecker --paper paper.pdf --llm-provider vllm --llm-endpoint http://localhost:8001/v1
 ```
 

{academic_refchecker-2.0.20 → academic_refchecker-2.0.21}/backend/database.py

@@ -144,6 +144,12 @@ class Database:
             """)
 
             await self._ensure_columns(db)
+            
+            # Create index for batch queries
+            await db.execute("""
+                CREATE INDEX IF NOT EXISTS idx_check_history_batch_id 
+                ON check_history(batch_id)
+            """)
             await db.commit()
 
     async def _ensure_columns(self, db: aiosqlite.Connection):
@@ -168,6 +174,12 @@ class Database:
             await db.execute("ALTER TABLE check_history ADD COLUMN thumbnail_path TEXT")
         if "bibliography_source_path" not in columns:
             await db.execute("ALTER TABLE check_history ADD COLUMN bibliography_source_path TEXT")
+        if "batch_id" not in columns:
+            await db.execute("ALTER TABLE check_history ADD COLUMN batch_id TEXT")
+        if "batch_label" not in columns:
+            await db.execute("ALTER TABLE check_history ADD COLUMN batch_label TEXT")
+        if "original_filename" not in columns:
+            await db.execute("ALTER TABLE check_history ADD COLUMN original_filename TEXT")
 
     async def save_check(self,
                          paper_title: str,
@@ -222,7 +234,8 @@ class Database:
                 SELECT id, paper_title, paper_source, custom_label, timestamp,
                        total_refs, errors_count, warnings_count, suggestions_count, unverified_count,
                        refs_with_errors, refs_with_warnings_only, refs_verified,
-                       llm_provider, llm_model, status, source_type
+                       llm_provider, llm_model, status, source_type, batch_id, batch_label,
+                       original_filename
                 FROM check_history
                 ORDER BY timestamp DESC
                 LIMIT ?
@@ -282,20 +295,27 @@ class Database:
                                     paper_source: str,
                                     source_type: str,
                                     llm_provider: Optional[str] = None,
-                                    llm_model: Optional[str] = None) -> int:
+                                    llm_model: Optional[str] = None,
+                                    batch_id: Optional[str] = None,
+                                    batch_label: Optional[str] = None,
+                                    original_filename: Optional[str] = None) -> int:
         """Create a pending check entry before verification starts"""
         async with aiosqlite.connect(self.db_path) as db:
             cursor = await db.execute("""
                 INSERT INTO check_history
                 (paper_title, paper_source, source_type, total_refs, errors_count, warnings_count,
-                 suggestions_count, unverified_count, results_json, llm_provider, llm_model, status)
-                VALUES (?, ?, ?, 0, 0, 0, 0, 0, '[]', ?, ?, 'in_progress')
+                 suggestions_count, unverified_count, results_json, llm_provider, llm_model, status,
+                 batch_id, batch_label, original_filename)
+                VALUES (?, ?, ?, 0, 0, 0, 0, 0, '[]', ?, ?, 'in_progress', ?, ?, ?)
             """, (
                 paper_title,
                 paper_source,
                 source_type,
                 llm_provider,
-                llm_model
+                llm_model,
+                batch_id,
+                batch_label,
+                original_filename
             ))
             await db.commit()
             return cursor.lastrowid
@@ -667,16 +687,35 @@ class Database:
         
         Returns the cached result if found, None otherwise.
         """
+        import time
+        import tempfile
+        from pathlib import Path
+        
+        debug_file = Path(tempfile.gettempdir()) / "refchecker_debug.log"
+        
+        start = time.time()
         cache_key = self._compute_reference_cache_key(reference)
+        key_time = time.time() - start
         
+        connect_start = time.time()
         async with aiosqlite.connect(self.db_path) as db:
+            connect_time = time.time() - connect_start
             await db.execute("PRAGMA busy_timeout=5000")
             db.row_factory = aiosqlite.Row
+            
+            query_start = time.time()
             async with db.execute(
                 "SELECT result_json FROM verification_cache WHERE cache_key = ?",
                 (cache_key,)
             ) as cursor:
                 row = await cursor.fetchone()
+                query_time = time.time() - query_start
+                
+                total_time = time.time() - start
+                if total_time > 0.05:
+                    with open(debug_file, "a") as f:
+                        f.write(f"[TIMING] Cache lookup: total={total_time:.3f}s, key={key_time:.3f}s, connect={connect_time:.3f}s, query={query_time:.3f}s\n")
+                
                 if row and row['result_json']:
                     try:
                         return json.loads(row['result_json'])
@@ -716,6 +755,88 @@ class Database:
             await db.commit()
             return cursor.rowcount
 
+    # Batch operations
+
+    async def get_batch_checks(self, batch_id: str) -> List[Dict[str, Any]]:
+        """Get all checks belonging to a batch"""
+        async with aiosqlite.connect(self.db_path) as db:
+            await db.execute("PRAGMA busy_timeout=5000")
+            db.row_factory = aiosqlite.Row
+            async with db.execute("""
+                SELECT id, paper_title, paper_source, custom_label, timestamp,
+                       total_refs, errors_count, warnings_count, suggestions_count, unverified_count,
+                       refs_with_errors, refs_with_warnings_only, refs_verified,
+                       llm_provider, llm_model, status, source_type, batch_id, batch_label
+                FROM check_history
+                WHERE batch_id = ?
+                ORDER BY timestamp ASC
+            """, (batch_id,)) as cursor:
+                rows = await cursor.fetchall()
+                return [dict(row) for row in rows]
+
+    async def get_batch_summary(self, batch_id: str) -> Optional[Dict[str, Any]]:
+        """Get aggregated summary for a batch"""
+        async with aiosqlite.connect(self.db_path) as db:
+            await db.execute("PRAGMA busy_timeout=5000")
+            db.row_factory = aiosqlite.Row
+            async with db.execute("""
+                SELECT 
+                    batch_id,
+                    batch_label,
+                    COUNT(*) as total_papers,
+                    SUM(CASE WHEN status = 'completed' THEN 1 ELSE 0 END) as completed_papers,
+                    SUM(CASE WHEN status = 'in_progress' THEN 1 ELSE 0 END) as in_progress_papers,
+                    SUM(CASE WHEN status = 'error' THEN 1 ELSE 0 END) as error_papers,
+                    SUM(CASE WHEN status = 'cancelled' THEN 1 ELSE 0 END) as cancelled_papers,
+                    SUM(total_refs) as total_refs,
+                    SUM(errors_count) as total_errors,
+                    SUM(warnings_count) as total_warnings,
+                    SUM(suggestions_count) as total_suggestions,
+                    SUM(unverified_count) as total_unverified,
+                    MIN(timestamp) as started_at
+                FROM check_history
+                WHERE batch_id = ?
+                GROUP BY batch_id
+            """, (batch_id,)) as cursor:
+                row = await cursor.fetchone()
+                if row:
+                    return dict(row)
+                return None
+
+    async def cancel_batch(self, batch_id: str) -> int:
+        """Cancel all in-progress checks in a batch. Returns count of cancelled checks."""
+        async with aiosqlite.connect(self.db_path) as db:
+            await db.execute("PRAGMA busy_timeout=5000")
+            cursor = await db.execute("""
+                UPDATE check_history 
+                SET status = 'cancelled' 
+                WHERE batch_id = ? AND status = 'in_progress'
+            """, (batch_id,))
+            await db.commit()
+            return cursor.rowcount
+
+    async def delete_batch(self, batch_id: str) -> int:
+        """Delete all checks in a batch. Returns count of deleted checks."""
+        async with aiosqlite.connect(self.db_path) as db:
+            await db.execute("PRAGMA busy_timeout=5000")
+            cursor = await db.execute(
+                "DELETE FROM check_history WHERE batch_id = ?",
+                (batch_id,)
+            )
+            await db.commit()
+            return cursor.rowcount
+
+    async def update_batch_label(self, batch_id: str, label: str) -> bool:
+        """Update the label for all checks in a batch"""
+        async with aiosqlite.connect(self.db_path) as db:
+            await db.execute("PRAGMA busy_timeout=5000")
+            await db.execute(
+                "UPDATE check_history SET batch_label = ? WHERE batch_id = ?",
+                (label, batch_id)
+            )
+            await db.commit()
+            return True
+
 
 # Global database instance
 db = Database()