fix: extractor subprocess reads table configs via stdin, not DuckDB

Subprocess cannot open system.duckdb (main process holds lock).
Now main process reads table_registry and passes configs as JSON
via stdin to subprocess. Subprocess never touches system.duckdb.

app/api/sync.py

@@ -38,26 +38,76 @@ def _get_data_dir() -> Path:
 def _run_sync(tables: Optional[List[str]] = None):
     """Run extractor as subprocess + orchestrator rebuild.
 
-    Extractor runs in a separate process to avoid DuckDB lock conflicts
-    with the main API process. Orchestrator rebuild runs in-process after
-    the extractor finishes (it only reads extract.duckdb files).
+    Reads table configs from DuckDB (in main process which has the shared
+    connection), passes them as JSON via stdin to the extractor subprocess.
+    This avoids DuckDB lock conflicts — subprocess never opens system.duckdb.
     """
+    import json as _json
     import subprocess
     import sys
 
     try:
-        # Run extractor as subprocess — completely separate DuckDB connections
+        from app.instance_config import get_data_source_type, get_value
+        from src.db import get_system_db
+        from src.repositories.table_registry import TableRegistryRepository
+
+        source_type = get_data_source_type()
+        data_dir = _get_data_dir()
+
+        # Read table configs in main process (has shared DuckDB connection)
+        sys_conn = get_system_db()
+        try:
+            repo = TableRegistryRepository(sys_conn)
+            if tables:
+                all_configs = [repo.get(t) for t in tables]
+                table_configs = [c for c in all_configs if c is not None]
+            else:
+                table_configs = repo.list_by_source(source_type) if source_type else repo.list_all()
+        finally:
+            sys_conn.close()
+
+        if not table_configs:
+            logger.warning("No tables to sync for source_type=%s", source_type)
+            return
+
+        # Serialize configs — strip non-serializable fields
+        serializable = []
+        for tc in table_configs:
+            serializable.append({k: (v.isoformat() if hasattr(v, 'isoformat') else v)
+                                 for k, v in tc.items() if v is not None})
+
+        # Run extractor subprocess with table configs via stdin
+        # Subprocess does NOT open system.duckdb — no lock conflict
         env = {**os.environ}
-        cmd = [sys.executable, "-m", "connectors.keboola.extractor"]
-        logger.info("Starting extractor subprocess: %s", " ".join(cmd))
+        cmd = [sys.executable, "-c", """
+import json, sys, os, logging
+from pathlib import Path
+logging.basicConfig(level=logging.INFO, format="%(levelname)s: %(message)s")
+
+configs = json.load(sys.stdin)
+url = os.environ.get("KEBOOLA_STACK_URL", "")
+token = os.environ.get("KEBOOLA_STORAGE_TOKEN", "")
+
+if not url or not token:
+    print("ERROR: Missing KEBOOLA_STACK_URL or KEBOOLA_STORAGE_TOKEN", file=sys.stderr)
+    sys.exit(1)
+
+from connectors.keboola.extractor import run
+data_dir = Path(os.environ.get("DATA_DIR", "./data"))
+result = run(str(data_dir / "extracts" / "keboola"), configs, url, token)
+print(json.dumps(result))
+"""]
+
+        logger.info("Starting extractor subprocess for %d tables", len(table_configs))
 
         result = subprocess.run(
-            cmd, capture_output=True, text=True, timeout=1800, env=env,
-            cwd=str(Path(__file__).parent.parent.parent),  # project root
+            cmd, input=_json.dumps(serializable), capture_output=True, text=True,
+            timeout=1800, env=env,
+            cwd=str(Path(__file__).parent.parent.parent),
         )
 
         if result.stdout:
-            logger.info("Extractor stdout: %s", result.stdout[-500:])
+            logger.info("Extractor result: %s", result.stdout.strip()[-500:])
         if result.stderr:
             logger.warning("Extractor stderr: %s", result.stderr[-500:])
         if result.returncode != 0:
@@ -70,7 +120,7 @@ def _run_sync(tables: Optional[List[str]] = None):
         logger.info("Orchestrator rebuild: %s", {k: len(v) for k, v in views.items()})
 
     except subprocess.TimeoutExpired:
-        logger.error("Extractor timed out after 600s")
+        logger.error("Extractor timed out after 1800s")
     except Exception as e:
         logger.error(f"Data sync failed: {e}\n{traceback.format_exc()}")