When rebuilding if a document does not exist anymore, re-embed the chunks instead of failing

src/haiku/rag/client.py

@@ -1,4 +1,5 @@
 import hashlib
+import logging
 import mimetypes
 import tempfile
 from collections.abc import AsyncGenerator
@@ -18,6 +19,8 @@ from haiku.rag.store.repositories.document import DocumentRepository
 from haiku.rag.store.repositories.settings import SettingsRepository
 from haiku.rag.utils import text_to_docling_document
 
+logger = logging.getLogger(__name__)
+
 
 class HaikuRAG:
     """High-level haiku-rag client."""
@@ -538,8 +541,8 @@ class HaikuRAG:
         """Rebuild the database by deleting all chunks and re-indexing all documents.
 
         For documents with URIs:
-        - Deletes the document and re-adds it from source if source exists
+        - Re-adds from source if source exists
-        - Skips documents where source no longer exists
+        - Re-embeds from existing content if source is missing
 
         For documents without URIs:
         - Re-creates chunks from existing content
@@ -559,29 +562,51 @@ class HaikuRAG:
         for doc in documents:
             assert doc.id is not None, "Document ID should not be None"
             if doc.uri:
-                # Document has a URI - delete and try to re-add from source
+                # Document has a URI - check if source is accessible
+                source_accessible = False
+                parsed_url = urlparse(doc.uri)
+
                 try:
-                    # Delete the old document first
+                    if parsed_url.scheme == "file":
-                    await self.delete_document(doc.id)
+                        # Check if file exists
+                        source_path = Path(parsed_url.path)
+                        source_accessible = source_path.exists()
+                    elif parsed_url.scheme in ("http", "https"):
+                        # For URLs, we'll try to create and catch errors
+                        source_accessible = True
+                    else:
+                        source_accessible = False
+                except Exception:
+                    source_accessible = False
 
-                    # Try to re-create from source (this creates the document with chunks)
+                if source_accessible:
-                    new_doc = await self.create_document_from_source(
+                    # Source exists - delete and recreate from source
-                        source=doc.uri, metadata=doc.metadata or {}
+                    try:
+                        await self.delete_document(doc.id)
+                        new_doc = await self.create_document_from_source(
+                            source=doc.uri, metadata=doc.metadata or {}
+                        )
+                        assert new_doc.id is not None, (
+                            "New document ID should not be None"
+                        )
+                        yield new_doc.id
+                    except Exception as e:
+                        logger.error(
+                            "Error recreating document from source %s: %s",
+                            doc.uri,
+                            e,
+                        )
+                        continue
+                else:
+                    # Source missing - re-embed from existing content
+                    logger.warning(
+                        "Source missing for %s, re-embedding from content", doc.uri
                     )
-
+                    docling_document = text_to_docling_document(doc.content)
-                    assert new_doc.id is not None, "New document ID should not be None"
+                    await self.chunk_repository.create_chunks_for_document(
-                    yield new_doc.id
+                        doc.id, docling_document
-
-                except (FileNotFoundError, ValueError, OSError) as e:
-                    # Source doesn't exist or can't be accessed - document already deleted, skip
-                    print(f"Skipping document with URI {doc.uri}: {e}")
-                    continue
-                except Exception as e:
-                    # Unexpected error - log it and skip
-                    print(
-                        f"Unexpected error processing document with URI {doc.uri}: {e}"
                     )
-                    continue
+                    yield doc.id
             else:
                 # Document without URI - re-create chunks from existing content
                 docling_document = text_to_docling_document(doc.content)

src/haiku/rag/monitor.py

@@ -1,13 +1,13 @@
+import logging
 from pathlib import Path
 
 from watchfiles import Change, DefaultFilter, awatch
 
 from haiku.rag.client import HaikuRAG
-from haiku.rag.logging import get_logger
 from haiku.rag.reader import FileReader
 from haiku.rag.store.models.document import Document
 
-logger = get_logger()
+logger = logging.getLogger(__name__)
 
 
 class FileFilter(DefaultFilter):

tests/test_rebuild.py

@@ -47,3 +47,40 @@ async def test_rebuild_database(qa_corpus: Dataset, temp_db_path):
                 chunks_after.extend(doc_chunks)
 
         assert len(chunks_after) > 0
+
+
+@pytest.mark.asyncio
+async def test_rebuild_with_missing_source(qa_corpus: Dataset, temp_db_path):
+    """Test rebuild functionality when document source is missing."""
+    async with HaikuRAG(temp_db_path) as client:
+        # Create document with content
+        content = qa_corpus["document_extracted"][0]
+        doc = await client.create_document(content=content)
+
+        # Manually set a URI that doesn't exist
+        assert doc.id is not None
+        doc_with_uri = await client.document_repository.get_by_id(doc.id)
+        assert doc_with_uri is not None
+        doc_with_uri.uri = "file:///nonexistent/path.txt"
+        await client.document_repository.update(doc_with_uri)
+
+        # Verify chunks exist before rebuild
+        chunks_before = await client.chunk_repository.get_by_document_id(doc.id)
+        assert len(chunks_before) > 0
+
+        # Perform rebuild
+        processed_doc_ids = []
+        async for doc_id in client.rebuild_database():
+            processed_doc_ids.append(doc_id)
+
+        # Document should still be processed (not skipped)
+        assert doc.id in processed_doc_ids
+
+        # Verify document still exists
+        doc_after = await client.document_repository.get_by_id(doc.id)
+        assert doc_after is not None
+        assert doc_after.content == content
+
+        # Verify chunks were recreated from content
+        chunks_after = await client.chunk_repository.get_by_document_id(doc.id)
+        assert len(chunks_after) > 0