import hashlib import json import logging import mimetypes import tempfile from pathlib import Path from typing import TYPE_CHECKING from urllib.parse import quote, unquote, urlparse from haiku.rag.client.exceptions import UnsupportedSourceError from haiku.rag.client.processing import ( ensure_chunks_embedded, get_extension_from_content_type_or_url, ) from haiku.rag.client.titles import resolve_title from haiku.rag.converters import get_converter from haiku.rag.ingester.sources import ( FetchResult, resolve_adhoc_fetcher, resolve_configured_source, ) from haiku.rag.store.models.chunk import Chunk from haiku.rag.store.models.document import Document from haiku.rag.store.models.document_item import extract_items from haiku.rag.telemetry import logfire if TYPE_CHECKING: from docling_core.types.doc.document import DoclingDocument from haiku.rag.client import HaikuRAG from haiku.rag.ingester.sources.base import Source logger = logging.getLogger(__name__) # Maximum length of an attachment chain rooted at a top-level ingest. With # value 3, a PDF whose attachments contain PDFs which themselves contain # PDFs is fully ingested (3 levels); a fourth nested level logs a warning # and is skipped. MAX_ATTACHMENT_DEPTH = 3 def parent_uri_filter(parent_uri: str) -> str: """SQL `WHERE` clause matching documents whose ``metadata.parent_uri`` equals ``parent_uri``. ``metadata`` is stored as a JSON string produced by the standard library's ``json.dumps`` (which inserts ``": "`` between key and value), so the match is a substring search over that serialized form — escape JSON-meaningful chars in the URI, then SQL-escape single quotes.""" json_fragment = json.dumps(parent_uri)[1:-1].replace("'", "''") return f'metadata LIKE \'%"parent_uri": "{json_fragment}"%\'' async def _store_document_with_chunks( client: "HaikuRAG", document: Document, chunks: list[Chunk], docling_document: "DoclingDocument", ) -> Document: """Store a document with chunks, embedding any that lack embeddings. Handles versioning/rollback on failure. """ chunks = await ensure_chunks_embedded(client._config, chunks, client.embedder) versions = await client.store.current_table_versions() created_doc = await client.document_repository.create(document) try: assert created_doc.id is not None, ( "Document ID should not be None after creation" ) for order, chunk in enumerate(chunks): chunk.document_id = created_doc.id chunk.order = order await client.chunk_repository.create(chunks) items = extract_items(created_doc.id, docling_document) await client.document_item_repository.create_items(created_doc.id, items) if client._config.storage.auto_vacuum: client._schedule_vacuum() return created_doc except Exception: await client.store.restore_table_versions(versions) raise async def _update_document_with_chunks( client: "HaikuRAG", document: Document, chunks: list[Chunk], docling_document: "DoclingDocument | None" = None, ) -> Document: """Update a document and replace its chunks, embedding any that lack embeddings. Handles versioning/rollback on failure. When `docling_document` is None, existing items are preserved. """ assert document.id is not None, "Document ID is required for update" # Snapshot existing picture bytes before deleting items so the post-delete # extract_items can merge them back when the live docling has had its # picture URIs stripped (rebuild / re-extract via the stored blob). existing_picture_data: dict[str, bytes] | None = None if docling_document is not None: existing_picture_data = ( await client.document_item_repository.get_all_picture_data(document.id) ) chunks = await ensure_chunks_embedded(client._config, chunks, client.embedder) versions = await client.store.current_table_versions() await client.chunk_repository.delete_by_document_id(document.id) try: updated_doc = await client.document_repository.update(document) assert updated_doc.id is not None for order, chunk in enumerate(chunks): chunk.document_id = updated_doc.id chunk.order = order await client.chunk_repository.create(chunks) if docling_document is not None: await client.document_item_repository.delete_by_document_id(updated_doc.id) items = extract_items( updated_doc.id, docling_document, existing_picture_data=existing_picture_data, ) await client.document_item_repository.create_items(updated_doc.id, items) if client._config.storage.auto_vacuum: client._schedule_vacuum() return updated_doc except Exception: await client.store.restore_table_versions(versions) raise async def create_document( client: "HaikuRAG", content: str, uri: str | None = None, title: str | None = None, metadata: dict | None = None, format: str = "md", ) -> Document: """Create a new document from text content. Converts the content, chunks it, and generates embeddings. """ from haiku.rag.embeddings import embed_chunks converter = get_converter(client._config) docling_document = await converter.convert_text(content, format=format) chunks = await client.chunk(docling_document) embedded_chunks = await embed_chunks(chunks, client.embedder, client._config) stored_content = docling_document.export_to_markdown() if title is None: title = await resolve_title(client._config, docling_document, stored_content) document = Document( content=stored_content, uri=uri, title=title, metadata=metadata or {}, ) document.set_docling(docling_document) return await _store_document_with_chunks( client, document, embedded_chunks, docling_document ) async def import_document( client: "HaikuRAG", docling_document: "DoclingDocument", chunks: list[Chunk], uri: str | None = None, title: str | None = None, metadata: dict | None = None, ) -> Document: """Import a pre-processed document with chunks. Use this when conversion, chunking, and embedding were done externally. Chunks without embeddings will be automatically embedded. """ content = docling_document.export_to_markdown() if title is None: title = await resolve_title(client._config, docling_document, content) document = Document( content=content, uri=uri, title=title, metadata=metadata or {}, ) document.set_docling(docling_document) return await _store_document_with_chunks(client, document, chunks, docling_document) async def _refresh_doc_metadata( client: "HaikuRAG", doc: Document, *, title: str | None, user_metadata: dict, source_metadata: dict | None, ) -> Document: """Update a document's title + metadata without re-chunking. Used by the cheap revision and MD5 short-circuits in create_document_from_source.""" updated = False if title is not None and title != doc.title: doc.title = title updated = True merged = {**(doc.metadata or {}), **user_metadata} if source_metadata: merged.update(source_metadata) if merged != doc.metadata: doc.metadata = merged updated = True if updated: return await client.document_repository.update(doc) return doc async def _ingest_fetch_result( client: "HaikuRAG", result: FetchResult, *, title: str | None, user_metadata: dict, stored_uri: str, existing_doc: Document | None, depth: int = 0, ) -> Document: """Convert / chunk / embed / store a fetched document. Replaces an existing document if one is supplied. ``depth`` tracks position in an attachment chain so the reconciliation step can bound recursion.""" from haiku.rag.embeddings import embed_chunks converter = get_converter(client._config) file_extension = get_extension_from_content_type_or_url( result.uri, result.content_type ) if file_extension not in converter.supported_extensions: raise UnsupportedSourceError( f"Unsupported content type/extension: {result.content_type}/{file_extension}" ) source_metadata: dict = { "content_type": result.content_type, "md5": result.content_hash, **result.extra_metadata, } if result.revision is not None: source_metadata["source_revision"] = result.revision if result.disk_path is not None: target_path = result.disk_path cleanup_path: Path | None = None else: with tempfile.NamedTemporaryFile( mode="wb", suffix=file_extension, delete=False ) as temp_file: temp_file.write(result.body) temp_file.flush() target_path = Path(temp_file.name) cleanup_path = target_path try: with logfire.span("document.convert", uri=result.uri): docling_document = await client.convert(target_path, source_uri=result.uri) with logfire.span("document.chunk", uri=result.uri) as chunk_span: chunks = await client.chunk(docling_document) chunk_span.set_attribute("chunks_created", len(chunks)) with logfire.span("document.embed", uri=result.uri): embedded_chunks = await embed_chunks( chunks, client.embedder, client._config ) finally: if cleanup_path is not None: cleanup_path.unlink(missing_ok=True) stored_content = docling_document.export_to_markdown() final_metadata = {**user_metadata, **source_metadata} if existing_doc: existing_doc.content = stored_content existing_doc.metadata = final_metadata existing_doc.set_docling(docling_document) if title is not None: existing_doc.title = title elif existing_doc.title is None: existing_doc.title = await resolve_title( client._config, docling_document, stored_content ) with logfire.span("document.store", uri=result.uri, op="update") as store_span: updated = await _update_document_with_chunks( client, existing_doc, embedded_chunks, docling_document ) store_span.set_attribute("document_id", updated.id) await _reconcile_pdf_attachments(client, updated, result.body, depth=depth) return updated if title is None: title = await resolve_title(client._config, docling_document, stored_content) document = Document( content=stored_content, uri=stored_uri, title=title, metadata=final_metadata, ) document.set_docling(docling_document) with logfire.span("document.store", uri=result.uri, op="create") as store_span: created = await _store_document_with_chunks( client, document, embedded_chunks, docling_document ) store_span.set_attribute("document_id", created.id) await _reconcile_pdf_attachments(client, created, result.body, depth=depth) return created async def _reconcile_pdf_attachments( client: "HaikuRAG", parent_doc: Document, parent_body: bytes, *, depth: int, ) -> None: """Diff the parent PDF's ``/EmbeddedFiles`` table against any children already linked via ``metadata.parent_uri`` and bring the child set in line: ingest additions, update changed bytes, cascade-delete removed names. Re-uses ``_ingest_fetch_result`` for each child so the standard conversion path runs uniformly — child PDFs recurse into this helper one level deeper, bounded by ``MAX_ATTACHMENT_DEPTH``. """ if not client._config.processing.extract_pdf_attachments: return if not parent_doc.uri: return if (parent_doc.metadata or {}).get("content_type") != "application/pdf": return import pypdfium2 as pdfium try: pdf = pdfium.PdfDocument(parent_body) except pdfium.PdfiumError as exc: logger.warning( "Cannot scan %s for embedded attachments: %s", parent_doc.uri, exc ) return try: attachment_count = pdf.count_attachments() if depth + 1 >= MAX_ATTACHMENT_DEPTH: if attachment_count > 0: logger.warning( "Attachment depth cap (%d) reached at %s; skipping %d nested " "attachment(s).", MAX_ATTACHMENT_DEPTH, parent_doc.uri, attachment_count, ) return new_attachments: dict[str, tuple[str, bytes, str, str]] = {} for i in range(attachment_count): att = pdf.get_attachment(i) name = att.get_name() if not name: continue data = bytes(att.get_data()) child_uri = f"{parent_doc.uri}#attachment={quote(name, safe='')}" content_type = mimetypes.guess_type(name)[0] or "application/octet-stream" content_hash = hashlib.md5(data, usedforsecurity=False).hexdigest() new_attachments[child_uri] = (name, data, content_type, content_hash) finally: pdf.close() existing = await client.list_documents(filter=parent_uri_filter(parent_doc.uri)) existing_by_uri: dict[str, Document] = {d.uri: d for d in existing if d.uri} for child_uri, (name, data, content_type, content_hash) in new_attachments.items(): existing_child = existing_by_uri.get(child_uri) if ( existing_child and (existing_child.metadata or {}).get("md5") == content_hash ): continue child_fr = FetchResult( uri=child_uri, body=data, content_type=content_type, content_hash=content_hash, extra_metadata={"parent_uri": parent_doc.uri}, ) try: await _ingest_fetch_result( client, child_fr, title=None, user_metadata={}, stored_uri=child_uri, existing_doc=existing_child, depth=depth + 1, ) except UnsupportedSourceError: logger.warning( "Skipping attachment %r in %s: unsupported content type %r", name, parent_doc.uri, content_type, ) for child_uri, child in existing_by_uri.items(): if child_uri not in new_attachments and child.id: await client.delete_document(child.id) async def create_document_from_source( client: "HaikuRAG", source: str | Path, title: str | None = None, metadata: dict | None = None, uri: str | None = None, storage_options: dict[str, str] | None = None, sources: "list[Source] | None" = None, source_id: str | None = None, ) -> Document | list[Document]: """Create or update document(s) from a file path, directory, or URL. Checks if a document with the same URI already exists: - If MD5 is unchanged, returns existing document - If MD5 changed, updates the document - If no document exists, creates a new one If ``uri`` is provided, it overrides the URI auto-derived from the source (which is normally ``file://`` for local files or the URL for remote sources). Not supported for directory sources, which produce one document per file. Returns a single Document for files/URLs, a list for directories. """ metadata = metadata or {} source_str = str(source) parsed_url = urlparse(source_str) # Directory case: recurse with the existing FS filter and produce one # document per file. Remote schemes (http/s3) never hit this branch. if parsed_url.scheme in ("", "file"): # file:// URIs URL-encode special characters ([, ], spaces, etc.); # unquote to get the real filesystem path before any stat/rglob. local_path = ( Path(unquote(parsed_url.path)) if parsed_url.scheme == "file" else (Path(source) if isinstance(source, str) else source) ) if local_path.is_dir(): if uri is not None: raise UnsupportedSourceError( "uri override is not supported for directory sources; each file " "produces its own document with its own auto-derived URI." ) from haiku.rag.ingester.sources.filter import FileFilter # One-shot CLI directory ingest uses the converter's supported # extensions but no include/ignore patterns. For pattern-based # filtering use `haiku-ingester serve` with an FS source. documents: list[Document] = [] filter = FileFilter() for child in local_path.rglob("*"): if child.is_file() and filter.include_file(str(child)): doc = await create_document_from_source( client, child, title=None, metadata=metadata ) assert isinstance(doc, Document) documents.append(doc) return documents if not local_path.exists(): raise UnsupportedSourceError(f"File does not exist: {local_path}") # Match the old _create_document_from_file behaviour: fail fast on # unsupported extension before reading any bytes. converter = get_converter(client._config) if local_path.suffix.lower() not in converter.supported_extensions: raise UnsupportedSourceError( f"Unsupported file extension: {local_path.suffix}" ) # Worker jobs carry source_id from the poller; strict lookup so a # renamed/removed source surfaces as a DLQ instead of silently dropping # credentials. Ad-hoc CLI calls (no source_id) fall back to scheme-based # adapters when no configured source matches. if source_id is not None: fetcher = resolve_configured_source(source_str, source_id, sources) else: fetcher = resolve_adhoc_fetcher( source_str, sources=sources, storage_options=storage_options ) # The stored URI is what we look up + persist by. For an explicit uri # override, use it as-is. For a file:// input the source string is # already canonical (URL-encoded); round-tripping via Path.as_uri() # would double-encode any escapes like %5B. For bare paths, canonicalize. if uri is not None: stored_uri = uri elif parsed_url.scheme == "file": stored_uri = source_str elif parsed_url.scheme == "": stored_uri = Path(source_str).absolute().as_uri() else: stored_uri = source_str existing_doc = await client.get_document_by_uri(stored_uri) # Cheap revision-based short-circuit: only worth a HEAD when we have a # stored revision to compare against. All sources persist their native # revision (mtime_ns for FS, ETag for S3, ETag/Last-Modified for HTTP) # under the canonical "source_revision" metadata key. stored_revision = ( (existing_doc.metadata or {}).get("source_revision") if existing_doc else None ) if existing_doc and stored_revision: current_revision = await fetcher.head(source_str) if current_revision == stored_revision: return await _refresh_doc_metadata( client, existing_doc, title=title, user_metadata=metadata, source_metadata=None, ) with logfire.span("document.fetch", uri=source_str) as fetch_span: result = await fetcher.fetch(source_str) fetch_span.set_attribute("bytes", len(result.body)) fetch_span.set_attribute("content_hash", result.content_hash) # MD5 short-circuit: the bytes are unchanged even if the revision wasn't. # Refresh the source-derived metadata (revision may have rolled) but skip # convert/embed/store entirely. if existing_doc and existing_doc.metadata.get("md5") == result.content_hash: source_meta: dict = { "content_type": result.content_type, "md5": result.content_hash, **result.extra_metadata, } if result.revision is not None: source_meta["source_revision"] = result.revision return await _refresh_doc_metadata( client, existing_doc, title=title, user_metadata=metadata, source_metadata=source_meta, ) return await _ingest_fetch_result( client, result, title=title, user_metadata=metadata, stored_uri=stored_uri, existing_doc=existing_doc, ) async def update_document( client: "HaikuRAG", document_id: str, content: str | None = None, metadata: dict | None = None, chunks: list[Chunk] | None = None, title: str | None = None, docling_document: "DoclingDocument | None" = None, ) -> Document: """Update a document by ID. Updates specified fields. When content or docling_document is provided, the document is rechunked and re-embedded. Updates to only metadata or title skip rechunking for efficiency. Raises: ValueError: If document not found, or if both content and docling_document are provided. """ from haiku.rag.embeddings import embed_chunks if content is not None and docling_document is not None: raise ValueError( "content and docling_document are mutually exclusive. " "Provide one or the other, not both." ) existing_doc = await client.get_document_by_id(document_id) if existing_doc is None: raise ValueError(f"Document with ID {document_id} not found") if title is not None: existing_doc.title = title if metadata is not None: existing_doc.metadata = metadata if content is None and chunks is None and docling_document is None: return await client.document_repository.update(existing_doc) if chunks is not None: if docling_document is not None: existing_doc.content = docling_document.export_to_markdown() existing_doc.set_docling(docling_document) elif content is not None: existing_doc.content = content return await _update_document_with_chunks( client, existing_doc, chunks, docling_document ) if docling_document is not None: existing_doc.content = docling_document.export_to_markdown() existing_doc.set_docling(docling_document) new_chunks = await client.chunk(docling_document) embedded_chunks = await embed_chunks( new_chunks, client.embedder, client._config ) return await _update_document_with_chunks( client, existing_doc, embedded_chunks, docling_document ) assert content is not None existing_doc.content = content converter = get_converter(client._config) converted_docling = await converter.convert_text(existing_doc.content, format="md") existing_doc.set_docling(converted_docling) new_chunks = await client.chunk(converted_docling) embedded_chunks = await embed_chunks(new_chunks, client.embedder, client._config) return await _update_document_with_chunks( client, existing_doc, embedded_chunks, converted_docling ) def check_source_accessible(uri: str) -> bool: """Check if a document's source URI is accessible.""" parsed_url = urlparse(uri) try: if parsed_url.scheme == "file": return Path(parsed_url.path).exists() elif parsed_url.scheme in ("http", "https", "s3"): return True return False except Exception: return False