morphik-core/core/services/document_service.py

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Python
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import base64
from io import BytesIO
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from typing import Dict, Any, List, Optional
from fastapi import UploadFile
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from core.models.chunk import Chunk, DocumentChunk
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from core.models.documents import (
Document,
ChunkResult,
DocumentContent,
DocumentResult,
)
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from ..models.auth import AuthContext
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from core.database.base_database import BaseDatabase
from core.storage.base_storage import BaseStorage
from core.vector_store.base_vector_store import BaseVectorStore
from core.embedding.base_embedding_model import BaseEmbeddingModel
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from core.parser.base_parser import BaseParser
from core.completion.base_completion import BaseCompletionModel
from core.models.completion import CompletionRequest, CompletionResponse, ChunkSource
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import logging
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from core.reranker.base_reranker import BaseReranker
from core.config import get_settings
from core.cache.base_cache import BaseCache
from core.cache.base_cache_factory import BaseCacheFactory
from core.services.rules_processor import RulesProcessor
from core.embedding.colpali_embedding_model import ColpaliEmbeddingModel
from core.vector_store.multi_vector_store import MultiVectorStore
import filetype
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from filetype.types import IMAGE # , DOCUMENT, document
import pdf2image
from PIL.Image import Image
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import tempfile
import os
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logger = logging.getLogger(__name__)
IMAGE = {im.mime for im in IMAGE}
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class DocumentService:
def __init__(
self,
database: BaseDatabase,
vector_store: BaseVectorStore,
storage: BaseStorage,
parser: BaseParser,
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embedding_model: BaseEmbeddingModel,
completion_model: BaseCompletionModel,
cache_factory: BaseCacheFactory,
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reranker: Optional[BaseReranker] = None,
enable_colpali: bool = False,
colpali_embedding_model: Optional[ColpaliEmbeddingModel] = None,
colpali_vector_store: Optional[MultiVectorStore] = None,
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):
self.db = database
self.vector_store = vector_store
self.storage = storage
self.parser = parser
self.embedding_model = embedding_model
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self.completion_model = completion_model
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self.reranker = reranker
self.cache_factory = cache_factory
self.rules_processor = RulesProcessor()
self.colpali_embedding_model = colpali_embedding_model
self.colpali_vector_store = colpali_vector_store
colpali_vector_store.initialize()
# Cache-related data structures
# Maps cache name to active cache object
self.active_caches: Dict[str, BaseCache] = {}
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async def retrieve_chunks(
self,
query: str,
auth: AuthContext,
filters: Optional[Dict[str, Any]] = None,
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k: int = 5,
min_score: float = 0.0,
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use_reranking: Optional[bool] = None,
use_colpali: Optional[bool] = None,
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) -> List[ChunkResult]:
"""Retrieve relevant chunks."""
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settings = get_settings()
should_rerank = use_reranking if use_reranking is not None else settings.USE_RERANKING
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# Get embedding for query
query_embedding_regular = await self.embedding_model.embed_for_query(query)
query_embedding_multivector = await self.colpali_embedding_model.embed_for_query(query) if use_colpali else None
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logger.info("Generated query embedding")
# Find authorized documents
doc_ids = await self.db.find_authorized_and_filtered_documents(auth, filters)
if not doc_ids:
logger.info("No authorized documents found")
return []
logger.info(f"Found {len(doc_ids)} authorized documents")
# Search chunks with vector similarity
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chunks = await self.vector_store.query_similar(
query_embedding_regular, k=10 * k if should_rerank else k, doc_ids=doc_ids
)
chunks_multivector = (
await self.colpali_vector_store.query_similar(
query_embedding_multivector, k=k, doc_ids=doc_ids
)
if use_colpali
else []
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)
logger.info(f"Found {len(chunks)} similar chunks via regular embedding")
if use_colpali:
logger.info(
f"Found {len(chunks_multivector)} similar chunks via multivector embedding since we are also using colpali"
)
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# Rerank chunks using the reranker if enabled and available
if chunks and should_rerank and self.reranker is not None:
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chunks = await self.reranker.rerank(query, chunks)
chunks.sort(key=lambda x: x.score, reverse=True)
chunks = chunks[:k]
logger.info(f"Reranked {k*10} chunks and selected the top {k}")
chunks = chunks_multivector + chunks
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# Create and return chunk results
results = await self._create_chunk_results(auth, chunks)
logger.info(f"Returning {len(results)} chunk results")
return results
async def retrieve_docs(
self,
query: str,
auth: AuthContext,
filters: Optional[Dict[str, Any]] = None,
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k: int = 5,
min_score: float = 0.0,
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use_reranking: Optional[bool] = None,
use_colpali: Optional[bool] = None,
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) -> List[DocumentResult]:
"""Retrieve relevant documents."""
# Get chunks first
chunks = await self.retrieve_chunks(
query, auth, filters, k, min_score, use_reranking, use_colpali
)
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# Convert to document results
results = await self._create_document_results(auth, chunks)
documents = list(results.values())
logger.info(f"Returning {len(documents)} document results")
return documents
async def batch_retrieve_documents(
self,
document_ids: List[str],
auth: AuthContext
) -> List[Document]:
"""
Retrieve multiple documents by their IDs in a single batch operation.
Args:
document_ids: List of document IDs to retrieve
auth: Authentication context
Returns:
List of Document objects that user has access to
"""
if not document_ids:
return []
# Use the database's batch retrieval method
documents = await self.db.get_documents_by_id(document_ids, auth)
logger.info(f"Batch retrieved {len(documents)} documents out of {len(document_ids)} requested")
return documents
async def batch_retrieve_chunks(
self,
chunk_ids: List[ChunkSource],
auth: AuthContext
) -> List[ChunkResult]:
"""
Retrieve specific chunks by their document ID and chunk number in a single batch operation.
Args:
chunk_ids: List of ChunkSource objects with document_id and chunk_number
auth: Authentication context
Returns:
List of ChunkResult objects
"""
if not chunk_ids:
return []
# Collect unique document IDs to check authorization in a single query
doc_ids = list({source.document_id for source in chunk_ids})
# Find authorized documents in a single query
authorized_docs = await self.batch_retrieve_documents(doc_ids, auth)
authorized_doc_ids = {doc.external_id for doc in authorized_docs}
# Filter sources to only include authorized documents
authorized_sources = [
source for source in chunk_ids
if source.document_id in authorized_doc_ids
]
if not authorized_sources:
return []
# Create list of (document_id, chunk_number) tuples for vector store query
chunk_identifiers = [
(source.document_id, source.chunk_number)
for source in authorized_sources
]
# Retrieve the chunks from vector store in a single query
chunks = await self.vector_store.get_chunks_by_id(chunk_identifiers)
# Convert to chunk results
results = await self._create_chunk_results(auth, chunks)
logger.info(f"Batch retrieved {len(results)} chunks out of {len(chunk_ids)} requested")
return results
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async def query(
self,
query: str,
auth: AuthContext,
filters: Optional[Dict[str, Any]] = None,
k: int = 20, # from contextual embedding paper
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min_score: float = 0.0,
max_tokens: Optional[int] = None,
temperature: Optional[float] = None,
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use_reranking: Optional[bool] = None,
use_colpali: Optional[bool] = None,
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) -> CompletionResponse:
"""Generate completion using relevant chunks as context."""
# Get relevant chunks
chunks = await self.retrieve_chunks(
query, auth, filters, k, min_score, use_reranking, use_colpali
)
documents = await self._create_document_results(auth, chunks)
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chunk_contents = [chunk.augmented_content(documents[chunk.document_id]) for chunk in chunks]
# Collect sources information
sources = [
ChunkSource(document_id=chunk.document_id, chunk_number=chunk.chunk_number)
for chunk in chunks
]
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# Generate completion
request = CompletionRequest(
query=query,
context_chunks=chunk_contents,
max_tokens=max_tokens,
temperature=temperature,
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)
response = await self.completion_model.complete(request)
# Add sources information at the document service level
response.sources = sources
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return response
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async def ingest_text(
self,
content: str,
filename: Optional[str] = None,
metadata: Optional[Dict[str, Any]] = None,
auth: AuthContext = None,
rules: Optional[List[str]] = None,
use_colpali: Optional[bool] = None,
) -> Document:
"""Ingest a text document."""
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if "write" not in auth.permissions:
logger.error(f"User {auth.entity_id} does not have write permission")
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raise PermissionError("User does not have write permission")
doc = Document(
content_type="text/plain",
filename=filename,
metadata=metadata or {},
owner={"type": auth.entity_type, "id": auth.entity_id},
access_control={
"readers": [auth.entity_id],
"writers": [auth.entity_id],
"admins": [auth.entity_id],
},
)
logger.info(f"Created text document record with ID {doc.external_id}")
# Apply rules if provided
if rules:
rule_metadata, modified_text = await self.rules_processor.process_rules(content, rules)
# Update document metadata with extracted metadata from rules
metadata.update(rule_metadata)
doc.metadata = metadata # Update doc metadata after rules
if modified_text:
content = modified_text
logger.info("Updated content with modified text from rules")
# Store full content before chunking
doc.system_metadata["content"] = content
# Split into chunks after all processing is done
chunks = await self.parser.split_text(content)
if not chunks:
raise ValueError("No content chunks extracted")
logger.info(f"Split processed text into {len(chunks)} chunks")
# Generate embeddings for chunks
embeddings = await self.embedding_model.embed_for_ingestion(chunks)
logger.info(f"Generated {len(embeddings)} embeddings")
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chunk_objects = self._create_chunk_objects(doc.external_id, chunks, embeddings)
logger.info(f"Created {len(chunk_objects)} chunk objects")
chunk_objects_multivector = []
if use_colpali:
embeddings_multivector = await self.colpali_embedding_model.embed_for_ingestion(chunks)
logger.info(
f"Generated {len(embeddings_multivector)} embeddings for multivector embedding"
)
chunk_objects_multivector = self._create_chunk_objects(
doc.external_id, chunks, embeddings_multivector
)
logger.info(
f"Created {len(chunk_objects_multivector)} chunk objects for multivector embedding"
)
# Create and store chunk objects
# Store everything
await self._store_chunks_and_doc(chunk_objects, doc, use_colpali, chunk_objects_multivector)
logger.info(f"Successfully stored text document {doc.external_id}")
return doc
async def ingest_file(
self,
file: UploadFile,
metadata: Dict[str, Any],
auth: AuthContext,
rules: Optional[List[str]] = None,
use_colpali: Optional[bool] = None,
) -> Document:
"""Ingest a file document."""
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if "write" not in auth.permissions:
raise PermissionError("User does not have write permission")
# Read file content
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file_content = await file.read()
file_type = filetype.guess(file_content)
# Parse file to text first
additional_metadata, text = await self.parser.parse_file_to_text(
file_content, file.filename
)
logger.info(f"Parsed file into text of length {len(text)}")
# Apply rules if provided
if rules:
rule_metadata, modified_text = await self.rules_processor.process_rules(text, rules)
# Update document metadata with extracted metadata from rules
metadata.update(rule_metadata)
if modified_text:
text = modified_text
logger.info("Updated text with modified content from rules")
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# Create document record
doc = Document(
content_type=file_type.mime or "",
filename=file.filename,
metadata=metadata,
owner={"type": auth.entity_type, "id": auth.entity_id},
access_control={
"readers": [auth.entity_id],
"writers": [auth.entity_id],
"admins": [auth.entity_id],
},
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additional_metadata=additional_metadata,
)
# Store full content
doc.system_metadata["content"] = text
logger.info(f"Created file document record with ID {doc.external_id}")
file_content_base64 = base64.b64encode(file_content).decode()
# Store the original file
storage_info = await self.storage.upload_from_base64(
file_content_base64, doc.external_id, file.content_type
)
doc.storage_info = {"bucket": storage_info[0], "key": storage_info[1]}
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logger.info(f"Stored file in bucket `{storage_info[0]}` with key `{storage_info[1]}`")
# Split into chunks after all processing is done
chunks = await self.parser.split_text(text)
if not chunks:
raise ValueError("No content chunks extracted")
logger.info(f"Split processed text into {len(chunks)} chunks")
# Generate embeddings for chunks
embeddings = await self.embedding_model.embed_for_ingestion(chunks)
logger.info(f"Generated {len(embeddings)} embeddings")
# Create and store chunk objects
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chunk_objects = self._create_chunk_objects(doc.external_id, chunks, embeddings)
logger.info(f"Created {len(chunk_objects)} chunk objects")
chunk_objects_multivector = []
logger.info(f"use_colpali: {use_colpali}")
if use_colpali:
chunks_multivector = self._create_chunks_multivector(
file_type, file_content_base64, file_content, chunks
)
logger.info(f"Created {len(chunks_multivector)} chunks for multivector embedding")
colpali_embeddings = await self.colpali_embedding_model.embed_for_ingestion(
chunks_multivector
)
logger.info(f"Generated {len(colpali_embeddings)} embeddings for multivector embedding")
chunk_objects_multivector = self._create_chunk_objects(
doc.external_id, chunks_multivector, colpali_embeddings
)
# Store everything
doc.chunk_ids = await self._store_chunks_and_doc(
chunk_objects, doc, use_colpali, chunk_objects_multivector
)
logger.info(f"Successfully stored file document {doc.external_id}")
return doc
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def img_to_base64_str(self, img: Image):
buffered = BytesIO()
img.save(buffered, format="PNG")
buffered.seek(0)
img_byte = buffered.getvalue()
img_str = "data:image/png;base64," + base64.b64encode(img_byte).decode()
return img_str
def _create_chunks_multivector(
self, file_type, file_content_base64: str, file_content: bytes, chunks: List[Chunk]
):
logger.info(f"Creating chunks for multivector embedding for file type {file_type.mime}")
match file_type.mime:
case file_type if file_type in IMAGE:
return [Chunk(content=file_content_base64, metadata={"is_image": True})]
case "application/pdf":
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logger.info("Working with PDF file!")
images = pdf2image.convert_from_bytes(file_content)
images_b64 = [self.img_to_base64_str(image) for image in images]
return [
Chunk(content=image_b64, metadata={"is_image": True})
for image_b64 in images_b64
]
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case "application/vnd.openxmlformats-officedocument.wordprocessingml.document" | "application/msword":
logger.info("Working with Word document!")
# Check if file content is empty
if not file_content or len(file_content) == 0:
logger.error("Word document content is empty")
return [
Chunk(content=chunk.content, metadata=(chunk.metadata | {"is_image": False}))
for chunk in chunks
]
# Convert Word document to PDF first
with tempfile.NamedTemporaryFile(suffix=".docx", delete=False) as temp_docx:
temp_docx.write(file_content)
temp_docx_path = temp_docx.name
with tempfile.NamedTemporaryFile(suffix=".pdf", delete=False) as temp_pdf:
temp_pdf_path = temp_pdf.name
try:
# Convert Word to PDF
import subprocess
# Get the base filename without extension
base_filename = os.path.splitext(os.path.basename(temp_docx_path))[0]
output_dir = os.path.dirname(temp_pdf_path)
expected_pdf_path = os.path.join(output_dir, f"{base_filename}.pdf")
result = subprocess.run(
["soffice", "--headless", "--convert-to", "pdf", "--outdir",
output_dir, temp_docx_path],
capture_output=True,
text=True
)
if result.returncode != 0:
logger.error(f"Failed to convert Word to PDF: {result.stderr}")
return [
Chunk(content=chunk.content, metadata=(chunk.metadata | {"is_image": False}))
for chunk in chunks
]
# LibreOffice creates the PDF with the same base name in the output directory
# Check if the expected PDF file exists
if not os.path.exists(expected_pdf_path) or os.path.getsize(expected_pdf_path) == 0:
logger.error(f"Generated PDF is empty or doesn't exist at expected path: {expected_pdf_path}")
return [
Chunk(content=chunk.content, metadata=(chunk.metadata | {"is_image": False}))
for chunk in chunks
]
# Now process the PDF using the correct path
with open(expected_pdf_path, "rb") as pdf_file:
pdf_content = pdf_file.read()
try:
images = pdf2image.convert_from_bytes(pdf_content)
if not images:
logger.warning("No images extracted from PDF")
return [
Chunk(content=chunk.content, metadata=(chunk.metadata | {"is_image": False}))
for chunk in chunks
]
images_b64 = [self.img_to_base64_str(image) for image in images]
return [
Chunk(content=image_b64, metadata={"is_image": True})
for image_b64 in images_b64
]
except Exception as pdf_error:
logger.error(f"Error converting PDF to images: {str(pdf_error)}")
return [
Chunk(content=chunk.content, metadata=(chunk.metadata | {"is_image": False}))
for chunk in chunks
]
except Exception as e:
logger.error(f"Error processing Word document: {str(e)}")
return [
Chunk(content=chunk.content, metadata=(chunk.metadata | {"is_image": False}))
for chunk in chunks
]
finally:
# Clean up temporary files
if os.path.exists(temp_docx_path):
os.unlink(temp_docx_path)
if os.path.exists(temp_pdf_path):
os.unlink(temp_pdf_path)
# Also clean up the expected PDF path if it exists and is different from temp_pdf_path
if 'expected_pdf_path' in locals() and os.path.exists(expected_pdf_path) and expected_pdf_path != temp_pdf_path:
os.unlink(expected_pdf_path)
# case filetype.get_type(ext="txt"):
# logger.info(f"Found text input: chunks for multivector embedding")
# return chunks.copy()
# TODO: Add support for office documents
# case document.Xls | document.Xlsx | document.Ods |document.Odp:
# logger.warning(f"Colpali is not supported for file type {file_type.mime} - skipping")
# case file_type if file_type in DOCUMENT:
# pass
case _:
logger.warning(
f"Colpali is not supported for file type {file_type.mime} - skipping"
)
return [
Chunk(content=chunk.content, metadata=(chunk.metadata | {"is_image": False}))
for chunk in chunks
]
def _create_chunk_objects(
self,
doc_id: str,
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chunks: List[Chunk],
embeddings: List[List[float]],
) -> List[DocumentChunk]:
"""Helper to create chunk objects"""
return [
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c.to_document_chunk(chunk_number=i, embedding=embedding, document_id=doc_id)
for i, (embedding, c) in enumerate(zip(embeddings, chunks))
]
async def _store_chunks_and_doc(
self,
chunk_objects: List[DocumentChunk],
doc: Document,
use_colpali: bool = False,
chunk_objects_multivector: Optional[List[DocumentChunk]] = None,
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) -> List[str]:
"""Helper to store chunks and document"""
# Store chunks in vector store
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success, result = await self.vector_store.store_embeddings(chunk_objects)
if not success:
raise Exception("Failed to store chunk embeddings")
logger.debug("Stored chunk embeddings in vector store")
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doc.chunk_ids = result
if use_colpali and chunk_objects_multivector is not None:
success, result_multivector = await self.colpali_vector_store.store_embeddings(
chunk_objects_multivector
)
if not success:
raise Exception("Failed to store multivector chunk embeddings")
logger.debug("Stored multivector chunk embeddings in vector store")
doc.chunk_ids += result_multivector
# Store document metadata
if not await self.db.store_document(doc):
raise Exception("Failed to store document metadata")
logger.debug("Stored document metadata in database")
logger.debug(f"Chunk IDs stored: {doc.chunk_ids}")
return doc.chunk_ids
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async def _create_chunk_results(
self, auth: AuthContext, chunks: List[DocumentChunk]
) -> List[ChunkResult]:
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"""Create ChunkResult objects with document metadata."""
results = []
for chunk in chunks:
# Get document metadata
doc = await self.db.get_document(chunk.document_id, auth)
if not doc:
logger.warning(f"Document {chunk.document_id} not found")
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continue
logger.debug(f"Retrieved metadata for document {chunk.document_id}")
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# Generate download URL if needed
download_url = None
if doc.storage_info:
download_url = await self.storage.get_download_url(
doc.storage_info["bucket"], doc.storage_info["key"]
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)
logger.debug(f"Generated download URL for document {chunk.document_id}")
metadata = doc.metadata
metadata["is_image"] = chunk.metadata.get("is_image", False)
results.append(
ChunkResult(
content=chunk.content,
score=chunk.score,
document_id=chunk.document_id,
chunk_number=chunk.chunk_number,
metadata=metadata,
content_type=doc.content_type,
filename=doc.filename,
download_url=download_url,
)
)
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logger.info(f"Created {len(results)} chunk results")
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return results
async def _create_document_results(
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self, auth: AuthContext, chunks: List[ChunkResult]
) -> Dict[str, DocumentResult]:
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"""Group chunks by document and create DocumentResult objects."""
# Group chunks by document and get highest scoring chunk per doc
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doc_chunks: Dict[str, ChunkResult] = {}
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for chunk in chunks:
if (
chunk.document_id not in doc_chunks
or chunk.score > doc_chunks[chunk.document_id].score
):
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doc_chunks[chunk.document_id] = chunk
logger.info(f"Grouped chunks into {len(doc_chunks)} documents")
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logger.info(f"Document chunks: {doc_chunks}")
results = {}
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for doc_id, chunk in doc_chunks.items():
# Get document metadata
doc = await self.db.get_document(doc_id, auth)
if not doc:
logger.warning(f"Document {doc_id} not found")
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continue
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logger.info(f"Retrieved metadata for document {doc_id}")
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# Create DocumentContent based on content type
if doc.content_type == "text/plain":
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content = DocumentContent(type="string", value=chunk.content, filename=None)
logger.debug(f"Created text content for document {doc_id}")
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else:
# Generate download URL for file types
download_url = await self.storage.get_download_url(
doc.storage_info["bucket"], doc.storage_info["key"]
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)
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content = DocumentContent(type="url", value=download_url, filename=doc.filename)
logger.debug(f"Created URL content for document {doc_id}")
results[doc_id] = DocumentResult(
score=chunk.score,
document_id=doc_id,
metadata=doc.metadata,
content=content,
additional_metadata=doc.additional_metadata,
)
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logger.info(f"Created {len(results)} document results")
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return results
async def create_cache(
self,
name: str,
model: str,
gguf_file: str,
docs: List[Document | None],
filters: Optional[Dict[str, Any]] = None,
) -> Dict[str, str]:
"""Create a new cache with specified configuration.
Args:
name: Name of the cache to create
model: Name of the model to use
gguf_file: Name of the GGUF file to use
filters: Optional metadata filters for documents to include
docs: Optional list of specific document IDs to include
"""
# Create cache metadata
metadata = {
"model": model,
"model_file": gguf_file,
"filters": filters,
"docs": [doc.model_dump_json() for doc in docs],
"storage_info": {
"bucket": "caches",
"key": f"{name}_state.pkl",
},
}
# Store metadata in database
success = await self.db.store_cache_metadata(name, metadata)
if not success:
logger.error(f"Failed to store cache metadata for cache {name}")
return {"success": False, "message": f"Failed to store cache metadata for cache {name}"}
# Create cache instance
cache = self.cache_factory.create_new_cache(
name=name, model=model, model_file=gguf_file, filters=filters, docs=docs
)
cache_bytes = cache.saveable_state
base64_cache_bytes = base64.b64encode(cache_bytes).decode()
bucket, key = await self.storage.upload_from_base64(
base64_cache_bytes,
key=metadata["storage_info"]["key"],
bucket=metadata["storage_info"]["bucket"],
)
return {
"success": True,
"message": f"Cache created successfully, state stored in bucket `{bucket}` with key `{key}`",
}
async def load_cache(self, name: str) -> bool:
"""Load a cache into memory.
Args:
name: Name of the cache to load
Returns:
bool: Whether the cache exists and was loaded successfully
"""
try:
# Get cache metadata from database
metadata = await self.db.get_cache_metadata(name)
if not metadata:
logger.error(f"No metadata found for cache {name}")
return False
# Get cache bytes from storage
cache_bytes = await self.storage.download_file(
metadata["storage_info"]["bucket"], "caches/" + metadata["storage_info"]["key"]
)
cache_bytes = cache_bytes.read()
cache = self.cache_factory.load_cache_from_bytes(
name=name, cache_bytes=cache_bytes, metadata=metadata
)
self.active_caches[name] = cache
return {"success": True, "message": "Cache loaded successfully"}
except Exception as e:
logger.error(f"Failed to load cache {name}: {e}")
# raise e
return {"success": False, "message": f"Failed to load cache {name}: {e}"}
def close(self):
"""Close all resources."""
# Close any active caches
self.active_caches.clear()