fix: strip null bytes from parsed file content before retain (#535)

* doc: split blog index into Hindsight and Hindsight Cloud sections

- Tag the document upload post with `hindsight-cloud`
- BlogListPage renders two sections, capping Cloud at 3 posts with a "View all →" link
- Swizzle BlogTagsPostsPage so /blog/tags/hindsight-cloud uses the custom grid layout

* doc: attribute blog posts to Nicolò Boschi with GitHub profile image

Replace the generic "Hindsight Team" author with the real author entry
(nicoloboschi) across all 15 blog posts. GitHub profile image is loaded
from https://github.com/nicoloboschi.png.

* doc: add Hindsight Team title to nicoloboschi author

* doc: assign blog posts to correct authors based on git blame

- Add benfrank241 (Ben Bartholomew) and chrislatimer (Chris Latimer) to authors.yml
- Assign 7 posts to Ben, 1 post to Chris, remainder stay with Nicolò

* fix: strip null bytes from parsed file content before retain

* test: add tests for sanitize_llm_output

* fix: retry retain DB transaction on deadlock during parallel document processing
This commit is contained in:
Nicolò Boschi 2026-03-10 16:24:11 +01:00 committed by GitHub
parent 28308a14d6
commit cd3a6a227b
No known key found for this signature in database
GPG key ID: B5690EEEBB952194
4 changed files with 282 additions and 227 deletions

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@ -58,10 +58,16 @@ async def retry_with_backoff(
last_exception = e last_exception = e
if attempt < max_retries: if attempt < max_retries:
delay = min(base_delay * (2**attempt), max_delay) delay = min(base_delay * (2**attempt), max_delay)
logger.warning( if isinstance(e, asyncpg.exceptions.DeadlockDetectedError):
f"Database operation failed (attempt {attempt + 1}/{max_retries + 1}): {e}. " logger.warning(
f"Retrying in {delay:.1f}s..." f"Deadlock detected during parallel document processing — this is expected and will resolve automatically "
) f"(attempt {attempt + 1}/{max_retries + 1}, retrying in {delay:.1f}s)"
)
else:
logger.warning(
f"Database operation failed (attempt {attempt + 1}/{max_retries + 1}): {e}. "
f"Retrying in {delay:.1f}s..."
)
await asyncio.sleep(delay) await asyncio.sleep(delay)
else: else:
logger.error(f"Database operation failed after {max_retries + 1} attempts: {e}") logger.error(f"Database operation failed after {max_retries + 1} attempts: {e}")

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@ -168,7 +168,7 @@ from enum import Enum
from ..metrics import get_metrics_collector from ..metrics import get_metrics_collector
from ..pg0 import EmbeddedPostgres, parse_pg0_url from ..pg0 import EmbeddedPostgres, parse_pg0_url
from .entity_resolver import EntityResolver from .entity_resolver import EntityResolver
from .llm_wrapper import LLMConfig, requires_api_key from .llm_wrapper import LLMConfig, requires_api_key, sanitize_llm_output
from .query_analyzer import QueryAnalyzer from .query_analyzer import QueryAnalyzer
from .reflect import run_reflect_agent from .reflect import run_reflect_agent
from .reflect.tools import tool_expand, tool_recall, tool_search_mental_models, tool_search_observations from .reflect.tools import tool_expand, tool_recall, tool_search_mental_models, tool_search_observations
@ -664,7 +664,7 @@ class MemoryEngine(MemoryEngineInterface):
filename=filename, filename=filename,
content_type=task_dict.get("content_type"), content_type=task_dict.get("content_type"),
) )
markdown_content = convert_result.content markdown_content = sanitize_llm_output(convert_result.content) or ""
winning_parser = convert_result.parser_name winning_parser = convert_result.parser_name
except Exception as e: except Exception as e:
# Re-raise with filename context for better error reporting # Re-raise with filename context for better error reporting

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@ -11,7 +11,7 @@ from collections.abc import Awaitable, Callable
from datetime import UTC, datetime from datetime import UTC, datetime
from typing import Any from typing import Any
from ..db_utils import acquire_with_retry from ..db_utils import acquire_with_retry, retry_with_backoff
from . import bank_utils from . import bank_utils
@ -269,9 +269,6 @@ async def retain_batch(
for extracted_fact, embedding in zip(extracted_facts, embeddings) for extracted_fact, embedding in zip(extracted_facts, embeddings)
] ]
# Track document IDs for logging
document_ids_added = []
# Group contents by document_id for document tracking and chunk storage # Group contents by document_id for document tracking and chunk storage
from collections import defaultdict from collections import defaultdict
@ -280,234 +277,249 @@ async def retain_batch(
doc_id = content_dict.get("document_id") doc_id = content_dict.get("document_id")
contents_by_doc[doc_id].append((idx, content_dict)) contents_by_doc[doc_id].append((idx, content_dict))
# Step 4: Database transaction # Step 4: Database transaction (retried on deadlock)
async with acquire_with_retry(pool) as conn: result_unit_ids: list[list[str]] = []
async with conn.transaction():
# Handle document tracking for all documents
step_start = time.time()
# Map None document_id to generated UUIDs
doc_id_mapping = {} # Maps original doc_id (including None) to actual doc_id used
if document_id: log_buffer_pre_db = len(log_buffer)
# Legacy: single document_id parameter
combined_content = "\n".join([c.get("content", "") for c in contents_dicts])
retain_params = {}
# Collect tags from all content items and merge with document_tags
all_tags = set(document_tags or [])
for item in contents_dicts:
item_tags = item.get("tags", []) or []
all_tags.update(item_tags)
merged_tags = list(all_tags)
if contents_dicts: async def _run_db_work() -> None:
first_item = contents_dicts[0] nonlocal result_unit_ids
if first_item.get("context"):
retain_params["context"] = first_item["context"]
if first_item.get("event_date"):
retain_params["event_date"] = (
first_item["event_date"].isoformat()
if hasattr(first_item["event_date"], "isoformat")
else str(first_item["event_date"])
)
if first_item.get("metadata"):
retain_params["metadata"] = first_item["metadata"]
await fact_storage.handle_document_tracking( # Reset per-fact mutations and log buffer so each retry attempt starts clean
conn, bank_id, document_id, combined_content, is_first_batch, retain_params, merged_tags del log_buffer[log_buffer_pre_db:]
) document_ids_added: list[str] = []
document_ids_added.append(document_id) for pf in processed_facts:
doc_id_mapping[None] = document_id # For backwards compatibility pf.document_id = None
else: pf.chunk_id = None
# Handle per-item document_ids (create documents if any item has document_id or if chunks exist)
has_any_doc_ids = any(item.get("document_id") for item in contents_dicts)
if has_any_doc_ids or chunks: async with acquire_with_retry(pool) as conn:
for original_doc_id, doc_contents in contents_by_doc.items(): async with conn.transaction():
actual_doc_id = original_doc_id # Handle document tracking for all documents
step_start = time.time()
# Map None document_id to generated UUIDs
doc_id_mapping = {} # Maps original doc_id (including None) to actual doc_id used
# Only create document record if: if document_id:
# 1. Item has explicit document_id, OR # Legacy: single document_id parameter
# 2. There are chunks (need document for chunk storage) combined_content = "\n".join([c.get("content", "") for c in contents_dicts])
should_create_doc = (original_doc_id is not None) or chunks retain_params = {}
# Collect tags from all content items and merge with document_tags
all_tags = set(document_tags or [])
for item in contents_dicts:
item_tags = item.get("tags", []) or []
all_tags.update(item_tags)
merged_tags = list(all_tags)
if should_create_doc: if contents_dicts:
if actual_doc_id is None: first_item = contents_dicts[0]
# No document_id but have chunks - generate one if first_item.get("context"):
actual_doc_id = str(uuid.uuid4()) retain_params["context"] = first_item["context"]
if first_item.get("event_date"):
# Store mapping for later use retain_params["event_date"] = (
doc_id_mapping[original_doc_id] = actual_doc_id first_item["event_date"].isoformat()
if hasattr(first_item["event_date"], "isoformat")
# Combine content for this document else str(first_item["event_date"])
combined_content = "\n".join([c.get("content", "") for _, c in doc_contents])
# Collect tags from all content items for this document and merge with document_tags
all_tags = set(document_tags or [])
for _, item in doc_contents:
item_tags = item.get("tags", []) or []
all_tags.update(item_tags)
merged_tags = list(all_tags)
# Extract retain params from first content item
retain_params = {}
if doc_contents:
first_item = doc_contents[0][1]
if first_item.get("context"):
retain_params["context"] = first_item["context"]
if first_item.get("event_date"):
retain_params["event_date"] = (
first_item["event_date"].isoformat()
if hasattr(first_item["event_date"], "isoformat")
else str(first_item["event_date"])
)
if first_item.get("metadata"):
retain_params["metadata"] = first_item["metadata"]
await fact_storage.handle_document_tracking(
conn,
bank_id,
actual_doc_id,
combined_content,
is_first_batch,
retain_params,
merged_tags,
) )
document_ids_added.append(actual_doc_id) if first_item.get("metadata"):
retain_params["metadata"] = first_item["metadata"]
await fact_storage.handle_document_tracking(
conn, bank_id, document_id, combined_content, is_first_batch, retain_params, merged_tags
)
document_ids_added.append(document_id)
doc_id_mapping[None] = document_id # For backwards compatibility
else:
# Handle per-item document_ids (create documents if any item has document_id or if chunks exist)
has_any_doc_ids = any(item.get("document_id") for item in contents_dicts)
if has_any_doc_ids or chunks:
for original_doc_id, doc_contents in contents_by_doc.items():
actual_doc_id = original_doc_id
# Only create document record if:
# 1. Item has explicit document_id, OR
# 2. There are chunks (need document for chunk storage)
should_create_doc = (original_doc_id is not None) or chunks
if should_create_doc:
if actual_doc_id is None:
# No document_id but have chunks - generate one
actual_doc_id = str(uuid.uuid4())
# Store mapping for later use
doc_id_mapping[original_doc_id] = actual_doc_id
# Combine content for this document
combined_content = "\n".join([c.get("content", "") for _, c in doc_contents])
# Collect tags from all content items for this document and merge with document_tags
all_tags = set(document_tags or [])
for _, item in doc_contents:
item_tags = item.get("tags", []) or []
all_tags.update(item_tags)
merged_tags = list(all_tags)
# Extract retain params from first content item
retain_params = {}
if doc_contents:
first_item = doc_contents[0][1]
if first_item.get("context"):
retain_params["context"] = first_item["context"]
if first_item.get("event_date"):
retain_params["event_date"] = (
first_item["event_date"].isoformat()
if hasattr(first_item["event_date"], "isoformat")
else str(first_item["event_date"])
)
if first_item.get("metadata"):
retain_params["metadata"] = first_item["metadata"]
await fact_storage.handle_document_tracking(
conn,
bank_id,
actual_doc_id,
combined_content,
is_first_batch,
retain_params,
merged_tags,
)
document_ids_added.append(actual_doc_id)
if document_ids_added:
log_buffer.append(
f"[2.5] Document tracking: {len(document_ids_added)} documents in {time.time() - step_start:.3f}s"
)
# Store chunks and map to facts for all documents
step_start = time.time()
chunk_id_map_by_doc = {} # Maps (doc_id, chunk_index) -> chunk_id
if chunks:
# Group chunks by their source document
chunks_by_doc = defaultdict(list)
for chunk in chunks:
# chunk.content_index tells us which content this chunk came from
original_doc_id = contents_dicts[chunk.content_index].get("document_id")
# Map to actual document_id (handles None -> generated UUID mapping)
actual_doc_id = doc_id_mapping.get(original_doc_id, original_doc_id)
if actual_doc_id is None and document_id:
actual_doc_id = document_id
chunks_by_doc[actual_doc_id].append(chunk)
# Store chunks for each document
for doc_id, doc_chunks in chunks_by_doc.items():
chunk_id_map = await chunk_storage.store_chunks_batch(conn, bank_id, doc_id, doc_chunks)
# Store mapping with document context
for chunk_idx, chunk_id in chunk_id_map.items():
chunk_id_map_by_doc[(doc_id, chunk_idx)] = chunk_id
log_buffer.append(
f"[3] Store chunks: {len(chunks)} chunks for {len(chunks_by_doc)} documents in {time.time() - step_start:.3f}s"
)
# Map chunk_ids and document_ids to facts
for fact, processed_fact in zip(extracted_facts, processed_facts):
# Get the original document_id for this fact's source content
original_doc_id = contents_dicts[fact.content_index].get("document_id")
# Map to actual document_id (handles None -> generated UUID mapping)
actual_doc_id = doc_id_mapping.get(original_doc_id, original_doc_id)
if actual_doc_id is None and document_id:
actual_doc_id = document_id
# Set document_id on the fact
processed_fact.document_id = actual_doc_id
# Map chunk_id if this fact came from a chunk
if fact.chunk_index is not None:
# Look up chunk_id using (doc_id, chunk_index)
chunk_id = chunk_id_map_by_doc.get((actual_doc_id, fact.chunk_index))
if chunk_id:
processed_fact.chunk_id = chunk_id
else:
# No chunks - still need to set document_id on facts
for fact, processed_fact in zip(extracted_facts, processed_facts):
original_doc_id = contents_dicts[fact.content_index].get("document_id")
# Map to actual document_id (handles None -> generated UUID mapping)
actual_doc_id = doc_id_mapping.get(original_doc_id, original_doc_id)
if actual_doc_id is None and document_id:
actual_doc_id = document_id
processed_fact.document_id = actual_doc_id
non_duplicate_facts = processed_facts
# Insert facts (document_id is now stored per-fact)
step_start = time.time()
unit_ids = await fact_storage.insert_facts_batch(conn, bank_id, non_duplicate_facts)
log_buffer.append(f"[5] Insert facts: {len(unit_ids)} units in {time.time() - step_start:.3f}s")
# Process entities
step_start = time.time()
# Build map of content_index -> user entities for merging
user_entities_per_content = {
idx: content.entities for idx, content in enumerate(contents) if content.entities
}
entity_links = await entity_processing.process_entities_batch(
entity_resolver,
conn,
bank_id,
unit_ids,
non_duplicate_facts,
log_buffer,
user_entities_per_content=user_entities_per_content,
entity_labels=getattr(config, "entity_labels", None),
)
log_buffer.append(f"[6] Process entities: {len(entity_links)} links in {time.time() - step_start:.3f}s")
# Create temporal links
step_start = time.time()
temporal_link_count = await link_creation.create_temporal_links_batch(conn, bank_id, unit_ids)
log_buffer.append(f"[7] Temporal links: {temporal_link_count} links in {time.time() - step_start:.3f}s")
# Create semantic links
step_start = time.time()
embeddings_for_links = [fact.embedding for fact in non_duplicate_facts]
semantic_link_count = await link_creation.create_semantic_links_batch(
conn, bank_id, unit_ids, embeddings_for_links
)
log_buffer.append(f"[8] Semantic links: {semantic_link_count} links in {time.time() - step_start:.3f}s")
# Insert entity links
step_start = time.time()
if entity_links:
await entity_processing.insert_entity_links_batch(conn, entity_links)
log_buffer.append(
f"[9] Entity links: {len(entity_links) if entity_links else 0} links in {time.time() - step_start:.3f}s"
)
# Create causal links
step_start = time.time()
causal_link_count = await link_creation.create_causal_links_batch(conn, unit_ids, non_duplicate_facts)
log_buffer.append(f"[10] Causal links: {causal_link_count} links in {time.time() - step_start:.3f}s")
# Map results back to original content items
result_unit_ids = _map_results_to_contents(contents, extracted_facts, unit_ids)
# Transactional outbox: queue any side-effect tasks (e.g. webhook deliveries)
# inside the same transaction so they are atomically committed with the retain data.
if outbox_callback:
await outbox_callback(conn)
# Flush entity stats (mention_count / last_seen) now that the transaction
# has committed. Uses a fresh pool connection — no locks held.
await entity_resolver.flush_pending_stats()
# Log final summary
total_time = time.time() - start_time
log_buffer.append(f"{'=' * 60}")
log_buffer.append(f"RETAIN_BATCH COMPLETE: {len(unit_ids)} units in {total_time:.3f}s")
if document_ids_added: if document_ids_added:
log_buffer.append( log_buffer.append(f"Documents: {', '.join(document_ids_added)}")
f"[2.5] Document tracking: {len(document_ids_added)} documents in {time.time() - step_start:.3f}s" log_buffer.append(f"{'=' * 60}")
)
# Store chunks and map to facts for all documents logger.info("\n" + "\n".join(log_buffer) + "\n")
step_start = time.time()
chunk_id_map_by_doc = {} # Maps (doc_id, chunk_index) -> chunk_id
if chunks: await retry_with_backoff(_run_db_work)
# Group chunks by their source document return result_unit_ids, usage
chunks_by_doc = defaultdict(list)
for chunk in chunks:
# chunk.content_index tells us which content this chunk came from
original_doc_id = contents_dicts[chunk.content_index].get("document_id")
# Map to actual document_id (handles None -> generated UUID mapping)
actual_doc_id = doc_id_mapping.get(original_doc_id, original_doc_id)
if actual_doc_id is None and document_id:
actual_doc_id = document_id
chunks_by_doc[actual_doc_id].append(chunk)
# Store chunks for each document
for doc_id, doc_chunks in chunks_by_doc.items():
chunk_id_map = await chunk_storage.store_chunks_batch(conn, bank_id, doc_id, doc_chunks)
# Store mapping with document context
for chunk_idx, chunk_id in chunk_id_map.items():
chunk_id_map_by_doc[(doc_id, chunk_idx)] = chunk_id
log_buffer.append(
f"[3] Store chunks: {len(chunks)} chunks for {len(chunks_by_doc)} documents in {time.time() - step_start:.3f}s"
)
# Map chunk_ids and document_ids to facts
for fact, processed_fact in zip(extracted_facts, processed_facts):
# Get the original document_id for this fact's source content
original_doc_id = contents_dicts[fact.content_index].get("document_id")
# Map to actual document_id (handles None -> generated UUID mapping)
actual_doc_id = doc_id_mapping.get(original_doc_id, original_doc_id)
if actual_doc_id is None and document_id:
actual_doc_id = document_id
# Set document_id on the fact
processed_fact.document_id = actual_doc_id
# Map chunk_id if this fact came from a chunk
if fact.chunk_index is not None:
# Look up chunk_id using (doc_id, chunk_index)
chunk_id = chunk_id_map_by_doc.get((actual_doc_id, fact.chunk_index))
if chunk_id:
processed_fact.chunk_id = chunk_id
else:
# No chunks - still need to set document_id on facts
for fact, processed_fact in zip(extracted_facts, processed_facts):
original_doc_id = contents_dicts[fact.content_index].get("document_id")
# Map to actual document_id (handles None -> generated UUID mapping)
actual_doc_id = doc_id_mapping.get(original_doc_id, original_doc_id)
if actual_doc_id is None and document_id:
actual_doc_id = document_id
processed_fact.document_id = actual_doc_id
non_duplicate_facts = processed_facts
# Insert facts (document_id is now stored per-fact)
step_start = time.time()
unit_ids = await fact_storage.insert_facts_batch(conn, bank_id, non_duplicate_facts)
log_buffer.append(f"[5] Insert facts: {len(unit_ids)} units in {time.time() - step_start:.3f}s")
# Process entities
step_start = time.time()
# Build map of content_index -> user entities for merging
user_entities_per_content = {
idx: content.entities for idx, content in enumerate(contents) if content.entities
}
entity_links = await entity_processing.process_entities_batch(
entity_resolver,
conn,
bank_id,
unit_ids,
non_duplicate_facts,
log_buffer,
user_entities_per_content=user_entities_per_content,
entity_labels=getattr(config, "entity_labels", None),
)
log_buffer.append(f"[6] Process entities: {len(entity_links)} links in {time.time() - step_start:.3f}s")
# Create temporal links
step_start = time.time()
temporal_link_count = await link_creation.create_temporal_links_batch(conn, bank_id, unit_ids)
log_buffer.append(f"[7] Temporal links: {temporal_link_count} links in {time.time() - step_start:.3f}s")
# Create semantic links
step_start = time.time()
embeddings_for_links = [fact.embedding for fact in non_duplicate_facts]
semantic_link_count = await link_creation.create_semantic_links_batch(
conn, bank_id, unit_ids, embeddings_for_links
)
log_buffer.append(f"[8] Semantic links: {semantic_link_count} links in {time.time() - step_start:.3f}s")
# Insert entity links
step_start = time.time()
if entity_links:
await entity_processing.insert_entity_links_batch(conn, entity_links)
log_buffer.append(
f"[9] Entity links: {len(entity_links) if entity_links else 0} links in {time.time() - step_start:.3f}s"
)
# Create causal links
step_start = time.time()
causal_link_count = await link_creation.create_causal_links_batch(conn, unit_ids, non_duplicate_facts)
log_buffer.append(f"[10] Causal links: {causal_link_count} links in {time.time() - step_start:.3f}s")
# Map results back to original content items
result_unit_ids = _map_results_to_contents(contents, extracted_facts, unit_ids)
# Transactional outbox: queue any side-effect tasks (e.g. webhook deliveries)
# inside the same transaction so they are atomically committed with the retain data.
if outbox_callback:
await outbox_callback(conn)
# Flush entity stats (mention_count / last_seen) now that the transaction
# has committed. Uses a fresh pool connection — no locks held.
await entity_resolver.flush_pending_stats()
# Log final summary
total_time = time.time() - start_time
log_buffer.append(f"{'=' * 60}")
log_buffer.append(f"RETAIN_BATCH COMPLETE: {len(unit_ids)} units in {total_time:.3f}s")
if document_ids_added:
log_buffer.append(f"Documents: {', '.join(document_ids_added)}")
log_buffer.append(f"{'=' * 60}")
logger.info("\n" + "\n".join(log_buffer) + "\n")
return result_unit_ids, usage
def _map_results_to_contents( def _map_results_to_contents(

View file

@ -0,0 +1,37 @@
import pytest
from hindsight_api.engine.llm_wrapper import sanitize_llm_output
@pytest.mark.parametrize(
"input_text, expected",
[
# Null bytes stripped
("hello\x00world", "helloworld"),
("FIRST\u0000PAGE", "FIRSTPAGE"),
# Multiple null bytes
("\x00\x00text\x00", "text"),
# Other control characters stripped (non-whitespace)
("text\x01\x02\x03end", "textend"),
("text\x08end", "textend"), # backspace
("text\x0cend", "textend"), # form feed
("text\x0bend", "textend"), # vertical tab
("text\x1fend", "textend"), # unit separator
("text\x7fend", "textend"), # DEL
# Whitespace preserved
("hello\tworld", "hello\tworld"),
("hello\nworld", "hello\nworld"),
("hello\r\nworld", "hello\r\nworld"),
# Unicode surrogates stripped
("text\ud800end", "textend"),
("text\udfffend", "textend"),
# Clean text unchanged
("normal text", "normal text"),
("unicode: café naïve", "unicode: café naïve"),
# Edge cases
("", ""),
(None, None),
],
)
def test_sanitize_llm_output(input_text, expected):
assert sanitize_llm_output(input_text) == expected