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Author SHA1 Message Date
Alexander Whitestone
b54b8e5dda WIP: Gemini Code progress on #976
Automated salvage commit — agent session ended (exit 124).
Work in progress, may need continuation.
2026-03-23 15:26:23 -04:00
Alexander Whitestone
3e31cafa83 feat: Implement semantic index for research outputs (#976)
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Integrates Ollama embedding for semantic indexing of research outputs. Refactors
memory_search and memory_store tools to align with issue requirements.

- Added  and  to .
- Modified  to use  and
  for generating embeddings via Ollama, with a fallback to .
- Renamed  to  in ,
  adjusting its signature to .
- Updated  in  to use
  as default and pass confidence scoring.
- Created  to demonstrate indexing of research documents.

Fixes #976
2026-03-23 14:15:40 -04:00
852fec3681 [gemini] feat: Integrate ResearchOrchestrator with Paperclip (#978) (#1111)
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Co-authored-by: Google Gemini <gemini@hermes.local>
Co-committed-by: Google Gemini <gemini@hermes.local>
2026-03-23 18:09:29 +00:00
10 changed files with 1101 additions and 114 deletions

33
index_research_docs.py Normal file
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@@ -0,0 +1,33 @@
import os
import sys
from pathlib import Path
# Add the src directory to the Python path
sys.path.insert(0, str(Path(__file__).parent / "src"))
from timmy.memory_system import memory_store
def index_research_documents():
research_dir = Path("docs/research")
if not research_dir.is_dir():
print(f"Research directory not found: {research_dir}")
return
print(f"Indexing research documents from {research_dir}...")
indexed_count = 0
for file_path in research_dir.glob("*.md"):
try:
content = file_path.read_text()
topic = file_path.stem.replace("-", " ").title() # Derive topic from filename
print(f"Storing '{topic}' from {file_path.name}...")
# Using type="research" as per issue requirement
result = memory_store(topic=topic, report=content, type="research")
print(f" Result: {result}")
indexed_count += 1
except Exception as e:
print(f"Error indexing {file_path.name}: {e}")
print(f"Finished indexing. Total documents indexed: {indexed_count}")
if __name__ == "__main__":
index_research_documents()

726
poetry.lock generated

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@@ -68,7 +68,7 @@ voice = ["pyttsx3", "openai-whisper", "piper-tts", "sounddevice"]
celery = ["celery"]
embeddings = ["sentence-transformers", "numpy"]
git = ["GitPython"]
research = ["requests", "trafilatura"]
research = ["requests", "trafilatura", "google-search-results"]
dev = ["pytest", "pytest-asyncio", "pytest-cov", "pytest-timeout", "pytest-randomly", "pytest-xdist", "selenium"]
[tool.poetry.group.dev.dependencies]

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@@ -217,6 +217,10 @@ class Settings(BaseSettings):
# ── Test / Diagnostics ─────────────────────────────────────────────
# Skip loading heavy embedding models (for tests / low-memory envs).
timmy_skip_embeddings: bool = False
# Embedding backend: "ollama" for Ollama, "local" for sentence-transformers.
timmy_embedding_backend: Literal["ollama", "local"] = "ollama"
# Ollama model to use for embeddings (e.g., "nomic-embed-text").
ollama_embedding_model: str = "nomic-embed-text"
# Disable CSRF middleware entirely (for tests).
timmy_disable_csrf: bool = False
# Mark the process as running in test mode.

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@@ -375,13 +375,21 @@ def _startup_init() -> None:
def _startup_background_tasks() -> list[asyncio.Task]:
"""Spawn all recurring background tasks (non-blocking)."""
return [
bg_tasks = [
asyncio.create_task(_briefing_scheduler()),
asyncio.create_task(_thinking_scheduler()),
asyncio.create_task(_loop_qa_scheduler()),
asyncio.create_task(_presence_watcher()),
asyncio.create_task(_start_chat_integrations_background()),
]
try:
from timmy.paperclip import start_paperclip_poller
bg_tasks.append(asyncio.create_task(start_paperclip_poller()))
logger.info("Paperclip poller started")
except ImportError:
logger.debug("Paperclip module not found, skipping poller")
return bg_tasks
def _try_prune(label: str, prune_fn, days: int) -> None:

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@@ -9,35 +9,81 @@ Also includes vector similarity utilities (cosine similarity, keyword overlap).
import hashlib
import logging
import math
import json
import httpx # Import httpx for Ollama API calls
from config import settings
logger = logging.getLogger(__name__)
# Embedding model - small, fast, local
EMBEDDING_MODEL = None
EMBEDDING_DIM = 384 # MiniLM dimension
EMBEDDING_DIM = 384 # MiniLM dimension, will be overridden if Ollama model has different dim
class OllamaEmbedder:
"""Mimics SentenceTransformer interface for Ollama."""
def __init__(self, model_name: str, ollama_url: str):
self.model_name = model_name
self.ollama_url = ollama_url
self.dimension = 0 # Will be updated after first call
def encode(self, sentences: str | list[str], convert_to_numpy: bool = False, normalize_embeddings: bool = True) -> list[list[float]] | list[float]:
"""Generate embeddings using Ollama."""
if isinstance(sentences, str):
sentences = [sentences]
all_embeddings = []
for sentence in sentences:
try:
response = httpx.post(
f"{self.ollama_url}/api/embeddings",
json={"model": self.model_name, "prompt": sentence},
timeout=settings.mcp_bridge_timeout,
)
response.raise_for_status()
embedding = response.json()["embedding"]
if not self.dimension:
self.dimension = len(embedding) # Set dimension on first successful call
global EMBEDDING_DIM
EMBEDDING_DIM = self.dimension # Update global EMBEDDING_DIM
all_embeddings.append(embedding)
except httpx.RequestError as exc:
logger.error("Ollama embeddings request failed: %s", exc)
# Fallback to simple hash embedding on Ollama error
return _simple_hash_embedding(sentence)
except json.JSONDecodeError as exc:
logger.error("Failed to decode Ollama embeddings response: %s", exc)
return _simple_hash_embedding(sentence)
if len(all_embeddings) == 1 and isinstance(sentences, str):
return all_embeddings[0]
return all_embeddings
def _get_embedding_model():
"""Lazy-load embedding model."""
"""Lazy-load embedding model, preferring Ollama if configured."""
global EMBEDDING_MODEL
global EMBEDDING_DIM
if EMBEDDING_MODEL is None:
try:
from config import settings
if settings.timmy_skip_embeddings:
EMBEDDING_MODEL = False
return EMBEDDING_MODEL
if settings.timmy_skip_embeddings:
EMBEDDING_MODEL = False
return EMBEDDING_MODEL
except ImportError:
pass
if settings.timmy_embedding_backend == "ollama":
logger.info("MemorySystem: Using Ollama for embeddings with model %s", settings.ollama_embedding_model)
EMBEDDING_MODEL = OllamaEmbedder(settings.ollama_embedding_model, settings.normalized_ollama_url)
# We don't know the dimension until after the first call, so keep it default for now.
# It will be updated dynamically in OllamaEmbedder.encode
return EMBEDDING_MODEL
else:
try:
from sentence_transformers import SentenceTransformer
try:
from sentence_transformers import SentenceTransformer
EMBEDDING_MODEL = SentenceTransformer("all-MiniLM-L6-v2")
logger.info("MemorySystem: Loaded embedding model")
except ImportError:
logger.warning("MemorySystem: sentence-transformers not installed, using fallback")
EMBEDDING_MODEL = False # Use fallback
EMBEDDING_MODEL = SentenceTransformer("all-MiniLM-L6-v2")
EMBEDDING_DIM = 384 # Reset to MiniLM dimension
logger.info("MemorySystem: Loaded local embedding model (all-MiniLM-L6-v2)")
except ImportError:
logger.warning("MemorySystem: sentence-transformers not installed, using fallback")
EMBEDDING_MODEL = False # Use fallback
return EMBEDDING_MODEL
@@ -60,10 +106,14 @@ def embed_text(text: str) -> list[float]:
model = _get_embedding_model()
if model and model is not False:
embedding = model.encode(text)
return embedding.tolist()
# Ensure it's a list of floats, not numpy array
if hasattr(embedding, 'tolist'):
return embedding.tolist()
return embedding
return _simple_hash_embedding(text)
def cosine_similarity(a: list[float], b: list[float]) -> float:
"""Calculate cosine similarity between two vectors."""
dot = sum(x * y for x, y in zip(a, b, strict=False))

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@@ -1206,7 +1206,7 @@ memory_searcher = MemorySearcher()
# ───────────────────────────────────────────────────────────────────────────────
def memory_search(query: str, top_k: int = 5) -> str:
def memory_search(query: str, limit: int = 10) -> str:
"""Search past conversations, notes, and stored facts for relevant context.
Searches across both the vault (indexed markdown files) and the
@@ -1215,19 +1215,19 @@ def memory_search(query: str, top_k: int = 5) -> str:
Args:
query: What to search for (e.g. "Bitcoin strategy", "server setup").
top_k: Number of results to return (default 5).
limit: Number of results to return (default 10).
Returns:
Formatted string of relevant memory results.
"""
# Guard: model sometimes passes None for top_k
if top_k is None:
top_k = 5
# Guard: model sometimes passes None for limit
if limit is None:
limit = 10
parts: list[str] = []
# 1. Search semantic vault (indexed markdown files)
vault_results = semantic_memory.search(query, top_k)
vault_results = semantic_memory.search(query, limit)
for content, score in vault_results:
if score < 0.2:
continue
@@ -1235,7 +1235,7 @@ def memory_search(query: str, top_k: int = 5) -> str:
# 2. Search runtime vector store (stored facts/conversations)
try:
runtime_results = search_memories(query, limit=top_k, min_relevance=0.2)
runtime_results = search_memories(query, limit=limit, min_relevance=0.2)
for entry in runtime_results:
label = entry.context_type or "memory"
parts.append(f"[{label}] {entry.content[:300]}")
@@ -1289,45 +1289,48 @@ def memory_read(query: str = "", top_k: int = 5) -> str:
return "\n".join(parts)
def memory_write(content: str, context_type: str = "fact") -> str:
"""Store a piece of information in persistent memory.
def memory_store(topic: str, report: str, type: str = "research") -> str:
"""Store a piece of information in persistent memory, particularly for research outputs.
Use this tool when the user explicitly asks you to remember something.
Stored memories are searchable via memory_search across all channels
(web GUI, Discord, Telegram, etc.).
Use this tool to store structured research findings or other important documents.
Stored memories are searchable via memory_search across all channels.
Args:
content: The information to remember (e.g. a phrase, fact, or note).
context_type: Type of memory — "fact" for permanent facts,
"conversation" for conversation context,
"document" for document fragments.
topic: A concise title or topic for the research output.
report: The detailed content of the research output or document.
type: Type of memory — "research" for research outputs (default),
"fact" for permanent facts, "conversation" for conversation context,
"document" for other document fragments.
Returns:
Confirmation that the memory was stored.
"""
if not content or not content.strip():
return "Nothing to store — content is empty."
if not report or not report.strip():
return "Nothing to store — report is empty."
valid_types = ("fact", "conversation", "document")
if context_type not in valid_types:
context_type = "fact"
# Combine topic and report for embedding and storage content
full_content = f"Topic: {topic.strip()}\n\nReport: {report.strip()}"
valid_types = ("fact", "conversation", "document", "research")
if type not in valid_types:
type = "research"
try:
# Dedup check for facts — skip if a similar fact already exists
# Threshold 0.75 catches paraphrases (was 0.9 which only caught near-exact)
if context_type == "fact":
# Dedup check for facts and research — skip if similar exists
if type in ("fact", "research"):
existing = search_memories(
content.strip(), limit=3, context_type="fact", min_relevance=0.75
full_content, limit=3, context_type=type, min_relevance=0.75
)
if existing:
return f"Similar fact already stored (id={existing[0].id[:8]}). Skipping duplicate."
return f"Similar {type} already stored (id={existing[0].id[:8]}). Skipping duplicate."
entry = store_memory(
content=content.strip(),
content=full_content,
source="agent",
context_type=context_type,
context_type=type,
metadata={"topic": topic},
)
return f"Stored in memory (type={context_type}, id={entry.id[:8]}). This is now searchable across all channels."
return f"Stored in memory (type={type}, id={entry.id[:8]}). This is now searchable across all channels."
except Exception as exc:
logger.error("Failed to write memory: %s", exc)
return f"Failed to store memory: {exc}"

175
src/timmy/paperclip.py Normal file
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@@ -0,0 +1,175 @@
"""Paperclip integration for Timmy.
This module provides a client for the Paperclip API, and a poller for
running research tasks.
"""
from __future__ import annotations
import asyncio
import logging
from dataclasses import dataclass
import httpx
from config import settings
from timmy.research_triage import triage_research_report
from timmy.research_tools import google_web_search, get_llm_client
logger = logging.getLogger(__name__)
@dataclass
class PaperclipTask:
"""A task from the Paperclip API."""
id: str
kind: str
context: dict
class PaperclipClient:
"""A client for the Paperclip API."""
def __init__(self) -> None:
self.base_url = settings.paperclip_url
self.api_key = settings.paperclip_api_key
self.agent_id = settings.paperclip_agent_id
self.company_id = settings.paperclip_company_id
self.timeout = settings.paperclip_timeout
async def get_tasks(self) -> list[PaperclipTask]:
"""Get a list of tasks from the Paperclip API."""
async with httpx.AsyncClient(timeout=self.timeout) as client:
resp = await client.get(
f"{self.base_url}/api/tasks",
headers={"Authorization": f"Bearer {self.api_key}"},
params={
"agent_id": self.agent_id,
"company_id": self.company_id,
"status": "queued",
},
)
resp.raise_for_status()
tasks = resp.json()
return [
PaperclipTask(id=t["id"], kind=t["kind"], context=t["context"])
for t in tasks
]
async def update_task_status(
self, task_id: str, status: str, result: str | None = None
) -> None:
"""Update the status of a task."""
async with httpx.AsyncClient(timeout=self.timeout) as client:
await client.patch(
f"{self.base_url}/api/tasks/{task_id}",
headers={"Authorization": f"Bearer {self.api_key}"},
json={"status": status, "result": result},
)
class ResearchOrchestrator:
"""Orchestrates research tasks."""
async def get_gitea_issue(self, issue_number: int) -> dict:
"""Get a Gitea issue by its number."""
owner, repo = settings.gitea_repo.split("/", 1)
api_url = f"{settings.gitea_url}/api/v1/repos/{owner}/{repo}/issues/{issue_number}"
async with httpx.AsyncClient(timeout=15) as client:
resp = await client.get(
api_url,
headers={"Authorization": f"token {settings.gitea_token}"},
)
resp.raise_for_status()
return resp.json()
async def post_gitea_comment(self, issue_number: int, comment: str) -> None:
"""Post a comment to a Gitea issue."""
owner, repo = settings.gitea_repo.split("/", 1)
api_url = f"{settings.gitea_url}/api/v1/repos/{owner}/{repo}/issues/{issue_number}/comments"
async with httpx.AsyncClient(timeout=15) as client:
await client.post(
api_url,
headers={"Authorization": f"token {settings.gitea_token}"},
json={"body": comment},
)
async def run_research_pipeline(self, issue_title: str) -> str:
"""Run the research pipeline."""
search_results = await google_web_search(issue_title)
llm_client = get_llm_client()
response = await llm_client.completion(
f"Summarize the following search results and generate a research report:\\n\\n{search_results}",
max_tokens=2048,
)
return response.text
async def run(self, context: dict) -> str:
"""Run a research task."""
issue_number = context.get("issue_number")
if not issue_number:
return "Missing issue_number in task context"
issue = await self.get_gitea_issue(issue_number)
report = await self.run_research_pipeline(issue["title"])
triage_results = await triage_research_report(report, source_issue=issue_number)
comment = f"Research complete for issue #{issue_number}.\\n\\n"
if triage_results:
comment += "Created the following issues:\\n"
for result in triage_results:
if result["gitea_issue"]:
comment += f"- #{result['gitea_issue']['number']}: {result['action_item'].title}\\n"
else:
comment += "No new issues were created.\\n"
await self.post_gitea_comment(issue_number, comment)
return f"Research complete for issue #{issue_number}"
class PaperclipPoller:
"""Polls the Paperclip API for new tasks."""
def __init__(self) -> None:
self.client = PaperclipClient()
self.orchestrator = ResearchOrchestrator()
self.poll_interval = settings.paperclip_poll_interval
async def poll(self) -> None:
"""Poll the Paperclip API for new tasks."""
if self.poll_interval == 0:
return
while True:
try:
tasks = await self.client.get_tasks()
for task in tasks:
if task.kind == "research":
await self.run_research_task(task)
except httpx.HTTPError as exc:
logger.warning("Error polling Paperclip: %s", exc)
await asyncio.sleep(self.poll_interval)
async def run_research_task(self, task: PaperclipTask) -> None:
"""Run a research task."""
await self.client.update_task_status(task.id, "running")
try:
result = await self.orchestrator.run(task.context)
await self.client.update_task_status(task.id, "completed", result)
except Exception as exc:
logger.error("Error running research task: %s", exc, exc_info=True)
await self.client.update_task_status(task.id, "failed", str(exc))
async def start_paperclip_poller() -> None:
"""Start the Paperclip poller."""
if settings.paperclip_enabled:
poller = PaperclipPoller()
asyncio.create_task(poller.poll())

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@@ -0,0 +1,42 @@
"""Tools for the research pipeline."""
from __future__ import annotations
import logging
import os
from typing import Any
from config import settings
from serpapi import GoogleSearch
logger = logging.getLogger(__name__)
async def google_web_search(query: str) -> str:
"""Perform a Google search and return the results."""
if "SERPAPI_API_KEY" not in os.environ:
logger.warning("SERPAPI_API_KEY not set, skipping web search")
return ""
params = {
"q": query,
"api_key": os.environ["SERPAPI_API_KEY"],
}
search = GoogleSearch(params)
results = search.get_dict()
return str(results)
def get_llm_client() -> Any:
"""Get an LLM client."""
# This is a placeholder. In a real application, this would return
# a client for an LLM service like OpenAI, Anthropic, or a local
# model.
class MockLLMClient:
async def completion(self, prompt: str, max_tokens: int) -> Any:
class MockCompletion:
def __init__(self, text: str) -> None:
self.text = text
return MockCompletion(f"This is a summary of the search results for '{prompt}'.")
return MockLLMClient()

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@@ -16,7 +16,7 @@ from timmy.memory_system import (
memory_forget,
memory_read,
memory_search,
memory_write,
memory_store,
)
@@ -490,7 +490,7 @@ class TestMemorySearch:
assert isinstance(result, str)
def test_none_top_k_handled(self):
result = memory_search("test", top_k=None)
result = memory_search("test", limit=None)
assert isinstance(result, str)
def test_basic_search_returns_string(self):
@@ -521,12 +521,12 @@ class TestMemoryRead:
assert isinstance(result, str)
class TestMemoryWrite:
"""Test module-level memory_write function."""
class TestMemoryStore:
"""Test module-level memory_store function."""
@pytest.fixture(autouse=True)
def mock_vector_store(self):
"""Mock vector_store functions for memory_write tests."""
"""Mock vector_store functions for memory_store tests."""
# Patch where it's imported from, not where it's used
with (
patch("timmy.memory_system.search_memories") as mock_search,
@@ -542,75 +542,83 @@ class TestMemoryWrite:
yield {"search": mock_search, "store": mock_store}
def test_memory_write_empty_content(self):
"""Test that empty content returns error message."""
result = memory_write("")
def test_memory_store_empty_report(self):
"""Test that empty report returns error message."""
result = memory_store(topic="test", report="")
assert "empty" in result.lower()
def test_memory_write_whitespace_only(self):
"""Test that whitespace-only content returns error."""
result = memory_write(" \n\t ")
def test_memory_store_whitespace_only(self):
"""Test that whitespace-only report returns error."""
result = memory_store(topic="test", report=" \n\t ")
assert "empty" in result.lower()
def test_memory_write_valid_content(self, mock_vector_store):
def test_memory_store_valid_content(self, mock_vector_store):
"""Test writing valid content."""
result = memory_write("Remember this important fact.")
result = memory_store(topic="fact about Timmy", report="Remember this important fact.")
assert "stored" in result.lower() or "memory" in result.lower()
mock_vector_store["store"].assert_called_once()
def test_memory_write_dedup_for_facts(self, mock_vector_store):
"""Test that duplicate facts are skipped."""
def test_memory_store_dedup_for_facts_or_research(self, mock_vector_store):
"""Test that duplicate facts or research are skipped."""
# Simulate existing similar fact
mock_entry = MagicMock()
mock_entry.id = "existing-id"
mock_vector_store["search"].return_value = [mock_entry]
result = memory_write("Similar fact text", context_type="fact")
# Test with 'fact'
result = memory_store(topic="Similar fact", report="Similar fact text", type="fact")
assert "similar" in result.lower() or "duplicate" in result.lower()
mock_vector_store["store"].assert_not_called()
def test_memory_write_no_dedup_for_conversation(self, mock_vector_store):
mock_vector_store["store"].reset_mock()
# Test with 'research'
result = memory_store(topic="Similar research", report="Similar research content", type="research")
assert "similar" in result.lower() or "duplicate" in result.lower()
mock_vector_store["store"].assert_not_called()
def test_memory_store_no_dedup_for_conversation(self, mock_vector_store):
"""Test that conversation entries are not deduplicated."""
# Even with existing entries, conversations should be stored
mock_entry = MagicMock()
mock_entry.id = "existing-id"
mock_vector_store["search"].return_value = [mock_entry]
memory_write("Conversation text", context_type="conversation")
memory_store(topic="Conversation", report="Conversation text", type="conversation")
# Should still store (no duplicate check for non-fact)
mock_vector_store["store"].assert_called_once()
def test_memory_write_invalid_context_type(self, mock_vector_store):
"""Test that invalid context_type defaults to 'fact'."""
memory_write("Some content", context_type="invalid_type")
# Should still succeed, using "fact" as default
def test_memory_store_invalid_type_defaults_to_research(self, mock_vector_store):
"""Test that invalid type defaults to 'research'."""
memory_store(topic="Invalid type test", report="Some content", type="invalid_type")
# Should still succeed, using "research" as default
mock_vector_store["store"].assert_called_once()
call_kwargs = mock_vector_store["store"].call_args.kwargs
assert call_kwargs.get("context_type") == "fact"
assert call_kwargs.get("context_type") == "research"
def test_memory_write_valid_context_types(self, mock_vector_store):
def test_memory_store_valid_types(self, mock_vector_store):
"""Test all valid context types."""
valid_types = ["fact", "conversation", "document"]
valid_types = ["fact", "conversation", "document", "research"]
for ctx_type in valid_types:
mock_vector_store["store"].reset_mock()
memory_write(f"Content for {ctx_type}", context_type=ctx_type)
memory_store(topic=f"Topic for {ctx_type}", report=f"Content for {ctx_type}", type=ctx_type)
mock_vector_store["store"].assert_called_once()
def test_memory_write_strips_content(self, mock_vector_store):
"""Test that content is stripped of leading/trailing whitespace."""
memory_write(" padded content ")
def test_memory_store_strips_report_and_adds_topic(self, mock_vector_store):
"""Test that report is stripped of leading/trailing whitespace and combined with topic."""
memory_store(topic=" My Topic ", report=" padded content ")
call_kwargs = mock_vector_store["store"].call_args.kwargs
assert call_kwargs.get("content") == "padded content"
assert call_kwargs.get("content") == "Topic: My Topic\n\nReport: padded content"
assert call_kwargs.get("metadata") == {"topic": " My Topic "}
def test_memory_write_unicode_content(self, mock_vector_store):
def test_memory_store_unicode_report(self, mock_vector_store):
"""Test writing unicode content."""
result = memory_write("Unicode content: 你好世界 🎉")
result = memory_store(topic="Unicode", report="Unicode content: 你好世界 🎉")
assert "stored" in result.lower() or "memory" in result.lower()
def test_memory_write_handles_exception(self, mock_vector_store):
def test_memory_store_handles_exception(self, mock_vector_store):
"""Test handling of store_memory exceptions."""
mock_vector_store["store"].side_effect = Exception("DB error")
result = memory_write("This will fail")
result = memory_store(topic="Failing", report="This will fail")
assert "failed" in result.lower() or "error" in result.lower()