From fb2d535552ba0376d95955d003f66b0f1e5f6464 Mon Sep 17 00:00:00 2001 From: Greg Hogue Date: Wed, 15 Jan 2025 12:38:38 -0500 Subject: [PATCH 01/10] remove unused conversational chain code --- src/conversational_chain/chain.py | 83 +++++++----------------------- src/conversational_chain/graph.py | 28 ++++++---- src/conversational_chain/memory.py | 26 ---------- src/retreival_chain.py | 4 -- 4 files changed, 38 insertions(+), 103 deletions(-) delete mode 100644 src/conversational_chain/memory.py diff --git a/src/conversational_chain/chain.py b/src/conversational_chain/chain.py index 4181b48..7828e42 100644 --- a/src/conversational_chain/chain.py +++ b/src/conversational_chain/chain.py @@ -4,74 +4,29 @@ from langchain.chains.retrieval import create_retrieval_chain from langchain_core.language_models.chat_models import BaseChatModel from langchain_core.retrievers import BaseRetriever +from langchain_core.runnables import Runnable from system_prompt.reactome_prompt import contextualize_q_prompt, qa_prompt -class RAGChainWithMemory: - def __init__(self, memory, retriever: BaseRetriever, llm: BaseChatModel): - """ - Initializes the Retrieval-Augmented Generation (RAG) chain with memory. - """ - self.memory = memory - self.llm = llm +def create_rag_chain(llm: BaseChatModel, retriever: BaseRetriever) -> Runnable: + # Create the history-aware retriever + history_aware_retriever: BaseRetriever = create_history_aware_retriever( + llm=llm, + retriever=retriever, + prompt=contextualize_q_prompt, + ) - # Create the history-aware retriever - self.history_aware_retriever = create_history_aware_retriever( - llm=self.llm, - retriever=retriever, - prompt=contextualize_q_prompt, - ) + # Create the documents chain + question_answer_chain: Runnable = create_stuff_documents_chain( + llm=llm.model_copy(update={"streaming": True}), + prompt=qa_prompt, + ) - # Create the documents chain - self.question_answer_chain = create_stuff_documents_chain( - llm=self.llm.model_copy(update={"streaming": True}), - prompt=qa_prompt, - ) + # Create the retrieval chain + rag_chain: Runnable = create_retrieval_chain( + retriever=history_aware_retriever, + combine_docs_chain=question_answer_chain, + ) - # Create the retrieval chain - self.rag_chain = create_retrieval_chain( - retriever=self.history_aware_retriever, - combine_docs_chain=self.question_answer_chain, - ) - - def invoke(self, user_input): - """ - Runs the chain synchronously. - """ - # Invoke the chain and get the parsed output - response = self.rag_chain.invoke( - { - "input": user_input, - "chat_history": self.memory.get_history(), - } - ) - - answer = response["answer"] - - # Update memory with user input and LLM response - self.memory.add_human_message(user_input) - self.memory.add_ai_message(answer) - - return answer - - async def ainvoke(self, user_input, callbacks=None): - """ - Runs the chain asynchronously. - """ - # Invoke the chain asynchronously - response = await self.rag_chain.ainvoke( - { - "input": user_input, - "chat_history": self.memory.get_history(), - }, - callbacks=callbacks, - ) - - answer = response["answer"] - - # Update memory with user input and LLM response - self.memory.add_human_message(user_input) - self.memory.add_ai_message(answer) - - return answer + return rag_chain diff --git a/src/conversational_chain/graph.py b/src/conversational_chain/graph.py index 45f098e..242f0d0 100644 --- a/src/conversational_chain/graph.py +++ b/src/conversational_chain/graph.py @@ -3,8 +3,11 @@ from typing import Annotated, Any, Sequence, TypedDict from langchain_core.callbacks.base import Callbacks +from langchain_core.documents import Document +from langchain_core.language_models.chat_models import BaseChatModel from langchain_core.messages import AIMessage, BaseMessage, HumanMessage -from langchain_core.runnables import RunnableConfig +from langchain_core.retrievers import BaseRetriever +from langchain_core.runnables import Runnable, RunnableConfig from langgraph.checkpoint.base import BaseCheckpointSaver from langgraph.checkpoint.memory import MemorySaver from langgraph.checkpoint.postgres.aio import AsyncPostgresSaver @@ -13,7 +16,7 @@ from psycopg import AsyncConnection from psycopg_pool import AsyncConnectionPool -from conversational_chain.chain import RAGChainWithMemory +from conversational_chain.chain import create_rag_chain from util.logging import logging LANGGRAPH_DB_URI = f"postgresql://{os.getenv('POSTGRES_USER')}:{os.getenv('POSTGRES_PASSWORD')}@postgres:5432/{os.getenv('POSTGRES_LANGGRAPH_DB')}?sslmode=disable" @@ -29,22 +32,29 @@ class ChatResponse(TypedDict): chat_history: Annotated[Sequence[BaseMessage], add_messages] - context: str - answer: str + context: list[Document] + answer: str # primary LLM response that is streamed to the user class ChatState(ChatResponse): input: str -class RAGGraphWithMemory(RAGChainWithMemory): - def __init__(self, **chain_kwargs) -> None: - super().__init__(**chain_kwargs) +class RAGGraphWithMemory: + def __init__(self, retriever: BaseRetriever, llm: BaseChatModel) -> None: + # Set up runnables + self.rag_chain: Runnable = create_rag_chain(llm, retriever) + + # Create graph state_graph: StateGraph = StateGraph(ChatState) + # Set up nodes state_graph.add_node("model", self.call_model) state_graph.set_entry_point("model") state_graph.set_finish_point("model") + self.uncompiled_graph: StateGraph = state_graph + + # The following are set asynchronously by calling initialize() self.graph: CompiledStateGraph | None = None self.pool: AsyncConnectionPool[AsyncConnection[dict[str, Any]]] | None = None @@ -90,7 +100,7 @@ async def call_model( async def ainvoke( self, user_input: str, callbacks: Callbacks, thread_id: str - ) -> str: + ) -> ChatState: if self.graph is None: self.graph = await self.initialize() response: dict[str, Any] = await self.graph.ainvoke( @@ -100,4 +110,4 @@ async def ainvoke( configurable={"thread_id": thread_id}, ), ) - return response["answer"] + return response diff --git a/src/conversational_chain/memory.py b/src/conversational_chain/memory.py deleted file mode 100644 index bbf35d6..0000000 --- a/src/conversational_chain/memory.py +++ /dev/null @@ -1,26 +0,0 @@ -from langchain.schema import AIMessage, HumanMessage - - -class ChatHistoryMemory: - """ - Manages the chat history for the conversation. - """ - - def __init__(self): - self.history = [] - - def add_human_message(self, content: str): - """Adds a human message to the chat history.""" - self.history.append(HumanMessage(content=content)) - - def add_ai_message(self, content: str): - """Adds an AI message to the chat history.""" - self.history.append(AIMessage(content=content)) - - def get_history(self): - """Returns the chat history.""" - return self.history - - def clear_history(self): - """Clears the chat history.""" - self.history = [] diff --git a/src/retreival_chain.py b/src/retreival_chain.py index 4cbb34d..8b25411 100644 --- a/src/retreival_chain.py +++ b/src/retreival_chain.py @@ -18,7 +18,6 @@ from langchain_openai import ChatOpenAI, OpenAIEmbeddings from conversational_chain.graph import RAGGraphWithMemory -from conversational_chain.memory import ChatHistoryMemory from reactome.metadata_info import descriptions_info, field_info @@ -59,8 +58,6 @@ def create_retrieval_chain( hf_model: Optional[str] = None, device: str = "cpu", ) -> RAGGraphWithMemory: - memory = ChatHistoryMemory() - callbacks: list[BaseCallbackHandler] = [] if commandline: callbacks = [StreamingStdOutCallbackHandler()] @@ -119,7 +116,6 @@ def create_retrieval_chain( reactome_retriever = MergerRetriever(retrievers=retriever_list) qa = RAGGraphWithMemory( - memory=memory, retriever=reactome_retriever, llm=llm, ) From fae8abd16f5b9c815ed57f49591f9c14e86882b8 Mon Sep 17 00:00:00 2001 From: Greg Hogue Date: Wed, 15 Jan 2025 12:57:04 -0500 Subject: [PATCH 02/10] add postprocess node to main graph; export feedbacks --- bin/chat-chainlit.py | 6 ++++-- bin/export_records.py | 30 +++++++++++++++++++++--------- src/conversational_chain/graph.py | 13 ++++++++++++- 3 files changed, 37 insertions(+), 12 deletions(-) diff --git a/bin/chat-chainlit.py b/bin/chat-chainlit.py index 90d045c..4fa42b6 100644 --- a/bin/chat-chainlit.py +++ b/bin/chat-chainlit.py @@ -8,7 +8,7 @@ from chainlit.types import ThreadDict from dotenv import load_dotenv -from conversational_chain.graph import RAGGraphWithMemory +from conversational_chain.graph import ChatState, RAGGraphWithMemory from retreival_chain import create_retrieval_chain from util.embedding_environment import EmbeddingEnvironment from util.logging import logging @@ -79,8 +79,10 @@ async def main(message: cl.Message) -> None: stream_final_answer=True, force_stream_final_answer=True, # we're not using prefix tokens ) - await llm_graph.ainvoke( + result: ChatState = await llm_graph.ainvoke( message.content, callbacks=[cb], thread_id=thread_id, ) + if len(result["additional_text"]) > 0: + await cl.Message(content=result["additional_text"]).send() diff --git a/bin/export_records.py b/bin/export_records.py index 9ea8882..17e44a6 100644 --- a/bin/export_records.py +++ b/bin/export_records.py @@ -15,16 +15,27 @@ def build_query(since_timestamp: str | None) -> str: if since_timestamp is None: since_timestamp = "" query = f""" - SELECT "threadId", "createdAt", name, type, output + SELECT + steps."threadId", + steps."createdAt", + steps.name, + steps.type, + steps.output, + feedbacks.value, + feedbacks.comment FROM steps + LEFT JOIN + feedbacks ON steps."parentId" = feedbacks."forId" WHERE - type IN ('user_message', 'assistant_message') AND - "createdAt" > '{since_timestamp}' - ORDER BY ( - SELECT MIN("createdAt") - FROM steps s - WHERE s."threadId" = steps."threadId" - ), "createdAt"; + steps.type IN ('user_message', 'assistant_message') AND + steps."createdAt" > '{since_timestamp}' + ORDER BY + ( + SELECT MIN(s."createdAt") + FROM steps s + WHERE s."threadId" = steps."threadId" + ), + steps."createdAt"; """ return query @@ -47,6 +58,7 @@ def main(records_dir: Path): with psycopg.connect(CHAINLIT_DB_URI) as conn: with conn.cursor() as cur: cur.execute(query) + header = [col.name for col in cur.description] records = cur.fetchall() if len(records) == 0: @@ -59,7 +71,7 @@ def main(records_dir: Path): with open(record_file, mode="w", newline="") as file: writer = csv.writer(file, lineterminator="\n") - writer.writerow(["threadId", "createdAt", "name", "type", "output"]) + writer.writerow(header) writer.writerows(records) print("Wrote", record_file) diff --git a/src/conversational_chain/graph.py b/src/conversational_chain/graph.py index 242f0d0..e62adf4 100644 --- a/src/conversational_chain/graph.py +++ b/src/conversational_chain/graph.py @@ -38,6 +38,7 @@ class ChatResponse(TypedDict): class ChatState(ChatResponse): input: str + additional_text: str # additional text to send after graph completes class RAGGraphWithMemory: @@ -49,8 +50,11 @@ def __init__(self, retriever: BaseRetriever, llm: BaseChatModel) -> None: state_graph: StateGraph = StateGraph(ChatState) # Set up nodes state_graph.add_node("model", self.call_model) + state_graph.add_node("postprocess", self.postprocess) + # Set up edges state_graph.set_entry_point("model") - state_graph.set_finish_point("model") + state_graph.add_edge("model", "postprocess") + state_graph.set_finish_point("postprocess") self.uncompiled_graph: StateGraph = state_graph @@ -98,6 +102,13 @@ async def call_model( "answer": response["answer"], } + async def postprocess( + self, state: ChatResponse, config: RunnableConfig + ) -> dict[str, str]: + return { + "additional_text": "", + } + async def ainvoke( self, user_input: str, callbacks: Callbacks, thread_id: str ) -> ChatState: From 4326344fb7491ee51f59240aa1bff20663784817 Mon Sep 17 00:00:00 2001 From: Greg Hogue Date: Wed, 15 Jan 2025 17:04:46 -0500 Subject: [PATCH 03/10] config.yml with customizable static messages --- .config.schema.yaml | 41 + bin/chat-chainlit.py | 24 +- config.yml | 44 + poetry.lock | 2715 ++++++++++++++++------------------ pyproject.toml | 1 + src/util/chainlit_helpers.py | 45 + src/util/config_yml.py | 127 ++ 7 files changed, 1586 insertions(+), 1411 deletions(-) create mode 100644 .config.schema.yaml create mode 100644 config.yml create mode 100644 src/util/chainlit_helpers.py create mode 100644 src/util/config_yml.py diff --git a/.config.schema.yaml b/.config.schema.yaml new file mode 100644 index 0000000..34011a8 --- /dev/null +++ b/.config.schema.yaml @@ -0,0 +1,41 @@ +$schema: "https://json-schema.org/draft/2020-12/schema" +type: object +properties: + messages: + type: object + additionalProperties: + type: object + properties: + message: + type: string + enabled: + type: boolean + recipients: + type: array + items: + type: string + oneOf: + - pattern: "@.+\\..+" + - enum: ["all", "logged_in", "guests"] + trigger: + type: object + properties: + event: + type: string + enum: ["on_chat_start", "on_chat_end", "on_chat_resume", "on_message"] + after_messages: + type: integer + start: + type: string + format: date-time + end: + type: string + format: date-time + freq_max: + type: string + pattern: "^[0-9]+[smhdw]$" + anyOf: + - required: ["event"] + - required: ["after_messages"] + required: ["message", "trigger"] +required: ["messages"] diff --git a/bin/chat-chainlit.py b/bin/chat-chainlit.py index 4fa42b6..c6ef80e 100644 --- a/bin/chat-chainlit.py +++ b/bin/chat-chainlit.py @@ -10,10 +10,13 @@ from conversational_chain.graph import ChatState, RAGGraphWithMemory from retreival_chain import create_retrieval_chain +from util.chainlit_helpers import static_messages +from util.config_yml import Config, TriggerEvent from util.embedding_environment import EmbeddingEnvironment from util.logging import logging load_dotenv() +config = Config.from_yaml() ENV = os.getenv("CHAT_ENV", "reactome") logging.info(f"Selected environment: {ENV}") @@ -58,22 +61,26 @@ async def chat_profile() -> list[cl.ChatProfile]: async def start() -> None: thread_id: str = cl.user_session.get("id") cl.user_session.set("thread_id", thread_id) - - chat_profile: str = cl.user_session.get("chat_profile") - initial_message = ( - f"Welcome to {chat_profile}, your interactive chatbot for exploring Reactome!" - " Ask me about biological pathways and processes." - ) - await cl.Message(content=initial_message).send() + await static_messages(config, TriggerEvent.on_chat_start) @cl.on_chat_resume async def resume(thread: ThreadDict) -> None: - pass # ChainLit/LangGraph Postgres integrations handle everything + await static_messages(config, TriggerEvent.on_chat_resume) + + +@cl.on_chat_end +async def end() -> None: + await static_messages(config, TriggerEvent.on_chat_end) @cl.on_message async def main(message: cl.Message) -> None: + await static_messages(config, TriggerEvent.on_message) + + message_count: int = cl.user_session.get("message_count", 0) + 1 + cl.user_session.set("message_count", message_count) + thread_id: str = cl.user_session.get("thread_id") cb = cl.AsyncLangchainCallbackHandler( stream_final_answer=True, @@ -86,3 +93,4 @@ async def main(message: cl.Message) -> None: ) if len(result["additional_text"]) > 0: await cl.Message(content=result["additional_text"]).send() + await static_messages(config, after_messages=message_count) diff --git a/config.yml b/config.yml new file mode 100644 index 0000000..5f14007 --- /dev/null +++ b/config.yml @@ -0,0 +1,44 @@ +# yaml-language-server: $schema=./.config.schema.yaml + +messages: + + welcome: + message: |- + Welcome to {chat_profile}, your interactive chatbot for exploring Reactome! + Ask me about biological pathways and processes. + trigger: + event: on_chat_start + + demo-message: + message: |- + Hello! + This is an example message from the `./config.yml` file. + Static messages can be defined here and triggered by events. + + **_Use an editor with YAML support for autocomplete and schema validation._** + enabled: false + trigger: + event: on_chat_start + + after3-example: + message: |- + This message will be triggered after the 3rd message of a chat, until the end of Jan '25. + This message only sends to non-authenticated users and users logged in with their GMail account. + enabled: false + recipients: + - guests + - "*@gmail.com" + trigger: + start: 2025-01-01T00:00:00Z + end: 2025-02-01T00:00:00Z + after_messages: 3 + + every-message-example: + message: |- + Hi, {user_id}. 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b/src/util/chainlit_helpers.py new file mode 100644 index 0000000..e1a5978 --- /dev/null +++ b/src/util/chainlit_helpers.py @@ -0,0 +1,45 @@ +from datetime import datetime +from typing import Iterable + +import chainlit as cl + +from util.config_yml import Config, TriggerEvent + + +def get_user_id() -> str | None: + user: cl.User | None = cl.user_session.get("user") + return user.identifier if user else None + + +async def send_messages(messages: Iterable[str]): + for message in messages: + await cl.Message(content=message).send() + + +async def static_messages( + config: Config, + event: TriggerEvent | None = None, + after_messages: int | None = None, +) -> None: + user_id: str | None = get_user_id() + last_static_messages: dict[str, datetime] = cl.user_session.get( + "last_static_messages", {} + ) + messages: dict[str, str] = config.get_messages( + user_id, event, after_messages, last_static_messages + ) + now: datetime = datetime.now() + for message_id in messages: + last_static_messages[message_id] = now + cl.user_session.set("last_static_messages", last_static_messages) + + chat_profile: str = cl.user_session.get("chat_profile") + + messages_formatted: Iterable[str] = map( + lambda msg: msg.format( + chat_profile=chat_profile, + user_id=user_id, + ), + messages.values(), + ) + await send_messages(messages_formatted) diff --git a/src/util/config_yml.py b/src/util/config_yml.py new file mode 100644 index 0000000..17a5a8e --- /dev/null +++ b/src/util/config_yml.py @@ -0,0 +1,127 @@ +import re +from datetime import datetime, timedelta +from enum import StrEnum, auto +from fnmatch import fnmatch +from pathlib import Path +from typing import Self + +import yaml +from pydantic import BaseModel, ValidationError + +from util.logging import logging + +CONFIG_YML = Path("config.yml") + +interval_units = { + "s": "seconds", + "m": "minutes", + "h": "hours", + "d": "days", + "w": "weeks", +} + + +def parse_interval(interval_str: str) -> timedelta: + re_match = re.fullmatch(r"([0-9]+)([smhdw])", interval_str) + value = int(re_match.group(1)) + unit = interval_units[re_match.group(2)] + return timedelta(**{unit: value}) + + +class TriggerEvent(StrEnum): + on_chat_start = auto() + on_chat_end = auto() + on_chat_resume = auto() + on_message = auto() + + +class Trigger(BaseModel): + event: TriggerEvent | None = None + after_messages: int | None = None + start: datetime | None = None + end: datetime | None = None + freq_max: str | None = None + + def match_trigger( + self, + event: TriggerEvent | None = None, + after_messages: int | None = None, + last_message: datetime | None = None, + ): + now = datetime.now() + if self.event and self.event != event: + return False + if self.after_messages and self.after_messages != after_messages: + return False + if self.start and self.start.replace(tzinfo=None) > now: + return False + if self.end and self.end.replace(tzinfo=None) < now: + return False + if ( + self.freq_max + and last_message + and parse_interval(self.freq_max) > now - last_message + ): + return False + return True + + +class Message(BaseModel): + message: str + enabled: bool = True + recipients: list[str] | None = None + trigger: Trigger + + def match_recipient(self, user_id: str | None) -> bool: + if not self.recipients: + return True + for entry in self.recipients: + logging.warning(entry) + if entry == "all": + return True + if user_id is None: + if entry == "guests": + return True + else: + if entry == "logged_in": + return True + elif entry[0] == "/" and entry[-1] == "/": + if re.search(entry[1:-1], user_id): + return True + else: + if fnmatch(user_id, entry): + return True + return False + + +class Config(BaseModel): + messages: dict[str, Message] + + def get_messages( + self, + user_id: str | None = None, + event: TriggerEvent | None = None, + after_messages: int | None = None, + last_messages: dict[str, datetime] | None = None, + ) -> dict[str, str]: + return { + message_id: message.message + for message_id, message in self.messages.items() + if ( + message.enabled + and message.match_recipient(user_id) + and message.trigger.match_trigger( + event, after_messages, last_messages.get(message_id, None) + ) + ) + } + + @classmethod + def from_yaml(cls, config_yml: Path = CONFIG_YML) -> Self | None: + with open(config_yml) as f: + yaml_data: dict = yaml.safe_load(f) + try: + return cls(**yaml_data) + except ValidationError as e: + logging.warning(e) + return None From e49c6ac0a145c7a88fafb7a66c2120c79b67c5fb Mon Sep 17 00:00:00 2001 From: Greg Hogue Date: Thu, 16 Jan 2025 13:12:09 -0500 Subject: [PATCH 04/10] upgrade to chainlit 2.0 (fixes pydantic version issue) --- .chainlit/config.toml | 60 ++++++-------------------------------- poetry.lock | 40 ++++++++++++------------- public/theme.json | 68 +++++++++++++++++++++++++++++++++++++++++++ pyproject.toml | 4 +-- 4 files changed, 97 insertions(+), 75 deletions(-) create mode 100644 public/theme.json diff --git a/.chainlit/config.toml b/.chainlit/config.toml index 2aee2e2..e2c7032 100644 --- a/.chainlit/config.toml +++ b/.chainlit/config.toml @@ -9,15 +9,15 @@ user_env = [] # Duration (in seconds) during which the session is saved when the connection is lost session_timeout = 3600 +# Duration (in seconds) of the user session expiry +user_session_timeout = 1296000 # 15 days + # Enable third parties caching (e.g LangChain cache) cache = false # Authorized origins allow_origins = ["*"] -# Follow symlink for asset mount (see https://github.com/Chainlit/chainlit/issues/317) -# follow_symlink = false - [features] # Process and display HTML in messages. This can be a security risk (see https://stackoverflow.com/questions/19603097/why-is-it-dangerous-to-render-user-generated-html-or-javascript) unsafe_allow_html = true @@ -39,29 +39,20 @@ edit_message = true max_size_mb = 500 [features.audio] - # Threshold for audio recording - min_decibels = -45 - # Delay for the user to start speaking in MS - initial_silence_timeout = 3000 - # Delay for the user to continue speaking in MS. If the user stops speaking for this duration, the recording will stop. - silence_timeout = 1500 - # Above this duration (MS), the recording will forcefully stop. - max_duration = 15000 - # Duration of the audio chunks in MS - chunk_duration = 1000 # Sample rate of the audio - sample_rate = 44100 + sample_rate = 24000 [UI] # Name of the assistant. name = "React-to-me" +# default_theme = "dark" + +# layout = "wide" + # Description of the assistant. This is used for HTML tags. # description = "" -# Large size content are by default collapsed for a cleaner ui -default_collapse_content = true - # Chain of Thought (CoT) display mode. Can be "hidden", "tool_call" or "full". cot = "hidden" @@ -76,9 +67,6 @@ github = "https://github.com/reactome/reactome_chatbot/issues" # The Javascript file can be served from the public directory. # custom_js = "/public/test.js" -# Specify a custom font url. -# custom_font = "https://fonts.googleapis.com/css2?family=Inter:wght@400;500;700&display=swap" - # Specify a custom meta image url. # custom_meta_image_url = "https://chainlit-cloud.s3.eu-west-3.amazonaws.com/logo/chainlit_banner.png" @@ -87,35 +75,5 @@ github = "https://github.com/reactome/reactome_chatbot/issues" # Be careful: If this is a relative path, it should not start with a slash. # custom_build = "./public/build" -[UI.theme] - default = "dark" - #layout = "wide" - #font_family = "Inter, sans-serif" -# Override default MUI light theme. (Check theme.ts) -[UI.theme.light] - #background = "#FAFAFA" - #paper = "#FFFFFF" - - [UI.theme.light.primary] - main = "#2F9EC2" - dark = "#0F5462" - light = "#E1F4FC" - [UI.theme.light.text] - #primary = "#212121" - #secondary = "#616161" - -# Override default MUI dark theme. (Check theme.ts) -[UI.theme.dark] - #background = "#FAFAFA" - #paper = "#FFFFFF" - - [UI.theme.dark.primary] - main = "#2F9EC2" - dark = "#0F5462" - light = "#E1F4FC" - [UI.theme.dark.text] - #primary = "#EEEEEE" - #secondary = "#BDBDBD" - [meta] -generated_by = "1.3.1" +generated_by = "2.0.3" diff --git a/poetry.lock b/poetry.lock index 15ea1fd..3e9f4ea 100644 --- a/poetry.lock +++ b/poetry.lock @@ -464,13 +464,13 @@ files = [ [[package]] name = "chainlit" -version = "1.3.2" +version = "2.0.3" description = "Build Conversational AI." optional = false python-versions = "<4.0.0,>=3.9" files = [ - {file = "chainlit-1.3.2-py3-none-any.whl", hash = "sha256:c0926e8b157a67aede511a8220307889d04e9458ff3f94176e004fe533662d74"}, - {file = "chainlit-1.3.2.tar.gz", hash = "sha256:5562246ca42c858a42e86efdd5a46c27fd93481706f6fe47416109c47ac41b77"}, + {file = "chainlit-2.0.3-py3-none-any.whl", hash = "sha256:d177b5e2e9cf55cb93a864e932cd30e6277aabdb11eb957a5f8f7111bc5275e8"}, + {file = "chainlit-2.0.3.tar.gz", hash = "sha256:a312879420f470eeeffff27823c70a20cace1d32ff5bb4f103b537870fa8b0a0"}, ] [package.dependencies] @@ -482,14 +482,13 @@ fastapi = ">=0.115.3,<0.116" filetype = ">=1.2.0,<2.0.0" httpx = ">=0.23.0" lazify = ">=0.4.0,<0.5.0" -literalai = "0.0.623" +literalai = "0.1.103" nest-asyncio = ">=1.6.0,<2.0.0" -numpy = ">=1.26,<2.0" packaging = ">=23.1,<24.0" pydantic = ">=1,<3" pyjwt = ">=2.8.0,<3.0.0" python-dotenv = ">=1.0.0,<2.0.0" -python-multipart = ">=0.0.9,<0.0.10" +python-multipart = ">=0.0.18,<0.0.19" python-socketio = ">=5.11.0,<6.0.0" starlette = ">=0.41.2,<0.42.0" syncer = ">=2.0.3,<3.0.0" @@ -1772,18 +1771,18 @@ langchain-core = ">=0.3.29,<0.4.0" [[package]] name = "langgraph" -version = "0.2.62" +version = "0.2.63" description = "Building stateful, multi-actor applications with LLMs" optional = false python-versions = "<4.0,>=3.9.0" files = [ - {file = "langgraph-0.2.62-py3-none-any.whl", hash = "sha256:51ae9e02a52485a837642eebe7ae43269af7d7305d62f8f69ac11589b2fbba26"}, - {file = "langgraph-0.2.62.tar.gz", hash = "sha256:0aac9fd55ffe669bc1312203e0f9ea2733c65cc276f196e7ff0d443cf4efbb89"}, + {file = "langgraph-0.2.63-py3-none-any.whl", hash = "sha256:7867108e045c0ee52cb705749edd478b08588dce74fbd4466b4197a04c4e718b"}, + {file = "langgraph-0.2.63.tar.gz", hash = "sha256:4bcdd6023b02d16c840b5ee612bfbafd1b9e0beef91622aa1827593374ee6e8e"}, ] [package.dependencies] langchain-core = ">=0.2.43,<0.3.0 || >0.3.0,<0.3.1 || >0.3.1,<0.3.2 || >0.3.2,<0.3.3 || >0.3.3,<0.3.4 || >0.3.4,<0.3.5 || >0.3.5,<0.3.6 || >0.3.6,<0.3.7 || >0.3.7,<0.3.8 || >0.3.8,<0.3.9 || >0.3.9,<0.3.10 || >0.3.10,<0.3.11 || >0.3.11,<0.3.12 || >0.3.12,<0.3.13 || >0.3.13,<0.3.14 || >0.3.14,<0.3.15 || >0.3.15,<0.3.16 || >0.3.16,<0.3.17 || >0.3.17,<0.3.18 || >0.3.18,<0.3.19 || >0.3.19,<0.3.20 || >0.3.20,<0.3.21 || >0.3.21,<0.3.22 || >0.3.22,<0.4.0" -langgraph-checkpoint = ">=2.0.4,<3.0.0" +langgraph-checkpoint = ">=2.0.10,<3.0.0" langgraph-sdk = ">=0.1.42,<0.2.0" [[package]] @@ -1803,13 +1802,13 @@ msgpack = ">=1.1.0,<2.0.0" [[package]] name = "langgraph-checkpoint-postgres" -version = "2.0.12" +version = "2.0.13" description = "Library with a Postgres implementation of LangGraph checkpoint saver." optional = false python-versions = "<4.0.0,>=3.9.0" files = [ - {file = "langgraph_checkpoint_postgres-2.0.12-py3-none-any.whl", hash = "sha256:2f85db16b15daa2d07c1bb9b345830d56bdc1a5e0f47c1a92f6dfd76d1e21721"}, - {file = "langgraph_checkpoint_postgres-2.0.12.tar.gz", hash = "sha256:6bd718a4cdd29e47516b993c137f71ac416a302234f1dee5a88869413e5e5a98"}, + {file = "langgraph_checkpoint_postgres-2.0.13-py3-none-any.whl", hash = "sha256:98fe99c07404541d87f50c277a0120f9c4d964b665e5f42aecd911e0f365ae59"}, + {file = "langgraph_checkpoint_postgres-2.0.13.tar.gz", hash = "sha256:cadab495a0b3d13534178ab3bd711f12dbfeccb9e5d0fb24905ea809a700b137"}, ] [package.dependencies] @@ -1888,12 +1887,12 @@ files = [ [[package]] name = "literalai" -version = "0.0.623" +version = "0.1.103" description = "An SDK for observability in Python applications" optional = false python-versions = "*" files = [ - {file = "literalai-0.0.623.tar.gz", hash = "sha256:d65c04dde6b1e99d585e4112a607e5fd574d282b70f600c55a671018340dfb0f"}, + {file = "literalai-0.1.103.tar.gz", hash = "sha256:060e86e63c0f53041a737b2183354ac092ee8cd9faec817dc95df639bb263a7d"}, ] [package.dependencies] @@ -3836,18 +3835,15 @@ docs = ["sphinx"] [[package]] name = "python-multipart" -version = "0.0.9" +version = "0.0.18" description = "A streaming multipart parser for Python" optional = false python-versions = ">=3.8" files = [ - {file = "python_multipart-0.0.9-py3-none-any.whl", hash = "sha256:97ca7b8ea7b05f977dc3849c3ba99d51689822fab725c3703af7c866a0c2b215"}, - {file = "python_multipart-0.0.9.tar.gz", hash = "sha256:03f54688c663f1b7977105f021043b0793151e4cb1c1a9d4a11fc13d622c4026"}, + {file = "python_multipart-0.0.18-py3-none-any.whl", hash = "sha256:efe91480f485f6a361427a541db4796f9e1591afc0fb8e7a4ba06bfbc6708996"}, + {file = "python_multipart-0.0.18.tar.gz", hash = "sha256:7a68db60c8bfb82e460637fa4750727b45af1d5e2ed215593f917f64694d34fe"}, ] -[package.extras] -dev = ["atomicwrites (==1.4.1)", "attrs (==23.2.0)", "coverage (==7.4.1)", "hatch", "invoke (==2.2.0)", "more-itertools (==10.2.0)", "pbr (==6.0.0)", "pluggy (==1.4.0)", "py (==1.11.0)", "pytest (==8.0.0)", "pytest-cov (==4.1.0)", "pytest-timeout (==2.2.0)", "pyyaml (==6.0.1)", "ruff (==0.2.1)"] - [[package]] name = "python-socketio" version = "5.12.1" @@ -5518,4 +5514,4 @@ type = ["pytest-mypy"] [metadata] lock-version = "2.0" python-versions = ">=3.12, <4" -content-hash = "a573340ef72feed9379108779bf00c8ced62e584d401970578cc49e64355d2a8" +content-hash = "bdf103c372372d702d379d189fde56a6c38b1fa373f5237312177023fa4929a0" diff --git a/public/theme.json b/public/theme.json new file mode 100644 index 0000000..1859863 --- /dev/null +++ b/public/theme.json @@ -0,0 +1,68 @@ +{ + "custom_fonts": [], + "variables": { + "light": { + "--font-sans": "'Inter', sans-serif", + "--font-mono": "source-code-pro, Menlo, Monaco, Consolas, 'Courier New', monospace", + "--background": "0 0% 100%", + "--foreground": "0 0% 5%", + "--card": "0 0% 100%", + "--card-foreground": "0 0% 5%", + "--popover": "0 0% 100%", + "--popover-foreground": "0 0% 5%", + "--primary": "195 61% 47.3%", + "--primary-foreground": "0 0% 100%", + "--secondary": "210 40% 96.1%", + "--secondary-foreground": "222.2 47.4% 11.2%", + "--muted": "0 0% 90%", + "--muted-foreground": "0 0% 36%", + "--accent": "0 0% 95%", + "--accent-foreground": "222.2 47.4% 11.2%", + "--destructive": "0 84.2% 60.2%", + "--destructive-foreground": "210 40% 98%", + "--border": "0 0% 90%", + "--input": "0 0% 90%", + "--ring": "195 61% 47.3%", + "--radius": "0.75rem", + "--sidebar-background": "0 0% 98%", + "--sidebar-foreground": "240 5.3% 26.1%", + "--sidebar-primary": "240 5.9% 10%", + "--sidebar-primary-foreground": "0 0% 98%", + "--sidebar-accent": "240 4.8% 95.9%", + "--sidebar-accent-foreground": "240 5.9% 10%", + "--sidebar-border": "220 13% 91%", + "--sidebar-ring": "217.2 91.2% 59.8%" + }, + "dark": { + "--font-sans": "'Inter', sans-serif", + "--font-mono": "source-code-pro, Menlo, Monaco, Consolas, 'Courier New', monospace", + "--background": "0 0% 13%", + "--foreground": "0 0% 93%", + "--card": "0 0% 18%", + "--card-foreground": "210 40% 98%", + "--popover": "0 0% 18%", + "--popover-foreground": "210 40% 98%", + "--primary": "195 61% 47.3%", + "--primary-foreground": "0 0% 100%", + "--secondary": "0 0% 19%", + "--secondary-foreground": "210 40% 98%", + "--muted": "0 1% 26%", + "--muted-foreground": "0 0% 71%", + "--accent": "0 0% 26%", + "--accent-foreground": "210 40% 98%", + "--destructive": "0 62.8% 30.6%", + "--destructive-foreground": "210 40% 98%", + "--border": "0 1% 26%", + "--input": "0 1% 26%", + "--ring": "195 61% 47.3%", + "--sidebar-background": "0 0% 9%", + "--sidebar-foreground": "240 4.8% 95.9%", + "--sidebar-primary": "224.3 76.3% 48%", + "--sidebar-primary-foreground": "0 0% 100%", + "--sidebar-accent": "0 0% 13%", + "--sidebar-accent-foreground": "240 4.8% 95.9%", + "--sidebar-border": "240 3.7% 15.9%", + "--sidebar-ring": "217.2 91.2% 59.8%" + } + } +} diff --git a/pyproject.toml b/pyproject.toml index cd89d34..88ff29b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -23,7 +23,7 @@ langchain-openai = "^0.2.3" neo4j = "4.3.6" python-dotenv = "^1.0.1" pyfiglet = "^1.0.2" -chainlit = "^1.3.1" +chainlit = "^2.0.3" asyncpg = "^0.30.0" sqlalchemy = "^2.0.30" langchain-community = "^0.3.3" @@ -42,7 +42,7 @@ langgraph = "^0.2.39" langgraph-checkpoint-postgres = "^2.0.2" rank-bm25 = "^0.2.2" psycopg = {extras = ["binary"], version = "^3.2.3"} -pydantic = "!=2.10.2" +pydantic = "^2.10.5" pyyaml = "^6.0.2" [tool.poetry.group.dev.dependencies] From 87ee1c7cd827e7ed958e556b59af665ca48a7f66 Mon Sep 17 00:00:00 2001 From: Greg Hogue Date: Thu, 16 Jan 2025 13:13:37 -0500 Subject: [PATCH 05/10] handle missing config.yml --- bin/chat-chainlit.py | 2 +- config.yml => config_template.yml | 0 src/util/chainlit_helpers.py | 4 +++- src/util/config_yml.py | 3 +++ 4 files changed, 7 insertions(+), 2 deletions(-) rename config.yml => config_template.yml (100%) diff --git a/bin/chat-chainlit.py b/bin/chat-chainlit.py index c6ef80e..a1a2734 100644 --- a/bin/chat-chainlit.py +++ b/bin/chat-chainlit.py @@ -16,7 +16,7 @@ from util.logging import logging load_dotenv() -config = Config.from_yaml() +config: Config | None = Config.from_yaml() ENV = os.getenv("CHAT_ENV", "reactome") logging.info(f"Selected environment: {ENV}") diff --git a/config.yml b/config_template.yml similarity index 100% rename from config.yml rename to config_template.yml diff --git a/src/util/chainlit_helpers.py b/src/util/chainlit_helpers.py index e1a5978..4afc8ef 100644 --- a/src/util/chainlit_helpers.py +++ b/src/util/chainlit_helpers.py @@ -17,10 +17,12 @@ async def send_messages(messages: Iterable[str]): async def static_messages( - config: Config, + config: Config | None, event: TriggerEvent | None = None, after_messages: int | None = None, ) -> None: + if not config: + return user_id: str | None = get_user_id() last_static_messages: dict[str, datetime] = cl.user_session.get( "last_static_messages", {} diff --git a/src/util/config_yml.py b/src/util/config_yml.py index 17a5a8e..1a3b18f 100644 --- a/src/util/config_yml.py +++ b/src/util/config_yml.py @@ -118,6 +118,9 @@ def get_messages( @classmethod def from_yaml(cls, config_yml: Path = CONFIG_YML) -> Self | None: + if not config_yml.exists(): + logging.warning(f"Config file not found: {config_yml}") + return None with open(config_yml) as f: yaml_data: dict = yaml.safe_load(f) try: From 5b7245fcc303e8e4524d444c37d688bba1ef0557 Mon Sep 17 00:00:00 2001 From: Greg Hogue Date: Thu, 16 Jan 2025 13:20:54 -0500 Subject: [PATCH 06/10] use a default config to avoid missing our starting message --- .gitignore | 1 + config_template.yml => config_default.yml | 0 src/util/config_yml.py | 7 +++++-- 3 files changed, 6 insertions(+), 2 deletions(-) rename config_template.yml => config_default.yml (100%) diff --git a/.gitignore b/.gitignore index 8b8e329..cea5f55 100644 --- a/.gitignore +++ b/.gitignore @@ -164,3 +164,4 @@ cython_debug/ csv_files/ embeddings/ records/ +config.yml diff --git a/config_template.yml b/config_default.yml similarity index 100% rename from config_template.yml rename to config_default.yml diff --git a/src/util/config_yml.py b/src/util/config_yml.py index 1a3b18f..cafbad6 100644 --- a/src/util/config_yml.py +++ b/src/util/config_yml.py @@ -11,6 +11,7 @@ from util.logging import logging CONFIG_YML = Path("config.yml") +CONFIG_DEFAULT_YML = Path("config_default.yml") interval_units = { "s": "seconds", @@ -119,8 +120,10 @@ def get_messages( @classmethod def from_yaml(cls, config_yml: Path = CONFIG_YML) -> Self | None: if not config_yml.exists(): - logging.warning(f"Config file not found: {config_yml}") - return None + logging.warning( + f"Config file not found: {config_yml} ; falling back to {CONFIG_DEFAULT_YML}" + ) + config_yml = CONFIG_DEFAULT_YML with open(config_yml) as f: yaml_data: dict = yaml.safe_load(f) try: From 7128922149b4f9c620b1a1c3032b3d58273cdc8c Mon Sep 17 00:00:00 2001 From: Greg Hogue Date: Thu, 16 Jan 2025 13:26:08 -0500 Subject: [PATCH 07/10] HTTPS middleware redirect; improved client host check ; 400 HTML response with "Try Again" button --- bin/chat-fastapi.py | 52 ++++++++++++++++++++++++++++++++++++--------- 1 file changed, 42 insertions(+), 10 deletions(-) diff --git a/bin/chat-fastapi.py b/bin/chat-fastapi.py index 9ff4f89..a70f4c9 100644 --- a/bin/chat-fastapi.py +++ b/bin/chat-fastapi.py @@ -1,11 +1,12 @@ import hashlib import hmac import os +from string import Template import requests from chainlit.utils import mount_chainlit from dotenv import load_dotenv -from fastapi import FastAPI, HTTPException, Request, Response +from fastapi import FastAPI, Request, Response from fastapi.responses import RedirectResponse load_dotenv() @@ -17,6 +18,20 @@ CLOUDFLARE_SECRET_KEY = os.getenv("CLOUDFLARE_SECRET_KEY") CLOUDFLARE_SITE_KEY = os.getenv("CLOUDFLARE_SITE_KEY") +ERROR_PAGE_TEMPLATE = Template( + f""" + + +

$error_title

+

If you believe this to be in error, please contact the maintainers to report an issue.

+
+ +
+ + +""" +) + def make_signature(value: str) -> str: if CLOUDFLARE_SECRET_KEY is None: @@ -56,6 +71,10 @@ async def verify_captcha_middleware(request: Request, call_next): response = await call_next(request) return response + if request.url.scheme == "http": + url = request.url.replace(scheme="https") + return RedirectResponse(url=str(url)) + # Check if the user has completed the CAPTCHA verification captcha_verified = request.cookies.get("captcha_verified") @@ -69,18 +88,14 @@ async def verify_captcha_middleware(request: Request, call_next): # Serve the CAPTCHA verification page (basic HTML form) @app.get(f"{CHAINLIT_URI}/verify_captcha_page") -async def captcha_page(request: Request): - - host = request.headers.get('X-Forwarded-Host', request.headers.get('Host')) - form_action = f"https://{host}{CHAINLIT_URI}/verify_captcha" - +async def captcha_page(): html_content = f""" -
+