From 1fd9bb4d7cd2411b77a7ce9d74a7615413698ae8 Mon Sep 17 00:00:00 2001 From: Ismail Pelaseyed Date: Sat, 10 Feb 2024 18:45:56 +0100 Subject: [PATCH 1/2] Feat/summarization pipeline (#26) * WIP * Add summarization pipeline * Fix formatting * Update .env.example --- .env.example | 3 +-- api/ingest.py | 29 ++++++++++++++++++++++------- requirements.txt | 3 ++- service/embedding.py | 29 ++++++++++++++++++++++------- service/router.py | 9 +++++++-- utils/__init__.py | 0 utils/summarise.py | 33 +++++++++++++++++++++++++++++++++ 7 files changed, 87 insertions(+), 19 deletions(-) create mode 100644 utils/__init__.py create mode 100644 utils/summarise.py diff --git a/.env.example b/.env.example index 35a872cb..b86ff61f 100644 --- a/.env.example +++ b/.env.example @@ -1,4 +1,3 @@ API_BASE_URL=https://rag.superagent.sh COHERE_API_KEY= -HUGGINGFACE_API_KEY= -JWT_SECRET= \ No newline at end of file +OPENAI_API_KEY= \ No newline at end of file diff --git a/api/ingest.py b/api/ingest.py index 8d9b7498..c6575abe 100644 --- a/api/ingest.py +++ b/api/ingest.py @@ -1,6 +1,7 @@ +import asyncio from typing import Dict -import requests +import aiohttp from fastapi import APIRouter from models.ingest import RequestPayload @@ -17,12 +18,26 @@ async def ingest(payload: RequestPayload) -> Dict: vector_credentials=payload.vector_database, ) documents = await embedding_service.generate_documents() - chunks = await embedding_service.generate_chunks(documents=documents) - await embedding_service.generate_embeddings(nodes=chunks) + summary_documents = await embedding_service.generate_summary_documents( + documents=documents + ) + chunks, summary_chunks = await asyncio.gather( + embedding_service.generate_chunks(documents=documents), + embedding_service.generate_chunks(documents=summary_documents), + ) + + await asyncio.gather( + embedding_service.generate_embeddings(nodes=chunks), + embedding_service.generate_embeddings( + nodes=summary_chunks, index_name=f"{payload.index_name}summary" + ), + ) if payload.webhook_url: - requests.post( - url=payload.webhook_url, - json={"index_name": payload.index_name, "status": "completed"}, - ) + async with aiohttp.ClientSession() as session: + await session.post( + url=payload.webhook_url, + json={"index_name": payload.index_name, "status": "completed"}, + ) + return {"success": True, "index_name": payload.index_name} diff --git a/requirements.txt b/requirements.txt index f29452f4..bfd74fbd 100644 --- a/requirements.txt +++ b/requirements.txt @@ -20,6 +20,7 @@ colorlog==6.8.2 cryptography==41.0.7 dataclasses-json==0.6.3 Deprecated==1.2.14 +dirtyjson==1.0.8 distro==1.9.0 dnspython==2.4.2 docx2txt==0.8 @@ -48,7 +49,7 @@ idna==3.6 importlib-metadata==6.11.0 Jinja2==3.1.3 joblib==1.3.2 -llama-index==0.9.30 +llama-index==0.9.46 loguru==0.7.2 lxml==5.1.0 MarkupSafe==2.1.3 diff --git a/service/embedding.py b/service/embedding.py index 2773e018..c6e977da 100644 --- a/service/embedding.py +++ b/service/embedding.py @@ -1,6 +1,7 @@ import asyncio +import copy from tempfile import NamedTemporaryFile -from typing import Any, List, Union +from typing import Any, List, Optional, Union import numpy as np import requests @@ -11,6 +12,7 @@ from models.file import File from service.vector_database import get_vector_service +from utils.summarise import completion class EmbeddingService: @@ -37,9 +39,9 @@ async def generate_documents(self) -> List[Document]: for file in tqdm(self.files, desc="Generating documents"): suffix = self._get_datasource_suffix(file.type.value) with NamedTemporaryFile(suffix=suffix, delete=True) as temp_file: - response = requests.get(url=file.url) - temp_file.write(response.content) - temp_file.flush() + with requests.get(url=file.url) as response: # Add context manager here + temp_file.write(response.content) + temp_file.flush() reader = SimpleDirectoryReader(input_files=[temp_file.name]) docs = reader.load_data() for doc in docs: @@ -55,8 +57,7 @@ async def generate_chunks( return nodes async def generate_embeddings( - self, - nodes: List[Union[Document, None]], + self, nodes: List[Union[Document, None]], index_name: Optional[str] = None ) -> List[tuple[str, list, dict[str, Any]]]: pbar = tqdm(total=len(nodes), desc="Generating embeddings") @@ -81,8 +82,22 @@ async def generate_embedding(node): embeddings = await asyncio.gather(*tasks) pbar.close() vector_service = get_vector_service( - index_name=self.index_name, credentials=self.vector_credentials + index_name=index_name or self.index_name, + credentials=self.vector_credentials, ) await vector_service.upsert(embeddings=[e for e in embeddings if e is not None]) return [e for e in embeddings if e is not None] + + async def generate_summary_documents( + self, documents: List[Document] + ) -> List[Document]: + pbar = tqdm(total=len(documents), desc="Summarizing documents") + summary_documents = [] + for document in documents: + doc_copy = copy.deepcopy(document) # Make a copy of the document + doc_copy.text = await completion(document=doc_copy) + summary_documents.append(doc_copy) + pbar.update() + pbar.close() + return summary_documents diff --git a/service/router.py b/service/router.py index 3c993673..58c8ef20 100644 --- a/service/router.py +++ b/service/router.py @@ -22,6 +22,7 @@ def create_route_layer() -> RouteLayer: score_threshold=0.5, ) ] + print(config("COHERE_API_KEY")) encoder = CohereEncoder(cohere_api_key=config("COHERE_API_KEY")) return RouteLayer(encoder=encoder, routes=routes) @@ -40,9 +41,13 @@ async def get_documents(vector_service: VectorService, payload: RequestPayload) async def query(payload: RequestPayload) -> List: rl = create_route_layer() decision = rl(payload.input).name - print(decision) + if decision == "summarize": - return [] + vector_service: VectorService = get_vector_service( + index_name=f"{payload.index_name}summary", + credentials=payload.vector_database, + ) + return await get_documents(vector_service, payload) vector_service: VectorService = get_vector_service( index_name=payload.index_name, credentials=payload.vector_database diff --git a/utils/__init__.py b/utils/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/utils/summarise.py b/utils/summarise.py new file mode 100644 index 00000000..ec46e6ac --- /dev/null +++ b/utils/summarise.py @@ -0,0 +1,33 @@ +from decouple import config +from llama_index import Document +from openai import AsyncOpenAI + +client = AsyncOpenAI( + api_key=config("OPENAI_API_KEY"), +) + + +def _generate_content(document: Document) -> str: + return f"""Make an in depth summary the block of text below. + +Text: +------------------------------------------ +{document.get_content()} +------------------------------------------ + +Your summary:""" + + +async def completion(document: Document): + content = _generate_content(document) + completion = await client.chat.completions.create( + messages=[ + { + "role": "user", + "content": content, + } + ], + model="gpt-3.5-turbo-16k", + ) + + return completion.choices[0].message.content From 3ded91819a9430a01c93ebdca383b5e94a897753 Mon Sep 17 00:00:00 2001 From: Simonas Jakubonis <20096648+simjak@users.noreply.github.com> Date: Sat, 10 Feb 2024 22:05:28 +0200 Subject: [PATCH 2/2] chore: Poetry + precommit (#27) * chore: Poetry + precommit * Remove uneccesary dependencies * Update github workflows * Add poetry version to github workflow * Update Makefile * Small tweaks --------- Co-authored-by: Ismail Pelaseyed --- .github/workflows/lint.yml | 12 +- .pre-commit-config.yaml | 77 + Makefile | 10 +- poetry.lock | 3231 ++++++++++++++++++++++++++++++++++++ pyproject.toml | 58 + requirements.txt | 118 -- service/embedding.py | 7 +- service/vector_database.py | 8 +- 8 files changed, 3388 insertions(+), 133 deletions(-) create mode 100644 .pre-commit-config.yaml create mode 100644 poetry.lock create mode 100644 pyproject.toml delete mode 100644 requirements.txt diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 44bab06a..269f1344 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -5,6 +5,9 @@ on: branches: [main] pull_request: +env: + POETRY_VERSION: "1.4.2" + jobs: build: runs-on: ubuntu-latest @@ -16,14 +19,17 @@ jobs: - "3.11" steps: - uses: actions/checkout@v4 + - name: Install poetry + run: | + pipx install poetry==$POETRY_VERSION - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} + cache: poetry - name: Install dependencies run: | - python -m pip install --upgrade pip - pip install -r requirements.txt + poetry install - name: Analysing the code with our lint run: | - make lint + make lint \ No newline at end of file diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 00000000..b24594f3 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,77 @@ +default_language_version: + python: python3.9 +repos: + - repo: meta + hooks: + - id: check-hooks-apply + - id: check-useless-excludes + + - repo: https://github.com/psf/black + rev: 23.9.1 + hooks: + - id: black + + - repo: https://github.com/asottile/blacken-docs + rev: 1.16.0 + hooks: + - id: blacken-docs + additional_dependencies: [black==22.10.0] + + - repo: https://github.com/alessandrojcm/commitlint-pre-commit-hook + rev: v9.11.0 + hooks: + - id: commitlint + stages: [commit-msg] + additional_dependencies: ['@commitlint/config-conventional'] + + - repo: https://github.com/codespell-project/codespell + rev: v2.2.4 + hooks: + - id: codespell + name: Run codespell to check for common misspellings in files + language: python + types: [ text ] + args: [ "--write-changes", "--ignore-words-list", "asend" ] + exclude: "poetry.lock" + + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.4.0 + hooks: + - id: check-vcs-permalinks + - id: end-of-file-fixer + - id: trailing-whitespace + args: [ --markdown-linebreak-ext=md ] + - id: debug-statements + - id: no-commit-to-branch + - id: check-merge-conflict + - id: check-toml + - id: check-yaml + args: [ '--unsafe' ] # for mkdocs.yml + - id: detect-private-key + + - repo: https://github.com/commitizen-tools/commitizen + rev: v3.13.0 + hooks: + - id: commitizen + - id: commitizen-branch + stages: + - post-commit + - push + + - repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.0.290 + hooks: + - id: ruff + types_or: [python, pyi, jupyter] + + # - repo: https://github.com/pre-commit/mirrors-mypy + # rev: v1.8.0 + # hooks: + # - id: mypy + # args: [--ignore-missing-imports] + + - repo: https://github.com/PyCQA/bandit + rev: 1.7.6 + hooks: + - id: bandit + args: ['-lll'] diff --git a/Makefile b/Makefile index 2596be0e..ffdb6dcb 100644 --- a/Makefile +++ b/Makefile @@ -1,11 +1,13 @@ format: - python -m black . - python -m ruff --select I --fix . + poetry run black . + poetry run ruff --select I --fix . + poetry run vulture . --exclude=venv PYTHON_FILES=. lint: PYTHON_FILES=. lint_diff: 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+weaviate-client = "^3.26.0" +llama-index = "^0.9.46" +pinecone-client = "^3.0.2" +qdrant-client = "^1.7.3" +ruff = "^0.2.1" +black = "^23.12.1" +flake8 = "^7.0.0" +vulture = "^2.11" +python-decouple = "^3.8" +semantic-router = "^0.0.20" +astrapy = "^0.7.4" +openai = "^1.12.0" +tqdm = "^4.66.2" +cohere = "^4.46" +cmake = "^3.28.1" +fastembed = "^0.2.1" +pypdf = "^4.0.1" +docx2txt = "^0.8" + +[tool.poetry.extras] +fastembed = ["fastembed"] + +[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" + + +[tool.vulture] +exclude = [ + "*/test_*.py", + "*/.venv/*.py", +] +ignore_decorators = ["@app.route", "@require_*"] +ignore_names = ["visit_*", "do_*"] +make_whitelist = true +min_confidence = 100 +paths = ["."] +sort_by_size = true +verbose = false + +[tool.ruff] +exclude = [ + "*/docs/*.py", + "*/test_*.py", + "*/.venv/*.py", +] \ No newline at end of file diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index bfd74fbd..00000000 --- a/requirements.txt +++ /dev/null @@ -1,118 +0,0 @@ -aiohttp==3.9.1 -aiosignal==1.3.1 -annotated-types==0.6.0 -anyio==4.2.0 -astrapy==0.7.0 -attrs==23.2.0 -Authlib==1.3.0 -backoff==2.2.1 -beautifulsoup4==4.12.2 -black==23.12.1 -cassandra-driver==3.29.0 -cassio==0.1.4 -certifi==2023.11.17 -cffi==1.16.0 -charset-normalizer==3.3.2 -click==8.1.7 -cohere==4.42 -coloredlogs==15.0.1 -colorlog==6.8.2 -cryptography==41.0.7 -dataclasses-json==0.6.3 -Deprecated==1.2.14 -dirtyjson==1.0.8 -distro==1.9.0 -dnspython==2.4.2 -docx2txt==0.8 -fastapi==0.109.0 -fastavro==1.9.3 -fastembed==0.1.3 -filelock==3.13.1 -flatbuffers==23.5.26 -frozenlist==1.4.1 -fsspec==2023.12.2 -geomet==0.2.1.post1 -greenlet==3.0.3 -grpcio==1.60.0 -grpcio-tools==1.60.0 -gunicorn==21.2.0 -h11==0.14.0 -h2==4.1.0 -hpack==4.0.0 -httpcore==1.0.2 -httptools==0.6.1 -httpx==0.25.2 -huggingface-hub==0.19.4 -humanfriendly==10.0 -hyperframe==6.0.1 -idna==3.6 -importlib-metadata==6.11.0 -Jinja2==3.1.3 -joblib==1.3.2 -llama-index==0.9.46 -loguru==0.7.2 -lxml==5.1.0 -MarkupSafe==2.1.3 -marshmallow==3.20.2 -mpmath==1.3.0 -multidict==6.0.4 -mypy-extensions==1.0.0 -nest-asyncio==1.5.8 -networkx==3.2.1 -nltk==3.8.1 -numpy==1.26.3 -onnx==1.15.0 -onnxruntime==1.17.0 -openai==1.10.0 -packaging==23.2 -pandas==2.1.4 -pathspec==0.12.1 -pillow==10.2.0 -pinecone-client==3.0.0 -platformdirs==4.1.0 -portalocker==2.8.2 -protobuf==4.25.2 -pycparser==2.21 -pydantic==2.6.0 -pydantic_core==2.16.1 -PyJWT==2.8.0 -pypdf==3.17.4 -python-dateutil==2.8.2 -python-decouple==3.8 -python-dotenv==1.0.0 -python-pptx==0.6.23 -pytz==2023.3.post1 -PyYAML==6.0.1 -qdrant-client==1.7.0 -regex==2023.12.25 -requests==2.31.0 -ruff==0.1.13 -safetensors==0.4.1 -semantic-router==0.0.20 -six==1.16.0 -sniffio==1.3.0 -soupsieve==2.5 -SQLAlchemy==2.0.25 -starlette==0.35.1 -sympy==1.12 -tenacity==8.2.3 -tiktoken==0.5.2 -tokenizers==0.15.0 -toml==0.10.2 -torch==2.1.2 -tqdm==4.66.1 -typing-inspect==0.9.0 -typing_extensions==4.9.0 -tzdata==2023.4 -urllib3==1.26.18 -uvicorn==0.25.0 -uvloop==0.19.0 -validators==0.22.0 -vulture==2.10 -watchfiles==0.21.0 -weaviate-client==3.26.0 -websockets==12.0 -wrapt==1.16.0 -XlsxWriter==3.1.9 -yarl==1.9.4 -zipp==3.17.0 diff --git a/service/embedding.py b/service/embedding.py index c6e977da..db40479b 100644 --- a/service/embedding.py +++ b/service/embedding.py @@ -5,7 +5,7 @@ import numpy as np import requests -from fastembed.embedding import FlagEmbedding as Embedding +from fastembed import TextEmbedding from llama_index import Document, SimpleDirectoryReader from llama_index.node_parser import SimpleNodeParser from tqdm import tqdm @@ -27,7 +27,6 @@ def _get_datasource_suffix(self, type: str) -> str: "PDF": ".pdf", "MARKDOWN": ".md", "DOCX": ".docx", - "PPTX": ".pptx", } try: return suffixes[type] @@ -63,8 +62,8 @@ async def generate_embeddings( async def generate_embedding(node): if node is not None: - embedding_model = Embedding( - model_name="sentence-transformers/all-MiniLM-L6-v2", max_length=512 + embedding_model = TextEmbedding( + model_name="sentence-transformers/all-MiniLM-L6-v2" ) embeddings: List[np.ndarray] = list(embedding_model.embed(node.text)) embedding = ( diff --git a/service/vector_database.py b/service/vector_database.py index 7258a6c9..5dae685f 100644 --- a/service/vector_database.py +++ b/service/vector_database.py @@ -5,7 +5,7 @@ import weaviate from astrapy.db import AstraDB from decouple import config -from fastembed.embedding import FlagEmbedding as Embedding +from fastembed import TextEmbedding from pinecone import Pinecone, ServerlessSpec from qdrant_client import QdrantClient from qdrant_client.http import models as rest @@ -36,9 +36,9 @@ async def convert_to_rerank_format(): async def delete(self, file_url: str): pass - async def _generate_vectors(sefl, input: str): - embedding_model = Embedding( - model_name="sentence-transformers/all-MiniLM-L6-v2", max_length=512 + async def _generate_vectors(self, input: str): + embedding_model = TextEmbedding( + model_name="sentence-transformers/all-MiniLM-L6-v2" ) embeddings: List[np.ndarray] = list(embedding_model.embed(input)) return embeddings[0].tolist()