diff --git a/.flake8 b/.flake8 new file mode 100644 index 0000000..ab0493d --- /dev/null +++ b/.flake8 @@ -0,0 +1,10 @@ +[flake8] +exclude = + venv + .venv + __pycache__ + notebooks + data +# Recommend matching the black line length (default 88), +# rather than using the flake8 default of 79: +max-line-length = 88 diff --git a/.github/workflows/update.yml b/.github/workflows/update.yml new file mode 100644 index 0000000..afa982f --- /dev/null +++ b/.github/workflows/update.yml @@ -0,0 +1,17 @@ +name: Push Event Workflow + +on: push + +jobs: + unit-testing: + runs-on: ubuntu-latest + + steps: + - name: Checkout code + uses: actions/checkout@v2 + + - name: Install Package + run: pip install flake8 + + - name: Run tests + run: flake8 insight_engine/embeddings.py diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..3d89c9b --- /dev/null +++ b/.gitignore @@ -0,0 +1,155 @@ +# Local data +data/local_data/ + +# Secrets +.streamlit/secrets.toml + +# VSCode +.vscode/ + +# TODO +TODO.md + +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ +cover/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +.pybuilder/ +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pdm +# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. +#pdm.lock +# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it +# in version control. +# https://pdm.fming.dev/#use-with-ide +.pdm.toml + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# pytype static type analyzer +.pytype/ + +# Cython debug symbols +cython_debug/ + +# PyCharm +# JetBrains specific template is maintained in a separate JetBrains.gitignore that can +# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore +# and can be added to the global gitignore or merged into this file. For a more nuclear +# option (not recommended) you can uncomment the following to ignore the entire idea folder. +#.idea/ + + diff --git a/.streamlit/config.toml b/.streamlit/config.toml new file mode 100644 index 0000000..acecf38 --- /dev/null +++ b/.streamlit/config.toml @@ -0,0 +1,2 @@ +[server] +maxUploadSize = 15 \ No newline at end of file diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..9ef3819 --- /dev/null +++ b/LICENSE @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2023 Glory Olusola + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/README.md b/README.md new file mode 100644 index 0000000..1587a0b --- /dev/null +++ b/README.md @@ -0,0 +1,40 @@ +
{wrap_text_in_html(doc)}
", unsafe_allow_html=True) + +button = st.button("Submit") +if button or st.session_state.get("submit"): + if not st.session_state.get("api_key_configured"): + st.error("Please configure your OpenAI API key!") + elif not index: + st.error("Please upload a document!") + elif not query: + st.error("Please enter a question!") + else: + st.session_state["submit"] = True + # Output Columns + answer_col, sources_col = st.columns(2) + sources = search_docs(index, query) + + try: + answer = get_answer(sources, query) + if not show_all_chunks: + # Get the sources for the answer + sources = get_sources(answer, sources) + + with answer_col: + st.markdown("#### Answer") + st.markdown(answer["output_text"].split("SOURCES: ")[0]) + + with sources_col: + st.markdown("#### Sources") + for source in sources: + st.markdown(source.page_content) + st.markdown(source.metadata["source"]) + st.markdown("---") + + except OpenAIError as e: + st.error(e._message) diff --git a/engine/prompts.py b/engine/prompts.py new file mode 100644 index 0000000..3456d17 --- /dev/null +++ b/engine/prompts.py @@ -0,0 +1,31 @@ +# flake8: noqa +from langchain.prompts import PromptTemplate + +## Use a shorter template to reduce the number of tokens in the prompt +template = """Create a final answer to the given questions using the provided document excerpts(in no particular order) as references. ALWAYS include a "SOURCES" section in your answer including only the minimal set of sources needed to answer the question. If you are unable to answer the question, simply state that you do not know. Do not attempt to fabricate an answer and leave the SOURCES section empty. + +--------- + +QUESTION: What is the purpose of ARPA-H? +========= +Content: More support for patients and families. \n\nTo get there, I call on Congress to fund ARPA-H, the Advanced Research Projects Agency for Health. \n\nItโs based on DARPAโthe Defense Department project that led to the Internet, GPS, and so much more. \n\nARPA-H will have a singular purposeโto drive breakthroughs in cancer, Alzheimerโs, diabetes, and more. +Source: 1-32 +Content: While weโre at it, letโs make sure every American can get the health care they need. \n\nWeโve already made historic investments in health care. \n\nWeโve made it easier for Americans to get the care they need, when they need it. \n\nWeโve made it easier for Americans to get the treatments they need, when they need them. \n\nWeโve made it easier for Americans to get the medications they need, when they need them. +Source: 1-33 +Content: The V.A. is pioneering new ways of linking toxic exposures to disease, already helping veterans get the care they deserve. \n\nWe need to extend that same care to all Americans. \n\nThatโs why Iโm calling on Congress to pass legislation that would establish a national registry of toxic exposures, and provide health care and financial assistance to those affected. +Source: 1-30 +========= +FINAL ANSWER: The purpose of ARPA-H is to drive breakthroughs in cancer, Alzheimerโs, diabetes, and more. +SOURCES: 1-32 + +--------- + +QUESTION: {question} +========= +{summaries} +========= +FINAL ANSWER:""" + +STUFF_PROMPT = PromptTemplate( + template=template, input_variables=["summaries", "question"] +) diff --git a/engine/utils.py b/engine/utils.py new file mode 100644 index 0000000..0824e3e --- /dev/null +++ b/engine/utils.py @@ -0,0 +1,160 @@ +import re +from io import BytesIO +from typing import Any, Dict, List + +import docx2txt +import streamlit as st +from langchain.chains.qa_with_sources import load_qa_with_sources_chain +from langchain.docstore.document import Document +from langchain.llms import OpenAI +from langchain.text_splitter import RecursiveCharacterTextSplitter +from langchain.vectorstores import VectorStore +from langchain.vectorstores.faiss import FAISS +from openai.error import AuthenticationError +from pypdf import PdfReader + +from engine.embeddings import OpenAIEmbeddings +from engine.prompts import STUFF_PROMPT + + +@st.cache_data +def parse_docx(file: BytesIO) -> str: + text = docx2txt.process(file) + # Remove multiple newlines + text = re.sub(r"\n\s*\n", "\n\n", text) + return text + + +@st.cache_data +def parse_pdf(file: BytesIO) -> List[str]: + pdf = PdfReader(file) + output = [] + for page in pdf.pages: + text = page.extract_text() + # Merge hyphenated words + text = re.sub(r"(\w+)-\n(\w+)", r"\1\2", text) + # Fix newlines in the middle of sentences + text = re.sub(r"(? str: + text = file.read().decode("utf-8") + # Remove multiple newlines + text = re.sub(r"\n\s*\n", "\n\n", text) + return text + + +@st.cache_data +def text_to_docs(text: str | List[str]) -> List[Document]: + """Converts a string or list of strings to a list of Documents + with metadata.""" + if isinstance(text, str): + # Take a single string as one page + text = [text] + page_docs = [Document(page_content=page) for page in text] + + # Add page numbers as metadata + for i, doc in enumerate(page_docs): + doc.metadata["page"] = i + 1 + + # Split pages into chunks + doc_chunks = [] + + for doc in page_docs: + text_splitter = RecursiveCharacterTextSplitter( + chunk_size=800, + separators=["\n\n", "\n", ".", "!", "?", ",", " ", ""], + chunk_overlap=0, + ) + chunks = text_splitter.split_text(doc.page_content) + for i, chunk in enumerate(chunks): + doc = Document( + page_content=chunk, metadata={"page": doc.metadata["page"], "chunk": i} + ) + # Add sources a metadata + doc.metadata["source"] = f"{doc.metadata['page']}-{doc.metadata['chunk']}" + doc_chunks.append(doc) + return doc_chunks + + +@st.cache_data +def embed_docs(docs: List[Document]) -> VectorStore: + """Embeds a list of Documents and returns a FAISS index""" + + if not st.session_state.get("OPENAI_API_KEY"): + raise AuthenticationError( + "Enter your OpenAI API key in the sidebar. You can get a key at" + " https://platform.openai.com/account/api-keys." + ) + else: + # Embed the chunks + embeddings = OpenAIEmbeddings( + openai_api_key=st.session_state.get("OPENAI_API_KEY") + ) # type: ignore + index = FAISS.from_documents(docs, embeddings) + + return index + + +@st.cache_data +def search_docs(index: VectorStore, query: str) -> List[Document]: + """Searches a FAISS index for similar chunks to the query + and returns a list of Documents.""" + + # Search for similar chunks + docs = index.similarity_search(query, k=5) + return docs + + +@st.cache_data +def get_answer(docs: List[Document], query: str) -> Dict[str, Any]: + """Gets an answer to a question from a list of Documents.""" + + # Get the answer + + chain = load_qa_with_sources_chain( + OpenAI( + temperature=0, openai_api_key=st.session_state.get("OPENAI_API_KEY") + ), # type: ignore + chain_type="stuff", + prompt=STUFF_PROMPT, + ) + + # Cohere doesn't work very well as of now. + # chain = load_qa_with_sources_chain( + # Cohere(temperature=0), chain_type="stuff", prompt=STUFF_PROMPT # type: ignore + # ) + answer = chain( + {"input_documents": docs, "question": query}, return_only_outputs=True + ) + return answer + + +@st.cache_data +def get_sources(answer: Dict[str, Any], docs: List[Document]) -> List[Document]: + """Gets the source documents for an answer.""" + + # Get sources for the answer + source_keys = [s for s in answer["output_text"].split("SOURCES: ")[-1].split(", ")] + + source_docs = [] + for doc in docs: + if doc.metadata["source"] in source_keys: + source_docs.append(doc) + + return source_docs + + +def wrap_text_in_html(text: str | List[str]) -> str: + """Wraps each text block separated by newlines intags""" + if isinstance(text, list): + # Add horizontal rules between pages + text = "\n
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