5770 lines
179 KiB
Plaintext
5770 lines
179 KiB
Plaintext
{
|
||
"cells": [
|
||
{
|
||
"cell_type": "markdown",
|
||
"id": "18d62071e34b0d53",
|
||
"metadata": {
|
||
"collapsed": false,
|
||
"id": "18d62071e34b0d53",
|
||
"jupyter": {
|
||
"outputs_hidden": false
|
||
}
|
||
},
|
||
"source": [
|
||
"# This is an experiment: create vectorized embeddings out of an EverNote DB (PDF, DOCX, HTML, TXT)\n"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "markdown",
|
||
"id": "aLpLL0Wy2A8M",
|
||
"metadata": {
|
||
"id": "aLpLL0Wy2A8M"
|
||
},
|
||
"source": [
|
||
"\n",
|
||
"## Features\n",
|
||
"\n",
|
||
"* vectorize text, html files, pdfs and docx into one vector store (FAISS)\n",
|
||
"* use local self-hosted embeddings (CPU or GPU computed)\n",
|
||
" * for sentences\n",
|
||
"* query a local vector store, use cache from LangChain (in-memory)\n",
|
||
"* use Ollama on-prem self-hosted Mistral for the response processing / prompt engineering"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "markdown",
|
||
"id": "stgrzM3K2C-o",
|
||
"metadata": {
|
||
"id": "stgrzM3K2C-o"
|
||
},
|
||
"source": [
|
||
"## Anti-Features\n",
|
||
"\n",
|
||
"* due to cost reasons the OpenAI embeddings don't get used. So sorry ... not."
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "markdown",
|
||
"id": "94517a27e3148ff4",
|
||
"metadata": {
|
||
"collapsed": false,
|
||
"id": "94517a27e3148ff4",
|
||
"jupyter": {
|
||
"outputs_hidden": false
|
||
}
|
||
},
|
||
"source": [
|
||
"# Setup and configuration\n",
|
||
"\n",
|
||
"⚠ This config is automated and executes a Bash script from a GitHub repo if you execute it on Goog Colab ⚠"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 23,
|
||
"id": "fd9747a54ea8fcef",
|
||
"metadata": {
|
||
"ExecuteTime": {
|
||
"end_time": "2024-04-05T11:27:09.463344Z",
|
||
"start_time": "2024-04-05T11:27:09.458830Z"
|
||
},
|
||
"id": "fd9747a54ea8fcef"
|
||
},
|
||
"outputs": [],
|
||
"source": [
|
||
"import sys\n",
|
||
"import os\n",
|
||
"import subprocess\n",
|
||
"\n",
|
||
"IN_COLAB = 'google.colab' in sys.modules\n",
|
||
"\n",
|
||
"if not IN_COLAB:\n",
|
||
" # The Evernote DB path containing the extracted data\n",
|
||
" # It will not be needed on Colab\n",
|
||
" extracted_evernote_db = \"/home/marius/data/it-sec-research-extracted/IT sec research\"\n",
|
||
"\n",
|
||
" # Output paths containing the Evernote text notes or documents data.\n",
|
||
" # These get generated by the data extraction process\n",
|
||
" output_path_extracted_notes = \"/home/marius/source/bookworm/export.txt\"\n",
|
||
" output_path_extracted_docs = \"/home/marius/source/bookworm/export.documents.txt\"\n",
|
||
"\n",
|
||
" # Resulting DB or vector store path.\n",
|
||
" result_db = \"/home/marius/source/bookworm/evernote.db\"\n",
|
||
"\n",
|
||
"else:\n",
|
||
" # For the Goog Colab env we use different paths\n",
|
||
" output_path_extracted_notes = \"/content/export.txt\"\n",
|
||
" output_path_extracted_docs = \"/content/export.documents.txt\"\n",
|
||
" result_db = \"/content/evernote.db\"\n",
|
||
"\n",
|
||
" # Download the data locally (just some txt files here)\n",
|
||
" # Install pip dependencies in Colab\n",
|
||
" subprocess.run('''\n",
|
||
" source <(curl -s https://raw.githubusercontent.com/norandom/project_bookworm/main/scripts/prepare_colab_env.sh)\n",
|
||
" ''',\n",
|
||
" shell=True, check=True, executable='/bin/bash')"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 24,
|
||
"id": "oHbFM-721Uwf",
|
||
"metadata": {
|
||
"ExecuteTime": {
|
||
"end_time": "2024-04-05T11:27:14.298345Z",
|
||
"start_time": "2024-04-05T11:27:14.295581Z"
|
||
},
|
||
"id": "oHbFM-721Uwf"
|
||
},
|
||
"outputs": [],
|
||
"source": [
|
||
"# To suppress some warnings\n",
|
||
"os.environ[\"TOKENIZERS_PARALLELISM\"] = \"False\""
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "markdown",
|
||
"id": "yuhXPdN_z2cW",
|
||
"metadata": {
|
||
"id": "yuhXPdN_z2cW"
|
||
},
|
||
"source": [
|
||
"## Checks"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 25,
|
||
"id": "6SPPaVEet9EO",
|
||
"metadata": {
|
||
"ExecuteTime": {
|
||
"end_time": "2024-04-05T11:27:18.222315Z",
|
||
"start_time": "2024-04-05T11:27:18.219343Z"
|
||
},
|
||
"colab": {
|
||
"base_uri": "https://localhost:8080/"
|
||
},
|
||
"id": "6SPPaVEet9EO",
|
||
"outputId": "e7cb63ec-8192-43a4-9320-83ff5b3b2122"
|
||
},
|
||
"outputs": [
|
||
{
|
||
"name": "stdout",
|
||
"output_type": "stream",
|
||
"text": [
|
||
"/home/marius/source/bookworm/export.txt\n"
|
||
]
|
||
}
|
||
],
|
||
"source": [
|
||
"print(output_path_extracted_notes)"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "markdown",
|
||
"id": "B02AY_Gez61T",
|
||
"metadata": {
|
||
"id": "B02AY_Gez61T"
|
||
},
|
||
"source": [
|
||
"## For the progress bars in Colab\n",
|
||
"\n",
|
||
"⚛ If you don't add this magic commands the `tqdm` progress bars will not update properly ⚛"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 5,
|
||
"id": "XGYNhuvrvnUD",
|
||
"metadata": {
|
||
"id": "XGYNhuvrvnUD"
|
||
},
|
||
"outputs": [],
|
||
"source": [
|
||
"%reload_ext autoreload\n",
|
||
"%autoreload 2"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "markdown",
|
||
"id": "a8c8692786d83c00",
|
||
"metadata": {
|
||
"collapsed": false,
|
||
"id": "a8c8692786d83c00",
|
||
"jupyter": {
|
||
"outputs_hidden": false
|
||
}
|
||
},
|
||
"source": [
|
||
"## Select key dependencies\n",
|
||
"\n",
|
||
"* `cryptography` is used to handle some PDF functions here (signatures)"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 6,
|
||
"id": "bb34db1ea75a1edf",
|
||
"metadata": {
|
||
"ExecuteTime": {
|
||
"end_time": "2024-04-04T10:08:32.520341Z",
|
||
"start_time": "2024-04-04T10:08:30.353678Z"
|
||
},
|
||
"colab": {
|
||
"base_uri": "https://localhost:8080/"
|
||
},
|
||
"id": "bb34db1ea75a1edf",
|
||
"outputId": "26af1f05-f9c1-4849-88e1-dc5c18cd3884"
|
||
},
|
||
"outputs": [
|
||
{
|
||
"name": "stdout",
|
||
"output_type": "stream",
|
||
"text": [
|
||
"Name: cryptography\n",
|
||
"Version: 42.0.5\n",
|
||
"Summary: cryptography is a package which provides cryptographic recipes and primitives to Python developers.\n",
|
||
"Home-page: \n",
|
||
"Author: \n",
|
||
"Author-email: The Python Cryptographic Authority and individual contributors <cryptography-dev@python.org>\n",
|
||
"License: Apache-2.0 OR BSD-3-Clause\n",
|
||
"Location: /usr/local/lib/python3.10/dist-packages\n",
|
||
"Requires: cffi\n",
|
||
"Required-by: pyOpenSSL\n"
|
||
]
|
||
}
|
||
],
|
||
"source": [
|
||
"%pip show cryptography"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "markdown",
|
||
"id": "297746c807e95fbf",
|
||
"metadata": {
|
||
"collapsed": false,
|
||
"id": "297746c807e95fbf",
|
||
"jupyter": {
|
||
"outputs_hidden": false
|
||
}
|
||
},
|
||
"source": [
|
||
"* `pikepdf` is used to repair some PDFs"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 7,
|
||
"id": "ebc8af0183532fc2",
|
||
"metadata": {
|
||
"ExecuteTime": {
|
||
"end_time": "2024-04-04T10:08:34.665865Z",
|
||
"start_time": "2024-04-04T10:08:32.522020Z"
|
||
},
|
||
"colab": {
|
||
"base_uri": "https://localhost:8080/"
|
||
},
|
||
"id": "ebc8af0183532fc2",
|
||
"outputId": "7966230e-ec57-4b64-acf2-09d013bb2608"
|
||
},
|
||
"outputs": [
|
||
{
|
||
"name": "stdout",
|
||
"output_type": "stream",
|
||
"text": [
|
||
"Name: pikepdf\n",
|
||
"Version: 8.13.0\n",
|
||
"Summary: Read and write PDFs with Python, powered by qpdf\n",
|
||
"Home-page: \n",
|
||
"Author: \n",
|
||
"Author-email: \"James R. Barlow\" <james@purplerock.ca>\n",
|
||
"License: MPL-2.0\n",
|
||
"Location: /usr/local/lib/python3.10/dist-packages\n",
|
||
"Requires: Deprecated, lxml, packaging, Pillow\n",
|
||
"Required-by: \n"
|
||
]
|
||
}
|
||
],
|
||
"source": [
|
||
"%pip show pikepdf"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "markdown",
|
||
"id": "7c7a7f6b0db3719e",
|
||
"metadata": {
|
||
"collapsed": false,
|
||
"id": "7c7a7f6b0db3719e",
|
||
"jupyter": {
|
||
"outputs_hidden": false
|
||
}
|
||
},
|
||
"source": [
|
||
"* `pypdf` with all features is needed because this DB consists of 100+ PDFs"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 8,
|
||
"id": "779f81e2ab00f73c",
|
||
"metadata": {
|
||
"ExecuteTime": {
|
||
"end_time": "2024-04-04T10:08:37.436449Z",
|
||
"start_time": "2024-04-04T10:08:35.269255Z"
|
||
},
|
||
"colab": {
|
||
"base_uri": "https://localhost:8080/"
|
||
},
|
||
"id": "779f81e2ab00f73c",
|
||
"outputId": "e1fcc840-7e3c-4d4a-9457-745be8db60c4"
|
||
},
|
||
"outputs": [
|
||
{
|
||
"name": "stdout",
|
||
"output_type": "stream",
|
||
"text": [
|
||
"Name: pypdf\n",
|
||
"Version: 4.0.2\n",
|
||
"Summary: A pure-python PDF library capable of splitting, merging, cropping, and transforming PDF files\n",
|
||
"Home-page: \n",
|
||
"Author: \n",
|
||
"Author-email: Mathieu Fenniak <biziqe@mathieu.fenniak.net>\n",
|
||
"License: \n",
|
||
"Location: /usr/local/lib/python3.10/dist-packages\n",
|
||
"Requires: \n",
|
||
"Required-by: \n"
|
||
]
|
||
}
|
||
],
|
||
"source": [
|
||
"%pip show \"pypdf\""
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "markdown",
|
||
"id": "A5l3rFo03NKq",
|
||
"metadata": {
|
||
"id": "A5l3rFo03NKq"
|
||
},
|
||
"source": [
|
||
"* `torch` is used for tensors, and GPU processing"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 9,
|
||
"id": "de3f715519fda6c4",
|
||
"metadata": {
|
||
"ExecuteTime": {
|
||
"end_time": "2024-04-04T10:08:39.729429Z",
|
||
"start_time": "2024-04-04T10:08:37.438498Z"
|
||
},
|
||
"colab": {
|
||
"base_uri": "https://localhost:8080/"
|
||
},
|
||
"id": "de3f715519fda6c4",
|
||
"outputId": "9f328109-f568-411b-c78a-0c1be41090bb"
|
||
},
|
||
"outputs": [
|
||
{
|
||
"name": "stdout",
|
||
"output_type": "stream",
|
||
"text": [
|
||
"Name: torch\n",
|
||
"Version: 2.2.1+cu121\n",
|
||
"Summary: Tensors and Dynamic neural networks in Python with strong GPU acceleration\n",
|
||
"Home-page: https://pytorch.org/\n",
|
||
"Author: PyTorch Team\n",
|
||
"Author-email: packages@pytorch.org\n",
|
||
"License: BSD-3\n",
|
||
"Location: /usr/local/lib/python3.10/dist-packages\n",
|
||
"Requires: filelock, fsspec, jinja2, networkx, nvidia-cublas-cu12, nvidia-cuda-cupti-cu12, nvidia-cuda-nvrtc-cu12, nvidia-cuda-runtime-cu12, nvidia-cudnn-cu12, nvidia-cufft-cu12, nvidia-curand-cu12, nvidia-cusolver-cu12, nvidia-cusparse-cu12, nvidia-nccl-cu12, nvidia-nvtx-cu12, sympy, triton, typing-extensions\n",
|
||
"Required-by: fastai, sentence-transformers, torchaudio, torchdata, torchtext, torchvision\n"
|
||
]
|
||
}
|
||
],
|
||
"source": [
|
||
"%pip show torch"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "markdown",
|
||
"id": "ZxyhRz6-3p-c",
|
||
"metadata": {
|
||
"id": "ZxyhRz6-3p-c"
|
||
},
|
||
"source": [
|
||
"* `faiss` is used in the CPU version as a general vector store library. The data is being serialzed with `LangChain`. FAISS CPU version uses AVX2. The GPU port has some implementation issues with disk persistance and merging."
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 10,
|
||
"id": "HARY_QMJvttI",
|
||
"metadata": {
|
||
"colab": {
|
||
"base_uri": "https://localhost:8080/"
|
||
},
|
||
"id": "HARY_QMJvttI",
|
||
"outputId": "bb7f5758-135e-435d-bf26-9aa3a1417e81"
|
||
},
|
||
"outputs": [
|
||
{
|
||
"name": "stdout",
|
||
"output_type": "stream",
|
||
"text": [
|
||
"Name: faiss-cpu\n",
|
||
"Version: 1.8.0\n",
|
||
"Summary: A library for efficient similarity search and clustering of dense vectors.\n",
|
||
"Home-page: \n",
|
||
"Author: \n",
|
||
"Author-email: Kota Yamaguchi <yamaguchi_kota@cyberagent.co.jp>\n",
|
||
"License: MIT License\n",
|
||
"Location: /usr/local/lib/python3.10/dist-packages\n",
|
||
"Requires: numpy\n",
|
||
"Required-by: \n"
|
||
]
|
||
}
|
||
],
|
||
"source": [
|
||
"%pip show faiss_cpu"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "markdown",
|
||
"id": "ce1350d2d6e3ed63",
|
||
"metadata": {
|
||
"collapsed": false,
|
||
"id": "ce1350d2d6e3ed63",
|
||
"jupyter": {
|
||
"outputs_hidden": false
|
||
}
|
||
},
|
||
"source": [
|
||
"## Text extraction\n",
|
||
"\n",
|
||
"⬛ This doesn't need to get executed if you already have the `*.txt` files.\n",
|
||
"\n",
|
||
"\n",
|
||
"* Here the html and text data is extracted into txt\n",
|
||
"* The PDF and DOCX data is extracted into another txt file. This will be used for weighted data fusion later.\n",
|
||
"\n",
|
||
"* the texts are normalized:\n",
|
||
" * unicode normalization\n",
|
||
" * surrogate characters get replaced\n",
|
||
" * html gets converted to text\n",
|
||
" * pdfs get repaired\n",
|
||
" * docx files get read\n",
|
||
"\n",
|
||
"* exceptions get handled (UTF-16 issues, PDF reference errors)"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 11,
|
||
"id": "yrzYeheF40jt",
|
||
"metadata": {
|
||
"id": "yrzYeheF40jt"
|
||
},
|
||
"outputs": [],
|
||
"source": [
|
||
"import glob\n",
|
||
"import os\n",
|
||
"\n",
|
||
"import unicodedata # to normalize text\n",
|
||
"import html2text # to convert html to text\n",
|
||
"from langchain.document_loaders import PyPDFLoader, Docx2txtLoader\n",
|
||
"import pikepdf # to repair PDFs\n",
|
||
"from pathlib import Path\n",
|
||
"from tqdm.notebook import tqdm\n",
|
||
"from concurrent.futures import ThreadPoolExecutor, as_completed"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": null,
|
||
"id": "b557444b8b1d4839",
|
||
"metadata": {
|
||
"ExecuteTime": {
|
||
"end_time": "2024-04-04T09:25:39.388933Z",
|
||
"start_time": "2024-04-04T09:25:39.320902Z"
|
||
},
|
||
"id": "b557444b8b1d4839"
|
||
},
|
||
"outputs": [],
|
||
"source": [
|
||
"def convert_html_to_text(html_blob: str) -> str:\n",
|
||
" \"\"\"\n",
|
||
" Converts a html blob into a string.\n",
|
||
" \"\"\"\n",
|
||
" h = html2text.HTML2Text()\n",
|
||
" h.mark_code = True\n",
|
||
" h.escape_snob = True\n",
|
||
" h.unicode_snob = True\n",
|
||
" # h.use_automatic_links = True\n",
|
||
" h.images_as_html = True\n",
|
||
" h.single_line_break = True\n",
|
||
" h.ignore_links = True\n",
|
||
" return h.handle(html_blob)\n",
|
||
"\n",
|
||
"def normalize_text(txt_blob: str) -> str:\n",
|
||
" \"\"\"\n",
|
||
" Normalize a text blob using NFKD normalization.\n",
|
||
" \"\"\"\n",
|
||
" return unicodedata.normalize(\"NFKD\", txt_blob)\n",
|
||
"\n",
|
||
"def repair_pdf(file_path: str) -> bool:\n",
|
||
" \"\"\"\n",
|
||
" Attempts to repair a PDF file using pikepdf.\n",
|
||
" \"\"\"\n",
|
||
" try:\n",
|
||
" with pikepdf.open(file_path, allow_overwriting_input=True) as pdf:\n",
|
||
" pdf.save(file_path)\n",
|
||
" return True\n",
|
||
" except pikepdf.PdfError as e:\n",
|
||
" print(f\"Failed to repair PDF {file_path}: {e}\")\n",
|
||
" return False\n",
|
||
"\n",
|
||
"def read_and_convert_file(file_path: str, is_html: bool, is_pdf: bool, is_docx: bool) -> str:\n",
|
||
" \"\"\"\n",
|
||
" Reads and converts a file from HTML, PDF, DOCX, or plain text to text.\n",
|
||
" :param file_path:\n",
|
||
" :param is_html:\n",
|
||
" :param is_pdf:\n",
|
||
" :param is_docx:\n",
|
||
" :return:\n",
|
||
" \"\"\"\n",
|
||
"\n",
|
||
" content = \"\"\n",
|
||
" if is_html:\n",
|
||
" try:\n",
|
||
" with open(file_path, 'r', encoding='utf-8') as file:\n",
|
||
" content = file.read()\n",
|
||
" return convert_html_to_text(content)\n",
|
||
" except Exception as e:\n",
|
||
" print(f\"Error reading {file_path}: {e}\")\n",
|
||
" return \"\"\n",
|
||
"\n",
|
||
" elif is_pdf:\n",
|
||
" try:\n",
|
||
" loader = PyPDFLoader(file_path)\n",
|
||
" # ... fixes \"Multiple definitions in dictionary at byte 0xb32 for key /ExtGState\" error\n",
|
||
" documents = loader.load()\n",
|
||
" content = \"\\n\".join(doc.page_content for doc in documents if hasattr(doc, 'page_content'))\n",
|
||
" except Exception as e:\n",
|
||
" print(f\"Error loading PDF {file_path}: {e}. Attempting to repair...\")\n",
|
||
" if repair_pdf(file_path):\n",
|
||
" try:\n",
|
||
" loader = PyPDFLoader(file_path)\n",
|
||
" documents = loader.load()\n",
|
||
" content = \"\\n\".join(doc.page_content for doc in documents if hasattr(doc, 'page_content'))\n",
|
||
" except Exception as e:\n",
|
||
" print(f\"Failed to process PDF {file_path} after repair: {e}\")\n",
|
||
" return \"\"\n",
|
||
" return normalize_text(content)\n",
|
||
"\n",
|
||
" elif is_docx:\n",
|
||
" try:\n",
|
||
" loader = Docx2txtLoader(file_path)\n",
|
||
" content = loader.load()\n",
|
||
" if isinstance(content, list):\n",
|
||
" content = \"\\n\".join(content)\n",
|
||
" except Exception as e:\n",
|
||
" print(f\"Error reading DOCX {file_path}: {e}\")\n",
|
||
" return \"\"\n",
|
||
" return normalize_text(content)\n",
|
||
"\n",
|
||
" else: # For plain text files\n",
|
||
" try:\n",
|
||
" with open(file_path, 'r', encoding='utf-8') as file:\n",
|
||
" return normalize_text(file.read())\n",
|
||
" except Exception as e:\n",
|
||
" print(f\"Error reading {file_path}: {e}\")\n",
|
||
" return \"\"\n",
|
||
"\n",
|
||
"def sanitize_text(text):\n",
|
||
" \"\"\"\n",
|
||
" Removes or replaces surrogate characters from a string.\n",
|
||
" \"\"\"\n",
|
||
" return text.encode('utf-8', 'replace').decode('utf-8')\n",
|
||
"\n",
|
||
"def append_to_output(data: str, is_pdf: bool, is_docx: bool, output_path: str):\n",
|
||
" \"\"\"\n",
|
||
" Appends sanitized data to an output file.\n",
|
||
" \"\"\"\n",
|
||
" sanitized_data = sanitize_text(data)\n",
|
||
" if is_pdf or is_docx:\n",
|
||
" output_path = str(Path(output_path).with_suffix('')) + \".documents.txt\"\n",
|
||
"\n",
|
||
" with open(output_path, \"a\", encoding='utf-8') as output_file:\n",
|
||
" output_file.write(sanitized_data)\n",
|
||
"\n",
|
||
"def process_file(file):\n",
|
||
" is_html = file.endswith('.html')\n",
|
||
" is_pdf = file.endswith('.pdf')\n",
|
||
" is_docx = file.endswith('.docx')\n",
|
||
"\n",
|
||
" file_content = read_and_convert_file(file, is_html, is_pdf, is_docx)\n",
|
||
" append_to_output(file_content, is_pdf, is_docx, output_path=output_path)\n",
|
||
"\n",
|
||
"def process_files_in_directory(directory: str):\n",
|
||
" txt_html_files = glob.glob(os.path.join(directory, \"*.txt\")) + glob.glob(os.path.join(directory, \"*.html\"))\n",
|
||
" pdf_docx_files = glob.glob(os.path.join(directory, \"img\", \"*.pdf\")) + glob.glob(os.path.join(directory, \"img\", \"*.docx\"))\n",
|
||
" all_files = txt_html_files + pdf_docx_files\n",
|
||
"\n",
|
||
" # Initialize the progress bar\n",
|
||
" pbar = tqdm(total=len(all_files), desc=\"Processing files\")\n",
|
||
"\n",
|
||
" with ThreadPoolExecutor(max_workers=3) as executor:\n",
|
||
" # Submit all files to the executor and store future objects\n",
|
||
" futures = [executor.submit(process_file, file) for file in all_files]\n",
|
||
"\n",
|
||
" # As tasks complete, update the progress bar\n",
|
||
" for future in as_completed(futures):\n",
|
||
" pbar.update(1) # Update the progress bar by one for each task completed\n",
|
||
"\n",
|
||
" # Ensure the progress bar is closed upon completion\n",
|
||
" pbar.close()\n",
|
||
"\n",
|
||
"process_files_in_directory(extracted_evernote_db)"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "markdown",
|
||
"id": "e1bcc07f980c865f",
|
||
"metadata": {
|
||
"collapsed": false,
|
||
"id": "e1bcc07f980c865f",
|
||
"jupyter": {
|
||
"outputs_hidden": false
|
||
}
|
||
},
|
||
"source": [
|
||
"# Chunking of the texts\n",
|
||
"\n",
|
||
"The texts need to get chunked (pre-processing) before the embedding process. We are processing text for the sake of similarity detection. Therefore we can use overlaps. For log-processing and detection engineering, overlaps would be counter-productive."
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 26,
|
||
"id": "de8d9f18d8342c57",
|
||
"metadata": {
|
||
"ExecuteTime": {
|
||
"end_time": "2024-04-05T11:28:01.724622Z",
|
||
"start_time": "2024-04-05T11:27:36.210305Z"
|
||
},
|
||
"colab": {
|
||
"base_uri": "https://localhost:8080/"
|
||
},
|
||
"id": "de8d9f18d8342c57",
|
||
"outputId": "31fd5ade-1af8-4592-8d18-aa2b8d635c44"
|
||
},
|
||
"outputs": [
|
||
{
|
||
"name": "stdout",
|
||
"output_type": "stream",
|
||
"text": [
|
||
"Now you have 723845 chunks in /home/marius/source/bookworm/export.txt\n",
|
||
"Now you have 151259 chunks in /home/marius/source/bookworm/export.documents.txt\n"
|
||
]
|
||
}
|
||
],
|
||
"source": [
|
||
"from langchain.text_splitter import RecursiveCharacterTextSplitter\n",
|
||
"\n",
|
||
"def chunk_text_data(txt_file=output_path_extracted_notes):\n",
|
||
"\n",
|
||
" with open(txt_file) as f:\n",
|
||
" text_notes = f.read()\n",
|
||
"\n",
|
||
" text_splitter = RecursiveCharacterTextSplitter(\n",
|
||
" chunk_size=100,\n",
|
||
" chunk_overlap=20,\n",
|
||
" length_function=len\n",
|
||
" )\n",
|
||
"\n",
|
||
" chunks = text_splitter.create_documents([text_notes])\n",
|
||
" print(f'Now you have {len(chunks)} chunks in {txt_file}')\n",
|
||
" return chunks\n",
|
||
"\n",
|
||
"# chunk individual text file containing the data\n",
|
||
"text_chunks = chunk_text_data(txt_file=output_path_extracted_notes)\n",
|
||
"doc_chunks = chunk_text_data(txt_file=output_path_extracted_docs)"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 28,
|
||
"id": "5c8dc13955c19d29",
|
||
"metadata": {
|
||
"ExecuteTime": {
|
||
"end_time": "2024-04-05T11:28:29.590616Z",
|
||
"start_time": "2024-04-05T11:28:29.586268Z"
|
||
},
|
||
"collapsed": false,
|
||
"jupyter": {
|
||
"outputs_hidden": false
|
||
}
|
||
},
|
||
"outputs": [
|
||
{
|
||
"data": {
|
||
"text/plain": [
|
||
"'fields. Primitive fields are those finite fields in which the exponent n is 1. In primitive fields'"
|
||
]
|
||
},
|
||
"execution_count": 28,
|
||
"metadata": {},
|
||
"output_type": "execute_result"
|
||
}
|
||
],
|
||
"source": [
|
||
"text_chunks[42].page_content"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "markdown",
|
||
"id": "aea7ceb111fed5f3",
|
||
"metadata": {
|
||
"collapsed": false,
|
||
"id": "aea7ceb111fed5f3",
|
||
"jupyter": {
|
||
"outputs_hidden": false
|
||
}
|
||
},
|
||
"source": [
|
||
"### Embedding costs - why no OpenAI?\n",
|
||
"\n",
|
||
"The OpenAI API has a cost for the embeddings.\n",
|
||
"At this point there seems to be no way to pre-estimate the costs reliably.\n",
|
||
"The following calculation is probably flawed. But if it's correct, I wish the OpenAPI team the best of luck with finding a new pricing model."
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 13,
|
||
"id": "afb2c8feb9ca0bb4",
|
||
"metadata": {
|
||
"colab": {
|
||
"base_uri": "https://localhost:8080/"
|
||
},
|
||
"id": "afb2c8feb9ca0bb4",
|
||
"outputId": "4bf4a714-b59e-4835-f3ac-3110b329b7b4"
|
||
},
|
||
"outputs": [
|
||
{
|
||
"name": "stdout",
|
||
"output_type": "stream",
|
||
"text": [
|
||
"Total Tokens: 15769414\n",
|
||
"Embedding Cost in USD: 473.08241999999996\n"
|
||
]
|
||
}
|
||
],
|
||
"source": [
|
||
"def print_embedding_cost(texts):\n",
|
||
" import tiktoken\n",
|
||
" enc = tiktoken.encoding_for_model('gpt-4')\n",
|
||
" total_tokens = sum([len(enc.encode(page.page_content)) for page in texts])\n",
|
||
" print(f'Total Tokens: {total_tokens}')\n",
|
||
" print(f'Embedding Cost in USD: { (0.03 / 1_000) * total_tokens}')\n",
|
||
"\n",
|
||
"print_embedding_cost(text_chunks)"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "markdown",
|
||
"id": "8012516604037e2f",
|
||
"metadata": {
|
||
"collapsed": false,
|
||
"id": "8012516604037e2f",
|
||
"jupyter": {
|
||
"outputs_hidden": false
|
||
}
|
||
},
|
||
"source": [
|
||
"# Use Hugging Face Embeddings Sentence Transformers\n",
|
||
"\n",
|
||
"Here we:\n",
|
||
"\n",
|
||
"* use a self-hosted on-premises model for the embedding and vectorization\n",
|
||
"* configure it for the use with the CPU or GPU\n",
|
||
"\n",
|
||
"This model is from the Beijing Academy of Artificial Intelligence\n",
|
||
"* https://huggingface.co/BAAI/bge-large-en-v1.5\n",
|
||
"* It uses: https://huggingface.co/docs/transformers/model_doc/auto\n",
|
||
"\n",
|
||
"It will produce embeddings of 1024 dimensions, roughly 500 less than OpenAI Embeddings I wanted to use initially."
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "markdown",
|
||
"id": "LJIwSxNf5sm7",
|
||
"metadata": {
|
||
"id": "LJIwSxNf5sm7"
|
||
},
|
||
"source": [
|
||
"## GPU detection (CUDA)\n",
|
||
"\n",
|
||
"Here we detect whether a GPU is present, and if that is the case, we initialize the model to use it later. If not, we can use the CPU as a fallback. But for this use-case / implementation the Nvidia V100 GPU is about 60x faster (estimation)."
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 13,
|
||
"id": "3081256c9cf22780",
|
||
"metadata": {
|
||
"ExecuteTime": {
|
||
"end_time": "2024-04-05T11:16:40.738173Z",
|
||
"start_time": "2024-04-05T11:16:39.380789Z"
|
||
},
|
||
"colab": {
|
||
"base_uri": "https://localhost:8080/"
|
||
},
|
||
"id": "3081256c9cf22780",
|
||
"outputId": "9b120f43-f2cd-47c2-b763-e089aca15ee2"
|
||
},
|
||
"outputs": [
|
||
{
|
||
"name": "stdout",
|
||
"output_type": "stream",
|
||
"text": [
|
||
"No CUDA available\n"
|
||
]
|
||
}
|
||
],
|
||
"source": [
|
||
"import torch\n",
|
||
"use_cuda = torch.cuda.is_available()\n",
|
||
"\n",
|
||
"USE_GPU=True\n",
|
||
"\n",
|
||
"if use_cuda:\n",
|
||
" print('__CUDNN VERSION:', torch.backends.cudnn.version())\n",
|
||
" print('__Number CUDA Devices:', torch.cuda.device_count())\n",
|
||
" print('__CUDA Device Name:',torch.cuda.get_device_name(0))\n",
|
||
" print('__CUDA Device Total Memory [GB]:',torch.cuda.get_device_properties(0).total_memory/1e9)\n",
|
||
" USE_GPU=True\n",
|
||
" print(\"GPU enabled\")\n",
|
||
"\n",
|
||
"if not use_cuda:\n",
|
||
" print('No CUDA available')\n",
|
||
" USE_GPU=False\n"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "markdown",
|
||
"id": "GY_nYdSO6JTc",
|
||
"metadata": {
|
||
"id": "GY_nYdSO6JTc"
|
||
},
|
||
"source": [
|
||
"## BAAI BERT Model\n",
|
||
"\n",
|
||
"The Beijing Academy of Artificial Intelligence (BAAI) is a leading organization, which provides state of the art models on HuggingFace. Here the model is being used to create the Embeddings. An Embedding here isn't a plain Word2Vec style projection of text to a vector space. It has a semantic integration. I still have to research the details.\n",
|
||
"\n",
|
||
"Bidirectional Encoder Representations from Transformers (BERT) is a language model based on the transformer architecture, notable for its dramatic improvement over previous state of the art models. It was introduced in October 2018 by researchers at Google."
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 14,
|
||
"id": "c1ca979bbc1610bb",
|
||
"metadata": {
|
||
"ExecuteTime": {
|
||
"end_time": "2024-04-05T11:16:41.041Z",
|
||
"start_time": "2024-04-05T11:16:41.037371Z"
|
||
},
|
||
"id": "c1ca979bbc1610bb"
|
||
},
|
||
"outputs": [],
|
||
"source": [
|
||
"from langchain.embeddings import HuggingFaceEmbeddings\n",
|
||
"\n",
|
||
"# pre-trained model path\n",
|
||
"modelPath = \"BAAI/bge-large-en-v1.5\"\n",
|
||
"\n",
|
||
"# Create a dictionary with model configuration options, specifying to use the CPU or GPU for computations\n",
|
||
"if not USE_GPU:\n",
|
||
" model_kwargs = {'device':'cpu'}\n",
|
||
"else:\n",
|
||
" model_kwargs = {}\n",
|
||
"\n",
|
||
"# Create a dictionary with encoding options, specifically setting 'normalize_embeddings' to True\n",
|
||
"encode_kwargs = {'normalize_embeddings': True}"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "markdown",
|
||
"id": "JSTLqLQj6ref",
|
||
"metadata": {
|
||
"id": "JSTLqLQj6ref"
|
||
},
|
||
"source": [
|
||
"### Initialization of the Embedding model"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 15,
|
||
"id": "3c2b9cd67f161714",
|
||
"metadata": {
|
||
"ExecuteTime": {
|
||
"end_time": "2024-04-05T11:16:47.504267Z",
|
||
"start_time": "2024-04-05T11:16:44.983827Z"
|
||
},
|
||
"colab": {
|
||
"base_uri": "https://localhost:8080/",
|
||
"height": 496,
|
||
"referenced_widgets": [
|
||
"a1b39dadf1fd474296d47c00498b1d97",
|
||
"ce3cebc4664b4b4094f965e3d98b1ec3",
|
||
"cbd1ebc865344b2cbe09aaad9341f447",
|
||
"1fe3e7dd24a143b38fcc1f16048fce75",
|
||
"26fcfd7ef3784d02bed4f621377600b0",
|
||
"40346f9f5293495ea35a8b6a2234e8e5",
|
||
"32675b12f59c4b04ae03d4246c67145c",
|
||
"8ae260f36b444619be6f189b02dc54a4",
|
||
"e70eeeff503c4f2a83757cb0c202e7d0",
|
||
"5afae079bdb047a9adbe1352ca91899c",
|
||
"defeecb0c9034ef0835df87438c046e2",
|
||
"1b1bb145deac4bcbb720559e5a9f4cde",
|
||
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||
]
|
||
},
|
||
"id": "3c2b9cd67f161714",
|
||
"outputId": "4c3c646e-6b4a-4ec3-e975-930d445c2144"
|
||
},
|
||
"outputs": [],
|
||
"source": [
|
||
"# Initialize an instance of HuggingFaceEmbeddings with the specified parameters\n",
|
||
"# this model requires sentence_transformers\n",
|
||
"\n",
|
||
"embeddings = HuggingFaceEmbeddings(\n",
|
||
" model_name=modelPath, # Provide the pre-trained model's path\n",
|
||
" model_kwargs=model_kwargs, # Pass the model configuration options\n",
|
||
" encode_kwargs=encode_kwargs # Pass the encoding options\n",
|
||
" )"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 16,
|
||
"id": "3b9ff8cad49442cf",
|
||
"metadata": {
|
||
"ExecuteTime": {
|
||
"end_time": "2024-04-05T11:16:56.483091Z",
|
||
"start_time": "2024-04-05T11:16:56.459721Z"
|
||
},
|
||
"colab": {
|
||
"base_uri": "https://localhost:8080/"
|
||
},
|
||
"id": "3b9ff8cad49442cf",
|
||
"outputId": "b289b59e-550c-4a81-f9c3-ef38b98e9761"
|
||
},
|
||
"outputs": [
|
||
{
|
||
"ename": "NameError",
|
||
"evalue": "name 'text_chunks' is not defined",
|
||
"output_type": "error",
|
||
"traceback": [
|
||
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
|
||
"\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)",
|
||
"Cell \u001b[0;32mIn[16], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m vector \u001b[38;5;241m=\u001b[39m embeddings\u001b[38;5;241m.\u001b[39membed_query(\u001b[43mtext_chunks\u001b[49m[\u001b[38;5;241m0\u001b[39m]\u001b[38;5;241m.\u001b[39mpage_content)\n\u001b[1;32m 2\u001b[0m \u001b[38;5;66;03m# print(vector)\u001b[39;00m\n\u001b[1;32m 3\u001b[0m n_dimensions \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlen\u001b[39m(vector)\n",
|
||
"\u001b[0;31mNameError\u001b[0m: name 'text_chunks' is not defined"
|
||
]
|
||
}
|
||
],
|
||
"source": [
|
||
"vector = embeddings.embed_query(text_chunks[0].page_content)\n",
|
||
"# print(vector)\n",
|
||
"n_dimensions = len(vector)\n",
|
||
"print(n_dimensions, \" dimensions are going to be used\")"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "markdown",
|
||
"id": "e6ev40az7JZY",
|
||
"metadata": {
|
||
"id": "e6ev40az7JZY"
|
||
},
|
||
"source": [
|
||
"This means that per line of the txt, this model creates 1024 dimensions (per vector)."
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "markdown",
|
||
"id": "b347fb5ee68daf60",
|
||
"metadata": {
|
||
"collapsed": false,
|
||
"id": "b347fb5ee68daf60",
|
||
"jupyter": {
|
||
"outputs_hidden": false
|
||
}
|
||
},
|
||
"source": [
|
||
"## Batch process the embedding\n",
|
||
"\n",
|
||
"Many data-science tasks require to split a larger processing operation into batch jobs.\n",
|
||
"Like in the good old Mainframe days.\n",
|
||
"\n",
|
||
"Initially I wanted to use the basic vector DB sqlite-vss again: https://github.com/asg017/sqlite-vss\n",
|
||
"\n",
|
||
"This is based on FAISS as well, but sqlite-vss doesn't seem to be able to handle concurrency. Recent sqlite versions can.\n",
|
||
"\n",
|
||
"### FAISS\n",
|
||
"\n",
|
||
"https://faiss.ai/ - a library for efficient similarity search and clustering of dense vectors.\n",
|
||
"\n",
|
||
"### Concurrency and batch processing\n",
|
||
"\n",
|
||
"We add vectors of 1024 dimensions per chunk (sentence, line break delimited) to a vector store based on FAISS and LangChain.\n",
|
||
"The processing is done in batches of 50 chunks, using 3 threads in parallel."
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 19,
|
||
"id": "b03bfcb6c666db1",
|
||
"metadata": {
|
||
"ExecuteTime": {
|
||
"end_time": "2024-04-04T10:10:08.134514Z",
|
||
"start_time": "2024-04-04T10:10:07.895943Z"
|
||
},
|
||
"id": "b03bfcb6c666db1"
|
||
},
|
||
"outputs": [],
|
||
"source": [
|
||
"from concurrent.futures import ThreadPoolExecutor, as_completed\n",
|
||
"import os\n",
|
||
"\n",
|
||
"from tqdm.notebook import tqdm\n",
|
||
"from typing import List\n",
|
||
"from langchain.schema.document import Document\n",
|
||
"\n",
|
||
"from langchain_community.vectorstores import FAISS"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 22,
|
||
"id": "e6ffc345c26298ad",
|
||
"metadata": {
|
||
"ExecuteTime": {
|
||
"end_time": "2024-04-04T10:32:48.905517Z",
|
||
"start_time": "2024-04-04T10:30:48.115043Z"
|
||
},
|
||
"colab": {
|
||
"base_uri": "https://localhost:8080/",
|
||
"height": 67,
|
||
"referenced_widgets": [
|
||
"592f37baf1c74e149577e80678db668f",
|
||
"2cdb27f1d7b14b558cf6f19fc0ab4fd9",
|
||
"ce8eed52d57c47479ab9a45b85296c04",
|
||
"a18c165ea7fc485c91e64df34974d685",
|
||
"090543e0523a4d0e8dbd89e0152a3a15",
|
||
"0fbb5a8dd8c64e6c862779496a0c1867",
|
||
"8c77c7def1804fd6884a601c76618fa7",
|
||
"4f06cc3b83e641cd81deba9aaea93fbb",
|
||
"b0e999f6c752439a8f4ba962815160ae",
|
||
"a18f27c970524c048b424be9672e106f",
|
||
"f6b2c8e5621143729c8d6e3129251f29"
|
||
]
|
||
},
|
||
"id": "e6ffc345c26298ad",
|
||
"outputId": "3d0276e2-aa07-4c66-c0a9-b20effd2cca5"
|
||
},
|
||
"outputs": [
|
||
{
|
||
"data": {
|
||
"application/vnd.jupyter.widget-view+json": {
|
||
"model_id": "592f37baf1c74e149577e80678db668f",
|
||
"version_major": 2,
|
||
"version_minor": 0
|
||
},
|
||
"text/plain": [
|
||
"Processing batches: 0%| | 0/1448 [00:00<?, ?it/s]"
|
||
]
|
||
},
|
||
"metadata": {},
|
||
"output_type": "display_data"
|
||
},
|
||
{
|
||
"name": "stdout",
|
||
"output_type": "stream",
|
||
"text": [
|
||
"All texts have been added to the database.\n"
|
||
]
|
||
}
|
||
],
|
||
"source": [
|
||
"def add_texts_in_batches(batch: List[Document], sqlite_table: str = \"evernote\", embeddings=embeddings) -> None:\n",
|
||
" \"\"\"\n",
|
||
" Using type hints is a good idea here, because error messages get swallowed by the ThreadPoolExecutor.\n",
|
||
" The exception handling serves the same purpose.\n",
|
||
" Exceptions can cost performance, but only on the CPU level here.\n",
|
||
" \"\"\"\n",
|
||
"\n",
|
||
" try:\n",
|
||
" db = FAISS.from_documents(batch, embeddings, distance_strategy=\"COSINE\")\n",
|
||
" return db\n",
|
||
"\n",
|
||
" except Exception as e:\n",
|
||
" print(f\"Exception occurred in add_texts_in_batches: {e}\")\n",
|
||
"\n",
|
||
"\n",
|
||
"def divide_chunks(chunks, n):\n",
|
||
" \"\"\"\n",
|
||
" Divide and conquer :)\n",
|
||
" \"\"\"\n",
|
||
" for i in range(0, len(chunks), n):\n",
|
||
" yield chunks[i:i + n]\n",
|
||
"\n",
|
||
"\n",
|
||
"def vectorize_data_in_batches(chunks, embeddings):\n",
|
||
" \"\"\"\n",
|
||
" This function orchestrates the embedding vectorization in batches.\n",
|
||
" \"\"\"\n",
|
||
"\n",
|
||
" num_workers = 3\n",
|
||
" batch_size = 500 # Adjust based on your needs and memory constraints\n",
|
||
"\n",
|
||
" batches = list(divide_chunks(chunks, batch_size))\n",
|
||
" faiss_db = None\n",
|
||
"\n",
|
||
" with ThreadPoolExecutor(max_workers=num_workers) as executor:\n",
|
||
" # Submit all the batches for processing\n",
|
||
" futures = {executor.submit(add_texts_in_batches, batch, embeddings=embeddings): batch for batch in batches}\n",
|
||
"\n",
|
||
" # Setup the tqdm progress bar\n",
|
||
" progress_bar = tqdm(total=len(futures), desc=\"Processing batches\")\n",
|
||
"\n",
|
||
" for future in as_completed(futures):\n",
|
||
" # Each time a future completes, update the progress and collect the result\n",
|
||
" progress_bar.update(1)\n",
|
||
" try:\n",
|
||
" db_result = future.result() # This is where you get the returned value from add_texts_in_batches\n",
|
||
" if faiss_db is not None:\n",
|
||
" faiss_db.merge_from(db_result)\n",
|
||
"\n",
|
||
" else:\n",
|
||
" faiss_db = db_result\n",
|
||
"\n",
|
||
" except Exception as e:\n",
|
||
" print(f\"An error occurred: {e}\")\n",
|
||
"\n",
|
||
" progress_bar.close() # Ensure the progress bar is closed at the end\n",
|
||
"\n",
|
||
" faiss_db.save_local(\"faiss_index_cosine\")\n",
|
||
" print(\"All texts have been added to the database.\")\n",
|
||
"\n",
|
||
"\n",
|
||
"vectorize_data_in_batches(chunks=text_chunks, embeddings=embeddings)"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "markdown",
|
||
"id": "WfjpAoJqE_L4",
|
||
"metadata": {
|
||
"id": "WfjpAoJqE_L4"
|
||
},
|
||
"source": [
|
||
"# Similarity and MMR search\n",
|
||
"\n",
|
||
"* this works on the FAISS index without a GPU\n",
|
||
"* you can retrieve the data from Kaggle: https://www.kaggle.com/mariusciepluch/faiss-text-db-infosec-archive\n",
|
||
"* the data is a FAISS index with cosine similarity\n",
|
||
"* you can use this FAISS index with MMR search\n",
|
||
"\n",
|
||
"\n",
|
||
"\"Maximal Marginal Relevance a.k.a. MMR has been introduced in the paper The Use of MMR, Diversity-Based Reranking for Reordering Documents and Producing Summaries. MMR tries to reduce the redundancy of results while at the same time maintaining query relevance of results for already ranked documents/phrases etc.\" (https://medium.com/tech-that-works/maximal-marginal-relevance-to-rerank-results-in-unsupervised-keyphrase-extraction-22d95015c7c5)\n",
|
||
"\n",
|
||
"MMR search provides better results here."
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 3,
|
||
"id": "96e60ed06157e62d",
|
||
"metadata": {
|
||
"ExecuteTime": {
|
||
"end_time": "2024-04-05T11:02:12.762744Z",
|
||
"start_time": "2024-04-05T11:02:12.759789Z"
|
||
},
|
||
"collapsed": false,
|
||
"jupyter": {
|
||
"outputs_hidden": false
|
||
}
|
||
},
|
||
"outputs": [],
|
||
"source": [
|
||
"from langchain_community.vectorstores import FAISS"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 10,
|
||
"id": "9ea3f5a0d14cada",
|
||
"metadata": {
|
||
"ExecuteTime": {
|
||
"end_time": "2024-04-05T11:11:46.382509Z",
|
||
"start_time": "2024-04-05T11:10:10.900581Z"
|
||
},
|
||
"collapsed": false,
|
||
"jupyter": {
|
||
"outputs_hidden": false
|
||
}
|
||
},
|
||
"outputs": [
|
||
{
|
||
"name": "stdout",
|
||
"output_type": "stream",
|
||
"text": [
|
||
"Downloading faiss-text-db-infosec-archive.zip to /home/marius/source/bookworm\r\n",
|
||
"100%|██████████████████████████████████████| 2.59G/2.59G [01:34<00:00, 35.9MB/s]\r\n",
|
||
"100%|██████████████████████████████████████| 2.59G/2.59G [01:34<00:00, 29.4MB/s]\r\n"
|
||
]
|
||
}
|
||
],
|
||
"source": [
|
||
"# DL FAISS index via API command (API key required afaik)\n",
|
||
"!/home/marius/miniconda3/envs/llm_langchain/bin/kaggle datasets download -d mariusciepluch/faiss-text-db-infosec-archive"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": null,
|
||
"id": "43458ad9399324dd",
|
||
"metadata": {
|
||
"collapsed": false,
|
||
"jupyter": {
|
||
"outputs_hidden": false
|
||
}
|
||
},
|
||
"outputs": [],
|
||
"source": [
|
||
"# Unzip the downloaded file\n",
|
||
"!7z x faiss-text-db-infosec-archive.zip"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 17,
|
||
"id": "nJG7eD8eFBnV",
|
||
"metadata": {
|
||
"ExecuteTime": {
|
||
"end_time": "2024-04-05T11:17:16.569043Z",
|
||
"start_time": "2024-04-05T11:17:06.997334Z"
|
||
},
|
||
"id": "nJG7eD8eFBnV"
|
||
},
|
||
"outputs": [],
|
||
"source": [
|
||
"loaded_db = FAISS.load_local(\"faiss_index_cosine\", embeddings, distance_strategy=\"COSINE\", allow_dangerous_deserialization=True)"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 34,
|
||
"id": "1e9cb08cdf9cc837",
|
||
"metadata": {
|
||
"ExecuteTime": {
|
||
"end_time": "2024-04-05T11:33:25.027401Z",
|
||
"start_time": "2024-04-05T11:33:24.742258Z"
|
||
},
|
||
"collapsed": false,
|
||
"jupyter": {
|
||
"outputs_hidden": false
|
||
}
|
||
},
|
||
"outputs": [
|
||
{
|
||
"name": "stdout",
|
||
"output_type": "stream",
|
||
"text": [
|
||
"[Document(page_content=\"`exploit'\"), Document(page_content='* **Exploit** : An exploit is a software or procedure that uses a vulnerability to effect some'), Document(page_content='exploit techniques disclosed?'), Document(page_content='Exploit-Entwicklung.')]\n"
|
||
]
|
||
}
|
||
],
|
||
"source": [
|
||
"results = loaded_db.search(search_type=\"mmr\", query=\"What is an exploit?\")\n",
|
||
"print(results)"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 35,
|
||
"id": "Wwbebp6wF9fG",
|
||
"metadata": {
|
||
"ExecuteTime": {
|
||
"end_time": "2024-04-05T11:34:00.277813Z",
|
||
"start_time": "2024-04-05T11:33:59.955815Z"
|
||
},
|
||
"id": "Wwbebp6wF9fG"
|
||
},
|
||
"outputs": [
|
||
{
|
||
"name": "stdout",
|
||
"output_type": "stream",
|
||
"text": [
|
||
"[(Document(page_content=\"`exploit'\"), 0.24956527), (Document(page_content=\"`exploit'\"), 0.24956527), (Document(page_content=\"`exploit'\"), 0.24956527), (Document(page_content=\"`exploit'\"), 0.24956527)]\n"
|
||
]
|
||
}
|
||
],
|
||
"source": [
|
||
"results_with_scores = loaded_db.similarity_search_with_score(\"What is an exploit?\")\n",
|
||
"print(results_with_scores)"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 32,
|
||
"id": "f4f39812d0cebde4",
|
||
"metadata": {
|
||
"ExecuteTime": {
|
||
"end_time": "2024-04-05T11:31:58.672502Z",
|
||
"start_time": "2024-04-05T11:31:58.284632Z"
|
||
},
|
||
"collapsed": false,
|
||
"jupyter": {
|
||
"outputs_hidden": false
|
||
}
|
||
},
|
||
"outputs": [
|
||
{
|
||
"name": "stdout",
|
||
"output_type": "stream",
|
||
"text": [
|
||
"[Document(page_content=\"`exploit'\"), Document(page_content='* **Exploit** : An exploit is a software or procedure that uses a vulnerability to effect some'), Document(page_content='exploit techniques disclosed?'), Document(page_content='Exploit-Entwicklung.')]\n"
|
||
]
|
||
}
|
||
],
|
||
"source": [
|
||
"retriever = loaded_db.as_retriever( search_type=\"mmr\",)\n",
|
||
"docs = retriever.invoke(\"What is an exploit?\")\n",
|
||
"print(docs)"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 41,
|
||
"id": "a650e47f9e73351f",
|
||
"metadata": {
|
||
"ExecuteTime": {
|
||
"end_time": "2024-04-05T11:40:04.650321Z",
|
||
"start_time": "2024-04-05T11:40:00.463436Z"
|
||
},
|
||
"collapsed": false,
|
||
"jupyter": {
|
||
"outputs_hidden": false
|
||
}
|
||
},
|
||
"outputs": [
|
||
{
|
||
"name": "stdout",
|
||
"output_type": "stream",
|
||
"text": [
|
||
"[Document(page_content='### Exploit Development'), Document(page_content='Reverse engineering, specific to computer science, is the act of deriving a'), Document(page_content='This article is about the reverse engineering of the exploit found in the leak'), Document(page_content='the Software Exploitation challenges and I designed all the Reverse\\nEngineering challenges.'), Document(page_content='understand the thought process behind reverse engineering modern malware of'), Document(page_content='# Gdbinit | Reverse Engineering Mac OS X\\n**Created:**| _1/3/2012 4:12:17 PM_ \\n---|---'), Document(page_content='series. First thing said: “what is an exploit?”. It could be described as a'), Document(page_content='How might an attacker benefit from capturing or modifying the data?'), Document(page_content='to do Reverse Engineering and exploit development, yet some of it is required'), Document(page_content='hacking, crack, hack, unlock, unprotect, break, reverse engineer, recover,'), Document(page_content='#### Putting it all together\\n\\nThe exploitation process is:'), Document(page_content='Place you reverse engineering questions for Linux related topics here... Tux'), Document(page_content='level bit hacks**. Bit hacks are ingenious little programming tricks that'), Document(page_content='was found and exploited?'), Document(page_content='**First things first how the hell does the dumping of Windows hashes actually'), Document(page_content='1. Using SDbgExt to aid your debugging and reverse engineering efforts \\\\(part 1\\\\). SDbgExt is the'), Document(page_content='hardware hackers, reverse-engineers and exploit developers.'), Document(page_content='\\\\[forum\\\\]reverse-engineering.net \\nReverse Engineering the World \\nReversing for Newbies'), Document(page_content='as anti-debugs, exception triggers, Get IPs...it uses several tricks to be'), Document(page_content='to understand more of the exploit process and more of how Internet Explorer\\nworked.'), Document(page_content='is exploited by hackers. Indeed, no open-software initiative helps explicitly with understanding'), Document(page_content='discuss the sandbox implementation itself, how it works, and also provide some'), Document(page_content='classic tools in order to debug the exploit. Furthermore, your structure'), Document(page_content='* **Exploit** : An exploit is a software or procedure that uses a vulnerability to effect some'), Document(page_content='# JAVA Exploit Kit Malware \\\\#1 | inREVERSE\\n**Created:**| _1/7/2010 1:29:44 PM_ \\n---|---'), Document(page_content='* Reverse Engineering Automation\\n * Binary Exploitation Techniques'), Document(page_content='exploit, because if you create the exploit yourself you should know exactly'), Document(page_content='The question is : How do exploit writers build their exploits ? What does the'), Document(page_content='using Metasploit’s pattern\\\\_create.rb tool to help us pinpoint the exact part'), Document(page_content='Description: A PowerShell Post-Exploitation Framework used in many PowerShell\\nattack tools.'), Document(page_content='and how they are exploited. Detailed technical information on how to exploit'), Document(page_content='gain a reverse shell. For the SQLi attack there are few basic steps :'), Document(page_content='* Struct Builder: Tool commonly used in game hacking to reverse data structures. This tool is'), Document(page_content='A Few Thoughts on Cryptographic Engineering: How does the NSA break SSL?\\nCreated:'), Document(page_content='**Answer:** Backdoors are tools used by attackers to help them maintain access'), Document(page_content='exploitation process. On the other hand, the “E” attribute has been removed'), Document(page_content='understand SEH in the context of exploit writing. I encourage you to read up'), Document(page_content='Exploit-DB. \\n \\nThe exploitation process for this vulnerability will examine overwritng EIP'), Document(page_content='boot process, the following files of a Windows 10 1607 build have been reverse-engineered:'), Document(page_content='process explaining some of the basics of exploiting. The whole topic can be'), Document(page_content='exploits. Low integrity processes are used for processing and handling of'), Document(page_content=\"I wanted to hack something in javascript to see how it's like to build\\nprototypes with it.\"), Document(page_content='The return-into-library technique is the root on which all return-oriented exploit approaches are'), Document(page_content='22. Down the Rabbit Hole \\nSummary of the Rogue File/Process'), Document(page_content='talent you have after reverse-engineering your star-exploit back in 2010'), Document(page_content='Labels: Exploitation, Reverse Engineering'), Document(page_content='What is the process for identifying and addressing vulnerabilities in the\\napplication?'), Document(page_content='But is this level of obfuscation where exploit countermeasures are headed? How'), Document(page_content='bug, they just say its a DoS. Then a really smart exploit developer comes along and says, \"Hey'), Document(page_content=\"iOS App Reverse Engineering is the world's 1st book of very detailed iOS App\")]\n"
|
||
]
|
||
}
|
||
],
|
||
"source": [
|
||
"retriever = loaded_db.as_retriever( search_type=\"mmr\", search_kwargs={'k': 50, 'fetch_k': 5000})\n",
|
||
"docs = retriever.invoke(\"What is an exploit and what is the process of creating it? How does reverse engineering contribute to exploit development?\")\n",
|
||
"print(docs)"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "markdown",
|
||
"id": "b8ad09a6a2b98e12",
|
||
"metadata": {
|
||
"collapsed": false,
|
||
"jupyter": {
|
||
"outputs_hidden": false
|
||
}
|
||
},
|
||
"source": [
|
||
"# Use the FAISS index with Mistral"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 42,
|
||
"id": "cfbc6c6bf2fd7caf",
|
||
"metadata": {
|
||
"ExecuteTime": {
|
||
"end_time": "2024-04-05T11:41:25.823973Z",
|
||
"start_time": "2024-04-05T11:41:24.910564Z"
|
||
},
|
||
"collapsed": false,
|
||
"jupyter": {
|
||
"outputs_hidden": false
|
||
}
|
||
},
|
||
"outputs": [],
|
||
"source": [
|
||
"from langchain_community.llms import Ollama\n",
|
||
"from langchain.globals import set_llm_cache\n",
|
||
"from langchain.cache import InMemoryCache\n",
|
||
"\n",
|
||
"set_llm_cache(InMemoryCache())\n",
|
||
"\n",
|
||
"llm = Ollama(model=\"mistral\")"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "markdown",
|
||
"id": "f75b4231f798edec",
|
||
"metadata": {
|
||
"collapsed": false,
|
||
"jupyter": {
|
||
"outputs_hidden": false
|
||
}
|
||
},
|
||
"source": [
|
||
"## Pass MMR search results to Mistral\n",
|
||
"\n",
|
||
"* I am using Ollama and Mistral, self-hosted\n",
|
||
"* The Mistral model is a large language model, which can be used for text generation and QA\n",
|
||
"* The Mistral model is being used to generate a response to the MMR search results"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 43,
|
||
"id": "56cc32c360a4bd3c",
|
||
"metadata": {
|
||
"ExecuteTime": {
|
||
"end_time": "2024-04-05T11:44:35.703318Z",
|
||
"start_time": "2024-04-05T11:44:34.995829Z"
|
||
},
|
||
"collapsed": false,
|
||
"jupyter": {
|
||
"outputs_hidden": false
|
||
}
|
||
},
|
||
"outputs": [],
|
||
"source": [
|
||
"from langchain.chains import RetrievalQA\n",
|
||
"\n",
|
||
"chain = RetrievalQA.from_chain_type(llm=llm, chain_type=\"stuff\", retriever=retriever)"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 45,
|
||
"id": "2fec48eac2aa2531",
|
||
"metadata": {
|
||
"ExecuteTime": {
|
||
"end_time": "2024-04-05T11:49:52.931101Z",
|
||
"start_time": "2024-04-05T11:49:42.877730Z"
|
||
},
|
||
"collapsed": false,
|
||
"jupyter": {
|
||
"outputs_hidden": false
|
||
}
|
||
},
|
||
"outputs": [
|
||
{
|
||
"name": "stdout",
|
||
"output_type": "stream",
|
||
"text": [
|
||
"{'query': 'What is an exploit and how does the process of reverse engineering contribute to exploit development?', 'result': \" An exploit is a software or procedure that uses a vulnerability to effect some unwanted or unintended action in a system. The process of reverse engineering contributes significantly to exploit development as it involves understanding the inner workings of a software or system, identifying vulnerabilities, and developing code (exploits) to take advantage of those vulnerabilities. Reverse engineering tools and techniques enable researchers and attackers to analyze software, disassemble code, and modify it to create exploits. Exploit development requires reverse engineering skills, custom shellcode payloads, and a deep understanding of the target system's vulnerabilities and exploitability.\"}\n"
|
||
]
|
||
}
|
||
],
|
||
"source": [
|
||
"query = \"What is an exploit and how does the process of reverse engineering contribute to exploit development?\"\n",
|
||
"answer = chain.invoke(query)\n",
|
||
"print(answer)"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "markdown",
|
||
"id": "82gFVyrNCYOF",
|
||
"metadata": {
|
||
"id": "82gFVyrNCYOF"
|
||
},
|
||
"source": [
|
||
"# Sandbox code - test area"
|
||
]
|
||
},
|
||
{
|
||
"cell_type": "code",
|
||
"execution_count": 26,
|
||
"id": "v6bhYHU5_9oo",
|
||
"metadata": {
|
||
"colab": {
|
||
"base_uri": "https://localhost:8080/"
|
||
},
|
||
"id": "v6bhYHU5_9oo",
|
||
"outputId": "a88691e1-3ee4-4a34-edbf-4fac688dd78d"
|
||
},
|
||
"outputs": [
|
||
{
|
||
"name": "stdout",
|
||
"output_type": "stream",
|
||
"text": [
|
||
"<class 'langchain_community.vectorstores.faiss.FAISS'>\n"
|
||
]
|
||
}
|
||
],
|
||
"source": [
|
||
"from langchain_community.vectorstores import FAISS\n",
|
||
"\n",
|
||
"texts = [\"FAISS is an important library\", \"LangChain supports FAISS\"]\n",
|
||
"faiss = FAISS.from_texts(texts, embeddings, distance_strategy=\"COSINE\")\n",
|
||
"print(type(faiss))\n",
|
||
"\n",
|
||
"faiss.save_local(\"test\")\n",
|
||
"\n",
|
||
"new_db = FAISS.load_local(\"test\", embeddings, allow_dangerous_deserialization=True)"
|
||
]
|
||
}
|
||
],
|
||
"metadata": {
|
||
"accelerator": "GPU",
|
||
"colab": {
|
||
"gpuType": "V100",
|
||
"machine_shape": "hm",
|
||
"provenance": []
|
||
},
|
||
"kernelspec": {
|
||
"display_name": "Python 3 (ipykernel)",
|
||
"language": "python",
|
||
"name": "python3"
|
||
},
|
||
"language_info": {
|
||
"codemirror_mode": {
|
||
"name": "ipython",
|
||
"version": 3
|
||
},
|
||
"file_extension": ".py",
|
||
"mimetype": "text/x-python",
|
||
"name": "python",
|
||
"nbconvert_exporter": "python",
|
||
"pygments_lexer": "ipython3",
|
||
"version": "3.11.8"
|
||
},
|
||
"widgets": {
|
||
"application/vnd.jupyter.widget-state+json": {
|
||
"00473551f93a45fe8e8337c15d677848": {
|
||
"model_module": "@jupyter-widgets/controls",
|
||
"model_module_version": "1.5.0",
|
||
"model_name": "HBoxModel",
|
||
"state": {
|
||
"_dom_classes": [],
|
||
"_model_module": "@jupyter-widgets/controls",
|
||
"_model_module_version": "1.5.0",
|
||
"_model_name": "HBoxModel",
|
||
"_view_count": null,
|
||
"_view_module": "@jupyter-widgets/controls",
|
||
"_view_module_version": "1.5.0",
|
||
"_view_name": "HBoxView",
|
||
"box_style": "",
|
||
"children": [
|
||
"IPY_MODEL_8bf13bfe911c43798e87e8bf9e49047a",
|
||
"IPY_MODEL_c7f64c8420074c469024b1b89ff0c114",
|
||
"IPY_MODEL_94b6362a788b4c15ac67cc41e9f1b4ce"
|
||
],
|
||
"layout": "IPY_MODEL_576c65f676f941bcb20c804191b1e63a"
|
||
}
|
||
},
|
||
"00f1718ef79a405eb83b4190b80bc95d": {
|
||
"model_module": "@jupyter-widgets/controls",
|
||
"model_module_version": "1.5.0",
|
||
"model_name": "DescriptionStyleModel",
|
||
"state": {
|
||
"_model_module": "@jupyter-widgets/controls",
|
||
"_model_module_version": "1.5.0",
|
||
"_model_name": "DescriptionStyleModel",
|
||
"_view_count": null,
|
||
"_view_module": "@jupyter-widgets/base",
|
||
"_view_module_version": "1.2.0",
|
||
"_view_name": "StyleView",
|
||
"description_width": ""
|
||
}
|
||
},
|
||
"012be145a1444889bfa30fae7812d62b": {
|
||
"model_module": "@jupyter-widgets/controls",
|
||
"model_module_version": "1.5.0",
|
||
"model_name": "HTMLModel",
|
||
"state": {
|
||
"_dom_classes": [],
|
||
"_model_module": "@jupyter-widgets/controls",
|
||
"_model_module_version": "1.5.0",
|
||
"_model_name": "HTMLModel",
|
||
"_view_count": null,
|
||
"_view_module": "@jupyter-widgets/controls",
|
||
"_view_module_version": "1.5.0",
|
||
"_view_name": "HTMLView",
|
||
"description": "",
|
||
"description_tooltip": null,
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