diff --git a/.github/workflows/ruff_format.yaml b/.github/workflows/ruff_format.yaml new file mode 100644 index 000000000..959b7fc4b --- /dev/null +++ b/.github/workflows/ruff_format.yaml @@ -0,0 +1,11 @@ +name: ruff format +on: [ pull_request ] + +jobs: + ruff: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - uses: astral-sh/ruff-action@v2 + with: + args: "format --check" diff --git a/.github/workflows/ruff_lint.yaml b/.github/workflows/ruff_lint.yaml new file mode 100644 index 000000000..214e8ec6d --- /dev/null +++ b/.github/workflows/ruff_lint.yaml @@ -0,0 +1,9 @@ +name: ruff lint +on: [ pull_request ] + +jobs: + ruff: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - uses: astral-sh/ruff-action@v2 diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 000000000..42f12ea51 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,20 @@ +# See https://pre-commit.com for more information +# See https://pre-commit.com/hooks.html for more hooks +repos: +- repo: https://github.com/pre-commit/pre-commit-hooks + rev: v3.2.0 + hooks: + - id: trailing-whitespace + - id: end-of-file-fixer + - id: check-yaml + - id: check-added-large-files +- repo: https://github.com/astral-sh/ruff-pre-commit + # Ruff version. + rev: v0.8.3 + hooks: + # Run the linter. + - id: ruff + types_or: [ python, pyi ] + # Run the formatter. + - id: ruff-format + types_or: [ python, pyi ] diff --git a/README.md b/README.md index 40005fc09..f35829783 100644 --- a/README.md +++ b/README.md @@ -17,6 +17,9 @@ Try it in a Google Colab Discord community +
+why cognee +
## 📦 Installation @@ -259,11 +262,7 @@ pip install cognee ## Vector & Graph Databases Implementation State - + | Name | Type | Current state | Known Issues | |----------|--------------------|-------------------|--------------| diff --git a/assets/cognee_benefits.png b/assets/cognee_benefits.png new file mode 100644 index 000000000..d435bed05 Binary files /dev/null and b/assets/cognee_benefits.png differ diff --git a/cognee-mcp/README.md b/cognee-mcp/README.md index a83c07bff..4ffa41e8f 100644 --- a/cognee-mcp/README.md +++ b/cognee-mcp/README.md @@ -12,6 +12,17 @@ A MCP server project 2. Install dependencies +``` +pip install uv +``` +``` +brew install postgresql +``` + +``` +brew install rust +``` + ```jsx cd cognee-mcp uv sync --dev --all-extras @@ -25,25 +36,42 @@ source .venv/bin/activate 4. Add the new server to your Claude config: -```json -"cognee": { - "command": "uv", - "args": [ - "--directory", - "/{Absolute path to cognee directory}/cognee-mcp", - "run", - "cognee" - ], - "env": { - "ENV": "local", - "TOKENIZERS_PARALLELISM": "false", - "LLM_API_KEY": "add_your_api_key_here", - } +The file should be located here: ~/Library/Application\ Support/Claude/ +You need to create claude_desktop_config.json in this folder if it doesn't exist + +``` + + +{ + "mcpServers": { + "cognee": { + "command": "/Users/{user}/cognee/.venv/bin/uv", + "args": [ + "--directory", + "/Users/{user}/cognee/cognee-mcp", + "run", + "cognee" + ], + "env": { + "ENV": "local", + "TOKENIZERS_PARALLELISM": "false", + "LLM_API_KEY": "sk-" + } + }, + "filesystem": { + "command": "npx", + "args": [ + "-y", + "@modelcontextprotocol/server-filesystem", + "/Users/{user}/Desktop", + "/Users/{user}/Projects" + ] + } + } } ``` -Then, edit the pyproject.toml in your new folder so that it includes packages from the cognee requirements. Use the pyproject.toml in your cognee library for this, but match the syntax of the automatically generated pyproject.toml so that it is compatible with uv. - +Restart your Claude desktop. ### Installing via Smithery diff --git a/cognee/infrastructure/databases/relational/sqlalchemy/SqlAlchemyAdapter.py b/cognee/infrastructure/databases/relational/sqlalchemy/SqlAlchemyAdapter.py index 8041aeaea..c197efc72 100644 --- a/cognee/infrastructure/databases/relational/sqlalchemy/SqlAlchemyAdapter.py +++ b/cognee/infrastructure/databases/relational/sqlalchemy/SqlAlchemyAdapter.py @@ -1,15 +1,23 @@ +import os from os import path +import logging from uuid import UUID from typing import Optional from typing import AsyncGenerator, List from contextlib import asynccontextmanager -from sqlalchemy import text, select, MetaData, Table +from sqlalchemy import text, select, MetaData, Table, delete from sqlalchemy.orm import joinedload +from sqlalchemy.exc import NoResultFound from sqlalchemy.ext.asyncio import AsyncSession, create_async_engine, async_sessionmaker from cognee.infrastructure.databases.exceptions import EntityNotFoundError +from cognee.modules.data.models.Data import Data + from ..ModelBase import Base + +logger = logging.getLogger(__name__) + class SQLAlchemyAdapter(): def __init__(self, connection_string: str): self.db_path: str = None @@ -86,9 +94,9 @@ class SQLAlchemyAdapter(): return [schema[0] for schema in result.fetchall()] return [] - async def delete_data_by_id(self, table_name: str, data_id: UUID, schema_name: Optional[str] = "public"): + async def delete_entity_by_id(self, table_name: str, data_id: UUID, schema_name: Optional[str] = "public"): """ - Delete data in given table based on id. Table must have an id Column. + Delete entity in given table based on id. Table must have an id Column. """ if self.engine.dialect.name == "sqlite": async with self.get_async_session() as session: @@ -107,6 +115,42 @@ class SQLAlchemyAdapter(): await session.commit() + async def delete_data_entity(self, data_id: UUID): + """ + Delete data and local files related to data if there are no references to it anymore. + """ + async with self.get_async_session() as session: + if self.engine.dialect.name == "sqlite": + # Foreign key constraints are disabled by default in SQLite (for backwards compatibility), + # so must be enabled for each database connection/session separately. + await session.execute(text("PRAGMA foreign_keys = ON;")) + + try: + data_entity = (await session.scalars(select(Data).where(Data.id == data_id))).one() + except (ValueError, NoResultFound) as e: + raise EntityNotFoundError(message=f"Entity not found: {str(e)}") + + # Check if other data objects point to the same raw data location + raw_data_location_entities = (await session.execute( + select(Data.raw_data_location).where(Data.raw_data_location == data_entity.raw_data_location))).all() + + # Don't delete local file unless this is the only reference to the file in the database + if len(raw_data_location_entities) == 1: + + # delete local file only if it's created by cognee + from cognee.base_config import get_base_config + config = get_base_config() + + if config.data_root_directory in raw_data_location_entities[0].raw_data_location: + if os.path.exists(raw_data_location_entities[0].raw_data_location): + os.remove(raw_data_location_entities[0].raw_data_location) + else: + # Report bug as file should exist + logger.error("Local file which should exist can't be found.") + + await session.execute(delete(Data).where(Data.id == data_id)) + await session.commit() + async def get_table(self, table_name: str, schema_name: Optional[str] = "public") -> Table: """ Dynamically loads a table using the given table name and schema name. diff --git a/cognee/modules/data/methods/delete_data.py b/cognee/modules/data/methods/delete_data.py index c0493a606..65abe714a 100644 --- a/cognee/modules/data/methods/delete_data.py +++ b/cognee/modules/data/methods/delete_data.py @@ -17,4 +17,4 @@ async def delete_data(data: Data): db_engine = get_relational_engine() - return await db_engine.delete_data_by_id(data.__tablename__, data.id) + return await db_engine.delete_data_entity(data.id) diff --git a/cognee/modules/data/methods/delete_dataset.py b/cognee/modules/data/methods/delete_dataset.py index c2205144d..96a2e7d71 100644 --- a/cognee/modules/data/methods/delete_dataset.py +++ b/cognee/modules/data/methods/delete_dataset.py @@ -4,4 +4,4 @@ from cognee.infrastructure.databases.relational import get_relational_engine async def delete_dataset(dataset: Dataset): db_engine = get_relational_engine() - return await db_engine.delete_data_by_id(dataset.__tablename__, dataset.id) + return await db_engine.delete_entity_by_id(dataset.__tablename__, dataset.id) diff --git a/cognee/tests/test_pgvector.py b/cognee/tests/test_pgvector.py index 9554a3f9d..417904089 100644 --- a/cognee/tests/test_pgvector.py +++ b/cognee/tests/test_pgvector.py @@ -2,12 +2,53 @@ import os import logging import pathlib import cognee + +from cognee.modules.data.models import Data from cognee.api.v1.search import SearchType from cognee.modules.retrieval.brute_force_triplet_search import brute_force_triplet_search from cognee.modules.users.methods import get_default_user logging.basicConfig(level=logging.DEBUG) +async def test_local_file_deletion(data_text, file_location): + from sqlalchemy import select + import hashlib + from cognee.infrastructure.databases.relational import get_relational_engine + + engine = get_relational_engine() + + async with engine.get_async_session() as session: + # Get hash of data contents + encoded_text = data_text.encode("utf-8") + data_hash = hashlib.md5(encoded_text).hexdigest() + # Get data entry from database based on hash contents + data = (await session.scalars(select(Data).where(Data.content_hash == data_hash))).one() + assert os.path.isfile(data.raw_data_location), f"Data location doesn't exist: {data.raw_data_location}" + # Test deletion of data along with local files created by cognee + await engine.delete_data_entity(data.id) + assert not os.path.exists( + data.raw_data_location), f"Data location still exists after deletion: {data.raw_data_location}" + + async with engine.get_async_session() as session: + # Get data entry from database based on file path + data = (await session.scalars(select(Data).where(Data.raw_data_location == file_location))).one() + assert os.path.isfile(data.raw_data_location), f"Data location doesn't exist: {data.raw_data_location}" + # Test local files not created by cognee won't get deleted + await engine.delete_data_entity(data.id) + assert os.path.exists(data.raw_data_location), f"Data location doesn't exists: {data.raw_data_location}" + +async def test_getting_of_documents(dataset_name_1): + # Test getting of documents for search per dataset + from cognee.modules.users.permissions.methods import get_document_ids_for_user + user = await get_default_user() + document_ids = await get_document_ids_for_user(user.id, [dataset_name_1]) + assert len(document_ids) == 1, f"Number of expected documents doesn't match {len(document_ids)} != 1" + + # Test getting of documents for search when no dataset is provided + user = await get_default_user() + document_ids = await get_document_ids_for_user(user.id) + assert len(document_ids) == 2, f"Number of expected documents doesn't match {len(document_ids)} != 2" + async def main(): cognee.config.set_vector_db_config( @@ -67,16 +108,7 @@ async def main(): from cognee.infrastructure.databases.vector import get_vector_engine - # Test getting of documents for search per dataset - from cognee.modules.users.permissions.methods import get_document_ids_for_user - user = await get_default_user() - document_ids = await get_document_ids_for_user(user.id, [dataset_name_1]) - assert len(document_ids) == 1, f"Number of expected documents doesn't match {len(document_ids)} != 1" - - # Test getting of documents for search when no dataset is provided - user = await get_default_user() - document_ids = await get_document_ids_for_user(user.id) - assert len(document_ids) == 2, f"Number of expected documents doesn't match {len(document_ids)} != 2" + await test_getting_of_documents(dataset_name_1) vector_engine = get_vector_engine() random_node = (await vector_engine.search("entity_name", "Quantum computer"))[0] @@ -106,6 +138,8 @@ async def main(): results = await brute_force_triplet_search('What is a quantum computer?') assert len(results) > 0 + await test_local_file_deletion(text, explanation_file_path) + await cognee.prune.prune_data() assert not os.path.isdir(data_directory_path), "Local data files are not deleted" diff --git a/poetry.lock b/poetry.lock index 261f85db5..989ad440b 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.5 and should not be changed by hand. [[package]] name = "aiofiles" @@ -586,17 +586,17 @@ css = ["tinycss2 (>=1.1.0,<1.5)"] [[package]] name = "boto3" -version = "1.35.84" +version = "1.35.85" description = "The AWS SDK for Python" optional = false python-versions = ">=3.8" files = [ - {file = "boto3-1.35.84-py3-none-any.whl", hash = "sha256:c94fc8023caf952f8740a48fc400521bba167f883cfa547d985c05fda7223f7a"}, - {file = "boto3-1.35.84.tar.gz", hash = "sha256:9f9bf72d92f7fdd546b974ffa45fa6715b9af7f5c00463e9d0f6ef9c95efe0c2"}, + {file = "boto3-1.35.85-py3-none-any.whl", hash = "sha256:f22678bdbdc91ca6022a45696284d236e1fbafa84ca3a69d108d4a155cdd823e"}, + {file = "boto3-1.35.85.tar.gz", hash = "sha256:6257cad97d92c2b5597aec6e5484b9cfed8c0c785297942ed37cfaf2dd0ec23c"}, ] [package.dependencies] -botocore = ">=1.35.84,<1.36.0" +botocore = ">=1.35.85,<1.36.0" jmespath = ">=0.7.1,<2.0.0" s3transfer = ">=0.10.0,<0.11.0" @@ -605,13 +605,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "botocore" -version = "1.35.84" +version = "1.35.85" description = "Low-level, data-driven core of boto 3." optional = false python-versions = ">=3.8" files = [ - {file = "botocore-1.35.84-py3-none-any.whl", hash = "sha256:b4dc2ac7f54ba959429e1debbd6c7c2fb2349baa1cd63803f0682f0773dbd077"}, - {file = "botocore-1.35.84.tar.gz", hash = "sha256:f86754882e04683e2e99a6a23377d0dd7f1fc2b2242844b2381dbe4dcd639301"}, + {file = "botocore-1.35.85-py3-none-any.whl", hash = "sha256:04c196905b0eebcb29f7594a9e4588772a5222deed1b381f54cab78d0f30e239"}, + {file = "botocore-1.35.85.tar.gz", hash = "sha256:5e7e8075e85427c9e0e6d15dcb7d13b3c843011b25d43981571fe1bfb3fd6985"}, ] [package.dependencies] @@ -726,6 +726,17 @@ files = [ [package.dependencies] pycparser = "*" +[[package]] +name = "cfgv" +version = "3.4.0" +description = "Validate configuration and produce human readable error messages." +optional = false +python-versions = ">=3.8" +files = [ + {file = "cfgv-3.4.0-py2.py3-none-any.whl", hash = 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"sha256:a0222f93f9a50d51b9962d88d16c2fc315e8223b756355e65eb9a1d5e1a8ae40"}, ] [package.dependencies] @@ -1380,6 +1391,17 @@ files = [ {file = "dirtyjson-1.0.8.tar.gz", hash = "sha256:90ca4a18f3ff30ce849d100dcf4a003953c79d3a2348ef056f1d9c22231a25fd"}, ] +[[package]] +name = "distlib" +version = "0.3.9" +description = "Distribution utilities" +optional = false +python-versions = "*" +files = [ + {file = "distlib-0.3.9-py2.py3-none-any.whl", hash = "sha256:47f8c22fd27c27e25a65601af709b38e4f0a45ea4fc2e710f65755fa8caaaf87"}, + {file = "distlib-0.3.9.tar.gz", hash = "sha256:a60f20dea646b8a33f3e7772f74dc0b2d0772d2837ee1342a00645c81edf9403"}, +] + [[package]] name = "distro" version = "1.9.0" @@ -2529,6 +2551,20 @@ files = [ {file = "hyperframe-6.0.1.tar.gz", hash = "sha256:ae510046231dc8e9ecb1a6586f63d2347bf4c8905914aa84ba585ae85f28a914"}, ] +[[package]] +name = "identify" +version = "2.6.3" +description = "File identification library for Python" +optional = false +python-versions = ">=3.9" +files = [ + {file = "identify-2.6.3-py2.py3-none-any.whl", hash = "sha256:9edba65473324c2ea9684b1f944fe3191db3345e50b6d04571d10ed164f8d7bd"}, + {file = "identify-2.6.3.tar.gz", hash = "sha256:62f5dae9b5fef52c84cc188514e9ea4f3f636b1d8799ab5ebc475471f9e47a02"}, +] + +[package.extras] +license = ["ukkonen"] + [[package]] name = "idna" version = "3.10" @@ -3055,13 +3091,13 @@ jupyter-server = ">=1.1.2" [[package]] name = "jupyter-server" -version = "2.14.2" +version = "2.15.0" description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications." optional = true -python-versions = ">=3.8" +python-versions = ">=3.9" files = [ - {file = "jupyter_server-2.14.2-py3-none-any.whl", hash = "sha256:47ff506127c2f7851a17bf4713434208fc490955d0e8632e95014a9a9afbeefd"}, - {file = "jupyter_server-2.14.2.tar.gz", hash = "sha256:66095021aa9638ced276c248b1d81862e4c50f292d575920bbe960de1c56b12b"}, + {file = "jupyter_server-2.15.0-py3-none-any.whl", hash = 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"sha256:3d71835c4c630db03a19757565046029e89ee96a4b06788892599d49bb3fc58a"}, + {file = "langchain_core-0.3.28-py3-none-any.whl", hash = "sha256:a02f81ca53a8eed757133797e5a602ca80c1324bbecb0c5d86ef7bd3d6625372"}, + {file = "langchain_core-0.3.28.tar.gz", hash = "sha256:407f7607e6b3c0ebfd6094da95d39b701e22e59966698ef126799782953e7f2c"}, ] [package.dependencies] @@ -4537,6 +4573,17 @@ plot = ["matplotlib"] tgrep = ["pyparsing"] twitter = ["twython"] +[[package]] +name = "nodeenv" +version = "1.9.1" +description = "Node.js virtual environment builder" +optional = false +python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" +files = [ + {file = "nodeenv-1.9.1-py2.py3-none-any.whl", hash = "sha256:ba11c9782d29c27c70ffbdda2d7415098754709be8a7056d79a737cd901155c9"}, + {file = "nodeenv-1.9.1.tar.gz", hash = "sha256:6ec12890a2dab7946721edbfbcd91f3319c6ccc9aec47be7c7e6b7011ee6645f"}, +] + [[package]] name = "notebook" version = "7.3.1" @@ -4964,8 +5011,8 @@ files = [ 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