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fix: Resolve issue with Kuzu graph database persistence on our local … (#1490)

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…Docker

<!-- .github/pull_request_template.md -->

## Description
Resolves issue with kuzu graph data persistence for Cognee backend
docker

## Type of Change
<!-- Please check the relevant option -->
- [x] Bug fix (non-breaking change that fixes an issue)
- [ ] New feature (non-breaking change that adds functionality)
- [ ] Breaking change (fix or feature that would cause existing
functionality to change)
- [ ] Documentation update
- [ ] Code refactoring
- [ ] Performance improvement
- [ ] Other (please specify):

## Pre-submission Checklist
<!-- Please check all boxes that apply before submitting your PR -->
- [ ] **I have tested my changes thoroughly before submitting this PR**
- [ ] **This PR contains minimal changes necessary to address the
issue/feature**
- [ ] My code follows the project's coding standards and style
guidelines
- [ ] I have added tests that prove my fix is effective or that my
feature works
- [ ] I have added necessary documentation (if applicable)
- [ ] All new and existing tests pass
- [ ] I have searched existing PRs to ensure this change hasn't been
submitted already
- [ ] I have linked any relevant issues in the description
- [ ] My commits have clear and descriptive messages

## DCO Affirmation
I affirm that all code in every commit of this pull request conforms to
the terms of the Topoteretes Developer Certificate of Origin.

---------

Co-authored-by: Boris <boris@topoteretes.com>
This commit is contained in:
Igor Ilic 2025-10-07 20:38:43 +02:00 • committed by GitHub
parent f81d427466
commit e7709f7bd0
No known key found for this signature in database
GPG key ID: B5690EEEBB952194
5 changed files with 90 additions and 70 deletions
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1
Dockerfile
View file

@ -22,6 +22,7 @@ RUN apt-get update && apt-get install -y \
libpq-dev \ libpq-dev \
git \ git \
curl \ curl \
cmake \
clang \ clang \
build-essential \ build-essential \
&& rm -rf /var/lib/apt/lists/* && rm -rf /var/lib/apt/lists/*

28
cognee/infrastructure/databases/graph/kuzu/adapter.py
View file

@ -48,6 +48,29 @@ class KuzuAdapter(GraphDBInterface):
def _initialize_connection(self) -> None: def _initialize_connection(self) -> None:
"""Initialize the Kuzu database connection and schema.""" """Initialize the Kuzu database connection and schema."""
def _install_json_extension():
"""
Function handles installing of the json extension for the current Kuzu version.
This has to be done with an empty graph db before connecting to an existing database otherwise
missing json extension errors will be raised.
"""
try:
with tempfile.NamedTemporaryFile(mode="w", delete=True) as temp_file:
temp_graph_file = temp_file.name
tmp_db = Database(
temp_graph_file,
buffer_pool_size=2048 * 1024 * 1024, # 2048MB buffer pool
max_db_size=4096 * 1024 * 1024,
)
tmp_db.init_database()
connection = Connection(tmp_db)
connection.execute("INSTALL JSON;")
except Exception as e:
logger.info(f"JSON extension already installed or not needed: {e}")
_install_json_extension()
try: try:
if "s3://" in self.db_path: if "s3://" in self.db_path:
with tempfile.NamedTemporaryFile(mode="w", delete=False) as temp_file: with tempfile.NamedTemporaryFile(mode="w", delete=False) as temp_file:
@ -109,11 +132,6 @@ class KuzuAdapter(GraphDBInterface):
self.db.init_database() self.db.init_database()
self.connection = Connection(self.db) self.connection = Connection(self.db)
try:
self.connection.execute("INSTALL JSON;")
except Exception as e:
logger.info(f"JSON extension already installed or not needed: {e}")
try: try:
self.connection.execute("LOAD EXTENSION JSON;") self.connection.execute("LOAD EXTENSION JSON;")
logger.info("Loaded JSON extension") logger.info("Loaded JSON extension")

79
poetry.lock generated
View file

@ -4414,49 +4414,50 @@ adal = ["adal (>=1.0.2)"]
[[package]] [[package]]
name = "kuzu" name = "kuzu"
version = "0.11.0" version = "0.11.2"
description = "Highly scalable, extremely fast, easy-to-use embeddable graph database" description = "Highly scalable, extremely fast, easy-to-use embeddable graph database"
optional = false optional = false
python-versions = "*" python-versions = "*"
groups = ["main"] groups = ["main"]
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{file = "kuzu-0.11.2.tar.gz", hash = "sha256:9f224ec218ab165a18acaea903695779780d70335baf402d9b7f59ba389db0bd"},
] ]
[[package]] [[package]]
@ -12776,4 +12777,4 @@ posthog = ["posthog"]
[metadata] [metadata]
lock-version = "2.1" lock-version = "2.1"
python-versions = ">=3.10,<=3.13" python-versions = ">=3.10,<=3.13"
content-hash = "c76267fe685339b5b5665342c81850a3e891cadaf760178bf3b04058f35b1014" content-hash = "874553043d02f0974213e040262fe0b1abf61b3c0be47c5e6d8e2db718f94ea2"

2
pyproject.toml
View file

@ -48,7 +48,7 @@ dependencies = [
"pympler>=1.1,<2.0.0", "pympler>=1.1,<2.0.0",
"onnxruntime<=1.22.1", "onnxruntime<=1.22.1",
"pylance>=0.22.0,<=0.36.0", "pylance>=0.22.0,<=0.36.0",
"kuzu (==0.11.0)", "kuzu (==0.11.2)",
"python-magic-bin<0.5 ; platform_system == 'Windows'", # Only needed for Windows "python-magic-bin<0.5 ; platform_system == 'Windows'", # Only needed for Windows
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50
uv.lock generated
View file

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