A Python wrapper API for operating and working with the Neo4j Graph Data Science (GDS) library

Related tags

Databasegdsclient
Overview

gdsclient

This repo hosts the sources for gdsclient, a Python wrapper API for operating and working with the Neo4j Graph Data Science (GDS) library. gdsclient enables users to write pure Python code to project graphs, run algorithms, and define and use machine learning pipelines in GDS. The API is designed to mimic the GDS Cypher procedure API, but in Python code. It abstracts the necessary operation of the Neo4j Python Driver to offer a simpler surface.

Please leave any feedback as issues on this repository. Happy coding!

Installation

To build and install gdsclient from this repository, simply run the following command:

pip3 install .

Documentation

A minimal example of using gdsclient to connect to a Neo4j database and run GDS algorithms:

from neo4j import GraphDatabase
from gdsclient import Neo4jQueryRunner, GraphDataScience

# Set up driver and gds module
URI = "bolt://localhost:7687" # Override according to your setup
driver = GraphDatabase.driver(URI) # You might also have auth set up in your db
runner = Neo4jQueryRunner(driver)
gds = GraphDataScience(runner)

# Project your graph
graph = gds.graph.create("graph", "*", "*")

# Run the PageRank algorithm with custom configuration
gds.pageRank.write(graph, tolerance=0.5, writeProperty="pagerank")

For extensive documentation of all operations supported by GDS, please refer to the GDS Manual.

Extensive end-to-end examples in Jupyter ready-to-run notebooks can be found in the examples directory:

Acknowledgements

This work has been inspired by the great work done in the following libraries:

Contributing

The gdsclient project does not yet have contribution guidelines.

License

See LICENSE file. All content is copyright © Neo4j Sweden AB.

Comments
  • streamNodeProperty() doesn't work with gds.run_cypher() as I guess

    streamNodeProperty() doesn't work with gds.run_cypher() as I guess

    graphdatascience 1.3

    I tried a query like this:

    query = f'''
   call gds.graph.streamNodeProperty(
      'xxx',
      'xxxx',
      ['xxxxx']
   )
yield nodeId as id, propertyValue as degree
return id, degree limit 100
...
result = gds.run_cypher(query)

    => KeyError: 'graph_name'

    I figured out to make it work like this:

    query = f'''
   ...
'''
params = {
   'graph_name': 'xxx',
   'properties': 'xxxx',
   'entities'" ['xxxxx'],
   'config': ''
}
result = gds.run_cypher(query, params)

    => No error, but it returned all rows(not limited to 100) as nodeId and propertyValue(not renamed as id and degree)

    Other cypher queries works with gds.run_cypher(query) as expected.

    opened by MOSSupport 27
  • Add IMDB data and loaders

    Add IMDB data and loaders

    Co-authored-by: Adam Schill Collberg [email protected]

    Thank you for your contribution to the Graph Data Science Client project.

    Before submitting this PR, please read Contributing to the Neo4j Ecosystem.

    Make sure:

    • [x] You signed the Neo4j CLA (Contributor License Agreement) so that we are allowed to ship your code in our library
    • [x] Your contribution is covered by tests
    REVIEW OK - MERGE ON HOLD 
    opened by brs96 10
  • Skip defaults tests when targeting AuraDS

    Skip defaults tests when targeting AuraDS

    Since the "neo4j" user lacks auth there.

    Thank you for your contribution to the Graph Data Science Client project.

    Before submitting this PR, please read Contributing to the Neo4j Ecosystem.

    Make sure:

    • [ ] You signed the Neo4j CLA (Contributor License Agreement) so that we are allowed to ship your code in our library
    • [ ] Your contribution is covered by tests
    opened by adamnsch 5
  • gds.degree.stream not respecting orientation?

    gds.degree.stream not respecting orientation?

    Describe the bug I'm trying to reproduce a similar result that I would get in GDS.

    To Reproduce Cypher code:

    call gds.graph.project('xdc-test-search', ['Event','Search'], { HAS_SEARCH:{orientation:'REVERSE'}})
call gds.degree.stream('xdc-test-search')
YIELD nodeId, score
return gds.util.asNode(nodeId).search_name_1 as SearchTerm, score As NumberOfSearches
Order by NumberOfSearches Descending, SearchTerm Limit 10;

    The above returns the Search nodes.

    Python code:

    node_projection = ["Event","Search"]
relationship_projection = {"HAS_SEARCH": {"orientation": "REVERSE"}}
G, _ = gds.graph.project("xdc-test-search", node_projection, relationship_projection)
degree_stream = gds.degree.stream(G)

    degree.stream above is returning the node ids of the Event nodes (other side of direction), even if I were to use G = gds.graph.get("xdc-test-search") and use the projection created with cypher.

    I'm sure it's something I'm doing on my end :)

    graphdatascience library version: 1.3 GDS plugin version: 2.1.7 Python version: 3.9.12 Neo4j version: 4.4.10 Operating system: macOS 12.6

    The image below is what I would expect from the python approach. image

    opened by bSharpCyclist 4
  • Support multiple dataframe input to CE construct

    Support multiple dataframe input to CE construct

    Thank you for your contribution to the Graph Data Science Client project.

    Before submitting this PR, please read Contributing to the Neo4j Ecosystem.

    Make sure:

    • [x] You signed the Neo4j CLA (Contributor License Agreement) so that we are allowed to ship your code in our library
    • [x] Your contribution is covered by tests
    opened by adamnsch 3
  • Expose undirected rel types in graph.construct and load_cora

    Expose undirected rel types in graph.construct and load_cora

    Thank you for your contribution to the Graph Data Science Client project.

    Before submitting this PR, please read Contributing to the Neo4j Ecosystem.

    Make sure:

    • [x] You signed the Neo4j CLA (Contributor License Agreement) so that we are allowed to ship your code in our library
    • [x] Your contribution is covered by tests
    opened by FlorentinD 3
  • Test graph.construct with nan properties

    Test graph.construct with nan properties

    • Enable arrow test against AuraDS
    • Test NaN and null handling in graph.construct

    Thank you for your contribution to the Graph Data Science Client project.

    Before submitting this PR, please read Contributing to the Neo4j Ecosystem.

    Make sure:

    • [x] You signed the Neo4j CLA (Contributor License Agreement) so that we are allowed to ship your code in our library
    • [x] Your contribution is covered by tests
    opened by FlorentinD 3
  • Handle gds.alpha.graph.nodeLabel.write

    Handle gds.alpha.graph.nodeLabel.write

    Thank you for your contribution to the Graph Data Science Client project.

    Before submitting this PR, please read Contributing to the Neo4j Ecosystem.

    Make sure:

    • [ ] You signed the Neo4j CLA (Contributor License Agreement) so that we are allowed to ship your code in our library
    • [ ] Your contribution is covered by tests
    opened by vnickolov 3
  • Relationship Orientation during graph construction with dataframes

    Relationship Orientation during graph construction with dataframes

    Hi, I'd like to understand if it is possible to construct a graph from data frames without orientation so that I can have an undirected relationship. I see from the schema here https://neo4j.com/docs/graph-data-science/current/graph-project-apache-arrow/#arrow-send-relationships that source and destination are mandatory but there is no special column for orientation.

    opened by valerio-piccioni 3
  • Add mapping for `gds.alpha.triangles`

    Add mapping for `gds.alpha.triangles`

    Thank you for your contribution to the Graph Data Science Client project.

    Before submitting this PR, please read Contributing to the Neo4j Ecosystem.

    Make sure:

    • [x] You signed the Neo4j CLA (Contributor License Agreement) so that we are allowed to ship your code in our library
    • [x] Your contribution is covered by tests
    opened by FlorentinD 3
  • Set target database within initial constructor call

    Set target database within initial constructor call

    Is your feature request related to a problem? Please describe. I would like to set the database I plan to use upon initializing my gds object GraphDataScience(URI, auth=creds, database='my-db') rather than having to call gds.set_database("my-db"). This would purely be a simple convenience to save a line of code.

    Describe the solution you would like Allow the setting of the database within the constructor call

    opened by seankrobinson 3
  • WIP: Hashgnn example notebook

    WIP: Hashgnn example notebook

    Based on #224

    Thank you for your contribution to the Graph Data Science Client project.

    Before submitting this PR, please read Contributing to the Neo4j Ecosystem.

    Make sure:

    • [ ] You signed the Neo4j CLA (Contributor License Agreement) so that we are allowed to ship your code in our library
    • [ ] Your contribution is covered by tests
    opened by adamnsch 1
  • Add convenience methods for loading OGB graphs

    Add convenience methods for loading OGB graphs

    Thank you for your contribution to the Graph Data Science Client project.

    Before submitting this PR, please read Contributing to the Neo4j Ecosystem.

    Make sure:

    • [ ] You signed the Neo4j CLA (Contributor License Agreement) so that we are allowed to ship your code in our library
    • [ ] Your contribution is covered by tests
    opened by adamnsch 1
  • WIP: Update query runner interface

    WIP: Update query runner interface

    Thank you for your contribution to the Graph Data Science Client project.

    Before submitting this PR, please read Contributing to the Neo4j Ecosystem.

    Make sure:

    • [ ] You signed the Neo4j CLA (Contributor License Agreement) so that we are allowed to ship your code in our library
    • [ ] Your contribution is covered by tests
    opened by adamnsch 1
Releases(1.5)

  • 1.5(Nov 2, 2022)

    We are happy to announce the release of graphdatascience, the GDS Python client, version 1.5! It is published to PyPI!

    Changes:

    • Fixed a bug where the client could not connect to the server when the default db was set in the GraphDataScience constructor.
    • For GDS admin users, gds.graph.get is now able to resolve graph names into Graph objects of other users graph projections.
    • Add support for gds.alpha.triangles.
    • Support calling gds.alpha.userLog to access hints and warnings for the recently run operations.
    • Add support for gds.alpha.backup and gds.alpha.restore.
    • Add support for gds.alpha.config.defaults.set and gds.alpha.config.defaults.list.

    The release can be pip installed with pip install graphdatascience==1.5.

    Source code(tar.gz)
    Source code(zip)

  • 1.4(Sep 30, 2022)

    We are happy to announce the release of graphdatascience, the GDS Python client, version 1.4! It is published to PyPI!

    Highlights:

    • The DataFrame returned by gds.beta.graph.relationships.stream now has a convenience method called by_rel_type.
    • Added a new optional string parameter database to GraphDataScience.run_cypher for overriding which database to target.
    • Added new method gds.graph.load_cora to load the CORA dataset into GDS.
    • Added a new optional string parameter database to the GraphDataScience constructor for specifying the targeted database.
    • Fix resolving Node regression pipelines created via gds.alpha.pipeline.nodeRegression.create.
    • Fix resolving Node regression models created via gds.alpha.pipeline.nodeRegression.train.
    • Fix an issue where run_cypher did not execute Cypher correctly in some edge cases.

    A full list of changes can be found in the changelog.

    The release can be pip installed with pip install graphdatascience==1.4.

    Source code(tar.gz)
    Source code(zip)

  • 1.3(Aug 23, 2022)

    We are happy to announce the release of graphdatascience, the GDS Python client, version 1.3! It is published to PyPI!

    Highlights:

    • New versioning scheme using only two numbers
    • Add MLP training method addMLP to link prediction and node classification pipelines.
    • Add support for new graph catalog API endpoints in GDS >= 2.2.0.
    • Add support for random walk with restarts sampling procedure.
    • Add support for graph property endpoints in GDS >= 2.2.0.
    • Add Arrow Flight specific parameters to the GraphDataScience constructor:
      • arrow_tls_root_certs
      • arrow_disable_server_verification
    • Add support for new stream graph relationships endpoint.
    • Dropped support for Python 3.6.

    A full list of changes can be found in the changelog.

    The release can be pip installed with pip install graphdatascience==1.3.

    Source code(tar.gz)
    Source code(zip)

  • 1.3.0a1(Aug 11, 2022)

    The first alpha release of version 1.3.0 of graphdatascience, the GDS Python client, has been published to PyPI!

    Highlights:

    • Add MLP training method addMLP to link prediction and node classification pipelines.
    • Add support for new graph catalog API endpoints in GDS >= 2.2.0.
    • Add support for random walk with restarts sampling procedure.
    • Add support for graph property endpoints in GDS >= 2.2.0.
    • Add Arrow Flight specific parameters to the GraphDataScience constructor:
      • arrow_tls_root_certs
      • arrow_disable_server_verification
    • Add support for new stream graph relationships endpoint.
    • Dropped support for Python 3.6.

    A full list of changes can be found in the changelog.

    The release can be pip installed with pip install graphdatascience==1.3.0a1.

    Source code(tar.gz)
    Source code(zip)

  • 1.2.0(Jul 5, 2022)

    Version 1.2.0 of graphdatascience, the GDS Python client, has been published to PyPI!

    Included are bug fixes for:

    • The separate_property_columns=True option of gds.graph.streamNodeProperties did not handle list node properties correctly.
    • An irrelevant warning was shown when creating a GraphDataScience object targeting an AuraDS instance with GDS server version >= 2.1.0.
    • Calling gds.alpha.graph.construct targeting an AuraDS instance would raise an exception.

    The release can be pip installed with pip install graphdatascience==1.2.0.

    Source code(tar.gz)
    Source code(zip)

  • 1.1.0(Jun 9, 2022)

    Version 1.1.0 of graphdatascience, the GDS Python client, has been published to PyPI!

    Changes highlights:

    • Support for GDS library version 2.1
    • Additional and improved convenience functionality on the Graph object
    • Supporting GDS Apache Arrow capabilities for graph catalog stream procedures
    • New method gds.alpha.graph.construct for loading a graph directly into GDS from client side pandas DataFrames
      • Greatly sped up by Apache Arrow if enabled

    A full list of changes can be found in the changelog.

    The release can be pip installed with pip install graphdatascience==1.1.0.

    Source code(tar.gz)
    Source code(zip)

  • 1.1.0rc1(Jun 2, 2022)

    The first release candidate of version 1.1.0 of graphdatascience, the GDS Python client, has been published to PyPI!

    Highlights:

    • Added support for auto tuning for machine learning pipelines.
    • Added support for providing ranges as length two tuples to addLogisticRegression and addRandomForest.
    • Added support for new GDS library 2.1 signature of gds.graph.removeNodeProperties.
    • Added support for new function gds.close which calls .close() on a GraphDataScience object's underlying Neo4j driver.
    • Added new method gds.alpha.graph.construct to construct a GDS graph from pandas DataFrames. When running against a GDS library with its Apache Arrow server enabled it will be a lot faster.
    • Added support for new nodeRegression pipelines.
    • New convenience methods on the Graph object.

    A full list of changes can be found in the changelog.

    The release can be pip installed with pip install graphdatascience==1.1.0rc1.

    Source code(tar.gz)
    Source code(zip)

  • 1.1.0a2(May 19, 2022)

    The second alpha release of version 1.1.0 of graphdatascience, the GDS Python client, has been published to PyPI!

    Highlights:

    • Added support for new configureAutoTuning method on NC and LP pipelines.
    • Added support for providing ranges as length two tuples to addLogisticRegression and addRandomForest.
    • Added new method auto_tuning_config to NC and LP pipelines for querying a pipelines auto-tuning config.
    • Added support for new GDS library 2.1 signature of gds.graph.removeNodeProperties.
    • Added support for new function gds.close which calls .close() on a GraphDataScience object's underlying Neo4j driver.
    • Added new method gds.alpha.graph.construct to construct a GDS graph from pandas DataFrames, which works if the GDS Flight server is enabled.
    • Added new function gds.database which can be used to see which database is currently being targeted.
    • Added support for new nodeRegression pipelines.

    The release can be pip installed with pip install graphdatascience==1.1.0a2.

    Source code(tar.gz)
    Source code(zip)

  • 1.1.0a1(May 6, 2022)

    The alpha release of version 1.1.0 of graphdatascience, the GDS Python client, has been published to PyPI!

    Highlights:

    • Added support for new configureAutoTuning method on NC and LP pipelines.
    • Added support for providing ranges as length two tuples to addLogisticRegression and addRandomForest.
    • Added support for new function gds.close which calls .close() on a GraphDataScience object's underlying Neo4j driver.
    • Added new method gds.alpha.graph.construct to construct a GDS graph from pandas DataFrames, which works if the GDS Flight server is enabled.
    • Added new function gds.database which can be used to see which database is currently being targeted.
    • The functions gds.graph.streamNodeProperty and gds.graph.streamRelationshipProperty can leverage the Arrow Flight server of GDS to improve throughput.

    The release can be pip installed with pip install graphdatascience==1.1.0a1.

    Source code(tar.gz)
    Source code(zip)

  • 1.0.0(Mar 24, 2022)

    The first official major release, 1.0.0, of graphdatascience, the GDS Python client, has been published to PyPI!

    Highlights:

    • Replaced all dict return types with pandas Series.
    • Replaced all list[dict,...] return types with pandas DataFrame.
    • Replaced NC and LP training pipelines method configureParams by new methods addLogisticRegression and addRandomForest.
    • All procedures of the GDS Pipeline catalog are supported.
    • The NC and LP training pipelines support estimating train via a train_estimate method.
    • All ML models support estimating predict via predict_[mode]_estimate methods.
    • Removed support for GDS 1.x graph.create syntax.

    Read more in the changelog.

    The release can be pip installed with pip install graphdatascience==1.0.0.

    Source code(tar.gz)
    Source code(zip)

  • 0.1.0(Feb 25, 2022)

    A new release 0.1.0 of graphdatascience, the GDS Python client, has been published at PyPI!

    Highlights:

    • When connecting to AuraDS, a specific user-agent will be set indicating that the graphdatascience client is used.
    • The methods of NCTrainingPipeline and LPTrainingPipeline for building the pipelines now return metadata from the underlying Cypher procedures called.
    • Methods creating Graph objects now additionally return the metadata from the underlying Cypher procedures called.
    • Methods creating Model objects now additionally return the metadata from the underlying Cypher procedures called.

    Read more in the changelog.

    The release can be pip installed with pip install graphdatascience==0.1.0.

    Source code(tar.gz)
    Source code(zip)

  • 0.0.9(Feb 3, 2022)

  • 0.0.8(Jan 24, 2022)

    A new release 0.0.8 of graphdatascience, which is the new and final name of the GDS Python client, formerly called gdsclient , has been published at PyPI!

    Highlights:

    • new library name!
    • new source repository (this repo)
    • support for all utility functions
    • support for all Similarity functions
    • simplified interface to construct GDS reference object (hidden driver)
    • simplified interface to run Cypher queries (hidden query runner)

    The release can be pip installed with pip install graphdatascience==0.0.8.

    Source code(tar.gz)
    Source code(zip)
Owner
Neo Technology
Neo Technology
GitHub Repository
Python function to extract all the rows from a SQLite database file while iterating over its bytes, such as while downloading it

Python function to extract all the rows from a SQLite database file while iterating over its bytes, such as while downloading it

Department for International Trade 16 Nov 09, 2022
securedb is a fast and lightweight Python framework to easily interact with JSON-based encrypted databases.

securedb securedb is a Python framework that lets you work with encrypted JSON databases. Features: newkey() to generate an encryption key write(key,

Filippo Romani 2 Nov 23, 2022
PathfinderMonsterDatabase - A database of all monsters in Pathfinder 1e, created by parsing aonprd.com

PathfinderMonsterDatabase A database of all monsters in Pathfinder 1e, created by parsing aonprd.com Setup Run the following line to install all requi

Yoni Lerner 11 Jun 12, 2022
Oh-My-PickleDB is an open source key-value store using Python's json module.

OH-MY-PICKLEDB oh-my-pickleDB is a lightweight, fast, and intuitive data manager written in python 📝 Table of Contents About Getting Started Deployme

Adrián Toral 6 Feb 20, 2022
EmployeeDB - Advanced Redis search functionalities on Python applied on an Employee management backend app

EmployeeDB - Advanced Redis search functionalities on Python applied on an Employee management backend app

Ahmad Bazzi 58 Oct 10, 2022
HTTP graph database built in Python 3

KiwiDB HTTP graph database built in Python 3. Reference Format References are strings in the format: { JanCraft 1 Dec 17, 2021

Shelf DB is a tiny document database for Python to stores documents or JSON-like data

Shelf DB Introduction Shelf DB is a tiny document database for Python to stores documents or JSON-like data. Get it $ pip install shelfdb shelfquery S

Um Nontasuwan 35 Nov 03, 2022
A simple GUI that interacts with a database to keep track of a collection of US coins.

CoinCollectorGUI A simple gui designed to interact with a database. The goal of the database is to make keeping track of collected coins simple. The G

Builder212 1 Nov 09, 2021
ClutterDB - Extremely simple JSON database made for infrequent changes which behaves like a dict

extremely simple JSON database made for infrequent changes which behaves like a dict this was made for ClutterBot

Clutter Development 1 Jan 12, 2022
A Painless Simple Way To Create Schema and Do Database Operations Quickly In Python

PainlessDB - Taking Your Pain away to the moon 🚀 Contribute · Community · Documentation 🎫 Introduction : PainlessDB is a Python-based free and open-

Aiden Ellis 3 Jul 15, 2022
Codeqlcompile - 自动反编译闭源应用，创建codeql数据库

codeql_compile 自动反编译闭源应用，创建codeql数据库 准备 首先下载ecj.jar和idea提供反编译的java-decompiler.ja

236 Jan 05, 2023
Simple embedded in memory json database

dbj dbj is a simple embedded in memory json database. It is easy to use, fast and has a simple query language. The code is fully documented, tested an

Pedro Gonring 25 Aug 12, 2022
LaikaDB, banco de dados para projetos simples.

LaikaDB LaikaDB é um banco de dados noSQL para uso local e simples, onde você pode realizar gravações e leituras de forma eficiente e simples. Todos o

Jaedson Silva 0 Jun 24, 2022
Decentralised graph database management system

Decentralised graph database management system To get started clone the repo, and run the command below. python3 database.py Now, create a new termina

Omkar Patil 2 Apr 18, 2022
Tiny local JSON database for Python.

Pylowdb Simple to use local JSON database 🦉 # This is pure python, not specific to pylowdb ;) db.data['posts'] = ({ 'id': 1, 'title': 'pylowdb is awe

Hussein Sarea 3 Jan 26, 2022
Metrics-advisor - Analyze reshaped metrics from TiDB cluster Prometheus and give some advice about anomalies and correlation.

metrics-advisor Analyze reshaped metrics from TiDB cluster Prometheus and give some advice about anomalies and correlation. Team freedeaths mashenjun

3 Jan 07, 2022
Enfilade: Tool to Detect Infections in MongoDB Instances

Enfilade: Tool to Detect Infections in MongoDB Instances

Aditya K Sood 7 Feb 21, 2022
ChaozzDBPy - A python implementation based on the original ChaozzDB from Chaozznl with some new features

ChaozzDBPy About ChaozzDBPy is a python implementation based on the original Cha

Igor Iglesias 1 May 25, 2022
A NoSQL database made in python.

CookieDB A NoSQL database made in python.

cookie 1 Nov 30, 2022
Connect Django Project to PostgreSQL

An application for learning things with creating quizzes and flashcards.Django, PostgresSQL are used for this project.

Cena Ashoori 1 Jan 25, 2022