Available Packages

GeneWeaver is a collection of python packages that are used to build the GeneWeaver web application.

These packages are also available for use in other projects. The packages are:

• geneweaver-core: Foundational shared functionality for the GeneWeaver project.
• geneweaver-client: A command line interface interacting with GeneWeaver ReST APIs.
• geneweaver-testing: GeneWeaver's shared automated tests.
• geneweaver-tools: A framework for creating analysis tools for the GeneWeaver project.
• geneweaver-boolean-algebra: A package for performing boolean algebra operations on GeneWeaver data.
• geneweaver-db: A package for interacting with the GeneWeaver database.

Development has moved to the GeneWeaver monorepo

geneweaver-core, geneweaver-db, geneweaver-client and geneweaver-tools are now developed in the GeneWeaver monorepo under packages/. The standalone repositories for geneweaver-db, geneweaver-client, geneweaver-tools, geneweaver-testing and geneweaver-boolean-algebra are archived. The PyPI releases above are still installable, but the monorepo is the source of truth and the published releases may lag it.

This matters most for geneweaver-tools: the published package contains the AbstractTool framework only. The GeneWeaver analysis tools themselves (BooleanAlgebra, Combine, DBSCAN, HyperGeometric, JaccardClustering, JaccardSimilarity, MSET, PhenomeMap, UpSet) live in the monorepo at packages/tools and have not been published to PyPI.

Package Relationships

The following diagram shows the relationships between the packages.

graph LR
    G[GeneWeaver Application]
    D[geneweaver-db]
    T[geneweaver-tools]
    BA[geneweaver-boolean-algebra]
    A[geneweaver-core]
    E[geneweaver-testing]
    C[geneweaver-client]
    T & E & A --> BA --> G
    E --> A & D --> G
    E & A --> C
    E --> G & T
    A --> D

The client consumes the ReST APIs provided by the GeneWeaver application.

sequenceDiagram
    geneweaver-client ->>+ GeneWeaver Application: ReST API Call
    GeneWeaver Application ->>+ Database: Database Query
    Database -->>- GeneWeaver Application: Database Response
    GeneWeaver Application -->>- geneweaver-client: ReST API Response

Next Steps

Researchers 🔬Educators & Students 📚Software Developers 💻

Researchers should consider using the GeneWeaver web application to upload and analyze their data. The web application is available at geneweaver.org.

Sometimes, it might be useful to use the command line interface to automate the uploading or downloading of data to/from the web application. This can be done using the python package called geneweaver-client, which can either be installed directly

pip install geneweaver-client

or into a virtual environment

python -m venv my-venv
source my-venv/bin/activate
pip install geneweaver-client

Coming Soon

Documentation for educators and students is coming soon.

Coming Soon

Documentation for software developers is coming soon.