GSoC 2020 project idea 18: Pyxnat: Enhanced interfacing with a neuroimaging data management platform in Python

The aim of this GSoC project is to extend the existing Python library (pyxnat). Pyxnat is an open source Python library which has been developed by the neuroimaging community to provide a programmatic interface with the widely-deployed data management platform XNAT. The project will cover the support of basic database operations i.e. collecting subject information or image collections to more advanced features including querying processing outputs/biomarker data or launching processing pipelines. Critical importance will be given to good development practices including version control, unit tests, code quality and documentation writing. Final outcomes of the project will impact on the open source library.

Required/desired skills:

  • Proficiency in Python and Unix-based systems
  • Familiar with databases and network programming
  • Comfortable with Git-based collaborative software development culture
  • Concerned with good practices in software development and open source software

We welcome candidates without all the skills, but they should show a strong motivation to acquire them.

The GSoC student will develop their skills working with Python (and/or web development for project 19) and with modern software testing tools for improved reproducibility and robustness of code, while learning about data analysis in neuroimaging. The interested candidate will also learn about code distribution and related matters (linting, testing, packaging, …)

Mentors: Greg Operto (goperto@barcelonabeta.org) and Jordi Huguet (jhuguet@barcelonabeta.org), BarcelonaBeta Brain Research Center, Spain

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@goperto @jhuguetn have began working on the above skills, please let me know if I can start contributing to the project in any way .

Thank you.

All interested candidates are invited to clone the code repository and run the suite of tests for continuous integration using nosetests.

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Hi everyone,

This is Agha Saad Fraz, I am pursuing Software Engineering and I am interested in applying to INCF for GSoC’20. I have seen the ideas, The idea I am interested in is:

Pyxnat: Enhanced interfacing with a neuroimaging data management platform in Python

I have selected this idea as this is aligned with my interests and my skills. I have been developing software for more than a year. I use python and its libraries for that. and I think this project would be the best thing for me to learn more about python, its libraries, and neuroimaging.

Guide me on how to get started. Thanks :slight_smile:

Hi @goperto @jhuguetn. I have cloned and followed the steps and tried to run nosetests command and got this and I am not sure if this is correct or not?

Hi @malin, @goperto, I wanted to ask if this project is still available for GSoC’20?

Hi @AghaSaad04,

Thank you for your interest in our project. Project is indeed still available, so if you are interested I encourage you to apply.

Your snapshot shows 23% coverage, it does not seem correct. Tip: check for Internet access issues since it looks like you might be running nose offline thus skipping most of the tests which require access to an open XNAT database.

If you get stuck at some point, please come back to us with specific questions/doubts based on the error messages/traces you might get. Contact us by email directly if you need a quick reply.

Good luck with it.

Regards,
Jordi

@jhuguetn I tried to run the docker-compose up command but getting this error:

Though I have given the permission to /var/lib/postgresql folder

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