Project Report, GSoC, 2019

INTRODUCTION

Hi all!

This project "Validation of Spatial Systems Biology Models in Java(TM)" was done as a part of the Google Summer of Code program, with the organization N.R.N.B.

My mentors for this project were Nicolas Rodriguez and Thomas M. Hamm, along with support and valuable suggestions from Lucian P. Smith, Jun.-Prof. Dr Andreas Draeger and Prof. Akira Funahashi.

The basic overview of the program and the project can be found in my introductory blog: 

https://gsoc19-spatial.blogspot.com/2019/05/starting-google-summer-of-code-2019.html.

For the in-depth background of the project, and detailed understanding of the working of the offline validator the readers are suggested to go through my proposal for the Google Summer of Code, 2019: 

https://drive.google.com/open?id=1Vail5-JzdCM13t2cGwD4UK08mne1xkRo.

WORK DETAILS

My GitHub fork for this project is https://github.com/bhavyejain/jsbml.

In the duration of this project, I implemented constraint classes for the spatial package and fixed issues with the existing spatial classes, consequently bringing most of them to the latest specification. My work in this repository is reflected in the following extension: https://github.com/bhavyejain/jsbml/tree/master/extensions/spatial/src/org/sbml/jsbml.

I made a pull request after implementing 2-3 constraint classes at a time so that it is easy to review the code from time to time. The test files of many classes also required corrections. The modified test files were uploaded to a master google drive and the corrections listed in a document for further reference. All the merged contributions have been compiled and tested before making the merge.

All of my commits can be viewed here:

https://github.com/sbmlteam/jsbml/commits?author=bhavyejain

Except for the new rules under construction, all my pull requests have been merged with the master branch of the product, and can be viewed here:

https://github.com/sbmlteam/jsbml/pulls?q=is%3Apr+author%3Abhavyejain+is%3Aclosed

The ongoing work is reflected in the open pull requests which will be merged as and when new rules are added successfully with simultaneous creation of test files. The open pull requests (if any active at the moment) authored by me can be viewed here:

https://github.com/sbmlteam/jsbml/pulls/bhavyejain

DELIVERABLES

All validation and consistency rules provided in the Spatial Processes SBML Level 3 Package Specification have been implemented and tested.

Existing source code has been updated to meet the latest requirements of the validator and the specification.

New code has been tested successfully on various test files.

CURRENT STATUS AND FURTHER DEVELOPMENT

Currently, work is being done to manually add more validation rules. Additional rules for around 13 classes have been identified and finalised, with more to be proposed in coming days. The procedure to add such rules has been decided upon and work is expected to proceed at a steady pace. Post final evaluation, I shall work upon completing the validation for spatial package, and include as many syntactic and possibly semantic error checks to make the validator robust. 

#10 Final Phase of Google Summer of Code, 2019!

Greeting everyone!

In the last week, the offline validator for spatial was completed as per the existing specification! The conflicts and errors (both semantic and syntactic) have been resolved to best of my knowledge, and the system seems to work as it should for the time being! In the complete process, I was able to bring many classes up to the latest specification and added (and fixed) some code in the SpatialParser as well.

The SpatialPoints class now extends AbstractSpatialNamedSBase to include the 'id' and 'name' attributes.

The issue with the SpatialParser where it was adding attributes to the UNKOWN_XML multiple times (duplicates) has been resolved. A processEndDocument() method has been added to handle missing SpatialReactionPlugin extension for the Reaction element.

Work has started on adding more rules by hand. Rather, the progress is good, and I am already in the process of implementing some additional rules. I figured out some rules by going through the specification and shared a Google Doc with my mentors. They helped me finalize the rules and give them a proper language. We started the numbering of the new rules from 50, example: 1220650 (In general, 12XXX50, 12XXX51 and so on). This was done to accommodate any future changes in the specification and the rules that the automatic generator would then produce. As of now, we have new rules for around 12 classes, with more to be added with time. Hopefully, the rules can be reflected in the upcoming draft of the spatial specification. 

Since most of the work is already done, the updated from here on could be really slow. Further work requires some discussion and finalization of things before starting to implement them. Nevertheless, all the work can be seen on the GitHub repository itself. 

I'll be posing the final report soon! :-D

Till next time,

Cheers!