Getting started with the CODEBASE



Greetings,

Our second meeting was scheduled for 21st May, but it was father's day in Germany and national holiday too. We talked a bit about father's day (me and Andreas), it was really a nice chat, and we decided to meet on the next day. I was asked last time to start with the code and was also assigned an issue to solve. The issue was quite simple, but it required agreement from various different communities that are using the JSON format for SBML models. We were not able to reach upon a common agreement, and hence I was not able to submit the PR corresponding to that. I solved it, though, on my local system, and during the meeting, we went through it once. Mentors suggested a few modifications, and I changed the code accordingly.

During the meeting, we selected one more issue to be solved by me in the following week and Matthias assigned me a few more tasks like pulling out the JSON schema (which was initially present inside json.py) and put it in an independent file so that other users can easily find it out and we can also work upon the jsoc_schema_v2, which is the main task of this project, and put both the schemas inside the same directory. We agreed that we should have version 2 for JSON schema because BiGG and other few tools depend heavily on JSON schema and changing the same schema can lead to breaking of things for them. So most of the time in the meeting, we discussed how should we proceed with the new changes so that things don't break for the tools relying upon json_schema_v1, and we agreed that we will try to make things as much backward compatible as possible, and bring backward-incompatible changes only when we have no choice left to correctly represent the model's component. We also discussed how should we make our discussion as open as possible so that communities of other tools depending upon the schema can participate and provide their suggestions. We decided to post an introductory mail on the mailing list of these communities to let them know about the project and invited them for the discussion going openly on Github for JSON related issues.

At last, I lost the internet connection when we were summarising the things. So we summarised it on our Slack discussion channel, thanks to the mentors for being very helpful and understanding. It was overall a good meeting.

Thanks for the reading.
See you next week.
Location: Rewari, Haryana, India

Comments

Post a Comment

Popular posts from this blog

The Week 12

Greetings, The last meeting was not too long, it ended in approximately 35 minutes. The mentors first went through the JSON schema-V2 to see the definitions of features added to JSON like group, user defined constraint, annotation etc. They suggested a few modifications like adding pattern properties for datetime and Id. The schema was otherwise all fine. After this, we started discussing the helper function for adding user defined constraints. I had implemented this method by parsing string by my own and extracting information out of it, which lead to various restrictions on defining the constraint. But Matthias suggested that the best way to handle expression inside a string is by using the Abstract Syntax Tree (AST). By using the tree, we can define our constraint expression more freely, with just a few restrictions. So I shall add this support using AST. The other important thing that we discussed was the JSON validation function. Currently, I was using the inbuilt JSON validation
Read more

The Week 13

 Greetings, Almost towards the end, we didn't have anything new to discuss in the last meeting, except the identifier (id) of COBRA model components. The 'id' of an SBML component is an important attribute and should not be manipulated. COBRApy, however, allows the user to pass a replacement function to manipulate the component ids. It also asks the user to pass a reverse replacement function to modify the ids while writing the model back. We discussed this thing and both of the mentors were having an opinion that ids should not be manipulated at all, it can create problems. Currently, the COBRApy writes the same manipulated ids in the JSON format, and if we apply the defined id pattern properties of SBML to these manipulated ids, these ids may get failed. So at the time of reading/writing the model from JSON, I have used the default replacement functions to fix the ids. Another thing which we discussed was the things which COBRApy communities have listed to port the code f
Read more

The Final Report

Image
Greetings everyone, I am glad to write the final report for the project "SBML-JSON converter and SBML scheme". It's been three months now since I am working on this project and about 5-6 months since I am involved in it. And I must say that I have learned quite a lot by now, thanks to Matthias and Andreas for all their help. It had been a very nice journey with both of them, marked by daily chats and weekly meetings.  We have actually covered all that we claimed in the initial proposal , and the complete code has been submitted to COBRApy . Two of our pull requests have got merged, one is under review and will get merged soon, and one may require some time because it contains some functionalities which will be used only after  libsbml (the interfacing library between SBML and COBRApy) incorporate fbc-v3 package.  All the pull requests submitted so far are summarised in this spreadsheet . Here is a summary of the work done in this project: The JSON schema v1 had some i
Read more