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 function (using the defined JSON schema), which throws error immediately when it encounters one. But in COBRApy, when validation of SBML model is performed, all the errors encountered in the model are put in a list and then the list is returned. So, we thought that it will be better to have a similar implementation for JSON too. Hence, I will be implementing this validation function by my own.

One more thing that Matthias told was that COBRApy community are going to drop support for python 2. So we shall also remove any python 2 usage in our implemented features. That was all we planned for this week.

Thanks for reading. See you next week.