converting an model.xml to model.json with cobra

Hi,

I have build a model in Python in xml format and want to convert it to a json format so i can use it for visualization with Escher. I loaded the xml model in Matlab but I can only get it converted into a .mat file and get an error when I want to get json format model. I tried the following:

1. outmodel = writeCbModel(model, 'format','json', 'fileName', 'TestModel.json')

Error using writeCbModel (line 229)

Unknown file format

Error in MBA_testfile (line 35)

outmodel = writeCbModel(model, 'format','json', 'fileName', 'TestModel.json')

2. cobra.io.json.to_json(model)

Unable to resolve the name cobra.io.json.to_json.

Error in MBA_testfile (line 20)

cobra.io.json.to_json(model)

Answer 1

[Ishan Gupta]

MATLAB has a built in function called “jsonencode()” to convert a struct to a JSON string.

Also, when writing into a file using “fprintf()" function the file Identifier which you created as the variable “fid” should be passed as the first argument to the function.

The following code might help you :

targets = load('targets.mat').targets; 
distractors = load('distractors.mat').distractors; 
level_number='Level 3' %example of a level number 
for y=1:12 
    JSONFILE_name= sprintf('%s_JSON%d.json',level_number,y); 
    fid=fopen(JSONFILE_name,'w') 
    s = struct("audioData", targets{y}, "DistractorData", distractors{y}); 
    encodedJSON = jsonencode(s); 
    fprintf(fid, encodedJSON); 
end 
fclose('all'); 

Refer to the following Links:

On “jsonencode()” function:

https://in.mathworks.com/help/matlab/ref/jsonencode.html

On “fprintf()” fucntion:

https://in.mathworks.com/help/matlab/ref/fprintf.html