fix: if organism is in KEGG multiple times

[edkerk]

Main improvements in this PR:

• fix:
  • fuzzyKcatMatching solves #277 when KEGG has multiple entries with the same organism name.

I hereby confirm that I have:

• [x] Selected develop as a target branch (top left drop-down menu)

[github-actions[bot]]

This PR has been automatically tested with GH Actions. Here is the output of the tests:

 
Running geckoCoreFunctionTests
================================================================================
Verification failed in geckoCoreFunctionTests/testsaveECModel_tc0009.
    ---------------------
    Framework Diagnostic:
    ---------------------
    verifyEqual failed.
    --> Path to failure: .rev
        --> The numeric values are not equal using "isequaln".
        --> Failure table:
                Index    Actual    Expected    Error    RelativeError
                _____    ______    ________    _____    _____________
            
                 12        1          0          1           Inf     
                 13        1          0          1           Inf     
                 14        1          0          1           Inf     
                 15        1          0          1           Inf     
                 16        1          0          1           Inf     
                 17        1          0          1           Inf     
        
        Actual double:
            17x1 double
        Expected double:
            17x1 double
    
    Actual Value:
      struct with fields:
    
               name: 'testModel'
                 id: 'testModel'
         annotation: [1x1 struct]
               date: '2023-03-20'
        description: ''
            version: ''
               rxns: {17x1 cell}
                  S: [10x17 double]
                rev: [17x1 double]
           metNames: {10x1 cell}
              comps: {2x1 cell}
          compNames: {2x1 cell}
           metComps: [10x1 double]
               mets: {10x1 cell}
            grRules: {17x1 cell}
         rxnGeneMat: [17x5 double]
              genes: {5x1 cell}
                 ub: [17x1 double]
                 lb: [17x1 double]
                  c: [17x1 double]
           rxnNames: {17x1 cell}
                  b: [10x1 double]
            eccodes: {17x1 cell}
           metNotes: {10x1 cell}
                 ec: [1x1 struct]
    Expected Value:
      struct with fields:
    
                 id: 'testModel'
               name: 'testModel'
        description: ''
            version: ''
               date: '2023-03-20'
         annotation: [1x1 struct]
               rxns: {17x1 cell}
           rxnNames: {17x1 cell}
               mets: {10x1 cell}
           metNames: {10x1 cell}
                  S: [10x17 double]
                 lb: [17x1 double]
                 ub: [17x1 double]
                rev: [17x1 double]
                  c: [17x1 double]
                  b: [10x1 double]
              genes: {5x1 cell}
            grRules: {17x1 cell}
         rxnGeneMat: [17x5 double]
            eccodes: {17x1 cell}
           metComps: [10x1 double]
           metNotes: {10x1 cell}
              comps: {2x1 cell}
          compNames: {2x1 cell}
                 ec: [1x1 struct]
    ------------------
    Stack Information:
    ------------------
    In /home/m/actions-runner/_work/GECKO/GECKO/test/unit_tests/geckoCoreFunctionTests.m (testsaveECModel_tc0009) at 232
================================================================================
Model-specific DLKcat input stored at /home/m/actions-runner/_work/GECKO/GECKO/test/unit_tests/ecTestGEM/data/DLKcat_input_test.tsv
Limit has been reached. Protein P5 seems to be problematic. Consider changing the kcat.
Done geckoCoreFunctionTests
__________

Failure Summary:

     Name                                           Failed  Incomplete  Reason(s)
    ============================================================================================
     geckoCoreFunctionTests/testsaveECModel_tc0009    X                 Failed by verification.

Note: In the case of multiple test runs, this post will be edited.

[ae-tafur]

Look good !

[mihai-sysbio]

The implementation of this fix can be very tricky to debug later on. If there is no better solution than choosing the first match, please also consider updating the documentation of this function.

[edkerk]

Fair point, will mention this in function documentation.

[edkerk]

See 886a15ec047cfdf32ed3ae24e50803f9ba2b97db and #295.