fillGapsSmallTests

run this test case with the command
results = runtests('fillGapsSmallTests.m')

0001 %run this test case with the command
0002 %results = runtests('fillGapsSmallTests.m')
0003 function tests = fillGapsSmallTests
0004 tests = functiontests(localfunctions);
0005 testGurobi = exist('gurobi','file')==3;
0006 if testGurobi
0007     try
0008         gurobi_read('solverTests.m');
0009     catch ME
0010         if ~startsWith(ME.message,'Gurobi error 10012') % Expected error code, others may indicate problems with license
0011            testGurobi = false;
0012         end
0013     end
0014 end
0015 if ~testGurobi
0016     disp('Gurobi not installed or not functional, some fillGapsSmallTests skipped.')
0017     skipTests = contains({tests.Name},'gurobi','IgnoreCase',true);
0018     tests(skipTests) = [];
0019 end
0020 if exist('scip','file')~=3
0021     disp('SCIP MEX binary not installed or not functional, some fillGapsSmallTests skipped.')
0022     skipTests = contains({tests.Name},'scip','IgnoreCase',true);
0023     tests(skipTests) = [];
0024 end
0025 end
0026 
0027 function testSmallSCIP(testCase)
0028 %Test using small model
0029 sourceDir = fileparts(which(mfilename));
0030 load([sourceDir,'/test_data/ecoli_textbook.mat'], 'model');
0031 modelDB=model; % Keep as database with reactions
0032 try
0033     oldSolver=getpref('RAVEN','solver');
0034 catch
0035 end
0036 setRavenSolver('scip');
0037 
0038 %Remove first 10 reactions
0039 model=removeReactions(modelDB,(1:10));
0040 modelDB.id='DB';
0041 try
0042     evalc('[newConnected,cannotConnect,addedRxns,model,exitFlag]=fillGaps(model,modelDB)');
0043 catch
0044     try
0045         setRavenSolver(oldSolver);
0046     catch
0047         rmpref('RAVEN','solver');
0048     end
0049     error('Solver not working')
0050 end
0051 sol=solveLP(model);
0052 try
0053     setRavenSolver(oldSolver);
0054 catch
0055     rmpref('RAVEN','solver');
0056 end
0057 %Should give non-zero flux
0058 verifyTrue(testCase,sol.f>0);
0059 end
0060 
0061 function testSmallGurobi(testCase)
0062 %Test using small model
0063 sourceDir = fileparts(which(mfilename));
0064 load([sourceDir,'/test_data/ecoli_textbook.mat'], 'model');
0065 modelDB=model; % Keep as database with reactions
0066 try
0067     oldSolver=getpref('RAVEN','solver');
0068 catch
0069 end
0070 setRavenSolver('gurobi');
0071 
0072 %Remove first 10 reactions
0073 model=removeReactions(modelDB,(1:10));
0074 
0075 modelDB.id='DB';
0076 try
0077     evalc('[newConnected,cannotConnect,addedRxns,model,exitFlag]=fillGaps(model,modelDB)');
0078 catch
0079     try
0080         setRavenSolver(oldSolver);
0081     catch
0082         rmpref('RAVEN','solver');
0083     end
0084     error('Solver not working')
0085 end
0086 sol=solveLP(model);
0087 try
0088     setRavenSolver(oldSolver);
0089 catch
0090     rmpref('RAVEN','solver');
0091 end
0092 %Expect at least 5% of the original growth
0093 verifyTrue(testCase,sol.f>0);
0094 end