checkInstallation.m

function checkInstallation()
% checkInstallation
%   The purpose of this function is to check if all necessary functions are
%   installed and working. It also checks whether there are any functions
%   with overlapping names between RAVEN and other toolboxes or
%   user-defined functions, which are accessible from MATLAB pathlist
%
%   Usage: checkInstallation()

%Check if RAVEN is in the MATLAB path list
paths=textscan(path,'%s','delimiter', pathsep);
paths=paths{1};

%Get the RAVEN path
[ST, I]=dbstack('-completenames');
[ravenDir,~,~]=fileparts(fileparts(ST(I).file));

%Print the RAVEN version if it is not the development version
if exist(fullfile(ravenDir,'version.txt'), 'file') == 2
    fprintf(['\n*** THE RAVEN TOOLBOX v.' fgetl(fopen(fullfile(ravenDir,'version.txt'))) ' ***\n\n']);
else
    fprintf('\n*** THE RAVEN TOOLBOX - DEVELOPMENT VERSION ***\n\n');
end

fprintf(['MATLAB R' version('-release') ' detected\n\n']);

fprintf('Checking if RAVEN is on the MATLAB path...\t\t\t\t\t\t\t\t\t');
if ismember(ravenDir,paths)
    fprintf('OK\n');
else
    fprintf('OK (just added)\n');
    subpath=regexp(genpath(ravenDir),pathsep,'split'); %List all subdirectories
    pathsToKeep=cellfun(@(x) isempty(strfind(x,'.git')),subpath) & cellfun(@(x) isempty(strfind(x,'doc')),subpath);
    addpath(strjoin(subpath(pathsToKeep),pathsep));
    savepath
end

%Add the required classes to the static Java path if not already added
addJavaPaths();

excelFile=fullfile(ravenDir,'tutorial','empty.xlsx');
xmlFile=fullfile(ravenDir,'tutorial','empty.xml');
matFile=fullfile(ravenDir,'tutorial','empty.mat');

%Check if it is possible to parse an Excel file
fprintf('Checking if it is possible to parse a model in Microsoft Excel format...\t');
try
    importExcelModel(excelFile,false,false,true);
    fprintf('OK\n');
catch
    fprintf('Not OK\n');
end

%Check if it is possible to import an SBML model using libSBML
fprintf('Checking if it is possible to import an SBML model using libSBML...\t\t\t');
try
    importModel(xmlFile);
    try
        libSBMLver=OutputSBML; % Only works in libSBML 5.17.0+
        fprintf('OK\n');
    catch
        fprintf(['Not OK\n\n'...
            'An older libSBML version was found, update to version 5.17.0 or higher\n'...
            'for a significant improvement of model import\n\n']);
    end
catch
    fprintf(['Not OK\nTo import SBML models, download libSBML from\n'...
        'http://sbml.org/Software/libSBML/Downloading_libSBML and add to MATLAB path\n']);
end

%Define values for keepSolver and workingSolvers, needed for solver
%functionality check
keepSolver=false;
workingSolvers='';
%Get current solver. Set it to 'none', if it is not set
if ~ispref('RAVEN','solver')
    fprintf('Solver found in preferences... NONE\n');
    setRavenSolver('none');
    curSolv=getpref('RAVEN','solver');
else
    curSolv=getpref('RAVEN','solver');
    fprintf(['Solver found in preferences... ',curSolv,'\n']);
end

%Check if it is possible to solve an LP problem using different solvers
solver={'gurobi','cobra'};

for i=1:numel(solver)
    fprintf(['Checking if it is possible to solve an LP problem using ',solver{i},'...\t\t\t']);
    try
        setRavenSolver(solver{i});
        load(matFile);
        solveLP(emptyModel);
        workingSolvers=strcat(workingSolvers,';',solver{i});
        fprintf('OK\n');
        if strcmp(curSolv,solver{i})
            keepSolver=true;
        end
    catch
        fprintf('Not OK\n');
    end
end

if keepSolver
    %The solver set in curSolv is functional, so the settings are restored
    %to the ones which were set before running checkInstallation
    setRavenSolver(curSolv);
    fprintf(['Preferred solver... KEPT\nSolver saved as preference... ',curSolv,'\n\n']);
elseif ~isempty(workingSolvers)
    %There are working solvers, but the none of them is the solver defined
    %by curSolv. The first working solver is therefore set as RAVEN solver
    workingSolvers=regexprep(workingSolvers,'^;','');
    workingSolvers=regexprep(workingSolvers,';.+$','');
    %Only one working solver should be left by now in workingSolvers
    setRavenSolver(workingSolvers);
    fprintf(['Preferred solver... NEW\nSolver saved as preference... ',workingSolvers,'\n\n']);
else
    %No functional solvers were found, so the setting is restored back to
    %original
    setRavenSolver(curSolv);
    fprintf(['WARNING: No working solver was found!\n'...
        'Install the solver, set it using setRavenSolver(''solverName'') and run checkInstallation again\n'...
        'Available solverName options are ''gurobi'' and ''cobra''\n\n']);
end

fprintf('Checking essential binary executables:\n');
fprintf('NOTE: Broken binary executables <strong>must be fixed</strong> before running RAVEN\n');

fprintf('\tBLAST+... ');
res=runtests('blastPlusTests.m','OutputDetail',0);
interpretResults(res);
fprintf('\tDIAMOND... ');
res=runtests('diamondTests.m','OutputDetail',0);
interpretResults(res);
fprintf('\tHMMER... ');
res=runtests('hmmerTests.m','OutputDetail',0);
interpretResults(res);
fprintf('Checking non-essential/development binary executables:\n');
fprintf('NOTE: Only fix these binaries if planning to use KEGG FTP dump files in getKEGGModelForOrganism\n');
fprintf('\tCD-HIT... ');
res=runtests('cdhitTests.m','OutputDetail',0);
interpretResults(res);
fprintf('\tMAFFT... ');
res=runtests('mafftTests.m','OutputDetail',0);
interpretResults(res);

fprintf('Checking whether RAVEN functions are non-redundant across MATLAB path...\t');
checkFunctionUniqueness();

fprintf('\n*** checkInstallation complete ***\n\n');
end

function interpretResults(results)
if results.Failed==0 && results.Incomplete==0
    fprintf('OK\n');
else
    fprintf('Not OK! Download/compile the binary and rerun checkInstallation\n');
end
end