runDLKcat.m

function runDLKcat(modelAdapter,filePath)
% runDLKcat
%   Runs DLKcat to predict kcat values from a Docker image. Once DLKcat is succesfully
%   run, the DLKcatFile will be overwritten with the DLKcat
%   output in the model-specific 'data' sub-folder taken from modelAdapter
%   (e.g. GECKO/tutorials/tutorial_yeast-GEM/data/DLKcat.tsv)
%
% Input
%   modelAdapter    a loaded model adapter. (Optional, will otherwise use
%                   the default model adapter)
%   filePath        path to the DLKcat.tsv file. (Optional, will otherwise
%                   assume data/DLKcat.tsv)
%
%   NOTE: 1. Requires Docker to be installed, and Docker Desktop running. Visit "https://www.docker.com"
%         2. Runtime will depend on whether the image is to be downloaded or not.

if nargin < 1 || isempty(modelAdapter)
    modelAdapter = ModelAdapterManager.getDefault();
    if isempty(modelAdapter)
        error('Either send in a modelAdapter or set the default model adapter in the ModelAdapterManager.')
    end
end
params = modelAdapter.params;
% Make sure path is full, not relative
[~, params.path] = fileattrib(params.path);
params.path=params.path.Name;

if nargin < 2 || isempty(filePath)
    filePath = fullfile(params.path,'data','DLKcat.tsv');
elseif strcmp(filePath(end),{'\','/'})
    filePath = fullfile(filePath,'DLKcat.tsv');
end
filePath = checkFileExistence(filePath,1);

copyfile(filePath, fullfile(params.path,'data','tempDLKcat.tsv'));
    

%% Check and install requirements
% On macOS, Docker might not be properly loaded if MATLAB is started via
% launcher and not terminal.
if ismac
    setenv('PATH', strcat('/usr/local/bin', ':', getenv("PATH")));
end

% Check if Docker is installed
[checks.docker.status, checks.docker.out] = system('docker --version');
if checks.docker.status ~= 0
    error('Cannot find Docker, make sure it is installed. If it is, it might be required to start Matlab from the command-line instead of the launcher in order for Docker to be detected and used.')
end

disp('Running DLKcat prediction, this may take many minutes, especially the first time.')
status = system(['docker run --rm -v "' fullfile(params.path,'/data') '":/data ghcr.io/sysbiochalmers/dlkcat-gecko:0.1 /bin/bash -c "python DLKcat.py /data/tempDLKcat.tsv /data/tempDLKcatOutput.tsv"']);
delete(fullfile(params.path,'/data/tempDLKcat.tsv'));

if status == 0 && exist(fullfile(params.path,'data/tempDLKcatOutput.tsv'))
    movefile(fullfile(params.path,'/data/tempDLKcatOutput.tsv'), filePath);
    disp('DKLcat prediction completed.');
else    
    error('DLKcat encountered an error or it did not create any output file.')
end