loadOmeroGateway.m

function [gateway,user,cred] = loadOmeroGateway(userName, password, host, varargin)
% loadOmeroGateway opens a connection to an OMERO server using Java gateway 
% (https://docs.openmicroscopy.org/latest/omero/developers/Java.html#gatewayconnect).
%
% SYNTAX
% [gateway,user,cred] = loadOmeroGateway(userName, password, host)
% [gateway,user,cred] = loadOmeroGateway(userName, password, host, port)
%
%
% INPUT ARGUMENTS
% userName    char row vector
%             OMERO user name.
%
% password    char row vector
%             OMERO login password.
%
% host        char row vector
%             host OMERO server. Not including 'http:\\' etc
%
% port        scalar integer
%             (Optional) Port number as an integer
%
%
% OUTPUT ARGUMENTS
% gateway     omero.gateway.Gateway Java object
%
%             # IMPORTANT #
%             In order to disconnet from OMERO.server, execute the below:
%          
%               gateway.disconnect();
%
% user        omero.gateway.model.ExperimenterData Java object
%
% cred        omero.gateway.LoginCredentials Java object
%
%
% NOTE
%
% Use gateway.close() to close the connection once you're done.
%
%
% Written by Kouichi C. Nakamura Ph.D.
% MRC Brain Network Dynamics Unit
% University of Oxford
% kouichi.c.nakamura@gmail.com
% 26-Sep-2018 23:53:43
%
% See also
% loadOmero
% https://javadoc.scijava.org/OMERO/omero/gateway/package-summary.html
%


% Check if "omero.client" is already on the classpath, if not
% then add the omero_client.jar to the javaclasspath.
if exist('omero.client','class') == 0
    
    disp('');
    disp('--------------------------');
    disp('OMERO.matlab Toolbox ');
    disp(omeroVersion);
    disp('--------------------------');
    disp('');
    
    % Add the JARs required by OMERO.matlab to the Java dynamic classpath
    % This will allow the import omero.* statement to pass successfully.
    omeroJars = getOmeroJars();
    cellfun(@javaaddpath, omeroJars);
    import omero.*;
    
    % Also add the OmeroM directory and its subdirectories to the path
    % so that functions and demos are available even if the user changes
    % directories. See the unloadOmero function for how to remove these
    % values.
    addpath(genpath(findOmero)); % OmeroM and subdirectories
    
    % If it does exist, then check that there aren't more than one
    % version active.
else
    
    w = which('omeroVersion','-ALL');
    sz = size(w);
    sz = sz(1);
    if sz > 1
        warning('OMERO:loadOmero','More than one OMERO version found!');
        disp(char(w));
    end
    
end

try
    bfCheckJavaPath; % add Bioformats MATLAB plugin java class paths
catch mexc1
    if strcmp(mexc1.identifier,'MATLAB:UndefinedFunction')
        error(['bfCheckJavaPath is not found. ',...
            'Check if Bioformats MATLAB toolbox is installed ',...
            'from https://www.openmicroscopy.org/bio-formats/downloads/ ',...
            'and the folder is added to the MATLAB search path.'])
    else
       throw(mexc1) 
    end
end

p = inputParser;
p.addRequired('userName',@(x) ischar(x) && isrow(x))
p.addRequired('password',@(x) ischar(x) && isrow(x))
p.addRequired('host',@(x) ischar(x) && isrow(x))
p.addOptional('port',[],@(x) isnumeric(x) && isscalar(x))
p.parse(userName, password, host, varargin{:});

port = p.Results.port;

if isempty(port)
    cred = omero.gateway.LoginCredentials(userName, password, host);    
else
    cred = omero.gateway.LoginCredentials(userName, password, host, port);
end


simpleLogger = omero.log.SimpleLogger();
gateway = omero.gateway.Gateway(simpleLogger);

user = gateway.connect(cred);

end