mjsWriteSshScript.m

function sshScriptFile = mjsWriteSshScript(jobScriptFile, varargin)
% Write a shell script that will invoke a given jobScriptFile via SSH.
%
% This saves us from having to write lots of SSH syntax by hand.
%
% sshScriptFile = mjsWriteSshScript(jobScriptFile) generates a shell
% script that will cause the given jobScriptFile be executed remotely,
% via SSH.
%
% mjsWriteSshScript( ... 'sshScriptFile', sshScriptFile) specify the name
% of the new SSH script that should be generated.  The default is chosen
% based on the jobScriptFile.
%
% mjsWriteSshScript( ... 'host', host) specify the address or hostname of
% the remote host to access via SSH.
%
% mjsWriteSshScript( ... 'port', port) specify the port to connect to on
% the remote host.
%
% mjsWriteSshScript( ... 'user', user) specify the usename to use when
% connecting to the remote host.
%
% mjsWriteSshScript( ... 'identity', identity) specify the path to an
% identity file (often .pem) to use for authenticating with the remote
% host.
%
% mjsWriteSshScript( ... 'knownHostsFile', knownHostsFile) specify the path
% to the ssh "known_hosts" file, where the ssh key of the given host can be
% automatically accepted.  The default is '~/.ssh/known_hosts'.
%
% sshScriptFile = mjsWriteSshScript(jobScriptFile, varargin)
%
% 2016-2017 Brainard Lab, University of Pennsylvania

arguments = mjsIncludeEnvironmentProfile(varargin{:});

parser = inputParser();
parser.KeepUnmatched = true;
parser.StructExpand = true;
parser.addRequired('jobScriptFile', @ischar);
parser.addParameter('sshScriptFile', '', @ischar);
parser.addParameter('sshScriptFid', [], @isnumeric);
parser.addParameter('host', 'localhost', @ischar);
parser.addParameter('port', [], @isnumeric);
parser.addParameter('user', '', @ischar);
parser.addParameter('identity', '', @ischar);
parser.addParameter('knownHostsFile', '', @ischar);
parser.parse(jobScriptFile, arguments);
jobScriptFile = parser.Results.jobScriptFile;
sshScriptFile = parser.Results.sshScriptFile;
sshScriptFid = parser.Results.sshScriptFid;
host = parser.Results.host;
port = parser.Results.port;
user = parser.Results.user;
identity = parser.Results.identity;
knownHostsFile = parser.Results.knownHostsFile;

% default ssh script name based on job script name
[jobScriptPath, jobScriptBase] = fileparts(jobScriptFile);
if isempty(sshScriptFile)
    sshScriptFile = fullfile(jobScriptPath, [jobScriptBase '-ssh.sh']);
end

% default SSH user is current Matlab user
if isempty(user)
    [~, user] = system('whoami');
end


%% Read job script into memory so we can embed it in the ssh script.
fid = fopen(jobScriptFile, 'r');
if -1 == fid
    error('mjsWriteSshScript:fopen', ...
        'Could not open file <%s> for reading.', jobScriptFile);
end
jobScriptText = fread(fid, '*char')';
fclose(fid);

% excape literal single quotes '
%   allows us to enclose the whole job script in strong quotes '...'
%   Matlab makes this look bad because it takes '''' to say '
jobScriptText = regexprep(jobScriptText, '''', '''\\''''');


%% Create the ssh script file.
scriptDir = fileparts(sshScriptFile);
if ~isempty(scriptDir) && 7 ~= exist(scriptDir, 'dir')
    mkdir(scriptDir);
end

if isempty(sshScriptFid)
    fid = fopen(sshScriptFile, 'w');
else
    % allow writing to an already-open file
    fid = sshScriptFid;
end
if -1 == fid
    error('mjsWriteSshScript:fopen', ...
        'Could not open file <%s> for writing.', sshScriptFile);
end

try
    if isempty(sshScriptFid)
        % don't need shebang when writing into an existing file
        fprintf(fid, '#!/bin/sh\n');
    end
    fprintf(fid, '## Begin script generated by mjsWriteSshScript.m\n');
    
    
    %% Embed the job command here in this script.
    fprintf(fid, '\n');
    fprintf(fid, '# embed the whole job script in strong quotes ''...''\n');
    fprintf(fid, 'COMMAND=''%s''\n', jobScriptText);
    
    
    %% Try to automatically accept the remote ssh key.
    %   avoids prompting the user to accept the key
    if ~isempty(knownHostsFile)
        fprintf(fid, '\n');
        fprintf(fid, '# auto-accept remote ssh key to avoid user prompt\n');
        fprintf(fid, 'ssh-keyscan -H "%s" >> "%s"\n', host, knownHostsFile);
    end
    
    
    %% Try to invoke the command on the remote host.
    if isempty(port)
        portOption = '';
    else
        portOption = sprintf('-p %d', port);
    end
    
    if isempty(identity)
        idOption = '';
    else
        idOption = sprintf('-i "%s"', identity);
    end
    
    fprintf(fid, '\n');
    fprintf(fid, '# invoke ssh with the whole job command\n');
    fprintf(fid, 'echo "Running command <$COMMAND> at host <%s> with identity <%s>"\n', host, idOption);
    fprintf(fid, 'ssh %s %s \\\n', portOption, idOption);
    fprintf(fid, '  "%s@%s" \\\n', user, host);
    fprintf(fid, '  "$COMMAND"\n');
    
    fprintf(fid, '\n');
    fprintf(fid, 'echo "Done."\n');
    fprintf(fid, 'date\n');

    fprintf(fid, '\n');
    fprintf(fid, '## End script generated by mjsWriteSshScript.m\n');
    fprintf(fid, '\n');
    
    if isempty(sshScriptFid)
        fclose(fid);
    end
    
catch err
    if isempty(sshScriptFid)
        fclose(fid);
    end
    rethrow(err);
end

if isempty(sshScriptFid)
    system(['chmod +x ' sshScriptFile]);
end