Module: RemoteWorkflow::SSH

Defined in:
lib/rbbt/workflow/remote_workflow/driver/ssh.rb

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.clean(url, input_id, jobname = nil) ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 138

def self.clean(url, input_id, jobname = nil)
  server, path = parse_url(url)

  script = path_script(path)
  script +=<<-EOF
job.clean
  EOF
  Misc.ssh_run(server, script)
end

.get_json(url, params = {}) ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 80

def self.get_json(url, params = {})
  server, path = parse_url(url)
  script = path_script(path)

  script +=<<-EOF
STDOUT.write res.to_json
  EOF

  JSON.parse(Misc.ssh_run(server, script))
end

.get_raw(url, params) ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 91

def self.get_raw(url, params)
  server, path = parse_url(url)
  script = path_script(path)

  script +=<<-EOF
STDOUT.write res
  EOF

  Misc.ssh_run(server, script)
end

.job_script(inputs_id, jobname = nil) ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 70

def self.job_script(inputs_id, jobname = nil)
  script =<<-EOF
jobname = #{jobname.nil? ? 'nil' : "'#{jobname}'"}
path = File.join(ENV["HOME"], '.rbbt/tmp/tmp-ssh_job_inputs/#{inputs_id}')
job_inputs = Workflow.load_inputs(path, task_info[:inputs], task_info[:input_types])
job = wf.job(task, jobname, job_inputs)
  EOF
  script
end

.parse_url(url) ⇒ Object

def self.run_log(server, script)

Log.debug "Run and monitor ssh script in #{server}:\n#{script}"
CMD.cmd("ssh '#{server}' 'shopt -s expand_aliases; bash -ic \"ruby\"' ", :in => script, :log => true)

end



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# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 13

def self.parse_url(url)
  m = url.match(/ssh:\/\/([^:]+):(.*)/)
  server = m.captures[0]
  path = m.captures[1]
  [server, path]
end

.path_script(path) ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 20

def self.path_script(path) 

  workflow, task, job, *rest = path.split("/")

  script =<<-EOF
require 'rbbt/workflow'
wf = Workflow.require_workflow "#{workflow}"
  EOF

  case task
  when nil
    script +=<<-EOF
task_info = {}
wf.tasks.keys.each do |task|
  task_info[task] = wf.task_info(task)
end
res = task_info
    EOF
  when 'documentation'
    script +=<<-EOF
res = documentation = wf.documentation
    EOF
  else
    if job.nil?
      script +=<<-EOF
task = '#{task}'
res = task_info = wf.task_info(task)
      EOF
    else
      case rest.first
      when nil
        script +=<<-EOF
task = '#{task}'
jobname = '#{job}'
res = job = wf.fast_load_id(File.join(task, jobname))
        EOF
      when "info"
        script +=<<-EOF
task = '#{task}'
jobname = '#{job}'
job = wf.fast_load_id(File.join(task, jobname))
res = job_info = job.info
        EOF
      else
        raise "Unkown path: #{[path, rest].inspect}"
      end
    end
  end
end

.post_job(url, inputs_id, jobname = nil) ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 102

def self.post_job(url, inputs_id, jobname = nil)
  server, path = parse_url(url)

  script = path_script(path)
  script += job_script(inputs_id, jobname)
  script +=<<-EOF
job.init_info
STDOUT.write job.name
  EOF
  @name = Misc.ssh_run(server, script)
end

.relay(workflow, task, jobname, inputs, server, options = {}) ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 161

def self.relay(workflow, task, jobname, inputs, server, options = {})
  options = Misc.add_defaults options, :search_path => 'user'
  search_path = options[:search_path]

  job = workflow.job(task, jobname, inputs)

  job.dependencies.each do |dep| 
    dep.produce 
  end

  override_dependencies = job.dependencies.collect{|dep| [dep.workflow.to_s, dep.task_name.to_s] * "#" << "=" << Rbbt.identify(dep.path)}

  job.dependencies.each do |dep| 
    Step.migrate(dep.path, search_path, :target => server)
  end

  remote = RemoteWorkflow.new("ssh://#{server}:#{workflow.to_s}", "#{workflow.to_s}")
  rjob = remote.job(task, jobname, {})
  rjob.override_dependencies = override_dependencies
  rjob.run
end

.run_job(url, input_id, jobname = nil) ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 114

def self.run_job(url, input_id, jobname = nil)
  server, path = parse_url(url)

  script = path_script(path)
  script += job_script(input_id, jobname)
  script +=<<-EOF
job.produce
STDOUT.write job.path
  EOF
  Misc.ssh_run(server, script)
end

.run_slurm_job(url, input_id, jobname = nil) ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 126

def self.run_slurm_job(url, input_id, jobname = nil)
  server, path = parse_url(url)

  script = path_script(path)
  script += job_script(input_id, jobname)
  script +=<<-EOF
job.produce
STDOUT.write job.path
  EOF
  Misc.ssh_run(server, script)
end

.upload_inputs(server, inputs, input_types, input_id) ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 148

def self.upload_inputs(server, inputs, input_types, input_id)
  TmpFile.with_file do |dir|
    if Step.save_inputs(inputs, input_types, dir)
      Dir.glob(File.join(dir, "*.as_step")).each do |file|
        path = Open.read(file).strip
        new = Step.migrate(path, :user, :target => server)
        Open.write(file, new)
      end
      CMD.cmd("ssh '#{server}' mkdir -p .rbbt/tmp/tmp-ssh_job_inputs/; scp -r '#{dir}' #{server}:.rbbt/tmp/tmp-ssh_job_inputs/#{input_id}")
    end
  end
end

Instance Method Details

#documentation ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 187

def documentation
  @documention ||= IndiferentHash.setup(RemoteWorkflow::SSH.get_json(File.join(url, "documentation")))
  @documention
end

#init_remote_tasks ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 232

def init_remote_tasks
  @task_info = IndiferentHash.setup(RemoteWorkflow::SSH.get_json(url))
  @exec_exports = @stream_exports = @synchronous_exports = []
  @asynchronous_exports = @task_info.keys
end

#task_dependencies ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 222

def task_dependencies
  @task_dependencies ||= Hash.new do |hash,task| 
    hash[task] = if exported_tasks.include? task
                   RemoteWorkflow::SSH.get_json(File.join(url, task.to_s, 'dependencies'))
                 else
                   []
                 end
  end
end

#task_info(task) ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 192

def task_info(task)
  @task_info ||= IndiferentHash.setup({})

  if @task_info[task].nil?
    task_info = RemoteWorkflow::SSH.get_json(File.join(@base_url, task.to_s))
    task_info = RemoteWorkflow::SSH.fix_hash(task_info)

    task_info[:result_type] = task_info[:result_type].to_sym if task_info[:result_type]
    task_info[:export] = task_info[:export].to_sym if task_info[:export]
    task_info[:input_types] = RemoteWorkflow::SSH.fix_hash(task_info[:input_types], true)
    task_info[:inputs] = task_info[:inputs].collect{|input| input.to_sym }

    @task_info[task] = IndiferentHash.setup(task_info)
  end

  IndiferentHash.setup(@task_info[task])
end

#tasks ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 210

def tasks
  @tasks ||= Hash.new do |hash,task_name| 
    raise Workflow::TaskNotFoundException, "Task #{task_name} not found in workflow #{self.to_s}" unless @task_info.include?(task_name)
    info = @task_info[task_name]
    task = Task.setup info do |*args|
      raise "This is a remote task" 
    end
    task.name = task_name.to_sym
    hash[task_name] = task
  end
end

#workflow_description ⇒ Object 



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# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 183

def workflow_description
  RemoteWorkflow::SSH.get_raw(File.join(url, 'description'))
end