Class: Bio::Conduit::Process

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/conduit/process.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(filename) ⇒ Process

Returns a new instance of Process.



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# File 'lib/bio/conduit/process.rb', line 103

def initialize(filename)
    yaml = YAML::load(File.open(filename))
    @steps = {}
    @name = yaml['pipeline']
    @resources = yaml['resources']
    @runninglist = []
    yaml['steps'].each_pair do |name, detail|
        @resources[name] = "../#{name}"
        @steps[name] = Bio::Conduit::Step.new(name, detail, @resources)
    end
end

Instance Attribute Details

#steps ⇒ Object (readonly)

Returns the value of attribute steps.



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# File 'lib/bio/conduit/process.rb', line 101

def steps
  @steps
end

Instance Method Details

#[](name) ⇒ Object 



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# File 'lib/bio/conduit/process.rb', line 115

def [](name)
    @steps[name]
end

#add_running_step(stepname) ⇒ Object 



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# File 'lib/bio/conduit/process.rb', line 119

def add_running_step(stepname)
    step = self[stepname]
    self.add_running_step(step.dependency) if step.dependence?
    if !@runninglist.include?(stepname)
        @runninglist.push(stepname)
    end
end

#run_steps(steps) ⇒ Object 



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# File 'lib/bio/conduit/process.rb', line 127

def run_steps(steps)

    @steps.keys.each do |name|
        self.add_running_step(name) if steps == nil || steps.include?(name)
    end

    combinestep = nil

    @runninglist.each do |stepname|
        if combinestep
            combinestep = combinestep + self[stepname]
        else
            combinestep = self[stepname]
        end
    end

    return combinestep
end