Class: JobStep

Inherits:
Object
  • Object
show all
Defined in:
lib/rpipe.rb

Direct Known Subclasses

Preprocessing, Reconstruction, Stats

Constant Summary collapse

COLLISION_POLICY =

options – :panic, :destroy, :overwrite

:panic

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(workflow_spec, job_spec) ⇒ JobStep

Intialize with two configuration option hashes - workflow_spec and job_spec



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# File 'lib/rpipe.rb', line 29

def initialize(workflow_spec, job_spec)
	# allow jobspec to override the workflow spec
	@subid        = job_spec['subid']       || workflow_spec['subid']
	@rawdir       = job_spec['rawdir']      || workflow_spec['rawdir']
	@origdir      = job_spec['origdir']     || workflow_spec['origdir']
	@procdir      = job_spec['procdir']     || workflow_spec['procdir']
	@statsdir     = job_spec['statsdir']    || workflow_spec['statsdir']
	@spmdir       = job_spec['spmdir']      || workflow_spec['spmdir'] || default_spmdir
	@scans        = job_spec['scans']       || workflow_spec['scans']
	@scan_labels  = job_spec['scan_labels'] || workflow_spec['scan_labels'] 
	@collision_policy = (job_spec['collision'] || workflow_spec['collision'] || COLLISION_POLICY).to_sym
	@step   = job_spec['step']
	@method = job_spec['method']
	include_custom_methods(@method)
	@libdir = File.dirname(Pathname.new(__FILE__).realpath)
	
	job_requires 'subid'
end

Instance Attribute Details

#collision_policy ⇒ Object

Returns the value of attribute collision_policy.



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# File 'lib/rpipe.rb', line 26

def collision_policy
  @collision_policy
end

#libdir ⇒ Object

Returns the value of attribute libdir.



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# File 'lib/rpipe.rb', line 26

def libdir
  @libdir
end

#origdir ⇒ Object

Returns the value of attribute origdir.



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# File 'lib/rpipe.rb', line 26

def origdir
  @origdir
end

#procdir ⇒ Object

Returns the value of attribute procdir.



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# File 'lib/rpipe.rb', line 26

def procdir
  @procdir
end

#rawdir ⇒ Object

Returns the value of attribute rawdir.



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# File 'lib/rpipe.rb', line 26

def rawdir
  @rawdir
end

#spmdir ⇒ Object

Returns the value of attribute spmdir.



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# File 'lib/rpipe.rb', line 26

def spmdir
  @spmdir
end

#statsdir ⇒ Object

Returns the value of attribute statsdir.



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# File 'lib/rpipe.rb', line 26

def statsdir
  @statsdir
end

#step ⇒ Object

Returns the value of attribute step.



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# File 'lib/rpipe.rb', line 26

def step
  @step
end

#subid ⇒ Object

Returns the value of attribute subid.



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# File 'lib/rpipe.rb', line 26

def subid
  @subid
end

Instance Method Details

#check_instance_vars(*args) ⇒ Object 



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# File 'lib/rpipe.rb', line 106

def check_instance_vars(*args)
  undefined_vars = []
  args.each do |arg|
    unless instance_variable_defined?("@" + arg) && eval("@" + arg).nil? == false
      undefined_vars << arg
    end
  end
  
  unless undefined_vars.size == 0
    yield undefined_vars
  end
end

#default_spmdir ⇒ Object

Raises:

  • (IOError) 


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# File 'lib/rpipe.rb', line 125

def default_spmdir
  spmdirs = %w{/Applications/spm/spm8/spm8_current /apps/spm/spm8_current}
  spmdirs.each do |dir|
    return dir if File.directory? dir
  end
  raise IOError, "Couldn't find default SPM directory in #{spmdirs.join("; ")}."
end

#include_custom_methods(module_name) ⇒ Object

Dynamically load custom methods for advanced processing.



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# File 'lib/rpipe.rb', line 49

def include_custom_methods(module_name)
	if module_name.nil? or ['default','wadrc'].include?(module_name)
		# do nothing, use default implementation
	else
     # Search the load path and require a file named after the custom method.
     # Include methods contained in the custom method module.  
	  # Ensure it's named properly according to file convention or it won't be correctly included.
		begin 
 			require module_name
	    extend self.class.const_get(module_name.dot_camelize)
		rescue LoadError => e
		  puts "Unable to find the specified method #{module_name}"
		  puts "Please either use a standard preprocessing step or put a method in app/methods/#{module_name}.rb"
		  puts "Looking in: #{$LOAD_PATH.join(":")}"
		  raise e
    rescue NameError => e
      $Log.error "Unable to include a module #{module_name.dot_camelize} (for custom #{@step} step)."
      puts "Please check app/methods/#{module_name}.rb and ensure that you declared a module named _exactly_ #{module_name.dot_camelize}."
      puts
      raise e
     end

	end
end

#job_requires(*args) ⇒ Object

Check for required keys in instance variables.



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# File 'lib/rpipe.rb', line 93

def job_requires(*args)
  check_instance_vars *args do |missing_vars|
    error = "
    Warning: Misconfiguration detected.
    You are missing the following required variables from your spec file:
    #{missing_vars.collect { |var| "\t  - #{var} \n" } }
    "
    
    puts error
    raise ScriptError, "Missing Vars: #{missing_vars.join(", ")}"
  end
end

#setup_directory(path, logging_tag) ⇒ Object

Setup directory path according to collision policy.



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# File 'lib/rpipe.rb', line 75

def setup_directory(path, logging_tag)
	if File.exist?(path)
		if @collision_policy == :destroy
			puts "#{logging_tag} :: Deleting directory #{path}"
			FileUtils.rm_rf(path)
			FileUtils.mkdir_p(path)
		elsif @collision_policy == :overwrite
			puts "#{logging_tag} :: Overwriting inside directory #{path}"
		else
			raise(IOError, "Directory already exists, exiting: #{path}")
		end
	else
		puts "#{logging_tag} :: Creating new directory #{path}"
		FileUtils.mkdir_p(path)
	end
end

#validate_existence_of(*args) ⇒ Object

Raises:

  • (ScriptError) 


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# File 'lib/rpipe.rb', line 119

def validate_existence_of(*args)
  missing_files = []
  args.flatten.collect { |file| missing_files << file unless File.exist?(file) }
  raise ScriptError, "Missing files: #{missing_files.join(", ")}" unless missing_files.empty?
end