Module: GeneValidatorApp::RunGeneValidator

Extended by:
Forwardable
Defined in:
lib/genevalidatorapp/genevalidator.rb

Overview

Module that runs GeneValidator

Defined Under Namespace

Classes: ArgumentError, RuntimeError

Class Attribute Summary collapse

Class Method Summary collapse

Class Attribute Details

.gv_dir ⇒ Object (readonly)

Returns the value of attribute gv_dir.



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# File 'lib/genevalidatorapp/genevalidator.rb', line 30

def gv_dir
  @gv_dir
end

.input_file ⇒ Object (readonly)

Returns the value of attribute input_file.



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# File 'lib/genevalidatorapp/genevalidator.rb', line 30

def input_file
  @input_file
end

.params ⇒ Object (readonly)

Returns the value of attribute params.



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# File 'lib/genevalidatorapp/genevalidator.rb', line 30

def params
  @params
end

.raw_seq ⇒ Object (readonly)

Returns the value of attribute raw_seq.



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# File 'lib/genevalidatorapp/genevalidator.rb', line 30

def raw_seq
  @raw_seq
end

.tmp_gv_dir ⇒ Object (readonly)

Returns the value of attribute tmp_gv_dir.



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# File 'lib/genevalidatorapp/genevalidator.rb', line 30

def tmp_gv_dir
  @tmp_gv_dir
end

.unique_id ⇒ Object (readonly)

Returns the value of attribute unique_id.



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# File 'lib/genevalidatorapp/genevalidator.rb', line 30

def unique_id
  @unique_id
end

.xml_file ⇒ Object (readonly)

Returns the value of attribute xml_file.



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# File 'lib/genevalidatorapp/genevalidator.rb', line 30

def xml_file
  @xml_file
end

Class Method Details

.init(url, params) ⇒ Object

Setting the scene



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# File 'lib/genevalidatorapp/genevalidator.rb', line 34

def init(url, params)
  create_unique_id
  create_subdir_in_main_tmpdir
  create_soft_link_from_tmpdir_to_gv_dir
  @params = params
  validate_params
  obtain_db_path
  @url = produce_result_url_link(url)
end

.run ⇒ Object

Run BLAST(X/P), get_raw_sequence and genevalidator

Returns html for just the table or a link to the page produced by GV



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# File 'lib/genevalidatorapp/genevalidator.rb', line 46

def run
  write_seq_to_file
  run_genevalidator
  copy_json_folder
  (@params[:result_link]) ? @url : output_json_file_path
  parse_output_json
end