Module: EcfClassify::Zenodo

Defined in:
lib/ecf_classify/zenodo.rb

Constant Summary collapse

PATH = 
""
RECORD_URL = 
'https://zenodo.org/record/3672544/'
FILES = 
{
  :general              => "ecf_general_model.hmm",
  :sigma3               => "Sigma70_r3.hmm",
  :sigma2_4             => "Sigma70_r2_r4.hmm",
  :groups               => "all_ecf_groups.hmm",
  :subgroups            => "all_ecf_subgroups.hmm",
  :groups_statistics    => "groups_statistics.txt",
  :subgroups_statistics => "subgroups_statistics.txt",
}
STATUS_FILE = 
"status.txt"

Class Method Summary collapse

Class Method Details

.check ⇒ Object 



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# File 'lib/ecf_classify/zenodo.rb', line 49

def self.check

end

.download ⇒ Object

downloads the current dataset

returns

true if everything is ok



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# File 'lib/ecf_classify/zenodo.rb', line 23

def self.download
  perma_record = open(RECORD_URL)
  FILES.each do |key,file|
    download = open(perma_record.base_uri.to_s + "/files/" + file)
    IO.copy_stream(download, path(key))
    if(file.split(".").last == "hmm")
      EcfClassify::HMMER.hmmpress(path(key))
    end
  end
  open(path(STATUS_FILE),"w"){ |f| f.puts perma_record.base_uri.to_s }
  true
end

.file ⇒ Object 



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# File 'lib/ecf_classify/zenodo.rb', line 53

def self.file

end

.path(name) ⇒ Object 



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# File 'lib/ecf_classify/zenodo.rb', line 57

def self.path(name)
  File.expand_path('../../../data/' + (FILES[name] || name.to_s) , __FILE__)
end

.status ⇒ Object

get the status of the download

returns the current doi if the dataset is complete returns nil if the data is not there or incomplete



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# File 'lib/ecf_classify/zenodo.rb', line 41

def self.status
  if File.exists? path(STATUS_FILE)
    return File.read(path(STATUS_FILE))
  else
    return nil
  end
end