Class: GeneCache

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

Overview

TODO: check we have working sqlite3 executable for fast import of data

Constant Summary collapse

@@db = 
SQLite3::Database.new GeneCache.db_path
@@tables = 
@@db.execute("SELECT name FROM sqlite_master where type = 'table'")

Class Method Summary collapse

Class Method Details

.convert(species, from, to, id) ⇒ Object 



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# File 'lib/genecache.rb', line 23

def self.convert(species, from, to, id)
  table = "#{species}_#{from}_#{to}"
  unless @@tables.include?([table])
    # TODO: Update table sometimes!
    self.download!(species, from, to)
  end

  r = @@db.execute "select #{to} from #{table} where #{from} = '#{id}'"
  r.flatten
end

.db_path ⇒ Object 



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# File 'lib/genecache.rb', line 15

def self.db_path
  FileUtils.mkdir_p ENV['HOME'] + "/.genecache"
  return ENV['HOME'] + "/.genecache/db.sqlite3"
end

.download!(species, from, to) ⇒ Object 



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# File 'lib/genecache.rb', line 34

def self.download!(species, from, to)
  table = "#{species}_#{from}_#{to}"
  $log.info "Downloading table: #{table}"
  @@db.execute "drop table if exists #{table}"
  @@db.execute "drop index if exists from_index"
  @@db.execute "drop index if exists to_index"

  url = "http://biodb.jp/tmp/#{table}.zip"
  zip_data = open(url).read

  Zip::Archive.open_buffer(zip_data) do |ar|
    ar.fopen(0) do |f|
      tmp = Tempfile.new 'biodb'
      data = f.read.split("\n")
      header = data.first.split
      throw "Invalid header!" if header.sort != [from, to].sort
      @@db.execute "create table #{table} (#{header.first} VARCHAR(255), #{header.last} VARCHAR(255))"

      rest = data[1..-5] * "\n"
      tmp.write rest
      tmp.close

      system(%$echo -e ".mode tabs \\n.import #{File.expand_path(tmp.path)} #{table}" | sqlite3 #{self.db_path}$)
      @@db.execute "create index from_index on #{table} (#{header.first})"
      @@db.execute "create index to_index on #{table} (#{header.last})"
    end

    # Update local list of tables
    @@tables = @@db.execute("SELECT name FROM sqlite_master where type = 'table' and name = '#{table}'")
  end
end