Class: KingdomDB

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

Constant Summary collapse

ROOT_ID = 
"1"
SCIENTIFIC_NAME = 
"scientific name"
DEFAULT_FILTER = 
[
 "Bacteria",
 "Archaea",
 "Viruses",
 "NONE"
]

Instance Method Summary collapse

Constructor Details

#initialize(server, user, password, database) ⇒ KingdomDB

Returns a new instance of KingdomDB.



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# File 'lib/kingdom_db.rb', line 14

def initialize(server, user, password, database)
  
  connect_string = 'mysql2://'+ server + '/' + database + '?user=' + user

  if !password.nil?
    connect_string = connect_string + '&password=' + password
  end

  if !defined?(RUBY_ENGINE)
    #This is most likey 1.8.7
  else
    if RUBY_ENGINE == 'jruby'
      #This is JRuby, using jdbc
      connect_string = 'jdbc:' + connect_string
    end
  end
  
  @database = Sequel.connect(connect_string)
  @filter_hit_cache = {}
  
end

Instance Method Details

#get_filter(name_array) ⇒ Object 



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# File 'lib/kingdom_db.rb', line 111

def get_filter(name_array)
  filter_hash = Hash[name_array.collect { |taxon_name|
                       [taxon_name, id_from_name(taxon_name)]
                     }]
  return filter_hash
end

#id_from_gi(gi_number) ⇒ Object 



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# File 'lib/kingdom_db.rb', line 94

def id_from_gi(gi_number)
  db_results = @database[:proteingiToTaxonId].filter(:gi => gi_number).map(:taxonid)
  
  if db_results.size == 0
    raise("No results for gi " + gi_number.to_s)
  elsif db_results.size > 1
    raise("Results not unique: " + db_results.inspect)
  else
    return db_results[0].to_s
  end
end

#id_from_name(taxon_name) ⇒ Object 



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# File 'lib/kingdom_db.rb', line 36

def id_from_name(taxon_name)
  db_results = @database[:names].select(:taxonid, :class).filter(:name => taxon_name).all

  if db_results.size > 1
    #If we get more than one result, check if we got a scientific name
    db_results.delete_if{|x| x[:class] != SCIENTIFIC_NAME}
  end

  if db_results.size > 1
    raise("Results not unique: " + db_results.inspect)
  end
          
  if db_results.size == 0
    raise("No results for taxon name " + taxon_name.to_s)
  end

  return db_results[0][:taxonid].to_s
end

#match_filter(taxon_name, filter_hash) ⇒ Object 



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# File 'lib/kingdom_db.rb', line 118

def match_filter(taxon_name, filter_hash)

  current_species_id = id_from_name(taxon_name)

  history = []
  
  while ((current_species_id.to_i > ROOT_ID.to_i)&&(!filter_hash.has_value?(current_species_id)))
    if @filter_hit_cache.has_key? current_species_id
      #Cache hit
      current_species_id = @filter_hit_cache[current_species_id]
      break
    else
      parent_id = parent_id_from_id(current_species_id)
      history << current_species_id
      current_species_id = parent_id
    end
  end
  
  history.each { |i|
    @filter_hit_cache[i] = current_species_id
  }
  
  if current_species_id == ROOT_ID
    return nil
  else
    return name_from_id(current_species_id)
  end
end

#name_from_gi(gi_number) ⇒ Object 



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

def name_from_gi(gi_number)
  taxonid = id_from_gi(gi_number)
  name_from_id(taxonid)
end

#name_from_id(taxon_id) ⇒ Object 



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# File 'lib/kingdom_db.rb', line 55

def name_from_id(taxon_id)
  db_results = @database[:names].filter(:taxonid => taxon_id.to_s, :class => SCIENTIFIC_NAME).map(:name)

  if db_results.size == 0
    raise("No results for taxon id " + taxon_id.to_s)
  elsif db_results.size > 1
    raise("Results not unique: " + db_results.inspect)
  else
    return db_results[0]
  end
end

#node_rank_from_id(taxon_id) ⇒ Object 



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# File 'lib/kingdom_db.rb', line 80

def node_rank_from_id(taxon_id)
  db_results = @database[:nodes].filter(:taxonid => taxon_id.to_s).map(:rank)


  if db_results.size == 0
    raise("No results for taxon id " + taxon_id.to_s)  
  elsif db_results.size > 1
    raise("Results not unique: " + db_results.inspect)
  else
    return db_results[0].to_s
  end
  
end

#parent_id_from_id(taxon_id) ⇒ Object 



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# File 'lib/kingdom_db.rb', line 67

def parent_id_from_id(taxon_id)
  db_results = @database[:nodes].filter(:taxonid => taxon_id.to_s).map(:parenttaxonid)

  if db_results.size == 0
    raise("No results for taxon id " + taxon_id.to_s)
  elsif db_results.size > 1
    raise("Results not unique: " + db_results.inspect)
  else
    return db_results[0].to_s
  end
  
end