Sha256: c29f8a0148670bdf1ffddce08bcb3fba49cc6dc759b74f387fdd4159f81612e1
Contents?: true
Size: 1.86 KB
Versions: 13
Compression:
Stored size: 1.86 KB
Contents
#require 'dm-ar-finders'
#require 'dm-core'
require 'erb'
require 'composite_primary_keys'
module Bio
class SQL
class DummyBase < ActiveRecord::Base
#NOTE: Using postgresql, not setting sequence name, system will discover the name by default.
#NOTE: this class will not establish the connection automatically
self.abstract_class = true
self.pluralize_table_names = false
#prepend table name to the usual id, avoid to specify primary id for every table
self.primary_key_prefix_type = :table_name_with_underscore
#biosql_configurations=YAML::load(ERB.new(IO.read(File.join(File.dirname(__FILE__),'./config', 'database.yml'))).result)
#self.configurations=biosql_configurations
#self.establish_connection "development"
end #DummyBase
require 'bio/io/biosql/ar-biosql'
# #no check is made
def self.establish_connection(configurations, env)
# #configurations is an hash similar what YAML returns.
#configurations.assert_valid_keys('development', 'production','test')
#configurations[env].assert_valid_keys('hostname','database','adapter','username','password')
DummyBase.configurations = configurations
connection = DummyBase.establish_connection "#{env}"
#Init of basis terms and ontologies
Ontology.first(:conditions => ["name = ?", 'Annotation Tags']) || Ontology.create({:name => 'Annotation Tags'})
Ontology.first(:conditions => ["name = ?", 'SeqFeature Keys']) || Ontology.create({:name => 'SeqFeature Keys'})
Ontology.first(:conditions => ["name = ?", 'SeqFeature Sources']) ||Ontology.create({:name => 'SeqFeature Sources'})
Term.first(:conditions => ["name = ?", 'EMBLGenBankSwit']) || Term.create({:name => 'EMBLGenBankSwit', :ontology => Ontology.first(:conditions => ["name = ?", 'SeqFeature Sources'])})
connection
end #establish_connection
end #SQL
end #Bio
Version data entries
13 entries across 13 versions & 4 rubygems