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Versions: 9
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Contents
module Bio
class SQL
class Biodatabase < DummyBase
has_many :bioentries, :class_name =>"Bioentry", :foreign_key => "biodatabase_id"
validates_uniqueness_of :name
end
end #SQL
end #Bio
if __FILE__ == $0
require 'rubygems'
require 'composite_primary_keys'
require 'bio'
require 'pp'
# pp connection = Bio::SQL.establish_connection('bio/io/biosql/config/database.yml','development')
pp connection = Bio::SQL.establish_connection({'test'=>{'database'=>"bio_test", 'adapter'=>"postgresql", 'username'=>"rails", 'password'=>nil}},'test')
#pp YAML::load(ERB.new(IO.read('bio/io/biosql/config/database.yml')).result)
if true
pp Bio::SQL.list_entries
puts "### GenBank"
if ARGV.size > 0
gb = Bio::GenBank.new(ARGF.read)
else
require 'bio/io/fetch'
gb = Bio::GenBank.new(Bio::Fetch.query('gb', 'AJ224122'))
end
biosequence = gb.to_biosequence
db=Bio::SQL::Biodatabase.new(:biodatabase_id=>3,:name=>"JEFF", :authority=>"ME", :description=>"YOU")
db.save!
#sqlseq = Bio::SQL::Sequence.new(:biosequence=>biosequence,:biodatabase_id=>db.id)
# bioseq = Bio::SQL.fetch_accession('AJ224122')
# pp bioseq
# pp bioseq.entry_id
#TODO create a test only for tables not sequence here
# pp bioseq.molecule_type
#pp bioseq.molecule_type.class
#bioseq.molecule_type_update('dna', 1)
pp Bio::SQL::Taxon.find(8121).taxon_names
#sqlseq.to_biosequence
#sqlseq.delete
end
#pp bioseq.molecule_type
#term = Bio::SQL::Term.find_by_name('mol_type')
#pp term
#pp bioseq.entry.bioentry_qualifier_values.create(:term=>term, :rank=>2, :value=>'pippo')
#pp bioseq.entry.bioentry_qualifier_values.inspect
#pp bioseq.entry.bioentry_qualifier_values.find_all_by_term_id(26)
#pp primo.class
# pp primo.value='dna'
# pp primo.save
#pp bioseq.molecule_type= 'prova'
#Bio::SQL::BioentryQualifierValue.delete(delete.bioentry_id,delete.term_id,delete.rank)
end
Version data entries
9 entries across 9 versions & 4 rubygems