class Bio::SQL

Constants

VERSION

Public Class Methods

delete_entry_accession(accession) click to toggle source
   # File lib/bio/io/sql.rb
73 def self.delete_entry_accession(accession)
74   Bio::SQL::Bioentry.find_by_accession(accession.upcase).destroy!
75 end
delete_entry_id(id) click to toggle source
   # File lib/bio/io/sql.rb
69 def self.delete_entry_id(id)
70   Bio::SQL::Bioentry.delete(id)
71 end
establish_connection(configurations, env) click to toggle source

no check is made

   # File lib/bio/io/biosql/biosql.rb
23 def self.establish_connection(configurations, env)
24   #  #configurations is an hash similar what YAML returns.
25 
26    #configurations.assert_valid_keys('development', 'production','test')
27    #configurations[env].assert_valid_keys('hostname','database','adapter','username','password')
28    DummyBase.configurations = configurations
29   connection = DummyBase.establish_connection "#{env}"
30   #Init of basis terms and ontologies
31   Ontology.first(:conditions => ["name = ?", 'Annotation Tags']) || Ontology.create({:name => 'Annotation Tags'})
32   Ontology.first(:conditions => ["name = ?", 'SeqFeature Keys']) || Ontology.create({:name => 'SeqFeature Keys'})
33   Ontology.first(:conditions => ["name = ?", 'SeqFeature Sources']) ||Ontology.create({:name => 'SeqFeature Sources'})
34   Term.first(:conditions => ["name = ?", 'EMBLGenBankSwit']) || Term.create({:name => 'EMBLGenBankSwit', :ontology => Ontology.first(:conditions => ["name = ?", 'SeqFeature Sources'])})
35   connection 
36 end
exists_accession(accession) click to toggle source
   # File lib/bio/io/sql.rb
47     def self.exists_accession(accession)
48 #      Bio::SQL::Bioentry.find_by_accession(accession.upcase).nil? ? false : true
49       !Bio::SQL::Bioentry.find_by_accession(accession.upcase).nil?
50     end
exists_database(name) click to toggle source
   # File lib/bio/io/sql.rb
52     def self.exists_database(name)
53 #      Bio::SQL::Biodatabase.find_by_name(name).nil? ? false : true
54       !Bio::SQL::Biodatabase.first(:name=>name).nil?
55     end
fetch_accession(accession) click to toggle source
   # File lib/bio/io/sql.rb
42     def self.fetch_accession(accession)
43 #     Bio::SQL::Bioentry.exists?(:accession => accession) ? Bio::SQL::Sequence.new(:entry=>Bio::SQL::Bioentry.find_by_accession(accession)) : nil
44       Bio::SQL::Sequence.new(:entry=>Bio::SQL::Bioentry.find_by_accession(accession.upcase))
45     end
fetch_id(id) click to toggle source
   # File lib/bio/io/sql.rb
38 def self.fetch_id(id)
39   Bio::SQL::Bioentry.find(id)
40 end
list_databases() click to toggle source
   # File lib/bio/io/sql.rb
63 def self.list_databases
64   Bio::SQL::Biodatabase.all.collect do|entry|
65     {:id=>entry.biodatabase_id, :name => entry.name}
66   end
67 end
list_entries() click to toggle source
   # File lib/bio/io/sql.rb
57 def self.list_entries
58   Bio::SQL::Bioentry.all.collect do|entry|
59     {:id=>entry.bioentry_id, :accession=>entry.accession}
60   end
61 end