Class Bio::SQL
In: lib/bio/db/biosql/sequence.rb
lib/bio/io/biosql/ar-biosql.rb
lib/bio/io/biosql/biosql.rb
lib/bio/io/sql.rb
Parent: Object

Methods

Classes and Modules

Class Bio::SQL::Biodatabase
Class Bio::SQL::Bioentry
Class Bio::SQL::BioentryDbxref
Class Bio::SQL::BioentryPath
Class Bio::SQL::BioentryQualifierValue
Class Bio::SQL::BioentryReference
Class Bio::SQL::BioentryRelationship
Class Bio::SQL::Biosequence
Class Bio::SQL::Comment
Class Bio::SQL::Dbxref
Class Bio::SQL::DbxrefQualifierValue
Class Bio::SQL::DummyBase
Class Bio::SQL::Location
Class Bio::SQL::LocationQualifierValue
Class Bio::SQL::Ontology
Class Bio::SQL::Reference
Class Bio::SQL::Seqfeature
Class Bio::SQL::SeqfeatureDbxref
Class Bio::SQL::SeqfeaturePath
Class Bio::SQL::SeqfeatureQualifierValue
Class Bio::SQL::SeqfeatureRelationship
Class Bio::SQL::Sequence
Class Bio::SQL::Taxon
Class Bio::SQL::TaxonName
Class Bio::SQL::Term
Class Bio::SQL::TermDbxref
Class Bio::SQL::TermPath
Class Bio::SQL::TermRelationship
Class Bio::SQL::TermRelationshipTerm
Class Bio::SQL::TermSynonym

Public Class methods

[Source]

    # File lib/bio/io/sql.rb, line 73
73:     def self.delete_entry_accession(accession)
74:       Bio::SQL::Bioentry.find_by_accession(accession.upcase).destroy!
75:     end

[Source]

    # File lib/bio/io/sql.rb, line 69
69:     def self.delete_entry_id(id)
70:       Bio::SQL::Bioentry.delete(id)
71:     end

no check is made

[Source]

    # File lib/bio/io/biosql/biosql.rb, line 23
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

[Source]

    # File lib/bio/io/sql.rb, line 47
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

[Source]

    # File lib/bio/io/sql.rb, line 52
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

[Source]

    # File lib/bio/io/sql.rb, line 42
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

[Source]

    # File lib/bio/io/sql.rb, line 38
38:     def self.fetch_id(id)
39:       Bio::SQL::Bioentry.find(id)
40:     end

[Source]

    # File lib/bio/io/sql.rb, line 63
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

[Source]

    # File lib/bio/io/sql.rb, line 57
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

[Validate]