Class Bio::SQL
In: lib/bio/io/sql.rb
lib/bio/io/biosql/bioentry.rb
lib/bio/io/biosql/term_synonym.rb
lib/bio/io/biosql/term_relationship_term.rb
lib/bio/io/biosql/location.rb
lib/bio/io/biosql/bioentry_qualifier_value.rb
lib/bio/io/biosql/biodatabase.rb
lib/bio/io/biosql/seqfeature_relationship.rb
lib/bio/io/biosql/biosequence.rb
lib/bio/io/biosql/dbxref_qualifier_value.rb
lib/bio/io/biosql/taxon.rb
lib/bio/io/biosql/bioentry_path.rb
lib/bio/io/biosql/dbxref.rb
lib/bio/io/biosql/bioentry_dbxref.rb
lib/bio/io/biosql/term_relationship.rb
lib/bio/io/biosql/seqfeature_dbxref.rb
lib/bio/io/biosql/seqfeature_path.rb
lib/bio/io/biosql/comment.rb
lib/bio/io/biosql/seqfeature_qualifier_value.rb
lib/bio/io/biosql/reference.rb
lib/bio/io/biosql/term_dbxref.rb
lib/bio/io/biosql/term_path.rb
lib/bio/io/biosql/taxon_name.rb
lib/bio/io/biosql/seqfeature.rb
lib/bio/io/biosql/location_qualifier_value.rb
lib/bio/io/biosql/bioentry_relationship.rb
lib/bio/io/biosql/term.rb
lib/bio/io/biosql/bioentry_reference.rb
lib/bio/io/biosql/ontology.rb
lib/bio/db/biosql/sequence.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 65
65:     def self.delete_entry_accession(accession)
66:       Bioentry.delete(Bioentry.find_by_accession(accession))
67:     end

[Source]

    # File lib/bio/io/sql.rb, line 61
61:     def self.delete_entry_id(id)
62:       Bioentry.delete(id)
63:     end

no check is made

[Source]

    # File lib/bio/io/sql.rb, line 23
23:     def self.establish_connection(configurations, env)
24:       #configurations is an hash similar what YAML returns.
25:       #{:database=>"biorails_development", :adapter=>"postgresql", :username=>"rails", :password=>nil}
26:       configurations.assert_valid_keys('development', 'production','test')
27:       configurations[env].assert_valid_keys('hostname','database','adapter','username','password')
28:       DummyBase.configurations = configurations
29:       DummyBase.establish_connection "#{env}"
30:     end

[Source]

    # File lib/bio/io/sql.rb, line 41
41:     def self.exists_accession(accession)
42:       Bio::SQL::Bioentry.find_by_accession(accession.upcase).nil? ? false : true
43:     end

[Source]

    # File lib/bio/io/sql.rb, line 45
45:     def self.exists_database(name)
46:       Bio::SQL::Biodatabase.find_by_name(name).nil? ? false : true
47:     end

[Source]

    # File lib/bio/io/sql.rb, line 36
36:     def self.fetch_accession(accession)
37:       accession = accession.upcase
38:       Bio::SQL::Bioentry.exists?(:accession => accession) ? Bio::SQL::Sequence.new(:entry=>Bio::SQL::Bioentry.find_by_accession(accession)) : nil                       
39:     end

[Source]

    # File lib/bio/io/sql.rb, line 32
32:     def self.fetch_id(id)
33:       Bio::SQL::Bioentry.find(id)
34:     end

[Source]

    # File lib/bio/io/sql.rb, line 55
55:     def self.list_databases
56:       Bio::SQL::Biodatabase.find(:all).collect{|entry|
57:         {:id=>entry.biodatabase_id, :name => entry.name}
58:       }
59:     end

[Source]

    # File lib/bio/io/sql.rb, line 49
49:     def self.list_entries
50:       Bio::SQL::Bioentry.find(:all).collect{|entry|
51:         {:id=>entry.bioentry_id, :accession=>entry.accession}
52:       }
53:     end

[Validate]