Class: Bio::SQL

Inherits:
Object show all
Defined in:
lib/bio/io/sql.rb,
lib/bio/io/biosql/term.rb,
lib/bio/io/biosql/taxon.rb,
lib/bio/io/biosql/dbxref.rb,
lib/bio/io/biosql/comment.rb,
lib/bio/db/biosql/sequence.rb,
lib/bio/io/biosql/bioentry.rb,
lib/bio/io/biosql/location.rb,
lib/bio/io/biosql/ontology.rb,
lib/bio/io/biosql/reference.rb,
lib/bio/io/biosql/term_path.rb,
lib/bio/io/biosql/seqfeature.rb,
lib/bio/io/biosql/taxon_name.rb,
lib/bio/io/biosql/biodatabase.rb,
lib/bio/io/biosql/biosequence.rb,
lib/bio/io/biosql/term_dbxref.rb,
lib/bio/io/biosql/term_synonym.rb,
lib/bio/io/biosql/bioentry_path.rb,
lib/bio/io/biosql/bioentry_dbxref.rb,
lib/bio/io/biosql/seqfeature_path.rb,
lib/bio/io/biosql/seqfeature_dbxref.rb,
lib/bio/io/biosql/term_relationship.rb,
lib/bio/io/biosql/bioentry_reference.rb,
lib/bio/io/biosql/bioentry_relationship.rb,
lib/bio/io/biosql/dbxref_qualifier_value.rb,
lib/bio/io/biosql/term_relationship_term.rb,
lib/bio/io/biosql/seqfeature_relationship.rb,
lib/bio/io/biosql/bioentry_qualifier_value.rb,
lib/bio/io/biosql/location_qualifier_value.rb,
lib/bio/io/biosql/seqfeature_qualifier_value.rb

Defined Under Namespace

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

Class Method Summary collapse

Class Method Details

.delete_entry_accession(accession) ⇒ Object 



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# File 'lib/bio/io/sql.rb', line 65

def self.delete_entry_accession(accession)
  Bioentry.delete(Bioentry.find_by_accession(accession))
end

.delete_entry_id(id) ⇒ Object 



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# File 'lib/bio/io/sql.rb', line 61

def self.delete_entry_id(id)
  Bioentry.delete(id)
end

.establish_connection(configurations, env) ⇒ Object

no check is made



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# File 'lib/bio/io/sql.rb', line 23

def self.establish_connection(configurations, env)
  #configurations is an hash similar what YAML returns.
  #{:database=>"biorails_development", :adapter=>"postgresql", :username=>"rails", :password=>nil}
  configurations.assert_valid_keys('development', 'production','test')
  configurations[env].assert_valid_keys('hostname','database','adapter','username','password')
  DummyBase.configurations = configurations
  DummyBase.establish_connection "#{env}"
end

.exists_accession(accession) ⇒ Object 



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# File 'lib/bio/io/sql.rb', line 41

def self.exists_accession(accession)
  Bio::SQL::Bioentry.find_by_accession(accession.upcase).nil? ? false : true
end

.exists_database(name) ⇒ Object 



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# File 'lib/bio/io/sql.rb', line 45

def self.exists_database(name)
  Bio::SQL::Biodatabase.find_by_name(name).nil? ? false : true
end

.fetch_accession(accession) ⇒ Object 



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# File 'lib/bio/io/sql.rb', line 36

def self.fetch_accession(accession)
  accession = accession.upcase
  Bio::SQL::Bioentry.exists?(:accession => accession) ? Bio::SQL::Sequence.new(:entry=>Bio::SQL::Bioentry.find_by_accession(accession)) : nil			
end

.fetch_id(id) ⇒ Object 



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# File 'lib/bio/io/sql.rb', line 32

def self.fetch_id(id)
  Bio::SQL::Bioentry.find(id)
end

.list_databases ⇒ Object 



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# File 'lib/bio/io/sql.rb', line 55

def self.list_databases
  Bio::SQL::Biodatabase.find(:all).collect{|entry|
    {:id=>entry.biodatabase_id, :name => entry.name}
  }
end

.list_entries ⇒ Object 



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# File 'lib/bio/io/sql.rb', line 49

def self.list_entries
  Bio::SQL::Bioentry.find(:all).collect{|entry|
    {:id=>entry.bioentry_id, :accession=>entry.accession}
  }
end