sql.rb in bioruby-bio-1.3.0.5000

- old
+ new
@@ -1,186 +1,79 @@
+#module Bio
+ # class SQL
+  #  #no check is made
+   # 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
 
-require 'rubygems'
-require 'erb'
-require 'composite_primary_keys'
+
+#require 'rubygems'
+#require 'composite_primary_keys'
+#require 'erb'
 # BiosqlPlug
 
 =begin
 Ok Hilmar gives to me some clarification
 1) "EMBL/GenBank/SwissProt" name in term table, is only a convention assuming data loaded by genbank embl ans swissprot formats.
-   If your features come from others ways for example blast or alignment ... whatever.. the user as to take care about the source. 
+   If your features come from others ways for example blast or alignment ... whatever.. the user as to take care about the source.
 
 
 =end
 =begin
 TODO:
 1) source_term_id => surce_term and check before if the source term is present or not and the level, the root should always be something "EMBL/GenBank/SwissProt" or contestualized.
-2) Into DummyBase class delete connection there and use Bio::ArSQL.establish_connection which reads info from a yml file. 
+2) Into DummyBase class delete connection there and use Bio::ArSQL.establish_connection which reads info from a yml file.
 3) Chk Locations in Biofeatures ArSQL
 =end
 module Bio
-  class SQL	
-    #no check is made
-    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
-    
+  class SQL
+
+    require 'bio/io/biosql/biosql'
+    autoload :Sequence, 'bio/db/biosql/sequence'
+
     def self.fetch_id(id)
       Bio::SQL::Bioentry.find(id)
     end
-    
+
     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			
+#     Bio::SQL::Bioentry.exists?(:accession => accession) ? Bio::SQL::Sequence.new(:entry=>Bio::SQL::Bioentry.find_by_accession(accession)) : nil
+      Bio::SQL::Sequence.new(:entry=>Bio::SQL::Bioentry.find_by_accession(accession.upcase))
     end
-    
+
     def self.exists_accession(accession)
-      Bio::SQL::Bioentry.find_by_accession(accession.upcase).nil? ? false : true
+#      Bio::SQL::Bioentry.find_by_accession(accession.upcase).nil? ? false : true
+      !Bio::SQL::Bioentry.find_by_accession(accession.upcase).nil?
     end
-    
+
     def self.exists_database(name)
-      Bio::SQL::Biodatabase.find_by_name(name).nil? ? false : true
+#      Bio::SQL::Biodatabase.find_by_name(name).nil? ? false : true
+      !Bio::SQL::Biodatabase.first(:name=>name).nil?
     end
-    
+
     def self.list_entries
-      Bio::SQL::Bioentry.find(:all).collect{|entry|
+      Bio::SQL::Bioentry.all.collect do|entry|
         {:id=>entry.bioentry_id, :accession=>entry.accession}
-      }
+      end
     end
-    
+
     def self.list_databases
-      Bio::SQL::Biodatabase.find(:all).collect{|entry|
+      Bio::SQL::Biodatabase.all.collect do|entry|
         {:id=>entry.biodatabase_id, :name => entry.name}
-      }
+      end
     end
-    
+
     def self.delete_entry_id(id)
-      Bioentry.delete(id)
+      Bio::SQL::Bioentry.delete(id)
     end
-    
+
     def self.delete_entry_accession(accession)
-      Bioentry.delete(Bioentry.find_by_accession(accession))
+      Bio::SQL::Bioentry.find_by_accession(accession.upcase).destroy!
     end
-    
-    
-    class DummyBase <  ActiveRecord::Base
-      #NOTE: Using postgresql, not setting sequence name, system will discover the name by default.
-      #NOTE: this class will not establish the connection automatically
-      self.abstract_class = true			
-      self.pluralize_table_names = false
-      #prepend table name to the usual id, avoid to specify primary id for every table
-      self.primary_key_prefix_type = :table_name_with_underscore
-      #biosql_configurations=YAML::load(ERB.new(IO.read(File.join(File.dirname(__FILE__),'../config', 'database.yml'))).result)
-      #self.configurations=biosql_configurations
-      #self.establish_connection "development"
-    end #DummyBase
-    
-    autoload :Biodatabase, 'bio/io/biosql/biodatabase'
-    autoload :Bioentry, 'bio/io/biosql/bioentry'
-    autoload :BioentryDbxref, 'bio/io/biosql/bioentry_dbxref'
-    autoload :BioentryPath, 'bio/io/biosql/bioentry_path'
-    autoload :BioentryQualifierValue, 'bio/io/biosql/bioentry_qualifier_value'
-    autoload :BioentryReference, 'bio/io/biosql/bioentry_reference'
-    autoload :BioentryRelationship, 'bio/io/biosql/bioentry_relationship'
-    autoload :Biosequence, 'bio/io/biosql/biosequence'
-    autoload :Comment, 'bio/io/biosql/comment'
-    autoload :Dbxref, 'bio/io/biosql/dbxref'
-    autoload :DbxrefQualifierValue, 'bio/io/biosql/dbxref_qualifier_value'
-    autoload :Location, 'bio/io/biosql/location'
-    autoload :LocationQualifierValue, 'bio/io/biosql/location_qualifier_value'
-    autoload :Ontology, 'bio/io/biosql/ontology'
-    autoload :Reference, 'bio/io/biosql/reference'
-    autoload :Seqfeature, 'bio/io/biosql/seqfeature'
-    autoload :SeqfeatureDbxref, 'bio/io/biosql/seqfeature_dbxref'
-    autoload :SeqfeaturePath, 'bio/io/biosql/seqfeature_path'
-    autoload :SeqfeatureQualifierValue, 'bio/io/biosql/seqfeature_qualifier_value'
-    autoload :SeqfeatureRelationship, 'bio/io/biosql/seqfeature_relationship'
-    autoload :Taxon, 'bio/io/biosql/taxon'
-    autoload :TaxonName, 'bio/io/biosql/taxon_name'
-    autoload :Term, 'bio/io/biosql/term'
-    autoload :TermDbxref, 'bio/io/biosql/term_dbxref'
-    autoload :TermPath, 'bio/io/biosql/term_path'
-    autoload :TermRelationship, 'bio/io/biosql/term_relationship'
-    autoload :TermRelationshipTerm, 'bio/io/biosql/term_relationship_term'
-    autoload :Sequence, 'bio/db/biosql/sequence'
+
   end #biosql
-  
-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')
-  connection = Bio::SQL.establish_connection({'development'=>{'database'=>"bio_test", 'adapter'=>"postgresql", 'username'=>"rails", 'password'=>nil}},'development')
-  #pp YAML::load(ERB.new(IO.read('bio/io/biosql/config/database.yml')).result)
-  if true
-    #Bio::SQL.list_entries
-
-#  	biosequence = data.to_biosequence
-#	puts biosequence.output(:genbank)
-	db=Bio::SQL::Biodatabase.new(:name=>'JEFF', :authority=>'ME', :description=>'YOU')
-	db.save!
-
-    puts "### FileFile.auto"
-    if ARGV.size > 0
-	#embl = Bio::FlatFile.auto(ARGF.read)
-	Bio::FlatFile.auto(ARGF) do |ff|
-		ff.each do |data|
-			biosequence=data.to_biosequence
-			puts biosequence.output(:fasta)
-			sqlseq = Bio::SQL::Sequence.new(:biosequence=>biosequence,:biodatabase_id=>db.biodatabase_id)
-			sqlseq.save
-			sqlseq.to_biosequence.output(:fasta)
-		end
-	end
-    else
-	require 'bio/io/fetch'
-	server = Bio::Fetch.new('http://www.ebi.ac.uk/cgi-bin/dbfetch')
-	data = Bio::EMBL.new(server.fetch('embl','AJ224123'))
-    end
-
-	
-#	sqlseq = Bio::SQL::Sequence.new(:biosequence=>biosequence,:biodatabase_id=>db.biodatabase_id)
-#	sqlseq.save
-#	sqlseq_bioseq=sqlseq.to_biosequence	
-#	puts sqlseq_bioseq.output(:genbank)
-
-
-
-	#    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
-	
-#	db.destroy
-  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
+end #Bio