bio-biosql 0.0.0
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- checksums.yaml +7 -0
- data/.gitignore +14 -0
- data/.project +17 -0
- data/BSDL +22 -0
- data/COPYING +56 -0
- data/COPYING.ja +51 -0
- data/Gemfile +4 -0
- data/LEGAL +9 -0
- data/README.md +69 -0
- data/Rakefile +19 -0
- data/bio-biosql.gemspec +36 -0
- data/lib/bio-biosql/version.rb +5 -0
- data/lib/bio/db/biosql/biosql_to_biosequence.rb +78 -0
- data/lib/bio/db/biosql/sequence.rb +444 -0
- data/lib/bio/io/biosql/ar-biosql.rb +257 -0
- data/lib/bio/io/biosql/biosql.rb +39 -0
- data/lib/bio/io/biosql/config/database.yml +21 -0
- data/lib/bio/io/sql.rb +79 -0
- data/test/bioruby_test_helper.rb +86 -0
- data/test/data/00dummy.txt +1 -0
- data/test/unit/bio/db/biosql/tc_biosql.rb +114 -0
- data/test/unit/bio/db/biosql/ts_suite_biosql.rb +8 -0
- metadata +176 -0
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module Bio
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class SQL
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class Biodatabase < DummyBase
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has_many :bioentries, :class_name =>"Bioentry", :foreign_key => "biodatabase_id"
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validates_uniqueness_of :name
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end
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class BioentryDbxref < DummyBase
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#delete set_sequence_name nil
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set_primary_key nil #bioentry_id,dbxref_id
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belongs_to :bioentry, :class_name => "Bioentry"
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belongs_to :dbxref, :class_name => "Dbxref"
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end
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class BioentryPath < DummyBase
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set_primary_key nil
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#delete set_sequence_name nil
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belongs_to :term, :class_name => "Term"
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#da sistemare per poter procedere.
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belongs_to :object_bioentry, :class_name=>"Bioentry"
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belongs_to :subject_bioentry, :class_name=>"Bioentry"
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end #BioentryPath
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class BioentryQualifierValue < DummyBase
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#NOTE: added rank to primary_keys, now it's finished.
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set_primary_keys :bioentry_id, :term_id, :rank
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belongs_to :bioentry, :class_name => "Bioentry"
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belongs_to :term, :class_name => "Term"
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end #BioentryQualifierValue
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class Bioentry < DummyBase
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belongs_to :biodatabase, :class_name => "Biodatabase"
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belongs_to :taxon, :class_name => "Taxon"
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has_one :biosequence
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#, :class_name => "Biosequence", :foreign_key => "bioentry_id"
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has_many :comments, :class_name =>"Comment", :order =>'rank'
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has_many :seqfeatures, :class_name => "Seqfeature", :order=>'rank'
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has_many :bioentry_references, :class_name=>"BioentryReference" #, :foreign_key => "bioentry_id"
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has_many :bioentry_dbxrefs, :class_name => "BioentryDbxref"
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has_many :object_bioentry_relationships, :class_name=>"BioentryRelationship", :foreign_key=>"object_bioentry_id" #non mi convince molto credo non funzioni nel modo corretto
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has_many :subject_bioentry_relationships, :class_name=>"BioentryRelationship", :foreign_key=>"subject_bioentry_id" #non mi convince molto credo non funzioni nel modo corretto
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has_many :object_bioentry_paths, :class_name=>"BioentryPath", :foreign_key=>"object_bioentry_id" #non mi convince molto credo non funzioni nel modo corretto
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has_many :subject_bioentry_paths, :class_name=>"BioentryPath", :foreign_key=>"subject_bioentry_id" #non mi convince molto credo non funzioni nel modo corretto
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has_many :cdsfeatures, :class_name=>"Seqfeature", :foreign_key =>"bioentry_id", :conditions=>["term.name='CDS'"], :include=>"type_term"
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has_many :references, :through=>:bioentry_references, :class_name => "Reference"
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has_many :terms, :through=>:bioentry_qualifier_values, :class_name => "Term"
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#NOTE: added order_by for multiple hit and manage ranks correctly
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has_many :bioentry_qualifier_values, :order=>"bioentry_id,term_id,rank", :class_name => "BioentryQualifierValue"
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#per la creazione richiesti:
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#name, accession, version
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# validates_uniqueness_of :accession, :scope=>[:biodatabase_id]
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# validates_uniqueness_of :name, :scope=>[:biodatabase_id]
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# validates_uniqueness_of :identifier, :scope=>[:biodatabase_id]
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end
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class BioentryReference < DummyBase
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set_primary_keys :bioentry_id, :reference_id, :rank
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belongs_to :bioentry, :class_name => "Bioentry"
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belongs_to :reference , :class_name => "Reference"
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end
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class BioentryRelationship < DummyBase
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#delete set_primary_key "bioentry_relationship_id"
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set_sequence_name "bieontry_relationship_pk_seq"
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belongs_to :object_bioentry, :class_name => "Bioentry"
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belongs_to :subject_bioentry, :class_name => "Bioentry"
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belongs_to :term
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end
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class Biosequence < DummyBase
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set_primary_keys :bioentry_id, :version
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#delete set_sequence_name "biosequence_pk_seq"
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belongs_to :bioentry, :foreign_key=>"bioentry_id"
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#has_one :bioentry
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#, :class_name => "Bioentry"
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end
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class Comment < DummyBase
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belongs_to :bioentry, :class_name => "Bioentry"
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end
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class DbxrefQualifierValue < DummyBase
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#think to use composite primary key
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set_primary_key nil #dbxref_id, term_id, rank
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#delete set_sequence_name nil
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belongs_to :dbxref, :class_name => "Dbxref"
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belongs_to :term, :class_name => "Term"
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end
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class Dbxref < DummyBase
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#set_sequence_name "dbxref_pk_seq"
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has_many :dbxref_qualifier_values, :class_name => "DbxrefQualifierValue"
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has_many :locations, :class_name => "Location"
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has_many :references, :class_name=>"Reference"
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has_many :term_dbxrefs, :class_name => "TermDbxref"
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has_many :bioentry_dbxrefs, :class_name => "BioentryDbxref"
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#TODO: check is with bioentry there is an has_and_belongs_to_many relationship has specified in schema overview.
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end
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class LocationQualifierValue < DummyBase
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set_primary_key nil #location_id, term_id
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#delete set_sequence_name nil
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belongs_to :location, :class_name => "Location"
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belongs_to :term, :class_name => "Term"
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end
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class Location < DummyBase
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#set_sequence_name "location_pk_seq"
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belongs_to :seqfeature, :class_name => "Seqfeature"
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belongs_to :dbxref, :class_name => "Dbxref"
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belongs_to :term, :class_name => "Term"
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has_many :location_qualifier_values, :class_name => "LocationQualifierValue"
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def to_s
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if strand==-1
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str="complement("+start_pos.to_s+".."+end_pos.to_s+")"
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else
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str=start_pos.to_s+".."+end_pos.to_s
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end
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return str
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end
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def sequence
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seq=""
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unless self.seqfeature.bioentry.biosequence.seq.nil?
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seq=Bio::Sequence::NA.new(self.seqfeature.bioentry.biosequence.seq[start_pos-1..end_pos-1])
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seq.reverse_complement! if strand==-1
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end
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return seq
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end
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end
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class Ontology < DummyBase
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has_many :terms, :class_name => "Term"
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has_many :term_paths, :class_name => "TermPath"
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has_many :term_relationships, :class_name => "TermRelationship"
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end
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class Reference < DummyBase
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belongs_to :dbxref, :class_name => "Dbxref"
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has_many :bioentry_references, :class_name=>"BioentryReference"
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has_many :bioentries, :through=>:bioentry_references
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end
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class SeqfeatureDbxref < DummyBase
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set_primary_keys :seqfeature_id, :dbxref_id
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#delete set_sequence_name nil
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belongs_to :seqfeature, :class_name => "Seqfeature", :foreign_key => "seqfeature_id"
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belongs_to :dbxref, :class_name => "Dbxref", :foreign_key => "dbxref_id"
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end
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class SeqfeaturePath < DummyBase
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set_primary_keys :object_seqfeature_id, :subject_seqfeature_id, :term_id
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set_sequence_name nil
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belongs_to :object_seqfeature, :class_name => "Seqfeature", :foreign_key => "object_seqfeature_id"
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belongs_to :subject_seqfeature, :class_name => "Seqfeature", :foreign_key => "subject_seqfeature_id"
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belongs_to :term, :class_name => "Term"
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end
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class SeqfeatureQualifierValue < DummyBase
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set_primary_keys :seqfeature_id, :term_id, :rank
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set_sequence_name nil
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belongs_to :seqfeature
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belongs_to :term, :class_name => "Term"
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end
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class Seqfeature <DummyBase
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set_sequence_name "seqfeature_pk_seq"
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belongs_to :bioentry
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#, :class_name => "Bioentry"
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belongs_to :type_term, :class_name => "Term", :foreign_key => "type_term_id"
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belongs_to :source_term, :class_name => "Term", :foreign_key =>"source_term_id"
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has_many :seqfeature_dbxrefs, :class_name => "SeqfeatureDbxref", :foreign_key => "seqfeature_id"
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has_many :seqfeature_qualifier_values, :order=>'rank', :foreign_key => "seqfeature_id"
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#, :class_name => "SeqfeatureQualifierValue"
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has_many :locations, :class_name => "Location", :order=>'rank'
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has_many :object_seqfeature_paths, :class_name => "SeqfeaturePath", :foreign_key => "object_seqfeature_id"
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has_many :subject_seqfeature_paths, :class_name => "SeqfeaturePath", :foreign_key => "subject_seqfeature_id"
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has_many :object_seqfeature_relationships, :class_name => "SeqfeatureRelationship", :foreign_key => "object_seqfeature_id"
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has_many :subject_seqfeature_relationships, :class_name => "SeqfeatureRelationship", :foreign_key => "subject_seqfeature_id"
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#get the subsequence described by the locations objects
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def sequence
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return self.locations.inject(Bio::Sequence::NA.new("")){|seq, location| seq<<location.sequence}
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end
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#translate the subsequences represented by the feature and its locations
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#not considering the qualifiers
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#Return a Bio::Sequence::AA object
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def translate(*args)
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self.sequence.translate(*args)
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end
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end
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class SeqfeatureRelationship <DummyBase
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set_sequence_name "seqfeatue_relationship_pk_seq"
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belongs_to :term, :class_name => "Term"
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belongs_to :object_seqfeature, :class_name => "Seqfeature"
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belongs_to :subject_seqfeature, :class_name => "Seqfeature"
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end
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class TaxonName < DummyBase
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set_primary_keys :taxon_id, :name, :name_class
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belongs_to :taxon, :class_name => "Taxon"
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end
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class Taxon < DummyBase
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set_sequence_name "taxon_pk_seq"
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has_many :taxon_names, :class_name => "TaxonName"
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has_one :taxon_scientific_name, :class_name => "TaxonName", :conditions=>"name_class = 'scientific name'"
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has_one :taxon_genbank_common_name, :class_name => "TaxonName", :conditions=>"name_class = 'genbank common name'"
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has_one :bioentry, :class_name => "Bioentry"
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end
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class TermDbxref < DummyBase
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set_primary_key nil #term_id, dbxref_id
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#delete set_sequence_name nil
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belongs_to :term, :class_name => "Term"
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belongs_to :dbxref, :class_name => "Dbxref"
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end
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class TermPath < DummyBase
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set_sequence_name "term_path_pk_seq"
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belongs_to :ontology, :class_name => "Ontology"
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belongs_to :subject_term, :class_name => "Term"
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belongs_to :object_term, :class_name => "Term"
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belongs_to :predicate_term, :class_name => "Term"
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end
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class Term < DummyBase
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belongs_to :ontology, :class_name => "Ontology"
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has_many :seqfeature_qualifier_values, :class_name => "SeqfeatureQualifierValue"
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has_many :dbxref_qualifier_values, :class_name => "DbxrefQualifierValue"
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has_many :bioentry_qualifer_values, :class_name => "BioentryQualifierValue"
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has_many :bioentries, :through=>:bioentry_qualifier_values
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has_many :locations, :class_name => "Location"
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has_many :seqfeature_relationships, :class_name => "SeqfeatureRelationship"
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has_many :term_dbxrefs, :class_name => "TermDbxref"
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has_many :term_relationship_terms, :class_name => "TermRelationshipTerm"
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has_many :term_synonyms, :class_name => "TermSynonym"
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has_many :location_qualifier_values, :class_name => "LocationQualifierValue"
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has_many :seqfeature_types, :class_name => "Seqfeature", :foreign_key => "type_term_id"
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has_many :seqfeature_sources, :class_name => "Seqfeature", :foreign_key => "source_term_id"
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has_many :term_path_subjects, :class_name => "TermPath", :foreign_key => "subject_term_id"
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has_many :term_path_predicates, :class_name => "TermPath", :foreign_key => "predicate_term_id"
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has_many :term_path_objects, :class_name => "TermPath", :foreign_key => "object_term_id"
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has_many :term_relationship_subjects, :class_name => "TermRelationship", :foreign_key =>"subject_term_id"
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has_many :term_relationship_predicates, :class_name => "TermRelationship", :foreign_key =>"predicate_term_id"
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has_many :term_relationship_objects, :class_name => "TermRelationship", :foreign_key =>"object_term_id"
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has_many :seqfeature_paths, :class_name => "SeqfeaturePath"
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end
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class TermRelationship < DummyBase
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set_sequence_name "term_relationship_pk_seq"
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belongs_to :ontology, :class_name => "Ontology"
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belongs_to :subject_term, :class_name => "Term"
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belongs_to :predicate_term, :class_name => "Term"
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belongs_to :object_term, :class_name => "Term"
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has_one :term_relationship_term, :class_name => "TermRelationshipTerm"
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end
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class TermRelationshipTerm < DummyBase
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#delete set_sequence_name nil
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set_primary_key :term_relationship_id
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belongs_to :term_relationship, :class_name => "TermRelationship"
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belongs_to :term, :class_name => "Term"
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end
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class TermSynonym < DummyBase
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#delete set_sequence_name nil
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set_primary_key nil
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belongs_to :term, :class_name => "Term"
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end
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end #SQL
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end #Bio
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#require 'dm-ar-finders'
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#require 'dm-core'
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require 'erb'
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require 'composite_primary_keys'
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module Bio
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class SQL
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class DummyBase < ActiveRecord::Base
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#NOTE: Using postgresql, not setting sequence name, system will discover the name by default.
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#NOTE: this class will not establish the connection automatically
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self.abstract_class = true
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self.pluralize_table_names = false
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#prepend table name to the usual id, avoid to specify primary id for every table
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self.primary_key_prefix_type = :table_name_with_underscore
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#biosql_configurations=YAML::load(ERB.new(IO.read(File.join(File.dirname(__FILE__),'./config', 'database.yml'))).result)
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#self.configurations=biosql_configurations
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#self.establish_connection "development"
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end #DummyBase
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require 'bio/io/biosql/ar-biosql'
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22
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+
# #no check is made
|
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 #establish_connection
|
37
|
+
|
38
|
+
end #SQL
|
39
|
+
end #Bio
|
@@ -0,0 +1,21 @@
|
|
1
|
+
#This is the database configuration specific for BioSQL
|
2
|
+
#User can configure it's db here
|
3
|
+
|
4
|
+
development:
|
5
|
+
adapter: jdbcmysql
|
6
|
+
database: bioseq
|
7
|
+
username: febo
|
8
|
+
password:
|
9
|
+
hostname: localhost
|
10
|
+
|
11
|
+
test:
|
12
|
+
adapter: postgresql
|
13
|
+
database: biorails_test
|
14
|
+
username: rails
|
15
|
+
password:
|
16
|
+
|
17
|
+
production:
|
18
|
+
adapter: postgresql
|
19
|
+
database: biorails_production
|
20
|
+
username: rails
|
21
|
+
password:
|
data/lib/bio/io/sql.rb
ADDED
@@ -0,0 +1,79 @@
|
|
1
|
+
#module Bio
|
2
|
+
# class SQL
|
3
|
+
# #no check is made
|
4
|
+
# def self.establish_connection(configurations, env)
|
5
|
+
# #configurations is an hash similar what YAML returns.
|
6
|
+
# #{:database=>"biorails_development", :adapter=>"postgresql", :username=>"rails", :password=>nil}
|
7
|
+
# configurations.assert_valid_keys('development', 'production','test')
|
8
|
+
# configurations[env].assert_valid_keys('hostname','database','adapter','username','password')
|
9
|
+
# DummyBase.configurations = configurations
|
10
|
+
# DummyBase.establish_connection "#{env}"
|
11
|
+
#end
|
12
|
+
|
13
|
+
|
14
|
+
#require 'rubygems'
|
15
|
+
#require 'composite_primary_keys'
|
16
|
+
#require 'erb'
|
17
|
+
# BiosqlPlug
|
18
|
+
|
19
|
+
=begin
|
20
|
+
Ok Hilmar gives to me some clarification
|
21
|
+
1) "EMBL/GenBank/SwissProt" name in term table, is only a convention assuming data loaded by genbank embl ans swissprot formats.
|
22
|
+
If your features come from others ways for example blast or alignment ... whatever.. the user as to take care about the source.
|
23
|
+
|
24
|
+
|
25
|
+
=end
|
26
|
+
=begin
|
27
|
+
TODO:
|
28
|
+
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.
|
29
|
+
2) Into DummyBase class delete connection there and use Bio::ArSQL.establish_connection which reads info from a yml file.
|
30
|
+
3) Chk Locations in Biofeatures ArSQL
|
31
|
+
=end
|
32
|
+
module Bio
|
33
|
+
class SQL
|
34
|
+
|
35
|
+
require 'bio/io/biosql/biosql'
|
36
|
+
autoload :Sequence, 'bio/db/biosql/sequence'
|
37
|
+
|
38
|
+
def self.fetch_id(id)
|
39
|
+
Bio::SQL::Bioentry.find(id)
|
40
|
+
end
|
41
|
+
|
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
|
46
|
+
|
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
|
51
|
+
|
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
|
56
|
+
|
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
|
62
|
+
|
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
|
68
|
+
|
69
|
+
def self.delete_entry_id(id)
|
70
|
+
Bio::SQL::Bioentry.delete(id)
|
71
|
+
end
|
72
|
+
|
73
|
+
def self.delete_entry_accession(accession)
|
74
|
+
Bio::SQL::Bioentry.find_by_accession(accession.upcase).destroy!
|
75
|
+
end
|
76
|
+
|
77
|
+
end #biosql
|
78
|
+
|
79
|
+
end #Bio
|
@@ -0,0 +1,86 @@
|
|
1
|
+
#
|
2
|
+
# test/bioruby_test_helper.rb - Helper module for testing bioruby
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2009 Naohisa Goto <ng@bioruby.org>
|
5
|
+
# License:: The Ruby License
|
6
|
+
#
|
7
|
+
|
8
|
+
require 'pathname'
|
9
|
+
|
10
|
+
unless defined? BioRubyTestDebug then
|
11
|
+
BioRubyTestDebug = ENV['BIORUBY_TEST_DEBUG'].to_s.empty? ? false : true
|
12
|
+
if BioRubyTestDebug then
|
13
|
+
$stderr.puts "BioRuby test debug enabled."
|
14
|
+
end
|
15
|
+
end #BioRubyTestDebug
|
16
|
+
|
17
|
+
unless defined? BioRubyTestGem then
|
18
|
+
gem_version = ENV['BIORUBY_TEST_GEM']
|
19
|
+
if gem_version then
|
20
|
+
$stderr.puts 'require "rubygems"' if BioRubyTestDebug
|
21
|
+
require "rubygems"
|
22
|
+
if gem_version.empty? then
|
23
|
+
$stderr.puts "gem 'bio'" if BioRubyTestDebug
|
24
|
+
gem 'bio'
|
25
|
+
else
|
26
|
+
$stderr.puts "gem 'bio', #{gem_version.inspect}" if BioRubyTestDebug
|
27
|
+
gem 'bio', gem_version
|
28
|
+
end
|
29
|
+
end
|
30
|
+
BioRubyTestGem = gem_version
|
31
|
+
end
|
32
|
+
|
33
|
+
unless defined? BioRubyTestLibPath then
|
34
|
+
libpath = ENV['BIORUBY_TEST_LIB']
|
35
|
+
unless libpath then
|
36
|
+
libpath = Pathname.new(File.join(File.dirname(__FILE__),
|
37
|
+
"..", "lib")).cleanpath.to_s
|
38
|
+
end
|
39
|
+
|
40
|
+
# do not add path to $: if BIORUBY_TEST_LIB is empty string
|
41
|
+
# or BioRubyTestGem is true.
|
42
|
+
if (libpath and libpath.empty?) or BioRubyTestGem then
|
43
|
+
libpath = nil
|
44
|
+
end
|
45
|
+
|
46
|
+
if libpath then
|
47
|
+
libpath.freeze
|
48
|
+
|
49
|
+
unless $:[0] == libpath then
|
50
|
+
$:.unshift(libpath)
|
51
|
+
if BioRubyTestDebug then
|
52
|
+
$stderr.puts "Added #{libpath.inspect} to $:."
|
53
|
+
end
|
54
|
+
else
|
55
|
+
if BioRubyTestDebug then
|
56
|
+
$stderr.puts "NOT added #{libpath.inspect} to $:. because it is already on the top of $:."
|
57
|
+
end
|
58
|
+
end
|
59
|
+
end
|
60
|
+
|
61
|
+
# (String or nil) Path to be added to $:.
|
62
|
+
# It may or may not be the path of bioruby.
|
63
|
+
BioRubyTestLibPath = libpath
|
64
|
+
|
65
|
+
if BioRubyTestDebug then
|
66
|
+
$stderr.print "$: = [", "\n"
|
67
|
+
$stderr.puts($:.collect { |x| "\t#{x.inspect}" }.join(",\n"))
|
68
|
+
$stderr.print "]", "\n"
|
69
|
+
end
|
70
|
+
end #BioRubyTestLibPath
|
71
|
+
|
72
|
+
unless defined? BioRubyTestDataPath and BioRubyTestDataPath
|
73
|
+
datapath = ENV['BIORUBY_TEST_DATA']
|
74
|
+
if datapath.to_s.empty? then
|
75
|
+
datapath = Pathname.new(File.join(File.dirname(__FILE__),
|
76
|
+
"data")).cleanpath.to_s
|
77
|
+
end
|
78
|
+
datapath.freeze
|
79
|
+
|
80
|
+
# (String) Path to the test data.
|
81
|
+
BioRubyTestDataPath = datapath
|
82
|
+
|
83
|
+
if BioRubyTestDebug then
|
84
|
+
$stderr.print "DataPath = ", BioRubyTestDataPath.inspect, "\n"
|
85
|
+
end
|
86
|
+
end
|