Module: Association
- Defined in:
- lib/rbbt/association.rb,
lib/rbbt/association/index.rb
Defined Under Namespace
Modules: Index
Class Attribute Summary collapse
-
.databases ⇒ Object
Returns the value of attribute databases.
Class Method Summary collapse
- .add_reciprocal(tsv) ⇒ Object
- .calculate_headers(key_field, fields, spec) ⇒ Object
-
.index(file, options = {}, persist_options = {}) ⇒ Object
def self.get_index(index_file, write = false) Persist.open_tokyocabinet(index_file, write, :list, TokyoCabinet::BDB).tap{|r| r.unnamed = true; Association::Index.setup r } end.
- .load_tsv(file, options) ⇒ Object
- .open(file, options = {}, persist_options = {}) ⇒ Object
-
.open_tsv(file, source, source_header, target, target_header, all_fields, options) ⇒ Object
{{{ Open.
- .parse_field_specification(spec) ⇒ Object
- .resolve_field(name, fields) ⇒ Object
- .specs(all_fields, options = {}) ⇒ Object
- .translate_tsv(tsv, source_final_format, target_final_format) ⇒ Object
Class Attribute Details
.databases ⇒ Object
Returns the value of attribute databases.
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# File 'lib/rbbt/association.rb', line 7 def databases @databases end |
Class Method Details
.add_reciprocal(tsv) ⇒ Object
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# File 'lib/rbbt/association.rb', line 13 def self.add_reciprocal(tsv) new = {} tsv.with_unnamed do tsv.through do |key, values| new[key] ||= values Misc.zip_fields(values).each do |fields| target, *rest = fields target_values = new[target] || tsv[target] || [[]] * values.length zipped_target_values = Misc.zip_fields(target_values) zipped_target_values << ([key].concat rest) new_values = Misc.zip_fields zipped_target_values new[target] = new_values end end end tsv.annotate(new) new end |
.calculate_headers(key_field, fields, spec) ⇒ Object
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# File 'lib/rbbt/association.rb', line 56 def self.calculate_headers(key_field, fields, spec) all_fields = [key_field].concat fields if fields and key_field field, header, format = parse_field_specification spec if spec if field and key_field == field and not all_fields.include? field field, header, format = resolve_field field, all_fields end [field, header, format] end |
.index(file, options = {}, persist_options = {}) ⇒ Object
def self.get_index(index_file, write = false)
Persist.open_tokyocabinet(index_file, write, :list, TokyoCabinet::BDB).tap{|r| r.unnamed = true; Association::Index.setup r }
end
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# File 'lib/rbbt/association.rb', line 251 def self.index(file, = {}, = {}) = {} if .nil? = Misc.add_defaults , :persist => true = {} if .nil? Persist.persist_tsv(file, nil, , {:persist => true, :prefix => "Association Index"}.merge().merge(:engine => TokyoCabinet::BDB, :serializer => :clean)) do |assocs| undirected = [:undirected] if file tsv = TSV === file ? file : Association.open(file, , .merge(:persist => false)) fields = tsv.fields key_field = [tsv.key_field, fields.first.split(":").last, undirected ? "undirected" : nil].compact * "~" TSV.setup(assocs, :key_field => key_field, :fields => fields[1..-1], :type => :list, :serializer => :list) tsv.with_unnamed do tsv.with_monitor :desc => "Extracting associations" do case tsv.type when :list tsv.through do |source, values| target, *rest = values next if source.nil? or source.empty? or target.nil? or target.empty? key = [source, target] * "~" assocs[key] = rest end when :flat tsv.through do |source, targets| next if source.nil? or source.empty? or targets.nil? or targets.empty? targets.each do |target| next if target.nil? or target.empty? key = [source, target] * "~" assocs[key] = nil end end when :double tsv.through do |source, values| next if values.empty? next if source.nil? next if values.empty? targets = values.first rest = Misc.zip_fields values[1..-1] annotations = rest.length > 1 ? targets.zip(rest) : targets.zip(rest * targets.length) annotations.each do |target, info| next if target.nil? key = [source, target] * "~" assocs[key] = info end end else raise "Type not supported: #{tsv.type}" end end end else key_field, fields = .values_at :key_field, :fields TSV.setup(assocs, :key_field => key_field, :fields => fields[1..-1], :type => :list, :serializer => :list) end assocs.close assocs end.tap do |assocs| Association::Index.setup assocs end end |
.load_tsv(file, options) ⇒ Object
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# File 'lib/rbbt/association.rb', line 191 def self.load_tsv(file, ) undirected = Misc. , :undirected case file when Proc return load_tsv(file.call, ) when TSV key_field, *fields = all_fields = file.all_fields else key_field, *fields = all_fields = TSV.parse_header(file, .merge(:fields => nil, :key_field => nil)).all_fields end source, source_header, source_format, target, target_header, target_format = specs(all_fields, ) Log.low("Loading associations from: #{ Misc.fingerprint file }") Log.low("sources: #{ [source, source_header, source_format].join(", ") }") Log.low("targets: #{ [target, target_header, target_format].join(", ") }") tsv = open_tsv(file, source, source_header, target, target_header, all_fields, ) tsv = translate_tsv(tsv, source_format, target_format) tsv = add_reciprocal(tsv) if undirected tsv end |
.open(file, options = {}, persist_options = {}) ⇒ Object
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# File 'lib/rbbt/association.rb', line 218 def self.open(file, = {}, = {}) = {} if .nil? = {} if .nil? namespace = [:namespace] old_file, file = file, file.sub('NAMESPACE', namespace) if namespace and String === file old_file.annotate file if Path === old_file Persist.persist_tsv(file, nil, , {:persist => true, :prefix => "Association"}.merge()) do |data| = .clone tsv = load_tsv(file, ) tsv.annotate(data) data.serializer = tsv.type if TokyoCabinet::HDB === data tsv.with_unnamed do tsv.each do |k,v| next if v.nil? data[k] = v end end data end end |
.open_tsv(file, source, source_header, target, target_header, all_fields, options) ⇒ Object
{{{ Open
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# File 'lib/rbbt/association.rb', line 69 def self.open_tsv(file, source, source_header, target, target_header, all_fields, ) fields = all_fields.dup fields.delete source fields.delete target fields.unshift target = .merge({ :persist => false, :key_field => all_fields.index(source), :fields => fields.collect{|f| String === f ? all_fields.index(f): f }, :type => [:type].to_s == :flat ? :flat : :double, :merge => [:type].to_s == :flat ? false : true }) # Preserve first line, which would have been considered a header otherwise ["header_hash"] = "#" if ["header_hash"] == "" field_headers = all_fields.values_at *[:fields] tsv = case file when TSV if file.fields == field_headers file else file.reorder(source, field_headers) end else TSV.open(file, ) end tsv.fields = field_headers tsv.key_field = source # Fix source header if source_header and tsv.key_field != source_header tsv.key_field = source_header end # Fix target header if target_header and tsv.fields.first != target_header tsv.fields = tsv.fields.collect{|f| f == target ? target_header : f } end tsv end |
.parse_field_specification(spec) ⇒ Object
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# File 'lib/rbbt/association.rb', line 46 def self.parse_field_specification(spec) return [2,nil,nil] if Fixnum === spec spec = spec.split "=>" unless Array === spec field_part, final_format = spec field, format = field_part.split "=~" [field, format, final_format] end |
.resolve_field(name, fields) ⇒ Object
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# File 'lib/rbbt/association.rb', line 39 def self.resolve_field(name, fields) entity_type = Entity.formats[name] return "Field #{ name } could not be resolved: #{fields}" if entity_type.nil? field = fields.select{|f| Entity.formats[f] == entity_type}.first [field, nil, name] end |
.specs(all_fields, options = {}) ⇒ Object
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# File 'lib/rbbt/association.rb', line 148 def self.specs(all_fields, = {}) source_spec, source_format, target_spec, target_format, format, key_field, fields = Misc. , :source, :source_format, :target, :target_format, :format, :key_field, :fields if key_field and all_fields key_pos = (Fixnum === key_field ? key_field : all_fields.index(key_field) ) key_field = all_fields[key_pos] else key_field = all_fields.first if all_fields end if fields and all_fields field_pos = fields.collect{|f| Fixnum === f ? f : fields.index(f) } fields = all_fields.values_at *field_pos else fields = all_fields[1..-1] if all_fields end source, source_header, orig_source_format = calculate_headers(key_field, fields, source_spec) source_format ||= orig_source_format source = key_field if source.nil? source = key_field if source == :key source_header ||= source target, target_header, orig_target_format = calculate_headers(key_field, fields, target_spec) target_format ||= orig_target_format target = (key_field == source ? fields.first : (([key_field] + fields) - [source]).first) if target.nil? target = key_field if target == :key target_header ||= target case format when String source_format ||= format if Entity.formats[source_header] == Entity.formats[format] target_format ||= format if Entity.formats[target_header] == Entity.formats[format] when Hash _type = Entity.formats[source_header].to_s source_format ||= format[_type] if format.include? _type _type = Entity.formats[target_header].to_s target_format ||= format[_type] if format.include? _type end [source, source_header, source_format, target, target_header, target_format] end |
.translate_tsv(tsv, source_final_format, target_final_format) ⇒ Object
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# File 'lib/rbbt/association.rb', line 115 def self.translate_tsv(tsv, source_final_format, target_final_format) source_field = tsv.key_field target_field = tsv.fields.first if source_final_format and source_field != source_final_format and Entity.formats[source_field] and Entity.formats[source_final_format].all_formats.include? source_field Log.debug("Changing source format from #{tsv.key_field} to #{source_final_format}") tsv.with_unnamed do tsv = tsv.change_key source_final_format, :identifiers => Organism.identifiers(tsv.namespace), :persist => true end end # Translate target if target_final_format and target_field != target_final_format and Entity.formats[target_field] and Entity.formats[target_field] == Entity.formats[target_final_format] Log.debug("Changing target format from #{tsv.fields.first} to #{target_final_format}") save_key_field = tsv.key_field tsv.key_field = "MASKED" tsv.with_unnamed do tsv = tsv.swap_id tsv.fields.first, target_final_format, :identifiers => Organism.identifiers(tsv.namespace), :persist => true end tsv.key_field = save_key_field end tsv end |