Module: BioCReader
- Defined in:
- lib/simple_bioc/bioc_reader.rb
Class Method Summary collapse
- .read(path, options) ⇒ Object
- .read_annotation(xml, annotation, options = {}) ⇒ Object
- .read_collection(xml, collection, options = {}) ⇒ Object
- .read_document(xml, document, options = {}) ⇒ Object
- .read_from_file_or_string(file_or_string, options) ⇒ Object
- .read_infon(xml, obj) ⇒ Object
- .read_int(xml, name) ⇒ Object
- .read_location(xml, location, options = {}) ⇒ Object
- .read_node(xml, node, options = {}) ⇒ Object
- .read_passage(xml, passage, options = {}) ⇒ Object
- .read_recursive(xml, obj, name, options = {}) ⇒ Object
- .read_relation(xml, relation, options = {}) ⇒ Object
- .read_sentence(xml, sentence, options = {}) ⇒ Object
- .read_text(xml, name) ⇒ Object
Class Method Details
.read(path, options) ⇒ Object
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# File 'lib/simple_bioc/bioc_reader.rb', line 7 def read(path, ) collection = nil File.open(path) do |file| collection = read_from_file_or_string(file, ) end collection end |
.read_annotation(xml, annotation, options = {}) ⇒ Object
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# File 'lib/simple_bioc/bioc_reader.rb', line 101 def read_annotation(xml, annotation, = {}) annotation.id = xml["id"] annotation.text = read_text(xml, "text") read_infon(xml, annotation) read_recursive(xml, annotation, "location") true end |
.read_collection(xml, collection, options = {}) ⇒ Object
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# File 'lib/simple_bioc/bioc_reader.rb', line 60 def read_collection(xml, collection, = {}) collection.source = read_text(xml, "source") collection.date = read_text(xml, "date") collection.key = read_text(xml, "key") read_infon(xml, collection) read_recursive(xml, collection, "document", ) end |
.read_document(xml, document, options = {}) ⇒ Object
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# File 'lib/simple_bioc/bioc_reader.rb', line 68 def read_document(xml, document, = {}) document.id = read_text(xml, "id") if [:documents].kind_of?(Array) && ![:documents].include?(document.id) return false end read_infon(xml, document) read_recursive(xml, document, "passage") read_recursive(xml, document, "relation") document.adjust_ref true end |
.read_from_file_or_string(file_or_string, options) ⇒ Object
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# File 'lib/simple_bioc/bioc_reader.rb', line 16 def read_from_file_or_string(file_or_string, ) collection = nil xml_doc = Nokogiri::XML(file_or_string) do |config| config.noent.strict.noblanks end xml = xml_doc.at_xpath("//collection") if xml.nil? fail 'Wrong format' end collection = SimpleBioC::Collection.new read_collection(xml, collection, ) collection end |
.read_infon(xml, obj) ⇒ Object
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# File 'lib/simple_bioc/bioc_reader.rb', line 42 def read_infon(xml, obj) ret = xml.xpath("infon") return if ret.nil? ret.each{ |i| obj.infons[i["key"]] = i.content} end |
.read_int(xml, name) ⇒ Object
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# File 'lib/simple_bioc/bioc_reader.rb', line 37 def read_int(xml, name) val = read_text(xml, name) val && val.to_i end |
.read_location(xml, location, options = {}) ⇒ Object
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# File 'lib/simple_bioc/bioc_reader.rb', line 116 def read_location(xml, location, = {}) location.offset = xml["offset"] location.length = xml["length"] location.original_offset = xml["original_offset"] true end |
.read_node(xml, node, options = {}) ⇒ Object
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# File 'lib/simple_bioc/bioc_reader.rb', line 123 def read_node(xml, node, = {}) node.refid = xml["refid"] node.role = xml["role"] true end |
.read_passage(xml, passage, options = {}) ⇒ Object
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# File 'lib/simple_bioc/bioc_reader.rb', line 80 def read_passage(xml, passage, = {}) passage.text = read_text(xml, "text") passage.offset = read_int(xml, "offset") read_infon(xml, passage) read_recursive(xml, passage, "sentence") read_recursive(xml, passage, "annotation") read_recursive(xml, passage, "relation") passage.adjust_annotation_offsets true end |
.read_recursive(xml, obj, name, options = {}) ⇒ Object
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# File 'lib/simple_bioc/bioc_reader.rb', line 48 def read_recursive(xml, obj, name, = {}) target_class = SimpleBioC.const_get(name.capitalize) ret = xml.xpath(name) return if ret.nil? ret.each do |node| instance = target_class.new(obj) ret = send(:"read_#{name}", node, instance, ) arr = obj.instance_variable_get(:"@#{name}s") arr << instance if ret && !arr.nil? end end |
.read_relation(xml, relation, options = {}) ⇒ Object
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# File 'lib/simple_bioc/bioc_reader.rb', line 109 def read_relation(xml, relation, = {}) relation.id = xml["id"] read_infon(xml, relation) read_recursive(xml, relation, "node") true end |
.read_sentence(xml, sentence, options = {}) ⇒ Object
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# File 'lib/simple_bioc/bioc_reader.rb', line 91 def read_sentence(xml, sentence, = {}) sentence.text = read_text(xml, "text") sentence.offset = read_int(xml, "offset") read_infon(xml, sentence) read_recursive(xml, sentence, "annotation") read_recursive(xml, sentence, "relation") sentence.adjust_annotation_offsets true end |
.read_text(xml, name) ⇒ Object
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# File 'lib/simple_bioc/bioc_reader.rb', line 32 def read_text(xml, name) node = xml.at_xpath(name) node && node.content end |