simple_bioc 0.0.20 → 0.0.21

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 974019424b72ab4bf3bd87d9444c6f2b04b009b4
+  metadata.gz: 344d68b7d1e117a05da96939c1ace1ff10cb630f
+  data.tar.gz: 549cfc037ec425cfa53815238aab5628044346c6
 SHA512:
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data/lib/simple_bioc/bioc_reader.rb

@@ -84,7 +84,6 @@ module BioCReader
     read_recursive(xml, passage, "sentence")
     read_recursive(xml, passage, "annotation")
     read_recursive(xml, passage, "relation")
-    passage.adjust_annotation_offsets
     true
   end
 
@@ -94,7 +93,6 @@ module BioCReader
     read_infon(xml, sentence)
     read_recursive(xml, sentence, "annotation")
     read_recursive(xml, sentence, "relation")
-    sentence.adjust_annotation_offsets
     true
   end
 

data/lib/simple_bioc/passage.rb

@@ -1,8 +1,5 @@
-require 'simple_bioc/location_adjuster'
 module SimpleBioC
   class Passage
-    include LocationAdjuster
-
     attr_accessor :offset, :text, :infons, :sentences, :annotations, :relations
     attr_reader :document
 

data/lib/simple_bioc/sentence.rb

@@ -1,8 +1,5 @@
-require 'simple_bioc/location_adjuster'
 module SimpleBioC
   class Sentence
-    include LocationAdjuster
-
     attr_accessor :offset, :text, :infons, :annotations, :relations
     attr_reader :passage
 

data/lib/simple_bioc/version.rb

@@ -1,3 +1,3 @@
 module SimpleBioC
-  VERSION = "0.0.20"
+  VERSION = "0.0.21"
 end

data/lib/simple_bioc.rb

@@ -42,10 +42,6 @@ module SimpleBioC
     BioCReader.read_from_file_or_string(file, options)
   end
 
-  def merge(dest_bioc, src_bioc)
-    return BioCMerger.merge(dest_bioc, src_bioc)
-  end
-
   # parse a BioC XML string and convert it into a collection instance
   # 
   # ==== Arguments

data/spec/file_check_spec.rb

@@ -11,62 +11,10 @@ describe "File Check" do
     end
   end
 
-  it "should merge documents successfully" do
-    col1 = SimpleBioC.from_xml("./xml/merge/9864355.xml")
-    col2 = SimpleBioC.from_xml("./xml/merge/9864355_1.xml")
-    col3 = SimpleBioC.from_xml("./xml/merge/9864355_2.xml")
-    col4 = SimpleBioC.from_xml("./xml/merge/9864355_3.xml")
-
-    SimpleBioC.merge(col1, col2)
-    SimpleBioC.merge(col1, col3)
-    SimpleBioC.merge(col1, col4)
-    output = SimpleBioC.to_xml(col1)
-    File.write("./xml/merge/output.xml", output)
-    puts "merge1"
-    col5 = SimpleBioC.from_xml("./xml/merge/output.xml")
-  end 
-
-  it "should merge same documents successfully" do
-    col1 = SimpleBioC.from_xml("./xml/10330397_gene.xml")
-    col2 = SimpleBioC.from_xml("./xml/10330397_ppimention.xml")
-
-    SimpleBioC.merge(col1, col2)
-    output = SimpleBioC.to_xml(col1)
-    File.write("./xml/merge/output_10330397.xml", output)
-    puts "merge2"
-    col5 = SimpleBioC.from_xml("./xml/merge/output_10330397.xml")
-  end 
-
   it "should fix location problem" do
     col1 = SimpleBioC.from_xml("./xml/merge/10366597_error.xml")
     output = SimpleBioC.to_xml(col1)
     File.write("./xml/merge/output_10366597.xml", output)
     col5 = SimpleBioC.from_xml("./xml/merge/output_10366597.xml")
   end 
-
-
-  it "should merge documents successfully with different order" do
-    col4 = SimpleBioC.from_xml("./xml/merge/9864355.xml")
-    col3 = SimpleBioC.from_xml("./xml/merge/9864355_1.xml")
-    col1 = SimpleBioC.from_xml("./xml/merge/9864355_2.xml")
-    col2 = SimpleBioC.from_xml("./xml/merge/9864355_3.xml")
-
-    SimpleBioC.merge(col1, col2)
-    SimpleBioC.merge(col1, col3)
-    SimpleBioC.merge(col1, col4)
-    output = SimpleBioC.to_xml(col1)
-    File.write("./xml/merge/output.xml", output)
-    puts "merge12"
-    col5 = SimpleBioC.from_xml("./xml/merge/output.xml")
-  end 
-
-  it "should load XML files successfully" do
-    Dir["./xml/*.xml"].each do |file_path|
-      puts "self-merge #{file_path}"
-      collection1 = SimpleBioC.from_xml(file_path)
-      collection2 = SimpleBioC.from_xml(file_path)
-      SimpleBioC.merge(collection1, collection2)
-      output = SimpleBioC.to_xml(collection1)
-    end
-  end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: simple_bioc
 version: !ruby/object:Gem::Version
-  version: 0.0.20
+  version: 0.0.21
 platform: ruby
 authors:
 - Dongseop Kwon
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-02-04 00:00:00.000000000 Z
+date: 2016-02-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri
@@ -185,13 +185,11 @@ files:
 - html/table_of_contents.html
 - lib/simple_bioc.rb
 - lib/simple_bioc/annotation.rb
-- lib/simple_bioc/bioc_merger.rb
 - lib/simple_bioc/bioc_reader.rb
 - lib/simple_bioc/bioc_writer.rb
 - lib/simple_bioc/collection.rb
 - lib/simple_bioc/document.rb
 - lib/simple_bioc/location.rb
-- lib/simple_bioc/location_adjuster.rb
 - lib/simple_bioc/node.rb
 - lib/simple_bioc/node_base.rb
 - lib/simple_bioc/passage.rb

data/lib/simple_bioc/bioc_merger.rb

@@ -1,229 +0,0 @@
-require 'nokogiri'
-
-Dir[File.dirname(__FILE__) + '/*.rb'].each {|file| require file }
-
-module BioCMerger
-  module_function
-
-  def merge(dest_collection, src_collection)
-    errors = []
-    warnings = []
-    id_map = {}
-
-    if dest_collection.documents.size != 1 || src_collection.documents.size != 1
-      warnings << 'Only the first documents will be merged'
-    end
-
-    doc_d = dest_collection.documents[0]
-    doc_s = src_collection.documents[0]
-
-    copy_infons(dest_collection, src_collection)
-    dest_collection.source = src_collection.source if dest_collection.source.nil? || dest_collection.source.empty?
-    dest_collection.date = src_collection.date if dest_collection.date.nil? || dest_collection.date.empty?
-    dest_collection.key = src_collection.key if dest_collection.key.nil? || dest_collection.key.empty?
-
-    copy_infons(doc_d, doc_s)
-    copy_relations(doc_d, doc_d, doc_s, id_map)
-
-    if doc_d.passages.size != doc_s.passages.size
-      warnings << 'Passages will not be merged because the numbers of passages in documents are different'
-    end
-
-    doc_d.passages.each_with_index do |p_d, index|
-      p_s = doc_s.passages[index]
-      if p_d.nil? || p_s.nil?
-        warnings << 'The number of sentences in pages should be the same'
-      elsif blank?(p_d.text) && blank?(p_s.text) && p_d.sentences.size != p_s.sentences.size
-        warnings << 'The number of sentences in pages should be the same'
-      end
-    end
-
-    doc_d.passages.each_with_index do |p_d, index|
-      p_s = doc_s.passages[index]
-      next if p_d.nil? || p_s.nil?
-      copy_relations(doc_d, p_d, p_s, id_map)
-      if p_d.sentences.size == p_s.sentences.size
-        p_d.sentences.each_with_index do |s_d, index|
-          s_s = p_s.sentences[index]
-          copy_infons(s_d, s_s)
-          copy_text(s_d, s_s)
-          copy_relations(doc_d, s_d, s_s, id_map)
-          copy_annotations(doc_d, s_d, s_s, id_map)
-          s_d.adjust_annotation_offsets
-        end
-      elsif p_d.sentences.size == 0
-        p_d.text = p_s.sentences.map{|s| s.text}.join(" ") if blank?(p_d.text)
-        p_s.sentences.each do |s|
-          copy_relations(doc_d, p_d, s, id_map)
-          copy_annotations(doc_d, p_d, s, id_map)
-        end
-      elsif p_s.sentences.size == 0
-        if p_d.sentences.size > 0
-          # dest has sentences, but src has only passages. 
-          p_d.text = p_d.sentences.map{|s| s.text}.join(" ") if blank?(p_d.text)
-          p_d.sentences.each do |s|
-            s.annotations.each do |a|
-              a.clear_sentence
-              p_d.annotations << a
-            end
-            s.relations.each do |r|
-              r.clear_sentence
-              p_d.relations << r
-            end
-          end
-          p_d.sentences.clear
-        else
-          copy_text(p_d, p_s)
-        end
-      end
-      copy_annotations(doc_d, p_d, p_s, id_map)
-      p_d.adjust_annotation_offsets
-    end
-    puts warnings
-  end
-
-  def adjust_relation_refids(doc, id_map)
-    adjust_relation_refid(doc, id_map)
-    doc.passages.each do |p|
-      adjust_relation_refid(p, id_map)
-      p.sentences.each do |s|
-        adjust_relation_refid(s, id_map)
-      end
-    end
-  end
-
-  def adjust_relation_refid(obj, id_map) 
-    return if obj.nil?
-    obj.relations.each do |r|
-      next if r.original.nil?
-      r.nodes.each do |n|
-        new_id = id_map[n.refid]
-        n.refid = new_id unless new_id.nil?
-        n.adjust_ref
-      end
-    end
-  end
-
-  def copy_relations(doc, dest, src, id_map)
-    return if src.nil?
-    src.relations.each do |r|
-      copy_relation(doc, dest, r, id_map)
-    end
-  end
-
-  def copy_annotations(doc, dest, src, id_map)
-    return if src.nil?
-    src.annotations.each do |a|
-      copy_annotation(doc, dest, a, id_map)
-    end
-  end
-  def copy_relation(doc, dest, relation, id_map)
-    new_r = nil
-    need_add = true
-    dest.relations.each do |r|
-      if r.id == relation.id
-        new_r = r
-        need_add = false
-        break
-      end
-    end
-    if new_r.nil?
-      new_r = SimpleBioC::Relation.new(dest)
-      new_r.id = choose_id(doc, relation.id, id_map)
-      new_r.original = relation
-    end
-
-    relation.nodes.each do |n|
-      found = false
-      new_r.nodes.each do |old_n|
-        if n.refid == old_n.refid && n.role == old_n.role
-          found = true
-          break
-        end
-      end
-      unless found
-        node = SimpleBioC::Node.new(new_r)
-        node.refid = n.refid
-        node.role = n.role
-        new_r.nodes << node
-      end
-    end
-    copy_infons(new_r, relation)
-    if need_add 
-      dest.relations << new_r
-    end
-  end
-
-  def copy_annotation(doc, dest, annotation, id_map)
-    new_a = nil
-    need_add = true
-    dest.annotations.each do |a|
-      if a.id == annotation.id && a.text == annotation.text
-        new_a = a
-        need_add = false
-        break
-      end
-    end
-    if new_a.nil?
-      new_a = SimpleBioC::Annotation.new(dest)
-      new_a.id = choose_id(doc, annotation.id, id_map)
-      new_a.text = annotation.text
-      new_a.locations = []
-    end
-
-    annotation.locations.each do |l|
-      found = false
-      new_a.locations.each do |old_l|
-        if l.offset == old_l.offset && l.length == old_l.length
-          found = true
-          break
-        end
-      end
-      unless found
-        new_l = SimpleBioC::Location.new(new_a)
-        new_l.offset = l.offset
-        new_l.length = l.length 
-        new_a.locations << new_l
-      end
-    end
-    copy_infons(new_a, annotation)
-    if need_add
-      dest.annotations << new_a
-    end
-  end
-
-  def choose_id(doc, id, id_map) 
-    new_id = id || "id"
-    node = doc.find_node(new_id)
-
-    until node.nil? do
-      new_id = new_id + "_c"
-      node = doc.find_node(new_id)
-    end
-
-    if new_id != id
-      id_map[id] = new_id
-    end
-    return new_id
-  end
-
-  def copy_text(dest, src)
-    if blank?(dest.text) && !blank?(src.text)
-      dest.text = src.text
-    end
-  end
-
-  def blank?(text)
-    return text.nil? || text.empty?
-  end
-
-  def copy_infons(dest, src)
-    src.infons.each do |k, v|
-      if dest.infons[k].nil?
-        dest.infons[k] = v
-      elsif dest.infons[k] != v
-        
-      end
-    end
-  end
-end

data/lib/simple_bioc/location_adjuster.rb

@@ -1,45 +0,0 @@
-module SimpleBioC
-  module LocationAdjuster
-    def adjust_annotation_offsets
-      obj = self
-      return if obj.nil? || obj.annotations.nil?
-      obj.annotations.each do |a|
-        positions = find_all_locations(obj, a.text)
-        next a.locations.nil?
-        a.locations.each do |l|
-          next if l.nil? || l == false
-          # l.original_offset = l.offset.to_i if l.original_offset.nil?
-          l.offset = choose_offset_candidate(l.offset, positions)
-        end
-      end
-    end
-    
-    module_function
-
-    def find_all_locations(obj, text)
-      positions = []
-      return positions if obj.nil? || obj.text.nil?
-      pos = obj.text.index(text)
-      until pos.nil? 
-        positions << (pos + obj.offset)
-        pos = obj.text.index(text, pos + 1)
-      end
-      return positions
-    end
-
-    def choose_offset_candidate(offset, positions)
-      return offset if positions.nil?
-      min_diff = 99999
-      offset = offset.to_i
-      ret = offset
-      positions.each do |p|
-        diff = (offset - p).abs
-        if diff < min_diff
-          ret = p 
-          min_diff = diff
-        end
-      end
-      return ret
-    end
-  end
-end