simple_bioc 0.0.16 → 0.0.17

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: feecd4ce8d52cafa27b5bc62c3da638352198bf4
-  data.tar.gz: 647f59cbc0be3c0aebccf06a07c1dfd6778c92b7
+  metadata.gz: 898191c87e6e9a0a46e7b7c6638370cffc0a5d25
+  data.tar.gz: 1bf48d3b2bdee74d55beefe4769a7376d066b8ce
 SHA512:
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-  data.tar.gz: ac121fdc97a23a85456681fdf6e532d6eae6cf6fe17788822d4a3f7ce1e97b1b9febcfdcc2499152ab9da0cddd190e3f895aefa51661f656b0718499d0238663
+  metadata.gz: 742f7bcc0521d1f4e92d1fd2027e613c9d959a272da3376660746edcd9fce4013ef43978859846e63616702d65ce87e46fb1f5c9e3c8de7ac312a072972ec22b
+  data.tar.gz: 52447cdb3c44fb1e13cafe44b45ad72139cde34322e920bdd039babc420c4f68fdf985a29154bb1fbfda078bf1f6d9a35879fb72776f0772d27f6dccd76d7961

data/lib/simple_bioc/annotation.rb

@@ -9,7 +9,7 @@ module SimpleBioC
     end
 
     def to_s
-      "Annotation:#{id} #{text}"
+      "Annotation:#{@id} #{@text}"
     end
   end
 end

data/lib/simple_bioc/bioc_reader.rb

@@ -40,12 +40,16 @@ module BioCReader
   end
 
   def read_infon(xml, obj)
-    xml.xpath("infon").each{ |i| obj.infons[i["key"]] = i.content}
+    ret = xml.xpath("infon")
+    return if ret.nil?
+    ret.each{ |i| obj.infons[i["key"]] = i.content}
   end
 
   def read_recursive(xml, obj, name, options = {})
     target_class = SimpleBioC.const_get(name.capitalize)
-    xml.xpath(name).each do |node|
+    ret = xml.xpath(name)
+    return if ret.nil?
+    ret.each do |node|
       instance = target_class.new(obj)
       ret = send(:"read_#{name}", node, instance, options)
       obj.instance_variable_get(:"@#{name}s")  << instance if ret

data/lib/simple_bioc/bioc_writer.rb

@@ -15,6 +15,7 @@ module BioCWriter
   end
 
   def write_infon(xml, obj)
+    return if obj.infons.nil?
     obj.infons.each do |k, v| 
       xml.infon(:key => k) {
         xml.text v
@@ -28,7 +29,7 @@ module BioCWriter
       xml.date collection.date
       xml.key collection.key
       write_infon(xml, collection)
-      collection.documents.each{|d| write_document(xml, d)}
+      collection.documents.each{|d| write_document(xml, d)} unless collection.documents.nil?
     }
   end
 
@@ -36,8 +37,8 @@ module BioCWriter
     xml.document {
       xml.id_ document.id
       write_infon(xml, document)
-      document.passages.each{|p| write_passage(xml, p)}
-      document.relations.each{|r| write_relation(xml, r)}
+      document.passages.each{|p| write_passage(xml, p)} unless document.passages.nil?
+      document.relations.each{|r| write_relation(xml, r)} unless document.relations.nil?
     }
   end
 
@@ -46,9 +47,9 @@ module BioCWriter
       write_infon(xml, passage)
       xml.offset passage.offset
       xml.text_ passage.text unless passage.text.nil?
-      passage.annotations.each{|a| write_annotation(xml, a)}
-      passage.sentences.each{|s| write_sentence(xml, s)}
-      passage.relations.each{|r| write_relation(xml, r)}
+      passage.annotations.each{|a| write_annotation(xml, a)} unless passage.annotations.nil?
+      passage.sentences.each{|s| write_sentence(xml, s)} unless passage.sentences.nil?
+      passage.relations.each{|r| write_relation(xml, r)} unless passage.relations.nil?
     }
   end
 
@@ -57,8 +58,8 @@ module BioCWriter
       write_infon(xml, sentence)
       xml.offset sentence.offset
       xml.text_ sentence.text unless sentence.text.nil?
-      sentence.annotations.each{|a| write_annotation(xml, a)}
-      sentence.relations.each{|r| write_relation(xml, r)}
+      sentence.annotations.each{|a| write_annotation(xml, a)} unless sentence.annotations.nil?
+      sentence.relations.each{|r| write_relation(xml, r)} unless sentence.relations.nil?
     }
   end
 
@@ -70,7 +71,7 @@ module BioCWriter
     end
     xml.annotation(attribute) {
       write_infon(xml, annotation)
-      annotation.locations.each{|l| write_location(xml, l)}
+      annotation.locations.each{|l| write_location(xml, l)} unless annotation.locations.nil?
       xml.text_ annotation.text
     }
   end
@@ -83,7 +84,7 @@ module BioCWriter
     end
     xml.relation(attribute) {
       write_infon(xml, relation)
-      relation.nodes.each{|n| write_node(xml, n)}
+      relation.nodes.each{|n| write_node(xml, n)} unless relation.nodes.nil?
     }
   end
 

data/lib/simple_bioc/document.rb

@@ -14,8 +14,8 @@ module SimpleBioC
     end
 
     def find_node(id)
-      relations.each{|r| return r if r.id == id}
-      passages.each do |p|
+      @relations.each{|r| return r if r.id == id}
+      @passages.each do |p|
         ret = p.find_node(id)
         return ret unless ret.nil?
       end
@@ -27,12 +27,12 @@ module SimpleBioC
     end
 
     def each_relation
-      relations.each{|r| yield r}
-      passages.each{|p| p.each_relation{|r| yield r}}
+      @relations.each{|r| yield r}
+      @passages.each{|p| p.each_relation{|r| yield r}}
     end
 
     def to_s
-      "Document:#{id}"
+      "Document:#{@id}"
     end
   end
 end

data/lib/simple_bioc/location_adjuster.rb

@@ -2,9 +2,10 @@ module SimpleBioC
   module LocationAdjuster
     def adjust_annotation_offsets
       obj = self
-      return if obj.nil?
+      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|
           l.original_offset = l.offset.to_i if l.original_offset.nil?
           l.offset = choose_offset_candidate(l.offset, positions)
@@ -26,6 +27,7 @@ module SimpleBioC
     end
 
     def choose_offset_candidate(offset, positions)
+      return offset if positions.nil?
       min_diff = 99999
       offset = offset.to_i
       ret = offset

data/lib/simple_bioc/node.rb

@@ -8,11 +8,11 @@ module SimpleBioC
     end
 
     def adjust_ref
-      @ref = relation.document.find_node(refid)
+      @ref = @relation.document.find_node(@refid)
     end
 
     def to_c
-      "Node @#{refid}: #{role})"
+      "Node @#{@refid}: #{@role})"
     end
   end
 end

data/lib/simple_bioc/node_base.rb

@@ -6,10 +6,10 @@ module SimpleBioC
 
     def initialize(parent)
       @infons = {}
+      @id = nil
       @document = parent if parent.is_a? Document
       @passage  = parent if parent.is_a? Passage
       @sentence = parent if parent.is_a? Sentence 
-
       @passage  = @sentence.passage unless @sentence.nil?
       @document = @passage.document unless @passage.nil?
     end

data/lib/simple_bioc/passage.rb

@@ -15,12 +15,12 @@ module SimpleBioC
     end
 
     def to_s
-      "Passage @#{offset}: #{text}"  
+      "Passage @#{@offset}: #{@text}"  
     end
 
     def find_node(id)
-      (relations+annotations).each{|n| return n if n.id == id}
-      sentences.each do |s|
+      (@relations+@annotations).each{|n| return n if n.id == id}
+      @sentences.each do |s|
         ret = s.find_node(id)
         return ret unless ret.nil?
       end
@@ -28,8 +28,8 @@ module SimpleBioC
     end
 
     def each_relation
-      relations.each{|r| yield r}
-      sentences.each{|s| s.each_relation{|r| yield r}}
+      @relations.each{|r| yield r}
+      @sentences.each{|s| s.each_relation{|r| yield r}}
     end
   end
 end

data/lib/simple_bioc/relation.rb

@@ -9,7 +9,7 @@ module SimpleBioC
     end
 
     def adjust_ref
-      nodes.each{|n| n.adjust_ref}
+      @nodes.each{|n| n.adjust_ref}
     end
 
     def to_c

data/lib/simple_bioc/sentence.rb

@@ -14,16 +14,16 @@ module SimpleBioC
     end
 
     def find_node(id)
-      (relations+annotations).each{|n| return n if n.id == id}
+      (@relations+@annotations).each{|n| return n if n.id == id}
       nil
     end
 
     def each_relation
-      relations.each{|r| yield r}
+      @relations.each{|r| yield r}
     end
 
     def to_c
-      "Sentence @#{offset}: #{text}"
+      "Sentence @#{@offset}: #{@text}"
     end
   end
 end

data/lib/simple_bioc/version.rb

@@ -1,3 +1,3 @@
 module SimpleBioC
-  VERSION = "0.0.16"
+  VERSION = "0.0.17"
 end