simple_bioc 0.0.9 → 0.0.10

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 8c14726b89b7d2f79ffc63b8db0ac5427d38640a
+  metadata.gz: 38665d005a277e7bd83304fe0773618a2f242d54
+  data.tar.gz: 7101cfef679db82fbebc46d209b132a5a0952b6b
 SHA512:
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+  metadata.gz: 9b57ddecef7b4ed0654736a34dbf64af7a9096cb7a7b10bef11ed48bf4caa01540053177e9ae39c30bfe68c5eab81e8f755ee7030c5cfec2fe1cae4afed8f4da
+  data.tar.gz: e306a112cf15ccc092e93478226e35ce9f391fc456371791e4f0e74838efcfe05a7f26c0216ebd5e1a0fd93dbef1ee469c5479596189003e5bc1d12be56c4e0a

data/lib/simple_bioc/bioc_merger.rb

@@ -128,32 +128,78 @@ module BioCMerger
     end
   end
   def copy_relation(doc, dest, relation, id_map)
-    new_r = SimpleBioC::Relation.new(dest)
-    new_r.id = choose_id(doc, relation.id, 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|
-      node = SimpleBioC::Node.new(new_r)
-      node.refid = n.refid
-      node.role = n.role
-      new_r.nodes << node
+      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)
-    new_r.original = relation
-    dest.relations << new_r
+    if need_add 
+      dest.relations << new_r
+    end
   end
 
   def copy_annotation(doc, dest, annotation, id_map)
-    new_a = SimpleBioC::Annotation.new(dest)
-    new_a.id = choose_id(doc, annotation.id, id_map)
-    new_a.text = annotation.text
-    new_a.locations = []
+    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|
-      new_l = SimpleBioC::Location.new(new_a)
-      new_l.offset = l.offset
-      new_l.length = l.length 
-      new_a.locations << new_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)
-    dest.annotations << new_a
+    if need_add
+      dest.annotations << new_a
+    end
   end
 
   def choose_id(doc, id, id_map) 

data/lib/simple_bioc/version.rb

@@ -1,3 +1,3 @@
 module SimpleBioC
-  VERSION = "0.0.9"
+  VERSION = "0.0.10"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: simple_bioc
 version: !ruby/object:Gem::Version
-  version: 0.0.9
+  version: 0.0.10
 platform: ruby
 authors:
 - Dongseop Kwon
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-12-14 00:00:00.000000000 Z
+date: 2016-01-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri