simple_bioc 0.0.8 → 0.0.9

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 2db1d0eca30d1829335e2953febac31c9d9278f7
-  data.tar.gz: 3ccb2c94824e37ffc5cf9576b15328d37f880a68
+  metadata.gz: 74a3d6d3513cdaa61df2b88050b9a44cf0852ed1
+  data.tar.gz: 8c14726b89b7d2f79ffc63b8db0ac5427d38640a
 SHA512:
-  metadata.gz: 81deae4a51d85fc659680359ba4e3dc0d8d09b006f8c5272041a8a8773b0c59b9f4f78d851dcc408ec0cd5d12197e9cde49aa98072ccbfb11965741be78fb542
-  data.tar.gz: c9fd968958871c146bcba7f468c04f152269daaf6b91425ee98cab129bb0a32d2445d227b4c914c88a3336feeae246106dc92f6dcefe9762482189e909aad95a
+  metadata.gz: 2559a63848b14f15b0a26a745ae7d1a58d677fbfd520b7f42467e76a2b69bdffda4eeedf73319c79a3d13abcbf7ad008f87899c36111dd6ae1e6591767a0e281
+  data.tar.gz: c25c91ce425ed2b1a4050898ae61415507c4720c9c54b660461d0ebb7535ffe1d821142cc0db9dc66d18e74c9153c3d74a7590395f4fa3c574958e06ba4332f6

data/lib/simple_bioc/bioc_merger.rb

@@ -45,7 +45,7 @@ module BioCMerger
       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, warnings)
+          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)
@@ -132,8 +132,8 @@ module BioCMerger
     new_r.id = choose_id(doc, relation.id, id_map)
     relation.nodes.each do |n|
       node = SimpleBioC::Node.new(new_r)
-      node.refid = relation.refid
-      node.role = relation.role
+      node.refid = n.refid
+      node.role = n.role
       new_r.nodes << node
     end
     copy_infons(new_r, relation)
@@ -157,7 +157,7 @@ module BioCMerger
   end
 
   def choose_id(doc, id, id_map) 
-    new_id = id
+    new_id = id || "id"
     node = doc.find_node(new_id)
 
     until node.nil? do
@@ -193,6 +193,7 @@ module BioCMerger
 
   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)

data/lib/simple_bioc/version.rb

@@ -1,3 +1,3 @@
 module SimpleBioC
-  VERSION = "0.0.8"
+  VERSION = "0.0.9"
 end

data/spec/file_check_spec.rb

@@ -41,15 +41,13 @@ describe "File Check" do
     col5 = SimpleBioC.from_xml("./xml/merge/output.xml")
   end 
 
-  it "should merge documents successfully with abbr" do
-    col1 = SimpleBioC.from_xml("./xml/merge/9864355.xml")
-    col2 = SimpleBioC.from_xml("./xml/abbr.xml")
-
-    SimpleBioC.merge(col1, col2)
-    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