simple_bioc 0.0.3 → 0.0.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: ac0961af71c5744bc71ea16221f5325af35e4583
-  data.tar.gz: 9f407b566a8dc6687d53f8145fc600f3d73039eb
+  metadata.gz: b3fa4051460fa744f5d6c1f48fc3d10350662750
+  data.tar.gz: 280387a719ad30f1b9eb4477a53a20fbab59cc01
 SHA512:
-  metadata.gz: ab77aa143472f5959a0ea97702ae68dba76bb6b75542086a065b625216234d8912a52d83a087f6acf3c553f0ee8adf5050ebafd94833171d9dd84d7a34124e0a
-  data.tar.gz: b02aa1b1d73ff1d0c6ed2650c0170ff88e22fd01a6e6df7d9508cf365e548bd6bf0413616a80a765b2fc35f9d3e1da2d20edf41cece737ceeb26577d39068251
+  metadata.gz: b3c76d3fc8ef4d863fdd589bd3bf4b6d81da1dade9d18a35b4e7cebd7bb59a77c2e4c6eb7dcc4897829898e5993e71605b3b6f06fbbd60a49750e6eab822e787
+  data.tar.gz: a1e6c5242c0d097efe64256276c27a293977906bb397be240852fd6a9552ee7c36dee56e1989790477326ce3201b2929cb31868bfa8f19f48f6964eed5be59e6

data/lib/simple_bioc/bioc_writer.rb

@@ -44,8 +44,8 @@ module BioCWriter
       write_infon(xml, passage)
       xml.offset passage.offset
       xml.text_ passage.text unless passage.text.nil?
-      passage.sentences.each{|s| write_sentence(xml, s)}
       passage.annotations.each{|a| write_annotation(xml, a)}
+      passage.sentences.each{|s| write_sentence(xml, s)}
       passage.relations.each{|r| write_relation(xml, r)}
     }
   end
@@ -68,8 +68,8 @@ module BioCWriter
     end
     xml.annotation(attribute) {
       write_infon(xml, annotation)
-      xml.text_ annotation.text
       annotation.locations.each{|l| write_location(xml, l)}
+      xml.text_ annotation.text
     }
   end
 

data/lib/simple_bioc/version.rb

@@ -1,3 +1,3 @@
 module SimpleBioC
-  VERSION = "0.0.3"
+  VERSION = "0.0.4"
 end

data/simple_bioc.gemspec

@@ -18,10 +18,11 @@ Gem::Specification.new do |spec|
   spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
   spec.require_paths = ["lib"]
 
-  spec.add_dependency("nokogiri",       [">= 1.3.2"])
+  spec.add_dependency "nokogiri", "~> 1.6"
 
   spec.add_development_dependency "bundler", "~> 1.3"
-  spec.add_development_dependency "rake"
-  spec.add_development_dependency("rspec-core", ["~> 2.2"])
-  spec.add_development_dependency("test-xml", ["~> 0.1.6"])
+  spec.add_development_dependency "rake", "~> 10.3"
+  spec.add_development_dependency "yard", "~> 0.8"
+  spec.add_development_dependency "rspec", "~> 3.2"
+  spec.add_development_dependency("test_xml", ["~> 0.1"])
 end

data/spec/simple_bioc_spec.rb

@@ -4,22 +4,28 @@ describe "Simple function" do
   it "should have a DTD declaration" do
     collection = SimpleBioC.from_xml("./xml/everything.xml")
     output = SimpleBioC.to_xml(collection)
-    output.should include('<!DOCTYPE collection SYSTEM "BioC.dtd">')
+    expect(output).to include('<!DOCTYPE collection SYSTEM "BioC.dtd">')
   end
   
   it "should no space when save_with = 0" do
     collection = SimpleBioC.from_xml("./xml/everything.xml")
     output = SimpleBioC.to_xml(collection, {save_with: 0})
-    output.should include('<collection><source>Made up file to test that everything is allowed and processed. Has text in the passage.</source><date>20130426</date><key>everything.key</key><infon key="collection-infon-key">collection-infon-value</infon><document><id>1</id><infon key="document-infon-key">document-infon-value</infon><passage><infon key="passage-infon-key">passage-infon-value</infon><offset>0</offset><text>text of passage</text><annotation id="P1"><infon key="annotation-infon-key">annotation-infon-value</infon><text>annotation text</text><location offset="1" length="2"/></annotation><relation id="RP1"><infon key="passage-relation-infon-key">passage-relation-infon-value</infon><node refid="RP1" role="passage-relation"/></relation></passage><relation id="D1"><infon key="document-relation-infon-key">document-relation-infon-value</infon><node refid="RD1" role="document-relation"/></relation></document></collection>')
+    expect(output).to include('<collection><source>Made up file to test that everything is allowed and processed. Has text in the passage.</source><date>20130426</date><key>everything.key</key><infon key="collection-infon-key">collection-infon-value</infon><document><id>1</id><infon key="document-infon-key">document-infon-value</infon><passage><infon key="passage-infon-key">passage-infon-value</infon><offset>0</offset><text>text of passage</text><annotation id="P1"><infon key="annotation-infon-key">annotation-infon-value</infon><location offset="1" length="2"/><text>annotation text</text></annotation><relation id="RP1"><infon key="passage-relation-infon-key">passage-relation-infon-value</infon><node refid="RP1" role="passage-relation"/></relation></passage><relation id="D1"><infon key="document-relation-infon-key">document-relation-infon-value</infon><node refid="RD1" role="document-relation"/></relation></document></collection>')
   end
 
   it "should process only one document by options" do
     collection = SimpleBioC.from_xml("./xml/lemma.xml", {documents:[21785578, 21488974]})
     output = SimpleBioC.to_xml(collection, {save_with: 0})
-    output.scan("<document>").size.should equal 2
-    output.should include("<document><id>21785578</id>")
-    output.should include("<document><id>21488974</id>")
-    output.should_not include("<document><id>21660417</id>")
-    output.should_not include("<document><id>21951408</id>")
+    expect(output.scan("<document>").size).to eq(2)
+    expect(output).to include("<document><id>21785578</id>")
+    expect(output).to include("<document><id>21488974</id>")
+    expect(output).not_to include("<document><id>21660417</id>")
+    expect(output).not_to include("<document><id>21951408</id>")
+  end
+
+  it "should have location node followed by text node" do
+    collection = SimpleBioC.from_xml("./xml/everything.xml")
+    output = SimpleBioC.to_xml(collection, {save_with: 0})
+    expect(output).to include('<location offset="1" length="2"/><text>annotation text</text>')
   end
 end

metadata

@@ -1,85 +1,99 @@
 --- !ruby/object:Gem::Specification
 name: simple_bioc
 version: !ruby/object:Gem::Version
-  version: 0.0.3
+  version: 0.0.4
 platform: ruby
 authors:
 - Dongseop Kwon
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-12-21 00:00:00.000000000 Z
+date: 2015-02-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.3.2
+        version: '1.6'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.3.2
+        version: '1.6'
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.3'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.3'
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '10.3'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - '>='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '10.3'
 - !ruby/object:Gem::Dependency
-  name: rspec-core
+  name: yard
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.2'
+        version: '0.8'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.2'
+        version: '0.8'
 - !ruby/object:Gem::Dependency
-  name: test-xml
+  name: rspec
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.1.6
+        version: '3.2'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.1.6
+        version: '3.2'
+- !ruby/object:Gem::Dependency
+  name: test_xml
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
 description: SimpleBioC is a simple parser / builder for BioC data format. BioC is
   a simple XML format to share text documents and annotations. You can find more information
   about BioC from the official BioC web site (http://www.ncbi.nlm.nih.gov/CBBresearch/Dogan/BioC/)
@@ -89,7 +103,7 @@ executables: []
 extensions: []
 extra_rdoc_files: []
 files:
-- .gitignore
+- ".gitignore"
 - Gemfile
 - LICENSE
 - LICENSE.txt
@@ -187,17 +201,17 @@ require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.1.9
+rubygems_version: 2.4.6
 signing_key: 
 specification_version: 4
 summary: Simple BioC parser/builder for ruby