ms-ident 0.0.2 → 0.0.3

data/VERSION

@@ -1 +1 @@
-0.0.2
+0.0.3

data/lib/ms/ident/pepxml.rb

@@ -18,6 +18,7 @@ end
 class Ms::Ident::Pepxml
   XML_STYLESHEET_LOCATION = '/tools/bin/TPP/tpp/schema/pepXML_std.xsl'
   DEFAULT_PEPXML_VERSION = MsmsPipelineAnalysis::PEPXML_VERSION
+  XML_ENCODING = 'UTF-8'
 
   attr_accessor :msms_pipeline_analysis
 
@@ -50,7 +51,7 @@ class Ms::Ident::Pepxml
   # if no outfile is given, an xml string is returned.  summary_xml should
   # have already been set and is not influenced by the outfile given here.
   def to_xml(outfile=nil)
-    builder = Nokogiri::XML::Builder.new
+    builder = Nokogiri::XML::Builder.new(:encoding => XML_ENCODING)
     msms_pipeline_analysis.to_xml(builder)
     add_stylesheet(builder.doc, Ms::Ident::Pepxml::XML_STYLESHEET_LOCATION)
     string = builder.doc.to_xml

data/spec/ms/ident/pepxml_spec.rb

@@ -13,6 +13,8 @@ describe "creating an Ms::Ident::Pepxml" do
   extend Ms::Ident
 
   it "can be creating in a nested fashion reflecting internal structure" do
+    tags_that_should_be_present = %w(msms_pipeline_analysis msms_run_summary sample_enzyme search_summary spectrum_query search_result search_hit modification_info mod_aminoacid_mass search_score)
+
     pepxml = Pepxml.new do |msms_pipeline_analysis|
       msms_pipeline_analysis.merge!(:summary_xml => "020.xml") do |msms_run_summary|
         # prep the sample enzyme and search_summary
@@ -84,8 +86,12 @@ describe "creating an Ms::Ident::Pepxml" do
         end
       end
     end
-    puts pepxml.to_xml
-    pepxml.to_xml.matches /<msms_pipeline_analysis /
+    xml = pepxml.to_xml
+    tags_that_should_be_present.each do |tag|
+      xml.matches /<#{tag} ?/
+    end
+    xml.matches /<\?xml version="1.0" encoding="UTF-8"\?>/
+    xml.matches %r{<\?xml-stylesheet type="text/xsl" href="/tools/bin/TPP/tpp/schema/pepXML_std.xsl"\?>}
   end
 end
 

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 0
-  - 2
-  version: 0.0.2
+  - 3
+  version: 0.0.3
 platform: ruby
 authors: 
 - John T. Prince
@@ -14,7 +14,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-02-26 00:00:00 -07:00
+date: 2011-02-28 00:00:00 -07:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -169,7 +169,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
-      hash: 642659304812034666
+      hash: 3918611084548908133
       segments: 
       - 0
       version: "0"