avoid holding huge xml file on memory

inutano · Feb 7, 2014 · a9828b7 · a9828b7
1 parent b870776
commit a9828b7
Showing 1 changed file with 5 additions and 10 deletions.
diff --git a/sra_metadata_parser.rb b/sra_metadata_parser.rb
@@ -6,8 +6,7 @@
 module SRAMetadataParser  
   class Submission
     def initialize(id, xml)
-      @nkgr = Nokogiri::XML(open(xml))
-      @submission = @nkgr.css("SUBMISSION").select{|n| n.attr("accession") == id }.first
+      @submission = Nokogiri::XML(open(xml)).css("SUBMISSION").select{|n| n.attr("accession") == id }.first
       raise NameError, "submission id not found" unless @submission
     end
 
@@ -45,8 +44,7 @@ def all
 
   class Study
     def initialize(id, xml)
-      @nkgr = Nokogiri::XML(open(xml))
-      @study = @nkgr.css("STUDY").select{|n| n.attr("accession") == id }.first
+      @study = Nokogiri::XML(open(xml)).css("STUDY").select{|n| n.attr("accession") == id }.first
       raise NameError, "study id not found" unless @study
     end
 
@@ -116,8 +114,7 @@ def all
 
   class Experiment
     def initialize(id, xml)
-      @nkgr = Nokogiri::XML(open(xml))
-      @exp = @nkgr.css("EXPERIMENT").select{|n| n.attr("accession") == id }.first
+      @exp = Nokogiri::XML(open(xml)).css("EXPERIMENT").select{|n| n.attr("accession") == id }.first
       raise NameError, "experiment id not found" unless @exp
     end
 
@@ -307,8 +304,7 @@ def all
 
   class Sample
     def initialize(id, xml)
-      @nkgr = Nokogiri::XML(open(xml))
-      @sample = @nkgr.css("SAMPLE").select{|n| n.attr("accession") == id }.first
+      @sample = Nokogiri::XML(open(xml)).css("SAMPLE").select{|n| n.attr("accession") == id }.first
       raise NameError, "sample id not found" unless @sample
     end
 
@@ -388,8 +384,7 @@ def all
 
   class Run
     def initialize(id, xml)
-      @nkgr = Nokogiri::XML(open(xml))
-      @run = @nkgr.css("RUN").select{|n| n.attr("accession").to_s == id }.first
+      @run = Nokogiri::XML(open(xml)).css("RUN").select{|n| n.attr("accession").to_s == id }.first
       raise NameError, "run id not found" unless @run
     end