ols 0.2.0 → 0.2.1

data/History.txt

@@ -1,3 +1,7 @@
+=== 0.2.1 2011-11-07
+
+* Cache bugfix.  Removed the use of 'Dir.chdir' as it was firing warnings.
+
 === 0.2.0 2011-11-07
 
 * Addition of a basic cache layer. Users can now cache regularly used ontologies on disk.

data/lib/ols/cache.rb

@@ -12,6 +12,7 @@ module OLS
     def initialize(args={})
       options = { :directory => Dir.getwd }.merge(args)
       @cache_directory = options[:directory]
+      @cache_directory.sub!(/\/$/,'')
 
       prepare_cache
     end
@@ -25,10 +26,8 @@ module OLS
       filename = @term_id_to_files[term_id].to_s
 
       unless filename.nil? || filename.empty?
-        Dir.chdir(@cache_directory) do
-          root_term = Marshal.load( File.open(filename) )
-          found_term = root_term.send(:find_in_graph,term_id)
-        end
+        root_term = Marshal.load( File.open("#{@cache_directory}/#{filename}") )
+        found_term = root_term.send(:find_in_graph,term_id)
       end
 
       found_term
@@ -50,17 +49,14 @@ module OLS
 
       new_filenames = []
 
-      Dir.chdir(@cache_directory) do
-        OLS.root_terms(ontology).each do |term|
-          term_filename = "#{term.term_id.gsub(':','')}.marshal"
-          term.focus_graph!
-          File.open("#{term_filename}",'w') { |f| f << Marshal.dump(term) }
-          @cached_ontologies[ontology] ||= { :filenames => [], :date => Date.today }
-          @cached_ontologies[ontology][:filenames].push(term_filename) unless @cached_ontologies[ontology][:filenames].include? term_filename
-          new_filenames.push(term_filename)
-        end
+     OLS.root_terms(ontology).each do |term|
+        term_filename = "#{term.term_id.gsub(':','')}.marshal"
+        term.focus_graph!
+        File.open("#{@cache_directory}/#{term_filename}",'w') { |f| f << Marshal.dump(term) }
+        @cached_ontologies[ontology] ||= { :filenames => [], :date => Date.today }
+        @cached_ontologies[ontology][:filenames].push(term_filename) unless @cached_ontologies[ontology][:filenames].include? term_filename
+        new_filenames.push(term_filename)
       end
-
       @cached_ontologies[ontology][:filenames].delete_if { |file| !new_filenames.include?(file) }
 
       write_cached_ontologies_to_disk
@@ -76,10 +72,8 @@ module OLS
     def remove_ontology_from_cache(ontology)
       raise ArgumentError, "'#{ontology}' is not part of the cache" unless OLS.ontologies.include?(ontology)
 
-      Dir.chdir(@cache_directory) do
-        @cached_ontologies[ontology][:filenames].each do |file|
-          File.delete(file)
-        end
+      @cached_ontologies[ontology][:filenames].each do |file|
+        File.delete("#{@cache_directory}/#{file}")
       end
 
       @cached_ontologies.delete(ontology)
@@ -92,9 +86,7 @@ module OLS
 
     # writes the @cached_ontologies variable to disk
     def write_cached_ontologies_to_disk
-      Dir.chdir(@cache_directory) do
-        File.open('cached_ontologies.yaml','w') { |f| f << @cached_ontologies.to_yaml }
-      end
+      File.open("#{@cache_directory}/cached_ontologies.yaml",'w') { |f| f << @cached_ontologies.to_yaml }
     end
 
     # Utility function to prepare the cache.
@@ -103,18 +95,18 @@ module OLS
       @term_id_to_files = {}
 
       Dir.mkdir(@cache_directory) unless Dir.exists?(@cache_directory)
-      Dir.chdir(@cache_directory) do
-        @cached_ontologies = YAML.load( File.open('cached_ontologies.yaml') ) if File.exists?('cached_ontologies.yaml')
-
-        @cached_ontologies.each do |ontology,details|
-          details[:filenames].each do |filename|
-            root_term = Marshal.load( File.open(filename) )
-            next unless root_term.is_a? OLS::Term
-            @term_id_to_files[ root_term.term_id ] = filename.to_sym
-            root_term.all_child_ids.each { |term_id| @term_id_to_files[term_id] = filename.to_sym }
-          end
+
+      @cached_ontologies = YAML.load( File.open("#{@cache_directory}/cached_ontologies.yaml") ) if File.exists?("#{@cache_directory}/cached_ontologies.yaml")
+
+      @cached_ontologies.each do |ontology,details|
+        details[:filenames].each do |filename|
+          root_term = Marshal.load( File.open("#{@cache_directory}/#{filename}") )
+          next unless root_term.is_a? OLS::Term
+          @term_id_to_files[ root_term.term_id ] = filename.to_sym
+          root_term.all_child_ids.each { |term_id| @term_id_to_files[term_id] = filename.to_sym }
         end
       end
     end
   end
-end
+end
+

data/lib/ols/version.rb

@@ -2,5 +2,5 @@
 
 module OLS
   # OLS::VERSION - The OLS gem version
-  VERSION = "0.2.0"
+  VERSION = "0.2.1"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: ols
 version: !ruby/object:Gem::Version
-  version: 0.2.0
+  version: 0.2.1
   prerelease: 
 platform: ruby
 authors:
@@ -13,7 +13,7 @@ date: 2011-11-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: savon
-  requirement: &2152592920 !ruby/object:Gem::Requirement
+  requirement: &2156971680 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2152592920
+  version_requirements: *2156971680
 - !ruby/object:Gem::Dependency
   name: rake
-  requirement: &2152592420 !ruby/object:Gem::Requirement
+  requirement: &2156971240 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,10 +32,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2152592420
+  version_requirements: *2156971240
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &2152591680 !ruby/object:Gem::Requirement
+  requirement: &2156970820 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -43,10 +43,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2152591680
+  version_requirements: *2156970820
 - !ruby/object:Gem::Dependency
   name: vcr
-  requirement: &2152590620 !ruby/object:Gem::Requirement
+  requirement: &2156970400 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2152590620
+  version_requirements: *2156970400
 - !ruby/object:Gem::Dependency
   name: webmock
-  requirement: &2152589180 !ruby/object:Gem::Requirement
+  requirement: &2156969980 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -65,10 +65,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2152589180
+  version_requirements: *2156969980
 - !ruby/object:Gem::Dependency
   name: simplecov
-  requirement: &2152587220 !ruby/object:Gem::Requirement
+  requirement: &2156969560 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -76,10 +76,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2152587220
+  version_requirements: *2156969560
 - !ruby/object:Gem::Dependency
   name: simplecov-rcov
-  requirement: &2152585760 !ruby/object:Gem::Requirement
+  requirement: &2156969140 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -87,10 +87,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2152585760
+  version_requirements: *2156969140
 - !ruby/object:Gem::Dependency
   name: mocha
-  requirement: &2152584200 !ruby/object:Gem::Requirement
+  requirement: &2156968720 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -98,7 +98,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2152584200
+  version_requirements: *2156968720
 description: ! "\n    OLS provides a simple interface to the EBI's Ontology Lookup
   Service (http://www.ebi.ac.uk/ontology-lookup/).\n    It provides an easy lookup
   of ontology terms and automagically builds up ontology trees for you.\n  "