ols 0.3.2 → 0.3.3

data/History.txt

@@ -1,7 +1,14 @@
+=== 0.3.3 2011-11-11
+
+* Minor cache modification - hold the marshaled strings in ram rather than repeadedly
+  read off disk.  This should ease pain when there are lots of concurrent requests to
+  a slow file system.
+
 === 0.3.2 2011-11-09
 
 * Bugfix - the term_name was getting lost off of the new nodes when we merged two graphs.
-* Small feature enhancement - when printing the graph to stdout, add an option to print out the term_name too.
+* Small feature enhancement - when printing the graph to stdout, add an option to print
+  out the term_name too.
 
 === 0.3.1 2011-11-08
 

data/README.rdoc

@@ -12,16 +12,16 @@ It provides an easy lookup of ontology terms and automagically builds up ontolog
 == Basic Usage
 
 Include the module in your code:
-  
+
   require 'rubygems'
   require 'ols'
-  
+
 Then, to lookup an ontology term:
-  
+
   ont = OLS.find_by_id('EMAP:3018')
-  
+
 This will create a simple tree object for the EMAP term EMAP:3018
-  
+
   ont.term_id             # => "EMAP:3018"
   ont.term_name           # => "TS18,nose"
 
@@ -142,4 +142,5 @@ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT.
 IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
 CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
 TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
-SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+

data/lib/ols/cache.rb

@@ -23,10 +23,10 @@ module OLS
     # @return [OLS::Term] The found OLS::Term object or +nil+
     def find_by_id(term_id)
       found_term = nil
-      filename = @term_id_to_files[term_id].to_s
+      filename = @term_id_to_files[term_id]
 
       unless filename.nil? || filename.empty?
-        root_term = Marshal.load( File.open("#{@cache_directory}/#{filename}") )
+        root_term = Marshal.load( @the_cache[filename] )
         found_term = root_term.send(:find_in_graph,term_id)
       end
 
@@ -49,7 +49,7 @@ module OLS
 
       new_filenames = []
 
-     OLS.root_terms(ontology).each do |term|
+      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) }
@@ -93,6 +93,7 @@ module OLS
     def prepare_cache
       @cached_ontologies = {}
       @term_id_to_files = {}
+      @the_cache = {}
 
       Dir.mkdir(@cache_directory) unless Dir.exists?(@cache_directory)
 
@@ -100,8 +101,11 @@ module OLS
 
       @cached_ontologies.each do |ontology,details|
         details[:filenames].each do |filename|
-          root_term = Marshal.load( File.open("#{@cache_directory}/#{filename}") )
+          file_contents = File.new("#{@cache_directory}/#{filename}",'rb').read
+          root_term = Marshal.load( file_contents )
           next unless root_term.is_a? OLS::Term
+
+          @the_cache[ filename.to_sym ] = file_contents
           @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

data/lib/ols/version.rb

@@ -2,5 +2,5 @@
 
 module OLS
   # OLS::VERSION - The OLS gem version
-  VERSION = "0.3.2"
+  VERSION = "0.3.3"
 end

data/test/test_helper.rb

@@ -43,7 +43,8 @@ VCR.config do |c|
   c.stub_with                :webmock
   c.ignore_localhost         = true
   c.default_cassette_options = {
-    :record            => :new_episodes,
-    :match_requests_on => [:uri, :method, :body]
+    :record             => :new_episodes,
+    :re_record_interval => 604800, # 7 days in seconds
+    :match_requests_on  => [:uri, :method, :body]
   }
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: ols
 version: !ruby/object:Gem::Version
-  version: 0.3.2
+  version: 0.3.3
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-11-09 00:00:00.000000000 Z
+date: 2011-11-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: savon
-  requirement: &2156771440 !ruby/object:Gem::Requirement
+  requirement: &2153022560 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2156771440
+  version_requirements: *2153022560
 - !ruby/object:Gem::Dependency
   name: rake
-  requirement: &2156771000 !ruby/object:Gem::Requirement
+  requirement: &2153022120 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,10 +32,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2156771000
+  version_requirements: *2153022120
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &2156770580 !ruby/object:Gem::Requirement
+  requirement: &2153021700 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -43,10 +43,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2156770580
+  version_requirements: *2153021700
 - !ruby/object:Gem::Dependency
   name: vcr
-  requirement: &2156770160 !ruby/object:Gem::Requirement
+  requirement: &2153021280 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2156770160
+  version_requirements: *2153021280
 - !ruby/object:Gem::Dependency
   name: webmock
-  requirement: &2156769740 !ruby/object:Gem::Requirement
+  requirement: &2153020860 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -65,10 +65,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2156769740
+  version_requirements: *2153020860
 - !ruby/object:Gem::Dependency
   name: simplecov
-  requirement: &2156769320 !ruby/object:Gem::Requirement
+  requirement: &2153020440 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -76,10 +76,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2156769320
+  version_requirements: *2153020440
 - !ruby/object:Gem::Dependency
   name: simplecov-rcov
-  requirement: &2156768900 !ruby/object:Gem::Requirement
+  requirement: &2153020020 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -87,10 +87,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2156768900
+  version_requirements: *2153020020
 - !ruby/object:Gem::Dependency
   name: mocha
-  requirement: &2156768480 !ruby/object:Gem::Requirement
+  requirement: &2153019600 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -98,7 +98,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2156768480
+  version_requirements: *2153019600
 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  "