ols 0.3.3 → 0.3.4

data/.gitignore

@@ -2,11 +2,9 @@
 .bundle
 .yardoc/*
 .rbx/*
-Gemfile.lock
 doc/*
 pkg/*
 coverage/*
-test/vcr_cassettes*
 *.dot
 *.png
-*.jpg
+*.jpg

data/.rbenv-version

@@ -0,0 +1 @@
+1.9.3-p0

data/.travis.yml

@@ -0,0 +1,10 @@
+language: ruby
+rvm:
+  - 1.8.7
+  - 1.9.2
+  - 1.9.3
+  # - jruby
+  # - rbx-18mode
+  # - rbx-19mode
+  # - ree
+script: bundle exec rake test

data/Gemfile.lock

@@ -0,0 +1,76 @@
+PATH
+  remote: .
+  specs:
+    ols (0.3.3)
+      savon
+
+GEM
+  remote: http://rubygems.org/
+  specs:
+    addressable (2.2.6)
+    akami (1.0.0)
+      gyoku (>= 0.4.0)
+    awesome_print (1.0.1)
+    builder (3.0.0)
+    coderay (0.9.8)
+    crack (0.3.1)
+    gyoku (0.4.4)
+      builder (>= 2.1.2)
+    httpi (0.9.5)
+      rack
+    metaclass (0.0.1)
+    method_source (0.6.7)
+      ruby_parser (>= 2.3.1)
+    mocha (0.10.0)
+      metaclass (~> 0.0.1)
+    multi_json (1.0.3)
+    nokogiri (1.5.0)
+    nori (1.0.2)
+    pry (0.9.7.4)
+      coderay (~> 0.9.8)
+      method_source (~> 0.6.7)
+      ruby_parser (>= 2.3.1)
+      slop (~> 2.1.0)
+    rack (1.3.5)
+    rake (0.9.2.2)
+    ruby_parser (2.3.1)
+      sexp_processor (~> 3.0)
+    savon (0.9.7)
+      akami (~> 1.0)
+      builder (>= 2.1.2)
+      gyoku (>= 0.4.0)
+      httpi (~> 0.9)
+      nokogiri (>= 1.4.0)
+      nori (~> 1.0)
+      wasabi (~> 2.0)
+    sexp_processor (3.0.10)
+    shoulda (2.11.3)
+    simplecov (0.5.4)
+      multi_json (~> 1.0.3)
+      simplecov-html (~> 0.5.3)
+    simplecov-html (0.5.3)
+    simplecov-rcov (0.2.3)
+      simplecov (>= 0.4.1)
+    slop (2.1.0)
+    vcr (1.11.3)
+    wasabi (2.0.0)
+      nokogiri (>= 1.4.0)
+    webmock (1.7.8)
+      addressable (~> 2.2, > 2.2.5)
+      crack (>= 0.1.7)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  awesome_print
+  jruby-openssl
+  mocha
+  ols!
+  pry
+  rake
+  shoulda
+  simplecov
+  simplecov-rcov
+  vcr
+  webmock

data/History.txt

@@ -1,3 +1,18 @@
+=== 0.3.4 2012-01-18
+
+* Minor update/clarification - the OLS::Term method .level() is now .depth(),
+  an alias is still in place for .level() though, and when this is called on a
+  term with multiple paths through the graph it will give a depth level for the
+  shortest route through the graph.
+* Bugfix - the cache functionallity (and test suite) will now work with Ruby 1.8.7.
+* Bugfix - the OLS::Term methods .all_children() and .all_parents() now return
+  arrays of uniq OLS::Term objects.
+* Bugfix - when using a cached copy of an ontology, we will now pull the root
+  term out of the cache rather than hitting the soap service.
+* Bugfix - when caching an ontology, we now grab the metadata for each term
+  and put that into the cache also.
+* Some code cleaning/refactoring.
+
 === 0.3.3 2011-11-11
 
 * Minor cache modification - hold the marshaled strings in ram rather than repeadedly

data/README.rdoc

@@ -1,5 +1,6 @@
-= OLS
+= OLS {<img src="https://secure.travis-ci.org/dazoakley/ols.png?branch=master" />}[http://travis-ci.org/dazoakley/ols] {<img src="https://gemnasium.com/dazoakley/ols.png?travis" />}[https://gemnasium.com/dazoakley/ols]
 
+http://rubygems.org/gems/ols
 http://github.com/dazoakley/ols
 
 OLS provides a simple interface to the EBI's Ontology Lookup Service (http://www.ebi.ac.uk/ontology-lookup/).
@@ -117,6 +118,7 @@ Different cache back-ends and other features will be built into future releases.
 
 Written by Darren Oakley (daz dot oakley at gmail dot com)
 
+http://rubygems.org/gems/ols
 http://github.com/dazoakley/ols
 
 == License

data/lib/ols.rb

@@ -62,15 +62,19 @@ module OLS
     # @return [Array] An array of OLS::Term objects for all root terms the requested ontology
     def root_terms(ontology)
       root_terms = []
-      response = request(:get_root_terms) { soap.body = { :ontologyName => ontology } }
+      root_terms = @cache.root_terms(ontology) if using_cache?
 
-      if response[:item].is_a? Array
-        response[:item].each do |term|
+      if root_terms.empty?
+        response = request(:get_root_terms) { soap.body = { :ontologyName => ontology } }
+
+        if response[:item].is_a? Array
+          response[:item].each do |term|
+            root_terms.push( OLS::Term.new(term[:key],term[:value]) )
+          end
+        else
+          term = response[:item]
           root_terms.push( OLS::Term.new(term[:key],term[:value]) )
         end
-      else
-        term = response[:item]
-        root_terms.push( OLS::Term.new(term[:key],term[:value]) )
       end
 
       root_terms
@@ -199,9 +203,7 @@ module OLS
   end
 end
 
-directory = File.expand_path(File.dirname(__FILE__))
-
-require File.join(directory, 'ols', 'version')
-require File.join(directory, 'ols', 'graph')
-require File.join(directory, 'ols', 'term')
-require File.join(directory, 'ols', 'cache')
+require 'ols/version'
+require 'ols/graph'
+require 'ols/term'
+require 'ols/cache'

data/lib/ols/cache.rb

@@ -25,7 +25,7 @@ module OLS
       found_term = nil
       filename = @term_id_to_files[term_id]
 
-      unless filename.nil? || filename.empty?
+      unless filename.nil? || filename.to_s.empty?
         root_term = Marshal.load( @the_cache[filename] )
         found_term = root_term.send(:find_in_graph,term_id)
       end
@@ -33,6 +33,21 @@ module OLS
       found_term
     end
 
+    # Pull root_terms (as OLS::Term objects) out of the cache. Returns an empty array
+    # if the specified ontology is not in the cache.
+    #
+    # @param [String] ontology The ontology name
+    # @return [Array] An array of root terms
+    def root_terms(ontology)
+      root_terms = []
+
+      if @cached_ontologies.keys.include? ontology
+        root_terms = @cached_ontologies[ontology][:root_terms].map { |term_id| self.find_by_id(term_id) }
+      end
+
+      root_terms
+    end
+
     # Returns a list of the cached ontologies.
     #
     # @return [Array] A list of the cached ontologies
@@ -47,17 +62,20 @@ module OLS
     def add_ontology_to_cache(ontology)
       raise ArgumentError, "'#{ontology}' is not a valid OLS ontology" unless OLS.ontologies.include?(ontology)
 
-      new_filenames = []
+      remove_ontology_from_cache(ontology) if @cached_ontologies.has_key?(ontology)
 
       OLS.root_terms(ontology).each do |term|
-        term_filename = "#{term.term_id.gsub(':','')}.marshal"
         term.focus_graph!
+        term.send(:get_term_metadata)
+        term.all_children.each { |child| child.send(:get_term_metadata) }
+
+        term_filename = "#{term.term_id.gsub(':','')}.marshal"
         File.open("#{@cache_directory}/#{term_filename}",'w') { |f| f << Marshal.dump(term) }
-        @cached_ontologies[ontology] ||= { :filenames => [], :date => Date.today }
+
+        @cached_ontologies[ontology] ||= { :root_terms => [], :filenames => [], :date => Date.today }
+        @cached_ontologies[ontology][:root_terms].push(term.term_id) unless @cached_ontologies[ontology][:root_terms].include? term.term_id
         @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
       prepare_cache
@@ -95,7 +113,7 @@ module OLS
       @term_id_to_files = {}
       @the_cache = {}
 
-      Dir.mkdir(@cache_directory) unless Dir.exists?(@cache_directory)
+      Dir.mkdir(@cache_directory) unless File.directory?(@cache_directory)
 
       @cached_ontologies = YAML.load( File.open("#{@cache_directory}/cached_ontologies.yaml") ) if File.exists?("#{@cache_directory}/cached_ontologies.yaml")
 

data/lib/ols/term.rb

@@ -93,12 +93,18 @@ module OLS
     #
     # Depth:: Length of the terms path to its root.  Depth of a root term is zero.
     #
+    # If this term has multiple parents (and more than one route through the graph to
+    # the root node) we will return the value for the shortest distance through the graph.
+    #
     # @return [Number] Depth of this node.
-    def level
+    # @since 0.3.4
+    def depth
       return 0 if self.is_root?
-      1 + parents.first.level
+      1 + parents.map(&:depth).sort.first
     end
 
+    alias :level :depth
+
     # Returns the root term for this ontology.
     #
     # @return [OLS::Term] The root term for this ontology
@@ -166,17 +172,17 @@ module OLS
         prev_parents = prev_parents.map(&:parents).flatten
       end
 
-      parentage_array.reverse.flatten
+      parentage_array.reverse.flatten.uniq
     end
 
     # Returns an array of all parent term_ids for this ontology term
     # (all the way to the top of the ontology).  The array is ordered
-    # with the root term first and the most direct parent(s) last. 
+    # with the root term first and the most direct parent(s) last.
     # Duplicates are also filtered out.
     #
     # @return [Array] An array of ontology term_ids
     def all_parent_ids
-      all_parents.map(&:term_id).uniq
+      all_parents.map(&:term_id)
     end
 
     # Returns an array of all parent term_names for this ontology term
@@ -186,7 +192,7 @@ module OLS
     #
     # @return [Array] An array of ontology term_names
     def all_parent_names
-      all_parents.map(&:term_name).uniq
+      all_parents.map(&:term_name)
     end
 
     alias :all_parent_term_ids :all_parent_ids
@@ -269,7 +275,7 @@ module OLS
         prev_children = prev_children.map(&:children).flatten
       end
 
-      children_array.flatten
+      children_array.flatten.uniq
     end
 
     # Returns an array of all child term_ids for this ontology term
@@ -311,13 +317,13 @@ module OLS
 
     # Flesh out and/or focus the ontology graph around this term.
     #
-    # This will fetch all children and parents for this term, and will also trick each 
-    # parent/child object into thinking the ontology graph is fully formed so no further 
-    # requests to OLS will be made (to further flesh out the graph).  It will also cut down 
+    # This will fetch all children and parents for this term, and will also trick each
+    # parent/child object into thinking the ontology graph is fully formed so no further
+    # requests to OLS will be made (to further flesh out the graph).  It will also cut down
     # a much larger ontology graph to just focus on the parents/descendants of this term.
     #
-    # *NOTE:* This method will totally clobber the existing ontology graph that this term 
-    # is part of by removing any term and relationship that is not supposed to be part of this 
+    # *NOTE:* This method will totally clobber the existing ontology graph that this term
+    # is part of by removing any term and relationship that is not supposed to be part of this
     # focused graph.  Use #focus_graph to pull out a copy and be non-destructive.
     #
     # i.e. This allows us to do the following
@@ -356,13 +362,13 @@ module OLS
 
     # Flesh out and/or focus the ontology graph around this term.
     #
-    # This will fetch all children and parents for this term, and will also trick each 
-    # parent/child object into thinking the ontology graph is fully formed so no further 
-    # requests to OLS will be made (to further flesh out the graph).  It will also cut down 
+    # This will fetch all children and parents for this term, and will also trick each
+    # parent/child object into thinking the ontology graph is fully formed so no further
+    # requests to OLS will be made (to further flesh out the graph).  It will also cut down
     # a much larger ontology graph to just focus on the parents/descendants of this term.
     #
-    # *NOTE:* This method does not affect self.  It returns a completley new OLS::Term 
-    # object containing a completley new internal OLS::Graph.  Use #focus_graph! if you 
+    # *NOTE:* This method does not affect self.  It returns a completley new OLS::Term
+    # object containing a completley new internal OLS::Graph.  Use #focus_graph! if you
     # wish to cut down the existing graph.
     #
     # i.e. This allows us to do the following
@@ -513,7 +519,7 @@ module OLS
       write_dot_and_image_file(dotfile,imgfile,fmt,nodes,node_ranks,edges)
     end
 
-    # Image drawing utility function.  This is responsible for writing the DOT 
+    # Image drawing utility function.  This is responsible for writing the DOT
     # source file and converting it into the desired image format.
     #
     # @param [String] dotfile The DOT filename

data/lib/ols/version.rb

@@ -2,5 +2,5 @@
 
 module OLS
   # OLS::VERSION - The OLS gem version
-  VERSION = "0.3.3"
+  VERSION = "0.3.4"
 end

data/ols.gemspec

@@ -1,5 +1,7 @@
-# -*- encoding: utf-8 -*-
-$:.push File.expand_path("../lib", __FILE__)
+# encoding: utf-8
+
+$LOAD_PATH << File.expand_path("../lib", __FILE__)
+
 require "ols/version"
 
 Gem::Specification.new do |s|
@@ -21,9 +23,9 @@ Gem::Specification.new do |s|
   s.test_files    = `git ls-files -- {test,spec,features}/*`.split("\n")
   s.executables   = `git ls-files -- bin/*`.split("\n").map{ |f| File.basename(f) }
   s.require_paths = ["lib"]
-  
+
   s.add_dependency "savon"
-  
+
   s.add_development_dependency "rake"
   s.add_development_dependency "shoulda"
   s.add_development_dependency "vcr"
@@ -31,4 +33,6 @@ Gem::Specification.new do |s|
   s.add_development_dependency "simplecov"
   s.add_development_dependency "simplecov-rcov"
   s.add_development_dependency "mocha"
+  s.add_development_dependency "awesome_print"
+  s.add_development_dependency "pry"
 end

data/script/console

@@ -1,9 +1,13 @@
 #!/usr/bin/env ruby
-# File: script/console
-irb = RUBY_PLATFORM =~ /(:?mswin|mingw)/ ? 'irb.bat' : 'irb'
 
-libs =  " -r irb/completion"
-libs <<  " -r #{File.dirname(__FILE__) + '/../lib/ols.rb'}"
+$LOAD_PATH << File.join(File.dirname(__FILE__) + '/../lib')
+
+require 'bundler/setup'
+require 'pry'
+require 'ols'
+
+puts "Welcome to the OLS console (note - you're using pry, not irb)"
+
+Pry.config.prompt = proc { "ols> " }
+Pry.start
 
-puts "Loading ols gem"
-exec "#{irb} #{libs} --simple-prompt"

data/test/fixtures/cached_ontologies.yaml

@@ -1,9 +1,13 @@
 ---
 EMAP:
+  :root_terms:
+  - EMAP:0
   :filenames:
   - EMAP0.marshal
-  :date: 2011-11-07
+  :date: 2012-01-10
 MP:
+  :root_terms:
+  - MP:0000001
   :filenames:
   - MP0000001.marshal
-  :date: 2011-11-07
+  :date: 2012-01-10

data/test/test_helper.rb

@@ -1,7 +1,7 @@
 # Add the lib directory to the search path
-$:.unshift( "#{File.expand_path(File.dirname(__FILE__))}/../lib" )
+$LOAD_PATH.unshift( "#{File.expand_path(File.dirname(__FILE__))}/../lib" )
 
-require 'rubygems'
+require 'bundler/setup'
 
 # Set-up SimpleCov (code coverage tool for Ruby 1.9)
 if /^1.9/ === RUBY_VERSION
@@ -25,11 +25,51 @@ if /^1.9/ === RUBY_VERSION
   end
 end
 
+require 'test/unit'
 require 'shoulda'
 require 'vcr'
+require 'webmock'
 require 'mocha'
+require 'awesome_print'
 require 'ols'
 
+# Backport some useful assertions from minitest
+if /^1\.8/ === RUBY_VERSION
+  module Test::Unit::Assertions
+    def assert_output stdout = nil, stderr = nil
+      out, err = capture_io do
+        yield
+      end
+
+      x = assert_equal stdout, out, "In stdout" if stdout
+      y = assert_equal stderr, err, "In stderr" if stderr
+
+      (!stdout || x) && (!stderr || y)
+    end
+
+    def assert_silent
+      assert_output "", "" do
+        yield
+      end
+    end
+
+    def capture_io
+      require 'stringio'
+
+      orig_stdout, orig_stderr         = $stdout, $stderr
+      captured_stdout, captured_stderr = StringIO.new, StringIO.new
+      $stdout, $stderr                 = captured_stdout, captured_stderr
+
+      yield
+
+      return captured_stdout.string, captured_stderr.string
+    ensure
+      $stdout = orig_stdout
+      $stderr = orig_stderr
+    end
+  end
+end
+
 # Set-up VCR for mocking up web requests.
 VCR.config do |c|
   if /^1\.8/ === RUBY_VERSION
@@ -43,8 +83,10 @@ VCR.config do |c|
   c.stub_with                :webmock
   c.ignore_localhost         = true
   c.default_cassette_options = {
-    :record             => :new_episodes,
-    :re_record_interval => 604800, # 7 days in seconds
+    # :record             => :new_episodes,
+    # :re_record_interval => 5184000, # 60 days in seconds
+    :record             => :none,
     :match_requests_on  => [:uri, :method, :body]
   }
 end
+