intermine 1.00.00 → 1.01.00

data/Rakefile

@@ -52,7 +52,6 @@ namespace :test do
         t.libs << "test"
         t.test_files = FileList['test/unit_tests.rb']
         t.verbose = true
-        puts "Running UNIT TESTS"
     end
 
     desc "Run the live integration tests"
@@ -60,7 +59,6 @@ namespace :test do
         t.libs << "test"
         t.test_files = FileList['test/live_test.rb'] << FileList['test/live_summary_test.rb'] << FileList['test/live_results.rb']
         t.verbose = false
-        puts "Running LIVE INTEGRATION TESTS"
     end
 
     desc "Run all tests"

data/lib/intermine/lists.rb

@@ -312,7 +312,7 @@ module InterMine::Lists
             @tags = @manager.tags_for(self)
         end
 
-        ENRICHMENT_DEFAULTS = {:correction => "Holm-Bonferroni", :maxp => 0.05}
+        ENRICHMENT_DEFAULTS = {:correction => "Holm-Bonferroni", :maxp => 0.05, :format => 'json'}
 
         # Retrieve the results of an enrichment calculation
         #

data/lib/intermine/model.rb

@@ -211,7 +211,7 @@ module Metadata
         #   organism = gene["organism"]
         #
         def [](key)
-            if @__cd__.has_field?(key):
+            if @__cd__.has_field?(key)
                 return self.send(key)
             end
             raise IndexError, "No field #{key} found for #{@__cd__.name}"

data/lib/intermine/service.rb

@@ -1,4 +1,3 @@
-require 'rubygems'
 require 'intermine/model'
 require "intermine/query"
 require "intermine/lists"
@@ -156,15 +155,22 @@ module InterMine
             end
             @root = root
             @token = token
-            begin
-                @version = fetch(@root + VERSION_PATH).to_i
-            rescue => e
-                raise ServiceError, "Error fetching version at #{@root + VERSION_PATH}: #{e.message}"
-            end
             @model = mock_model
             @_templates = nil
             @broken_templates = []
             @list_manager = InterMine::Lists::ListManager.new(self)
+
+            root_uri = URI.parse(@root)
+            @root_path = root_uri.path
+
+            @http = Net::HTTP.new(root_uri.host, root_uri.port)
+
+            v_path = @root + VERSION_PATH
+            begin
+                @version = fetch(v_path).to_i
+            rescue Exception => e
+                raise ServiceError, "Error fetching version at #{ v_path }: #{e.message}"
+            end
         end
 
         # Return the release string
@@ -223,21 +229,19 @@ module InterMine
         # Returns all the templates available to query against in the service 
         #
         def templates 
-            if @_templates.nil?
-                @_templates = {}
-                parser = InterMine::PathQuery::Template.parser(model)
-                template_xml = fetch(@root + TEMPLATES_PATH)
-                doc = REXML::Document.new(template_xml)
-                doc.elements.each("template-queries/template") do |t|
-                    begin
-                        temp = parser.parse(t)
-                        @_templates[temp.name] = temp
-                    rescue
-                        @broken_templates.push(t.attribute("name").value)
-                    end
+            parsed = {}
+            parser = InterMine::PathQuery::Template.parser(model)
+            template_xml = fetch(@root + TEMPLATES_PATH)
+            doc = REXML::Document.new(template_xml)
+            doc.elements.each("template-queries/template") do |t|
+                begin
+                    temp = parser.parse(t)
+                    parsed[temp.name] = temp
+                rescue
+                    @broken_templates.push(t.attribute("name").value)
                 end
             end
-            return @_templates
+            return parsed
         end
 
         # Get all the names of the available templates, in 
@@ -261,9 +265,19 @@ module InterMine
 
         # Retrieves data from a url with a get request.
         def fetch(url)
-            uri = URI.parse(url)
-            qs = params.map { |k,v| "#{k}=#{CGI::escape(v.to_s)}" }.join('&')
-            return Net::HTTP.get(uri.host, uri.path + (params.empty? ? "" : "?#{qs}"))
+            ps = params
+            qs = ps.empty? ? '' : '?' + ps.map{ |k,v| "#{k}=#{CGI::escape(v.to_s)}" }.join('&')
+            uri = URI.parse(url + qs)
+
+            req = Net::HTTP::Get.new(uri.path + qs)
+            resp = @http.request req
+
+            return case resp
+            when Net::HTTPSuccess
+                resp.body
+            else
+                raise ServiceError, resp.code, resp.body
+            end
         end
     end
 

data/lib/intermine/version.rb

@@ -3,6 +3,8 @@ module Intermine
     # Webservice Client Version number
     #
     # Changes:
+    #   1.01.00 - Test compatibility with 1.8.7, 1.9.2, 2.0.0-rc1
+    #             Numerous bug fixes.
     #   1.00.00 - Up to make use of new features of the InterMine 1.0 API
     #             * Enrichment queries
     #             * Range constraints
@@ -15,5 +17,6 @@ module Intermine
     #   0.98.10 - Added status property to lists
     #   0.98.09 - Major changes to results - now with thorough-going Enumerable support
     #   0.98.08 - Added column summary support
-    VERSION = "1.00.00"
+    #
+    VERSION = "1.01.00"
 end

data/test/live_results.rb

@@ -1,3 +1,4 @@
+# encoding: UTF-8
 require File.dirname(__FILE__) + "/test_helper.rb"
 
 require "test/unit"
@@ -12,7 +13,7 @@ class LiveResultsTest < Test::Unit::TestCase
         @q = @service.query("Employee").select("*", "department.*").where(:age => {:lt => @max})
         @empty = @service.query("Employee").where(:name => "some-non-existant-value")
         @exp_count = 82
-        @expected_last = "Didier Legu\303\251lec"
+        @expected_last = "Didier Leguélec"
         @expected_last_summary = "Vincent"
         @expected_last_obj = "Both Quotes '\""
         @expected_target = 37.02439

data/test/live_test.rb

@@ -10,9 +10,8 @@ class LiveDemoTest <  Test::Unit::TestCase
         @temp_lists = []
     end
 
-
     def teardown
-        @temp_lists.each do |l| 
+        (@temp_lists || []).each do |l| 
             begin
                 @service.delete_lists(l)
             rescue

data/test/test_query.rb

@@ -1,3 +1,5 @@
+# encoding: UTF-8
+
 require File.dirname(__FILE__) + "/test_helper.rb"
 require "intermine/query"
 require "intermine/model"
@@ -38,27 +40,25 @@ class TestQuery < Test::Unit::TestCase
             "Employee.age", 
             "Employee.department.name"
         ]
-        expected = views.to_s
-
 
         query = InterMine::PathQuery::Query.new(@model)
         query.add_views("Employee.name", "Employee.age", 
                         "Employee.department.name")
-        assert_equal(query.views.to_s, expected)
+        assert_equal(query.views.map{ |x| x.to_s }, views)
             
 
         query = InterMine::PathQuery::Query.new(@model, "Employee")
         query.add_views("Employee.name", "Employee.age", 
                         "Employee.department.name")
-        assert_equal(query.views.to_s, expected)
+        assert_equal(query.views.map{ |x| x.to_s }, views)
 
         query = InterMine::PathQuery::Query.new(@model)
         query.add_views(views)
-        assert_equal(query.views.to_s, expected)
+        assert_equal(query.views.map{ |x| x.to_s }, views)
 
         query = InterMine::PathQuery::Query.new(@model, "Employee")
         query.add_views(views)
-        assert_equal(query.views.to_s, expected)
+        assert_equal(query.views.map{ |x| x.to_s }, views)
     end
 
     def test_bad_viewpath
@@ -83,15 +83,15 @@ class TestQuery < Test::Unit::TestCase
             "Employee.age", 
             "Employee.department.name"
         ]
-        expected = views.to_s
+        expected = views
 
         query = InterMine::PathQuery::Query.new(@model, "Employee")
         query.add_views("name", "age", "department.name")
-        assert_equal(query.views.to_s, expected)
+        assert_equal(query.views.map {|x| x.to_s }, expected)
 
         query = InterMine::PathQuery::Query.new(@model, "Employee")
         query.add_views(["name", "age", "department.name"])
-        assert_equal(query.views.to_s, expected)
+        assert_equal(query.views.map {|x| x.to_s }, expected)
     end
 
     def test_bad_unqualified_path
@@ -166,8 +166,8 @@ class TestQuery < Test::Unit::TestCase
             :sub_class => "Manager"
         })
         query.add_views("Department.employees.seniority")
-        expected = ["Department.employees.seniority"].to_s
-        assert_equal(query.views.to_s, expected)
+        expected = ["Department.employees.seniority"]
+        assert_equal(query.views.map {|x| x.to_s }, expected)
 
         query = InterMine::PathQuery::Query.new(@model)
         assert_raise InterMine::Metadata::PathException do
@@ -570,7 +570,7 @@ class TestQuery < Test::Unit::TestCase
         assert_equal(conA.loopPath.to_s, "Employee.department.company.departments")
     end
 
-    def test_bad_lookup_constraint
+    def test_bad_loop_constraint
         query = InterMine::PathQuery::Query.new(@model, "Employee")
         assert_raise ArgumentError do
             query.add_constraint({

data/test/test_sugar.rb

@@ -1,11 +1,13 @@
 require File.dirname(__FILE__) + "/test_helper.rb"
+require "test/unit"
+
 require "intermine/query"
 require "intermine/model"
 require "intermine/lists"
 require "intermine/service"
-require "test/unit"
 
-class Service
+# Open Service class and mock the fetch method.
+class InterMine::Service
     def fetch(x)
         return 100
     end
@@ -15,10 +17,10 @@ class TestQuerySugar < Test::Unit::TestCase
 
     def initialize(name)
         super
-        file = File.new(
-            File.dirname(__FILE__) + "/data/model.json", "r")
-        data = file.read
-        @model = InterMine::Metadata::Model.new(data)
+        modelf = File.dirname(__FILE__) + "/data/model.json"
+        File.open(modelf, "r") do |f|
+            @model = InterMine::Metadata::Model.new f.read
+        end
         @service = InterMine::Service.new("foo", "bar", @model)
         @model.send(:set_service, @service) 
         @list = InterMine::Lists::List.new({"name" => "test-list"})

metadata

@@ -1,126 +1,70 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: intermine
-version: !ruby/object:Gem::Version 
-  hash: 23
+version: !ruby/object:Gem::Version
+  version: 1.01.00
   prerelease: 
-  segments: 
-  - 1
-  - 0
-  - 0
-  version: 1.00.00
 platform: ruby
-authors: 
+authors:
 - Alex Kalderimis
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2012-10-08 00:00:00 Z
-dependencies: 
-- !ruby/object:Gem::Dependency 
+date: 2013-03-01 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
   name: json
-  prerelease: false
-  requirement: &id001 !ruby/object:Gem::Requirement 
+  requirement: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 3
-        segments: 
-        - 0
-        version: "0"
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :runtime
-  version_requirements: *id001
-description: |
-  = Webservice Client Library for InterMine Data-Warehouses
-  
-  This library provides an interface to the InterMine webservices
-  API. It makes construction and execution of queries more 
-  straightforward, safe and convenient, and allows for results
-  to be used directly in Ruby code. As well as traditional row based
-  access, the library provides an object-orientated record result
-  format (similar to ActiveRecords), and allows for fast, memory 
-  efficient iteration of result sets.
-  
-  == Example
-  
-  Get all protein domains associated with a set of genes and print their names:
-  
-      require "intermine/service"
-  
-      Service.new("www.flymine.org/query").
-          new_query("Pathway")
-          select(:name).
-          where("genes.symbol" => ["zen", "hox", "h", "bib"]).
-          each_row { |row| puts row[:name]}
-  
-  == Who is this for?
-  
-  InterMine data warehouses are typically constructed to hold
-  Biological data, and as this library facilitates programmatic
-  access to these data, this install is primarily aimed at 
-  bioinformaticians. In particular, users of the following services
-  may find it especially useful:
-   * FlyMine (http://www.flymine.org/query)
-   * YeastMine (http://yeastmine.yeastgenome.org/yeastmine)
-   * RatMine (http://ratmine.mcw.edu/ratmine)
-   * modMine (http://intermine.modencode.org/release-23)
-   * metabolicMine (http://www.metabolicmine.org/beta)
-  
-  == How to use this library:
-  
-  We have tried to construct an interface to this library that
-  does not require you to learn an entirely new set of concepts. 
-  As such, as well as the underlying methods that are common
-  to all libraries, there is an additional set of aliases and sugar
-  methods that emulate the DSL style of SQL:
-  
-  === SQL style
-  
-    service = Service.new("www.flymine.org/query")
-    service.model.
-       table("Gene").
-       select("*", "pathways.*").
-       where(:symbol => "zen").
-       order_by(:symbol).
-       outerjoin(:pathways).
-       each_row do |r|
-         puts r
-       end
-  
-  === Common InterMine interface
-  
-    service = Service.new("www.flymine.org/query")
-    query = service.new_query("Gene")
-    query.add_views("*", "pathways.*")
-    query.add_constraint("symbol", "=", "zen")
-    query.add_sort_order(:symbol)
-    query.add_join(:pathways)
-    query.each_row do |r|
-      puts r
-    end
-  
-  For more details, see the accompanying documentation and the unit tests
-  for interface examples. Further documentation is available at www.intermine.org.
-  
-  == Support
-  
-  Support is available on our development mailing list: dev@intermine.org
-  
-  == License
-  
-  This code is Open Source under the LGPL. Source code for all InterMine code
-  can be checked out from svn://subversion.flymine.org/flymine
-
-email: 
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+description: ! "= Webservice Client Library for InterMine Data-Warehouses\n\nThis
+  library provides an interface to the InterMine webservices\nAPI. It makes construction
+  and execution of queries more \nstraightforward, safe and convenient, and allows
+  for results\nto be used directly in Ruby code. As well as traditional row based\naccess,
+  the library provides an object-orientated record result\nformat (similar to ActiveRecords),
+  and allows for fast, memory \nefficient iteration of result sets.\n\n== Example\n\nGet
+  all protein domains associated with a set of genes and print their names:\n\n    require
+  \"intermine/service\"\n\n    Service.new(\"www.flymine.org/query\").\n        new_query(\"Pathway\")\n
+  \       select(:name).\n        where(\"genes.symbol\" => [\"zen\", \"hox\", \"h\",
+  \"bib\"]).\n        each_row { |row| puts row[:name]}\n\n== Who is this for?\n\nInterMine
+  data warehouses are typically constructed to hold\nBiological data, and as this
+  library facilitates programmatic\naccess to these data, this install is primarily
+  aimed at \nbioinformaticians. In particular, users of the following services\nmay
+  find it especially useful:\n * FlyMine (http://www.flymine.org/query)\n * YeastMine
+  (http://yeastmine.yeastgenome.org/yeastmine)\n * RatMine (http://ratmine.mcw.edu/ratmine)\n
+  * modMine (http://intermine.modencode.org/release-23)\n * metabolicMine (http://www.metabolicmine.org/beta)\n\n==
+  How to use this library:\n\nWe have tried to construct an interface to this library
+  that\ndoes not require you to learn an entirely new set of concepts. \nAs such,
+  as well as the underlying methods that are common\nto all libraries, there is an
+  additional set of aliases and sugar\nmethods that emulate the DSL style of SQL:\n\n===
+  SQL style\n\n  service = Service.new(\"www.flymine.org/query\")\n  service.model.\n
+  \    table(\"Gene\").\n     select(\"*\", \"pathways.*\").\n     where(:symbol =>
+  \"zen\").\n     order_by(:symbol).\n     outerjoin(:pathways).\n     each_row do
+  |r|\n       puts r\n     end\n\n=== Common InterMine interface\n\n  service = Service.new(\"www.flymine.org/query\")\n
+  \ query = service.new_query(\"Gene\")\n  query.add_views(\"*\", \"pathways.*\")\n
+  \ query.add_constraint(\"symbol\", \"=\", \"zen\")\n  query.add_sort_order(:symbol)\n
+  \ query.add_join(:pathways)\n  query.each_row do |r|\n    puts r\n  end\n\nFor more
+  details, see the accompanying documentation and the unit tests\nfor interface examples.
+  Further documentation is available at www.intermine.org.\n\n== Support\n\nSupport
+  is available on our development mailing list: dev@intermine.org\n\n== License\n\nThis
+  code is Open Source under the LGPL. Source code for all InterMine code\ncan be checked
+  out from svn://subversion.flymine.org/flymine\n"
+email:
 - dev@intermine.org
 executables: []
-
 extensions: []
-
 extra_rdoc_files: []
-
-files: 
+files:
 - lib/intermine/lists.rb
 - lib/intermine/model.rb
 - lib/intermine/query.rb
@@ -153,41 +97,40 @@ files:
 - Gemfile
 - contact_header.rdoc
 homepage: http://www.intermine.org
-licenses: 
+licenses:
 - LGPL
 post_install_message: 
-rdoc_options: 
+rdoc_options:
 - --title
 - InterMine Webservice Client
 - --main
 - README.rdoc
 - --line-numbers
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
+required_ruby_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
       - 0
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
+      hash: 150304175
+required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
       - 0
-      version: "0"
+      hash: 150304175
 requirements: []
-
 rubyforge_project: intermine
-rubygems_version: 1.8.15
+rubygems_version: 1.8.25
 signing_key: 
 specification_version: 3
 summary: Webservice Client Library for InterMine Data-Warehouses
-test_files: 
+test_files:
 - test/unit_tests.rb