intermine 1.03.00 → 1.04.00

checksums.yaml

@@ -0,0 +1,7 @@
+---
+!binary "U0hBMQ==":
+  metadata.gz: 7acd7d68334244919bb203d2924ac0d83383f49e
+  data.tar.gz: b7b72e0ed38c01cc710ce038848698ec152c5729
+!binary "U0hBNTEy":
+  metadata.gz: 6a6ff85383c7cc8593ed654f3dc5319cf04f115e2fb7884581c7ceac21b9ca189e9e134ef2c2f2f5bd947fa49929fc52847569d535c4e79e671949e8853d2c83
+  data.tar.gz: 1fdd048f8a47b4ed646b89f4791fda7e0731069f960207a39ea43ce3d478beeb0e13c45acec19cdd8569a3af7b698cb4ea6eb90bee4d2d7b5e06499d433a073b

data/lib/intermine/model.rb

@@ -518,12 +518,35 @@ module Metadata
 
                 klass = Module.new
                 fd_names = @fields.values.map { |x| x.name }
+                fds = @fields.values
                 attr_names = @fields.values.select { |x| x.is_a?(AttributeDescriptor)}.map {|x| x.name}
                 klass.class_eval do
                     include *supers
                     attr_reader *attr_names
                 end
 
+                klass.class_eval do
+
+                    define_method(:to_h) do
+                        ret = Hash.new
+                        fds.each do |fd|
+                            if fd.is_a?(AttributeDescriptor)
+                                ret.store(fd.name, send(fd.name))
+                            elsif fd.is_a?(CollectionDescriptor)
+                                ret.store(fd.name, send(fd.name).map {|v| v.to_h})
+                            else
+                                ret.store(fd.name, send(fd.name).to_h)
+                            end
+                        end
+                        ret.store("id", objectId)
+                        return ret
+                    end
+
+                    define_method(:to_json) do |*a|
+                        to_h.to_json(*a)
+                    end
+                end
+
                 @fields.values.each do |fd|
                     if fd.is_a?(CollectionDescriptor)
                         klass.class_eval do

data/lib/intermine/version.rb

@@ -3,6 +3,7 @@ module Intermine
     # Webservice Client Version number
     #
     # Changes:
+    #   1.04.00 - Added to_h and to_json methods for result objects
     #   1.03.00 - Add support for indexed sequence service
     #   1.02.00 - Allow the lazy fetching to be optional
     #   1.01.01 - Improved lazy reference fetching
@@ -21,5 +22,5 @@ module Intermine
     #   0.98.09 - Major changes to results - now with thorough-going Enumerable support
     #   0.98.08 - Added column summary support
     #
-    VERSION = "1.03.00"
+    VERSION = "1.04.00"
 end

data/test/test_model.rb

@@ -1,5 +1,6 @@
 require File.dirname(__FILE__) + "/test_helper.rb"
 require "intermine/model"
+require "json"
 
 require "test/unit"
 
@@ -220,6 +221,58 @@ class TestModel < Test::Unit::TestCase
 
     end
 
+    def test_to_h
+
+        manager = @model.make_new("Manager", {
+            "name" => "David Brent",
+            "seniority" => 42,
+            "age" => 39,
+            "fullTime" => true,
+            "department" => {
+                "name" => "Sales",
+                "employees" => [
+                    { "name" => "Tom" },
+                    { "name" => "Dick" },
+                    { "name" => "Harry" }
+                ]
+            }
+        })
+
+        manager_h = manager.to_h
+
+        assert_equal(manager_h["name"], "David Brent")
+        assert_equal(manager_h["age"], 39)
+        assert_equal(manager_h["department"]["name"], "Sales")
+        assert_equal(manager_h["department"]["employees"][1]["name"], "Dick")
+        assert_equal(manager_h["department"]["employees"].size, 3)
+    end
+
+    def test_to_json
+
+        manager = @model.make_new("Manager", {
+            "name" => "David Brent",
+            "seniority" => 42,
+            "age" => 39,
+            "fullTime" => true,
+            "department" => {
+                "name" => "Sales",
+                "employees" => [
+                    { "name" => "Tom" },
+                    { "name" => "Dick" },
+                    { "name" => "Harry" }
+                ]
+            }
+        })
+
+        manager_h = JSON[manager.to_h.to_json]
+
+        assert_equal(manager_h["name"], "David Brent")
+        assert_equal(manager_h["age"], 39)
+        assert_equal(manager_h["department"]["name"], "Sales")
+        assert_equal(manager_h["department"]["employees"][1]["name"], "Dick")
+        assert_equal(manager_h["department"]["employees"].size, 3)
+    end
+
     def test_inheritance
 
         manager = @model.make_new("Manager", { "name" => "David Brent" })

metadata

@@ -1,185 +1,126 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: intermine
-version: !ruby/object:Gem::Version 
-  prerelease: 
-  version: 1.03.00
+version: !ruby/object:Gem::Version
+  version: 1.04.00
 platform: ruby
-authors: 
-  - Alex Kalderimis
+authors:
+- Alex Kalderimis
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2013-07-04 00:00:00 Z
-dependencies: 
-  - !ruby/object:Gem::Dependency 
-    name: json
-    version_requirements: &id001 !ruby/object:Gem::Requirement 
-      none: false
-      requirements: 
-        - - ">="
-          - !ruby/object:Gem::Version 
-            version: "0"
-    requirement: *id001
-    prerelease: false
-    type: :runtime
-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: 
-  - dev@intermine.org
+date: 2013-07-08 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: json
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    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: 
-  - lib/intermine/lists.rb
-  - lib/intermine/model.rb
-  - lib/intermine/query.rb
-  - lib/intermine/results.rb
-  - lib/intermine/service.rb
-  - lib/intermine/version.rb
-  - test/data/lists.json
-  - test/data/model.json
-  - test/data/resultobjs.json
-  - test/data/resultrow.json
-  - test/data/resultset.json
-  - test/data/testmodel_model.xml
-  - test/live_results.rb
-  - test/live_summary_test.rb
-  - test/live_test.rb
-  - test/test.rb
-  - test/test_helper.rb
-  - test/test_lists.rb
-  - test/test_model.rb
-  - test/test_query.rb
-  - test/test_result_row.rb
-  - test/test_results.rb
-  - test/test_service.rb
-  - test/test_sugar.rb
-  - test/unit_tests.rb
-  - MANIFEST
-  - LICENCE
-  - Rakefile
-  - README.rdoc
-  - Gemfile
-  - contact_header.rdoc
+files:
+- lib/intermine/lists.rb
+- lib/intermine/model.rb
+- lib/intermine/query.rb
+- lib/intermine/results.rb
+- lib/intermine/service.rb
+- lib/intermine/version.rb
+- test/data/lists.json
+- test/data/model.json
+- test/data/resultobjs.json
+- test/data/resultrow.json
+- test/data/resultset.json
+- test/data/testmodel_model.xml
+- test/live_results.rb
+- test/live_summary_test.rb
+- test/live_test.rb
+- test/test.rb
+- test/test_helper.rb
+- test/test_lists.rb
+- test/test_model.rb
+- test/test_query.rb
+- test/test_result_row.rb
+- test/test_results.rb
+- test/test_service.rb
+- test/test_sugar.rb
+- test/unit_tests.rb
+- MANIFEST
+- LICENCE
+- Rakefile
+- README.rdoc
+- Gemfile
+- contact_header.rdoc
 homepage: http://www.intermine.org
-licenses: 
-  - LGPL
+licenses:
+- LGPL
+metadata: {}
 post_install_message: 
-rdoc_options: 
-  - --title
-  - InterMine Webservice Client
-  - --main
-  - README.rdoc
-  - --line-numbers
-require_paths: 
-  - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
-  none: false
-  requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 2
-        segments: 
-          - 0
-        version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
-  none: false
-  requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 2
-        segments: 
-          - 0
-        version: "0"
+rdoc_options:
+- "--title"
+- InterMine Webservice Client
+- "--main"
+- README.rdoc
+- "--line-numbers"
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: intermine
-rubygems_version: 1.8.25
+rubygems_version: 2.0.0.preview3.1
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: Webservice Client Library for InterMine Data-Warehouses
-test_files: 
-  - test/unit_tests.rb
+test_files:
+- test/unit_tests.rb