intermine 0.98.10 → 0.98.11

data/lib/intermine/lists.rb

@@ -46,6 +46,8 @@ module InterMine::Lists
     #
     class List
 
+        include Enumerable
+
         # The name of the list. This can be changed at any time.
         attr_reader :name
 
@@ -164,23 +166,10 @@ module InterMine::Lists
         #   end
         #  
         def each
-            query.each_result {|r| yield r}
+            query.results.each {|r| yield r}
             return self
         end
 
-        # Return a list composed of the results of the elements of 
-        # this list process by the given block
-        #
-        #   symbols = list.map {|gene| gene.symbol}
-        #
-        def map 
-            ret = []
-            query.each_result {|r|
-                ret.push(yield r)
-            }
-            return ret
-        end
-
         # Used to create a new list from the contents of this one. This can be used
         # to define a sub-list
         #
@@ -298,6 +287,31 @@ module InterMine::Lists
             return self
         end
 
+        # Add tags to the list
+        #
+        # Updates the current tags by adding tags to the list.
+        #
+        def add_tags(*tags)
+            @tags = @manager.add_tags(self, tags)
+        end
+
+        # Remove one or more tags from the list
+        #
+        # If the tags are not currently associated with the list, 
+        # they will be ignored. 
+        #
+        def remove_tags(*tags)
+            to_remove = tags.select {|t| @tags.include? t}
+            unless to_remove.empty?
+                @tags = @manager.remove_tags(self, to_remove)
+            end
+        end
+
+        # Update this lists tags with the current tags on the server.
+        def update_tags
+            @tags = @manager.tags_for(self)
+        end
+
         private
 
         # Used to interpret arguments to add and remove
@@ -585,6 +599,51 @@ module InterMine::Lists
             return ret
         end
 
+        # Add tags to a list. 
+        #
+        # Returns the current tags
+        #
+        def add_tags(list, *tags)
+            uri = URI.parse(@service.root + Service::LIST_TAG_PATH)
+            params = @service.params.merge("name" => list.name, "tags" => tags.join(";"))
+            res = Net::HTTP.post_form(uri, params)
+            check_response_for_error(res)
+            return JSON.parse(res.body)["tags"]
+        end
+
+        # Remove tags from a list
+        #
+        # Returns the current tags
+        #
+        def remove_tags(list, *tags)
+            uri = URI.parse(@service.root + Service::LIST_TAG_PATH)
+            params = @service.params.merge(
+                "name" => list.name, 
+                "tags" => tags.join(";")
+            )
+            req_path = uri.path + "?" + params_to_query_string(params)
+            req = Net::HTTP::Delete.new(req_path)
+            res = Net::HTTP.start(uri.host, uri.port) do |http|
+                http.request(req)
+            end
+            check_response_for_error(res)
+            return JSON.parse(res.body)["tags"]
+        end
+
+        # Get the current tags for a list
+        def tags_for(list)
+            uri = URI.parse(@service.root + Service::LIST_TAG_PATH)
+            params = @service.params.merge(
+                "name" => list.name
+            )
+            req_path = uri.path + "?" + params_to_query_string(params)
+            res = Net::HTTP.start(uri.host, uri.port) {|http|
+                  http.get(req_path)
+            }
+            check_response_for_error(res)
+            return JSON.parse(res.body)["tags"]
+        end
+
         # only handles single value keys!
         def params_to_query_string(p)
             return @service.params.merge(p).map { |k,v| "#{k}=#{CGI::escape(v.to_s)}" }.join('&')

data/lib/intermine/model.rb

@@ -509,10 +509,10 @@ module Metadata
 
                 klass = Module.new
                 fd_names = @fields.values.map { |x| x.name }
+                attr_names = @fields.values.select { |x| x.is_a?(AttributeDescriptor)}.map {|x| x.name}
                 klass.class_eval do
                     include *supers
-                    attr_reader *fd_names
-
+                    attr_reader *attr_names
                 end
 
                 @fields.values.each do |fd|
@@ -535,6 +535,20 @@ module Metadata
                             end
                         end
                     end
+                    
+                    if fd.is_a?(ReferenceDescriptor)
+                        klass.class_eval do 
+                            define_method(fd.name) do 
+                                if instance_variable_get("@" + fd.name).nil?
+                                    q = __cd__.select(fd.name + ".*").where(:id => objectId)
+                                    instance_var = q.results.first[fd.name]
+                                    instance_variable_set("@" + fd.name, instance_var)
+                                end
+                                return instance_variable_get("@" + fd.name)
+                            end
+                        end
+                    end
+
                     klass.class_eval do
                         define_method(fd.name + "=") do |val|
                             if fd.is_a?(AttributeDescriptor)

data/lib/intermine/service.rb

@@ -108,6 +108,7 @@ module InterMine
         LIST_DIFFERENCE_PATH = "/lists/diff/json"
         LIST_INTERSECTION_PATH = "/lists/intersect/json"
         LIST_SUBTRACTION_PATH = "/lists/subtract/json"
+        LIST_TAG_PATH = "/list/tags/json"
 
         # The webservice version. An integer that 
         # supplies information about what features are supported.
@@ -122,11 +123,13 @@ module InterMine
         
         # A collection of the names of any templates that this service was not able to parse,
         # and you will thus not be able to access.
-        :broken_templates
+        attr_reader :broken_templates
 
         def_delegators :@list_manager, 
-            :lists, :list, :list_names, :create_list, :delete_lists, :get_lists_with_tags,
-            :union_of, :intersection_of, :symmetric_difference_of, :subtract
+            :lists, :list, :list_names, :create_list, :delete_lists, 
+            :get_lists_with_tags,
+            :union_of, :intersection_of, :symmetric_difference_of, 
+            :subtract
 
         # Construct a new service.
         #

data/lib/intermine/version.rb

@@ -3,8 +3,14 @@ module Intermine
     # Webservice Client Version number
     #
     # Changes:
+    #   0.98.11 - * InterMineObjects now lazily fetch their references 
+    #             if nil. Note that while extremely convenient, 
+    #             explicit prefetching will be much more efficient 
+    #             (how much depends on the number of extra requests, but
+    #             a factor of 10 seems pretty common).
+    #             * Added support for list tagging
     #   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 = "0.98.10"
+    VERSION = "0.98.11"
 end

data/test/live_test.rb

@@ -7,6 +7,17 @@ class LiveDemoTest <  Test::Unit::TestCase
 
     def setup
         @service = Service.new("http://localhost/intermine-test", "Z1a3D3U16cicCdS0T6y4bdN1SQh")
+        @temp_lists = []
+    end
+
+
+    def teardown
+        @temp_lists.each do |l| 
+            begin
+                @service.delete_lists(l)
+            rescue
+            end
+        end
     end
 
     def testVersion
@@ -34,4 +45,89 @@ class LiveDemoTest <  Test::Unit::TestCase
         assert_match("CURRENT", list.status)
     end
 
+    def testListEnumerability
+        list = @service.list("My-Favourite-Employees")
+        names = list.map {|emp| emp.name }
+        exp = ["Bernd Stromberg", "David Brent", "Neil Godwin", "Timo Becker"]
+        assert_equal(exp, names)
+
+        old = list.select {|emp| emp.age > 55}
+        assert_equal(1, old.size)
+        assert_equal("David Brent", old.first.name)
+
+        sum = list.reduce(0) {|m, i| m + i.age}
+        assert_equal(185, sum)
+    end
+
+    def testLazyReferenceFetching
+        list = @service.list("My-Favourite-Employees")
+
+        deps = list.map {|emp| emp.department.name }
+        exp = ["Schadensregulierung M-Z", "Sales", 
+            "Human Resources", "Schadensregulierung"]
+        assert_equal(exp, deps)
+
+        comps = list.map {|emp| emp.department.company.name }
+        exp = ["Capitol Versicherung AG", "Wernham-Hogg",
+              "Wernham-Hogg", "Capitol Versicherung AG"]
+        assert_equal(exp, comps)
+    end
+
+    def testLazyCollectionFetching
+        list = @service.list("My-Favourite-Employees")
+        emps = list.map {|manager| manager.department.employees.map {|employee| employee.age} }
+        exp = [[42, 28, 29, 46, 28, 48],
+            [62, 64, 58, 35, 36, 46],
+            [41, 57, 36],
+            [63, 37, 61, 55, 58, 45]]
+        assert_equal(exp, emps)
+
+        sum = list.reduce(0) {|m, manager| m + manager.department.employees.reduce(0) {|n, emp| n + emp.age}}
+        assert_equal(975, sum)
+    end
+
+    def testListCreation
+        ids = %{Alex Brenda Carol David Edgar}
+        new_list = @service.create_list(ids, "Employee")
+        @temp_lists << new_list
+        assert_equal(3, new_list.size)
+    end
+
+    def testListTagging
+        ids = %{Alex Brenda Carol David Edgar}
+        new_list = @service.create_list(ids, "Employee")
+        @temp_lists << new_list
+        assert_equal([], new_list.tags)
+        new_list.add_tags("a-tag", "another-tag")
+        assert_equal(2, new_list.tags.size)
+        assert_equal(["a-tag", "another-tag"].sort, new_list.tags.sort)
+    end
+
+    def testListTagRemoval
+        ids = %{Alex Brenda Carol David Edgar}
+        tags = ["a-tag", "another-tag"]
+        new_list = @service.create_list(ids, "Employee", tags)
+        @temp_lists << new_list
+        assert_equal(2, new_list.tags.size)
+        new_list.remove_tags("another-tag")
+        assert_equal(["a-tag"], new_list.tags)
+        new_list.remove_tags("a-tag")
+        assert_equal([], new_list.tags)
+        new_list.remove_tags("a-non-existent-tag")
+        assert_equal([], new_list.tags)
+    end
+
+    def testListTagUpdating
+        ids = %{Alex Brenda Carol David Edgar}
+        tags = ["a-tag", "another-tag"]
+        new_list = @service.create_list(ids, "Employee")
+        @temp_lists << new_list
+        assert_equal([], new_list.tags)
+        manager = @service.instance_variable_get("@list_manager")
+        assert_equal(2, manager.add_tags(new_list, tags).size)
+        assert_equal([], new_list.tags)
+        new_list.update_tags
+        assert_equal(tags.sort, new_list.tags.sort)
+    end
+
 end

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: intermine
 version: !ruby/object:Gem::Version 
-  hash: 387
+  hash: 385
   prerelease: false
   segments: 
   - 0
   - 98
-  - 10
-  version: 0.98.10
+  - 11
+  version: 0.98.11
 platform: ruby
 authors: 
 - Alex Kalderimis
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-10-28 00:00:00 +01:00
+date: 2011-11-01 00:00:00 +00:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency