intermine 0.98.01
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/Gemfile +4 -0
 - data/LICENCE +165 -0
 - data/MANIFEST +0 -0
 - data/README.rdoc +79 -0
 - data/Rakefile +67 -0
 - data/lib/intermine/lists.rb +716 -0
 - data/lib/intermine/model.rb +867 -0
 - data/lib/intermine/query.rb +1569 -0
 - data/lib/intermine/results.rb +196 -0
 - data/lib/intermine/service.rb +253 -0
 - data/lib/intermine/version.rb +3 -0
 - data/test/data/lists.json +29 -0
 - data/test/data/model.json +3 -0
 - data/test/data/resultobjs.json +3 -0
 - data/test/data/resultrow.json +1 -0
 - data/test/data/resultset.json +3 -0
 - data/test/data/testmodel_model.xml +94 -0
 - data/test/live_test.rb +35 -0
 - data/test/test.rb +84 -0
 - data/test/test_helper.rb +67 -0
 - data/test/test_lists.rb +68 -0
 - data/test/test_model.rb +417 -0
 - data/test/test_query.rb +1202 -0
 - data/test/test_result_row.rb +114 -0
 - data/test/test_results.rb +22 -0
 - data/test/test_service.rb +86 -0
 - data/test/test_sugar.rb +219 -0
 - data/test/unit_tests.rb +6 -0
 - metadata +192 -0
 
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            # Classes that represent the data model of an InterMine data-warehouse,
         
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            # and elements within that data model. 
         
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            #
         
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            require 'rubygems'
         
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            require 'json'
         
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            module InterMine
         
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            module Metadata
         
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                # 
         
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                # == Description
         
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                #
         
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                # A representation of the data model of an InterMine data warehouse. 
         
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                # This class contains access to all aspects of the model, including the tables
         
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                # of data stored, and the kinds of data in those tables. It is also the
         
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                # mechanism for creating objects which are representations of data within 
         
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                # the data model, including records, paths and columns.
         
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                #
         
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                #   model = Model.new(data)
         
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                #
         
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                #   model.classes.each do |c|
         
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                #       puts "#{c.name} has #{c.fields.size} fields"
         
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                #   end
         
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                #
         
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                #:include:contact_header.rdoc
         
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                #
         
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                class Model
         
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                    # The name of the model
         
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                    attr_reader :name
         
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                    # The classes within this model
         
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                    attr_reader :classes
         
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                    # The Service this model belongs to
         
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                    attr_reader :service
         
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                    # Construct a new model from its textual json representation
         
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                    #
         
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                    # Arguments:
         
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                    # [+model_data+] The JSON serialization of the model
         
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                    # [+service+] The Service this model belongs to
         
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                    #
         
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                    #   model = Model.new(json)
         
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                    #
         
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                    def initialize(model_data, service=nil) 
         
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                        result = JSON.parse(model_data)
         
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                        @model = result["model"]
         
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                        @service = service
         
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                        @name = @model["name"]
         
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                        @classes = {}
         
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                        @model["classes"].each do |k, v| 
         
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                            @classes[k] = ClassDescriptor.new(v, self)
         
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                        end
         
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                        @classes.each do |name, cld| 
         
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                            cld.fields.each do |fname, fd|
         
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                                if fd.respond_to?(:referencedType)
         
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                                    refCd = self.get_cd(fd.referencedType)
         
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                                    fd.referencedType = refCd
         
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                                end
         
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                            end
         
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                        end
         
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                    end
         
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                    # call-seq:
         
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                    #   get_cd(name) => ClassDescriptor
         
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                    #
         
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                    # Get a ClassDescriptor from the model by name.
         
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                    #
         
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                    # If a ClassDescriptor itself is passed as the argument,
         
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                    # it will be passed through.
         
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                    #
         
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                    def get_cd(cls)
         
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                        if cls.is_a?(ClassDescriptor)
         
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                            return cls
         
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                        else
         
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                            return @classes[cls.to_s]
         
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                        end
         
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                    end
         
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                    alias cd get_cd
         
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                    alias table get_cd
         
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                    # call-seq:
         
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                    #   make_new(name=nil, opts={}) => InterMineObject
         
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                    #
         
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                    # Make a new InterMineObject which is an instantiation of a class a ClassDescriptor represents
         
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                    #
         
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                    # Arguments:
         
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                    # [+name+] The name of the class to instantiate
         
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                    # [+opts+] The values to assign to the new object
         
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                    #
         
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                    #   gene = model.make_new 'Gene', {
         
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                    #       "symbol" => "zen",
         
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                    #       "name" => "zerknullt",
         
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                    #       "organism => {
         
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                    #           "shortName" => "D. melanogaster",
         
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                    #           "taxonId" => 7217
         
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                    #       }
         
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                    #   }
         
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                    #
         
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                    #   puts gene.organism.taxonId
         
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                    #   >>> 7217
         
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                    #
         
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                    def make_new(class_name=nil, opts={})
         
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                        # Support calling with just opts
         
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                        if class_name.is_a?(Hash)
         
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                            opts = class_name
         
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                            class_name = nil
         
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                        end
         
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                        if class_name && opts["class"] && (class_name != opts["class"]) && !get_cd(opts["class"]).subclass_of?(class_name)
         
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                            raise ArgumentError, "class name in options hash is not compatible with passed class name: #{opts["class"]} is not a subclass of #{class_name}"
         
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                        end
         
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                        # Prefer the options value to the passed value
         
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                        cd_name = opts["class"] || class_name
         
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                        cls = get_cd(cd_name).to_class
         
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                        obj = cls.new(opts)
         
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                        obj.send(:__cd__=, get_cd(cd_name))
         
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                        return obj
         
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                    end
         
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                    # === Resolve the value referred to by a path on an object
         
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                    #
         
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                    # The path may be either a string such as "Department.employees[2].name", 
         
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                    # or a Path object
         
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                    def resolve_path(obj, path)
         
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                        return obj._resolve(path)
         
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                    end
         
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                    private
         
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                    # For mocking in tests
         
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                    def set_service(service)
         
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                        @service = service
         
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                    end
         
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                end
         
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                # == A base class for all objects instantiated from a ClassDescriptor
         
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                #
         
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                # This class described the common behaviour for all objects instantiated 
         
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                # as representations of classes defined by a ClassDescriptor. It is not intended
         
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                # to be instantiated directly, but inherited from.
         
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                #
         
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                #:include:contact_header.rdoc
         
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                #
         
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                class InterMineObject
         
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                    # The database internal id in the originating mine. Serves as a guarantor
         
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                    # of object identity.
         
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                    attr_reader :objectId
         
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                    # The ClassDescriptor for this object
         
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                    attr_reader :__cd__
         
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                    # Arguments:
         
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                    # hash:: The properties of this object represented as a Hash. Nested 
         
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                    #        Arrays and Hashes are expected for collections and references.
         
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                    #
         
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                    def initialize(hash=nil)
         
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                        hash ||= {}
         
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                        hash.each do |key, value|
         
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                            if key.to_s != "class"
         
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                                self.send(key.to_s + "=", value)
         
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                            end
         
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                        end
         
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                    end
         
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                    # call-seq:
         
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                    #   is_a?(other) => bool
         
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                    #
         
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                    # Determine if this class is a subclass of other.
         
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                    #
         
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                    # Overridden to provide support for querying against ClassDescriptors and Strings.
         
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                    #
         
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                    def is_a?(other)
         
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                        if other.is_a?(ClassDescriptor)
         
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                            return is_a?(other.to_module)
         
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                        elsif other.is_a?(String)
         
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                            return is_a?(@__cd__.model.cd(other))
         
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                        else
         
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                            return super
         
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                        end
         
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                    end
         
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                    # call-seq:
         
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                    #   to_s() => human-readable string
         
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                    #
         
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                    # Serialise to a readable representation
         
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                    def to_s
         
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                        parts = [@__cd__.name + ':' + self.objectId.to_s]
         
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                        self.instance_variables.reject{|var| var.to_s.end_with?("objectId")}.each do |var|
         
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                            parts << "#{var}=#{self.instance_variable_get(var).inspect}"
         
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                        end
         
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                        return "<#{parts.join(' ')}>"
         
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                    end
         
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                    # call-seq:
         
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                    #   [key] => value
         
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                    #
         
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                    # Alias property fetches as item retrieval, so the following are equivalent:
         
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                    #
         
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                    #   organism = gene.organism
         
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                    #   organism = gene["organism"]
         
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                    #
         
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                    def [](key)
         
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                        if @__cd__.has_field?(key):
         
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                            return self.send(key)
         
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                        end
         
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                        raise IndexError, "No field #{key} found for #{@__cd__.name}"
         
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                    end
         
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                    # call-seq:
         
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| 
      
 217 
     | 
    
         
            +
                    #   _resolve(path) => value
         
     | 
| 
      
 218 
     | 
    
         
            +
                    #
         
     | 
| 
      
 219 
     | 
    
         
            +
                    # Resolve a path represented as a String or as a Path into a value
         
     | 
| 
      
 220 
     | 
    
         
            +
                    #
         
     | 
| 
      
 221 
     | 
    
         
            +
                    # This is designed to automate access to values in deeply nested objects. So:
         
     | 
| 
      
 222 
     | 
    
         
            +
                    #
         
     | 
| 
      
 223 
     | 
    
         
            +
                    #   name = gene._resolve('Gene.organism.name')
         
     | 
| 
      
 224 
     | 
    
         
            +
                    #
         
     | 
| 
      
 225 
     | 
    
         
            +
                    # Array indices are supported:
         
     | 
| 
      
 226 
     | 
    
         
            +
                    #  
         
     | 
| 
      
 227 
     | 
    
         
            +
                    #   symbol = gene._resolve('Gene.alleles[3].symbol')
         
     | 
| 
      
 228 
     | 
    
         
            +
                    #
         
     | 
| 
      
 229 
     | 
    
         
            +
                    def _resolve(path)
         
     | 
| 
      
 230 
     | 
    
         
            +
                        begin
         
     | 
| 
      
 231 
     | 
    
         
            +
                            parts = path.split(/(?:\.|\[|\])/).reject {|x| x.empty?}
         
     | 
| 
      
 232 
     | 
    
         
            +
                        rescue NoMethodError
         
     | 
| 
      
 233 
     | 
    
         
            +
                            parts = path.elements.map { |x| x.name }
         
     | 
| 
      
 234 
     | 
    
         
            +
                        end
         
     | 
| 
      
 235 
     | 
    
         
            +
                        root = parts.shift
         
     | 
| 
      
 236 
     | 
    
         
            +
                        if !is_a?(root)
         
     | 
| 
      
 237 
     | 
    
         
            +
                            raise ArgumentError, "Incompatible path '#{path}': #{self} is not a #{root}"
         
     | 
| 
      
 238 
     | 
    
         
            +
                        end
         
     | 
| 
      
 239 
     | 
    
         
            +
                        begin
         
     | 
| 
      
 240 
     | 
    
         
            +
                            res = parts.inject(self) do |memo, part| 
         
     | 
| 
      
 241 
     | 
    
         
            +
                                part = part.to_i if (memo.is_a?(Array) and part.to_i.to_s == part)
         
     | 
| 
      
 242 
     | 
    
         
            +
                                begin
         
     | 
| 
      
 243 
     | 
    
         
            +
                                    new = memo[part]
         
     | 
| 
      
 244 
     | 
    
         
            +
                                rescue TypeError
         
     | 
| 
      
 245 
     | 
    
         
            +
                                    raise ArgumentError, "Incompatible path '#{path}' for #{self}, expected an index"
         
     | 
| 
      
 246 
     | 
    
         
            +
                                end
         
     | 
| 
      
 247 
     | 
    
         
            +
                                new
         
     | 
| 
      
 248 
     | 
    
         
            +
                            end
         
     | 
| 
      
 249 
     | 
    
         
            +
                        rescue IndexError => e
         
     | 
| 
      
 250 
     | 
    
         
            +
                            raise ArgumentError, "Incompatible path '#{path}' for #{self}, #{e}"
         
     | 
| 
      
 251 
     | 
    
         
            +
                        end
         
     | 
| 
      
 252 
     | 
    
         
            +
                        return res
         
     | 
| 
      
 253 
     | 
    
         
            +
                    end
         
     | 
| 
      
 254 
     | 
    
         
            +
             
     | 
| 
      
 255 
     | 
    
         
            +
                    alias inspect to_s
         
     | 
| 
      
 256 
     | 
    
         
            +
             
     | 
| 
      
 257 
     | 
    
         
            +
                    private 
         
     | 
| 
      
 258 
     | 
    
         
            +
             
     | 
| 
      
 259 
     | 
    
         
            +
                    def __cd__=(cld)
         
     | 
| 
      
 260 
     | 
    
         
            +
                        @__cd__ = cld
         
     | 
| 
      
 261 
     | 
    
         
            +
                    end
         
     | 
| 
      
 262 
     | 
    
         
            +
                    
         
     | 
| 
      
 263 
     | 
    
         
            +
                    def objectId=(val)
         
     | 
| 
      
 264 
     | 
    
         
            +
                        @objectId = val
         
     | 
| 
      
 265 
     | 
    
         
            +
                    end
         
     | 
| 
      
 266 
     | 
    
         
            +
                end
         
     | 
| 
      
 267 
     | 
    
         
            +
             
     | 
| 
      
 268 
     | 
    
         
            +
                # == A base module that provides helpers for setting up classes bases on the contents of a Hash
         
     | 
| 
      
 269 
     | 
    
         
            +
                #
         
     | 
| 
      
 270 
     | 
    
         
            +
                #  ClassDescriptors and FieldDescriptors are instantiated 
         
     | 
| 
      
 271 
     | 
    
         
            +
                #  with hashes that provide their properties. This module
         
     | 
| 
      
 272 
     | 
    
         
            +
                #  makes sure that the appropriate instance variables are set
         
     | 
| 
      
 273 
     | 
    
         
            +
                #
         
     | 
| 
      
 274 
     | 
    
         
            +
                #:include:contact_header.rdoc
         
     | 
| 
      
 275 
     | 
    
         
            +
                #
         
     | 
| 
      
 276 
     | 
    
         
            +
                module SetHashKey 
         
     | 
| 
      
 277 
     | 
    
         
            +
             
     | 
| 
      
 278 
     | 
    
         
            +
                    # call-seq:
         
     | 
| 
      
 279 
     | 
    
         
            +
                    #   set_key_value(key, value)
         
     | 
| 
      
 280 
     | 
    
         
            +
                    #
         
     | 
| 
      
 281 
     | 
    
         
            +
                    # Set up instance variables based on the contents of a hash
         
     | 
| 
      
 282 
     | 
    
         
            +
                    def set_key_value(k, v)
         
     | 
| 
      
 283 
     | 
    
         
            +
                        if (k == "type")
         
     | 
| 
      
 284 
     | 
    
         
            +
                            k = "dataType"
         
     | 
| 
      
 285 
     | 
    
         
            +
                        end
         
     | 
| 
      
 286 
     | 
    
         
            +
                        ## create and initialize an instance variable for this 
         
     | 
| 
      
 287 
     | 
    
         
            +
                        ## key/value pair
         
     | 
| 
      
 288 
     | 
    
         
            +
                        self.instance_variable_set("@#{k}", v) 
         
     | 
| 
      
 289 
     | 
    
         
            +
                        ## create the getter that returns the instance variable
         
     | 
| 
      
 290 
     | 
    
         
            +
                        self.class.send(:define_method, k, 
         
     | 
| 
      
 291 
     | 
    
         
            +
                            proc{self.instance_variable_get("@#{k}")})  
         
     | 
| 
      
 292 
     | 
    
         
            +
                        ## create the setter that sets the instance variable
         
     | 
| 
      
 293 
     | 
    
         
            +
                        self.class.send(:define_method, "#{k}=", 
         
     | 
| 
      
 294 
     | 
    
         
            +
                            proc{|v| self.instance_variable_set("@#{k}", v)})  
         
     | 
| 
      
 295 
     | 
    
         
            +
                        return
         
     | 
| 
      
 296 
     | 
    
         
            +
                    end
         
     | 
| 
      
 297 
     | 
    
         
            +
             
     | 
| 
      
 298 
     | 
    
         
            +
                    # call-seq: 
         
     | 
| 
      
 299 
     | 
    
         
            +
                    #   inspect() => readable-string
         
     | 
| 
      
 300 
     | 
    
         
            +
                    #
         
     | 
| 
      
 301 
     | 
    
         
            +
                    # Produce a readable string
         
     | 
| 
      
 302 
     | 
    
         
            +
                    def inspect
         
     | 
| 
      
 303 
     | 
    
         
            +
                        parts = []
         
     | 
| 
      
 304 
     | 
    
         
            +
                        self.instance_variables.each do |x|
         
     | 
| 
      
 305 
     | 
    
         
            +
                            var = self.instance_variable_get(x)
         
     | 
| 
      
 306 
     | 
    
         
            +
                            if var.is_a?(ClassDescriptor) || var.is_a?(Model)
         
     | 
| 
      
 307 
     | 
    
         
            +
                                parts << x.to_s + "=" + var.to_s
         
     | 
| 
      
 308 
     | 
    
         
            +
                            else
         
     | 
| 
      
 309 
     | 
    
         
            +
                                parts << x.to_s + "=" + var.inspect
         
     | 
| 
      
 310 
     | 
    
         
            +
                            end
         
     | 
| 
      
 311 
     | 
    
         
            +
                        end
         
     | 
| 
      
 312 
     | 
    
         
            +
                        return "<#{parts.join(' ')}>"
         
     | 
| 
      
 313 
     | 
    
         
            +
                    end
         
     | 
| 
      
 314 
     | 
    
         
            +
                end
         
     | 
| 
      
 315 
     | 
    
         
            +
             
     | 
| 
      
 316 
     | 
    
         
            +
                # == A class representing a table in the InterMine data model
         
     | 
| 
      
 317 
     | 
    
         
            +
                #
         
     | 
| 
      
 318 
     | 
    
         
            +
                # A class descriptor represents a logical abstraction of a table in the 
         
     | 
| 
      
 319 
     | 
    
         
            +
                # InterMine model, and contains information about the columns in the table
         
     | 
| 
      
 320 
     | 
    
         
            +
                # and the other tables that are referenced by this table.
         
     | 
| 
      
 321 
     | 
    
         
            +
                #
         
     | 
| 
      
 322 
     | 
    
         
            +
                # It can be used to construct queries directly, when obtained from a webservice.
         
     | 
| 
      
 323 
     | 
    
         
            +
                #
         
     | 
| 
      
 324 
     | 
    
         
            +
                #   cld = service.model.table('Gene')
         
     | 
| 
      
 325 
     | 
    
         
            +
                #   cld.where(:symbol => 'zen').each_row {|row| puts row}       
         
     | 
| 
      
 326 
     | 
    
         
            +
                #
         
     | 
| 
      
 327 
     | 
    
         
            +
                #:include:contact_header.rdoc
         
     | 
| 
      
 328 
     | 
    
         
            +
                #
         
     | 
| 
      
 329 
     | 
    
         
            +
                class ClassDescriptor
         
     | 
| 
      
 330 
     | 
    
         
            +
                    include SetHashKey
         
     | 
| 
      
 331 
     | 
    
         
            +
             
     | 
| 
      
 332 
     | 
    
         
            +
                    # The InterMine Model
         
     | 
| 
      
 333 
     | 
    
         
            +
                    attr_reader :model
         
     | 
| 
      
 334 
     | 
    
         
            +
             
     | 
| 
      
 335 
     | 
    
         
            +
                    # The Hash containing the fields of this model
         
     | 
| 
      
 336 
     | 
    
         
            +
                    attr_reader :fields
         
     | 
| 
      
 337 
     | 
    
         
            +
             
     | 
| 
      
 338 
     | 
    
         
            +
                    # ClassDescriptors are constructed automatically when the model itself is 
         
     | 
| 
      
 339 
     | 
    
         
            +
                    # parsed. They should not be constructed on their own.
         
     | 
| 
      
 340 
     | 
    
         
            +
                    #
         
     | 
| 
      
 341 
     | 
    
         
            +
                    # Arguments:
         
     | 
| 
      
 342 
     | 
    
         
            +
                    # [+opts+] A Hash containing the information to initialise this ClassDescriptor.
         
     | 
| 
      
 343 
     | 
    
         
            +
                    # [+model+] The model this ClassDescriptor belongs to.
         
     | 
| 
      
 344 
     | 
    
         
            +
                    #
         
     | 
| 
      
 345 
     | 
    
         
            +
                    def initialize(opts, model)
         
     | 
| 
      
 346 
     | 
    
         
            +
                        @model = model
         
     | 
| 
      
 347 
     | 
    
         
            +
                        @fields = {}
         
     | 
| 
      
 348 
     | 
    
         
            +
                        @klass = nil
         
     | 
| 
      
 349 
     | 
    
         
            +
                        @module = nil
         
     | 
| 
      
 350 
     | 
    
         
            +
             
     | 
| 
      
 351 
     | 
    
         
            +
                        field_types = {
         
     | 
| 
      
 352 
     | 
    
         
            +
                            "attributes" => AttributeDescriptor,
         
     | 
| 
      
 353 
     | 
    
         
            +
                            "references" => ReferenceDescriptor,
         
     | 
| 
      
 354 
     | 
    
         
            +
                            "collections" => CollectionDescriptor
         
     | 
| 
      
 355 
     | 
    
         
            +
                        }
         
     | 
| 
      
 356 
     | 
    
         
            +
             
     | 
| 
      
 357 
     | 
    
         
            +
                        opts.each do |k,v|
         
     | 
| 
      
 358 
     | 
    
         
            +
                            if (field_types.has_key?(k))
         
     | 
| 
      
 359 
     | 
    
         
            +
                                v.each do |name, field| 
         
     | 
| 
      
 360 
     | 
    
         
            +
                                    @fields[name] = field_types[k].new(field, model)
         
     | 
| 
      
 361 
     | 
    
         
            +
                                end
         
     | 
| 
      
 362 
     | 
    
         
            +
                            else
         
     | 
| 
      
 363 
     | 
    
         
            +
                                set_key_value(k, v)
         
     | 
| 
      
 364 
     | 
    
         
            +
                            end
         
     | 
| 
      
 365 
     | 
    
         
            +
                        end
         
     | 
| 
      
 366 
     | 
    
         
            +
                    end
         
     | 
| 
      
 367 
     | 
    
         
            +
             
     | 
| 
      
 368 
     | 
    
         
            +
                    # call-seq: 
         
     | 
| 
      
 369 
     | 
    
         
            +
                    #   new_query => PathQuery::Query
         
     | 
| 
      
 370 
     | 
    
         
            +
                    #
         
     | 
| 
      
 371 
     | 
    
         
            +
                    # Construct a new query for the service this ClassDescriptor belongs to
         
     | 
| 
      
 372 
     | 
    
         
            +
                    # rooted on this table.
         
     | 
| 
      
 373 
     | 
    
         
            +
                    #
         
     | 
| 
      
 374 
     | 
    
         
            +
                    #   query = model.table('Gene').new_query
         
     | 
| 
      
 375 
     | 
    
         
            +
                    #
         
     | 
| 
      
 376 
     | 
    
         
            +
                    def new_query
         
     | 
| 
      
 377 
     | 
    
         
            +
                        q = @model.service.new_query(self.name)
         
     | 
| 
      
 378 
     | 
    
         
            +
                        return q
         
     | 
| 
      
 379 
     | 
    
         
            +
                    end
         
     | 
| 
      
 380 
     | 
    
         
            +
             
     | 
| 
      
 381 
     | 
    
         
            +
                    alias query new_query
         
     | 
| 
      
 382 
     | 
    
         
            +
             
     | 
| 
      
 383 
     | 
    
         
            +
                    # call-seq:
         
     | 
| 
      
 384 
     | 
    
         
            +
                    #   select(*columns) => PathQuery::Query
         
     | 
| 
      
 385 
     | 
    
         
            +
                    #
         
     | 
| 
      
 386 
     | 
    
         
            +
                    # Construct a new query on this table in the originating
         
     | 
| 
      
 387 
     | 
    
         
            +
                    # service with given columns selected for output.
         
     | 
| 
      
 388 
     | 
    
         
            +
                    #
         
     | 
| 
      
 389 
     | 
    
         
            +
                    #   query = model.table('Gene').select(:symbol, :name, "organism.name", "alleles.*")
         
     | 
| 
      
 390 
     | 
    
         
            +
                    #
         
     | 
| 
      
 391 
     | 
    
         
            +
                    #   query.each_result do |gene|
         
     | 
| 
      
 392 
     | 
    
         
            +
                    #       puts "#{gene.symbol} (#{gene.organism.name}): #{gene.alleles.size} Alleles"
         
     | 
| 
      
 393 
     | 
    
         
            +
                    #   end
         
     | 
| 
      
 394 
     | 
    
         
            +
                    #
         
     | 
| 
      
 395 
     | 
    
         
            +
                    def select(*cols)
         
     | 
| 
      
 396 
     | 
    
         
            +
                        q = new_query
         
     | 
| 
      
 397 
     | 
    
         
            +
                        q.add_views(cols)
         
     | 
| 
      
 398 
     | 
    
         
            +
                        return q
         
     | 
| 
      
 399 
     | 
    
         
            +
                    end
         
     | 
| 
      
 400 
     | 
    
         
            +
             
     | 
| 
      
 401 
     | 
    
         
            +
                    # call-seq: 
         
     | 
| 
      
 402 
     | 
    
         
            +
                    #   where(*constraints) => PathQuery::Query
         
     | 
| 
      
 403 
     | 
    
         
            +
                    #
         
     | 
| 
      
 404 
     | 
    
         
            +
                    # Returns a new query on this table in the originating
         
     | 
| 
      
 405 
     | 
    
         
            +
                    # service will all attribute columns selected for output 
         
     | 
| 
      
 406 
     | 
    
         
            +
                    # and the given constraints applied.
         
     | 
| 
      
 407 
     | 
    
         
            +
                    #
         
     | 
| 
      
 408 
     | 
    
         
            +
                    #   zen = model.table('Gene').where(:symbol => 'zen').one
         
     | 
| 
      
 409 
     | 
    
         
            +
                    #   puts "Zen is short for #{zen.name}, and has a length of #{zen.length}"
         
     | 
| 
      
 410 
     | 
    
         
            +
                    #
         
     | 
| 
      
 411 
     | 
    
         
            +
                    def where(*args)
         
     | 
| 
      
 412 
     | 
    
         
            +
                        q = new_query
         
     | 
| 
      
 413 
     | 
    
         
            +
                        q.select("*")
         
     | 
| 
      
 414 
     | 
    
         
            +
                        q.where(*args)
         
     | 
| 
      
 415 
     | 
    
         
            +
                        return q
         
     | 
| 
      
 416 
     | 
    
         
            +
                    end
         
     | 
| 
      
 417 
     | 
    
         
            +
             
     | 
| 
      
 418 
     | 
    
         
            +
                    # call-seq:
         
     | 
| 
      
 419 
     | 
    
         
            +
                    #   get_field(name) => FieldDescriptor
         
     | 
| 
      
 420 
     | 
    
         
            +
                    #
         
     | 
| 
      
 421 
     | 
    
         
            +
                    # Returns the field of the given name if it exists in the
         
     | 
| 
      
 422 
     | 
    
         
            +
                    # referenced table.
         
     | 
| 
      
 423 
     | 
    
         
            +
                    #
         
     | 
| 
      
 424 
     | 
    
         
            +
                    def get_field(name)
         
     | 
| 
      
 425 
     | 
    
         
            +
                        return @fields[name]
         
     | 
| 
      
 426 
     | 
    
         
            +
                    end
         
     | 
| 
      
 427 
     | 
    
         
            +
             
     | 
| 
      
 428 
     | 
    
         
            +
                    alias field get_field
         
     | 
| 
      
 429 
     | 
    
         
            +
             
     | 
| 
      
 430 
     | 
    
         
            +
                    # call-seq:
         
     | 
| 
      
 431 
     | 
    
         
            +
                    #   has_field?(name) => bool
         
     | 
| 
      
 432 
     | 
    
         
            +
                    #
         
     | 
| 
      
 433 
     | 
    
         
            +
                    # Returns true if the table has a field of the given name.
         
     | 
| 
      
 434 
     | 
    
         
            +
                    #
         
     | 
| 
      
 435 
     | 
    
         
            +
                    def has_field?(name)
         
     | 
| 
      
 436 
     | 
    
         
            +
                        return @fields.has_key?(name)
         
     | 
| 
      
 437 
     | 
    
         
            +
                    end
         
     | 
| 
      
 438 
     | 
    
         
            +
             
     | 
| 
      
 439 
     | 
    
         
            +
                    # call-seq:
         
     | 
| 
      
 440 
     | 
    
         
            +
                    #   attributes => Array[AttributeDescriptor]
         
     | 
| 
      
 441 
     | 
    
         
            +
                    #
         
     | 
| 
      
 442 
     | 
    
         
            +
                    # Returns an Array of all fields in the current table that represent 
         
     | 
| 
      
 443 
     | 
    
         
            +
                    # attributes (ie. columns that can hold values, rather than references to 
         
     | 
| 
      
 444 
     | 
    
         
            +
                    # other tables.)
         
     | 
| 
      
 445 
     | 
    
         
            +
                    #
         
     | 
| 
      
 446 
     | 
    
         
            +
                    def attributes
         
     | 
| 
      
 447 
     | 
    
         
            +
                        return @fields.select {|k, v| v.is_a?(AttributeDescriptor)}.map {|pair| pair[1]}
         
     | 
| 
      
 448 
     | 
    
         
            +
                    end
         
     | 
| 
      
 449 
     | 
    
         
            +
             
     | 
| 
      
 450 
     | 
    
         
            +
                    # Returns a human readable string
         
     | 
| 
      
 451 
     | 
    
         
            +
                    def to_s
         
     | 
| 
      
 452 
     | 
    
         
            +
                        return "#{@model.name}.#{@name}"
         
     | 
| 
      
 453 
     | 
    
         
            +
                    end
         
     | 
| 
      
 454 
     | 
    
         
            +
             
     | 
| 
      
 455 
     | 
    
         
            +
                    # Return a fuller string representation.
         
     | 
| 
      
 456 
     | 
    
         
            +
                    def inspect 
         
     | 
| 
      
 457 
     | 
    
         
            +
                        return "<#{self.class.name}:#{self.object_id} #{to_s}>"
         
     | 
| 
      
 458 
     | 
    
         
            +
                    end
         
     | 
| 
      
 459 
     | 
    
         
            +
             
     | 
| 
      
 460 
     | 
    
         
            +
                    # call-seq:
         
     | 
| 
      
 461 
     | 
    
         
            +
                    #   subclass_of?(other) => bool
         
     | 
| 
      
 462 
     | 
    
         
            +
                    #
         
     | 
| 
      
 463 
     | 
    
         
            +
                    # Returns true if the class this ClassDescriptor describes is a
         
     | 
| 
      
 464 
     | 
    
         
            +
                    # subclass of the class the other element evaluates to. The other
         
     | 
| 
      
 465 
     | 
    
         
            +
                    # may be a ClassDescriptor, or a Path, or a String describing a path.
         
     | 
| 
      
 466 
     | 
    
         
            +
                    #
         
     | 
| 
      
 467 
     | 
    
         
            +
                    #   model.table('Gene').subclass_of?(model.table('SequenceFeature'))
         
     | 
| 
      
 468 
     | 
    
         
            +
                    #   >>> true
         
     | 
| 
      
 469 
     | 
    
         
            +
                    #
         
     | 
| 
      
 470 
     | 
    
         
            +
                    #   model.table('Gene').subclass_of?(model.table('Protein'))
         
     | 
| 
      
 471 
     | 
    
         
            +
                    #   >>> false
         
     | 
| 
      
 472 
     | 
    
         
            +
                    #
         
     | 
| 
      
 473 
     | 
    
         
            +
                    def subclass_of?(other)
         
     | 
| 
      
 474 
     | 
    
         
            +
                        path = Path.new(other, @model)
         
     | 
| 
      
 475 
     | 
    
         
            +
                        if @extends.include? path.end_type
         
     | 
| 
      
 476 
     | 
    
         
            +
                            return true
         
     | 
| 
      
 477 
     | 
    
         
            +
                        else
         
     | 
| 
      
 478 
     | 
    
         
            +
                            @extends.each do |x|
         
     | 
| 
      
 479 
     | 
    
         
            +
                                superCls = @model.get_cd(x)
         
     | 
| 
      
 480 
     | 
    
         
            +
                                if superCls.subclass_of?(path)
         
     | 
| 
      
 481 
     | 
    
         
            +
                                    return true
         
     | 
| 
      
 482 
     | 
    
         
            +
                                end
         
     | 
| 
      
 483 
     | 
    
         
            +
                            end
         
     | 
| 
      
 484 
     | 
    
         
            +
                        end
         
     | 
| 
      
 485 
     | 
    
         
            +
                        return false
         
     | 
| 
      
 486 
     | 
    
         
            +
                    end
         
     | 
| 
      
 487 
     | 
    
         
            +
             
     | 
| 
      
 488 
     | 
    
         
            +
                    # call-seq: 
         
     | 
| 
      
 489 
     | 
    
         
            +
                    #   to_module => Module
         
     | 
| 
      
 490 
     | 
    
         
            +
                    #
         
     | 
| 
      
 491 
     | 
    
         
            +
                    # Produces a module containing the logic this ClassDescriptor represents,
         
     | 
| 
      
 492 
     | 
    
         
            +
                    # suitable for including into a class definition.
         
     | 
| 
      
 493 
     | 
    
         
            +
                    #
         
     | 
| 
      
 494 
     | 
    
         
            +
                    # The use of modules enables multiple inheritance, which is supported in 
         
     | 
| 
      
 495 
     | 
    
         
            +
                    # the InterMine data model, to be represented in the classes instantiated
         
     | 
| 
      
 496 
     | 
    
         
            +
                    # in the client.
         
     | 
| 
      
 497 
     | 
    
         
            +
                    #
         
     | 
| 
      
 498 
     | 
    
         
            +
                    def to_module
         
     | 
| 
      
 499 
     | 
    
         
            +
                        if @module.nil?
         
     | 
| 
      
 500 
     | 
    
         
            +
                            nums = ["Float", "Double", "float", "double"]
         
     | 
| 
      
 501 
     | 
    
         
            +
                            ints = ["Integer", "int"]
         
     | 
| 
      
 502 
     | 
    
         
            +
                            bools = ["Boolean", "boolean"]
         
     | 
| 
      
 503 
     | 
    
         
            +
             
     | 
| 
      
 504 
     | 
    
         
            +
                            supers = @extends.map { |x| @model.get_cd(x).to_module }
         
     | 
| 
      
 505 
     | 
    
         
            +
             
     | 
| 
      
 506 
     | 
    
         
            +
                            klass = Module.new
         
     | 
| 
      
 507 
     | 
    
         
            +
                            fd_names = @fields.values.map { |x| x.name }
         
     | 
| 
      
 508 
     | 
    
         
            +
                            klass.class_eval do
         
     | 
| 
      
 509 
     | 
    
         
            +
                                include *supers
         
     | 
| 
      
 510 
     | 
    
         
            +
                                attr_reader *fd_names
         
     | 
| 
      
 511 
     | 
    
         
            +
             
     | 
| 
      
 512 
     | 
    
         
            +
                            end
         
     | 
| 
      
 513 
     | 
    
         
            +
             
     | 
| 
      
 514 
     | 
    
         
            +
                            @fields.values.each do |fd|
         
     | 
| 
      
 515 
     | 
    
         
            +
                                if fd.is_a?(CollectionDescriptor)
         
     | 
| 
      
 516 
     | 
    
         
            +
                                    klass.class_eval do
         
     | 
| 
      
 517 
     | 
    
         
            +
                                        define_method("add" + fd.name.capitalize) do |*vals|
         
     | 
| 
      
 518 
     | 
    
         
            +
                                            type = fd.referencedType
         
     | 
| 
      
 519 
     | 
    
         
            +
                                            instance_var = instance_variable_get("@" + fd.name)
         
     | 
| 
      
 520 
     | 
    
         
            +
                                            instance_var ||= []
         
     | 
| 
      
 521 
     | 
    
         
            +
                                            vals.each do |item|
         
     | 
| 
      
 522 
     | 
    
         
            +
                                                if item.is_a?(Hash)
         
     | 
| 
      
 523 
     | 
    
         
            +
                                                    item = type.model.make_new(type.name, item)
         
     | 
| 
      
 524 
     | 
    
         
            +
                                                end
         
     | 
| 
      
 525 
     | 
    
         
            +
                                                if !item.is_a?(type)
         
     | 
| 
      
 526 
     | 
    
         
            +
                                                    raise ArgumentError, "Arguments to #{fd.name} in #{@name} must be #{type.name}s"
         
     | 
| 
      
 527 
     | 
    
         
            +
                                                end
         
     | 
| 
      
 528 
     | 
    
         
            +
                                                instance_var << item
         
     | 
| 
      
 529 
     | 
    
         
            +
                                            end
         
     | 
| 
      
 530 
     | 
    
         
            +
                                            instance_variable_set("@" + fd.name, instance_var)
         
     | 
| 
      
 531 
     | 
    
         
            +
                                        end
         
     | 
| 
      
 532 
     | 
    
         
            +
                                    end
         
     | 
| 
      
 533 
     | 
    
         
            +
                                end
         
     | 
| 
      
 534 
     | 
    
         
            +
                                klass.class_eval do
         
     | 
| 
      
 535 
     | 
    
         
            +
                                    define_method(fd.name + "=") do |val|
         
     | 
| 
      
 536 
     | 
    
         
            +
                                        if fd.is_a?(AttributeDescriptor)
         
     | 
| 
      
 537 
     | 
    
         
            +
                                            type = fd.dataType
         
     | 
| 
      
 538 
     | 
    
         
            +
                                            if nums.include?(type)
         
     | 
| 
      
 539 
     | 
    
         
            +
                                                if !val.is_a?(Numeric)
         
     | 
| 
      
 540 
     | 
    
         
            +
                                                    raise ArgumentError, "Arguments to #{fd.name} in #{@name} must be numeric"
         
     | 
| 
      
 541 
     | 
    
         
            +
                                                end
         
     | 
| 
      
 542 
     | 
    
         
            +
                                            elsif ints.include?(type)
         
     | 
| 
      
 543 
     | 
    
         
            +
                                                if !val.is_a?(Integer)
         
     | 
| 
      
 544 
     | 
    
         
            +
                                                    raise ArgumentError,  "Arguments to #{fd.name} in #{@name} must be integers"
         
     | 
| 
      
 545 
     | 
    
         
            +
                                                end
         
     | 
| 
      
 546 
     | 
    
         
            +
                                            elsif bools.include?(type)
         
     | 
| 
      
 547 
     | 
    
         
            +
                                                if !val.is_a?(TrueClass) && !val.is_a?(FalseClass)
         
     | 
| 
      
 548 
     | 
    
         
            +
                                                    raise ArgumentError,   "Arguments to #{fd.name} in #{@name} must be booleans"
         
     | 
| 
      
 549 
     | 
    
         
            +
                                                end
         
     | 
| 
      
 550 
     | 
    
         
            +
                                            end
         
     | 
| 
      
 551 
     | 
    
         
            +
                                            instance_variable_set("@" + fd.name, val)
         
     | 
| 
      
 552 
     | 
    
         
            +
                                        else
         
     | 
| 
      
 553 
     | 
    
         
            +
                                            type = fd.referencedType
         
     | 
| 
      
 554 
     | 
    
         
            +
                                            if fd.is_a?(CollectionDescriptor)
         
     | 
| 
      
 555 
     | 
    
         
            +
                                                instance_var = []
         
     | 
| 
      
 556 
     | 
    
         
            +
                                                val.each do |item|
         
     | 
| 
      
 557 
     | 
    
         
            +
                                                    if item.is_a?(Hash)
         
     | 
| 
      
 558 
     | 
    
         
            +
                                                        item = type.model.make_new(type.name, item)
         
     | 
| 
      
 559 
     | 
    
         
            +
                                                    end
         
     | 
| 
      
 560 
     | 
    
         
            +
                                                    if !item.is_a?(type)
         
     | 
| 
      
 561 
     | 
    
         
            +
                                                        raise ArgumentError, "Arguments to #{fd.name} in #{@name} must be #{type.name}s"
         
     | 
| 
      
 562 
     | 
    
         
            +
                                                    end
         
     | 
| 
      
 563 
     | 
    
         
            +
                                                    instance_var << item
         
     | 
| 
      
 564 
     | 
    
         
            +
                                                end
         
     | 
| 
      
 565 
     | 
    
         
            +
                                                instance_variable_set("@" + fd.name, instance_var)
         
     | 
| 
      
 566 
     | 
    
         
            +
                                            else
         
     | 
| 
      
 567 
     | 
    
         
            +
                                                if val.is_a?(Hash)
         
     | 
| 
      
 568 
     | 
    
         
            +
                                                    val = type.model.make_new(type.name, val)
         
     | 
| 
      
 569 
     | 
    
         
            +
                                                end
         
     | 
| 
      
 570 
     | 
    
         
            +
                                                if !val.is_a?(type)
         
     | 
| 
      
 571 
     | 
    
         
            +
                                                    raise ArgumentError, "Arguments to #{fd.name} in #{@name} must be #{type.name}s"
         
     | 
| 
      
 572 
     | 
    
         
            +
                                                end
         
     | 
| 
      
 573 
     | 
    
         
            +
                                                instance_variable_set("@" + fd.name, val)
         
     | 
| 
      
 574 
     | 
    
         
            +
                                            end
         
     | 
| 
      
 575 
     | 
    
         
            +
                                        end
         
     | 
| 
      
 576 
     | 
    
         
            +
                                    end
         
     | 
| 
      
 577 
     | 
    
         
            +
             
     | 
| 
      
 578 
     | 
    
         
            +
                                end
         
     | 
| 
      
 579 
     | 
    
         
            +
                            end
         
     | 
| 
      
 580 
     | 
    
         
            +
                            @module = klass
         
     | 
| 
      
 581 
     | 
    
         
            +
                        end
         
     | 
| 
      
 582 
     | 
    
         
            +
                        return @module
         
     | 
| 
      
 583 
     | 
    
         
            +
                    end
         
     | 
| 
      
 584 
     | 
    
         
            +
             
     | 
| 
      
 585 
     | 
    
         
            +
                    # call-seq:
         
     | 
| 
      
 586 
     | 
    
         
            +
                    #   to_class => Class
         
     | 
| 
      
 587 
     | 
    
         
            +
                    #
         
     | 
| 
      
 588 
     | 
    
         
            +
                    # Returns a Class that can be used to instantiate new objects
         
     | 
| 
      
 589 
     | 
    
         
            +
                    # representing rows of data in the InterMine database.
         
     | 
| 
      
 590 
     | 
    
         
            +
                    #
         
     | 
| 
      
 591 
     | 
    
         
            +
                    def to_class
         
     | 
| 
      
 592 
     | 
    
         
            +
                        if @klass.nil?
         
     | 
| 
      
 593 
     | 
    
         
            +
                            mod = to_module
         
     | 
| 
      
 594 
     | 
    
         
            +
                            kls = Class.new(InterMineObject)
         
     | 
| 
      
 595 
     | 
    
         
            +
                            cd = self
         
     | 
| 
      
 596 
     | 
    
         
            +
                            kls.class_eval do
         
     | 
| 
      
 597 
     | 
    
         
            +
                                include mod
         
     | 
| 
      
 598 
     | 
    
         
            +
                                @__cd__ = cd
         
     | 
| 
      
 599 
     | 
    
         
            +
                            end
         
     | 
| 
      
 600 
     | 
    
         
            +
                            @klass = kls
         
     | 
| 
      
 601 
     | 
    
         
            +
                        end
         
     | 
| 
      
 602 
     | 
    
         
            +
                        return @klass
         
     | 
| 
      
 603 
     | 
    
         
            +
                    end
         
     | 
| 
      
 604 
     | 
    
         
            +
             
     | 
| 
      
 605 
     | 
    
         
            +
                end
         
     | 
| 
      
 606 
     | 
    
         
            +
             
     | 
| 
      
 607 
     | 
    
         
            +
                # A representation of a database column. The characteristics of 
         
     | 
| 
      
 608 
     | 
    
         
            +
                # these classes are defined by the model information received 
         
     | 
| 
      
 609 
     | 
    
         
            +
                # from the webservice
         
     | 
| 
      
 610 
     | 
    
         
            +
                class FieldDescriptor
         
     | 
| 
      
 611 
     | 
    
         
            +
                    include SetHashKey
         
     | 
| 
      
 612 
     | 
    
         
            +
             
     | 
| 
      
 613 
     | 
    
         
            +
                    # The data model this field descriptor belongs to.
         
     | 
| 
      
 614 
     | 
    
         
            +
                    attr_accessor :model
         
     | 
| 
      
 615 
     | 
    
         
            +
             
     | 
| 
      
 616 
     | 
    
         
            +
                    # Constructor. 
         
     | 
| 
      
 617 
     | 
    
         
            +
                    #
         
     | 
| 
      
 618 
     | 
    
         
            +
                    # [+opts+]  The hash of parameters received from the webservice
         
     | 
| 
      
 619 
     | 
    
         
            +
                    # [+model+] The parental data model
         
     | 
| 
      
 620 
     | 
    
         
            +
                    #
         
     | 
| 
      
 621 
     | 
    
         
            +
                    def initialize(opts, model) 
         
     | 
| 
      
 622 
     | 
    
         
            +
                        @model = model
         
     | 
| 
      
 623 
     | 
    
         
            +
                        opts.each do |k, v|
         
     | 
| 
      
 624 
     | 
    
         
            +
                            set_key_value(k, v)
         
     | 
| 
      
 625 
     | 
    
         
            +
                        end
         
     | 
| 
      
 626 
     | 
    
         
            +
                    end
         
     | 
| 
      
 627 
     | 
    
         
            +
             
     | 
| 
      
 628 
     | 
    
         
            +
                end
         
     | 
| 
      
 629 
     | 
    
         
            +
             
     | 
| 
      
 630 
     | 
    
         
            +
                # A class representing columns that contain data.
         
     | 
| 
      
 631 
     | 
    
         
            +
                class AttributeDescriptor < FieldDescriptor
         
     | 
| 
      
 632 
     | 
    
         
            +
                end
         
     | 
| 
      
 633 
     | 
    
         
            +
             
     | 
| 
      
 634 
     | 
    
         
            +
                # A class representing columns that reference other tables.
         
     | 
| 
      
 635 
     | 
    
         
            +
                class ReferenceDescriptor < FieldDescriptor
         
     | 
| 
      
 636 
     | 
    
         
            +
                end
         
     | 
| 
      
 637 
     | 
    
         
            +
             
     | 
| 
      
 638 
     | 
    
         
            +
                # A class representing a virtual column that contains multiple references.
         
     | 
| 
      
 639 
     | 
    
         
            +
                class CollectionDescriptor < ReferenceDescriptor
         
     | 
| 
      
 640 
     | 
    
         
            +
                end
         
     | 
| 
      
 641 
     | 
    
         
            +
             
     | 
| 
      
 642 
     | 
    
         
            +
                # A representation of a path through the data model, starting at a table/class,
         
     | 
| 
      
 643 
     | 
    
         
            +
                # and descending ultimately to an attribute. A path represents a valid 
         
     | 
| 
      
 644 
     | 
    
         
            +
                # sequence of joins and column accesses according to the webservice's database schema.
         
     | 
| 
      
 645 
     | 
    
         
            +
                #
         
     | 
| 
      
 646 
     | 
    
         
            +
                # In string format, a path can be represented using dotted notation:
         
     | 
| 
      
 647 
     | 
    
         
            +
                #
         
     | 
| 
      
 648 
     | 
    
         
            +
                #   Gene.proteins.proteinDomains.name
         
     | 
| 
      
 649 
     | 
    
         
            +
                #
         
     | 
| 
      
 650 
     | 
    
         
            +
                # Which is a valid path through the data-model, starting in the gene table, following
         
     | 
| 
      
 651 
     | 
    
         
            +
                # a reference to the protein table (via x-to-many relationship) and then to the 
         
     | 
| 
      
 652 
     | 
    
         
            +
                # protein-domain table and then finally to the name column in the protein domain table.
         
     | 
| 
      
 653 
     | 
    
         
            +
                # Joins are implicitly implied.
         
     | 
| 
      
 654 
     | 
    
         
            +
                #
         
     | 
| 
      
 655 
     | 
    
         
            +
                #:include:contact_header.rdoc
         
     | 
| 
      
 656 
     | 
    
         
            +
                #
         
     | 
| 
      
 657 
     | 
    
         
            +
                class Path
         
     | 
| 
      
 658 
     | 
    
         
            +
             
     | 
| 
      
 659 
     | 
    
         
            +
                    # The data model that this path describes.
         
     | 
| 
      
 660 
     | 
    
         
            +
                    attr_reader :model
         
     | 
| 
      
 661 
     | 
    
         
            +
             
     | 
| 
      
 662 
     | 
    
         
            +
                    # The objects represented by each section of the path. The first is always a ClassDescriptor.
         
     | 
| 
      
 663 
     | 
    
         
            +
                    attr_reader :elements
         
     | 
| 
      
 664 
     | 
    
         
            +
                    
         
     | 
| 
      
 665 
     | 
    
         
            +
                    # The subclass information used to create this path. 
         
     | 
| 
      
 666 
     | 
    
         
            +
                    attr_reader :subclasses
         
     | 
| 
      
 667 
     | 
    
         
            +
                    
         
     | 
| 
      
 668 
     | 
    
         
            +
                    # The root class of this path. This is the same as the first element.
         
     | 
| 
      
 669 
     | 
    
         
            +
                    attr_reader :rootClass
         
     | 
| 
      
 670 
     | 
    
         
            +
             
     | 
| 
      
 671 
     | 
    
         
            +
                    # Construct a Path
         
     | 
| 
      
 672 
     | 
    
         
            +
                    #
         
     | 
| 
      
 673 
     | 
    
         
            +
                    # The standard mechanism is to parse a string representing a path 
         
     | 
| 
      
 674 
     | 
    
         
            +
                    # with information about the model and the subclasses that are in force. 
         
     | 
| 
      
 675 
     | 
    
         
            +
                    # However, it is also possible to clone a path by passing a Path through
         
     | 
| 
      
 676 
     | 
    
         
            +
                    # as the first element, and also to construct a path from a ClassDescriptor. 
         
     | 
| 
      
 677 
     | 
    
         
            +
                    # In both cases the new Path will inherit the model of the object used to
         
     | 
| 
      
 678 
     | 
    
         
            +
                    # construct it, this avoid the need for a model in these cases.
         
     | 
| 
      
 679 
     | 
    
         
            +
                    #
         
     | 
| 
      
 680 
     | 
    
         
            +
                    def initialize(pathstring, model=nil, subclasses={})
         
     | 
| 
      
 681 
     | 
    
         
            +
                        @model = model
         
     | 
| 
      
 682 
     | 
    
         
            +
                        @subclasses = subclasses
         
     | 
| 
      
 683 
     | 
    
         
            +
                        @elements = []
         
     | 
| 
      
 684 
     | 
    
         
            +
                        @rootClass = nil
         
     | 
| 
      
 685 
     | 
    
         
            +
                        parse(pathstring)
         
     | 
| 
      
 686 
     | 
    
         
            +
                    end
         
     | 
| 
      
 687 
     | 
    
         
            +
             
     | 
| 
      
 688 
     | 
    
         
            +
                    # call-seq:
         
     | 
| 
      
 689 
     | 
    
         
            +
                    #   end_type => String
         
     | 
| 
      
 690 
     | 
    
         
            +
                    #
         
     | 
| 
      
 691 
     | 
    
         
            +
                    # Return the string that describes the kind of thing this path represents.
         
     | 
| 
      
 692 
     | 
    
         
            +
                    # eg:
         
     | 
| 
      
 693 
     | 
    
         
            +
                    # [+Gene+] "Gene"
         
     | 
| 
      
 694 
     | 
    
         
            +
                    # [+Gene.symbol+] "java.lang.String"
         
     | 
| 
      
 695 
     | 
    
         
            +
                    # [+Gene.proteins+] "Protein"
         
     | 
| 
      
 696 
     | 
    
         
            +
                    #
         
     | 
| 
      
 697 
     | 
    
         
            +
                    def end_type
         
     | 
| 
      
 698 
     | 
    
         
            +
                        last = @elements.last
         
     | 
| 
      
 699 
     | 
    
         
            +
                        if last.is_a?(ClassDescriptor)
         
     | 
| 
      
 700 
     | 
    
         
            +
                            return last.name
         
     | 
| 
      
 701 
     | 
    
         
            +
                        elsif last.respond_to?(:referencedType)
         
     | 
| 
      
 702 
     | 
    
         
            +
                            return last.referencedType.name
         
     | 
| 
      
 703 
     | 
    
         
            +
                        else
         
     | 
| 
      
 704 
     | 
    
         
            +
                            return last.dataType
         
     | 
| 
      
 705 
     | 
    
         
            +
                        end
         
     | 
| 
      
 706 
     | 
    
         
            +
                    end
         
     | 
| 
      
 707 
     | 
    
         
            +
             
     | 
| 
      
 708 
     | 
    
         
            +
                    # call-seq:
         
     | 
| 
      
 709 
     | 
    
         
            +
                    #   end_cd => ClassDescriptor
         
     | 
| 
      
 710 
     | 
    
         
            +
                    #
         
     | 
| 
      
 711 
     | 
    
         
            +
                    # Return the last ClassDescriptor mentioned in this path. 
         
     | 
| 
      
 712 
     | 
    
         
            +
                    # eg:
         
     | 
| 
      
 713 
     | 
    
         
            +
                    # [+Gene+] Gene
         
     | 
| 
      
 714 
     | 
    
         
            +
                    # [+Gene.symbol+] Gene
         
     | 
| 
      
 715 
     | 
    
         
            +
                    # [+Gene.proteins+] Protein
         
     | 
| 
      
 716 
     | 
    
         
            +
                    # [+Gene.proteins.name+] Protein
         
     | 
| 
      
 717 
     | 
    
         
            +
                    #
         
     | 
| 
      
 718 
     | 
    
         
            +
                    def end_cd
         
     | 
| 
      
 719 
     | 
    
         
            +
                        last = @elements.last
         
     | 
| 
      
 720 
     | 
    
         
            +
                        if last.is_a?(ClassDescriptor)
         
     | 
| 
      
 721 
     | 
    
         
            +
                            return last
         
     | 
| 
      
 722 
     | 
    
         
            +
                        elsif last.respond_to?(:referencedType)
         
     | 
| 
      
 723 
     | 
    
         
            +
                            return last.referencedType
         
     | 
| 
      
 724 
     | 
    
         
            +
                        else
         
     | 
| 
      
 725 
     | 
    
         
            +
                            penult = @elements[-2]
         
     | 
| 
      
 726 
     | 
    
         
            +
                            if penult.is_a?(ClassDescriptor)
         
     | 
| 
      
 727 
     | 
    
         
            +
                                return penult
         
     | 
| 
      
 728 
     | 
    
         
            +
                            else
         
     | 
| 
      
 729 
     | 
    
         
            +
                                return penult.referencedType
         
     | 
| 
      
 730 
     | 
    
         
            +
                            end
         
     | 
| 
      
 731 
     | 
    
         
            +
                        end
         
     | 
| 
      
 732 
     | 
    
         
            +
                    end
         
     | 
| 
      
 733 
     | 
    
         
            +
             
     | 
| 
      
 734 
     | 
    
         
            +
                    # Two paths can be said to be equal when they stringify to the same representation.
         
     | 
| 
      
 735 
     | 
    
         
            +
                    def ==(other)
         
     | 
| 
      
 736 
     | 
    
         
            +
                        return self.to_s == other.to_s
         
     | 
| 
      
 737 
     | 
    
         
            +
                    end
         
     | 
| 
      
 738 
     | 
    
         
            +
             
     | 
| 
      
 739 
     | 
    
         
            +
                    # Get the number of elements in the path
         
     | 
| 
      
 740 
     | 
    
         
            +
                    def length
         
     | 
| 
      
 741 
     | 
    
         
            +
                        return @elements.length
         
     | 
| 
      
 742 
     | 
    
         
            +
                    end
         
     | 
| 
      
 743 
     | 
    
         
            +
             
     | 
| 
      
 744 
     | 
    
         
            +
                    # Return the string representation of this path, eg: "Gene.proteins.name"
         
     | 
| 
      
 745 
     | 
    
         
            +
                    def to_s 
         
     | 
| 
      
 746 
     | 
    
         
            +
                        return @elements.map {|x| x.name}.join(".")
         
     | 
| 
      
 747 
     | 
    
         
            +
                    end
         
     | 
| 
      
 748 
     | 
    
         
            +
             
     | 
| 
      
 749 
     | 
    
         
            +
                    # Returns a string as to_s without the first element. eg: "proteins.name"
         
     | 
| 
      
 750 
     | 
    
         
            +
                    def to_headless_s
         
     | 
| 
      
 751 
     | 
    
         
            +
                        return @elements[1, @elements.size - 1].map {|x| x.name}.join(".")
         
     | 
| 
      
 752 
     | 
    
         
            +
                    end
         
     | 
| 
      
 753 
     | 
    
         
            +
             
     | 
| 
      
 754 
     | 
    
         
            +
                    # Return true if the Path ends in an attribute
         
     | 
| 
      
 755 
     | 
    
         
            +
                    def is_attribute?
         
     | 
| 
      
 756 
     | 
    
         
            +
                        return @elements.last.is_a?(AttributeDescriptor)
         
     | 
| 
      
 757 
     | 
    
         
            +
                    end
         
     | 
| 
      
 758 
     | 
    
         
            +
             
     | 
| 
      
 759 
     | 
    
         
            +
                    # Return true if the last element is a class (ie. a path of length 1)
         
     | 
| 
      
 760 
     | 
    
         
            +
                    def is_class?
         
     | 
| 
      
 761 
     | 
    
         
            +
                        return @elements.last.is_a?(ClassDescriptor)
         
     | 
| 
      
 762 
     | 
    
         
            +
                    end
         
     | 
| 
      
 763 
     | 
    
         
            +
             
     | 
| 
      
 764 
     | 
    
         
            +
                    # Return true if the last element is a reference.
         
     | 
| 
      
 765 
     | 
    
         
            +
                    def is_reference?
         
     | 
| 
      
 766 
     | 
    
         
            +
                        return @elements.last.is_a?(ReferenceDescriptor)
         
     | 
| 
      
 767 
     | 
    
         
            +
                    end
         
     | 
| 
      
 768 
     | 
    
         
            +
             
     | 
| 
      
 769 
     | 
    
         
            +
                    # Return true if the last element is a collection
         
     | 
| 
      
 770 
     | 
    
         
            +
                    def is_collection?
         
     | 
| 
      
 771 
     | 
    
         
            +
                        return @elements.last.is_a?(CollectionDescriptor)
         
     | 
| 
      
 772 
     | 
    
         
            +
                    end
         
     | 
| 
      
 773 
     | 
    
         
            +
             
     | 
| 
      
 774 
     | 
    
         
            +
                    private
         
     | 
| 
      
 775 
     | 
    
         
            +
             
     | 
| 
      
 776 
     | 
    
         
            +
                    # Perform the parsing of the input into a sequence of elements.
         
     | 
| 
      
 777 
     | 
    
         
            +
                    def parse(pathstring)
         
     | 
| 
      
 778 
     | 
    
         
            +
                        if pathstring.is_a?(ClassDescriptor)
         
     | 
| 
      
 779 
     | 
    
         
            +
                            @rootClass = pathstring
         
     | 
| 
      
 780 
     | 
    
         
            +
                            @elements << pathstring
         
     | 
| 
      
 781 
     | 
    
         
            +
                            @model = pathstring.model
         
     | 
| 
      
 782 
     | 
    
         
            +
                            return
         
     | 
| 
      
 783 
     | 
    
         
            +
                        elsif pathstring.is_a?(Path)
         
     | 
| 
      
 784 
     | 
    
         
            +
                            @rootClass = pathstring.rootClass
         
     | 
| 
      
 785 
     | 
    
         
            +
                            @elements = pathstring.elements
         
     | 
| 
      
 786 
     | 
    
         
            +
                            @model = pathstring.model
         
     | 
| 
      
 787 
     | 
    
         
            +
                            @subclasses = pathstring.subclasses
         
     | 
| 
      
 788 
     | 
    
         
            +
                            return
         
     | 
| 
      
 789 
     | 
    
         
            +
                        end
         
     | 
| 
      
 790 
     | 
    
         
            +
             
     | 
| 
      
 791 
     | 
    
         
            +
                        bits = pathstring.split(".")
         
     | 
| 
      
 792 
     | 
    
         
            +
                        rootName = bits.shift
         
     | 
| 
      
 793 
     | 
    
         
            +
                        @rootClass = @model.get_cd(rootName)
         
     | 
| 
      
 794 
     | 
    
         
            +
                        if @rootClass.nil?
         
     | 
| 
      
 795 
     | 
    
         
            +
                            raise PathException.new(pathstring, subclasses, "Invalid root class '#{rootName}'")
         
     | 
| 
      
 796 
     | 
    
         
            +
                        end
         
     | 
| 
      
 797 
     | 
    
         
            +
             
     | 
| 
      
 798 
     | 
    
         
            +
                        @elements << @rootClass
         
     | 
| 
      
 799 
     | 
    
         
            +
                        processed = [rootName]
         
     | 
| 
      
 800 
     | 
    
         
            +
             
     | 
| 
      
 801 
     | 
    
         
            +
                        current_cd = @rootClass
         
     | 
| 
      
 802 
     | 
    
         
            +
             
     | 
| 
      
 803 
     | 
    
         
            +
                        while (bits.length > 0)
         
     | 
| 
      
 804 
     | 
    
         
            +
                            this_bit = bits.shift
         
     | 
| 
      
 805 
     | 
    
         
            +
                            fd = current_cd.get_field(this_bit)
         
     | 
| 
      
 806 
     | 
    
         
            +
                            if fd.nil?
         
     | 
| 
      
 807 
     | 
    
         
            +
                                subclassKey = processed.join(".")
         
     | 
| 
      
 808 
     | 
    
         
            +
                                if @subclasses.has_key?(subclassKey)
         
     | 
| 
      
 809 
     | 
    
         
            +
                                    subclass = model.get_cd(@subclasses[subclassKey])
         
     | 
| 
      
 810 
     | 
    
         
            +
                                    if subclass.nil?
         
     | 
| 
      
 811 
     | 
    
         
            +
                                        raise PathException.new(pathstring, subclasses,
         
     | 
| 
      
 812 
     | 
    
         
            +
                "'#{subclassKey}' constrained to be a '#{@subclasses[subclassKey]}', but that is not a valid class in the model")
         
     | 
| 
      
 813 
     | 
    
         
            +
                                    end
         
     | 
| 
      
 814 
     | 
    
         
            +
                                    current_cd = subclass
         
     | 
| 
      
 815 
     | 
    
         
            +
                                    fd = current_cd.get_field(this_bit)
         
     | 
| 
      
 816 
     | 
    
         
            +
                                end
         
     | 
| 
      
 817 
     | 
    
         
            +
                                if fd.nil?
         
     | 
| 
      
 818 
     | 
    
         
            +
                                    raise PathException.new(pathstring, subclasses,
         
     | 
| 
      
 819 
     | 
    
         
            +
                "giving up at '#{subclassKey}.#{this_bit}'. Could not find '#{this_bit}' in '#{current_cd}'")
         
     | 
| 
      
 820 
     | 
    
         
            +
                                end
         
     | 
| 
      
 821 
     | 
    
         
            +
                            end
         
     | 
| 
      
 822 
     | 
    
         
            +
                            @elements << fd
         
     | 
| 
      
 823 
     | 
    
         
            +
                            if fd.respond_to?(:referencedType)
         
     | 
| 
      
 824 
     | 
    
         
            +
                                current_cd = fd.referencedType
         
     | 
| 
      
 825 
     | 
    
         
            +
                            elsif bits.length > 0
         
     | 
| 
      
 826 
     | 
    
         
            +
                                raise PathException.new(pathstring, subclasses, 
         
     | 
| 
      
 827 
     | 
    
         
            +
                "Attributes must be at the end of the path. Giving up at '#{this_bit}'")
         
     | 
| 
      
 828 
     | 
    
         
            +
                            else
         
     | 
| 
      
 829 
     | 
    
         
            +
                                current_cd = nil
         
     | 
| 
      
 830 
     | 
    
         
            +
                            end
         
     | 
| 
      
 831 
     | 
    
         
            +
                            processed << this_bit
         
     | 
| 
      
 832 
     | 
    
         
            +
                        end
         
     | 
| 
      
 833 
     | 
    
         
            +
                    end
         
     | 
| 
      
 834 
     | 
    
         
            +
                end
         
     | 
| 
      
 835 
     | 
    
         
            +
             
     | 
| 
      
 836 
     | 
    
         
            +
                # An exception class for handling path parsing errors.
         
     | 
| 
      
 837 
     | 
    
         
            +
                class PathException < RuntimeError
         
     | 
| 
      
 838 
     | 
    
         
            +
             
     | 
| 
      
 839 
     | 
    
         
            +
                    attr_reader :pathstring, :subclasses
         
     | 
| 
      
 840 
     | 
    
         
            +
             
     | 
| 
      
 841 
     | 
    
         
            +
                    def initialize(pathstring=nil, subclasses={}, message=nil)
         
     | 
| 
      
 842 
     | 
    
         
            +
                        @pathstring = pathstring
         
     | 
| 
      
 843 
     | 
    
         
            +
                        @subclasses = subclasses
         
     | 
| 
      
 844 
     | 
    
         
            +
                        @message = message
         
     | 
| 
      
 845 
     | 
    
         
            +
                    end
         
     | 
| 
      
 846 
     | 
    
         
            +
             
     | 
| 
      
 847 
     | 
    
         
            +
                    # The string representation.
         
     | 
| 
      
 848 
     | 
    
         
            +
                    def to_s
         
     | 
| 
      
 849 
     | 
    
         
            +
                        if @pathstring.nil?
         
     | 
| 
      
 850 
     | 
    
         
            +
                            if @message.nil?
         
     | 
| 
      
 851 
     | 
    
         
            +
                                return self.class.name
         
     | 
| 
      
 852 
     | 
    
         
            +
                            else
         
     | 
| 
      
 853 
     | 
    
         
            +
                                return @message
         
     | 
| 
      
 854 
     | 
    
         
            +
                            end
         
     | 
| 
      
 855 
     | 
    
         
            +
                        end
         
     | 
| 
      
 856 
     | 
    
         
            +
                        preamble = "Unable to resolve '#{@pathstring}': "
         
     | 
| 
      
 857 
     | 
    
         
            +
                        footer = " (SUBCLASSES => #{@subclasses.inspect})"
         
     | 
| 
      
 858 
     | 
    
         
            +
                        if @message.nil?
         
     | 
| 
      
 859 
     | 
    
         
            +
                            return preamble + footer
         
     | 
| 
      
 860 
     | 
    
         
            +
                        else
         
     | 
| 
      
 861 
     | 
    
         
            +
                            return preamble + @message + footer
         
     | 
| 
      
 862 
     | 
    
         
            +
                        end
         
     | 
| 
      
 863 
     | 
    
         
            +
                    end
         
     | 
| 
      
 864 
     | 
    
         
            +
                end
         
     | 
| 
      
 865 
     | 
    
         
            +
            end
         
     | 
| 
      
 866 
     | 
    
         
            +
            end
         
     | 
| 
      
 867 
     | 
    
         
            +
             
     |