intermine 0.98.01
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- 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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# _resolve(path) => value
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#
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# Resolve a path represented as a String or as a Path into a value
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#
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# This is designed to automate access to values in deeply nested objects. So:
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#
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# name = gene._resolve('Gene.organism.name')
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#
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# Array indices are supported:
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#
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# symbol = gene._resolve('Gene.alleles[3].symbol')
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#
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def _resolve(path)
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begin
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parts = path.split(/(?:\.|\[|\])/).reject {|x| x.empty?}
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rescue NoMethodError
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parts = path.elements.map { |x| x.name }
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end
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root = parts.shift
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if !is_a?(root)
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raise ArgumentError, "Incompatible path '#{path}': #{self} is not a #{root}"
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end
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begin
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res = parts.inject(self) do |memo, part|
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part = part.to_i if (memo.is_a?(Array) and part.to_i.to_s == part)
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begin
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new = memo[part]
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rescue TypeError
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raise ArgumentError, "Incompatible path '#{path}' for #{self}, expected an index"
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end
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new
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end
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rescue IndexError => e
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raise ArgumentError, "Incompatible path '#{path}' for #{self}, #{e}"
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end
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return res
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end
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alias inspect to_s
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private
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def __cd__=(cld)
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@__cd__ = cld
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end
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def objectId=(val)
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@objectId = val
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end
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end
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# == A base module that provides helpers for setting up classes bases on the contents of a Hash
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#
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# ClassDescriptors and FieldDescriptors are instantiated
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# with hashes that provide their properties. This module
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# makes sure that the appropriate instance variables are set
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#
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#:include:contact_header.rdoc
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#
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module SetHashKey
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# call-seq:
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# set_key_value(key, value)
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#
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# Set up instance variables based on the contents of a hash
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def set_key_value(k, v)
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if (k == "type")
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k = "dataType"
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end
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## create and initialize an instance variable for this
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## key/value pair
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self.instance_variable_set("@#{k}", v)
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## create the getter that returns the instance variable
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self.class.send(:define_method, k,
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proc{self.instance_variable_get("@#{k}")})
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## create the setter that sets the instance variable
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self.class.send(:define_method, "#{k}=",
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proc{|v| self.instance_variable_set("@#{k}", v)})
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return
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end
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# call-seq:
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# inspect() => readable-string
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#
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# Produce a readable string
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def inspect
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parts = []
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self.instance_variables.each do |x|
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var = self.instance_variable_get(x)
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if var.is_a?(ClassDescriptor) || var.is_a?(Model)
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parts << x.to_s + "=" + var.to_s
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else
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parts << x.to_s + "=" + var.inspect
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end
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end
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return "<#{parts.join(' ')}>"
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end
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end
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# == A class representing a table in the InterMine data model
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#
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# A class descriptor represents a logical abstraction of a table in the
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# InterMine model, and contains information about the columns in the table
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# and the other tables that are referenced by this table.
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#
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# It can be used to construct queries directly, when obtained from a webservice.
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#
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# cld = service.model.table('Gene')
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# cld.where(:symbol => 'zen').each_row {|row| puts row}
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#
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#:include:contact_header.rdoc
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#
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class ClassDescriptor
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include SetHashKey
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# The InterMine Model
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attr_reader :model
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# The Hash containing the fields of this model
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attr_reader :fields
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# ClassDescriptors are constructed automatically when the model itself is
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# parsed. They should not be constructed on their own.
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#
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# Arguments:
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# [+opts+] A Hash containing the information to initialise this ClassDescriptor.
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# [+model+] The model this ClassDescriptor belongs to.
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#
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def initialize(opts, model)
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@model = model
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@fields = {}
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@klass = nil
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@module = nil
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field_types = {
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"attributes" => AttributeDescriptor,
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"references" => ReferenceDescriptor,
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"collections" => CollectionDescriptor
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}
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opts.each do |k,v|
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if (field_types.has_key?(k))
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v.each do |name, field|
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@fields[name] = field_types[k].new(field, model)
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end
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else
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set_key_value(k, v)
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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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# new_query => PathQuery::Query
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#
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# Construct a new query for the service this ClassDescriptor belongs to
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# rooted on this table.
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#
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# query = model.table('Gene').new_query
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#
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def new_query
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q = @model.service.new_query(self.name)
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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
|
+
|