intermine 0.98.01

data/test/data/lists.json

@@ -0,0 +1,29 @@
+{"lists":[
+    {
+        "name":"test-list-1", 
+        "title":"test1", 
+        "description":"An example test list",
+        "type": "Employee",
+        "size": 42,
+        "dateCreated": "2011-05-07T19:52:03",
+        "authorized": true,
+        "tags": ["tag1", "tag2", "tag3"]
+    },
+    {
+        "name":"test-list-2", 
+        "title":"test2", 
+        "description":"Another example test list",
+        "type": "Manager",
+        "size": 7,
+        "dateCreated": "2011-05-07T10:11:12",
+        "authorized": false
+    },
+    {
+        "name":"test-list-3", 
+        "title":"test3", 
+        "description":"Yet Another example test list",
+        "type": "CEO",
+        "size": 8,
+        "dateCreated": "2011-05-07T10:11:12"
+    }
+],"wasSuccessful":true,"error":null,"statusCode":200}

data/test/data/model.json

@@ -0,0 +1,3 @@
+{"model":{
+"name":"testmodel","classes":{"Broke":{"name":"Broke","extends":[],"isInterface":true,"attributes":{"debt":{"name":"debt","type":"int"},"id":{"name":"id","type":"java.lang.Integer"}},"references":{"bank":{"name":"bank","referencedType":"Bank","reverseReference":"debtors"}},"collections":{}},"Thing":{"name":"Thing","extends":[],"isInterface":true,"attributes":{"id":{"name":"id","type":"java.lang.Integer"}},"references":{},"collections":{}},"Employable":{"name":"Employable","extends":["Thing"],"isInterface":true,"attributes":{"name":{"name":"name","type":"java.lang.String"},"id":{"name":"id","type":"java.lang.Integer"}},"references":{},"collections":{}},"HasAddress":{"name":"HasAddress","extends":[],"isInterface":true,"attributes":{"id":{"name":"id","type":"java.lang.Integer"}},"references":{"address":{"name":"address","referencedType":"Address"}},"collections":{}},"HasSecretarys":{"name":"HasSecretarys","extends":[],"isInterface":true,"attributes":{"id":{"name":"id","type":"java.lang.Integer"}},"references":{},"collections":{"secretarys":{"name":"secretarys","referencedType":"Secretary"}}},"Contractor":{"name":"Contractor","extends":["Employable","ImportantPerson"],"isInterface":false,"attributes":{"name":{"name":"name","type":"java.lang.String"},"id":{"name":"id","type":"java.lang.Integer"},"seniority":{"name":"seniority","type":"java.lang.Integer"}},"references":{"personalAddress":{"name":"personalAddress","referencedType":"Address"},"businessAddress":{"name":"businessAddress","referencedType":"Address"}},"collections":{"companys":{"name":"companys","referencedType":"Company","reverseReference":"contractors"},"oldComs":{"name":"oldComs","referencedType":"Company","reverseReference":"oldContracts"}}},"Manager":{"name":"Manager","extends":["Employee","ImportantPerson"],"isInterface":false,"attributes":{"title":{"name":"title","type":"java.lang.String"},"fullTime":{"name":"fullTime","type":"boolean"},"age":{"name":"age","type":"int"},"end":{"name":"end","type":"java.lang.String"},"name":{"name":"name","type":"java.lang.String"},"id":{"name":"id","type":"java.lang.Integer"},"seniority":{"name":"seniority","type":"java.lang.Integer"}},"references":{"department":{"name":"department","referencedType":"Department","reverseReference":"employees"},"departmentThatRejectedMe":{"name":"departmentThatRejectedMe","referencedType":"Department","reverseReference":"rejectedEmployee"},"address":{"name":"address","referencedType":"Address"}},"collections":{"simpleObjects":{"name":"simpleObjects","referencedType":"SimpleObject","reverseReference":"employee"}}},"Employee":{"name":"Employee","extends":["Employable","HasAddress"],"isInterface":false,"attributes":{"fullTime":{"name":"fullTime","type":"boolean"},"age":{"name":"age","type":"int"},"end":{"name":"end","type":"java.lang.String"},"name":{"name":"name","type":"java.lang.String"},"id":{"name":"id","type":"java.lang.Integer"}},"references":{"department":{"name":"department","referencedType":"Department","reverseReference":"employees"},"departmentThatRejectedMe":{"name":"departmentThatRejectedMe","referencedType":"Department","reverseReference":"rejectedEmployee"},"address":{"name":"address","referencedType":"Address"}},"collections":{"simpleObjects":{"name":"simpleObjects","referencedType":"SimpleObject","reverseReference":"employee"}}},"Department":{"name":"Department","extends":["RandomInterface"],"isInterface":false,"attributes":{"name":{"name":"name","type":"java.lang.String"},"id":{"name":"id","type":"java.lang.Integer"}},"references":{"company":{"name":"company","referencedType":"Company","reverseReference":"departments"},"manager":{"name":"manager","referencedType":"Manager"}},"collections":{"employees":{"name":"employees","referencedType":"Employee","reverseReference":"department"},"rejectedEmployee":{"name":"rejectedEmployee","referencedType":"Employee","reverseReference":"departmentThatRejectedMe"}}},"Company":{"name":"Company","extends":["RandomInterface","HasAddress","HasSecretarys"],"isInterface":true,"attributes":{"name":{"name":"name","type":"java.lang.String"},"vatNumber":{"name":"vatNumber","type":"int"},"id":{"name":"id","type":"java.lang.Integer"}},"references":{"CEO":{"name":"CEO","referencedType":"CEO","reverseReference":"company"},"address":{"name":"address","referencedType":"Address"}},"collections":{"departments":{"name":"departments","referencedType":"Department","reverseReference":"company"},"contractors":{"name":"contractors","referencedType":"Contractor","reverseReference":"companys"},"oldContracts":{"name":"oldContracts","referencedType":"Contractor","reverseReference":"oldComs"},"secretarys":{"name":"secretarys","referencedType":"Secretary"}}},"Address":{"name":"Address","extends":["Thing"],"isInterface":false,"attributes":{"address":{"name":"address","type":"java.lang.String"},"id":{"name":"id","type":"java.lang.Integer"}},"references":{},"collections":{}},"RandomInterface":{"name":"RandomInterface","extends":[],"isInterface":true,"attributes":{"id":{"name":"id","type":"java.lang.Integer"}},"references":{},"collections":{}},"CEO":{"name":"CEO","extends":["Manager","HasSecretarys"],"isInterface":false,"attributes":{"salary":{"name":"salary","type":"int"},"title":{"name":"title","type":"java.lang.String"},"fullTime":{"name":"fullTime","type":"boolean"},"age":{"name":"age","type":"int"},"end":{"name":"end","type":"java.lang.String"},"name":{"name":"name","type":"java.lang.String"},"id":{"name":"id","type":"java.lang.Integer"},"seniority":{"name":"seniority","type":"java.lang.Integer"}},"references":{"company":{"name":"company","referencedType":"Company","reverseReference":"CEO"},"department":{"name":"department","referencedType":"Department","reverseReference":"employees"},"departmentThatRejectedMe":{"name":"departmentThatRejectedMe","referencedType":"Department","reverseReference":"rejectedEmployee"},"address":{"name":"address","referencedType":"Address"}},"collections":{"simpleObjects":{"name":"simpleObjects","referencedType":"SimpleObject","reverseReference":"employee"},"secretarys":{"name":"secretarys","referencedType":"Secretary"}}},"ImportantPerson":{"name":"ImportantPerson","extends":[],"isInterface":true,"attributes":{"seniority":{"name":"seniority","type":"java.lang.Integer"},"id":{"name":"id","type":"java.lang.Integer"}},"references":{},"collections":{}},"Secretary":{"name":"Secretary","extends":[],"isInterface":false,"attributes":{"name":{"name":"name","type":"java.lang.String"},"id":{"name":"id","type":"java.lang.Integer"}},"references":{},"collections":{}},"Types":{"name":"Types","extends":[],"isInterface":false,"attributes":{"name":{"name":"name","type":"java.lang.String"},"booleanType":{"name":"booleanType","type":"boolean"},"floatType":{"name":"floatType","type":"float"},"doubleType":{"name":"doubleType","type":"double"},"shortType":{"name":"shortType","type":"short"},"intType":{"name":"intType","type":"int"},"longType":{"name":"longType","type":"long"},"booleanObjType":{"name":"booleanObjType","type":"java.lang.Boolean"},"floatObjType":{"name":"floatObjType","type":"java.lang.Float"},"doubleObjType":{"name":"doubleObjType","type":"java.lang.Double"},"shortObjType":{"name":"shortObjType","type":"java.lang.Short"},"intObjType":{"name":"intObjType","type":"java.lang.Integer"},"longObjType":{"name":"longObjType","type":"java.lang.Long"},"bigDecimalObjType":{"name":"bigDecimalObjType","type":"java.math.BigDecimal"},"dateObjType":{"name":"dateObjType","type":"java.util.Date"},"stringObjType":{"name":"stringObjType","type":"java.lang.String"},"clobObjType":{"name":"clobObjType","type":"org.intermine.objectstore.query.ClobAccess"},"id":{"name":"id","type":"java.lang.Integer"}},"references":{},"collections":{}},"Bank":{"name":"Bank","extends":[],"isInterface":false,"attributes":{"name":{"name":"name","type":"java.lang.String"},"id":{"name":"id","type":"java.lang.Integer"}},"references":{},"collections":{"debtors":{"name":"debtors","referencedType":"Broke","reverseReference":"bank"}}},"SimpleObject":{"name":"SimpleObject","extends":["java.lang.Object"],"isInterface":false,"attributes":{"name":{"name":"name","type":"java.lang.String"}},"references":{"employee":{"name":"employee","referencedType":"Employee","reverseReference":"simpleObjects"}},"collections":{}},"Range":{"name":"Range","extends":[],"isInterface":false,"attributes":{"rangeStart":{"name":"rangeStart","type":"int"},"rangeEnd":{"name":"rangeEnd","type":"int"},"name":{"name":"name","type":"java.lang.String"},"id":{"name":"id","type":"java.lang.Integer"}},"references":{"parent":{"name":"parent","referencedType":"Company"}},"collections":{}}}
+},"wasSuccessful":true,"error":null,"statusCode":200}

data/test/data/resultobjs.json

@@ -0,0 +1,3 @@
+{"rootClass":"Pathway","modelName":"genomic","start":0,"views":["Pathway.identifier","Pathway.name","Pathway.genes.secondaryIdentifier","Pathway.genes.symbol"],"results":[
+{"objectId":388000112,"genes":[{"symbol":"CG12398","objectId":355194908,"class":"Gene","secondaryIdentifier":"CG12398"},{"symbol":"Zw","objectId":355077327,"class":"Gene","secondaryIdentifier":"CG12529"},{"symbol":"CG12539","objectId":355713082,"class":"Gene","secondaryIdentifier":"CG12539"},{"symbol":"CG13369","objectId":355219881,"class":"Gene","secondaryIdentifier":"CG13369"},{"symbol":"CG15093","objectId":355220032,"class":"Gene","secondaryIdentifier":"CG15093"},{"symbol":"CG17010","objectId":355512718,"class":"Gene","secondaryIdentifier":"CG17010"},{"symbol":"CG17333","objectId":355223984,"class":"Gene","secondaryIdentifier":"CG17333"},{"symbol":"Tal","objectId":355205655,"class":"Gene","secondaryIdentifier":"CG2827"},{"symbol":"CG30410","objectId":355505527,"class":"Gene","secondaryIdentifier":"CG30410"},{"symbol":"CG30499","objectId":355006231,"class":"Gene","secondaryIdentifier":"CG30499"},{"symbol":"fbp","objectId":355206294,"class":"Gene","secondaryIdentifier":"CG31692"},{"symbol":"Pgd","objectId":355110188,"class":"Gene","secondaryIdentifier":"CG3724"},{"symbol":"Pfk","objectId":355129877,"class":"Gene","secondaryIdentifier":"CG4001"},{"symbol":"CG5103","objectId":355532927,"class":"Gene","secondaryIdentifier":"CG5103"},{"symbol":"Pgm","objectId":355115908,"class":"Gene","secondaryIdentifier":"CG5165"},{"symbol":"CG5432","objectId":355442677,"class":"Gene","secondaryIdentifier":"CG5432"},{"symbol":"Ald","objectId":355087230,"class":"Gene","secondaryIdentifier":"CG6058"},{"symbol":"CG6767","objectId":355117375,"class":"Gene","secondaryIdentifier":"CG6767"},{"symbol":"CG7140","objectId":355023087,"class":"Gene","secondaryIdentifier":"CG7140"},{"symbol":"CG8036","objectId":355032410,"class":"Gene","secondaryIdentifier":"CG8036"},{"symbol":"Pgi","objectId":355130643,"class":"Gene","secondaryIdentifier":"CG8251"},{"symbol":"CG8525","objectId":355214438,"class":"Gene","secondaryIdentifier":"CG8525"}],"name":"Pentose phosphate pathway","class":"Pathway","identifier":"00030"}
+],"executionTime":"2011.07.13 10:03::13","wasSuccessful":true,"error":null,"statusCode":200}

data/test/data/resultrow.json

@@ -0,0 +1 @@
+[{"id":320000014,"value":"DepartmentA1","class":"Department","url":"/report.do?id=320000014"},{"id":320000015,"value":"EmployeeA1","class":"Manager","url":"/report.do?id=320000015"}]

data/test/data/resultset.json

@@ -0,0 +1,3 @@
+{"rootClass":"Company","modelName":"testmodel","start":0,"views":["Company.departments.name","Company.departments.manager.name"],"results":[
+[{"id":320000014,"value":"DepartmentA1","class":"Department","url":"/report.do?id=320000014"},{"id":320000015,"value":"EmployeeA1","class":"Manager","url":"/report.do?id=320000015"}]
+],"executionTime":"2011.07.09 11:52::30","wasSuccessful":true,"error":null,"statusCode":200}

data/test/data/testmodel_model.xml

@@ -0,0 +1,94 @@
+<model name="testmodel" package="org.intermine.model.testmodel">
+    <class name="Broke" is-interface="true">
+        <attribute name="debt" type="int"/>
+        <reference name="bank" referenced-type="Bank" reverse-reference="debtors"/>
+    </class>
+    <class name="Thing" is-interface="true"></class>
+    <class name="Employable" extends="Thing" is-interface="true">
+        <attribute name="name" type="java.lang.String"/>
+    </class>
+    <class name="HasAddress" is-interface="true">
+        <reference name="address" referenced-type="Address"/>
+    </class>
+    <class name="HasSecretarys" is-interface="true">
+        <collection name="secretarys" referenced-type="Secretary"/>
+    </class>
+    <class name="Contractor" extends="Employable ImportantPerson" is-interface="false">
+        <reference name="personalAddress" referenced-type="Address"/>
+        <reference name="businessAddress" referenced-type="Address"/>
+        <collection name="companys" referenced-type="Company" reverse-reference="contractors"/>
+        <collection name="oldComs" referenced-type="Company" reverse-reference="oldContracts"/>
+    </class>
+    <class name="Manager" extends="Employee ImportantPerson" is-interface="false">
+        <attribute name="title" type="java.lang.String"/>
+    </class>
+    <class name="Employee" extends="Employable HasAddress" is-interface="false">
+        <attribute name="fullTime" type="boolean"/>
+        <attribute name="age" type="int"/>
+        <attribute name="end" type="java.lang.String"/>
+        <reference name="department" referenced-type="Department" reverse-reference="employees"/>
+        <reference name="departmentThatRejectedMe" referenced-type="Department" reverse-reference="rejectedEmployee"/>
+        <collection name="simpleObjects" referenced-type="SimpleObject" reverse-reference="employee"/>
+    </class>
+    <class name="Department" extends="RandomInterface" is-interface="false">
+        <attribute name="name" type="java.lang.String"/>
+        <reference name="company" referenced-type="Company" reverse-reference="departments"/>
+        <reference name="manager" referenced-type="Manager"/>
+        <collection name="employees" referenced-type="Employee" reverse-reference="department"/>
+        <collection name="rejectedEmployees" referenced-type="Employee" reverse-reference="departmentThatRejectedMe"/>
+    </class>
+    <class name="Company" extends="RandomInterface HasAddress HasSecretarys" is-interface="true">
+        <attribute name="name" type="java.lang.String"/>
+        <attribute name="vatNumber" type="int"/>
+        <reference name="CEO" referenced-type="CEO" reverse-reference="company"/>
+        <collection name="departments" referenced-type="Department" reverse-reference="company"/>
+        <collection name="contractors" referenced-type="Contractor" reverse-reference="companys"/>
+        <collection name="oldContracts" referenced-type="Contractor" reverse-reference="oldComs"/>
+    </class>
+    <class name="Address" extends="Thing" is-interface="false">
+        <attribute name="address" type="java.lang.String"/>
+    </class>
+    <class name="RandomInterface" is-interface="true"></class>
+    <class name="CEO" extends="Manager HasSecretarys" is-interface="false">
+        <attribute name="salary" type="int"/>
+        <reference name="company" referenced-type="Company" reverse-reference="CEO"/>
+    </class>
+    <class name="ImportantPerson" is-interface="true">
+        <attribute name="seniority" type="java.lang.Integer"/>
+    </class>
+    <class name="Secretary" is-interface="false">
+        <attribute name="name" type="java.lang.String"/>
+    </class>
+    <class name="Types" is-interface="false">
+        <attribute name="name" type="java.lang.String"/>
+        <attribute name="booleanType" type="boolean"/>
+        <attribute name="floatType" type="float"/>
+        <attribute name="doubleType" type="double"/>
+        <attribute name="shortType" type="short"/>
+        <attribute name="intType" type="int"/>
+        <attribute name="longType" type="long"/>
+        <attribute name="booleanObjType" type="java.lang.Boolean"/>
+        <attribute name="floatObjType" type="java.lang.Float"/>
+        <attribute name="doubleObjType" type="java.lang.Double"/>
+        <attribute name="shortObjType" type="java.lang.Short"/>
+        <attribute name="intObjType" type="java.lang.Integer"/>
+        <attribute name="longObjType" type="java.lang.Long"/>
+        <attribute name="bigDecimalObjType" type="java.math.BigDecimal"/>
+        <attribute name="dateObjType" type="java.util.Date"/>
+        <attribute name="stringObjType" type="java.lang.String"/>
+    </class>
+    <class name="Bank" is-interface="false">
+        <attribute name="name" type="java.lang.String"/>
+        <collection name="debtors" referenced-type="Broke" reverse-reference="bank"/>
+    </class>
+    <class name="SimpleObject" is-interface="false" extends="java.lang.Object">
+        <attribute name="name" type="java.lang.String"/>
+        <reference name="employee" referenced-type="Employee" reverse-reference="simpleObjects"/>
+    </class>
+    <class name="Range" is-interface="false">
+        <attribute name="rangeStart" type="int"/>
+        <attribute name="rangeEnd" type="int"/>
+        <attribute name="name" type="java.lang.String"/>
+        <reference name="parent" referenced-type="Company"/>
+    </class>
+</model>

data/test/live_test.rb

@@ -0,0 +1,35 @@
+require File.dirname(__FILE__) + "/test_helper.rb"
+
+require "test/unit"
+require "intermine/service"
+
+class LiveTest < Test::Unit::TestCase
+
+    def setup
+        @service = Service.new("www.flymine.org/query")
+    end
+
+    # Tests a number of integrated features:
+    #  * Getting a template
+    #  * Passing template parameters
+    #  * getting counts
+    #  * getting rows
+    #  * getting records
+    #
+    def testBigResultSet
+        template = @service.template("Chromosome_Gene")
+        args = {"A" => {"!=" => '2L'}}
+        size = template.count(args)
+        i = 0
+        template.each_row(args) do |r|
+            i += 1
+        end
+        assert_equal(size, i)
+        i = 0
+        template.each_result(args) do |r|
+            i += 1
+        end
+        assert_equal(size, i)
+    end
+end
+

data/test/test.rb

@@ -0,0 +1,84 @@
+require "query"
+require "model"
+
+query = PathQuery::Query.new("Employee")
+query.name = "Ruby Query"
+query.model = "testmodel"
+query.title = "A query made in ruby"
+query.sort_order = "Employee asc"
+query.add_views("Employee.name", "Employee.age")
+query.add_views("fullTime", "department.name")
+
+bin_params = {:path => "Employee.name", :op => "=", :value => "Foo"}
+bin2_params = {:path => "age", :op => ">", :value => "26"}
+unary_params = {:path => "Employee.name", :op => "IS NULL"}
+sub_params = {:path => "Employee", :sub_class => "Manager"}
+lookup_params = {:path => "Employee", :op => "LOOKUP", :extra_value => "Foo", :value => "bar" }
+lookup_params2 = {:path => "Employee", :op => "LOOKUP", :value => "bar" }
+multi_params = {:path => "Employee.name", :op => "ONE OF", :values => ["one", "two", "three"]}
+loop_params = {:path => "Employee.name", :op => "IS", :loopPath => "Manager"}
+list_params = {:path => "Employee.name", :op => "IN", :value => "a list"}
+
+query.add_constraint(bin_params)
+query.add_constraint(bin2_params)
+query.add_constraint(sub_params)
+query.add_constraint(lookup_params)
+query.add_constraint(lookup_params2)
+query.add_constraint(multi_params)
+query.add_constraint(unary_params)
+query.add_constraint(loop_params)
+query.add_constraint(list_params)
+
+query.add_join("Employee.department", "OUTER")
+query.add_join("Employee.department.company")
+query.add_join("Employee.department.company", "INNER")
+
+puts query.to_xml
+
+file = File.new("model.json", "r")
+
+data = file.read
+model = Model.new(data)
+
+p model.get_class("Employee").get_field("department").referencedType
+p model.get_class("Employee").get_field("department").reverseReference
+p model.get_class("Employee").get_field("department").referencedType.get_field("company").referencedType
+p model.get_class("Employee").get_field("department").referencedType.get_field("company").referencedType.name
+
+path = Path.new("Employee.name", model)
+puts path, path.length
+
+path = Path.new("Employee.department.company.departments", model)
+puts path, path.length
+
+path = Path.new("Employee.department.company.departments.employees.address.address", model)
+puts path, path.length
+
+path = Path.new("Department.employees.seniority", model, {"Department.employees" => "Manager"})
+puts path, path.length
+
+begin
+    path = Path.new("Department.employees.foo", model, {"Department.employees" => "Manager"})
+rescue Exception => e
+    p e
+end
+
+begin
+    path = Path.new("Department.employees.seniority", model, {"Department.employees" => "Foo"})
+rescue Exception => e
+    p e
+end
+
+begin
+    path = Path.new("Employee.department.name.departments", model)
+rescue Exception => e
+    p e
+end
+
+begin
+    path = Path.new("Foo.bar", model)
+rescue Exception => e
+    p e
+end
+
+

data/test/test_helper.rb

@@ -0,0 +1,67 @@
+$LOAD_PATH << File.expand_path( File.dirname(__FILE__) + '/../lib' )
+require "rexml/document"
+require "test/unit"
+
+include Test::Unit::Assertions
+
+def compare_xml(a, b)
+    require "rexml/document"
+    docA = REXML::Document.new(a.to_s)
+    docB = REXML::Document.new(b.to_s)
+
+    a_elems = docA.elements.to_a
+    b_elems = docB.elements.to_a
+
+    (0 ... a_elems.size).each do |idx|
+        compare_elements(a_elems[idx], b_elems[idx])
+    end
+end
+
+private
+
+def fail_xml_compare(elemA, elemB, problem, e)
+    formatter = REXML::Formatters::Pretty.new
+    elemA_str = String.new
+    elemB_str = String.new
+    formatter.write(elemA, elemA_str)
+    formatter.write(elemB, elemB_str)
+    first_part = "#{elemA_str}\nis not equal to\n#{elemB_str}\n"
+    
+    raise Test::Unit::AssertionFailedError, "#{first_part}because #{problem} - #{e.message}" 
+end
+
+def compare_elements(elemA, elemB)
+
+    begin
+        assert_equal(elemA.name, elemB.name)
+    rescue Test::Unit::AssertionFailedError => e
+        fail_xml_compare(elemA, elemB, "names of element differ", e)
+    end
+
+    begin
+        assert_equal(elemA.attributes, elemB.attributes)
+    rescue Test::Unit::AssertionFailedError => e
+        fail_xml_compare(elemA, elemB, "attributes of element differ", e)
+    end
+
+    begin
+        assert_equal(elemA.text, elemB.text)
+    rescue Test::Unit::AssertionFailedError => e
+        fail_xml_compare(elemA, elemB, "text contents of element differ", e)
+    end
+
+    begin
+        assert_equal(elemA.elements.size, elemB.elements.size)
+    rescue Test::Unit::AssertionFailedError => e
+        fail_xml_compare(elemA, elemB, "number of children of element differ", e)
+    end
+
+    a_elems = elemA.elements.to_a
+    b_elems = elemB.elements.to_a
+
+    (0 ... a_elems.size).each do |idx|
+        compare_elements(a_elems[idx], b_elems[idx])
+    end
+end
+
+

data/test/test_lists.rb

@@ -0,0 +1,68 @@
+require File.dirname(__FILE__) + "/test_helper.rb"
+
+require "test/unit"
+require "intermine/lists"
+require "intermine/model"
+require "intermine/query"
+
+include Lists
+
+class FakeService
+
+    attr_reader :get_list_data, :root
+
+    def initialize(data, model)
+        @get_list_data = data
+        @model = model
+        @root = "FAKE_ROOT"
+    end
+
+    def query(rootClass=nil?)
+        return PathQuery::Query.new(@model, rootClass, self)
+    end
+
+end
+
+class TestList < Test::Unit::TestCase
+
+    def initialize(name)
+        super
+        d = File.dirname(__FILE__) + "/data"
+        lf = File.new(d + "/lists.json", "r")
+        mf = File.new(d + "/model.json", "r")
+        model = Model.new(mf.read)
+        @service = FakeService.new(lf.read, model)
+    end
+    
+    def setup
+        @manager = ListManager.new(@service)
+    end
+
+    def testParse
+        assert_equal(@manager.lists.size, 3)
+
+        list_a = @manager.lists.first
+        assert_equal(list_a.name, "test-list-1")
+        assert_equal(list_a.title, "test1")
+        assert_equal(list_a.description, "An example test list")
+        assert_equal(list_a.size, 42)
+        assert_equal(list_a.dateCreated, "2011-05-07T19:52:03")
+        assert_equal(list_a.tags, %w{tag1 tag2 tag3})
+        assert_equal(list_a.is_authorized?, true)
+
+        list_b = @manager.lists[1]
+        assert_equal(list_b.tags, [])
+        assert_equal(list_b.is_authorized?, false)
+
+        list_c = @manager.lists.last
+        assert_equal(list_c.is_authorized?, true)
+    end
+
+    def testListToQuery
+        list_a = @manager.lists.first
+        q = list_a.query
+        expected = %q!<query model='testmodel' view='Employee.name Employee.end Employee.id Employee.fullTime Employee.age' sortOrder='Employee.name ASC'><constraint op='IN' code='A' value='test-list-1' path='Employee'/></query>!
+        assert_equal(q.to_xml.to_s, expected)
+    end
+end
+    

data/test/test_model.rb

@@ -0,0 +1,417 @@
+require File.dirname(__FILE__) + "/test_helper.rb"
+require "intermine/model"
+
+require "test/unit"
+
+class TestModel < Test::Unit::TestCase
+
+    def initialize(name)
+        super
+        file = File.new(
+            File.dirname(__FILE__) + "/data/model.json", "r")
+        data = file.read
+        file.close
+        @model = InterMine::Metadata::Model.new(data)
+    end
+
+    def test_parse
+        assert_equal(@model.classes.size, 19)
+
+        dept = @model.get_cd("Department")
+        assert_equal("Department", dept.name)
+        assert_equal(false, dept.isInterface)
+        assert_equal(6, dept.fields.size)
+        assert_equal(dept.fields.keys.sort, ["company", "employees", "id", "manager", "name", "rejectedEmployee"])
+
+        assert_equal(dept.get_field("company").referencedType, @model.get_cd("Company"))
+
+        manager = @model.get_cd("Manager")
+        assert(manager.subclass_of?(@model.get_cd("Employee")))
+        assert(manager.subclass_of?("Employee"))
+        assert(manager.subclass_of?("HasAddress"))
+        assert(!manager.subclass_of?("Company"))
+        assert(manager.subclass_of?("Company.departments.employees"))
+        assert(!manager.subclass_of?("Company.name"))
+        assert_raise(InterMine::Metadata::PathException) {manager.subclass_of?("Foo")}
+    end
+
+    def test_attributes
+        dept = @model.get_cd("Department")
+        assert_equal(2, dept.attributes.size)
+
+        manager = @model.get_cd("Manager")
+        assert_equal(7, manager.attributes.size)
+    end
+
+    def test_sugar
+        dept = @model.get_cd("Department")
+
+        table = @model.table("Department")
+
+        assert_equal(dept, table)
+    end
+
+
+    def test_good_paths
+
+        path = InterMine::Metadata::Path.new("Employee.name", @model)
+        assert_equal(2, path.length)
+        assert_equal("java.lang.String", path.end_type)
+
+        path = InterMine::Metadata::Path.new("Employee.department.company.departments", @model)
+        assert_equal(4, path.length)
+        assert_equal("Department", path.end_type)
+
+        path = InterMine::Metadata::Path.new("Employee.department.company.departments.employees.address.address", @model)
+        assert_equal(7, path.length)
+        assert_equal("java.lang.String", path.end_type)
+
+        path = InterMine::Metadata::Path.new("Department.employees.seniority", @model, {"Department.employees" => "Manager"})
+        assert_equal(3, path.length)
+        assert_equal("java.lang.Integer", path.end_type)
+
+        path = InterMine::Metadata::Path.new("Department.employees.id", @model)
+        assert_equal(3, path.length)
+        assert_equal("java.lang.Integer", path.end_type)
+
+    end
+
+    def test_bad_paths
+
+        assert_raise(InterMine::Metadata::PathException) do
+            InterMine::Metadata::Path.new("Foo.bar", @model)
+        end
+
+        assert_raise(InterMine::Metadata::PathException) do
+            InterMine::Metadata::Path.new("Department.employees.foo", @model, {"Department.employees" => "Manager"})
+        end
+
+        assert_raise(InterMine::Metadata::PathException) do
+            InterMine::Metadata::Path.new("Department.employees.seniority", @model, {"Department.employees" => "Foo"})
+        end
+
+        assert_raise(InterMine::Metadata::PathException) do
+            InterMine::Metadata::Path.new("Employee.department.name.departments", @model)
+        end
+
+    end
+
+    def test_item_creation_bean_style
+        cd = @model.get_cd("Employee")
+        emp_kls = cd.to_class
+
+        emp = emp_kls.new
+        emp.name = "John Doe"
+        emp.age = 42
+        emp.fullTime = false
+
+        dep = @model.make_new("Department")
+        dep.name = "Sales"
+
+        emp.department = dep
+
+        assert_equal(emp.name, "John Doe")
+        assert_equal(emp.age, 42)
+        assert_equal(emp.fullTime, false)
+        assert_equal(emp.department.name, "Sales")
+    end
+
+    def test_item_creation_with_arguments
+        emp_kls = @model.get_cd("Employee").to_class
+        emp = emp_kls.new({
+            "name" => "John Doe",
+            "age" => 25,
+            "fullTime" => true
+        })
+        assert_equal(emp.name, "John Doe")
+        assert_equal(emp.age, 25)
+        assert_equal(emp.fullTime, true)
+
+        dep_kls = @model.get_cd("Department").to_class
+        dep = dep_kls.new({
+            "name" => "Sales"
+        })
+
+        emp.department = dep
+
+        assert_equal(emp.department.name, "Sales")
+
+        dep.addEmployees(emp)
+
+        assert_equal(dep.employees.first, emp)
+
+        emp2 = emp_kls.new({
+            "name" => "Jane Doe",
+            "age" => 26,
+            "fullTime" => false
+        })
+
+        dep.employees = [emp, emp2]
+        assert_equal(dep.employees.map { |x| x.name }, ["John Doe", "Jane Doe"])
+
+        emp3 = emp_kls.new({
+            "name" => "Jill Doe",
+            "age" => 26,
+            "fullTime" => false
+        })
+        emp4 = emp_kls.new({
+            "name" => "Jonas Doe",
+            "age" => 26,
+            "fullTime" => false
+        })
+
+        dep.addEmployees(emp3, emp4)
+        assert_equal(dep.employees.map { |x| x.name }, ["John Doe", "Jane Doe", "Jill Doe", "Jonas Doe"])
+    end
+
+    def test_item_creation_with_nested_coercion
+
+        emp_kls = @model.get_cd("Employee").to_class
+
+        emp5 = emp_kls.new({
+            "name" => "Jonas Doe",
+            "age" => 26,
+            "fullTime" => false,
+            "department" => { "name" => "Marketing" , "company" => { "name" => "Aperture Science", "vatNumber" => 12345}}
+        })
+
+        assert_equal(emp5.department.name, "Marketing")
+        assert_equal(emp5.department.company.name, "Aperture Science")
+        assert_equal(emp5.department.company.vatNumber, 12345)
+
+        dep = @model.get_cd("Department").to_class.new({ "name" => "Sales" })
+        dep.addEmployees({ "name" => "Jeremiah Doe", "age" => 42}, { "name" => "Jodie Doe" })
+        assert_equal(dep.employees.map { |x| x.name }, ["Jeremiah Doe", "Jodie Doe"])
+
+        assert_equal(dep.employees.first.age, 42)
+        assert_equal(dep.employees.last.age, nil)
+    end
+
+    def test_item_creation_from_model
+
+        manager = @model.make_new("Manager", {
+            "name" => "David Brent",
+            "seniority" => 42,
+            "age" => 39,
+            "fullTime" => true,
+            "department" => { "name" => "Sales" }
+        })
+
+        assert_equal(manager.name, "David Brent")
+        assert_equal(manager.seniority, 42)
+        assert_equal(manager.age, 39)
+        assert_equal(manager.fullTime, true)
+        assert_equal(manager.department.name, "Sales")
+
+        dep = @model.make_new("Department", {
+            "name" => "Janitorial", 
+            "employees" => [
+                { "name" => "A" },
+                { "name" => "B" }
+            ]
+        })
+
+        assert_equal(dep.name, "Janitorial")
+        assert_equal(dep.employees[0].name, "A")
+        assert_equal(dep.employees[1].name, "B")
+
+        dep.addEmployees({ "name" => "C" })
+        assert_equal(dep.employees[2].name, "C")
+
+    end
+
+    def test_inheritance
+
+        manager = @model.make_new("Manager", { "name" => "David Brent" })
+        employee = @model.make_new("Employee", { "name" => "Tim Canterbury" })
+
+        dep = @model.make_new("Department", { "name" => "Sales" })
+
+        dep.addEmployees(manager, employee)
+
+        assert_equal(dep.employees[0].name, "David Brent")
+        assert_equal(dep.employees[1].name, "Tim Canterbury")
+
+        mod = @model.get_cd("Employee").to_module
+        dep.employees.each do |emp|
+            assert_kind_of(mod, emp)
+        end
+
+        assert_kind_of(@model.get_cd("HasAddress").to_module, manager)
+
+        comp = @model.make_new("Company")
+        assert_raise ArgumentError do
+            dep.addEmployees(comp)
+        end
+    end
+
+    def test_creation_from_hash_alone
+
+        emp = @model.make_new({
+            "class" => "Employee",
+            "name" => "John Doe",
+            "age" => 25
+        })
+
+        assert_kind_of(@model.get_cd("Employee").to_module, emp)
+        assert_equal(emp.name, "John Doe")
+        assert_equal(emp.age, 25)
+    end
+
+    def test_prefer_hash_class
+
+        emp = @model.make_new("Employee", {
+            "class" => "Manager",
+            "name" => "John Doe",
+            "age" => 25
+        })
+
+        assert_kind_of(@model.get_cd("Employee").to_module, emp)
+        assert_kind_of(@model.get_cd("Manager").to_module, emp)
+        assert_equal(emp.name, "John Doe")
+        assert_equal(emp.age, 25)
+    end
+
+    def test_subclass_coercion
+
+        dep = @model.make_new("Department")
+
+        dep.addEmployees(
+            { "name" => "A" },
+            { "class" => "Manager", "name" => "B" },
+            { "class" => "CEO", "name" => "C" }
+        )
+
+        assert_equal(dep.employees[0].name, "A")
+        assert_equal(dep.employees[1].name, "B")
+        assert_equal(dep.employees[2].name, "C")
+
+        dep.employees.each do |emp|
+            assert_kind_of(@model.get_cd("Employee").to_module, emp)
+        end
+
+        dep.employees.slice(1, 2).each do |manager|
+            assert_kind_of(@model.get_cd("Manager").to_module, manager)
+        end
+
+        assert_kind_of(@model.get_cd("Manager").to_module, dep.employees.last)
+    end
+
+    def test_overridden_isa
+
+        manager = @model.make_new("Manager")
+
+        assert(manager.is_a?(@model.get_cd("Employee")))
+    end
+
+    def test_refuse_to_make_objects_with_conflicting_class_names
+
+        assert_raise ArgumentError do
+            @model.make_new("Employee", { "class" => "Company", "name" => "Aperture Science" })
+        end
+    end
+
+    def test_item_ids
+
+        dep = @model.make_new("Department", {
+            "name" => "Sales",
+            "objectId" => 12345
+        })
+
+        assert_equal(dep.objectId, 12345)
+    end
+
+    def test_item_creation_problems
+
+        emp_kls = @model.get_cd("Employee").to_class
+
+        assert_raise ArgumentError do
+            emp_kls.new({
+                "name" => "John Doe",
+                "age" => "foo",
+            })
+        end
+
+        assert_raise ArgumentError do
+            emp_kls.new({
+                "name" => "John Doe",
+                "age" => 14.75
+            })
+        end
+
+        assert_raise ArgumentError do
+            emp = emp_kls.new
+            emp.age = 13.5
+        end
+
+        assert_raise ArgumentError do
+            emp_kls.new({
+                "name" => "John Doe",
+                "fullTime" => "foo",
+            })
+        end
+
+        assert_raise NoMethodError do
+            emp_kls.new({
+                "name" => "Not for this world",
+                "foo" => "bar"
+            })
+        end
+
+    end
+
+    def test_path_resolution
+
+        dep = @model.make_new("Department", {
+            "name" => "Sales",
+            "company" => { 
+                "name" => "Werhnam-Hogg",
+                "CEO" => {
+                    "name" => "Jennifer",
+                    "address" => {
+                        "address" => "42 Some st"
+                    }
+                }
+            },
+            "employees" => [
+                { "name" => "A" },
+                { "name" => "B" }
+            ]
+        })
+
+        # Test chained path resolution
+        pathstr = "Department.company.CEO.address.address"
+        obj = @model.resolve_path(dep, pathstr)
+        assert_equal(obj, "42 Some st")
+        assert_equal(dep._resolve(pathstr), "42 Some st")
+
+        # Test resolving using Path objects
+        path = InterMine::Metadata::Path.new(pathstr, @model)
+        obj = @model.resolve_path(dep, path)
+        assert_equal(obj, "42 Some st")
+        assert_equal(dep._resolve(path), "42 Some st")
+
+        # Test resolving items in collections
+        pathstr_with_index = "Department.employees[1].name"
+        obj = @model.resolve_path(dep, pathstr_with_index)
+        assert_equal(obj, "B")
+        assert_equal(dep._resolve(pathstr_with_index), "B")
+
+        # Check bad paths
+        assert_raise ArgumentError do
+            @model.resolve_path(dep, "Department.company.foo")
+        end
+
+        # Check legal but irrelevant paths
+        assert_raise ArgumentError do
+            @model.resolve_path(dep, "Employee.department.name")
+        end
+
+        # Check non-indexed collection lookup
+        assert_raise ArgumentError do
+            @model.resolve_path(dep, "Department.employees.name")
+        end
+
+    end
+
+end