intermine 0.98.01

data/test/test_result_row.rb

@@ -0,0 +1,114 @@
+require File.dirname(__FILE__) + "/test_helper.rb"
+require "intermine/results"
+require 'rubygems'
+require "json"
+require "test/unit"
+
+class TestResults < Test::Unit::TestCase
+
+    include Results
+
+    def initialize(name)
+        super
+        file = File.new(
+            File.dirname(__FILE__) + "/data/resultrow.json", "r")
+        @data = file.read
+        @json = JSON.parse(@data)
+        @view = ["Company.departments.name","Company.departments.manager.name"]
+        @bad_view = ["Company.departments.name","Company.departments.manager.name", "Comany.name"]
+    end
+
+    def test_initialize
+        rr = ResultsRow.new(@data, @view)
+        assert_kind_of(ResultsRow, rr)
+
+        rr = ResultsRow.new(@json, @view)
+        assert_kind_of(ResultsRow, rr)
+
+        assert_raise ArgumentError do
+            ResultsRow.new
+        end
+
+        assert_raise ArgumentError do
+            ResultsRow.new(@data)
+        end
+
+        assert_raise ArgumentError do
+            ResultsRow.new(@data, @bad_view)
+        end
+
+        assert_raise ArgumentError do
+            ResultsRow.new(@json, @bad_view)
+        end
+    end
+
+    def test_array_access
+
+        rr = ResultsRow.new(@data, @view)
+
+        assert_equal(rr[0], "DepartmentA1")
+        assert_equal(rr[1], "EmployeeA1")
+
+        rr = ResultsRow.new(@json, @view)
+
+        assert_equal(rr[0], "DepartmentA1")
+        assert_equal(rr[1], "EmployeeA1")
+
+        rr = ResultsRow.new(@json, @view)
+
+        assert_raise IndexError do
+            rr[3]
+        end
+
+    end
+
+    def test_hash_access
+
+        rr = ResultsRow.new(@data, @view)
+
+        assert_equal(rr["Company.departments.name"], "DepartmentA1")
+        assert_equal(rr["Company.departments.manager.name"], "EmployeeA1")
+
+        rr = ResultsRow.new(@json, @view)
+
+        assert_equal(rr["Company.departments.name"], "DepartmentA1")
+        assert_equal(rr["Company.departments.manager.name"], "EmployeeA1")
+
+        rr = ResultsRow.new(@json, @view)
+
+        assert_raise IndexError do
+            rr["foo"]
+        end
+
+    end
+
+    def test_to_a
+
+        expected =  %w{DepartmentA1 EmployeeA1}
+
+        rr = ResultsRow.new(@data, @view)
+
+        assert_equal(expected, rr.to_a)
+
+        rr = ResultsRow.new(@json, @view)
+
+        assert_equal(expected, rr.to_a)
+    end
+
+    def test_to_h
+
+        rr = ResultsRow.new(@data, @view)
+
+        expected = {
+            "Company.departments.name" => "DepartmentA1",
+            "Company.departments.manager.name" => "EmployeeA1"
+        }
+        assert_equal(expected, rr.to_h)
+
+        rr = ResultsRow.new(@json, @view)
+
+        assert_equal(expected, rr.to_h)
+    end
+
+
+end

data/test/test_results.rb

@@ -0,0 +1,22 @@
+$LOAD_PATH << File.expand_path( File.dirname(__FILE__) + '/../lib' )
+require "intermine/model"
+require "intermine/query"
+require "intermine/results"
+include PathQuery
+
+d = File.new(File.dirname(__FILE__) + "/data/model.json").read
+m = Model.new(d)
+q = Query.new(m, "Employee")
+q.add_views("name", "age")
+q.add_constraint({:path => "age", :op => ">", :value => 40})
+q.add_sort_order("age")
+params = {"query" => q.to_xml, "format" => "jsonrows"}
+uri = "http://squirrel.flymine.org/intermine-test/service/query/results"
+rr = Results::ResultsReader.new(uri, params, q.views)
+sum, total = 0, 0
+rr.each_row {|emp| 
+    puts emp
+    sum += emp["age"]
+    total += 1
+}
+puts "Average age: #{sum/total} years"

data/test/test_service.rb

@@ -0,0 +1,86 @@
+$LOAD_PATH << File.expand_path( File.dirname(__FILE__) + '/../lib' )
+require "intermine/service"
+
+service = Service.new("http://squirrel.flymine.org/intermine-test/service")
+
+p service.version
+p service.model.name
+
+sum, total = 0, 0
+
+service.model.table("Employee").
+    select("name", "age").
+    where(:age => {">" => 60}).
+    order_by("age", "desc").each_row do |emp|
+        puts emp
+        sum += emp["age"]
+        total += 1
+end
+
+puts "Average => #{sum/total} - #{total} employees"
+puts
+
+tok_service = Service.new("http://squirrel.flymine.org/intermine-test/service", "a1v3V1X0f3hdmaybq0l6b7Z4eVG")
+
+q = tok_service.new_query("Employee")
+q.add_views("name", "age")
+q.add_constraint(:path => "Employee", :op => "IN", :value => "My-Favourite-Employees")
+
+sum = 0
+q.each_row do |emp|
+    puts emp
+    sum += emp["age"]
+end
+
+total = q.count
+puts "Average => #{sum/total} - #{total} employees"
+puts
+
+q = tok_service.new_query("Department").add_views("name")
+
+q.add_constraint(:path => "employees", :op => "IN", :value => "My-Favourite-Employees")
+
+q.each_row do |emp|
+    puts emp
+end
+
+sum, total,current_dep = 0, 0, nil
+service.model.table("Employee").
+    select(:name, :age, "department.name").
+    where(:age => {"<" => 27}).
+    where("department.name" => "S*").
+    order_by("department.name").
+    order_by(:age, :desc).
+    set_logic("A or B").each_row do |emp|
+    if (current_dep.nil? or current_dep != emp["department.name"])
+        current_dep = emp["department.name"] 
+        puts "\n#{current_dep}\n#{"-" * current_dep.length}"
+    end
+    puts "#{emp["name"]} (#{emp["age"]})"
+    sum += emp["age"]
+    total += 1
+end
+
+puts
+puts "Average => #{sum/total} - #{total} employees"
+
+service.model.table("Employee").
+    select("*", "department.*").
+    where(:age => {"<" => 30}).
+    each_row do |emp|
+        puts emp
+end
+
+Service.new("http://www.flymine.org/query/service").
+    model.
+    table(:Gene).
+    select(:symbol, "alleles.*").
+    where(:symbol => %w{zen h H bib}).
+    outerjoin(:alleles).
+    each_result do |gene| 
+        #puts gene
+
+        puts "#{"-" * 30}\n#{gene.symbol}: #{gene.alleles.size} Alleles"
+        puts "#{gene.alleles.map {|a| a.symbol}.join(", ")}"
+    end
+

data/test/test_sugar.rb

@@ -0,0 +1,219 @@
+require File.dirname(__FILE__) + "/test_helper.rb"
+require "intermine/query"
+require "intermine/model"
+require "intermine/lists"
+require "intermine/service"
+require "test/unit"
+
+class Service
+    def fetch(x)
+        return 100
+    end
+end
+
+class TestQuerySugar < Test::Unit::TestCase
+
+    def initialize(name)
+        super
+        file = File.new(
+            File.dirname(__FILE__) + "/data/model.json", "r")
+        data = file.read
+        @model = InterMine::Metadata::Model.new(data)
+        @service = InterMine::Service.new("foo", "bar", @model)
+        @model.send(:set_service, @service) 
+        @list = InterMine::Lists::List.new({"name" => "test-list"})
+    end
+
+    def test_select_statement
+        q = @model.table("Employee").select("Employee.name")
+        assert_kind_of(PathQuery::Query, q)
+        assert_equal(q.views, ["Employee.name"])
+    end
+
+    def test_view_expansion
+        q = @model.table("Employee").select("*", "department.*")
+        expected = ["Employee.name",
+         "Employee.end",
+         "Employee.id",
+         "Employee.fullTime",
+         "Employee.age",
+         "Employee.department.name",
+         "Employee.department.id"]
+
+        assert_equal(expected, q.views.map {|x| x.to_s})
+    end
+
+    def test_sugary_null_cons
+        q = @model.table("Employee").
+                   select("*").
+                   where(:age => nil).
+                   where(:name => {"=" => nil}).
+                   where(:fullTime => {"!=" => nil})
+
+        expected = "<query model='testmodel' sortOrder='Employee.name ASC' view='Employee.name Employee.end Employee.id Employee.fullTime Employee.age'>" +
+                        "<constraint op='IS NULL' code='A' path='Employee.age'/>" +
+                        "<constraint op='IS NULL' code='B' path='Employee.name'/>" +
+                        "<constraint op='IS NOT NULL' code='C' path='Employee.fullTime'/>" + 
+                "</query>"
+        
+        compare_xml(expected, q.to_xml)
+    end
+
+    def test_sugary_binaries
+        
+        q = @model.table("Employee").
+                   where(:name => "foo").
+                   where(:age => 10).
+                   where(:end => {"<" => 200}).
+                   where("department.name" => {:contains => "foo"}).
+                   where(:name => {"!=" => "bar"})
+
+        expected = "<query model='testmodel' sortOrder='Employee.name ASC' view='Employee.name Employee.end Employee.id Employee.fullTime Employee.age'>" +
+                        "<constraint op='=' code='A' value='foo' path='Employee.name'/>" + 
+                        "<constraint op='=' code='B' value='10' path='Employee.age'/>" + 
+                        "<constraint op='&lt;' code='C' value='200' path='Employee.end'/>" +
+                        "<constraint op='CONTAINS' code='D' value='foo' path='Employee.department.name'/>" +
+                        "<constraint op='!=' code='E' value='bar' path='Employee.name'/>" + 
+                "</query>"
+        
+        compare_xml(expected, q.to_xml)
+    end
+
+    def test_sugary_binary_aliases
+        
+        q = @model.table("Employee").
+                   where(:age => {:lt => 100}).
+                   where(:age => {:gt => 200}).
+                   where(:age => {:le => 300}).
+                   where(:age => {:ge => 400}).
+                   where("department.name" => {:eq => "foo"}).
+                   where(:name => {:ne => "bar"}).
+                   where(:name => {:== => "zop"})
+
+        expected = "<query model='testmodel' sortOrder='Employee.name ASC' view='Employee.name Employee.end Employee.id Employee.fullTime Employee.age'>" +
+                        "<constraint op='&lt;' code='A' value='100' path='Employee.age'/>" + 
+                        "<constraint op='&gt;' code='B' value='200' path='Employee.age'/>" + 
+                        "<constraint op='&lt;=' code='C' value='300' path='Employee.age'/>" + 
+                        "<constraint op='&gt;=' code='D' value='400' path='Employee.age'/>" + 
+                        "<constraint op='=' code='E' value='foo' path='Employee.department.name'/>" +
+                        "<constraint op='!=' code='F' value='bar' path='Employee.name'/>" + 
+                        "<constraint op='=' code='G' value='zop' path='Employee.name'/>" + 
+                "</query>"
+        
+        compare_xml(expected, q.to_xml)
+    end
+
+
+    def test_sugary_lookups
+
+        q = @model.table("Employee").
+                   where(:department => {:lookup => "foo"}).
+                   where("department.company" => {:lookup => "foo", :with => "extra"})
+
+        expected = "<query model='testmodel' sortOrder='Employee.name ASC' view='Employee.name Employee.end Employee.id Employee.fullTime Employee.age'>" +
+                        "<constraint op='LOOKUP' code='A' value='foo' path='Employee.department'/>" + 
+                        "<constraint extraValue='extra' op='LOOKUP' code='B' value='foo' path='Employee.department.company'/>" + 
+                "</query>"
+        
+        compare_xml(expected, q.to_xml)
+    end
+
+    def test_sugary_lists
+
+        q = @model.table("Employee").
+                   where(:Employee => @list).
+                   where("Employee.department.manager" => {"=" => @list}).
+                   where("Employee.department.manager" => {"!=" => @list}).
+                   where("Employee.department" => {:in => "a list"}).
+                   where("Employee.department.company" => {:not_in => "a list"})
+
+        expected = "<query model='testmodel' sortOrder='Employee.name ASC' view='Employee.name Employee.end Employee.id Employee.fullTime Employee.age'>" +
+                        "<constraint op='IN' code='A' value='test-list' path='Employee'/>" +
+                        "<constraint op='IN' code='B' value='test-list' path='Employee.department.manager'/>" +
+                        "<constraint op='NOT IN' code='C' value='test-list' path='Employee.department.manager'/>" +
+                        "<constraint op='IN' code='D' value='a list' path='Employee.department'/>" +
+                        "<constraint op='NOT IN' code='E' value='a list' path='Employee.department.company'/>" +
+                "</query>"
+        
+        compare_xml(expected, q.to_xml)
+    end
+
+    def test_sugary_multis
+
+        q = @model.table("Employee").
+                   where(:age => 30 .. 35).
+                   where("department.manager.name" => %w{zip zop zap}).
+                   where(:age => {'=' => 35 .. 36}).
+                   where(:end => {"!=" => 37 .. 39}).
+                   where(:age => {"=" => [1, 2, 3]}).
+                   where(:end => {"!=" => [3, 4, 5]}).
+                   where("department.manager.age" => {:none_of => 40 .. 45}).
+                   where("department.manager.end" => {:one_of => 50 .. 55}).
+                   where("department.manager.age" => {:none_of => [46, 47]}).
+                   where("department.manager.end" => {:one_of => [56, 57]})
+
+        expected = "<query model='testmodel' sortOrder='Employee.name ASC' view='Employee.name Employee.end Employee.id Employee.fullTime Employee.age'>" +
+                       "<constraint op='ONE OF' code='A' path='Employee.age'>" + 
+                            "<value>30</value><value>31</value><value>32</value><value>33</value><value>34</value><value>35</value>" +
+                       "</constraint>" + 
+                       "<constraint op='ONE OF' code='B' path='Employee.department.manager.name'>" + 
+                            "<value>zip</value><value>zop</value><value>zap</value>" + 
+                       "</constraint>" + 
+                       "<constraint op='ONE OF' code='C' path='Employee.age'>" + 
+                            "<value>35</value><value>36</value>" + 
+                        "</constraint>" +
+                        "<constraint op='NONE OF' code='D' path='Employee.end'>" + 
+                            "<value>37</value><value>38</value><value>39</value>" + 
+                        "</constraint>" + 
+                        "<constraint op='ONE OF' code='E' path='Employee.age'>" + 
+                            "<value>1</value><value>2</value><value>3</value>" + 
+                        "</constraint>" + 
+                        "<constraint op='NONE OF' code='F' path='Employee.end'>" + 
+                            "<value>3</value><value>4</value><value>5</value>" + 
+                        "</constraint>" + 
+                        "<constraint op='NONE OF' code='G' path='Employee.department.manager.age'>" +
+                            "<value>40</value><value>41</value><value>42</value><value>43</value><value>44</value><value>45</value>" +
+                        "</constraint>" + 
+                        "<constraint op='ONE OF' code='H' path='Employee.department.manager.end'>" +
+                            "<value>50</value><value>51</value><value>52</value><value>53</value><value>54</value><value>55</value>" +
+                        "</constraint>" +
+                        "<constraint op='NONE OF' code='I' path='Employee.department.manager.age'>" + 
+                            "<value>46</value><value>47</value>" + 
+                        "</constraint>" + 
+                        "<constraint op='ONE OF' code='J' path='Employee.department.manager.end'>" +
+                            "<value>56</value><value>57</value>" + 
+                        "</constraint>" + 
+                "</query>"
+        
+        compare_xml(expected, q.to_xml)
+    end
+
+    def test_sugary_loops
+
+        q = @model.table("Employee").
+                   where("department.company.CEO" => {:is => "department.manager"}).
+                   where("department.company.CEO" => {:is_not => "department.employees"})
+
+        expected = "<query model='testmodel' sortOrder='Employee.name ASC' view='Employee.name Employee.end Employee.id Employee.fullTime Employee.age'>" +
+                        "<constraint op='=' loopPath='Employee.department.manager' code='A' path='Employee.department.company.CEO'/>" + 
+                        "<constraint op='!=' loopPath='Employee.department.employees' code='B' path='Employee.department.company.CEO'/>" + 
+                "</query>"
+        
+        compare_xml(expected, q.to_xml)
+    end
+
+    def test_sugary_subclasses
+        manager = @model.table("Manager")
+
+        q = @model.table("Employee").
+                   where("department.employees" => manager).
+                   where("department.employees" => {:sub_class => "CEO"})
+
+        expected = "<query model='testmodel' sortOrder='Employee.name ASC' view='Employee.name Employee.end Employee.id Employee.fullTime Employee.age'>" +
+                        "<constraint type='Manager' path='Employee.department.employees'/>" +
+                        "<constraint type='CEO' path='Employee.department.employees'/>" +
+                "</query>"
+        
+        compare_xml(expected, q.to_xml)
+    end
+end

data/test/unit_tests.rb

@@ -0,0 +1,6 @@
+$LOAD_PATH << File.expand_path( File.dirname(__FILE__) )
+
+require 'test/unit'
+require 'test_model'
+require 'test_query'
+require 'test_sugar'