nbproject/project.properties nbproject/project.xml @@ -138,7 +138,7 @@ class LabController < ApplicationController :het => @species.phenotype_from(character, 1,0).to_s, :rec => @species.phenotype_from(character, 0,0).to_s, :location => @species.position_of(@species.gene_number_of(character)), - :sex_linked => @species.is_sex_linked?(character) ? "yes" : "no", + :sex_linked => @species.sex_linked?(character) ? "yes" : "no", :randomizable => @species.alternate_phenotypes(character) != [] ? "yes" : "no" } end end app/controllers/lab_controller.rb @@ -1,2 +1,11 @@ class Genotype < ActiveRecord::Base + belongs_to :fly + + def genotype_for?(character) + gene_number == species.gene_number_of(character) + end + + def species + fly.species + end end app/models/genotype.rb @@ -38,8 +38,12 @@ class Species @gene_numbers[character] end - def is_sex_linked?(character) - character != :sex and position_of(gene_number_of(character)) == 0.0 + def sex_linked?(character) + character != :sex and position_of(gene_number_of(character)) == position_of(gene_number_of(:sex)) + end + + def sex_linked_characters + @sex_linked_character ||= @characters.select { |c| sex_linked?(c) } end def position_of(gene_number) app/models/species.rb @@ -11,10 +11,10 @@ class Vial < ActiveRecord::Base validates_presence_of :label validates_presence_of :rack_id validates_numericality_of :number_of_requested_flies, :only_integer => true, - :on => :create + :on => :create validates_inclusion_of :number_of_requested_flies, :in => 0..255, - :message => "should be between 0 and 255", - :on => :create + :message => "should be between 0 and 255", + :on => :create validates_presence_of :mom_id, :if => Proc.new { |vial| vial.offspring_vial? } validates_presence_of :dad_id, :if => Proc.new { |vial| vial.offspring_vial? } @@ -22,7 +22,7 @@ class Vial < ActiveRecord::Base vial = Vial.new(vial_params) allele_frequencies[:sex] = 0.5 unless allele_frequencies[:sex] vial.species.characters.each do |character| - allele_frequencies[character] = 0.13 + (rand 37) / 100.0 unless allele_frequencies[character] + allele_frequencies[character] = 0.13 + (rand * (0.50 - 0.13)) unless allele_frequencies[character] end if vial.save vial.fill_from_field(bit_generator, allele_frequencies) @@ -96,8 +96,8 @@ class Vial < ActiveRecord::Base def combinations_of_phenotypes(characters = species.characters) cartesian_product( characters.collect do |character| - phenotypes = phenotypes_for_table(character) - end ) + phenotypes_for_table(character) + end ) end def number_of_flies (characters, phenotypes) @@ -136,9 +136,9 @@ class Vial < ActiveRecord::Base species.phenotypes(row_character).each do |row_phenotype| species.phenotypes(column_character).each do |column_phenotype| key = renamed_phenotype(row_character, row_phenotype).to_s + "$" + - renamed_phenotype(column_character, column_phenotype).to_s + renamed_phenotype(column_character, column_phenotype).to_s counts[key] = number_of_flies([row_character, column_character], - [row_phenotype, column_phenotype]) + [row_phenotype, column_phenotype]) end end counts @@ -147,7 +147,7 @@ class Vial < ActiveRecord::Base def renamed_phenotype(character, phenotype) phenotype_alternate = owner.phenotype_alternates.select do |pa| pa.scenario_id == owner.current_scenario.id and - pa.affected_character.intern == character and pa.original_phenotype.intern == phenotype + pa.affected_character.intern == character and pa.original_phenotype.intern == phenotype end.first if phenotype_alternate phenotype_alternate.renamed_phenotype.intern @@ -158,23 +158,28 @@ class Vial < ActiveRecord::Base def fill_from_field(bit_generator, allele_frequencies) number_of_requested_flies.times do |i| - new_fly = Fly.create! - species.characters.each do |character| - if character == :sex # could this be handled better? - new_fly.genotypes << Genotype.create!(:fly_id => new_fly.id, :gene_number => species.gene_number_of(:sex), - :mom_allele => 1, :dad_allele => bit_generator.random_bit(allele_frequencies[:sex])) - else - new_fly.genotypes << Genotype.create!(:fly_id => new_fly.id, :gene_number => species.gene_number_of(character), - :mom_allele => bit_generator.random_bit(allele_frequencies[character]), - :dad_allele => bit_generator.random_bit(allele_frequencies[character])) - end - end - species.characters.each do |character| - if species.is_sex_linked?(character) and new_fly.male? - new_fly.genotypes.select { |g| g.gene_number == species.gene_number_of(character) }.first.dad_allele = 0 - end # this assumes that 0 represents recessiveness... and some other things - end - flies << new_fly + new_fly = Fly.create! + species.characters.each do |character| + if character == :sex + new_fly.genotypes << Genotype.create!(:fly_id => new_fly.id, + :gene_number => species.gene_number_of(:sex), + :mom_allele => 1, + :dad_allele => bit_generator.random_bit(allele_frequencies[:sex])) + else + new_fly.genotypes << Genotype.create!(:fly_id => new_fly.id, + :gene_number => species.gene_number_of(character), + :mom_allele => bit_generator.random_bit(allele_frequencies[character]), + :dad_allele => bit_generator.random_bit(allele_frequencies[character])) + end + end + if new_fly.male? + species.sex_linked_characters.each do |character| + genotype = new_fly.genotypes.detect { |g| g.genotype_for?(character) } + genotype.dad_allele = 0 + genotype.save! + end + end + flies << new_fly end self end app/models/vial.rb @@ -1,10 +1,19 @@ require File.dirname(__FILE__) + '/../test_helper' class GenotypeTest < Test::Unit::TestCase - fixtures :genotypes + fixtures :genotypes, :flies, :vials - # Replace this with your real tests. - def test_truth - assert true + def test_belongs_to_fly + assert_equal flies(:fly_00), genotypes(:fly_00_eye_color).fly + end + + def test_genotype_for? + assert genotypes(:fly_00_eye_color).genotype_for?(:"eye color") + assert !genotypes(:fly_00_eye_color).genotype_for?(:antenna) + assert !genotypes(:fly_00_eye_color).genotype_for?(:sex) + + assert !genotypes(:fly_00_antenna).genotype_for?(:"eyecolor") + assert genotypes(:fly_00_antenna).genotype_for?(:antenna) + assert !genotypes(:fly_00_antenna).genotype_for?(:sex) end end test/unit/genotype_test.rb @@ -62,14 +62,19 @@ class SpeciesTest < Test::Unit::TestCase # is it ok to get negatives when the gene_numbers are backwards? end - def test_is_sex_linked? - assert !Species.singleton.is_sex_linked?(:"eye color") - assert !Species.singleton.is_sex_linked?(:wings) - assert !Species.singleton.is_sex_linked?(:legs) - assert !Species.singleton.is_sex_linked?(:sex) - assert !Species.singleton.is_sex_linked?(:seizure) + def test_sex_linked? + assert !Species.singleton.sex_linked?(:"eye color") + assert !Species.singleton.sex_linked?(:wings) + assert !Species.singleton.sex_linked?(:legs) + assert !Species.singleton.sex_linked?(:sex) + assert !Species.singleton.sex_linked?(:seizure) - assert Species.singleton.is_sex_linked?(:antenna) + assert Species.singleton.sex_linked?(:antenna) + end + + def test_sex_linked + assert_equal [:antenna], Species.singleton.sex_linked_characters + assert_equal [:antenna], Species.singleton.sex_linked_characters, "shouldn't break with caching" end end \ No newline at end of file test/unit/species_test.rb @@ -21,16 +21,16 @@ class VialTest < Test::Unit::TestCase def test_number_requested_validations ["4", "0", "255"].each do |number| vial = Vial.new(:label => 'foo', :rack_id => 1, - :number_of_requested_flies => number - ) + :number_of_requested_flies => number + ) assert vial.valid?, "should be valid" assert !vial.errors.invalid?(:number_of_requested_flies) end ['xxx', '-4', '-1', '256', '888'].each do |number| vial = Vial.new(:label => 'foo', :rack_id => 1, - :number_of_requested_flies => number - ) + :number_of_requested_flies => number + ) assert !vial.valid? assert vial.errors.invalid?(:number_of_requested_flies) end @@ -59,7 +59,7 @@ class VialTest < Test::Unit::TestCase assert_equal 0, vials(:vial_empty).flies.size, "should be no flies" assert_equal [flies(:fly_01)].to_set, vials(:vial_with_a_fly).flies.to_set assert_equal [flies(:fly_00), flies(:fly_10), flies(:fly_11), flies(:bob)].to_set, - vials(:vial_with_many_flies).flies.to_set + vials(:vial_with_many_flies).flies.to_set end def test_count_of_flies @@ -101,24 +101,24 @@ class VialTest < Test::Unit::TestCase def test_flies_are_destroyed_along_with_vial assert_dependents_destroyed(Vial, Fly, :foreign_key => "vial_id", - :fixture_id => 6, :number_of_dependents => 2) + :fixture_id => 6, :number_of_dependents => 2) end def test_combinations_of_phenotypes assert_equal [:sex, :"eye color", :wings, :legs, :antenna, :seizure], vials(:vial_one).species.characters assert_equal cartesian_product([[:female, :male], - [:red, :white], - [:curly, :straight], - [:hairy, :smooth], - [:long, :short], - [:"20% seizure", :"40% seizure", :"no seizure"]]), - vials(:vial_one).combinations_of_phenotypes + [:red, :white], + [:curly, :straight], + [:hairy, :smooth], + [:long, :short], + [:"20% seizure", :"40% seizure", :"no seizure"]]), + vials(:vial_one).combinations_of_phenotypes assert_equal cartesian_product([[:female, :male], - [:red, :white]]), - vials(:vial_one).combinations_of_phenotypes([:sex, :"eye color"]) + [:red, :white]]), + vials(:vial_one).combinations_of_phenotypes([:sex, :"eye color"]) assert_equal cartesian_product([[:red, :white], - [:hairy, :smooth]]), - vials(:vial_one).combinations_of_phenotypes([:"eye color", :legs]) + [:hairy, :smooth]]), + vials(:vial_one).combinations_of_phenotypes([:"eye color", :legs]) end def test_phenotypes_for_table @@ -154,10 +154,10 @@ class VialTest < Test::Unit::TestCase def test_collect_four_flies_from_field new_vial = Vial.collect_from_field({ - :label => "four fly vial", :rack_id => 1, - :number_of_requested_flies => "4" - }, - CookedBitGenerator.new([1])) + :label => "four fly vial", :rack_id => 1, + :number_of_requested_flies => "4" + }, + CookedBitGenerator.new([1])) assert_equal(([:female] * 4), phenotypes_of(new_vial, :sex)) assert_equal(([:red] * 4), phenotypes_of(new_vial, :"eye color")) assert_equal(([:straight] * 4), phenotypes_of(new_vial, :wings)) @@ -167,73 +167,89 @@ class VialTest < Test::Unit::TestCase def test_collect_nine_flies_from_field new_vial = Vial.collect_from_field({ - :label => "nine fly vial", :rack_id => 1, - :number_of_requested_flies => "9" }, - CookedBitGenerator.new([0, 1, 0, 0])) + :label => "nine fly vial", :rack_id => 1, + :number_of_requested_flies => "9" }, + CookedBitGenerator.new([0, 1, 0, 0])) assert_equal_set(([:male] * 7 + [:female] * 2), - new_vial.flies.map {|fly| fly.phenotype(:sex)}) + new_vial.flies.map {|fly| fly.phenotype(:sex)}) assert_equal_set(([:red] * 5 + [:white] * 4), - new_vial.flies.map {|fly| fly.phenotype(:"eye color")}) + new_vial.flies.map {|fly| fly.phenotype(:"eye color")}) assert_equal_set(([:straight] * 4 + [:curly] * 5), - new_vial.flies.map {|fly| fly.phenotype(:wings)}) + new_vial.flies.map {|fly| fly.phenotype(:wings)}) assert_equal_set(([:hairy] * 5 + [:smooth] * 4), - new_vial.flies.map {|fly| fly.phenotype(:legs)}) + new_vial.flies.map {|fly| fly.phenotype(:legs)}) assert_equal_set(([:long] * 4 + [:short] * 5), - new_vial.flies.map {|fly| fly.phenotype(:antenna)}) + new_vial.flies.map {|fly| fly.phenotype(:antenna)}) assert_equal 2, new_vial.flies_of_type([:sex, :legs],[:female, :smooth]).size assert_equal 1, new_vial.pedigree_number end def test_collecting_field_vial_with_allele_frequencies recessive_vial = Vial.collect_from_field({ - :label => "white-eyed curly and shaven flies", - :rack_id => 1, - :number_of_requested_flies => "14" }, - RandomBitGenerator.new, - { :"eye color" => 0.0, :wings => 0.0, :legs => 0.0} ) + :label => "white-eyed curly and shaven flies", + :rack_id => 1, + :number_of_requested_flies => "14" }, + RandomBitGenerator.new, + { :"eye color" => 0.0, :wings => 0.0, :legs => 0.0} ) assert_equal 14, recessive_vial.number_of_flies([:"eye color"],[:white]) assert_equal 14, recessive_vial.number_of_flies([:wings],[:curly]) assert_equal 14, recessive_vial.number_of_flies([:legs],[:smooth]) dominant_vial = Vial.collect_from_field({ - :label => "red-eyed gruff flies", :rack_id => 1, - :number_of_requested_flies => '15' }, - RandomBitGenerator.new, - { :"eye color" => 1.0, :wings => 1.0, :legs => 1.0} ) + :label => "red-eyed gruff flies", :rack_id => 1, + :number_of_requested_flies => '15' }, + RandomBitGenerator.new, + { :"eye color" => 1.0, :wings => 1.0, :legs => 1.0} ) assert_equal 15, dominant_vial.number_of_flies([:"eye color"],[:red]) assert_equal 15, dominant_vial.number_of_flies([:wings],[:straight]) assert_equal 15, dominant_vial.number_of_flies([:legs],[:hairy]) strange_male_vial = Vial.collect_from_field({ - :label => "wasp flies", :rack_id => 1, - :number_of_requested_flies => 16 }, - RandomBitGenerator.new, - { :"eye color" => 0.0, :sex => 0.0} ) + :label => "wasp flies", :rack_id => 1, + :number_of_requested_flies => 16 }, + RandomBitGenerator.new, + { :"eye color" => 0.0, :sex => 0.0} ) assert_equal 16, strange_male_vial.number_of_flies([:"eye color"],[:white]) assert_equal 16, strange_male_vial.number_of_flies([:sex],[:male]) end - def test_sex_linkage_in_field_vials + def test_sex_linkage_in_field_vials_with_males antenna_flies_vial = Vial.collect_from_field({ - :label => "flies with antenna", :rack_id => 1, - :number_of_requested_flies => "11" }, - RandomBitGenerator.new, - { :sex => 0.0 } ) + :label => "flies with antenna", :rack_id => 1, + :number_of_requested_flies => "11" }, + RandomBitGenerator.new, + { :sex => 0.0, :antenna => 1.0 } ) + + antenna_flies_vial.reload antenna_flies_vial.flies.each do |fly| - fly_dad_allele = fly.genotypes.select do |g| - g.gene_number == fly.species.gene_number_of(:antenna) - end.first.dad_allele - assert_equal 0, fly_dad_allele + assert fly.male? + assert_equal 0, + fly.genotypes.detect { |g| g.genotype_for?(:antenna) }.dad_allele + end + end + + def test_sex_linkage_in_field_vials_with_females + antenna_flies_vial = Vial.collect_from_field({ + :label => "flies with antenna", :rack_id => 1, + :number_of_requested_flies => "11" }, + RandomBitGenerator.new, + { :sex => 1.0, :antenna => 1.0 } ) + + antenna_flies_vial.reload + antenna_flies_vial.flies.each do |fly| + assert fly.female? + assert_equal 1, + fly.genotypes.detect { |g| g.genotype_for?(:antenna) }.dad_allele end end def test_making_three_babies_and_a_vial new_vial = Vial.make_babies_and_vial({ - :label => "three fly syblings", :rack_id => 1, - :mom_id => "6", :dad_id => "1", - :number_of_requested_flies => "3", - :creator => users(:steve) }, - CookedBitGenerator.new([0]) ) + :label => "three fly syblings", :rack_id => 1, + :mom_id => "6", :dad_id => "1", + :number_of_requested_flies => "3", + :creator => users(:steve) }, + CookedBitGenerator.new([0]) ) assert new_vial.valid? assert_equal(([:female] * 3), phenotypes_of(new_vial, :sex)) @@ -245,50 +261,50 @@ class VialTest < Test::Unit::TestCase def test_making_seven_babies_and_a_vial new_vial = Vial.make_babies_and_vial({ - :label => "seven fly syblings", :rack_id => 1, - :mom_id => "4", :dad_id => "3", - :number_of_requested_flies => "7", - :creator => users(:steve) }, - CookedBitGenerator.new([0,1,1,0,0,0,1]) ) + :label => "seven fly syblings", :rack_id => 1, + :mom_id => "4", :dad_id => "3", + :number_of_requested_flies => "7", + :creator => users(:steve) }, + CookedBitGenerator.new([0,1,1,0,0,0,1]) ) assert new_vial.valid? assert_equal_set(([:male] * 3 + [:female] * 4), - new_vial.flies.map {|fly| fly.phenotype(:sex)}) + new_vial.flies.map {|fly| fly.phenotype(:sex)}) assert_equal_set(([:red] * 7 + [:white] * 0), - new_vial.flies.map {|fly| fly.phenotype(:"eye color")}) + new_vial.flies.map {|fly| fly.phenotype(:"eye color")}) assert_equal_set(([:straight] * 3 + [:curly] * 4), - new_vial.flies.map {|fly| fly.phenotype(:wings)}) + new_vial.flies.map {|fly| fly.phenotype(:wings)}) assert_equal_set(([:hairy] * 4 + [:smooth] * 3), - new_vial.flies.map {|fly| fly.phenotype(:legs)}) + new_vial.flies.map {|fly| fly.phenotype(:legs)}) assert_equal_set(([:long] * 7 + [:short] * 0), - new_vial.flies.map {|fly| fly.phenotype(:antenna)}) + new_vial.flies.map {|fly| fly.phenotype(:antenna)}) assert_equal_set(([:"no seizure"] * 1 + [:"20% seizure"] * 4 + [:"40% seizure"] * 2), - new_vial.flies.map {|fly| fly.phenotype(:seizure)}) + new_vial.flies.map {|fly| fly.phenotype(:seizure)}) assert_equal 2, new_vial.flies_of_type([:wings, :legs],[:curly, :smooth]).size assert_equal 2, new_vial.pedigree_number end def test_offspring_vial? new_vial = Vial.make_babies_and_vial({ - :label => "three fly syblings", :rack_id => 1, - :mom_id => "6", :dad_id => "1", - :number_of_requested_flies => "3" }, - CookedBitGenerator.new([0]) ) + :label => "three fly syblings", :rack_id => 1, + :mom_id => "6", :dad_id => "1", + :number_of_requested_flies => "3" }, + CookedBitGenerator.new([0]) ) assert new_vial.offspring_vial?, - "should be an offspring vial because of the method called to create it" + "should be an offspring vial because of the method called to create it" new_vial = Vial.make_babies_and_vial({ - :label => "seven fly syblings", :rack_id => 1, - :mom_id => "4", :dad_id => "3", - :number_of_requested_flies => "7" }, - CookedBitGenerator.new([0,1,1,0,0,0,1]) ) + :label => "seven fly syblings", :rack_id => 1, + :mom_id => "4", :dad_id => "3", + :number_of_requested_flies => "7" }, + CookedBitGenerator.new([0,1,1,0,0,0,1]) ) assert new_vial.offspring_vial?, - "should be an offspring vial because of the method called to create it" + "should be an offspring vial because of the method called to create it" assert !vials(:vial_one).offspring_vial? assert !vials(:vial_with_many_flies).offspring_vial? assert vials(:destroyable_vial).offspring_vial?, - "should give sane answer for vials from database with parents" + "should give sane answer for vials from database with parents" end def test_sex_linkage_of_antenna @@ -311,10 +327,10 @@ class VialTest < Test::Unit::TestCase def test_make_babies_and_vial_fails_missing_data_validations vial = Vial.make_babies_and_vial({ - :label => "failure", :rack_id => 1, - :mom_id => nil, :dad_id => nil, - :number_of_requested_flies => -12, - :creator => users(:steve) }) + :label => "failure", :rack_id => 1, + :mom_id => nil, :dad_id => nil, + :number_of_requested_flies => -12, + :creator => users(:steve) }) assert !vial.valid? assert vial.errors.invalid?(:number_of_requested_flies) assert vial.errors.invalid?(:mom_id), "mom should not be missing" @@ -323,9 +339,9 @@ class VialTest < Test::Unit::TestCase def test_make_babies_and_vial_fails_missing_creator vial = Vial.make_babies_and_vial({ - :label => "failure", :rack_id => 1, - :mom_id => 6, :dad_id => 1, - :number_of_requested_flies => 12 }) + :label => "failure", :rack_id => 1, + :mom_id => 6, :dad_id => 1, + :number_of_requested_flies => 12 }) assert !vial.valid? assert vial.errors.invalid?(:creator) end @@ -333,30 +349,30 @@ class VialTest < Test::Unit::TestCase def test_make_babies_and_vial_fails_when_creator_does_not_own_rack assert_raise ApplicationController::InvalidOwner do Vial.make_babies_and_vial({ - :label => "failure", :rack_id => 1, - :mom_id => 8, :dad_id => 9, - :number_of_requested_flies => 12, - :creator => users(:jeremy) }) + :label => "failure", :rack_id => 1, + :mom_id => 8, :dad_id => 9, + :number_of_requested_flies => 12, + :creator => users(:jeremy) }) end end def test_make_babies_and_vial_fails_when_creator_does_not_own_mom assert_raise ApplicationController::InvalidOwner do Vial.make_babies_and_vial({ - :label => "failure", :rack_id => 4, - :mom_id => 4, :dad_id => 9, - :number_of_requested_flies => 12, - :creator => users(:jeremy) }) + :label => "failure", :rack_id => 4, + :mom_id => 4, :dad_id => 9, + :number_of_requested_flies => 12, + :creator => users(:jeremy) }) end end def test_make_babies_and_vial_fails_when_creator_does_not_own_dad assert_raise ApplicationController::InvalidOwner do Vial.make_babies_and_vial({ - :label => "failure", :rack_id => 4, - :mom_id => 8, :dad_id => 1, - :number_of_requested_flies => 12, - :creator => users(:jeremy) }) + :label => "failure", :rack_id => 4, + :mom_id => 8, :dad_id => 1, + :number_of_requested_flies => 12, + :creator => users(:jeremy) }) end end test/unit/vial_test.rb 1b4e2d7b21b698a85ef36991d3aedce64e9d6719 Jeremy D. Frens jdfrens@gmail.com http://github.com/jdfrens/yags/commit/b6c6e735b7b94d45a53b5fbac286c745d3d03137 b6c6e735b7b94d45a53b5fbac286c745d3d03137 2008-02-22T14:22:19-08:00 2008-02-22T14:22:19-08:00 Fixed bug with sex-linked genotype (test didn't reload vial and genotype save was needed). Refactored and cleaned up some of the code. Added NetBeans configuration 38a8622e8701cedc92fda04363efc6af685e035a Jeremy D. Frens jdfrens@gmail.com