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|
#
# test/bio/tc_pathway.rb - Unit test for Bio::Pathway
#
# Copyright:: Copyright (C) 2004
# Moses Hohman <mmhohman@northwestern.edu>
# License:: The Ruby License
#
# $Id:$
#
# loading helper routine for testing bioruby
require 'pathname'
load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 2,
'bioruby_test_helper.rb')).cleanpath.to_s
# libraries needed for the tests
require 'test/unit'
require 'bio/pathway'
module Bio
class TestMyGraph < Test::Unit::TestCase
def test_cliquishness
graph = Pathway.new([
Relation.new(1, 3, 1),
Relation.new(2, 3, 1),
Relation.new(1, 5, 1),
Relation.new(2, 6, 1),
Relation.new(3, 6, 1),
Relation.new(4, 6, 1),
Relation.new(5, 6, 1),
], true)
assert_equal(0, graph.cliquishness(1), "1's cliquishness wrong")
assert_equal(1, graph.cliquishness(2), "2's cliquishness wrong")
assert_in_delta(0.33, graph.cliquishness(3), 0.01, "3's cliquishness wrong")
# Because cliquishness (clustering coefficient) for a node
# that has only one neighbor node is undefined, test for
# node 4 is commented out.
#assert_equal(1, graph.cliquishness(4), "4's cliquishness wrong")
assert_equal(0, graph.cliquishness(5), "5's cliquishness wrong")
assert_in_delta(0.16, graph.cliquishness(6), 0.01, "6's cliquishness wrong")
end
end
class TestRelation < Test::Unit::TestCase
def setup
@r1 = Relation.new('a', 'b', 1)
@r2 = Relation.new('b', 'a', 1)
@r3 = Relation.new('b', 'a', 2)
@r4 = Relation.new('a', 'b', 1)
end
def test_comparison_operator
assert(@r1 === @r2, "@r1 === @r2 not true, === not symmetric wrt nodes")
assert(!(@r1 === @r3), "@r1 === @r3 not false, === does not take edge into account")
assert(@r1 === @r4, "@r1 === @r4 not true, === is not reflexive wrt nodes")
assert(@r1.eql?(@r2), "@r1 not eql @r2")
assert(!@r3.eql?(@r2), "@r3 eql to @r2")
end
def test_uniq
a = [ @r1, @r2, @r3, @r4 ].uniq
# Array#uniq does not guarantee that the first value is always
# chosen, though the "bug" is fixed.
# (https://bugs.ruby-lang.org/issues/9340 )
# (https://github.com/bioruby/bioruby/issues/92 )
# #assert_equal([@r1, @r3], a, "uniq did not have expected effect")
assert_equal(2, a.size)
assert(@r1 === a[0])
assert(@r3 === a[1])
end
end
class TestSampleGraph < Test::Unit::TestCase
TheInfinity = 1/0.0
# Sample Graph :
# +----------------+
# | |
# v |
# +---------(q)-->(t)------->(y)<----(r)
# | | | ^ |
# v | v | |
# +--(s)<--+ | (x)<---+ (u)<-----+
# | | | | |
# v | | v |
# (v)----->(w)<---+ (z)----+
def setup
@data = [
[ 'q', 's', 1, ],
[ 'q', 't', 1, ],
[ 'q', 'w', 1, ],
[ 'r', 'u', 1, ],
[ 'r', 'y', 1, ],
[ 's', 'v', 1, ],
[ 't', 'x', 1, ],
[ 't', 'y', 1, ],
[ 'u', 'y', 1, ],
[ 'v', 'w', 1, ],
[ 'w', 's', 1, ],
[ 'x', 'z', 1, ],
[ 'y', 'q', 1, ],
[ 'z', 'x', 1, ],
]
@graph = Pathway.new(@data.collect { |x| Relation.new(*x) })
end
def test_to_matrix
matrix = @graph.to_matrix(0)
index = @graph.index
# expected values
source_matrix =
[
#v w x y z q r s t u
[0, 1, 0, 0, 0, 0, 0, 0, 0, 0], #v
[0, 0, 0, 0, 0, 0, 0, 1, 0, 0], #w
[0, 0, 0, 0, 1, 0, 0, 0, 0, 0], #x
[0, 0, 0, 0, 0, 1, 0, 0, 0, 0], #y
[0, 0, 1, 0, 0, 0, 0, 0, 0, 0], #z
[0, 1, 0, 0, 0, 0, 0, 1, 1, 0], #q
[0, 0, 0, 1, 0, 0, 0, 0, 0, 1], #r
[1, 0, 0, 0, 0, 0, 0, 0, 0, 0], #s
[0, 0, 1, 1, 0, 0, 0, 0, 0, 0], #t
[0, 0, 0, 1, 0, 0, 0, 0, 0, 0] #u
]
source_index = {
"v"=>0, "w"=>1, "x"=>2, "y"=>3, "z"=>4,
"q"=>5, "r"=>6, "s"=>7, "t"=>8, "u"=>9
}
# test index size
assert_equal(10, source_index.size)
# test index keys
assert_equal(source_index.keys.sort, index.keys.sort)
# test index values
assert_equal(source_index.values.sort, index.values.sort)
# prepare expected matrix
ary = Array.new(index.size)
ary.collect! { |a| Array.new(index.size) }
index.each do |row_k, row_v|
src_row = source_index[row_k]
index.each do |col_k, col_v|
src_col = source_index[col_k]
ary[row_v][col_v] = source_matrix[src_row][src_col]
end
end
expected_matrix = Matrix.rows(ary)
# test the matrix
assert_equal(expected_matrix, matrix, "matrix wrong")
end
def test_to_matrix_fixed_index
# begin workaround removing depencency to order of Hash#each
%w( v w x y z q r s t u ).each_with_index do |x, i|
@graph.index[x] = i
end
# end workaround removing depencency to order of Hash#each
assert_equal(Matrix[
[0, 1, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 1, 0, 0],
[0, 0, 0, 0, 1, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 1, 0, 0, 0, 0],
[0, 0, 1, 0, 0, 0, 0, 0, 0, 0],
[0, 1, 0, 0, 0, 0, 0, 1, 1, 0],
[0, 0, 0, 1, 0, 0, 0, 0, 0, 1],
[1, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 1, 1, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 1, 0, 0, 0, 0, 0, 0]
], @graph.to_matrix(0), "matrix wrong")
assert_equal({"v"=>0,"w"=>1,"x"=>2,"y"=>3,"z"=>4,"q"=>5,"r"=>6,"s"=>7,"t"=>8,"u"=>9}, @graph.index, "node --> matrix index order wrong")
end
def test_dump_matrix
# begin workaround removing depencency to order of Hash#each
%w( v w x y z q r s t u ).each_with_index do |x, i|
@graph.index[x] = i
end
# end workaround removing depencency to order of Hash#each
dumped = "[" +
"# v, w, x, y, z, q, r, s, t, u\n" +
" [0, 1, 0, 0, 0, 0, 0, 0, 0, 0],\n" + # v
" [0, 0, 0, 0, 0, 0, 0, 1, 0, 0],\n" + # w
" [0, 0, 0, 0, 1, 0, 0, 0, 0, 0],\n" + # x
" [0, 0, 0, 0, 0, 1, 0, 0, 0, 0],\n" + # y
" [0, 0, 1, 0, 0, 0, 0, 0, 0, 0],\n" + # z
" [0, 1, 0, 0, 0, 0, 0, 1, 1, 0],\n" + # q
" [0, 0, 0, 1, 0, 0, 0, 0, 0, 1],\n" + # r
" [1, 0, 0, 0, 0, 0, 0, 0, 0, 0],\n" + # s
" [0, 0, 1, 1, 0, 0, 0, 0, 0, 0],\n" + # t
" [0, 0, 0, 1, 0, 0, 0, 0, 0, 0]\n]" # u
assert_equal(dumped, @graph.dump_matrix(0))
end
def test_dump_list
# begin workaround removing depencency to order of Hash#each
%w( v w x y z q r s t u ).each_with_index do |x, i|
@graph.index[x] = i
end
# end workaround removing depencency to order of Hash#each
dumped = "v => w (1)\n" +
"w => s (1)\n" +
"x => z (1)\n" +
"y => q (1)\n" +
"z => x (1)\n" +
"q => w (1), s (1), t (1)\n" +
"r => y (1), u (1)\n" +
"s => v (1)\n" +
"t => x (1), y (1)\n" +
"u => y (1)\n"
assert_equal(dumped, @graph.dump_list)
end
def test_extract_subgraph_by_label
hash = { 'q' => "L1", 's' => "L2", 'v' => "L3", 'w' => "L4" }
@graph.label = hash
subgraph = @graph.subgraph
# begin workaround removing depencency to order of Hash#each
%w( v w q s ).each_with_index do |x, i|
subgraph.index[x] = i
end
# end workaround removing depencency to order of Hash#each
dumped =
"v => w (1)\n" +
"w => s (1)\n" +
"q => w (1), s (1)\n" +
"s => v (1)\n"
assert_equal(dumped, subgraph.dump_list)
end
def test_extract_subgraph_by_list
subgraph = @graph.subgraph(['q', 't', 'x', 'y', 'z'])
# begin workaround removing depencency to order of Hash#each
%w( x y z q t ).each_with_index do |x, i|
subgraph.index[x] = i
end
# end workaround removing depencency to order of Hash#each
dumped =
"x => z (1)\n" +
"y => q (1)\n" +
"z => x (1)\n" +
"q => t (1)\n" +
"t => x (1), y (1)\n"
assert_equal(dumped, subgraph.dump_list)
end
def test_extract_subgraph_retains_disconnected_nodes
assert_equal(4, @graph.subgraph(['r', 's', 'v', 'w']).nodes, "wrong number of nodes")
end
# Sample Graph :
# +----------------+
# | |
# v |
# +---------(q)-->(t)------->(y)<----(r)
# | | | ^ |
# v | v | |
# +--(s)<--+ | (x)<---+ (u)<-----+
# | | | | |
# v | | v |
# (v)----->(w)<---+ (z)----+
def test_undirected_cliquishness
@graph.undirected
assert_in_delta(0.33, @graph.cliquishness('q'), 0.01)
end
def test_small_world_aka_node_degree_histogram
expected = {1=>7, 2=>2, 3=>1}
expected.default = 0
assert_equal(expected, @graph.small_world)
end
# Sample Graph :
# +----------------+
# | |
# v |
# +---------(q)-->(t)------->(y)<----(r)
# | | | ^ |
# v | v | |
# +--(s)<--+ | (x)<---+ (u)<-----+
# | | | | |
# v | | v |
# (v)----->(w)<---+ (z)----+
def test_breadth_first_search
distances, predecessors = @graph.breadth_first_search('q')
assert_equal({
"v"=>2,
"w"=>1,
"x"=>2,
"y"=>2,
"z"=>3,
"q"=>0,
"s"=>1,
"t"=>1}, distances, "distances wrong")
assert_equal({
"v"=>"s",
"w"=>"q",
"x"=>"t",
"y"=>"t",
"z"=>"x",
"q"=>nil,
"s"=>"q",
"t"=>"q"}, predecessors, "predecessors wrong")
end
def test_bfs_shortest_path
step, path = @graph.bfs_shortest_path('y', 'w')
assert_equal(2, step, "wrong # of steps")
assert_equal(["y", "q", "w"], path, "wrong path")
end
def test_depth_first_search
# fixing node order to aviod dependency of Hash#each_key
%w( v w x y z q r s t u ).each_with_index do |x, i|
@graph.index[x] = i
end
# exec dfs
timestamp, tree, back, cross, forward =
@graph.depth_first_search
assert_equal({
"v"=>[1, 6],
"w"=>[2, 5],
"x"=>[7, 10],
"y"=>[11, 16],
"z"=>[8, 9],
"q"=>[12, 15],
"r"=>[17, 20],
"s"=>[3, 4],
"t"=>[13, 14],
"u"=>[18, 19]}, timestamp, "timestamps wrong")
assert_equal({
"w"=>"v",
"z"=>"x",
"q"=>"y",
"s"=>"w",
"t"=>"q",
"u"=>"r"}, tree, "tree edges wrong")
assert_equal({
"z"=>"x",
"s"=>"v",
"t"=>"y"}, back, "back edges wrong")
assert_equal({
"q"=>"s",
"r"=>"y",
"t"=>"x",
"u"=>"y"}, cross, "cross edges wrong")
assert_equal({}, forward, "forward edges wrong")
end
# Sample Graph :
# +----------------+
# | |
# v |
# +---------(q)-->(t)------->(y)<----(r)
# | | | ^ |
# v | v | |
# +--(s)<--+ | (x)<---+ (u)<-----+
# | | | | |
# v | | v |
# (v)----->(w)<---+ (z)----+
def test_dijkstra
distances, predecessors = @graph.dijkstra('q')
assert_equal({
"v"=>2,
"w"=>1,
"x"=>2,
"y"=>2,
"z"=>3,
"q"=>0,
"r"=>TheInfinity,
"s"=>1,
"t"=>1,
"u"=>TheInfinity}, distances, "distances wrong")
assert_equal({
"v"=>"s",
"w"=>"q",
"x"=>"t",
"y"=>"t",
"z"=>"x",
"q"=>nil,
"r"=>nil,
"s"=>"q",
"t"=>"q",
"u"=>nil}, predecessors, "predecessors wrong")
end
def test_bellman_ford
distances, predecessors = @graph.bellman_ford('q')
assert_equal({
"v"=>2,
"w"=>1,
"x"=>2,
"y"=>2,
"z"=>3,
"q"=>0,
"r"=>TheInfinity,
"s"=>1,
"t"=>1,
"u"=>TheInfinity}, distances, "distances wrong")
assert_equal({
"v"=>"s",
"w"=>"q",
"x"=>"t",
"y"=>"t",
"z"=>"x",
"q"=>nil,
"r"=>nil,
"s"=>"q",
"t"=>"q",
"u"=>nil}, predecessors, "predecessors wrong")
end
end
class TestTopologicalSort < Test::Unit::TestCase
#
# Professor Bumstead topologically sorts his clothing when getting dressed.
#
# "undershorts" "socks"
# | | |
# v | v "watch"
# "pants" --+-------> "shoes"
# |
# v
# "belt" <----- "shirt" ----> "tie" ----> "jacket"
# | ^
# `---------------------------------------'
#
def test_dfs_topological_sort
dag = Pathway.new([
Relation.new("undershorts", "pants", true),
Relation.new("undershorts", "shoes", true),
Relation.new("socks", "shoes", true),
Relation.new("watch", "watch", true),
Relation.new("pants", "belt", true),
Relation.new("pants", "shoes", true),
Relation.new("shirt", "belt", true),
Relation.new("shirt", "tie", true),
Relation.new("tie", "jacket", true),
Relation.new("belt", "jacket", true),
])
sorted = dag.dfs_topological_sort
assert(sorted.index("socks") < sorted.index("shoes"), "socks >= shoes")
assert(sorted.index("undershorts") < sorted.index("pants"), "undershorts >= pants")
assert(sorted.index("undershorts") < sorted.index("shoes"), "undershorts >= shoes")
assert(sorted.index("pants") < sorted.index("shoes"), "pants >= shoes")
assert(sorted.index("pants") < sorted.index("belt"), "pants >= belt")
assert(sorted.index("shirt") < sorted.index("belt"), "shirt >= belt")
assert(sorted.index("shirt") < sorted.index("tie"), "shirt >= tie")
assert(sorted.index("belt") < sorted.index("jacket"), "belt >= jacket")
assert(sorted.index("tie") < sorted.index("jacket"), "tie >= jacket")
end
end
#TODO: verify the below
class TestWeightedGraph < Test::Unit::TestCase
# 'a' --> 'b'
# | 1 | 3
# |5 v
# `----> 'c'
def setup
r1 = Relation.new('a', 'b', 1)
r2 = Relation.new('a', 'c', 5)
r3 = Relation.new('b', 'c', 3)
@w_graph = Pathway.new([r1, r2, r3])
end
def test_dijkstra_on_weighted_graph
distances, predecessors = @w_graph.dijkstra('a')
assert_equal({
"a"=>0,
"b"=>1,
"c"=>4}, distances, "distances wrong")
assert_equal({
"a"=>nil,
"b"=>"a",
"c"=>"b"}, predecessors, "predecessors wrong")
end
def test_bellman_ford_on_negative_weighted_graph
# ,-- 'a' --> 'b'
# | | 1 | 3
# | |5 v
# | `----> 'c'
# | ^
# |2 | -5
# `--> 'd' ----'
r4 = Relation.new('a', 'd', 2)
r5 = Relation.new('d', 'c', -5)
@w_graph.append(r4)
@w_graph.append(r5)
distances, predecessors = @w_graph.bellman_ford('a')
assert_equal({
"a"=>0,
"b"=>1,
"c"=>-3,
"d"=>2}, distances, "distances wrong")
assert_equal({
"a"=>nil,
"b"=>"a",
"c"=>"d",
"d"=>"a"}, predecessors, "predecessors wrong")
end
end
end
|
