1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
|
require_relative "setup.rb"
class DataEntryTest < MiniTest::Test
def test_create
# add features
features = ["test1", "test2"].collect do |title|
NumericBioAssay.find_or_create_by( :title => title, :numeric => true)
end
compounds = []
input = [
["c1ccccc1NN",1,2],
["CC(C)N",4,5],
["C1C(C)CCCC1",6,7],
]
input.each do |row|
smi = row.shift
compound = Compound.find_or_create_by(:smiles => smi)
compounds << compound
row.each_with_index do |value,i|
DataEntry.find_or_create compound, features[i], value
end
end
assert_equal 3, compounds.size
assert_equal 2, features.size
input.each_with_index do |row,i|
row.each_with_index do |v,j|
assert_equal DataEntry[compounds[i],features[j]], input[i][j]
end
end
end
def test_create_from_file
d = OpenTox::Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.mini.csv")
assert_equal OpenTox::Dataset, d.class
refute_nil d.warnings
assert_match /row 13/, d.warnings.join
assert_match "EPAFHM.mini.csv", d.source
assert_equal 1, d.features.size
feature = d.features.first
assert_kind_of NumericBioAssay, feature
assert_match "EPAFHM.mini.csv", feature.source
assert_equal 0.0113, DataEntry[d.compounds.first, feature]
assert_equal 0.0113, d[d.compounds.first, feature]
assert_equal 0.00323, DataEntry[d.compounds[5], feature]
assert_equal 0.00323, d[d.compounds[5], feature]
end
def test_upload_kazius
d = OpenTox::Dataset.from_csv_file File.join DATA_DIR, "kazius.csv"
assert_empty d.warnings
# 493 COC1=C(C=C(C(=C1)Cl)OC)Cl,1
c = d.compounds[491]
assert_equal c.smiles, "COc1cc(c(cc1Cl)OC)Cl"
assert_equal DataEntry[c,d.features.first], 1
end
def test_upload_feature_dataset
t = Time.now
f = File.join DATA_DIR, "rat_feature_dataset.csv"
d = OpenTox::Dataset.from_csv_file f
assert_equal 458, d.features.size
d.save
p "Upload: #{Time.now-t}"
d2 = OpenTox::Dataset.find d.id
t = Time.now
assert_equal d.features.size, d2.features.size
csv = CSV.read f
csv.shift # remove header
assert_equal csv.size, d2.compounds.size
assert_equal csv.first.size-1, d2.features.size
d2.compounds.each_with_index do |compound,i|
row = csv[i]
row.shift # remove compound
assert_equal row, d2.fingerprint(compound)
end
p "Dowload: #{Time.now-t}"
d2.delete
assert_raises Mongoid::Errors::DocumentNotFound do
Dataset.find d.id
end
end
end
|
