summaryrefslogtreecommitdiff
path: root/test/dataset.rb
blob: b5275d491ef200a9ea08d8ed5eb8c5b9e7a01eeb (plain)
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
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
# TODO; check compound/data_entry sequences with missing and duplicated values

require_relative "setup.rb"

class DatasetTest < MiniTest::Test

  def test_all
    d1 = Dataset.new 
    d1.save
    datasets = Dataset.all 
    assert_equal Dataset, datasets.first.class
    d1.delete
  end

  def test_create_empty
    d = Dataset.new
    assert_equal Dataset, d.class
    refute_nil d.id
    assert_kind_of BSON::ObjectId, d.id
  end

  def test_client_create
    d = Dataset.new
    assert_equal Dataset, d.class
    d.name = "Create dataset test"

    # features not set
    # << operator was removed for efficiency reasons (CH)
    #assert_raises BadRequestError do
    #  d << [Compound.from_smiles("c1ccccc1NN"), 1,2]
    #end

    # add data entries
    d.features = ["test1", "test2"].collect do |title|
      f = Feature.new 
      f.name = title
      f.numeric = true
      f.save
      f
    end

    # wrong feature size
    # << operator was removed for efficiency reasons (CH)
    #assert_raises BadRequestError do
    #  d << [Compound.from_smiles("c1ccccc1NN"), 1,2,3]
    #end
    
    # manual low-level insertions without consistency checks for runtime efficiency
    data_entries = []
    d.compound_ids << Compound.from_smiles("c1ccccc1NN").id
    data_entries << [1,2]
    d.compound_ids << Compound.from_smiles("CC(C)N").id
    data_entries << [4,5]
    d.compound_ids << Compound.from_smiles("C1C(C)CCCC1").id
    data_entries << [6,7]
    d.data_entries = data_entries
    assert_equal 3, d.compounds.size
    assert_equal 2, d.features.size
    assert_equal [[1,2],[4,5],[6,7]], d.data_entries
    d.save_all
    # check if dataset has been saved correctly
    new_dataset = Dataset.find d.id
    assert_equal 3, new_dataset.compounds.size
    assert_equal 2, new_dataset.features.size
    assert_equal [[1,2],[4,5],[6,7]], new_dataset.data_entries
    d.delete
    assert_raises Mongoid::Errors::DocumentNotFound do
      Dataset.find d.id
    end
    assert_raises Mongoid::Errors::DocumentNotFound do
      Dataset.find new_dataset.id
    end
  end

  def test_dataset_accessors
    d = Dataset.from_csv_file "#{DATA_DIR}/multicolumn.csv"
    # create empty dataset
    new_dataset = Dataset.find d.id
    # get metadata
    assert_match "multicolumn.csv",  new_dataset.source
    assert_equal "multicolumn.csv",  new_dataset.name
    # get features
    assert_equal 6, new_dataset.features.size
    assert_equal 7, new_dataset.compounds.size
    assert_equal ["1", nil, "false", nil, nil, 1.0], new_dataset.data_entries.last
    d.delete
  end

  def test_create_from_file
    d = Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.mini.csv")
    assert_equal Dataset, d.class
    refute_nil d.warnings
    assert_match "EPAFHM.mini.csv",  d.source
    assert_equal "EPAFHM.mini.csv",  d.name
    d.delete 
    #assert_equal false, URI.accessible?(d.uri)
  end

  def test_create_from_file_with_wrong_smiles_compound_entries
    d = Dataset.from_csv_file File.join(DATA_DIR,"wrong_dataset.csv")
    refute_nil d.warnings
    assert_match /2|3|4|5|6|7|8/, d.warnings.join
    d.delete
  end

  def test_multicolumn_csv
    d = Dataset.from_csv_file "#{DATA_DIR}/multicolumn.csv"
    refute_nil d.warnings
    assert d.warnings.grep(/Duplicate compound/)  
    assert d.warnings.grep(/3, 5/)  
    assert_equal 6, d.features.size
    assert_equal 7, d.compounds.size
    assert_equal 5, d.compounds.collect{|c| c.inchi}.uniq.size
    assert_equal [["1", "1", "true", "true", "test", 1.1], ["1", "2", "false", "7.5", "test", 0.24], ["1", "3", "true", "5", "test", 3578.239], ["0", "4", "false", "false", "test", -2.35], ["1", "2", "true", "4", "test_2", 1], ["1", "2", "false", "false", "test", -1.5], ["1", nil, "false", nil, nil, 1.0]], d.data_entries
    assert_equal "c1ccc[nH]1,1,,false,,,1.0", d.to_csv.split("\n")[7]
    csv = CSV.parse(d.to_csv)
    original_csv = CSV.read("#{DATA_DIR}/multicolumn.csv")
    csv.shift
    original_csv.shift
    csv.each_with_index do |row,i|
      compound = Compound.from_smiles row.shift
      original_compound = Compound.from_smiles original_csv[i].shift
      assert_equal original_compound.inchi, compound.inchi
      row.each_with_index do |v,j|
        if v.numeric?
          assert_equal original_csv[i][j].strip.to_f, row[j].to_f
        else
          assert_equal original_csv[i][j].strip, row[j].to_s
        end
      end
    end
    d.delete 
  end

  def test_from_csv
    d = Dataset.from_csv_file "#{DATA_DIR}/hamster_carcinogenicity.csv"
    assert_equal Dataset, d.class
    assert_equal 1, d.features.size
    assert_equal 85, d.compounds.size
    assert_equal 85, d.data_entries.size
    csv = CSV.read("#{DATA_DIR}/hamster_carcinogenicity.csv")
    csv.shift
    assert_equal csv.collect{|r| r[1]}, d.data_entries.flatten
    d.delete 
    #assert_equal false, URI.accessible?(d.uri)
  end

  def test_from_csv_classification
    ["int", "float", "string"].each do |mode|
      d = Dataset.from_csv_file "#{DATA_DIR}/hamster_carcinogenicity.mini.bool_#{mode}.csv"
      csv = CSV.read("#{DATA_DIR}/hamster_carcinogenicity.mini.bool_#{mode}.csv")
      csv.shift
      entries = d.data_entries.flatten
      csv.each_with_index do |r, i|
        assert_equal r[1].to_s, entries[i]
      end
      d.delete 
    end
  end

  def test_from_csv2
    File.open("#{DATA_DIR}/temp_test.csv", "w+") { |file| file.write("SMILES,Hamster\nCC=O,true\n ,true\nO=C(N),true") }
    dataset = Dataset.from_csv_file "#{DATA_DIR}/temp_test.csv"
    assert_equal "Cannot parse SMILES compound ' ' at position 3, all entries are ignored.",  dataset.warnings.join
    File.delete "#{DATA_DIR}/temp_test.csv"
    dataset.features.each{|f| feature = Feature.find f.id; feature.delete}
    dataset.delete
  end

  def test_same_feature
    datasets = []
    features = []
    2.times do |i|
      d = Dataset.from_csv_file "#{DATA_DIR}/hamster_carcinogenicity.mini.csv"
      features << d.features.first
      assert features[0].id==features[-1].id,"re-upload should find old feature, but created new one"
      datasets << d
    end
    datasets.each{|d| d.delete}
  end

  def test_create_from_file
    d = Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.mini.csv")
    assert_equal 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_equal 0.0113, d.data_entries[0][0]
    assert_equal 0.00323, d.data_entries[5][0]
    d2 = Dataset.find d.id
    assert_equal 0.0113, d2.data_entries[0][0]
    assert_equal 0.00323, d2.data_entries[5][0]
  end

end