370 lines
19 KiB
Haskell
370 lines
19 KiB
Haskell
{-# LANGUAGE OverloadedStrings #-}
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import Test.Hspec
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import GEval.Core
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import GEval.OptionsParser
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import GEval.BLEU
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import GEval.ClippEU
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import GEval.PrecisionRecall
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import GEval.ClusteringMetrics
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import GEval.BIO
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import GEval.LineByLine
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import Data.Attoparsec.Text
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import Options.Applicative
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import Data.Text
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import Text.EditDistance
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import Data.Conduit.List (consume)
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import qualified Test.HUnit as HU
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import Data.Conduit.SmartSource
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import qualified Data.Conduit.Text as CT
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import Data.Conduit
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import Control.Monad.Trans.Resource
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import qualified Data.Conduit.List as CL
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informationRetrievalBookExample :: [(String, Int)]
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informationRetrievalBookExample = [("o", 2), ("o", 2), ("d", 2), ("x", 3), ("d", 3),
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("x", 1), ("o", 1), ("x", 1), ( "x", 1), ("x", 1), ("x", 1),
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("x", 2), ("o", 2), ("o", 2),
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("x", 3), ("d", 3), ("d", 3)]
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perfectClustering :: [(Int, Char)]
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perfectClustering = [(0, 'a'), (2, 'b'), (3, 'c'), (2, 'b'), (2, 'b'), (1, 'd'), (0, 'a')]
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stupidClusteringOneBigCluster :: [(Int, Int)]
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stupidClusteringOneBigCluster = [(0, 2), (2, 2), (1, 2), (2, 2), (0, 2), (0, 2), (0, 2), (0, 2), (1, 2), (1, 2)]
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stupidClusteringManySmallClusters :: [(Int, Int)]
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stupidClusteringManySmallClusters = [(0, 0), (2, 1), (1, 2), (2, 3), (0, 4), (0, 5), (0, 6), (0, 7), (1, 8), (1, 9)]
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main :: IO ()
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main = hspec $ do
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describe "root mean square error" $ do
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it "simple test" $ do
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(fmap Prelude.head (geval (defaultGEvalSpecification {gesExpectedDirectory=Just "test/rmse-simple/rmse-simple", gesOutDirectory="test/rmse-simple/rmse-simple-solution"}))) `shouldReturnAlmost` 0.64549722436790
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describe "mean square error" $ do
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it "simple test with arguments" $
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runGEvalTest "mse-simple" `shouldReturnAlmost` 0.4166666666666667
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describe "BLEU" $ do
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it "trivial example from Wikipedia" $
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runGEvalTest "bleu-trivial" `shouldReturnAlmost` 0.0
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it "complex example" $
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runGEvalTest "bleu-complex" `shouldReturnAlmost` 0.6211
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it "perfect translation" $
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runGEvalTest "bleu-perfect" `shouldReturnAlmost` 1.0000
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it "empty translation" $
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runGEvalTest "bleu-empty" `shouldReturnAlmost` 0.0000
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describe "Accuracy" $ do
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it "simple example" $
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runGEvalTest "accuracy-simple" `shouldReturnAlmost` 0.6
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it "with probs" $
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runGEvalTest "accuracy-probs" `shouldReturnAlmost` 0.4
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describe "F-measure" $ do
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it "simple example" $
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runGEvalTest "f-measure-simple" `shouldReturnAlmost` 0.57142857
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it "perfect classifier" $
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runGEvalTest "f-measure-perfect" `shouldReturnAlmost` 1.0
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it "stupid classifier" $
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runGEvalTest "f-measure-stupid" `shouldReturnAlmost` 0.0
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it "all false" $
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runGEvalTest "f-measure-all-false" `shouldReturnAlmost` 1.0
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it "F2-measure" $
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runGEvalTest "f2-simple" `shouldReturnAlmost` 0.714285714
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describe "precision count" $ do
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it "simple test" $ do
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precisionCount [["Alice", "has", "a", "cat" ]] ["Ala", "has", "cat"] `shouldBe` 2
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it "none found" $ do
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precisionCount [["Alice", "has", "a", "cat" ]] ["for", "bar", "baz"] `shouldBe` 0
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it "multiple values" $ do
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precisionCount [["bar", "bar", "bar", "bar", "foo", "xyz", "foo"]] ["foo", "bar", "foo", "baz", "bar", "foo"] `shouldBe` 4
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it "multiple refs" $ do
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precisionCount [["foo", "baz"], ["bar"], ["baz", "xyz"]] ["foo", "bar", "foo"] `shouldBe` 2
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describe "purity (in flat clustering)" $ do
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it "the example from Information Retrieval Book" $ do
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purity informationRetrievalBookExample `shouldBeAlmost` 0.70588
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describe "NMI (in flat clustering)" $ do
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it "the example from Information Retrieval Book" $ do
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normalizedMutualInformation informationRetrievalBookExample `shouldBeAlmost` 0.36456
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it "perfect clustering" $ do
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normalizedMutualInformation perfectClustering `shouldBeAlmost` 1.0
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it "stupid clustering with one big cluster" $ do
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normalizedMutualInformation stupidClusteringOneBigCluster `shouldBeAlmost` 0.0
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it "stupid clustering with many small clusters" $ do
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normalizedMutualInformation stupidClusteringManySmallClusters `shouldBeAlmost` 0.61799
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describe "NMI challenge" $ do
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it "complex test" $ do
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runGEvalTest "nmi-complex" `shouldReturnAlmost` 0.36456
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describe "LogLossHashed challenge" $ do
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it "simple example" $ do
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runGEvalTest "log-loss-hashed-simple" `shouldReturnAlmost` 2.398479083333333
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it "example with unnormalized values" $ do
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runGEvalTest "log-loss-hashed-not-normalized" `shouldReturnAlmost` 1.0468455186722887
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it "with probs instead of log probs" $ do
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runGEvalTest "log-loss-hashed-probs" `shouldReturnAlmost` 4.11631293099392
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it "with probs instead of log probs (with normalization)" $ do
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runGEvalTest "log-loss-hashed-probs-normalized" `shouldReturnAlmost` 1.55537749098853
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it "with log probs whose probs are summing up to less than 1.0" $ do
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runGEvalTest "log-loss-hashed-normalization" `shouldReturnAlmost` 5.16395069238851
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describe "LikelihoodHashed challenge" $ do
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it "example with unnormalized values" $ do
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runGEvalTest "likelihood-hashed-not-normalized" `shouldReturnAlmost` 0.351043364110715
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describe "reading options" $ do
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it "can get the metric" $ do
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extractMetric "bleu-complex" `shouldReturn` (Just BLEU)
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describe "error handling" $ do
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it "too few lines are handled" $ do
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runGEvalTest "error-too-few-lines" `shouldThrow` (== TooFewLines)
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it "too many lines are handled" $ do
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runGEvalTest "error-too-many-lines" `shouldThrow` (== TooManyLines)
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it "empty output is handled" $ do
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runGEvalTest "empty-output" `shouldThrow` (== EmptyOutput)
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it "unexpected data is handled" $
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runGEvalTest "unexpected-data" `shouldThrow` (== UnexpectedData 3 "input does not start with a digit")
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it "unwanted data is handled" $
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runGEvalTest "unwanted-data" `shouldThrow` (== UnexpectedData 2 "number expected")
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describe "precision and recall" $ do
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it "null test" $ do
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precision neverMatch ['a', 'b', 'c'] [0, 1, 2, 3, 4, 5] `shouldBeAlmost` 0.0
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recall neverMatch ['a', 'b', 'c'] [0, 1, 2, 3, 4, 5] `shouldBeAlmost` 0.0
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f1Measure neverMatch ['a', 'b', 'c'] [0, 1, 2, 3, 4, 5] `shouldBeAlmost` 0.0
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it "basic test" $ do
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precision testMatchFun ['a', 'b', 'c'] [0, 1, 2, 3, 4, 5] `shouldBeAlmost` 0.3333333333333333
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recall testMatchFun ['a', 'b', 'c'] [0, 1, 2, 3, 4, 5] `shouldBeAlmost` 0.66666666666666666
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f1Measure testMatchFun ['a', 'b', 'c'] [0, 1, 2, 3, 4, 5] `shouldBeAlmost` 0.444444444444444
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it "perfect result" $ do
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precision alwaysMatch ['a', 'b', 'c'] [0, 1, 2] `shouldBeAlmost` 1.0
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recall alwaysMatch ['a', 'b', 'c'] [0, 1, 2] `shouldBeAlmost` 1.0
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f1Measure alwaysMatch ['a', 'b', 'c'] [0, 1, 2] `shouldBeAlmost` 1.0
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it "full match" $ do
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precision alwaysMatch ['a', 'b', 'c'] [0, 1, 2, 3, 4, 5] `shouldBeAlmost` 0.5
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recall alwaysMatch ['a', 'b', 'c'] [0, 1, 2, 3, 4, 5] `shouldBeAlmost` 1.0
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f1Measure alwaysMatch ['a', 'b', 'c'] [0, 1, 2, 3 , 4, 5] `shouldBeAlmost` 0.66666666666666
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describe "ClippEU" $ do
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it "parsing rectangles" $ do
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let (Right r) = parseOnly (lineClippingsParser <* endOfInput) "2/0,0,2,3 10/20,30,40,50 18/0,1,500,3 "
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r `shouldBe` [Clipping (PageNumber 2) (Rectangle (Point 0 0) (Point 2 3)),
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Clipping (PageNumber 10) (Rectangle (Point 20 30) (Point 40 50)),
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Clipping (PageNumber 18) (Rectangle (Point 0 1) (Point 500 3))]
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it "no rectangles" $ do
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let (Right r) = parseOnly (lineClippingsParser <* endOfInput) ""
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r `shouldBe` []
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it "just spaces" $ do
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let (Right r) = parseOnly lineClippingsParser " "
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r `shouldBe` []
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it "parsing specs" $ do
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let (Right r) = parseOnly lineClippingSpecsParser " 2/0,0,2,3/5 10/20,30,40,50/10"
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r `shouldBe` [ClippingSpec (PageNumber 2) (Rectangle (Point 5 5) (Point 0 0))
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(Rectangle (Point 0 0) (Point 7 8)),
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ClippingSpec (PageNumber 10) (Rectangle (Point 30 40) (Point 30 40))
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(Rectangle (Point 10 20) (Point 50 60))]
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it "full test" $ do
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runGEvalTest "clippeu-simple" `shouldReturnAlmost` 0.399999999999
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describe "evaluation metric specification is parsed" $ do
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it "for simple names" $ do
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let metrics = [RMSE, MSE, BLEU, Accuracy, ClippEU]
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let parsedMetrics = Prelude.map (read . show) metrics
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metrics `shouldBe` parsedMetrics
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it "for F-Measure" $ do
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read "F2" `shouldBe` (FMeasure 2.0)
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read "F1" `shouldBe` (FMeasure 1.0)
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read "F0.5" `shouldBe` (FMeasure 0.5)
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describe "test edit-distance library" $ do
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it "for handling UTF8" $ do
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levenshteinDistance defaultEditCosts "źdźbło" "źd好bło" `shouldBe` 1
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levenshteinDistance defaultEditCosts "źdźbło" "źdźcło" `shouldBe` 1
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describe "CharMatch" $ do
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it "simple test" $ do
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runGEvalTest "charmatch-simple" `shouldReturnAlmost` 0.3571428571428571
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it "perfect solution" $ do
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runGEvalTest "charmatch-perfect" `shouldReturnAlmost` 1.0
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it "more complex test" $ do
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runGEvalTest "charmatch-complex" `shouldReturnAlmost` 0.1923076923076923
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it "broken test without input" $ do
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runGEvalTest "charmatch-no-input" `shouldThrow` (== NoInputFile "test/charmatch-no-input/charmatch-no-input/test-A/in.tsv")
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describe "MAP" $ do
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it "one result" $ do
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(calculateMAPForOneResult ["Berlin", "London", "Warsaw"]
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["Warsaw", "Moscow", "Berlin", "Prague"]) `shouldBeAlmost` 0.55555555
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it "check whether you cannot cheat with duplicated results" $ do
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(calculateMAPForOneResult ["one", "two"]
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["one", "one"]) `shouldBeAlmost` 0.5
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it "simple test" $ do
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runGEvalTest "map-simple" `shouldReturnAlmost` 0.444444444
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describe "LogLoss" $ do
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it "simple" $ do
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runGEvalTest "logloss-simple" `shouldReturnAlmost` 0.31824
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it "perfect" $ do
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runGEvalTest "logloss-perfect" `shouldReturnAlmost` 0.0
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describe "Likelihood" $ do
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it "simple" $ do
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runGEvalTest "likelihood-simple" `shouldReturnAlmost` 0.72742818469866
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describe "evaluating single lines" $ do
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it "RMSE" $ do
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gevalCoreOnSingleLines RMSE (LineInFile (FilePathSpec "stub1") 1 "blabla")
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(LineInFile (FilePathSpec "stub2") 1 "3.4")
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(LineInFile (FilePathSpec "stub3") 1 "2.6") `shouldReturnAlmost` 0.8
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describe "BIO format" $ do
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it "just parse" $ do
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let (Right r) = parseOnly (bioSequenceParser <* endOfInput) "O B-city/NEW_YORK I-city B-city/KALISZ I-city O B-name"
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r `shouldBe` [Outside,
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Beginning "city" (Just "NEW_YORK"),
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Inside "city" Nothing,
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Beginning "city" (Just "KALISZ"),
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Inside "city" Nothing,
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Outside,
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Beginning "name" Nothing]
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it "simplest entity" $ do
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let (Right ents) = parseBioSequenceIntoEntities "B-city"
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ents `shouldBe` [TaggedEntity (TaggedSpan 1 1) "city" Nothing]
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it "multi-word entity" $ do
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let (Right ents) = parseBioSequenceIntoEntities "B-date I-date"
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ents `shouldBe` [TaggedEntity (TaggedSpan 1 2) "date" Nothing]
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it "multi-word entity with normalized text" $ do
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let (Right ents) = parseBioSequenceIntoEntities "B-date/FOO I-date/BAR"
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ents `shouldBe` [TaggedEntity (TaggedSpan 1 2) "date" (Just "FOO_BAR")]
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it "simplest entity with something outside" $ do
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let (Right ents) = parseBioSequenceIntoEntities "O B-city"
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ents `shouldBe` [TaggedEntity (TaggedSpan 2 2) "city" Nothing]
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it "another simple case" $ do
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let (Right ents) = parseBioSequenceIntoEntities "B-city B-city"
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ents `shouldBe` [TaggedEntity (TaggedSpan 1 1) "city" Nothing,
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TaggedEntity (TaggedSpan 2 2) "city" Nothing]
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it "just parse into entities" $ do
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let (Right ents) = parseBioSequenceIntoEntities "O O B-city/LOS_ANGELES I-city B-city/KLUCZBORK O B-name O B-person/JOHN I-person/VON I-person/NEUMANN"
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ents `shouldBe` [TaggedEntity (TaggedSpan 3 4) "city" (Just "LOS_ANGELES"),
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TaggedEntity (TaggedSpan 5 5) "city" (Just "KLUCZBORK"),
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TaggedEntity (TaggedSpan 7 7) "name" (Nothing),
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TaggedEntity (TaggedSpan 9 11) "person" (Just "JOHN_VON_NEUMANN")]
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it "another entity parse" $ do
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let (Right ents) = parseBioSequenceIntoEntities "B-month/JULY B-month/JULY O O B-foo/bar"
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ents `shouldBe` [TaggedEntity (TaggedSpan 1 1) "month" (Just "JULY"),
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TaggedEntity (TaggedSpan 2 2) "month" (Just "JULY"),
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TaggedEntity (TaggedSpan 5 5) "foo" (Just "bar")]
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it "another entity parse" $ do
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let (Right ents) = parseBioSequenceIntoEntities "B-city/LOS I-city/ANGELES O B-city/NEW I-city/YORK"
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ents `shouldBe` [TaggedEntity (TaggedSpan 1 2) "city" (Just "LOS_ANGELES"),
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TaggedEntity (TaggedSpan 4 5) "city" (Just "NEW_YORK")]
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it "parse entity" $ do
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let (Right ents) = parseBioSequenceIntoEntities "B-surname/BROWN B-surname/SMITH"
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ents `shouldBe` [TaggedEntity (TaggedSpan 1 1) "surname" (Just "BROWN"),
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TaggedEntity (TaggedSpan 2 2) "surname" (Just "SMITH")]
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it "parse entity" $ do
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let (Right ents) = parseBioSequenceIntoEntities "O B-surname/SMITH"
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ents `shouldBe` [TaggedEntity (TaggedSpan 2 2) "surname" (Just "SMITH")]
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it "check counting" $ do
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gatherCountsForBIO [TaggedEntity (TaggedSpan 2 2) "surname" (Just "SMITH")] [TaggedEntity (TaggedSpan 1 1) "surname" (Just "BROWN"),
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TaggedEntity (TaggedSpan 2 2) "surname" (Just "SMITH")] `shouldBe` (1, 1, 2)
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it "check F1 on a more complicated example" $ do
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runGEvalTest "bio-f1-complex" `shouldReturnAlmost` 0.625
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it "check F1 on labels only" $ do
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runGEvalTest "bio-f1-complex-labels" `shouldReturnAlmost` 0.6666666666
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it "calculate F1" $ do
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runGEvalTest "bio-f1-simple" `shouldReturnAlmost` 0.5
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it "calculate F1 with underscores rather than minus signs" $ do
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runGEvalTest "bio-f1-simple-underscores" `shouldReturnAlmost` 0.5
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it "check perfect score" $ do
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runGEvalTest "bio-f1-perfect" `shouldReturnAlmost` 1.0
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it "check inconsistent input" $ do
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runGEvalTest "bio-f1-error" `shouldThrow` (== UnexpectedData 2 "inconsistent label sequence `B-NAME/JOHN I-FOO/SMITH I-FOO/X`")
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describe "automatic decompression" $ do
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it "more complex test" $ do
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runGEvalTest "charmatch-complex-compressed" `shouldReturnAlmost` 0.1923076923076923
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describe "line by line mode" $ do
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let sampleChallenge =
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GEvalSpecification
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{ gesOutDirectory = "test/likelihood-simple/likelihood-simple-solution",
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gesExpectedDirectory = Just "test/likelihood-simple/likelihood-simple",
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gesTestName = "test-A",
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gesOutFile = "out.tsv",
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gesExpectedFile = "expected.tsv",
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gesInputFile = "in.tsv",
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gesMetrics = [Likelihood],
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gesPrecision = Nothing }
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it "simple test" $ do
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results <- runLineByLineGeneralized KeepTheOriginalOrder sampleChallenge Data.Conduit.List.consume
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Prelude.map (\(LineRecord inp _ _ _ _) -> inp) results `shouldBe` ["foo",
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"bar",
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"baz",
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"baq"]
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it "test sorting" $ do
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results <- runLineByLineGeneralized FirstTheWorst sampleChallenge Data.Conduit.List.consume
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Prelude.head (Prelude.map (\(LineRecord inp _ _ _ _) -> inp) results) `shouldBe` "baq"
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describe "handle --alt-metric option" $ do
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it "accuracy instead of likelihood" $ do
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runGEvalTestExtraOptions ["--alt-metric", "Accuracy"] "likelihood-simple" `shouldReturnAlmost` 0.75
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it "accuracy instead of log loss" $ do
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runGEvalTestExtraOptions ["--alt-metric", "Accuracy"] "log-loss-hashed-probs" `shouldReturnAlmost` 0.4
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describe "smart sources" $ do
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it "smart specs are obtained" $ do
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getSmartSourceSpec "foo" "" "" `shouldReturn` Left NoSpecGiven
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getSmartSourceSpec "foo" "out.tsv" "-" `shouldReturn` Right Stdin
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getSmartSourceSpec "foo" "out.sv" "http://gonito.net/foo" `shouldReturn` (Right $ Http "http://gonito.net/foo")
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getSmartSourceSpec "foo" "in.tsv" "https://gonito.net" `shouldReturn` (Right $ Https "https://gonito.net")
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it "sources are accessed" $ do
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readFromSmartSource "baz" "out.tsv" "test/files/foo.txt" `shouldReturn` ["foo\n"]
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readFromSmartSource "" "" "https://httpbin.org/robots.txt" `shouldReturn`
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["User-agent: *\nDisallow: /deny\n"]
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readFromSmartSource :: FilePath -> FilePath -> String -> IO [String]
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readFromSmartSource defaultDir defaultFile specS = do
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(Right spec) <- getSmartSourceSpec defaultDir defaultFile specS
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let source = smartSource spec
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contents <- runResourceT (source $$ CT.decodeUtf8Lenient =$ CL.consume)
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return $ Prelude.map unpack contents
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neverMatch :: Char -> Int -> Bool
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neverMatch _ _ = False
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alwaysMatch :: Char -> Int -> Bool
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alwaysMatch _ _ = True
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testMatchFun :: Char -> Int -> Bool
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testMatchFun 'a' 1 = True
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testMatchFun 'a' 2 = True
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testMatchFun 'a' 3 = True
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testMatchFun 'b' 1 = True
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testMatchFun 'c' 1 = True
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testMatchFun _ _ = False
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extractVal :: (Either (ParserResult GEvalOptions) (Maybe [MetricValue])) -> IO MetricValue
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extractVal (Right (Just (val:_))) = return val
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runGEvalTest = runGEvalTestExtraOptions []
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runGEvalTestExtraOptions extraOptions testName = (runGEval ([
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"--expected-directory",
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"test/" ++ testName ++ "/" ++ testName,
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"--out-directory",
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"test/" ++ testName ++ "/" ++ testName ++ "-solution"] ++ extraOptions)) >>= extractVal
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extractMetric :: String -> IO (Maybe Metric)
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extractMetric testName = do
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result <- getOptions ["--expected-directory", "test/" ++ testName ++ "/" ++ testName]
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return $ case result of
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Left _ -> Nothing
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Right opts -> Just $ gesMainMetric $ geoSpec opts
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class AEq a where
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(=~) :: a -> a -> Bool
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instance AEq Double where
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x =~ y = abs ( x - y ) < (1.0e-4 :: Double)
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(@=~?) :: (Show a, AEq a) => a -> a -> HU.Assertion
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(@=~?) actual expected = expected =~ actual HU.@? assertionMsg
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where
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assertionMsg = "Expected : " ++ show expected ++
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"\nActual : " ++ show actual
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shouldBeAlmost got expected = got @=~? expected
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shouldReturnAlmost :: (AEq a, Show a, Eq a) => IO a -> a -> Expectation
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shouldReturnAlmost action expected = action >>= (@=~? expected)
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