Trying to get references
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@ -90,6 +90,7 @@ library
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, integration
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, Chart
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, Chart-cairo
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, errors
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default-language: Haskell2010
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executable geval
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@ -3,7 +3,7 @@
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module GEval.Annotation
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(parseAnnotations, Annotation(..),
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parseObtainedAnnotations, ObtainedAnnotation(..),
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matchScore, getProbabilisticSoftCounts)
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matchScore, getProbabilisticSoftCounts, intSetParser)
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where
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import qualified Data.IntSet as IS
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@ -291,7 +291,8 @@ data GEvalSpecification = GEvalSpecification
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gesTokenizer :: Maybe Tokenizer,
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gesGonitoHost :: Maybe String,
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gesToken :: Maybe String,
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gesGonitoGitAnnexRemote :: Maybe String}
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gesGonitoGitAnnexRemote :: Maybe String,
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gesReferences :: Maybe String }
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gesMainMetric :: GEvalSpecification -> Metric
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@ -378,7 +379,8 @@ defaultGEvalSpecification = GEvalSpecification {
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gesTokenizer = Nothing,
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gesGonitoHost = Nothing,
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gesToken = Nothing,
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gesGonitoGitAnnexRemote = Nothing }
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gesGonitoGitAnnexRemote = Nothing,
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gesReferences = Nothing}
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isEmptyFile :: FilePath -> IO (Bool)
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isEmptyFile path = do
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@ -17,19 +17,32 @@ module GEval.FeatureExtractor
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ExistentialFactor(..),
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AtomicFactor(..),
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FeatureNamespace(..),
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References(..),
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ReferencesData(..),
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filterExistentialFactors)
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where
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import Data.Text
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import Data.List
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import Data.Monoid ((<>))
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import Data.Maybe (catMaybes)
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import Data.Maybe (catMaybes, fromMaybe)
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import Text.Tokenizer
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import Text.WordShape
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import GEval.BlackBoxDebugging
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import GEval.Common
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import Text.Read (readMaybe)
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import Control.Error.Util (hush)
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import Data.Attoparsec.Text
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import Data.Attoparsec.Combinator
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import Control.Applicative
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import qualified Data.HashMap.Strict as H
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import GEval.Annotation
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import qualified Data.IntSet as IS
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data Feature = UnaryFeature PeggedExistentialFactor
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| CartesianFeature PeggedExistentialFactor PeggedExistentialFactor
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| NumericalFeature FeatureNamespace NumericalType NumericalDirection
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@ -124,6 +137,38 @@ instance Show FeatureNamespace where
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show (FeatureNamespace namespace) = unpack namespace
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show (FeatureTabbedNamespace namespace column) = ((unpack namespace) ++ "<" ++ (show column) ++ ">")
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data References = References (H.HashMap Integer Text)
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data ReferencesData = ReferencesData {
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referencesDataReferences :: References,
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referencesDataCurrentId :: Maybe Integer }
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data ReferencePointer = ReferencePointer Integer IS.IntSet
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getReferenced :: References -> ReferencePointer -> Maybe Text
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getReferenced (References references) (ReferencePointer refId indexSet) = case H.lookup refId references of
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Just t -> Just (getFrag t indexSet)
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Nothing -> Nothing
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getDirectOrReferenced :: Maybe References -> Text -> Text
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getDirectOrReferenced Nothing record = record
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getDirectOrReferenced (Just references) record = case parseReferencePointer record of
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Just pointer -> fromMaybe record (getReferenced references pointer)
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Nothing -> record
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getFrag :: Text -> IS.IntSet -> Text
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getFrag t indexSet = pack $ Data.List.map (\ix -> index t ix) $ IS.toAscList indexSet
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parseReferencePointer :: Text -> Maybe ReferencePointer
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parseReferencePointer t = hush $ parseOnly (referencePointerParser <* endOfInput) t
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referencePointerParser :: Parser ReferencePointer
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referencePointerParser = do
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refId <- decimal
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string " "
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indexSet <- intSetParser
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return $ ReferencePointer refId indexSet
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tokenizeForFactors :: (Maybe Tokenizer) -> Text -> [Text]
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tokenizeForFactors Nothing t = Data.List.filter (not . Data.Text.null) $ split splitPred t
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where splitPred c = c == ' ' || c == '\t' || c == ':'
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@ -150,19 +195,19 @@ extractSimpleFactors mTokenizer bbdo t = Data.List.concat $ (Prelude.map (Prelud
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numericalFactor t = [NumericalFactor (readMaybe $ unpack t) (Data.Text.length t)]
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extractFactorsFromField :: (Maybe Tokenizer) -> BlackBoxDebuggingOptions -> FeatureNamespace -> Text -> [PeggedFactor]
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extractFactorsFromField mTokenizer bbdo namespace record =
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extractFactorsFromField :: (Maybe Tokenizer) -> BlackBoxDebuggingOptions -> Maybe ReferencesData -> FeatureNamespace -> Text -> [PeggedFactor]
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extractFactorsFromField mTokenizer bbdo mReferenceData namespace record =
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Prelude.map (\af -> PeggedFactor namespace af)
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$ extractSimpleFactors mTokenizer bbdo record
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$ extractSimpleFactors mTokenizer bbdo (getDirectOrReferenced (referencesDataReferences <$> mReferenceData) record)
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extractFactors :: (Maybe Tokenizer) -> BlackBoxDebuggingOptions -> Text -> Text -> [PeggedFactor]
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extractFactors mTokenizer bbdo namespace record =
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extractFactorsFromField mTokenizer bbdo (FeatureNamespace namespace) record
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extractFactorsFromTabbed :: (Maybe Tokenizer) -> BlackBoxDebuggingOptions -> Text -> Text -> [PeggedFactor]
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extractFactorsFromTabbed mTokenizer bbdo namespace record =
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extractFactors :: (Maybe Tokenizer) -> BlackBoxDebuggingOptions -> Maybe ReferencesData -> Text -> Text -> [PeggedFactor]
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extractFactors mTokenizer bbdo mReferencesData namespace record = extractFactorsFromField mTokenizer bbdo mReferencesData (FeatureNamespace namespace) record
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extractFactorsFromTabbed :: (Maybe Tokenizer) -> BlackBoxDebuggingOptions -> Maybe ReferencesData -> Text -> Text -> [PeggedFactor]
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extractFactorsFromTabbed mTokenizer bbdo mReferencesData namespace record =
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Data.List.concat
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$ Prelude.map (\(n, t) -> extractFactorsFromField mTokenizer bbdo (FeatureTabbedNamespace namespace n) t)
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$ Prelude.map (\(n, t) -> extractFactorsFromField mTokenizer bbdo mReferencesData (FeatureTabbedNamespace namespace n) t)
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$ Prelude.zip [1..] (splitOn "\t" record)
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addCartesianFactors :: BlackBoxDebuggingOptions -> [LineWithPeggedFactors] -> [LineWithFactors]
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@ -61,16 +61,33 @@ import Statistics.Distribution (cumulative)
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import Statistics.Distribution.Normal (normalDistr)
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import Data.Statistics.Kendall (kendallZ)
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import Data.Conduit.Binary (sourceFile)
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import qualified Data.HashMap.Strict as H
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import qualified Data.Map.Strict as M
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import qualified Data.Set as S
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data LineRecord = LineRecord Text Text Text Word32 MetricValue
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deriving (Eq, Show)
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readReferences :: FilePath -> IO References
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readReferences referencesFilePath = do
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h <- runResourceT $ runConduit $ (sourceFile referencesFilePath
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.| CC.decodeUtf8Lenient
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.| CT.lines
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.| CC.map parseReferenceEntry
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.| CC.foldl (\h (refId, t) -> H.insert refId t h) H.empty)
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return $ References h
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parseReferenceEntry :: Text -> (Integer, Text)
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parseReferenceEntry line = (read $ unpack refId, t)
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where [refId, t] = splitOn "\t" line
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runLineByLine :: ResultOrdering -> Maybe String -> GEvalSpecification -> BlackBoxDebuggingOptions -> IO ()
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runLineByLine ordering featureFilter spec bbdo = runLineByLineGeneralized ordering spec consum
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where consum :: ConduitT LineRecord Void (ResourceT IO) ()
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consum = (runFeatureFilter featureFilter spec bbdo .| CL.map (encodeUtf8 . formatOutput) .| CC.unlinesAscii .| CC.stdout)
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where consum :: Maybe References -> ConduitT LineRecord Void (ResourceT IO) ()
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consum = (\mReferences -> (runFeatureFilter featureFilter spec bbdo mReferences .| CL.map (encodeUtf8 . formatOutput) .| CC.unlinesAscii .| CC.stdout))
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formatOutput (LineRecord inp exp out _ score) = Data.Text.intercalate "\t" [
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formatScore score,
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escapeTabs inp,
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@ -79,25 +96,25 @@ runLineByLine ordering featureFilter spec bbdo = runLineByLineGeneralized orderi
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formatScore :: MetricValue -> Text
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formatScore = Data.Text.pack . printf "%f"
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runFeatureFilter :: (Monad m, FeatureSource s) => Maybe String -> GEvalSpecification -> BlackBoxDebuggingOptions -> ConduitT s s m ()
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runFeatureFilter Nothing _ _ = doNothing
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runFeatureFilter (Just feature) spec bbdo = CC.map (\l -> (fakeRank, l))
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.| featureExtractor mTokenizer bbdo
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.| CC.filter (checkFeature feature)
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.| CC.map fst
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runFeatureFilter :: (Monad m, FeatureSource s) => Maybe String -> GEvalSpecification -> BlackBoxDebuggingOptions -> Maybe References -> ConduitT s s m ()
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runFeatureFilter Nothing _ _ _ = doNothing
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runFeatureFilter (Just feature) spec bbdo mReferences = CC.map (\l -> (fakeRank, l))
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.| featureExtractor mTokenizer bbdo mReferences
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.| CC.filter (checkFeature feature)
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.| CC.map fst
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where mTokenizer = gesTokenizer spec
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fakeRank = 0.0
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checkFeature feature (_, LineWithFactors _ _ fs) = feature `elem` (Prelude.map show fs)
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runWorstFeatures :: ResultOrdering -> GEvalSpecification -> BlackBoxDebuggingOptions -> IO ()
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runWorstFeatures ordering spec bbdo = runLineByLineGeneralized ordering' spec (worstFeaturesPipeline False spec bbdo)
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runWorstFeatures ordering spec bbdo = runLineByLineGeneralized ordering' spec (\mReferences -> worstFeaturesPipeline False spec bbdo mReferences)
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where ordering' = forceSomeOrdering ordering
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worstFeaturesPipeline :: Bool -> GEvalSpecification -> BlackBoxDebuggingOptions -> ConduitT LineRecord Void (ResourceT IO) ()
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worstFeaturesPipeline reversed spec bbdo = rank (lessByMetric reversed $ gesMainMetric spec)
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.| evalStateC 0 (extractFeaturesAndPValues spec bbdo)
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worstFeaturesPipeline :: Bool -> GEvalSpecification -> BlackBoxDebuggingOptions -> Maybe References -> ConduitT LineRecord Void (ResourceT IO) ()
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worstFeaturesPipeline reversed spec bbdo mReferences = rank (lessByMetric reversed $ gesMainMetric spec)
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.| evalStateC 0 (extractFeaturesAndPValues spec bbdo mReferences)
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.| CC.filter (\(FeatureWithPValue _ p _ _) -> not $ isNaN p) -- NaN values would poison sorting
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.| gobbleAndDo (sortBy featureOrder)
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.| filtreCartesian (bbdoCartesian bbdo)
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@ -120,10 +137,10 @@ forceSomeOrdering :: ResultOrdering -> ResultOrdering
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forceSomeOrdering FirstTheBest = FirstTheBest
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forceSomeOrdering _ = FirstTheWorst
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extractFeaturesAndPValues :: Monad m => GEvalSpecification -> BlackBoxDebuggingOptions -> ConduitT (Double, LineRecord) FeatureWithPValue (StateT Integer m) ()
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extractFeaturesAndPValues spec bbdo =
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extractFeaturesAndPValues :: Monad m => GEvalSpecification -> BlackBoxDebuggingOptions -> Maybe References -> ConduitT (Double, LineRecord) FeatureWithPValue (StateT Integer m) ()
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extractFeaturesAndPValues spec bbdo mReferences =
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totalCounter
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.| rankedFeatureExtractor spec bbdo
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.| rankedFeatureExtractor spec bbdo mReferences
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.| uScoresCounter (bbdoMinFrequency bbdo)
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@ -143,11 +160,11 @@ formatFeatureWithPValue (FeatureWithPValue f p avg c) =
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(pack $ printf "%0.8f" avg),
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(pack $ printf "%0.20f" p)]
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rankedFeatureExtractor :: Monad m => GEvalSpecification -> BlackBoxDebuggingOptions -> ConduitT (Double, LineRecord) RankedFactor m ()
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rankedFeatureExtractor spec bbdo = featureExtractor mTokenizer bbdo
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.| CC.map snd
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.| CC.map unwrapFeatures
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.| CC.concat
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rankedFeatureExtractor :: Monad m => GEvalSpecification -> BlackBoxDebuggingOptions -> Maybe References -> ConduitT (Double, LineRecord) RankedFactor m ()
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rankedFeatureExtractor spec bbdo mReferences = featureExtractor mTokenizer bbdo mReferences
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.| CC.map snd
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.| CC.map unwrapFeatures
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.| CC.concat
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where mTokenizer = gesTokenizer spec
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unwrapFeatures (LineWithFactors rank score fs) = Prelude.map (\f -> RankedFactor f rank score) fs
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@ -163,11 +180,11 @@ instance FeatureSource (LineRecord, LineRecord) where
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getScore (LineRecord _ _ _ _ scoreA, LineRecord _ _ _ _ scoreB) = scoreB - scoreA
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mainLineRecord (_, l) = l
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featureExtractor :: (Monad m, FeatureSource s) => Maybe Tokenizer -> BlackBoxDebuggingOptions -> ConduitT (Double, s) (s, LineWithFactors) m ()
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featureExtractor mTokenizer bbdo = CC.map extract
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.| finalFeatures (bbdoCartesian bbdo) (fromMaybe (bbdoMinFrequency bbdo) (bbdoMinCartesianFrequency bbdo))
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featureExtractor :: (Monad m, FeatureSource s) => Maybe Tokenizer -> BlackBoxDebuggingOptions -> Maybe References -> ConduitT (Double, s) (s, LineWithFactors) m ()
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featureExtractor mTokenizer bbdo mReferences = CC.map extract
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.| finalFeatures (bbdoCartesian bbdo) (fromMaybe (bbdoMinFrequency bbdo) (bbdoMinCartesianFrequency bbdo))
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where extract (rank, line) =
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(line, LineWithPeggedFactors rank (getScore line) $ getFeatures mTokenizer bbdo (mainLineRecord line))
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(line, LineWithPeggedFactors rank (getScore line) $ getFeatures mTokenizer bbdo mReferences (mainLineRecord line))
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finalFeatures :: Monad m => Bool -> Integer -> ConduitT (a, LineWithPeggedFactors) (a, LineWithFactors) m ()
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finalFeatures False _ = CC.map (\(l, p) -> (l, peggedToUnaryLine p))
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@ -199,12 +216,17 @@ filtreCartesian True = CC.concatMapAccum step S.empty
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peggedToUnaryLine :: LineWithPeggedFactors -> LineWithFactors
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peggedToUnaryLine (LineWithPeggedFactors rank score fs) = LineWithFactors rank score (Prelude.map UnaryFactor fs)
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getFeatures :: Maybe Tokenizer -> BlackBoxDebuggingOptions -> LineRecord -> [PeggedFactor]
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getFeatures mTokenizer bbdo (LineRecord inLine expLine outLine _ _) =
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getFeatures :: Maybe Tokenizer -> BlackBoxDebuggingOptions -> Maybe References -> LineRecord -> [PeggedFactor]
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getFeatures mTokenizer bbdo mReferences (LineRecord inLine expLine outLine _ _) =
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Data.List.concat [
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extractFactors mTokenizer bbdo "exp" expLine,
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extractFactorsFromTabbed mTokenizer bbdo "in" inLine,
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extractFactors mTokenizer bbdo "out" outLine]
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extractFactors mTokenizer bbdo mReferencesData "exp" expLine,
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extractFactorsFromTabbed mTokenizer bbdo mReferencesData "in" inLine,
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extractFactors mTokenizer bbdo mReferencesData "out" outLine]
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where mReferencesData = case mReferences of
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Just references -> Just $ ReferencesData {
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referencesDataReferences = references,
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referencesDataCurrentId = Nothing }
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Nothing -> Nothing
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data FeatureAggregate = ExistentialFactorAggregate Double MetricValue Integer
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| NumericalValueAggregate [Double] [MetricValue] [Int] [MetricValue]
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@ -327,10 +349,15 @@ lessByMetric reversed metric = lessByMetric' reversed (getMetricOrdering metric)
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(\(LineRecord _ _ _ _ scoreA) (LineRecord _ _ _ _ scoreB) ->
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scoreA < scoreB)
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runLineByLineGeneralized :: ResultOrdering -> GEvalSpecification -> ConduitT LineRecord Void (ResourceT IO) a -> IO a
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runLineByLineGeneralized :: ResultOrdering -> GEvalSpecification -> (Maybe References -> ConduitT LineRecord Void (ResourceT IO) a) -> IO a
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runLineByLineGeneralized ordering spec consum = do
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mReferences <- case gesReferences spec of
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Just referencesFp -> do
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references <- readReferences referencesFp
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return $ Just references
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Nothing -> return Nothing
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(inputFilePath, expectedFilePath, outFilePath) <- checkAndGetFilesSingleOut True spec
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gevalLineByLineCore metric mSelector preprocess inputFilePath expectedFilePath outFilePath (sorter ordering .| consum)
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gevalLineByLineCore metric mSelector preprocess inputFilePath expectedFilePath outFilePath (sorter ordering .| consum mReferences)
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where metric = gesMainMetric spec
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mSelector = gesSelector spec
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preprocess = gesPreprocess spec
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@ -340,6 +367,7 @@ runLineByLineGeneralized ordering spec consum = do
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sortOrder FirstTheBest TheLowerTheBetter = compareScores
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sortOrder _ _ = flip compareScores
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compareScores (LineRecord _ _ _ _ s1) (LineRecord _ _ _ _ s2) = s1 `compare` s2
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mReferences = Nothing
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gobbleAndDo :: Monad m => ([a] -> [b]) -> ConduitT a b m ()
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gobbleAndDo fun = do
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@ -348,12 +376,12 @@ gobbleAndDo fun = do
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runDiff :: ResultOrdering -> Maybe String -> FilePath -> GEvalSpecification -> BlackBoxDebuggingOptions -> IO ()
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runDiff ordering featureFilter otherOut spec bbdo = runDiffGeneralized ordering otherOut spec consum
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where consum :: ConduitT (LineRecord, LineRecord) Void (ResourceT IO) ()
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consum = CL.filter shouldBeShown
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.| runFeatureFilter featureFilter spec bbdo
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.| CL.map (encodeUtf8 . formatOutput)
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.| CC.unlinesAscii
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.| CC.stdout
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where consum :: Maybe References -> ConduitT (LineRecord, LineRecord) Void (ResourceT IO) ()
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consum = \mReferences -> CL.filter shouldBeShown
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.| runFeatureFilter featureFilter spec bbdo mReferences
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.| CL.map (encodeUtf8 . formatOutput)
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.| CC.unlinesAscii
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.| CC.stdout
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shouldBeShown (LineRecord _ _ outA _ scoreA, LineRecord _ _ outB _ scoreB) =
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outA /= outB && scoreA /= scoreB
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formatOutput (LineRecord inp exp outA _ scoreA, LineRecord _ _ outB _ scoreB) = Data.Text.intercalate "\t" [
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@ -366,21 +394,22 @@ runDiff ordering featureFilter otherOut spec bbdo = runDiffGeneralized ordering
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formatScoreDiff = Data.Text.pack . printf "%f"
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runMostWorseningFeatures :: ResultOrdering -> FilePath -> GEvalSpecification -> BlackBoxDebuggingOptions -> IO ()
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runMostWorseningFeatures ordering otherOut spec bbdo = runDiffGeneralized ordering' otherOut spec consum
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runMostWorseningFeatures ordering otherOut spec bbdo = runDiffGeneralized ordering' otherOut spec consum
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where ordering' = forceSomeOrdering ordering
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reversed = case ordering of
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KeepTheOriginalOrder -> False
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FirstTheWorst -> False
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FirstTheBest -> True
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consum :: ConduitT (LineRecord, LineRecord) Void (ResourceT IO) ()
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consum = CC.map prepareFakeLineRecord
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.| (worstFeaturesPipeline reversed spec bbdo)
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consum :: Maybe References -> ConduitT (LineRecord, LineRecord) Void (ResourceT IO) ()
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consum = \mReferences -> CC.map prepareFakeLineRecord
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.| (worstFeaturesPipeline reversed spec bbdo mReferences)
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prepareFakeLineRecord :: (LineRecord, LineRecord) -> LineRecord
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prepareFakeLineRecord (LineRecord _ _ _ _ scorePrev, LineRecord inp exp out c score) =
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LineRecord inp exp out c (score - scorePrev)
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mReferences = Nothing
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runDiffGeneralized :: ResultOrdering -> FilePath -> GEvalSpecification -> ConduitT (LineRecord, LineRecord) Void (ResourceT IO) a -> IO a
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runDiffGeneralized :: ResultOrdering -> FilePath -> GEvalSpecification -> (Maybe References -> ConduitT (LineRecord, LineRecord) Void (ResourceT IO) a) -> IO a
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runDiffGeneralized ordering otherOut spec consum = do
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(inputSource, expectedSource, outSource) <- checkAndGetFilesSingleOut True spec
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ooss <- getSmartSourceSpec ((gesOutDirectory spec) </> (gesTestName spec)) "out.tsv" otherOut
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@ -394,7 +423,7 @@ runDiffGeneralized ordering otherOut spec consum = do
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runResourceT $ runConduit $
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((getZipSource $ (,)
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<$> ZipSource sourceA
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<*> ZipSource sourceB) .| sorter ordering .| consum)
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<*> ZipSource sourceB) .| sorter ordering .| consum mReferences)
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where metric = gesMainMetric spec
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preprocess = gesPreprocess spec
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mSelector = gesSelector spec
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@ -406,6 +435,7 @@ runDiffGeneralized ordering otherOut spec consum = do
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compareScores ((LineRecord _ _ _ _ o1), (LineRecord _ _ _ _ n1))
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((LineRecord _ _ _ _ o2), (LineRecord _ _ _ _ n2))
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= (n1 - o1) `compare` (n2 - o2)
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mReferences = Nothing
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escapeTabs :: Text -> Text
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@ -177,6 +177,12 @@ specParser = GEvalSpecification
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<> help "Submit ONLY: Specification of a git-annex remote."
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)
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)
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<*> ( optional . strOption $
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( long "references"
|
||||
<> metavar "FILE"
|
||||
<> help "External text file referenced"
|
||||
)
|
||||
)
|
||||
|
||||
defaultMinFrequency :: Integer
|
||||
defaultMinFrequency = 1
|
||||
|
||||
@ -401,15 +401,16 @@ main = hspec $ do
|
||||
gesTokenizer = Nothing,
|
||||
gesGonitoHost = Nothing,
|
||||
gesToken = Nothing,
|
||||
gesGonitoGitAnnexRemote = Nothing}
|
||||
gesGonitoGitAnnexRemote = Nothing,
|
||||
gesReferences = Nothing }
|
||||
it "simple test" $ do
|
||||
results <- runLineByLineGeneralized KeepTheOriginalOrder sampleChallenge Data.Conduit.List.consume
|
||||
results <- runLineByLineGeneralized KeepTheOriginalOrder sampleChallenge (const Data.Conduit.List.consume)
|
||||
Prelude.map (\(LineRecord inp _ _ _ _) -> inp) results `shouldBe` ["foo",
|
||||
"bar",
|
||||
"baz",
|
||||
"baq"]
|
||||
it "test sorting" $ do
|
||||
results <- runLineByLineGeneralized FirstTheWorst sampleChallenge Data.Conduit.List.consume
|
||||
results <- runLineByLineGeneralized FirstTheWorst sampleChallenge (const Data.Conduit.List.consume)
|
||||
Prelude.head (Prelude.map (\(LineRecord inp _ _ _ _) -> inp) results) `shouldBe` "baq"
|
||||
describe "handle --alt-metric option" $ do
|
||||
it "accuracy instead of likelihood" $ do
|
||||
@ -546,7 +547,7 @@ main = hspec $ do
|
||||
bbdoCartesian = False,
|
||||
bbdoMinCartesianFrequency = Nothing,
|
||||
bbdoConsiderNumericalFeatures = True }
|
||||
(sort $ extractFactorsFromTabbed Nothing bbdo "in" "I like this\t34.3\ttests") `shouldBe` [
|
||||
(sort $ extractFactorsFromTabbed Nothing bbdo Nothing "in" "I like this\t34.3\ttests") `shouldBe` [
|
||||
PeggedFactor (FeatureTabbedNamespace "in" 1)
|
||||
(SimpleExistentialFactor (SimpleAtomicFactor (TextFactor "I"))),
|
||||
PeggedFactor (FeatureTabbedNamespace "in" 1)
|
||||
|
||||
Loading…
Reference in New Issue
Block a user