first tokenizer
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@ -39,7 +39,8 @@ module GEval.Core
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checkAndGetFilesSingleOut,
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checkMultipleOuts,
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checkMultipleOutsCore,
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gesMainMetric
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gesMainMetric,
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gesPreprocess
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) where
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import Data.Conduit
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@ -222,6 +223,9 @@ gesMainMetric spec = case gesMetrics spec of
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(metric:_) -> metric
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otherwise -> error "no metric given"
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gesPreprocess :: GEvalSpecification -> (Text -> Text)
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gesPreprocess spec = tokenizeTabSeparatedWithSpaces (gesTokenizer spec)
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getExpectedDirectory :: GEvalSpecification -> FilePath
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getExpectedDirectory spec = fromMaybe outDirectory $ gesExpectedDirectory spec
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where outDirectory = gesOutDirectory spec
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@ -295,7 +299,7 @@ isEmptyFile path = do
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return ((fileSize stat) == 0)
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data LineSource m = LineSource (ConduitT () Text m ()) SourceSpec Word32
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data LineSource m = LineSource (ConduitT () Text m ()) (Text -> Text) SourceSpec Word32
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geval :: GEvalSpecification -> IO [(SourceSpec, [MetricValue])]
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geval gevalSpec = do
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@ -305,9 +309,10 @@ geval gevalSpec = do
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gevalOnSingleOut :: GEvalSpecification -> SourceSpec -> SourceSpec -> SourceSpec -> IO (SourceSpec, [MetricValue])
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gevalOnSingleOut gevalSpec inputSource expectedSource outSource = do
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vals <- Prelude.mapM (\metric -> gevalCore metric inputSource expectedSource outSource) metrics
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vals <- Prelude.mapM (\metric -> gevalCore metric preprocess inputSource expectedSource outSource) metrics
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return (outSource, vals)
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where metrics = gesMetrics gevalSpec
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preprocess = gesPreprocess gevalSpec
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checkAndGetFilesSingleOut :: Bool -> GEvalSpecification -> IO (SourceSpec, SourceSpec, SourceSpec)
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checkAndGetFilesSingleOut forceInput gevalSpec = do
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@ -394,35 +399,36 @@ getInputSourceIfNeeded forced metrics directory inputFilePath
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Right sourceSpec -> return sourceSpec
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| otherwise = return NoSource
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fileAsLineSource :: SourceSpec -> LineSource (ResourceT IO)
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fileAsLineSource spec =
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LineSource ((smartSource spec) $= autoDecompress $= CT.decodeUtf8Lenient =$= CT.lines) spec 1
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fileAsLineSource :: SourceSpec -> (Text -> Text) -> LineSource (ResourceT IO)
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fileAsLineSource spec preprocess =
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LineSource ((smartSource spec) $= autoDecompress $= CT.decodeUtf8Lenient =$= CT.lines) preprocess spec 1
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gevalCoreOnSingleLines :: Metric -> LineInFile -> LineInFile -> LineInFile -> IO (MetricValue)
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gevalCoreOnSingleLines metric inpLine expLine outLine =
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gevalCoreOnSources metric (singleLineAsLineSource inpLine)
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(singleLineAsLineSource expLine)
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(singleLineAsLineSource outLine)
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gevalCoreOnSingleLines :: Metric -> (Text -> Text) -> LineInFile -> LineInFile -> LineInFile -> IO (MetricValue)
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gevalCoreOnSingleLines metric preprocess inpLine expLine outLine =
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gevalCoreOnSources metric (singleLineAsLineSource inpLine preprocess)
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(singleLineAsLineSource expLine preprocess)
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(singleLineAsLineSource outLine preprocess)
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singleLineAsLineSource :: LineInFile -> LineSource (ResourceT IO)
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singleLineAsLineSource (LineInFile sourceSpec lineNo line) =
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LineSource (CL.sourceList [line]) sourceSpec lineNo
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singleLineAsLineSource :: LineInFile -> (Text -> Text) -> LineSource (ResourceT IO)
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singleLineAsLineSource (LineInFile sourceSpec lineNo line) preprocess =
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LineSource (CL.sourceList [line]) preprocess sourceSpec lineNo
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-- | Runs evaluation for a given metric using the sources specified
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-- for input, expected output and output. Returns the metric value.
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-- Throws @GEvalException@ if something was wrong in the data (e.g.
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-- inconsistent number of lines in the sources).
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gevalCore :: Metric -- ^ evaluation metric
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-> (Text -> Text) -- ^ preprocessing function (e.g. tokenization)
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-> SourceSpec -- ^ source specification for the input values
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-> SourceSpec -- ^ source specification for the expected output
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-> SourceSpec -- ^ source specification for the output
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-> IO (MetricValue) -- ^ metric value for the output against the expected output
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gevalCore metric inputSource expectedSource outSource = do
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gevalCore metric preprocess inputSource expectedSource outSource = do
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whenM (isEmptyFileSource outSource) $ throwM $ EmptyOutput
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gevalCoreOnSources metric
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(fileAsLineSource inputSource)
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(fileAsLineSource expectedSource)
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(fileAsLineSource outSource)
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(fileAsLineSource inputSource preprocess)
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(fileAsLineSource expectedSource preprocess)
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(fileAsLineSource outSource preprocess)
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isEmptyFileSource :: SourceSpec -> IO Bool
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isEmptyFileSource (FilePathSpec filePath) = isEmptyFile filePath
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@ -690,9 +696,9 @@ instance (MonadUnliftIO m, MonadIO m, MonadThrow m) => EvaluationContext (Withou
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data ParserSpec (WithoutInput m e o) = ParserSpecWithoutInput (Text -> Either String e) (Text -> Either String o)
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data WrappedParsedRecord (WithoutInput m e o) = WrappedParsedRecordWithoutInput (SourceItem e) (SourceItem o)
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data ParsedRecord (WithoutInput m e o) = ParsedRecordWithoutInput e o
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getFirstLineNo _ (WithoutInput _ (LineSource _ _ lineNo)) = lineNo
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getExpectedSource (WithoutInput (LineSource _ expectedSource _) _) = expectedSource
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getOutSource (WithoutInput _ (LineSource _ outSource _)) = outSource
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getFirstLineNo _ (WithoutInput _ (LineSource _ _ _ lineNo)) = lineNo
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getExpectedSource (WithoutInput (LineSource _ _ expectedSource _) _) = expectedSource
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getOutSource (WithoutInput _ (LineSource _ _ outSource _)) = outSource
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recordSource (WithoutInput expectedLineSource outLineSource) (ParserSpecWithoutInput expParser outParser) = getZipSource $ WrappedParsedRecordWithoutInput
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<$> ZipSource (items expectedLineSource expParser)
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<*> ZipSource (items outLineSource outParser)
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@ -713,15 +719,15 @@ instance (MonadUnliftIO m, MonadIO m, MonadThrow m) => EvaluationContext (Withou
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data WithInput m i e o = WithInput (LineSource (ResourceT m)) (LineSource (ResourceT m)) (LineSource (ResourceT m))
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getInputFilePath (WithInput (LineSource _ inputFilePath _) _ _) = inputFilePath
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getInputFilePath (WithInput (LineSource _ _ inputFilePath _) _ _) = inputFilePath
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instance (MonadUnliftIO m, MonadIO m, MonadThrow m) => EvaluationContext (WithInput m i e o) m where
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data ParserSpec (WithInput m i e o) = ParserSpecWithInput (Text -> Either String i) (Text -> Either String e) (Text -> Either String o)
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data WrappedParsedRecord (WithInput m i e o) = WrappedParsedRecordWithInput (SourceItem i) (SourceItem e) (SourceItem o)
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data ParsedRecord (WithInput m i e o) = ParsedRecordWithInput i e o
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getFirstLineNo _ (WithInput _ _ (LineSource _ _ lineNo)) = lineNo
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getExpectedSource (WithInput _ (LineSource _ expectedSource _) _) = expectedSource
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getOutSource (WithInput _ _ (LineSource _ outSource _)) = outSource
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getFirstLineNo _ (WithInput _ _ (LineSource _ _ _ lineNo)) = lineNo
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getExpectedSource (WithInput _ (LineSource _ _ expectedSource _) _) = expectedSource
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getOutSource (WithInput _ _ (LineSource _ _ outSource _)) = outSource
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recordSource (WithInput inputLineSource expectedLineSource outLineSource) (ParserSpecWithInput inpParser expParser outParser) = getZipSource $ (\x (y,z) -> WrappedParsedRecordWithInput x y z)
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<$> ZipSource (items inputLineSource inpParser) <*> (ZipSource $ getZipSource $ (,)
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<$> ZipSource (items expectedLineSource expParser)
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@ -756,8 +762,8 @@ averageC = getZipSink
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<*> ZipSink CC.length
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items :: MonadResource m => LineSource m -> (Text -> Either String a) -> ConduitT () (SourceItem a) m ()
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items (LineSource lineSource _ _) parser =
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(lineSource =$= CL.map (toItem . parser)) >> yield Done
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items (LineSource lineSource preprocess _ _) parser =
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(lineSource =$= CL.map (toItem . parser . preprocess)) >> yield Done
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where toItem (Right x) = Got x
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toItem (Left m) = Wrong m
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@ -192,8 +192,9 @@ lessByMetric reversed metric = lessByMetric' reversed (getMetricOrdering metric)
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runLineByLineGeneralized :: ResultOrdering -> GEvalSpecification -> ConduitT LineRecord Void (ResourceT IO) a -> IO a
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runLineByLineGeneralized ordering spec consum = do
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(inputFilePath, expectedFilePath, outFilePath) <- checkAndGetFilesSingleOut True spec
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gevalLineByLineCore metric inputFilePath expectedFilePath outFilePath (sorter ordering .| consum)
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gevalLineByLineCore metric preprocess inputFilePath expectedFilePath outFilePath (sorter ordering .| consum)
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where metric = gesMainMetric spec
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preprocess = gesPreprocess spec
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sorter KeepTheOriginalOrder = doNothing
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sorter ordering = gobbleAndDo $ sortBy (sortOrder ordering (getMetricOrdering metric))
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sortOrder FirstTheWorst TheHigherTheBetter = compareScores
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@ -245,13 +246,14 @@ runDiffGeneralized ordering otherOut spec consum = do
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Left (NoFile fp) -> throwM $ NoOutFile fp
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Left (NoDirectory d) -> throwM $ NoOutFile otherOut
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Right otherOutSource -> do
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let sourceA = gevalLineByLineSource metric inputSource expectedSource otherOutSource
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let sourceB = gevalLineByLineSource metric inputSource expectedSource outSource
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let sourceA = gevalLineByLineSource metric preprocess inputSource expectedSource otherOutSource
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let sourceB = gevalLineByLineSource metric preprocess inputSource expectedSource outSource
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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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where metric = gesMainMetric spec
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preprocess = gesPreprocess spec
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sorter KeepTheOriginalOrder = doNothing
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sorter ordering = gobbleAndDo $ sortBy (sortOrder ordering (getMetricOrdering metric))
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sortOrder FirstTheWorst TheHigherTheBetter = compareScores
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@ -265,24 +267,24 @@ runDiffGeneralized ordering otherOut spec consum = do
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escapeTabs :: Text -> Text
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escapeTabs = Data.Text.replace "\t" "<tab>"
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gevalLineByLineCore :: Metric -> SourceSpec -> SourceSpec -> SourceSpec -> ConduitT LineRecord Void (ResourceT IO) a -> IO a
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gevalLineByLineCore metric inputSource expectedSource outSource consum =
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gevalLineByLineCore :: Metric -> (Text -> Text) -> SourceSpec -> SourceSpec -> SourceSpec -> ConduitT LineRecord Void (ResourceT IO) a -> IO a
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gevalLineByLineCore metric preprocess inputSource expectedSource outSource consum =
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runResourceT $ runConduit $
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((gevalLineByLineSource metric inputSource expectedSource outSource) .| consum)
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((gevalLineByLineSource metric preprocess inputSource expectedSource outSource) .| consum)
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gevalLineByLineSource :: Metric -> SourceSpec -> SourceSpec -> SourceSpec -> ConduitT () LineRecord (ResourceT IO) ()
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gevalLineByLineSource metric inputSource expectedSource outSource =
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gevalLineByLineSource :: Metric -> (Text -> Text) -> SourceSpec -> SourceSpec -> SourceSpec -> ConduitT () LineRecord (ResourceT IO) ()
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gevalLineByLineSource metric preprocess inputSource expectedSource outSource =
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(getZipSource $ (,)
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<$> ZipSource (CL.sourceList [1..])
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<*> (ZipSource $ recordSource context parserSpec)) .| CL.mapM (checkStepM evaluateLine) .| CL.catMaybes
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where parserSpec = (ParserSpecWithInput (Right . id) (Right . id) (Right . id))
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context = (WithInput inputLineSource expectedLineSource outputLineSource)
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inputLineSource = fileAsLineSource inputSource
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expectedLineSource = fileAsLineSource expectedSource
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outputLineSource = fileAsLineSource outSource
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inputLineSource = fileAsLineSource inputSource id
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expectedLineSource = fileAsLineSource expectedSource id
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outputLineSource = fileAsLineSource outSource id
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justLine (LineInFile _ _ l) = l
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evaluateLine (lineNo, ParsedRecordWithInput inp exp out) = do
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s <- liftIO $ gevalCoreOnSingleLines metric (LineInFile inputSource lineNo inp)
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(LineInFile expectedSource lineNo exp)
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(LineInFile outSource lineNo out)
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s <- liftIO $ gevalCoreOnSingleLines metric preprocess (LineInFile inputSource lineNo inp)
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(LineInFile expectedSource lineNo exp)
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(LineInFile outSource lineNo out)
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return $ LineRecord inp exp out lineNo s
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@ -21,6 +21,13 @@ instance Read Tokenizer where
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tokenize :: Maybe Tokenizer -> T.Text -> [T.Text]
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tokenize mTokenizer = T.words . (tokenizeWithSpaces mTokenizer)
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tokenizeTabSeparatedWithSpaces :: Maybe Tokenizer -> T.Text -> T.Text
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tokenizeTabSeparatedWithSpaces Nothing t = t -- special case for efficiency
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tokenizeTabSeparatedWithSpaces tokenizer@(Just _) t =
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T.intercalate "\t"
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$ map (tokenizeWithSpaces tokenizer)
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$ T.splitOn "\t" t
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tokenizeWithSpaces :: Maybe Tokenizer -> T.Text -> T.Text
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tokenizeWithSpaces Nothing t = t
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tokenizeWithSpaces (Just V13a) t = T.strip tTokenized
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@ -232,9 +232,9 @@ main = hspec $ do
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runGEvalTest "multilabel-likelihood-simple" `shouldReturnAlmost` 0.115829218528827
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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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gevalCoreOnSingleLines RMSE id (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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@ -311,7 +311,8 @@ main = hspec $ do
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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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gesPrecision = Nothing,
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gesTokenizer = 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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