automatic decompression

geval.cabal

@@ -27,6 +27,7 @@ library
                      , GEval.CharMatch
                      , GEval.LineByLine
                      , GEval.BIO
+                     , Data.Conduit.AutoDecompress
   build-depends:       base >= 4.7 && < 5
                      , cond
                      , conduit
@@ -49,6 +50,12 @@ library
                      , vector
                      , mtl
                      , edit-distance
+                     , bytestring
+                     , word8
+                     , primitive
+                     , transformers-base
+                     , bzlib-conduit
+                     , lzma-conduit
   default-language:    Haskell2010
 
 executable geval

src/Data/Conduit/AutoDecompress.hs

@@ -0,0 +1,44 @@
+{-# LANGUAGE AllowAmbiguousTypes #-}
+
+module Data.Conduit.AutoDecompress
+       (autoDecompress)
+       where
+
+import Data.Conduit
+import Data.Conduit.Combinators
+import Data.ByteString
+import Data.Conduit.Zlib
+import Data.Word8
+import Control.Monad.Trans.Resource (MonadThrow, MonadResource)
+import Control.Monad.Primitive (PrimMonad)
+import Control.Monad.Base (MonadBase)
+import qualified Data.Conduit.Lzma as XZ
+import qualified Data.Conduit.BZlib as BZ
+
+autoDecompress :: (MonadResource m, MonadBase base m, MonadThrow m, PrimMonad base) => ConduitM ByteString ByteString m ()
+autoDecompress = do
+  f <- await
+  case f of
+    Just chunk -> if Data.ByteString.length chunk > 1
+                   then
+                     do
+                       let firstByte = Data.ByteString.head chunk
+                       let secondByte = Data.ByteString.index chunk 1
+                       leftover chunk
+                       lookAtMagicNumbers (firstByte, secondByte)
+                   else
+                     do
+                      leftover chunk
+                      doNothing
+
+    Nothing -> return ()
+
+
+lookAtMagicNumbers :: (MonadResource m, MonadBase base m, MonadThrow m, PrimMonad base) => (Word8, Word8) -> Conduit ByteString m ByteString
+lookAtMagicNumbers (31, 139) = ungzip
+lookAtMagicNumbers (66, 90) = BZ.bunzip2
+lookAtMagicNumbers (253, 55) = XZ.decompress Nothing
+lookAtMagicNumbers _ = doNothing
+
+doNothing :: Monad m => Conduit ByteString m ByteString
+doNothing = Data.Conduit.Combinators.filter (const True)

src/GEval/Core.hs

@@ -57,7 +57,7 @@ import Data.Tuple
 import qualified Data.List.Split as DLS
 
 import Control.Monad.IO.Class
-import Control.Monad ((<=<))
+import Control.Monad ((<=<), filterM)
 
 import Data.Attoparsec.Text (parseOnly)
 
@@ -69,6 +69,7 @@ import GEval.ClusteringMetrics
 import GEval.LogLossHashed
 import GEval.CharMatch
 import GEval.BIO
+import Data.Conduit.AutoDecompress
 
 import qualified Data.HashMap.Strict as M
 
@@ -239,11 +240,14 @@ checkAndGetFiles gevalSpec = do
   unlessM (D.doesDirectoryExist expectedDirectory) $ throwM $ NoExpectedDirectory expectedDirectory
   unlessM (D.doesDirectoryExist outTestDirectory) $ throwM $ NoOutTestDirectory outTestDirectory
   unlessM (D.doesDirectoryExist expectedTestDirectory) $ throwM $ NoExpectedTestDirectory expectedTestDirectory
+  inputFilePath <- lookForCompressedFiles inputFilePath'
+  expectedFilePath <- lookForCompressedFiles expectedFilePath'
+  outFilePath <- lookForCompressedFiles outFilePath'
   checkInputFileIfNeeded metric inputFilePath
   return (inputFilePath, expectedFilePath, outFilePath)
-   where expectedFilePath = expectedTestDirectory </> (gesExpectedFile gevalSpec)
-         outFilePath = getOutFile gevalSpec (gesOutFile gevalSpec)
-         inputFilePath = expectedTestDirectory </> (gesInputFile gevalSpec)
+   where expectedFilePath' = expectedTestDirectory </> (gesExpectedFile gevalSpec)
+         outFilePath' = getOutFile gevalSpec (gesOutFile gevalSpec)
+         inputFilePath' = expectedTestDirectory </> (gesInputFile gevalSpec)
          expectedTestDirectory = expectedDirectory </> testName
          outTestDirectory = outDirectory </> testName
          expectedDirectory = getExpectedDirectory gevalSpec
@@ -251,6 +255,24 @@ checkAndGetFiles gevalSpec = do
          testName = gesTestName gevalSpec
          metric = gesMetric gevalSpec
 
+lookForCompressedFiles :: FilePath -> IO FilePath
+lookForCompressedFiles = lookForAlternativeFiles [".gz", ".xz", ".bz2"]
+
+lookForAlternativeFiles :: [String] -> FilePath -> IO FilePath
+lookForAlternativeFiles suffixes filePath
+   | takeExtension filePath `Prelude.elem` suffixes = return filePath
+   | otherwise = do
+       fileIsThere <- D.doesFileExist filePath
+       if fileIsThere
+         then
+           return filePath
+         else
+           do
+             found <- Control.Monad.filterM D.doesFileExist $ Prelude.map (filePath <.>) suffixes
+             return $ case found of
+                        [fp] -> fp
+                        _ -> filePath
+
 getOutFile :: GEvalSpecification -> FilePath -> FilePath
 getOutFile gevalSpec out = outDirectory </> testName </> out
   where outDirectory = gesOutDirectory gevalSpec
@@ -264,7 +286,7 @@ checkInputFileIfNeeded _ _ = return ()
 
 fileAsLineSource :: FilePath -> LineSource (ResourceT IO)
 fileAsLineSource filePath =
-  LineSource (CB.sourceFile filePath $= CT.decodeUtf8Lenient =$= CT.lines) filePath 1
+  LineSource (CB.sourceFile filePath $= autoDecompress =$= CT.decodeUtf8Lenient =$= CT.lines) filePath 1
 
 gevalCoreOnSingleLines :: Metric -> LineInFile -> LineInFile -> LineInFile -> IO (MetricValue)
 gevalCoreOnSingleLines metric inpLine expLine outLine =

test/Spec.hs

@@ -252,6 +252,10 @@ main = hspec $ do
       runGEvalTest "bio-f1-simple" `shouldReturnAlmost` 0.5
     it "check perfect score" $ do
       runGEvalTest "bio-f1-perfect" `shouldReturnAlmost` 1.0
+  describe "automatic decompression" $ do
+    it "more complex test" $ do
+      runGEvalTest "charmatch-complex-compressed" `shouldReturnAlmost` 0.1923076923076923
+
 
 neverMatch :: Char -> Int -> Bool
 neverMatch _ _ = False

test/charmatch-complex-compressed/charmatch-complex-compressed/config.txt

@@ -0,0 +1 @@
+--metric CharMatch