RFCT Use Control.Monad.{findM,firstJustM}

NGLess/BuiltinModules/Samples.hs

@@ -22,6 +22,7 @@ import qualified Data.Aeson.KeyMap as Aeson
 import qualified Data.Aeson.Key as Aeson
 import qualified Data.Yaml as Yaml
 import qualified Data.Vector as V
+import           Control.Monad.Extra (findM)
 import           Control.Monad.IO.Class (liftIO)
 import           System.FilePath ((</>), isAbsolute)
 
@@ -31,7 +32,6 @@ import Language
 import Data.FastQ
 import Modules
 import NGLess
-import Utils.Utils (findM)
 
 data SampleData = SampleData
     { sampleName :: !T.Text
@@ -118,11 +118,8 @@ executeLoadSample fname kwargs = do
     samples <- executeLoadSampleList fname []
     case samples of
         NGOList l -> do
-            found <- findM l $ \case
-                s@(NGOReadSet n _) ->
-                    if n == sample
-                        then return (Just s)
-                        else return Nothing
+            found <- flip findM l $ \case
+                NGOReadSet n _ -> return (n == sample)
                 _ -> throwShouldNotOccur "load_sample_from_yaml: sample list is not a list of samples"
             case found of
                 Just s -> return s

NGLess/FileManagement.hs

@@ -40,6 +40,7 @@ import qualified Conduit as C
 import           Conduit ((.|))
 import           System.FilePath (takeDirectory, (</>), (<.>), (-<.>))
 import           Control.Monad (unless, forM_, when)
+import           Control.Monad.Extra (firstJustM)
 import           System.Posix.Files (setFileMode, createSymbolicLink)
 import           System.Posix.Internals (c_getpid)
 import           Data.List (isSuffixOf, isPrefixOf)
@@ -63,7 +64,7 @@ import NGLess.NGLEnvironment
 import qualified Dependencies.Embedded as Deps
 import NGLess.NGError
 import Utils.LockFile
-import Utils.Utils (findM, withOutputFile)
+import Utils.Utils (withOutputFile)
 
 
 {- Note on temporary files
@@ -277,7 +278,7 @@ binPath User = ((</> "bin") . nConfUserDirectory) <$> nglConfiguration
 -- | Attempts to find the absolute path for the requested binary (checks permissions)
 findBin :: FilePath -> NGLessIO (Maybe FilePath)
 findBin fname = do
-        nglPath <- findM [Root, User] $ \p -> do
+        nglPath <- flip firstJustM [Root, User] $ \p -> do
             path <- (</> fname) <$> binPath p
             ex <- canExecute path
             if ex
@@ -388,18 +389,12 @@ expandPath fbase = do
         searchpath <- nConfSearchPath <$> nglConfiguration
         outputListLno' TraceOutput ["Looking for file '", fbase, "' (search path is ", show searchpath, ")"]
         let candidates = expandPath' fbase searchpath
-        findMaybeM candidates $ \p -> do
+        flip firstJustM candidates $ \p -> do
             outputListLno' TraceOutput ["Looking for file (", fbase, ") in ", p]
             exists <- liftIO (SD.doesFileExist p)
             return $! if exists
                             then Just p
                             else Nothing
-    where
-        findMaybeM :: Monad m => [a] -> (a -> m (Maybe b)) -> m (Maybe b)
-        findMaybeM [] _ = return Nothing
-        findMaybeM (x:xs) f = f x >>= \case
-            Nothing -> findMaybeM xs f
-            val -> return val
 
 expandPath' :: FilePath -> [FilePath] -> [FilePath]
 expandPath' fbase search = case RE.matchedText $ fbase RE.?=~ [RE.re|<(@{%id})?>|] of

NGLess/ReferenceDatabases.hs

@@ -24,6 +24,7 @@ import Data.Foldable
 import Data.Maybe
 
 import Control.Monad (liftM2)
+import Control.Monad.Extra (firstJustM)
 import Control.Applicative ((<|>))
 import Control.Monad.IO.Class (liftIO)
 import Control.Monad.Trans.Resource(release)
@@ -39,7 +40,7 @@ import NGLess
 import Dependencies.Versions (bwaVersion)
 import Utils.Network (downloadExpandTar, downloadOrCopyFile, downloadFile, isUrl)
 import Utils.LockFile (withLockFile, LockParameters(..), WhenExistsStrategy(..))
-import Utils.Utils (findM, withOutputFile)
+import Utils.Utils (withOutputFile)
 
 data ReferenceFilePaths = ReferenceFilePaths
     { rfpFaFile :: Maybe FilePath
@@ -108,8 +109,8 @@ downloadIfUrl basedir fname (Just path)
 moduleDirectReference :: T.Text -> NGLessIO (Maybe ReferenceFilePaths)
 moduleDirectReference rname = do
     mods <- ngleLoadedModules <$> nglEnvironment
-    findM mods $ \m ->
-        findM (modReferences m) $ \case
+    flip firstJustM mods $ \m ->
+        flip firstJustM (modReferences m) $ \case
             ExternalReference eref fafile gtffile mapfile
                 | eref == rname -> do
                     fafile'  <- downloadIfUrl (modPath m) (T.unpack rname <.> "fna.gz") (Just fafile)

NGLess/Utils/Utils.hs

@@ -1,4 +1,4 @@
-{- Copyright 2015-2019 NGLess Authors
+{- Copyright 2015-2024 NGLess Authors
  - License: MIT
  -}
 
@@ -9,7 +9,6 @@ module Utils.Utils
     , maybeM
     , mapMaybeM
     , fmapMaybeM
-    , findM
     , uniq
     , allSame
     , passthrough
@@ -74,15 +73,6 @@ moveOrCopy oldfp newfp = renameFile oldfp newfp `catch` (\e -> case ioeGetErrorT
             UnsupportedOperation -> copyFile oldfp newfp
             _ -> ioError e)
 
--- | Monadic version of find: returns the result of the first application of
--- the argument which is not 'Nothing' or, if all applications fail, return
--- 'Nothing'
-findM :: Monad m => [a] -> (a -> m (Maybe b)) -> m (Maybe b)
-findM [] _ = return Nothing
-findM (x:xs) f = f x >>= \case
-    Nothing -> findM xs f
-    val -> return val
-
 secondM :: Monad m => (a -> m b) -> (c,a) -> m (c,b)
 secondM f (a,c) = (a,) <$> f c
 {-# INLINE secondM #-}