ENH Make write() return the filename used

Also, internally refactor the code by adding a __builtin__ module as in Python, thus making the code more regular (there is no special `builtinFunctions` list anymore, just a special module that gets handled like all the other modules)
ngless-toolkit · Mar 19, 2021 · 66a08e5 · 66a08e5
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diff --git a/ChangeLog b/ChangeLog
@@ -1,3 +1,6 @@
+Unreleased
+	* write() returns the filename used
+
 Version 1.3.0 2021-01-28 by luispedro
 	* Validate count() headers on --validate-only
 	* Better error message if the user attempts to use the non-existent <\>

diff --git a/Execs/Main.hs b/Execs/Main.hs
@@ -80,6 +80,7 @@ import Utils.Batch (getNcpus)
 import Utils.Suggestion
 import CWL (writeCWL)
 
+import           BuiltinFunctions (builtinModule)
 import qualified BuiltinModules.Argv as ModArgv
 import qualified BuiltinModules.Assemble as ModAssemble
 import qualified BuiltinModules.Checks as Checks
@@ -144,7 +145,7 @@ runNGLessIO context (NGLessIO act) = try (runResourceT act) >>= \case
             exitFailure
         Right v -> return v
 
--- | Load both automatically imported modules are user-requested one
+-- | Load both automatically imported modules and user-requested ones
 loadModules :: NGLVersion -> [ModInfo] -> NGLessIO [Module]
 loadModules av mods  = do
     mA <- ModAsReads.loadModule ("" :: T.Text)
@@ -157,7 +158,8 @@ loadModules av mods  = do
     mStats <- ModQCStats.loadModule ("" :: T.Text)
     mOrfFind <- ModORFFind.loadModule ("0.6" :: T.Text)
     imported <- loadStdlibModules mods
-    let loaded = [mOrfFind | av >= NGLVersion 0 6]
+    let loaded = [builtinModule av]
+                    ++ [mOrfFind | av >= NGLVersion 0 6]
                     ++ [mLoadDirectory | av >= NGLVersion 1 2]
                     ++ [mReadlines, mArgv, mAssemble, mA, mChecks, mRemove, mStats] ++ imported
     forM_ loaded registerModule

diff --git a/NGLess/BuiltinFunctions.hs b/NGLess/BuiltinFunctions.hs
@@ -1,15 +1,19 @@
-{- Copyright 2013-2020 NGLess Authors
+{- Copyright 2013-2021 NGLess Authors
  - License: MIT
  -}
 module BuiltinFunctions
     ( MethodName(..)
     , MethodInfo(..)
-    , builtinFunctions
+    , builtinModule
     , builtinMethods
     , findFunction
     ) where
 
 import Data.List (find)
+import Data.Default (def)
+import qualified Data.Text as T
+
+import NGLess.NGLEnvironment (NGLVersion(..))
 import Modules
 import Language
 
@@ -24,9 +28,17 @@ data MethodInfo = MethodInfo
     } deriving (Eq, Show)
 
 findFunction :: [Module] -> FuncName -> Maybe Function
-findFunction mods fn = find ((==fn) . funcName) $ builtinFunctions ++ concat (modFunctions <$> mods)
+-- findFunction mods fn = trace (show mods) $ trace (show fn) $ find ((==fn) . funcName) $ concat (modFunctions <$> mods)
+findFunction mods fn = find ((==fn) . funcName) $ concat (modFunctions <$> mods)
+
+builtinModule :: NGLVersion -> Module
+builtinModule ver@(NGLVersion majV minV) = def
+    { modInfo = ModInfo "__builtin__" (T.pack $ show majV ++ "." ++ show minV)
+    , modPath = ""
+    , modFunctions = builtinFunctions ver
+    }
 
-builtinFunctions =
+builtinFunctions ver =
     [Function (FuncName "fastq") (Just NGLString) [ArgCheckFileReadable] NGLReadSet fastqArgs False []
     ,Function (FuncName "paired") (Just NGLString) [ArgCheckFileReadable] NGLReadSet pairedArgs False []
     ,Function (FuncName "group") (Just (NGList NGLReadSet)) [] NGLReadSet groupArgs False []
@@ -42,7 +54,7 @@ builtinFunctions =
     ,Function (FuncName "count") (Just NGLMappedReadSet) [] NGLCounts countArgs False [FunctionCheckReturnAssigned]
     ,Function (FuncName "__check_count") (Just NGLMappedReadSet) [] NGLCounts countCheckArgs False []
     ,Function (FuncName "countfile") (Just NGLString) [ArgCheckFileReadable] NGLCounts [] False [FunctionCheckReturnAssigned]
-    ,Function (FuncName "write") (Just NGLAny) [] NGLVoid writeArgs False []
+    ,Function (FuncName "write") (Just NGLAny) [] (if ver >= NGLVersion 1 4 then NGLString else NGLVoid) writeArgs False []
 
     ,Function (FuncName "print") (Just NGLAny) [] NGLVoid [] False []
 
@@ -151,6 +163,7 @@ smoothtrimArgs =
     ,ArgInformation "window" True NGLInteger []
     ]
 
+builtinMethods :: [MethodInfo]
 builtinMethods =
     [
      -- NGLMappedReadSet

diff --git a/NGLess/Transform.hs b/NGLess/Transform.hs
@@ -30,7 +30,7 @@ import Output (outputListLno', OutputType(..))
 import NGLess
 import Utils.Utils (uniq, secondM)
 import NGLess.NGLEnvironment
-import BuiltinFunctions
+import BuiltinFunctions (findFunction)
 
 
 {-| NOTE

diff --git a/NGLess/Types.hs b/NGLess/Types.hs
@@ -279,11 +279,9 @@ checkindexable expr = do
             errorInLineC ["List expected. Type ", show e , " provided."]
             return $ Just NGLVoid
 
-allFunctions = (builtinFunctions ++) <$> moduleFunctions
-moduleFunctions = asks (concatMap modFunctions)
 
 funcInfo fn = do
-    fs <- allFunctions
+    fs <- asks (concatMap modFunctions)
     let matched = filter ((==fn) . funcName) fs
     case matched of
         [fi] -> return fi

diff --git a/NGLess/Validation.hs b/NGLess/Validation.hs
@@ -23,7 +23,7 @@ import           Data.Foldable (asum)
 import Language
 import Modules
 import NGLess.NGError
-import BuiltinFunctions
+import BuiltinFunctions (MethodInfo(..), builtinMethods, findFunction)
 import Utils.Suggestion
 
 

diff --git a/NGLess/ValidationIO.hs b/NGLess/ValidationIO.hs
@@ -19,7 +19,7 @@ import NGLess
 import Output
 import Modules
 import Language
-import BuiltinFunctions
+import BuiltinFunctions (findFunction)
 import FileManagement
 import Utils.Suggestion
 import ReferenceDatabases

diff --git a/Tests-Src/Tests/Types.hs b/Tests-Src/Tests/Types.hs
@@ -11,22 +11,27 @@ import qualified Data.Text as T
 import Tests.Utils
 import Types
 import Language
+import BuiltinFunctions (builtinModule)
+import NGLess.NGLEnvironment (NGLVersion(..))
 
 tgroup_Types = $(testGroupGenerator)
 
+
+mods = [builtinModule (NGLVersion 1 3)]
+
 isOkTypes :: Script -> IO ()
-isOkTypes script = case checktypes [] script of
+isOkTypes script = case checktypes mods script of
     (Right _) -> return ()
     (Left err) -> assertFailure ("Type error on good code (error was '"++show err++"'")
 
-isOkTypesText scriptText = case parsetest scriptText >>= checktypes [] of
+isOkTypesText scriptText = case parsetest scriptText >>= checktypes mods of
     (Right _) -> return ()
     (Left err) -> assertFailure ("Type error on good code (error was '"++show err++"') for script: '"++T.unpack scriptText++"'")
 
-isErrorText scriptText = isError $ parsetest scriptText>>= checktypes []
+isErrorText scriptText = isError $ parsetest scriptText>>= checktypes mods
 
 
-case_bad_type_fastq = isError $ checktypes [] (Script Nothing [(0,FunctionCall (FuncName "fastq") (ConstInt 3) [] Nothing)])
+case_bad_type_fastq = isError $ checktypes mods (Script Nothing [(0,FunctionCall (FuncName "fastq") (ConstInt 3) [] Nothing)])
 case_good_type_fastq = isOkTypes (Script Nothing [(0,FunctionCall (FuncName "fastq") (ConstStr "fastq.fq") [] Nothing)])
 
 case_type_complete = isOkTypesText
@@ -49,7 +54,7 @@ case_indent_empty_line = isOkTypesText
     \        discard\n"
 
 
-case_invalid_func_fastq = isError $ checktypes [] $
+case_invalid_func_fastq = isError $ checktypes mods $
     Script Nothing [(0,FunctionCall (FuncName "fastq") (ConstStr "fastq.fq") [(Variable "fname", ConstInt 10)] Nothing)]
 
 -- unique

diff --git a/Tests-Src/Tests/Validation.hs b/Tests-Src/Tests/Validation.hs
@@ -14,15 +14,19 @@ import Tests.Utils
 import Validation
 import ValidationIO
 import Utils.Here
+import BuiltinFunctions (builtinModule)
+import NGLess.NGLEnvironment (NGLVersion(..))
 
 tgroup_Validation = $(testGroupGenerator)
 
 -- Pure Validation
 
-isValidateOk ftext = case parsetest ftext >>= validate [] of
+mods = [builtinModule (NGLVersion 1 3)]
+
+isValidateOk ftext = case parsetest ftext >>= validate mods of
     Right _ -> return ()
     Left err -> assertFailure ("Validation should have passed for script "++T.unpack ftext++"; instead picked up error: '"++show err++"'")
-isValidateError ftext = isErrorMsg ("Validation should have picked error for script '"++T.unpack ftext++"'") (parsetest ftext >>= validate [])
+isValidateError ftext = isErrorMsg ("Validation should have picked error for script '"++T.unpack ftext++"'") (parsetest ftext >>= validate mods)
 
 case_bad_function_attr_count = isValidateError
     "ngless '0.0'\n\
@@ -49,13 +53,13 @@ write(
 -- Validate IO
 
 validateIO_Ok script = do
-    err <- testNGLessIO $ validateIO [] (fromRight . parsetest $ script)
+    err <- testNGLessIO $ validateIO mods (fromRight . parsetest $ script)
     case err of
         Nothing -> assertBool "" True
         Just errmsg -> assertFailure (concat ["Expected no errors in validation, got ", show errmsg, ".\nScript was::\n\n", show script])
 
 validateIO_error script = do
-    err <- testNGLessIO $ validateIO [] (fromRight . parsetest $ script)
+    err <- testNGLessIO $ validateIO mods (fromRight . parsetest $ script)
     case err of
         Nothing -> assertFailure (concat ["ValidateIO should have detected an error on the script ", show script])
         Just _ -> return ()

diff --git a/docs/sources/Functions.rst b/docs/sources/Functions.rst
@@ -747,7 +747,10 @@ Any
 Return:
 ~~~~~~~
 
-Void
+.. versionadded:: NGLess 1.4
+    Prior to version 1.4, ``write()`` returned nothing
+
+String: the file name used
 
 Arguments by value:
 ~~~~~~~~~~~~~~~~~~~