diff --git a/Changelog b/Changelog --- a/Changelog +++ b/Changelog @@ -1,3 +1,10 @@ +1.8.12 [2024-08-02] + +* Add flag "use-hdf5-serial" to switch between "hdf5" and "hdf5-serial" as a pkgconfig dependency +* Add pipeline ensuring the project compiles and the tests run with ghcup and ghc 9.0, 9.2, 9.4 and 9.6. +* Fixes to support different versions of hdf5 simultaneously +* Add upper version bounds to conform wiht the Haskell PVP document + 1.8.11 [2023-10-10] ------ diff --git a/cbits/H5E_inline.c b/cbits/H5E_inline.c --- a/cbits/H5E_inline.c +++ b/cbits/H5E_inline.c @@ -26,7 +26,9 @@ BC_INLINE_(H5E_RS, hid_t) BC_INLINE_(H5E_HEAP, hid_t) BC_INLINE_(H5E_OHDR, hid_t) +#if !H5_VERSION_GE(1,8,14) BC_INLINE_(H5E_ATOM, hid_t) +#endif BC_INLINE_(H5E_ATTR, hid_t) BC_INLINE_(H5E_NONE_MAJOR, hid_t) BC_INLINE_(H5E_IO, hid_t) @@ -120,7 +122,9 @@ BC_INLINE_(H5E_TRUNCATED, hid_t) BC_INLINE_(H5E_MOUNT, hid_t) +#if !H5_VERSION_GE(1,8,14) BC_INLINE_(H5E_BADATOM, hid_t) +#endif BC_INLINE_(H5E_BADGROUP, hid_t) BC_INLINE_(H5E_CANTREGISTER, hid_t) BC_INLINE_(H5E_CANTINC, hid_t) diff --git a/cbits/H5FD_inline.c b/cbits/H5FD_inline.c --- a/cbits/H5FD_inline.c +++ b/cbits/H5FD_inline.c @@ -1,4 +1,7 @@ #include +#if H5_VERSION_GE(1,14,0) +#include +#endif #include diff --git a/hdf5.cabal b/hdf5.cabal --- a/hdf5.cabal +++ b/hdf5.cabal @@ -1,5 +1,5 @@ name: hdf5 -version: 1.8.11 +version: 1.8.12 stability: provisional cabal-version: >= 1.10 @@ -23,6 +23,11 @@ type: git location: git://github.com/picca/hs-hdf5.git +flag use-hdf5-serial + default: False + manual: True + description: Use Debian's hdf5-serial as a dependency instead of plain hdf5 + Library hs-source-dirs: src default-language: Haskell2010 @@ -30,7 +35,6 @@ default-extensions: ForeignFunctionInterface ghc-options: -Wall - cc-options: -Wno-format exposed-modules: Bindings.HDF5 , Bindings.HDF5.Attribute , Bindings.HDF5.Raw @@ -104,18 +108,21 @@ include-dirs: include - build-depends: base >= 3 && < 5 - , bindings-DSL - , bytestring - , libffi - , lifted-base - , monad-control - , primitive - , tagged - , vector - , transformers + build-depends: base >= 3 && < 5, + bindings-DSL >= 1.0.25 && < 1.1, + bytestring >= 0.10.0 && < 0.12, + libffi >= 0.1 && < 0.3, + lifted-base >= 0.2.3 && < 0.3, + monad-control >= 1.0.3 && < 1.1, + transformers >= 0.5.0 && < 0.7, + primitive >= 0.7.0 && < 0.9, + tagged >= 0.8.0 && < 0.9, + vector >= 0.12.0 && < 0.14 - pkgconfig-depends: hdf5-serial, libffi + if flag(use-hdf5-serial) + pkgconfig-depends: hdf5-serial + else + pkgconfig-depends: hdf5 test-suite hdf5-test diff --git a/src/Bindings/HDF5/Dataspace.hs b/src/Bindings/HDF5/Dataspace.hs deleted file mode 100644 --- a/src/Bindings/HDF5/Dataspace.hs +++ /dev/null @@ -1,372 +0,0 @@ -{-# LANGUAGE GeneralizedNewtypeDeriving #-} -module Bindings.HDF5.Dataspace - ( Dataspace - , DataspaceClass(..) - , SelectionOperator(..) - , SelectionType(..) - - , createDataspace - , createSimpleDataspace - , createExpandableDataspace - - , copyDataspace - - , closeDataspace - - , encodeDataspace - , decodeDataspace - - , getSimpleDataspaceExtentNPoints - , getSimpleDataspaceExtentNDims - , getSimpleDataspaceExtent - - , isSimpleDataspace - - , getDataspaceSelectionNPoints - - , selectHyperslab - , selectElements - - , getSimpleDataspaceExtentType - - , setDataspaceExtentNone - , copyDataspaceExtent - , dataspaceExtentsEqual - - , selectAll - , selectNone - - , offsetSimpleDataspaceSelection - - , selectionValid - - , getHyperslabSelection - , getHyperslabSelectionNBlocks - , getHyperslabSelectionBlockList - - , getElementSelection - , getElementSelectionNPoints - , getElementSelectionPointList - - , getSelectionBounds - - , getSelectionType - ) where - -import Bindings.HDF5.Core -import Bindings.HDF5.Error -import Bindings.HDF5.Object -import Bindings.HDF5.Raw.H5I -import Bindings.HDF5.Raw.H5S -import Control.Exception (assert) -import Control.Monad -import qualified Data.ByteString as BS -import qualified Data.ByteString.Unsafe as BS -import Data.List -import Data.Maybe -import Data.Tagged -import qualified Data.Vector as V -import qualified Data.Vector.Storable as SV -import Foreign hiding (And, Xor) -import Foreign.C -import Foreign.Ptr.Conventions - -newtype Dataspace = Dataspace HId_t - deriving (Eq, HId, FromHId, HDFResultType) - -instance Object Dataspace where - staticObjectType = Tagged (Just DataspaceObj) - -data DataspaceClass - = Scalar - | Simple - | Null - deriving (Eq, Ord, Enum, Bounded, Read, Show) - -rawDataspaceClass :: DataspaceClass -> H5S_class_t -rawDataspaceClass Scalar = h5s_SCALAR -rawDataspaceClass Simple = h5s_SIMPLE -rawDataspaceClass Null = h5s_NULL - -dataspaceClass :: H5S_class_t -> DataspaceClass -dataspaceClass c - | c == h5s_SCALAR = Scalar - | c == h5s_SIMPLE = Simple - | c == h5s_NULL = Null - | otherwise = error ("unknown dataspace class: " ++ show c) - -createDataspace :: DataspaceClass -> IO Dataspace -createDataspace cls = - fmap Dataspace $ - withErrorCheck $ - h5s_create (rawDataspaceClass cls) - -createSimpleDataspace :: [HSize] -> IO Dataspace -createSimpleDataspace dims = - fmap Dataspace $ - withErrorCheck $ - withInList (map hSize dims) $ \idims -> - h5s_create_simple n idims (InArray nullPtr) - where n = genericLength dims - -createExpandableDataspace :: [(HSize, Maybe HSize)] -> IO Dataspace -createExpandableDataspace dims = - fmap Dataspace $ - withErrorCheck $ - withInList (map hSize dimSizes) $ \idimSizes -> - withInList (map (maybe h5s_UNLIMITED hSize) dimLimits) $ \idimLimits -> - h5s_create_simple n idimSizes idimLimits - where - n = genericLength dims - (dimSizes, dimLimits) = unzip dims - -copyDataspace :: Dataspace -> IO Dataspace -copyDataspace (Dataspace space_id) = - fmap Dataspace $ - withErrorCheck $ - h5s_copy space_id - -closeDataspace :: Dataspace -> IO () -closeDataspace (Dataspace space_id) = - withErrorCheck_ $ - h5s_close space_id - -encodeDataspace :: Dataspace -> IO BS.ByteString -encodeDataspace (Dataspace space_id) = - withOutByteString $ \buf bufSz -> - withInOut_ bufSz $ \ioBufSz -> - withErrorCheck_ $ - h5s_encode space_id buf ioBufSz - -decodeDataspace :: BS.ByteString -> IO Dataspace -decodeDataspace bs = BS.unsafeUseAsCString bs $ \buf -> - fmap Dataspace $ - withErrorCheck $ - h5s_decode (InArray buf) - -getSimpleDataspaceExtentNPoints :: Dataspace -> IO HSize -getSimpleDataspaceExtentNPoints (Dataspace space_id) = - fmap fromIntegral $ - withErrorWhen (< 0) $ - h5s_get_simple_extent_npoints space_id - -getSimpleDataspaceExtentNDims :: Dataspace -> IO CInt -getSimpleDataspaceExtentNDims (Dataspace space_id) = - withErrorWhen (< 0) $ - h5s_get_simple_extent_ndims space_id - -getSimpleDataspaceExtent :: Dataspace -> IO ([HSize], [Maybe HSize]) -getSimpleDataspaceExtent space@(Dataspace space_id) = do - n <- getSimpleDataspaceExtentNDims space - - (dims, (maxDims, n')) <- - withOutList (fromIntegral n) $ \dims -> - withOutList (fromIntegral n) $ \maxDims -> - withErrorWhen (< 0) $ - h5s_get_simple_extent_dims space_id dims maxDims - - assert (n==n') $ return - ( map HSize dims - , [ if d == h5s_UNLIMITED then Nothing else Just (HSize d) | d <- maxDims] - ) - -isSimpleDataspace :: Dataspace -> IO Bool -isSimpleDataspace (Dataspace space_id) = - htriToBool $ - h5s_is_simple space_id - -getDataspaceSelectionNPoints :: Dataspace -> IO HSize -getDataspaceSelectionNPoints (Dataspace space_id) = - fmap fromIntegral $ - withErrorWhen (< 0) $ - h5s_get_select_npoints space_id - -data SelectionOperator - = Set - | Or - | And - | Xor - | NotB - | NotA - | Append - | Prepend - deriving (Eq, Ord, Enum, Bounded, Read, Show) - -rawSelectionOperator :: SelectionOperator -> H5S_seloper_t -rawSelectionOperator Set = h5s_SELECT_SET -rawSelectionOperator Or = h5s_SELECT_OR -rawSelectionOperator And = h5s_SELECT_AND -rawSelectionOperator Xor = h5s_SELECT_XOR -rawSelectionOperator NotB = h5s_SELECT_NOTB -rawSelectionOperator NotA = h5s_SELECT_NOTA -rawSelectionOperator Append = h5s_SELECT_APPEND -rawSelectionOperator Prepend = h5s_SELECT_PREPEND - -selectHyperslab :: Dataspace -> SelectionOperator -> [(HSize, Maybe HSize, HSize, Maybe HSize)] -> IO () -selectHyperslab space@(Dataspace space_id) oper hyperSlab = do - nDims <- getSimpleDataspaceExtentNDims space - - when (length hyperSlab /= fromIntegral nDims) - (fail "selectHyperslab: the given hyperslab has the wrong number of dimensions for this dataspace") - - withErrorCheck_ $ - withInList' start $ \istart -> - maybe withNull withInList' stride $ \istride -> - withInList' count $ \icount -> - maybe withNull withInList' block $ \iblock -> - h5s_select_hyperslab space_id (rawSelectionOperator oper) istart istride icount iblock - where - (start, mbStrides, count, mbBlocks) = unzip4 hyperSlab - stride - | any isJust mbStrides = Just (map (fromMaybe 1) mbStrides) - | otherwise = Nothing - block - | any isJust mbBlocks = Just (map (fromMaybe 1) mbBlocks) - | otherwise = Nothing - withNull f = f (InArray nullPtr) - withInList' = withInList . map hSize - -selectElements :: Dataspace -> SelectionOperator -> V.Vector (SV.Vector HSize) -> IO () -selectElements space@(Dataspace space_id) oper elems = do - nDims <- getSimpleDataspaceExtentNDims space - - let nElems = V.length elems - packed = SV.generate (nElems * fromIntegral nDims) $ \i -> - case i `divMod` nElems of - (dim, elt) -> elems V.! elt SV.! dim - - withErrorCheck_ $ - withInVector packed $ \ielems -> - h5s_select_elements space_id (rawSelectionOperator oper) (fromIntegral nElems) (castWrappedPtr ielems) - --- TODO: determine whether to throw an exception or simply report it --- when the returned value is invalid. -getSimpleDataspaceExtentType :: Dataspace -> IO DataspaceClass -getSimpleDataspaceExtentType (Dataspace space_id) = - fmap dataspaceClass $ - withErrorWhen (\(H5S_class_t c) -> c < 0) $ - h5s_get_simple_extent_type space_id - -setDataspaceExtentNone :: Dataspace -> IO () -setDataspaceExtentNone (Dataspace space_id) = - withErrorCheck_ $ - h5s_set_extent_none space_id - -copyDataspaceExtent :: Dataspace -> Dataspace -> IO () -copyDataspaceExtent (Dataspace dst) (Dataspace src) = - withErrorCheck_ $ - h5s_extent_copy dst src - -dataspaceExtentsEqual :: Dataspace -> Dataspace -> IO Bool -dataspaceExtentsEqual (Dataspace s1) (Dataspace s2) = - htriToBool $ - h5s_extent_equal s1 s2 - -selectAll :: Dataspace -> IO () -selectAll (Dataspace space_id) = - withErrorCheck_ $ - h5s_select_all space_id - -selectNone :: Dataspace -> IO () -selectNone (Dataspace space_id) = - withErrorCheck_ $ - h5s_select_none space_id - -offsetSimpleDataspaceSelection :: Dataspace -> SV.Vector HSSize -> IO () -offsetSimpleDataspaceSelection space@(Dataspace space_id) offsets = do - nDims <- getSimpleDataspaceExtentNDims space - - when (fromIntegral nDims /= SV.length offsets) - (fail "offsetSimpleDataspaceSelection: offset vector's length must equal number dimensions in dataspace") - - withErrorCheck_ $ - withInVector offsets $ \ioffsets -> - h5s_offset_simple space_id (castWrappedPtr ioffsets) - -selectionValid :: Dataspace -> IO Bool -selectionValid (Dataspace space_id) = - htriToBool $ - h5s_select_valid space_id - -getHyperslabSelection :: Dataspace -> IO (V.Vector (SV.Vector HSize, SV.Vector HSize)) -getHyperslabSelection space = getHyperslabSelectionBlockList space 0 maxBound - -getHyperslabSelectionNBlocks :: Dataspace -> IO HSize -getHyperslabSelectionNBlocks (Dataspace space_id) = - fmap fromIntegral $ - withErrorWhen (< 0) $ - h5s_get_select_hyper_nblocks space_id - -getHyperslabSelectionBlockList :: Dataspace -> HSize -> HSize -> IO (V.Vector (SV.Vector HSize, SV.Vector HSize)) -getHyperslabSelectionBlockList space@(Dataspace space_id) startBlock numBlocks = do - n <- getHyperslabSelectionNBlocks space - nDims <- getSimpleDataspaceExtentNDims space - - let nBlks = min numBlocks (n - startBlock) - blkSize = 2 * fromIntegral nDims - numSizes = nBlks * blkSize - - - sizes <- withOutVector_ (fromIntegral numSizes) $ \buf -> - withErrorCheck_ $ - h5s_get_select_hyper_blocklist space_id (hSize startBlock) (hSize nBlks) (castWrappedPtr buf) - - let decodePt i = SV.slice i (fromIntegral nDims) sizes - decodeBlock i = (decodePt b, decodePt (b + fromIntegral nDims)) - where b = i * fromIntegral blkSize - return $! V.generate (fromIntegral nBlks) decodeBlock - -getElementSelection :: Dataspace -> IO (V.Vector (SV.Vector HSize)) -getElementSelection space = getElementSelectionPointList space 0 maxBound - -getElementSelectionNPoints :: Dataspace -> IO HSize -getElementSelectionNPoints (Dataspace space_id) = - fmap fromIntegral $ - withErrorWhen (< 0) $ - h5s_get_select_elem_npoints space_id - -getElementSelectionPointList :: Dataspace -> HSize -> HSize -> IO (V.Vector (SV.Vector HSize)) -getElementSelectionPointList space@(Dataspace space_id) startPoint numPoints = do - n <- getElementSelectionNPoints space - nDims <- getSimpleDataspaceExtentNDims space - - let nPts = min numPoints (n - startPoint) - sz = nPts * fromIntegral nDims - - rawPoints <- withOutVector_ (fromIntegral sz) $ \buf -> - withErrorCheck_ $ - h5s_get_select_elem_pointlist space_id (hSize startPoint) (hSize nPts) (castWrappedPtr buf) - - let unpackPt i = SV.generate (fromIntegral nDims) $ \j -> rawPoints SV.! (i + j * fromIntegral nPts) - - return $! V.generate (fromIntegral nPts) unpackPt - -getSelectionBounds :: Dataspace -> IO [(HSize, HSize)] -getSelectionBounds space@(Dataspace space_id) = do - n <- getSimpleDataspaceExtentNDims space - - (start, end) <- - withOutList (fromIntegral n) $ \start -> - withOutList_ (fromIntegral n) $ \end -> - withErrorCheck_ $ - h5s_get_select_bounds space_id start end - - return [(HSize s, HSize e) | (s,e) <- zip start end] - -data SelectionType - = Points - | Hyperslabs - deriving (Eq, Ord, Bounded, Enum, Read, Show) - -selectionType :: H5S_sel_type -> Maybe SelectionType -selectionType c - | c == h5s_SEL_NONE = Nothing - | c == h5s_SEL_POINTS = Just Points - | c == h5s_SEL_HYPERSLABS = Just Hyperslabs - | otherwise = error ("unknown h5s_SEL value" ++ show c) - -getSelectionType :: Dataspace -> IO (Maybe SelectionType) -getSelectionType (Dataspace space_id) = - fmap selectionType $ - withErrorWhen (\(H5S_sel_type c) -> c < 0) $ - h5s_get_select_type space_id diff --git a/src/Bindings/HDF5/Dataspace.hsc b/src/Bindings/HDF5/Dataspace.hsc new file mode 100644 --- /dev/null +++ b/src/Bindings/HDF5/Dataspace.hsc @@ -0,0 +1,375 @@ +#include +#include +{-# LANGUAGE GeneralizedNewtypeDeriving #-} +{-# LANGUAGE CPP #-} +module Bindings.HDF5.Dataspace + ( Dataspace + , DataspaceClass(..) + , SelectionOperator(..) + , SelectionType(..) + + , createDataspace + , createSimpleDataspace + , createExpandableDataspace + + , copyDataspace + + , closeDataspace + + , encodeDataspace + , decodeDataspace + + , getSimpleDataspaceExtentNPoints + , getSimpleDataspaceExtentNDims + , getSimpleDataspaceExtent + + , isSimpleDataspace + + , getDataspaceSelectionNPoints + + , selectHyperslab + , selectElements + + , getSimpleDataspaceExtentType + + , setDataspaceExtentNone + , copyDataspaceExtent + , dataspaceExtentsEqual + + , selectAll + , selectNone + + , offsetSimpleDataspaceSelection + + , selectionValid + + , getHyperslabSelection + , getHyperslabSelectionNBlocks + , getHyperslabSelectionBlockList + + , getElementSelection + , getElementSelectionNPoints + , getElementSelectionPointList + + , getSelectionBounds + + , getSelectionType + ) where + +import Bindings.HDF5.Core +import Bindings.HDF5.Error +import Bindings.HDF5.Object +import Bindings.HDF5.Raw.H5I +import Bindings.HDF5.Raw.H5S +import Control.Exception (assert) +import Control.Monad +import qualified Data.ByteString as BS +import qualified Data.ByteString.Unsafe as BS +import Data.List +import Data.Maybe +import Data.Tagged +import qualified Data.Vector as V +import qualified Data.Vector.Storable as SV +import Foreign(nullPtr) +import Foreign.C +import Foreign.Ptr.Conventions + +newtype Dataspace = Dataspace HId_t + deriving (Eq, HId, FromHId, HDFResultType) + +instance Object Dataspace where + staticObjectType = Tagged (Just DataspaceObj) + +data DataspaceClass + = Scalar + | Simple + | Null + deriving (Eq, Ord, Enum, Bounded, Read, Show) + +rawDataspaceClass :: DataspaceClass -> H5S_class_t +rawDataspaceClass Scalar = h5s_SCALAR +rawDataspaceClass Simple = h5s_SIMPLE +rawDataspaceClass Null = h5s_NULL + +dataspaceClass :: H5S_class_t -> DataspaceClass +dataspaceClass c + | c == h5s_SCALAR = Scalar + | c == h5s_SIMPLE = Simple + | c == h5s_NULL = Null + | otherwise = error ("unknown dataspace class: " ++ show c) + +createDataspace :: DataspaceClass -> IO Dataspace +createDataspace cls = + fmap Dataspace $ + withErrorCheck $ + h5s_create (rawDataspaceClass cls) + +createSimpleDataspace :: [HSize] -> IO Dataspace +createSimpleDataspace dims = + fmap Dataspace $ + withErrorCheck $ + withInList (map hSize dims) $ \idims -> + h5s_create_simple n idims (InArray nullPtr) + where n = genericLength dims + +createExpandableDataspace :: [(HSize, Maybe HSize)] -> IO Dataspace +createExpandableDataspace dims = + fmap Dataspace $ + withErrorCheck $ + withInList (map hSize dimSizes) $ \idimSizes -> + withInList (map (maybe h5s_UNLIMITED hSize) dimLimits) $ \idimLimits -> + h5s_create_simple n idimSizes idimLimits + where + n = genericLength dims + (dimSizes, dimLimits) = unzip dims + +copyDataspace :: Dataspace -> IO Dataspace +copyDataspace (Dataspace space_id) = + fmap Dataspace $ + withErrorCheck $ + h5s_copy space_id + +closeDataspace :: Dataspace -> IO () +closeDataspace (Dataspace space_id) = + withErrorCheck_ $ + h5s_close space_id + +encodeDataspace :: Dataspace -> IO BS.ByteString +encodeDataspace (Dataspace space_id) = + withOutByteString $ \buf bufSz -> + withInOut_ bufSz $ \ioBufSz -> + withErrorCheck_ $ + h5s_encode space_id buf ioBufSz + +decodeDataspace :: BS.ByteString -> IO Dataspace +decodeDataspace bs = BS.unsafeUseAsCString bs $ \buf -> + fmap Dataspace $ + withErrorCheck $ + h5s_decode (InArray buf) + +getSimpleDataspaceExtentNPoints :: Dataspace -> IO HSize +getSimpleDataspaceExtentNPoints (Dataspace space_id) = + fmap fromIntegral $ + withErrorWhen (< 0) $ + h5s_get_simple_extent_npoints space_id + +getSimpleDataspaceExtentNDims :: Dataspace -> IO CInt +getSimpleDataspaceExtentNDims (Dataspace space_id) = + withErrorWhen (< 0) $ + h5s_get_simple_extent_ndims space_id + +getSimpleDataspaceExtent :: Dataspace -> IO ([HSize], [Maybe HSize]) +getSimpleDataspaceExtent space@(Dataspace space_id) = do + n <- getSimpleDataspaceExtentNDims space + + (dims, (maxDims, n')) <- + withOutList (fromIntegral n) $ \dims -> + withOutList (fromIntegral n) $ \maxDims -> + withErrorWhen (< 0) $ + h5s_get_simple_extent_dims space_id dims maxDims + + assert (n==n') $ return + ( map HSize dims + , [ if d == h5s_UNLIMITED then Nothing else Just (HSize d) | d <- maxDims] + ) + +isSimpleDataspace :: Dataspace -> IO Bool +isSimpleDataspace (Dataspace space_id) = + htriToBool $ + h5s_is_simple space_id + +getDataspaceSelectionNPoints :: Dataspace -> IO HSize +getDataspaceSelectionNPoints (Dataspace space_id) = + fmap fromIntegral $ + withErrorWhen (< 0) $ + h5s_get_select_npoints space_id + +data SelectionOperator + = Set + | Or + | And + | Xor + | NotB + | NotA + | Append + | Prepend + deriving (Eq, Ord, Enum, Bounded, Read, Show) + +rawSelectionOperator :: SelectionOperator -> H5S_seloper_t +rawSelectionOperator Set = h5s_SELECT_SET +rawSelectionOperator Or = h5s_SELECT_OR +rawSelectionOperator And = h5s_SELECT_AND +rawSelectionOperator Xor = h5s_SELECT_XOR +rawSelectionOperator NotB = h5s_SELECT_NOTB +rawSelectionOperator NotA = h5s_SELECT_NOTA +rawSelectionOperator Append = h5s_SELECT_APPEND +rawSelectionOperator Prepend = h5s_SELECT_PREPEND + +selectHyperslab :: Dataspace -> SelectionOperator -> [(HSize, Maybe HSize, HSize, Maybe HSize)] -> IO () +selectHyperslab space@(Dataspace space_id) oper hyperSlab = do + nDims <- getSimpleDataspaceExtentNDims space + + when (length hyperSlab /= fromIntegral nDims) + (fail "selectHyperslab: the given hyperslab has the wrong number of dimensions for this dataspace") + + withErrorCheck_ $ + withInList' start $ \istart -> + maybe withNull withInList' stride $ \istride -> + withInList' count $ \icount -> + maybe withNull withInList' block $ \iblock -> + h5s_select_hyperslab space_id (rawSelectionOperator oper) istart istride icount iblock + where + (start, mbStrides, count, mbBlocks) = unzip4 hyperSlab + stride + | any isJust mbStrides = Just (map (fromMaybe 1) mbStrides) + | otherwise = Nothing + block + | any isJust mbBlocks = Just (map (fromMaybe 1) mbBlocks) + | otherwise = Nothing + withNull f = f (InArray nullPtr) + withInList' = withInList . map hSize + +selectElements :: Dataspace -> SelectionOperator -> V.Vector (SV.Vector HSize) -> IO () +selectElements space@(Dataspace space_id) oper elems = do + nDims <- getSimpleDataspaceExtentNDims space + + let nElems = V.length elems + packed = SV.generate (nElems * fromIntegral nDims) $ \i -> + case i `divMod` nElems of + (dim, elt) -> elems V.! elt SV.! dim + + withErrorCheck_ $ + withInVector packed $ \ielems -> + h5s_select_elements space_id (rawSelectionOperator oper) (fromIntegral nElems) (castWrappedPtr ielems) + +-- TODO: determine whether to throw an exception or simply report it +-- when the returned value is invalid. +getSimpleDataspaceExtentType :: Dataspace -> IO DataspaceClass +getSimpleDataspaceExtentType (Dataspace space_id) = + fmap dataspaceClass $ + withErrorWhen (\(H5S_class_t c) -> c < 0) $ + h5s_get_simple_extent_type space_id + +setDataspaceExtentNone :: Dataspace -> IO () +setDataspaceExtentNone (Dataspace space_id) = + withErrorCheck_ $ + h5s_set_extent_none space_id + +copyDataspaceExtent :: Dataspace -> Dataspace -> IO () +copyDataspaceExtent (Dataspace dst) (Dataspace src) = + withErrorCheck_ $ + h5s_extent_copy dst src + +dataspaceExtentsEqual :: Dataspace -> Dataspace -> IO Bool +dataspaceExtentsEqual (Dataspace s1) (Dataspace s2) = + htriToBool $ + h5s_extent_equal s1 s2 + +selectAll :: Dataspace -> IO () +selectAll (Dataspace space_id) = + withErrorCheck_ $ + h5s_select_all space_id + +selectNone :: Dataspace -> IO () +selectNone (Dataspace space_id) = + withErrorCheck_ $ + h5s_select_none space_id + +offsetSimpleDataspaceSelection :: Dataspace -> SV.Vector HSSize -> IO () +offsetSimpleDataspaceSelection space@(Dataspace space_id) offsets = do + nDims <- getSimpleDataspaceExtentNDims space + + when (fromIntegral nDims /= SV.length offsets) + (fail "offsetSimpleDataspaceSelection: offset vector's length must equal number dimensions in dataspace") + + withErrorCheck_ $ + withInVector offsets $ \ioffsets -> + h5s_offset_simple space_id (castWrappedPtr ioffsets) + +selectionValid :: Dataspace -> IO Bool +selectionValid (Dataspace space_id) = + htriToBool $ + h5s_select_valid space_id + +getHyperslabSelection :: Dataspace -> IO (V.Vector (SV.Vector HSize, SV.Vector HSize)) +getHyperslabSelection space = getHyperslabSelectionBlockList space 0 maxBound + +getHyperslabSelectionNBlocks :: Dataspace -> IO HSize +getHyperslabSelectionNBlocks (Dataspace space_id) = + fmap fromIntegral $ + withErrorWhen (< 0) $ + h5s_get_select_hyper_nblocks space_id + +getHyperslabSelectionBlockList :: Dataspace -> HSize -> HSize -> IO (V.Vector (SV.Vector HSize, SV.Vector HSize)) +getHyperslabSelectionBlockList space@(Dataspace space_id) startBlock numBlocks = do + n <- getHyperslabSelectionNBlocks space + nDims <- getSimpleDataspaceExtentNDims space + + let nBlks = min numBlocks (n - startBlock) + blkSize = 2 * fromIntegral nDims + numSizes = nBlks * blkSize + + + sizes <- withOutVector_ (fromIntegral numSizes) $ \buf -> + withErrorCheck_ $ + h5s_get_select_hyper_blocklist space_id (hSize startBlock) (hSize nBlks) (castWrappedPtr buf) + + let decodePt i = SV.slice i (fromIntegral nDims) sizes + decodeBlock i = (decodePt b, decodePt (b + fromIntegral nDims)) + where b = i * fromIntegral blkSize + return $! V.generate (fromIntegral nBlks) decodeBlock + +getElementSelection :: Dataspace -> IO (V.Vector (SV.Vector HSize)) +getElementSelection space = getElementSelectionPointList space 0 maxBound + +getElementSelectionNPoints :: Dataspace -> IO HSize +getElementSelectionNPoints (Dataspace space_id) = + fmap fromIntegral $ + withErrorWhen (< 0) $ + h5s_get_select_elem_npoints space_id + +getElementSelectionPointList :: Dataspace -> HSize -> HSize -> IO (V.Vector (SV.Vector HSize)) +getElementSelectionPointList space@(Dataspace space_id) startPoint numPoints = do + n <- getElementSelectionNPoints space + nDims <- getSimpleDataspaceExtentNDims space + + let nPts = min numPoints (n - startPoint) + sz = nPts * fromIntegral nDims + + rawPoints <- withOutVector_ (fromIntegral sz) $ \buf -> + withErrorCheck_ $ + h5s_get_select_elem_pointlist space_id (hSize startPoint) (hSize nPts) (castWrappedPtr buf) + + let unpackPt i = SV.generate (fromIntegral nDims) $ \j -> rawPoints SV.! (i + j * fromIntegral nPts) + + return $! V.generate (fromIntegral nPts) unpackPt + +getSelectionBounds :: Dataspace -> IO [(HSize, HSize)] +getSelectionBounds space@(Dataspace space_id) = do + n <- getSimpleDataspaceExtentNDims space + + (start, end) <- + withOutList (fromIntegral n) $ \start -> + withOutList_ (fromIntegral n) $ \end -> + withErrorCheck_ $ + h5s_get_select_bounds space_id start end + + return [(HSize s, HSize e) | (s,e) <- zip start end] + +data SelectionType + = Points + | Hyperslabs + deriving (Eq, Ord, Bounded, Enum, Read, Show) + +selectionType :: H5S_sel_type -> Maybe SelectionType +selectionType c + | c == h5s_SEL_NONE = Nothing + | c == h5s_SEL_POINTS = Just Points + | c == h5s_SEL_HYPERSLABS = Just Hyperslabs + | otherwise = error ("unknown h5s_SEL value" ++ show c) + +getSelectionType :: Dataspace -> IO (Maybe SelectionType) +getSelectionType (Dataspace space_id) = + fmap selectionType $ + withErrorWhen (\(H5S_sel_type c) -> c < 0) $ + h5s_get_select_type space_id diff --git a/src/Bindings/HDF5/ErrorCodes.hs b/src/Bindings/HDF5/ErrorCodes.hs deleted file mode 100644 --- a/src/Bindings/HDF5/ErrorCodes.hs +++ /dev/null @@ -1,500 +0,0 @@ -{-# LANGUAGE DeriveDataTypeable, FlexibleInstances #-} -module Bindings.HDF5.ErrorCodes - ( MajorErrCode(..), majorErrorCode, majorErrorFromCode - , MinorErrCode(..), minorErrorCode, minorErrorFromCode - - ) where -import Data.Maybe - -import Bindings.HDF5.Raw.H5E -import Bindings.HDF5.Raw.H5I -import Data.Typeable (Typeable) -import Foreign - -data MajorErrCode - -- |Dataset - = Dataset - -- |Function entry/exit - | Func - -- |Data storage - | Storage - -- |File accessability - | File - -- |Shared Object Header Messages - | SOHM - -- |Symbol table - | Sym - -- |Virtual File Layer - | VFL - -- |Internal error (too specific to document in detail) - | Internal - -- |B-Tree node - | BTree - -- |References - | Reference - -- |Dataspace - | Dataspace - -- |Resource unavailable - | Resource - -- |Property lists - | PList - -- |Links - | Link - -- |Datatype - | Datatype - -- |Reference Counted Strings - | RS - -- |Heap - | Heap - -- |Object header - | OHDR - -- |Object atom - | Atom - -- |Attribute - | Attr - -- |Low-level I/O - | IO - -- |Skip Lists - | SList - -- |External file list - | EFL - -- |Ternary Search Trees - | TST - -- |Invalid arguments to routine - | Args - -- |Error API - | Error - -- |Data filters - | PLine - -- |Free Space Manager - | FSpace - -- |Object cache - | Cache - - -- |Unrecognized major error code - | UnknownMajor HId_t - deriving (Eq, Ord, Show, Typeable) - -rawMajorErrCodesInv :: [(HId_t, Maybe MajorErrCode)] -rawMajorErrCodesInv = [(a,b) | (b,a) <- rawMajorErrCodes] - -rawMajorErrCodes :: [(Maybe MajorErrCode, HId_t)] -rawMajorErrCodes = - [ (Nothing, h5e_NONE_MAJOR) - , (Just Dataset, h5e_DATASET) - , (Just Func, h5e_FUNC) - , (Just Storage, h5e_STORAGE) - , (Just File, h5e_FILE) - , (Just SOHM, h5e_SOHM) - , (Just Sym, h5e_SYM) - , (Just VFL, h5e_VFL) - , (Just Internal, h5e_INTERNAL) - , (Just BTree, h5e_BTREE) - , (Just Reference, h5e_REFERENCE) - , (Just Dataspace, h5e_DATASPACE) - , (Just Resource, h5e_RESOURCE) - , (Just PList, h5e_PLIST) - , (Just Link, h5e_LINK) - , (Just Datatype, h5e_DATATYPE) - , (Just RS, h5e_RS) - , (Just Heap, h5e_HEAP) - , (Just OHDR, h5e_OHDR) - , (Just Atom, h5e_ATOM) - , (Just Attr, h5e_ATTR) - , (Just IO, h5e_IO) - , (Just SList, h5e_SLIST) - , (Just EFL, h5e_EFL) - , (Just TST, h5e_TST) - , (Just Args, h5e_ARGS) - , (Just Error, h5e_ERROR) - , (Just PLine, h5e_PLINE) - , (Just FSpace, h5e_FSPACE) - , (Just Cache, h5e_CACHE) - ] - -majorErrorCode :: Maybe MajorErrCode -> Maybe HId_t -majorErrorCode (Just (UnknownMajor code)) = Just code -majorErrorCode err = lookup err rawMajorErrCodes - -majorErrorFromCode :: HId_t -> Maybe MajorErrCode -majorErrorFromCode code = - fromMaybe (Just (UnknownMajor code)) - (lookup code rawMajorErrCodesInv) - -instance Storable (Maybe MajorErrCode) where - sizeOf _ = sizeOf (undefined :: HId_t) - alignment _ = alignment (undefined :: HId_t) - - peek = fmap majorErrorFromCode . peek . castPtr - poke p err = case majorErrorCode err of - Nothing -> fail ("Unknown major error code: " ++ show err) - Just code -> poke (castPtr p) code - -data MinorErrCode - = SeekError - -- |Read failed - | ReadError - -- |Write failed - | WriteError - -- |Close failed - | CloseError - -- |Address overflowed - | Overflow - -- |File control (fcntl) failed - | FCNTL - -- |No space available for allocation - | NoSpace - -- |Can't allocate space - | CantAlloc - -- |Unable to copy object - | CantCopy - -- |Unable to free object - | CantFree - -- |Object already exists - | AlreadyExists - -- |Unable to lock object - | CantLock - -- |Unable to unlock object - | CantUnlock - -- |Unable to garbage collect - | CantGC - -- |Unable to compute size - | CantGetSize - -- |Object is already open - | ObjOpen - -- |Can't restore condition - | CantRestore - -- |Can't compute value - | CantCompute - -- |Can't extend heap's space - | CantExtend - -- |Can't attach object - | CantAttach - -- |Can't update object - | CantUpdate - -- |Can't operate on object - | CantOperate - -- |Unable to initialize object - | CantInit - -- |Object already initialized - | AlreadyInit - -- |Unable to release object - | CantRelease - -- |Can't get value - | CantGet - -- |Can't set value - | CantSet - -- |Duplicate class name in parent class - | DupClass - -- |Can't merge objects - | CantMerge - -- |Can't revive object - | CantRevive - -- |Can't shrink container - | CantShrink - -- |Bad object header link count - | LinkCount - -- |Wrong version number - | Version - -- |Alignment error - | Alignment - -- |Unrecognized message - | BadMesg - -- |Can't delete message - | CantDelete - -- |Iteration failed - | BadIter - -- |Can't pack messages - | CantPack - -- |Can't reset object - | CantReset - -- |Unable to rename object - | CantRename - -- |System error message - | SysErrStr - -- |Requested filter is not available - | NoFilter - -- |Callback failed - | Callback - -- |Error from filter 'can apply' callback - | CanApply - -- |Error from filter 'set local' callback - | SetLocal - -- |Filter present but encoding disabled - | NoEncoder - -- |Filter operation failed - | CantFilter - -- |Can't open object - | CantOpenObj - -- |Can't close object - | CantCloseObj - -- |Name component is too long - | CompLen - -- |Problem with path to object - | Path - -- |File already exists - | FileExists - -- |File already open - | FileOpen - -- |Unable to create file - | CantCreate - -- |Unable to open file - | CantOpenFile - -- |Unable to close file - | CantCloseFile - -- |Not an HDF5 file - | NotHDF5 - -- |Bad file ID accessed - | BadFile - -- |File has been truncated - | Truncated - -- |File mount error - | Mount - -- |Unable to find atom information (already closed?) - | BadAtom - -- |Unable to find ID group information - | BadGroup - -- |Unable to register new atom - | CantRegister - -- |Unable to increment reference count - | CantInc - -- |Unable to decrement reference count - | CantDec - -- |Out of IDs for group - | NoIds - -- |Unable to flush data from cache - | CantFlush - -- |Unable to serialize data from cache - | CantSerialize - -- |Unable to load metadata into cache - | CantLoad - -- |Protected metadata error - | Protect - -- |Metadata not currently cached - | NotCached - -- |Internal error detected - | System - -- |Unable to insert metadata into cache - | CantIns - -- |Unable to protect metadata - | CantProtect - -- |Unable to unprotect metadata - | CanTUnprotect - -- |Unable to pin cache entry - | CantPin - -- |Unable to un-pin cache entry - | CantUnpin - -- |Unable to mark a pinned entry as dirty - | CantMarkDirty - -- |Unable to mark metadata as dirty - | CantDirty - -- |Unable to expunge a metadata cache entry - | CantExpunge - -- |Unable to resize a metadata cache entry - | CantResize - -- |Link traversal failure - | Traverse - -- |Too many soft links in path - | NLinks - -- |Link class not registered - | NotRegistered - -- |Can't move object - | CantMove - -- |Can't sort objects - | CantSort - -- |Some MPI function failed - | MPI - -- |MPI Error String - | MPIErrStr - -- |Can't receive data - | CantRecv - -- |Can't clip hyperslab region - | CantClip - -- |Can't count elements - | CantCount - -- |Can't select hyperslab - | CantSelect - -- |Can't move to next iterator location - | CantNext - -- |Invalid selection - | BadSelect - -- |Can't compare objects - | CantCompare - -- |Information is uinitialized - | Uninitialized - -- |Feature is unsupported - | Unsupported - -- |Inappropriate type - | BadType - -- |Out of range - | BadRange - -- |Bad value - | BadValue - -- |Object not found - | NotFound - -- |Object already exists - | Exists - -- |Unable to encode value - | CantEncode - -- |Unable to decode value - | CantDecode - -- |Unable to split node - | CantSplit - -- |Unable to redistribute records - | CantRedistribute - -- |Unable to swap records - | CantSwap - -- |Unable to insert object - | CantInsert - -- |Unable to list node - | CantList - -- |Unable to modify record - | CantModify - -- |Unable to remove object - | CantRemove - -- |Can't convert datatypes - | CantConvert - -- |Bad size for object - | BadSize - - -- |Unrecognized minor error code - | UnknownMinor HId_t - deriving (Eq, Ord, Show, Typeable) - -rawMinorErrCodesInv :: [(HId_t, Maybe MinorErrCode)] -rawMinorErrCodesInv = [(a,b) | (b,a) <- rawMinorErrCodes] -rawMinorErrCodes :: [(Maybe MinorErrCode, HId_t)] -rawMinorErrCodes = - [ (Nothing, h5e_NONE_MINOR) - , (Just SeekError, h5e_SEEKERROR) - , (Just ReadError, h5e_READERROR) - , (Just WriteError, h5e_WRITEERROR) - , (Just CloseError, h5e_CLOSEERROR) - , (Just Overflow, h5e_OVERFLOW) - , (Just FCNTL, h5e_FCNTL) - , (Just NoSpace, h5e_NOSPACE) - , (Just CantAlloc, h5e_CANTALLOC) - , (Just CantCopy, h5e_CANTCOPY) - , (Just CantFree, h5e_CANTFREE) - , (Just AlreadyExists, h5e_ALREADYEXISTS) - , (Just CantLock, h5e_CANTLOCK) - , (Just CantUnlock, h5e_CANTUNLOCK) - , (Just CantGC, h5e_CANTGC) - , (Just CantGetSize, h5e_CANTGETSIZE) - , (Just ObjOpen, h5e_OBJOPEN) - , (Just CantRestore, h5e_CANTRESTORE) - , (Just CantCompute, h5e_CANTCOMPUTE) - , (Just CantExtend, h5e_CANTEXTEND) - , (Just CantAttach, h5e_CANTATTACH) - , (Just CantUpdate, h5e_CANTUPDATE) - , (Just CantOperate, h5e_CANTOPERATE) - , (Just CantInit, h5e_CANTINIT) - , (Just AlreadyInit, h5e_ALREADYINIT) - , (Just CantRelease, h5e_CANTRELEASE) - , (Just CantGet, h5e_CANTGET) - , (Just CantSet, h5e_CANTSET) - , (Just DupClass, h5e_DUPCLASS) - , (Just CantMerge, h5e_CANTMERGE) - , (Just CantRevive, h5e_CANTREVIVE) - , (Just CantShrink, h5e_CANTSHRINK) - , (Just LinkCount, h5e_LINKCOUNT) - , (Just Version, h5e_VERSION) - , (Just Alignment, h5e_ALIGNMENT) - , (Just BadMesg, h5e_BADMESG) - , (Just CantDelete, h5e_CANTDELETE) - , (Just BadIter, h5e_BADITER) - , (Just CantPack, h5e_CANTPACK) - , (Just CantReset, h5e_CANTRESET) - , (Just CantRename, h5e_CANTRENAME) - , (Just SysErrStr, h5e_SYSERRSTR) - , (Just NoFilter, h5e_NOFILTER) - , (Just Callback, h5e_CALLBACK) - , (Just CanApply, h5e_CANAPPLY) - , (Just SetLocal, h5e_SETLOCAL) - , (Just NoEncoder, h5e_NOENCODER) - , (Just CantFilter, h5e_CANTFILTER) - , (Just CantOpenObj, h5e_CANTOPENOBJ) - , (Just CantCloseObj, h5e_CANTCLOSEOBJ) - , (Just CompLen, h5e_COMPLEN) - , (Just Path, h5e_PATH) - , (Just FileExists, h5e_FILEEXISTS) - , (Just FileOpen, h5e_FILEOPEN) - , (Just CantCreate, h5e_CANTCREATE) - , (Just CantOpenFile, h5e_CANTOPENFILE) - , (Just CantCloseFile, h5e_CANTCLOSEFILE) - , (Just NotHDF5, h5e_NOTHDF5) - , (Just BadFile, h5e_BADFILE) - , (Just Truncated, h5e_TRUNCATED) - , (Just Mount, h5e_MOUNT) - , (Just BadAtom, h5e_BADATOM) - , (Just BadGroup, h5e_BADGROUP) - , (Just CantRegister, h5e_CANTREGISTER) - , (Just CantInc, h5e_CANTINC) - , (Just CantDec, h5e_CANTDEC) - , (Just NoIds, h5e_NOIDS) - , (Just CantFlush, h5e_CANTFLUSH) - , (Just CantSerialize, h5e_CANTSERIALIZE) - , (Just CantLoad, h5e_CANTLOAD) - , (Just Protect, h5e_PROTECT) - , (Just NotCached, h5e_NOTCACHED) - , (Just System, h5e_SYSTEM) - , (Just CantIns, h5e_CANTINS) - , (Just CantProtect, h5e_CANTPROTECT) - , (Just CanTUnprotect, h5e_CANTUNPROTECT) - , (Just CantPin, h5e_CANTPIN) - , (Just CantUnpin, h5e_CANTUNPIN) - , (Just CantMarkDirty, h5e_CANTMARKDIRTY) - , (Just CantDirty, h5e_CANTDIRTY) - , (Just CantExpunge, h5e_CANTEXPUNGE) - , (Just CantResize, h5e_CANTRESIZE) - , (Just Traverse, h5e_TRAVERSE) - , (Just NLinks, h5e_NLINKS) - , (Just NotRegistered, h5e_NOTREGISTERED) - , (Just CantMove, h5e_CANTMOVE) - , (Just CantSort, h5e_CANTSORT) - , (Just MPI, h5e_MPI) - , (Just MPIErrStr, h5e_MPIERRSTR) - , (Just CantRecv, h5e_CANTRECV) - , (Just CantClip, h5e_CANTCLIP) - , (Just CantCount, h5e_CANTCOUNT) - , (Just CantSelect, h5e_CANTSELECT) - , (Just CantNext, h5e_CANTNEXT) - , (Just BadSelect, h5e_BADSELECT) - , (Just CantCompare, h5e_CANTCOMPARE) - , (Just Uninitialized, h5e_UNINITIALIZED) - , (Just Unsupported, h5e_UNSUPPORTED) - , (Just BadType, h5e_BADTYPE) - , (Just BadRange, h5e_BADRANGE) - , (Just BadValue, h5e_BADVALUE) - , (Just NotFound, h5e_NOTFOUND) - , (Just Exists, h5e_EXISTS) - , (Just CantEncode, h5e_CANTENCODE) - , (Just CantDecode, h5e_CANTDECODE) - , (Just CantSplit, h5e_CANTSPLIT) - , (Just CantRedistribute, h5e_CANTREDISTRIBUTE) - , (Just CantSwap, h5e_CANTSWAP) - , (Just CantInsert, h5e_CANTINSERT) - , (Just CantList, h5e_CANTLIST) - , (Just CantModify, h5e_CANTMODIFY) - , (Just CantRemove, h5e_CANTREMOVE) - , (Just CantConvert, h5e_CANTCONVERT) - , (Just BadSize, h5e_BADSIZE) - ] - -minorErrorCode :: Maybe MinorErrCode -> Maybe HId_t -minorErrorCode (Just (UnknownMinor code)) = Just code -minorErrorCode err = lookup err rawMinorErrCodes - -minorErrorFromCode :: HId_t -> Maybe MinorErrCode -minorErrorFromCode code = - fromMaybe (Just (UnknownMinor code)) - (lookup code rawMinorErrCodesInv) - -instance Storable (Maybe MinorErrCode) where - sizeOf _ = sizeOf (undefined :: HId_t) - alignment _ = alignment (undefined :: HId_t) - - peek = fmap minorErrorFromCode . peek . castPtr - poke p err = case minorErrorCode err of - Nothing -> fail ("Unknown minor error code: " ++ show err) - Just code -> poke (castPtr p) code diff --git a/src/Bindings/HDF5/ErrorCodes.hsc b/src/Bindings/HDF5/ErrorCodes.hsc new file mode 100644 --- /dev/null +++ b/src/Bindings/HDF5/ErrorCodes.hsc @@ -0,0 +1,508 @@ +#include +#include + +{-# LANGUAGE DeriveDataTypeable, FlexibleInstances #-} +{-# LANGUAGE CPP #-} +module Bindings.HDF5.ErrorCodes + ( MajorErrCode(..), majorErrorCode, majorErrorFromCode + , MinorErrCode(..), minorErrorCode, minorErrorFromCode + + ) where +import Data.Maybe + +import Bindings.HDF5.Raw.H5E +import Bindings.HDF5.Raw.H5I +import Data.Typeable (Typeable) +import Foreign + +data MajorErrCode + -- |Dataset + = Dataset + -- |Function entry/exit + | Func + -- |Data storage + | Storage + -- |File accessability + | File + -- |Shared Object Header Messages + | SOHM + -- |Symbol table + | Sym + -- |Virtual File Layer + | VFL + -- |Internal error (too specific to document in detail) + | Internal + -- |B-Tree node + | BTree + -- |References + | Reference + -- |Dataspace + | Dataspace + -- |Resource unavailable + | Resource + -- |Property lists + | PList + -- |Links + | Link + -- |Datatype + | Datatype + -- |Reference Counted Strings + | RS + -- |Heap + | Heap + -- |Object header + | OHDR + -- |Object atom + | Atom + -- |Attribute + | Attr + -- |Low-level I/O + | IO + -- |Skip Lists + | SList + -- |External file list + | EFL + -- |Ternary Search Trees + | TST + -- |Invalid arguments to routine + | Args + -- |Error API + | Error + -- |Data filters + | PLine + -- |Free Space Manager + | FSpace + -- |Object cache + | Cache + + -- |Unrecognized major error code + | UnknownMajor HId_t + deriving (Eq, Ord, Show, Typeable) + +rawMajorErrCodesInv :: [(HId_t, Maybe MajorErrCode)] +rawMajorErrCodesInv = [(a,b) | (b,a) <- rawMajorErrCodes] + +rawMajorErrCodes :: [(Maybe MajorErrCode, HId_t)] +rawMajorErrCodes = + [ (Nothing, h5e_NONE_MAJOR) + , (Just Dataset, h5e_DATASET) + , (Just Func, h5e_FUNC) + , (Just Storage, h5e_STORAGE) + , (Just File, h5e_FILE) + , (Just SOHM, h5e_SOHM) + , (Just Sym, h5e_SYM) + , (Just VFL, h5e_VFL) + , (Just Internal, h5e_INTERNAL) + , (Just BTree, h5e_BTREE) + , (Just Reference, h5e_REFERENCE) + , (Just Dataspace, h5e_DATASPACE) + , (Just Resource, h5e_RESOURCE) + , (Just PList, h5e_PLIST) + , (Just Link, h5e_LINK) + , (Just Datatype, h5e_DATATYPE) + , (Just RS, h5e_RS) + , (Just Heap, h5e_HEAP) + , (Just OHDR, h5e_OHDR) +#if !H5_VERSION_GE(1,8,14) + , (Just Atom, h5e_ATOM) +#endif + , (Just Attr, h5e_ATTR) + , (Just IO, h5e_IO) + , (Just SList, h5e_SLIST) + , (Just EFL, h5e_EFL) + , (Just TST, h5e_TST) + , (Just Args, h5e_ARGS) + , (Just Error, h5e_ERROR) + , (Just PLine, h5e_PLINE) + , (Just FSpace, h5e_FSPACE) + , (Just Cache, h5e_CACHE) + ] + +majorErrorCode :: Maybe MajorErrCode -> Maybe HId_t +majorErrorCode (Just (UnknownMajor code)) = Just code +majorErrorCode err = lookup err rawMajorErrCodes + +majorErrorFromCode :: HId_t -> Maybe MajorErrCode +majorErrorFromCode code = + fromMaybe (Just (UnknownMajor code)) + (lookup code rawMajorErrCodesInv) + +instance Storable (Maybe MajorErrCode) where + sizeOf _ = sizeOf (undefined :: HId_t) + alignment _ = alignment (undefined :: HId_t) + + peek = fmap majorErrorFromCode . peek . castPtr + poke p err = case majorErrorCode err of + Nothing -> fail ("Unknown major error code: " ++ show err) + Just code -> poke (castPtr p) code + +data MinorErrCode + = SeekError + -- |Read failed + | ReadError + -- |Write failed + | WriteError + -- |Close failed + | CloseError + -- |Address overflowed + | Overflow + -- |File control (fcntl) failed + | FCNTL + -- |No space available for allocation + | NoSpace + -- |Can't allocate space + | CantAlloc + -- |Unable to copy object + | CantCopy + -- |Unable to free object + | CantFree + -- |Object already exists + | AlreadyExists + -- |Unable to lock object + | CantLock + -- |Unable to unlock object + | CantUnlock + -- |Unable to garbage collect + | CantGC + -- |Unable to compute size + | CantGetSize + -- |Object is already open + | ObjOpen + -- |Can't restore condition + | CantRestore + -- |Can't compute value + | CantCompute + -- |Can't extend heap's space + | CantExtend + -- |Can't attach object + | CantAttach + -- |Can't update object + | CantUpdate + -- |Can't operate on object + | CantOperate + -- |Unable to initialize object + | CantInit + -- |Object already initialized + | AlreadyInit + -- |Unable to release object + | CantRelease + -- |Can't get value + | CantGet + -- |Can't set value + | CantSet + -- |Duplicate class name in parent class + | DupClass + -- |Can't merge objects + | CantMerge + -- |Can't revive object + | CantRevive + -- |Can't shrink container + | CantShrink + -- |Bad object header link count + | LinkCount + -- |Wrong version number + | Version + -- |Alignment error + | Alignment + -- |Unrecognized message + | BadMesg + -- |Can't delete message + | CantDelete + -- |Iteration failed + | BadIter + -- |Can't pack messages + | CantPack + -- |Can't reset object + | CantReset + -- |Unable to rename object + | CantRename + -- |System error message + | SysErrStr + -- |Requested filter is not available + | NoFilter + -- |Callback failed + | Callback + -- |Error from filter 'can apply' callback + | CanApply + -- |Error from filter 'set local' callback + | SetLocal + -- |Filter present but encoding disabled + | NoEncoder + -- |Filter operation failed + | CantFilter + -- |Can't open object + | CantOpenObj + -- |Can't close object + | CantCloseObj + -- |Name component is too long + | CompLen + -- |Problem with path to object + | Path + -- |File already exists + | FileExists + -- |File already open + | FileOpen + -- |Unable to create file + | CantCreate + -- |Unable to open file + | CantOpenFile + -- |Unable to close file + | CantCloseFile + -- |Not an HDF5 file + | NotHDF5 + -- |Bad file ID accessed + | BadFile + -- |File has been truncated + | Truncated + -- |File mount error + | Mount + -- |Unable to find atom information (already closed?) + | BadAtom + -- |Unable to find ID group information + | BadGroup + -- |Unable to register new atom + | CantRegister + -- |Unable to increment reference count + | CantInc + -- |Unable to decrement reference count + | CantDec + -- |Out of IDs for group + | NoIds + -- |Unable to flush data from cache + | CantFlush + -- |Unable to serialize data from cache + | CantSerialize + -- |Unable to load metadata into cache + | CantLoad + -- |Protected metadata error + | Protect + -- |Metadata not currently cached + | NotCached + -- |Internal error detected + | System + -- |Unable to insert metadata into cache + | CantIns + -- |Unable to protect metadata + | CantProtect + -- |Unable to unprotect metadata + | CanTUnprotect + -- |Unable to pin cache entry + | CantPin + -- |Unable to un-pin cache entry + | CantUnpin + -- |Unable to mark a pinned entry as dirty + | CantMarkDirty + -- |Unable to mark metadata as dirty + | CantDirty + -- |Unable to expunge a metadata cache entry + | CantExpunge + -- |Unable to resize a metadata cache entry + | CantResize + -- |Link traversal failure + | Traverse + -- |Too many soft links in path + | NLinks + -- |Link class not registered + | NotRegistered + -- |Can't move object + | CantMove + -- |Can't sort objects + | CantSort + -- |Some MPI function failed + | MPI + -- |MPI Error String + | MPIErrStr + -- |Can't receive data + | CantRecv + -- |Can't clip hyperslab region + | CantClip + -- |Can't count elements + | CantCount + -- |Can't select hyperslab + | CantSelect + -- |Can't move to next iterator location + | CantNext + -- |Invalid selection + | BadSelect + -- |Can't compare objects + | CantCompare + -- |Information is uinitialized + | Uninitialized + -- |Feature is unsupported + | Unsupported + -- |Inappropriate type + | BadType + -- |Out of range + | BadRange + -- |Bad value + | BadValue + -- |Object not found + | NotFound + -- |Object already exists + | Exists + -- |Unable to encode value + | CantEncode + -- |Unable to decode value + | CantDecode + -- |Unable to split node + | CantSplit + -- |Unable to redistribute records + | CantRedistribute + -- |Unable to swap records + | CantSwap + -- |Unable to insert object + | CantInsert + -- |Unable to list node + | CantList + -- |Unable to modify record + | CantModify + -- |Unable to remove object + | CantRemove + -- |Can't convert datatypes + | CantConvert + -- |Bad size for object + | BadSize + + -- |Unrecognized minor error code + | UnknownMinor HId_t + deriving (Eq, Ord, Show, Typeable) + +rawMinorErrCodesInv :: [(HId_t, Maybe MinorErrCode)] +rawMinorErrCodesInv = [(a,b) | (b,a) <- rawMinorErrCodes] +rawMinorErrCodes :: [(Maybe MinorErrCode, HId_t)] +rawMinorErrCodes = + [ (Nothing, h5e_NONE_MINOR) + , (Just SeekError, h5e_SEEKERROR) + , (Just ReadError, h5e_READERROR) + , (Just WriteError, h5e_WRITEERROR) + , (Just CloseError, h5e_CLOSEERROR) + , (Just Overflow, h5e_OVERFLOW) + , (Just FCNTL, h5e_FCNTL) + , (Just NoSpace, h5e_NOSPACE) + , (Just CantAlloc, h5e_CANTALLOC) + , (Just CantCopy, h5e_CANTCOPY) + , (Just CantFree, h5e_CANTFREE) + , (Just AlreadyExists, h5e_ALREADYEXISTS) + , (Just CantLock, h5e_CANTLOCK) + , (Just CantUnlock, h5e_CANTUNLOCK) + , (Just CantGC, h5e_CANTGC) + , (Just CantGetSize, h5e_CANTGETSIZE) + , (Just ObjOpen, h5e_OBJOPEN) + , (Just CantRestore, h5e_CANTRESTORE) + , (Just CantCompute, h5e_CANTCOMPUTE) + , (Just CantExtend, h5e_CANTEXTEND) + , (Just CantAttach, h5e_CANTATTACH) + , (Just CantUpdate, h5e_CANTUPDATE) + , (Just CantOperate, h5e_CANTOPERATE) + , (Just CantInit, h5e_CANTINIT) + , (Just AlreadyInit, h5e_ALREADYINIT) + , (Just CantRelease, h5e_CANTRELEASE) + , (Just CantGet, h5e_CANTGET) + , (Just CantSet, h5e_CANTSET) + , (Just DupClass, h5e_DUPCLASS) + , (Just CantMerge, h5e_CANTMERGE) + , (Just CantRevive, h5e_CANTREVIVE) + , (Just CantShrink, h5e_CANTSHRINK) + , (Just LinkCount, h5e_LINKCOUNT) + , (Just Version, h5e_VERSION) + , (Just Alignment, h5e_ALIGNMENT) + , (Just BadMesg, h5e_BADMESG) + , (Just CantDelete, h5e_CANTDELETE) + , (Just BadIter, h5e_BADITER) + , (Just CantPack, h5e_CANTPACK) + , (Just CantReset, h5e_CANTRESET) + , (Just CantRename, h5e_CANTRENAME) + , (Just SysErrStr, h5e_SYSERRSTR) + , (Just NoFilter, h5e_NOFILTER) + , (Just Callback, h5e_CALLBACK) + , (Just CanApply, h5e_CANAPPLY) + , (Just SetLocal, h5e_SETLOCAL) + , (Just NoEncoder, h5e_NOENCODER) + , (Just CantFilter, h5e_CANTFILTER) + , (Just CantOpenObj, h5e_CANTOPENOBJ) + , (Just CantCloseObj, h5e_CANTCLOSEOBJ) + , (Just CompLen, h5e_COMPLEN) + , (Just Path, h5e_PATH) + , (Just FileExists, h5e_FILEEXISTS) + , (Just FileOpen, h5e_FILEOPEN) + , (Just CantCreate, h5e_CANTCREATE) + , (Just CantOpenFile, h5e_CANTOPENFILE) + , (Just CantCloseFile, h5e_CANTCLOSEFILE) + , (Just NotHDF5, h5e_NOTHDF5) + , (Just BadFile, h5e_BADFILE) + , (Just Truncated, h5e_TRUNCATED) + , (Just Mount, h5e_MOUNT) +#if !H5_VERSION_GE(1,8,14) + , (Just BadAtom, h5e_BADATOM) +#endif + , (Just BadGroup, h5e_BADGROUP) + , (Just CantRegister, h5e_CANTREGISTER) + , (Just CantInc, h5e_CANTINC) + , (Just CantDec, h5e_CANTDEC) + , (Just NoIds, h5e_NOIDS) + , (Just CantFlush, h5e_CANTFLUSH) + , (Just CantSerialize, h5e_CANTSERIALIZE) + , (Just CantLoad, h5e_CANTLOAD) + , (Just Protect, h5e_PROTECT) + , (Just NotCached, h5e_NOTCACHED) + , (Just System, h5e_SYSTEM) + , (Just CantIns, h5e_CANTINS) + , (Just CantProtect, h5e_CANTPROTECT) + , (Just CanTUnprotect, h5e_CANTUNPROTECT) + , (Just CantPin, h5e_CANTPIN) + , (Just CantUnpin, h5e_CANTUNPIN) + , (Just CantMarkDirty, h5e_CANTMARKDIRTY) + , (Just CantDirty, h5e_CANTDIRTY) + , (Just CantExpunge, h5e_CANTEXPUNGE) + , (Just CantResize, h5e_CANTRESIZE) + , (Just Traverse, h5e_TRAVERSE) + , (Just NLinks, h5e_NLINKS) + , (Just NotRegistered, h5e_NOTREGISTERED) + , (Just CantMove, h5e_CANTMOVE) + , (Just CantSort, h5e_CANTSORT) + , (Just MPI, h5e_MPI) + , (Just MPIErrStr, h5e_MPIERRSTR) + , (Just CantRecv, h5e_CANTRECV) + , (Just CantClip, h5e_CANTCLIP) + , (Just CantCount, h5e_CANTCOUNT) + , (Just CantSelect, h5e_CANTSELECT) + , (Just CantNext, h5e_CANTNEXT) + , (Just BadSelect, h5e_BADSELECT) + , (Just CantCompare, h5e_CANTCOMPARE) + , (Just Uninitialized, h5e_UNINITIALIZED) + , (Just Unsupported, h5e_UNSUPPORTED) + , (Just BadType, h5e_BADTYPE) + , (Just BadRange, h5e_BADRANGE) + , (Just BadValue, h5e_BADVALUE) + , (Just NotFound, h5e_NOTFOUND) + , (Just Exists, h5e_EXISTS) + , (Just CantEncode, h5e_CANTENCODE) + , (Just CantDecode, h5e_CANTDECODE) + , (Just CantSplit, h5e_CANTSPLIT) + , (Just CantRedistribute, h5e_CANTREDISTRIBUTE) + , (Just CantSwap, h5e_CANTSWAP) + , (Just CantInsert, h5e_CANTINSERT) + , (Just CantList, h5e_CANTLIST) + , (Just CantModify, h5e_CANTMODIFY) + , (Just CantRemove, h5e_CANTREMOVE) + , (Just CantConvert, h5e_CANTCONVERT) + , (Just BadSize, h5e_BADSIZE) + ] + +minorErrorCode :: Maybe MinorErrCode -> Maybe HId_t +minorErrorCode (Just (UnknownMinor code)) = Just code +minorErrorCode err = lookup err rawMinorErrCodes + +minorErrorFromCode :: HId_t -> Maybe MinorErrCode +minorErrorFromCode code = + fromMaybe (Just (UnknownMinor code)) + (lookup code rawMinorErrCodesInv) + +instance Storable (Maybe MinorErrCode) where + sizeOf _ = sizeOf (undefined :: HId_t) + alignment _ = alignment (undefined :: HId_t) + + peek = fmap minorErrorFromCode . peek . castPtr + poke p err = case minorErrorCode err of + Nothing -> fail ("Unknown minor error code: " ++ show err) + Just code -> poke (castPtr p) code diff --git a/src/Bindings/HDF5/File.hs b/src/Bindings/HDF5/File.hs deleted file mode 100644 --- a/src/Bindings/HDF5/File.hs +++ /dev/null @@ -1,284 +0,0 @@ -{-# LANGUAGE GeneralizedNewtypeDeriving #-} -{-# LANGUAGE FlexibleInstances #-} -module Bindings.HDF5.File - ( AccFlags(..) - , ObjType(..) - , Scope(..) - - , isHDF5 - - , File - , createFile - , openFile - , reopenFile - , flushFile - , closeFile - - , mountFile - , unmountFile - - , getFileSize - , getFileCreatePlist - , getFileAccessPlist - - , FileInfo(..) - , getFileInfo - , getFileIntent - , getFileName - , getFileObjCount - - , getOpenObjects - , getFileFreespace --- , get_mdc_config --- , get_mdc_hit_rate --- , get_mdc_size --- , clear_elink_file_cache --- , reset_mdc_hit_rate_stats --- , set_mdc_config - ) where - -import Bindings.HDF5.Core -import Bindings.HDF5.Error -import Bindings.HDF5.Object -import Bindings.HDF5.PropertyList.FAPL -import Bindings.HDF5.PropertyList.FCPL -import Bindings.HDF5.PropertyList.FMPL -import Bindings.HDF5.Raw.H5 -import Bindings.HDF5.Raw.H5F -import Bindings.HDF5.Raw.H5I -import Bindings.HDF5.Raw.H5P -import Data.Bits -import Data.Maybe -import qualified Data.ByteString as BS -import qualified Data.Vector.Storable as SV -import Foreign.C -import Foreign.Ptr -import Foreign.Ptr.Conventions -import Foreign.Storable - --- TODO: determine whether all of these are valid for _both_ create and open. --- any that are not should be converted to Bool inputs to the corresponding function. --- It very well may be best to separate several of them out like that anyway. -data AccFlags - = ReadOnly - | ReadWrite - | Truncate - | FailIfExists - | Debug - | Create - deriving (Eq, Ord, Enum, Bounded, Read, Show) - -accFlagToInt :: AccFlags -> CUInt -accFlagToInt ReadOnly = h5f_ACC_RDONLY -accFlagToInt ReadWrite = h5f_ACC_RDWR -accFlagToInt Truncate = h5f_ACC_TRUNC -accFlagToInt FailIfExists = h5f_ACC_EXCL -accFlagToInt Debug = h5f_ACC_DEBUG -accFlagToInt Create = h5f_ACC_CREAT - -accFlagsToInt :: [AccFlags] -> CUInt -accFlagsToInt = foldl (.|.) 0 . map accFlagToInt - -intToAccFlags :: CUInt -> [AccFlags] -intToAccFlags x = - [ f - | f <- [minBound .. maxBound] - , accFlagToInt f .&. x /= 0 - ] - -instance Storable [AccFlags] where - sizeOf _ = sizeOf (0 :: CUInt) - alignment _ = alignment (0 :: CUInt) - peek = fmap intToAccFlags . peek . castPtr - poke p = poke (castPtr p) . accFlagsToInt - -data ObjType - = Files - | Datasets - | Groups - | Datatypes - | Attrs - | All - deriving (Eq, Ord, Enum, Bounded, Read, Show) - -objTypeToInt :: ObjType -> CUInt -objTypeToInt Files = h5f_OBJ_FILE -objTypeToInt Datasets = h5f_OBJ_DATASET -objTypeToInt Groups = h5f_OBJ_GROUP -objTypeToInt Datatypes = h5f_OBJ_DATATYPE -objTypeToInt Attrs = h5f_OBJ_ATTR -objTypeToInt All = h5f_OBJ_ALL - -objTypesToInt :: [ObjType] -> CUInt -objTypesToInt = foldl (.|.) 0 . map objTypeToInt - -intToObjTypes :: CUInt -> [ObjType] -intToObjTypes x = - [ f - | f <- [minBound .. maxBound] - , objTypeToInt f .&. x /= 0 - ] - -instance Storable [ObjType] where - sizeOf _ = sizeOf (0 :: CUInt) - alignment _ = alignment (0 :: CUInt) - peek = fmap intToObjTypes . peek . castPtr - poke p = poke (castPtr p) . objTypesToInt - -data Scope - = Local - | Global - deriving (Eq, Ord, Enum, Bounded, Read, Show) - -scopeCode :: Scope -> H5F_scope_t -scopeCode Local = h5f_SCOPE_LOCAL -scopeCode Global = h5f_SCOPE_GLOBAL - -data CloseDegree - = Weak - | Semi - | Strong - deriving (Eq, Ord, Enum, Bounded, Read, Show) - -rawCloseDegreesInv :: [(H5F_close_degree_t, Maybe CloseDegree)] -rawCloseDegreesInv = [(a,b) | (b,a) <- rawCloseDegrees] -rawCloseDegrees :: [(Maybe CloseDegree, H5F_close_degree_t)] -rawCloseDegrees = - [ (Nothing, h5f_CLOSE_DEFAULT) - , (Just Weak, h5f_CLOSE_WEAK) - , (Just Semi, h5f_CLOSE_SEMI) - , (Just Strong, h5f_CLOSE_STRONG) - ] - -closeDegreeFromCode :: H5F_close_degree_t -> Maybe CloseDegree -closeDegreeFromCode c = fromMaybe Nothing (lookup c rawCloseDegreesInv) - -closeDegreeToCode :: Maybe CloseDegree -> H5F_close_degree_t -closeDegreeToCode c = - fromMaybe (error ("closeDegreeToCode: unrecognized H5F_close_degree_t: " ++ show c)) - (lookup c rawCloseDegrees) - -instance Storable (Maybe CloseDegree) where - sizeOf _ = sizeOf (undefined :: H5F_close_degree_t) - alignment _ = alignment (undefined :: H5F_close_degree_t) - peek = fmap closeDegreeFromCode . peek . castPtr - poke p = poke (castPtr p) . closeDegreeToCode - -isHDF5 :: BS.ByteString -> IO Bool -isHDF5 filename = htriToBool (BS.useAsCString filename h5f_is_hdf5) - -newtype File = File HId_t - deriving (Eq, HId, FromHId, HDFResultType) - -instance Location File -instance Object File where - staticObjectType = Tagged (Just FileObj) - -createFile :: BS.ByteString -> [AccFlags] -> Maybe FCPL -> Maybe FAPL -> IO File -createFile filename flags create_plist access_plist = - fmap File $ - withErrorCheck $ - BS.useAsCString filename $ \cfilename -> - h5f_create cfilename (accFlagsToInt flags) (maybe h5p_DEFAULT hid create_plist) (maybe h5p_DEFAULT hid access_plist) - -openFile :: BS.ByteString -> [AccFlags] -> Maybe FAPL -> IO File -openFile filename flags access_plist = - fmap File $ - withErrorCheck $ - BS.useAsCString filename $ \cfilename -> - h5f_open cfilename (accFlagsToInt flags) (maybe h5p_DEFAULT hid access_plist) - -reopenFile :: File -> IO File -reopenFile (File file_id) = - fmap File $ - withErrorCheck $ - h5f_reopen file_id - -flushFile :: File -> Scope -> IO () -flushFile (File file_id) scope = - withErrorCheck_ $ - h5f_flush file_id (scopeCode scope) - -closeFile :: File -> IO () -closeFile (File file_id) = - withErrorCheck_ (h5f_close file_id) - -mountFile :: Location loc => loc -> BS.ByteString -> File -> Maybe FMPL -> IO () -mountFile loc groupname (File file_id) mount_plist = - withErrorCheck_ $ - BS.useAsCString groupname $ \cgroupname -> - h5f_mount (hid loc) cgroupname file_id (maybe h5p_DEFAULT hid mount_plist) - -unmountFile :: Location loc => loc -> BS.ByteString -> IO () -unmountFile loc groupname = - withErrorCheck_ $ - BS.useAsCString groupname $ \cgroupname -> - h5f_unmount (hid loc) cgroupname - -getFileSize :: File -> IO HSize -getFileSize (File file_id) = - fmap HSize $ - withOut_ $ \sz -> - withErrorCheck $ - h5f_get_filesize file_id sz - -getFileCreatePlist :: File -> IO FCPL -getFileCreatePlist (File file_id) = - fmap uncheckedFromHId $ - withErrorCheck $ - h5f_get_create_plist file_id - -getFileAccessPlist :: File -> IO FAPL -getFileAccessPlist (File file_id) = - fmap uncheckedFromHId $ - withErrorCheck $ - h5f_get_access_plist file_id - -data FileInfo = FileInfo - { superExtSize :: !HSize - , sohmHdrSize :: !HSize - , sohmMsgsInfo :: !IH_Info - } deriving (Eq, Ord, Read, Show) - -readFileInfo :: H5F_info_t -> FileInfo -readFileInfo (H5F_info_t a b (H5_ih_info_t c d)) = FileInfo (HSize a) (HSize b) (IH_Info (HSize c) (HSize d)) - -getFileInfo :: Object obj => obj -> IO FileInfo -getFileInfo obj = - fmap readFileInfo $ - withOut_ $ \info -> - withErrorCheck $ - h5f_get_info (hid obj) info - -getFileIntent :: File -> IO [AccFlags] -getFileIntent (File file_id) = - fmap intToAccFlags $ - withOut_ $ \intent -> - withErrorCheck_ $ - h5f_get_intent file_id intent - -getFileName :: File -> IO BS.ByteString -getFileName (File file_id) = - withOutByteString' $ \buf bufSz -> - withErrorWhen (< 0) $ - h5f_get_name file_id buf bufSz - -getFileObjCount :: Maybe File -> Bool -> [ObjType] -> IO CSize -getFileObjCount mbFile local objTypes = - fmap fromIntegral $ - withErrorWhen (< 0) $ - h5f_get_obj_count (maybe (HId_t h5f_OBJ_ALL) hid mbFile) (objTypesToInt objTypes .|. if local then 0 else h5f_OBJ_LOCAL) - -getOpenObjects :: Maybe File -> Bool -> [ObjType] -> IO (SV.Vector ObjectId) -getOpenObjects mbFile local objTypes = do - n <- getFileObjCount mbFile local objTypes - - withOutVector' (fromIntegral n) $ \objects -> - withErrorWhen (< 0) $ - h5f_get_obj_ids (maybe (HId_t h5f_OBJ_ALL) hid mbFile) (objTypesToInt objTypes .|. if local then 0 else h5f_OBJ_LOCAL) n (castWrappedPtr objects) - -getFileFreespace :: File -> IO HSize -getFileFreespace (File file_id) = - fmap fromIntegral $ - withErrorWhen (< 0) $ - h5f_get_freespace file_id diff --git a/src/Bindings/HDF5/File.hsc b/src/Bindings/HDF5/File.hsc new file mode 100644 --- /dev/null +++ b/src/Bindings/HDF5/File.hsc @@ -0,0 +1,292 @@ +#include +#include +{-# LANGUAGE GeneralizedNewtypeDeriving #-} +{-# LANGUAGE FlexibleInstances #-} +module Bindings.HDF5.File + ( AccFlags(..) + , ObjType(..) + , Scope(..) + + , isHDF5 + + , File + , createFile + , openFile + , reopenFile + , flushFile + , closeFile + + , mountFile + , unmountFile + + , getFileSize + , getFileCreatePlist + , getFileAccessPlist + + , FileInfo(..) + , getFileInfo + , getFileIntent + , getFileName + , getFileObjCount + + , getOpenObjects + , getFileFreespace +-- , get_mdc_config +-- , get_mdc_hit_rate +-- , get_mdc_size +-- , clear_elink_file_cache +-- , reset_mdc_hit_rate_stats +-- , set_mdc_config + ) where + +import Bindings.HDF5.Core +import Bindings.HDF5.Error +import Bindings.HDF5.Object +import Bindings.HDF5.PropertyList.FAPL +import Bindings.HDF5.PropertyList.FCPL +import Bindings.HDF5.PropertyList.FMPL +import Bindings.HDF5.Raw.H5 +import Bindings.HDF5.Raw.H5F +import Bindings.HDF5.Raw.H5I +import Bindings.HDF5.Raw.H5P +import Data.Bits +import Data.Maybe +import qualified Data.ByteString as BS +import qualified Data.Vector.Storable as SV +import Foreign.C +import Foreign.Ptr +import Foreign.Ptr.Conventions +import Foreign.Storable + +-- TODO: determine whether all of these are valid for _both_ create and open. +-- any that are not should be converted to Bool inputs to the corresponding function. +-- It very well may be best to separate several of them out like that anyway. +data AccFlags + = ReadOnly + | ReadWrite + | Truncate + | FailIfExists + | Debug + | Create + deriving (Eq, Ord, Enum, Bounded, Read, Show) + +accFlagToInt :: AccFlags -> CUInt +accFlagToInt ReadOnly = h5f_ACC_RDONLY +accFlagToInt ReadWrite = h5f_ACC_RDWR +accFlagToInt Truncate = h5f_ACC_TRUNC +accFlagToInt FailIfExists = h5f_ACC_EXCL +accFlagToInt Debug = h5f_ACC_DEBUG +accFlagToInt Create = h5f_ACC_CREAT + +accFlagsToInt :: [AccFlags] -> CUInt +accFlagsToInt = foldl (.|.) 0 . map accFlagToInt + +intToAccFlags :: CUInt -> [AccFlags] +intToAccFlags x = + [ f + | f <- [minBound .. maxBound] + , accFlagToInt f .&. x /= 0 + ] + +instance Storable [AccFlags] where + sizeOf _ = sizeOf (0 :: CUInt) + alignment _ = alignment (0 :: CUInt) + peek = fmap intToAccFlags . peek . castPtr + poke p = poke (castPtr p) . accFlagsToInt + +data ObjType + = Files + | Datasets + | Groups + | Datatypes + | Attrs + | All + deriving (Eq, Ord, Enum, Bounded, Read, Show) + +objTypeToInt :: ObjType -> CUInt +objTypeToInt Files = h5f_OBJ_FILE +objTypeToInt Datasets = h5f_OBJ_DATASET +objTypeToInt Groups = h5f_OBJ_GROUP +objTypeToInt Datatypes = h5f_OBJ_DATATYPE +objTypeToInt Attrs = h5f_OBJ_ATTR +objTypeToInt All = h5f_OBJ_ALL + +objTypesToInt :: [ObjType] -> CUInt +objTypesToInt = foldl (.|.) 0 . map objTypeToInt + +intToObjTypes :: CUInt -> [ObjType] +intToObjTypes x = + [ f + | f <- [minBound .. maxBound] + , objTypeToInt f .&. x /= 0 + ] + +instance Storable [ObjType] where + sizeOf _ = sizeOf (0 :: CUInt) + alignment _ = alignment (0 :: CUInt) + peek = fmap intToObjTypes . peek . castPtr + poke p = poke (castPtr p) . objTypesToInt + +data Scope + = Local + | Global + deriving (Eq, Ord, Enum, Bounded, Read, Show) + +scopeCode :: Scope -> H5F_scope_t +scopeCode Local = h5f_SCOPE_LOCAL +scopeCode Global = h5f_SCOPE_GLOBAL + +data CloseDegree + = Weak + | Semi + | Strong + deriving (Eq, Ord, Enum, Bounded, Read, Show) + +rawCloseDegreesInv :: [(H5F_close_degree_t, Maybe CloseDegree)] +rawCloseDegreesInv = [(a,b) | (b,a) <- rawCloseDegrees] +rawCloseDegrees :: [(Maybe CloseDegree, H5F_close_degree_t)] +rawCloseDegrees = + [ (Nothing, h5f_CLOSE_DEFAULT) + , (Just Weak, h5f_CLOSE_WEAK) + , (Just Semi, h5f_CLOSE_SEMI) + , (Just Strong, h5f_CLOSE_STRONG) + ] + +closeDegreeFromCode :: H5F_close_degree_t -> Maybe CloseDegree +closeDegreeFromCode c = fromMaybe Nothing (lookup c rawCloseDegreesInv) + +closeDegreeToCode :: Maybe CloseDegree -> H5F_close_degree_t +closeDegreeToCode c = + fromMaybe (error ("closeDegreeToCode: unrecognized H5F_close_degree_t: " ++ show c)) + (lookup c rawCloseDegrees) + +instance Storable (Maybe CloseDegree) where + sizeOf _ = sizeOf (undefined :: H5F_close_degree_t) + alignment _ = alignment (undefined :: H5F_close_degree_t) + peek = fmap closeDegreeFromCode . peek . castPtr + poke p = poke (castPtr p) . closeDegreeToCode + +isHDF5 :: BS.ByteString -> IO Bool +isHDF5 filename = htriToBool (BS.useAsCString filename h5f_is_hdf5) + +newtype File = File HId_t + deriving (Eq, HId, FromHId, HDFResultType) + +instance Location File +instance Object File where + staticObjectType = Tagged (Just FileObj) + +createFile :: BS.ByteString -> [AccFlags] -> Maybe FCPL -> Maybe FAPL -> IO File +createFile filename flags create_plist access_plist = + fmap File $ + withErrorCheck $ + BS.useAsCString filename $ \cfilename -> + h5f_create cfilename (accFlagsToInt flags) (maybe h5p_DEFAULT hid create_plist) (maybe h5p_DEFAULT hid access_plist) + +openFile :: BS.ByteString -> [AccFlags] -> Maybe FAPL -> IO File +openFile filename flags access_plist = + fmap File $ + withErrorCheck $ + BS.useAsCString filename $ \cfilename -> + h5f_open cfilename (accFlagsToInt flags) (maybe h5p_DEFAULT hid access_plist) + +reopenFile :: File -> IO File +reopenFile (File file_id) = + fmap File $ + withErrorCheck $ + h5f_reopen file_id + +flushFile :: File -> Scope -> IO () +flushFile (File file_id) scope = + withErrorCheck_ $ + h5f_flush file_id (scopeCode scope) + +closeFile :: File -> IO () +closeFile (File file_id) = + withErrorCheck_ (h5f_close file_id) + +mountFile :: Location loc => loc -> BS.ByteString -> File -> Maybe FMPL -> IO () +mountFile loc groupname (File file_id) mount_plist = + withErrorCheck_ $ + BS.useAsCString groupname $ \cgroupname -> + h5f_mount (hid loc) cgroupname file_id (maybe h5p_DEFAULT hid mount_plist) + +unmountFile :: Location loc => loc -> BS.ByteString -> IO () +unmountFile loc groupname = + withErrorCheck_ $ + BS.useAsCString groupname $ \cgroupname -> + h5f_unmount (hid loc) cgroupname + +getFileSize :: File -> IO HSize +getFileSize (File file_id) = + fmap HSize $ + withOut_ $ \sz -> + withErrorCheck $ + h5f_get_filesize file_id sz + +getFileCreatePlist :: File -> IO FCPL +getFileCreatePlist (File file_id) = + fmap uncheckedFromHId $ + withErrorCheck $ + h5f_get_create_plist file_id + +getFileAccessPlist :: File -> IO FAPL +getFileAccessPlist (File file_id) = + fmap uncheckedFromHId $ + withErrorCheck $ + h5f_get_access_plist file_id + +data FileInfo = FileInfo + { superExtSize :: !HSize + , sohmHdrSize :: !HSize + , sohmMsgsInfo :: !IH_Info + } deriving (Eq, Ord, Read, Show) + +readFileInfo :: H5F_info_t -> FileInfo +#if H5Fget_info_vers == 1 +readFileInfo (H5F_info_t a b (H5_ih_info_t c d)) = FileInfo (HSize a) (HSize b) (IH_Info (HSize c) (HSize d)) +#elif H5Fget_info_vers == 2 +readFileInfo (H5F_info_t _superVersion _superSize superExtSize' _freeVersion _metaSize _totSpace _sohmVersion sohmHdrSize' (H5_ih_info_t c d)) = FileInfo (HSize superExtSize') (HSize sohmHdrSize') (IH_Info (HSize c) (HSize d)) +#else +#error unknown H5Fget_info_vers +#endif + +getFileInfo :: Object obj => obj -> IO FileInfo +getFileInfo obj = + fmap readFileInfo $ + withOut_ $ \info -> + withErrorCheck $ + h5f_get_info (hid obj) info + +getFileIntent :: File -> IO [AccFlags] +getFileIntent (File file_id) = + fmap intToAccFlags $ + withOut_ $ \intent -> + withErrorCheck_ $ + h5f_get_intent file_id intent + +getFileName :: File -> IO BS.ByteString +getFileName (File file_id) = + withOutByteString' $ \buf bufSz -> + withErrorWhen (< 0) $ + h5f_get_name file_id buf bufSz + +getFileObjCount :: Maybe File -> Bool -> [ObjType] -> IO CSize +getFileObjCount mbFile local objTypes = + fmap fromIntegral $ + withErrorWhen (< 0) $ + h5f_get_obj_count (maybe (HId_t h5f_OBJ_ALL) hid mbFile) (objTypesToInt objTypes .|. if local then 0 else h5f_OBJ_LOCAL) + +getOpenObjects :: Maybe File -> Bool -> [ObjType] -> IO (SV.Vector ObjectId) +getOpenObjects mbFile local objTypes = do + n <- getFileObjCount mbFile local objTypes + + withOutVector' (fromIntegral n) $ \objects -> + withErrorWhen (< 0) $ + h5f_get_obj_ids (maybe (HId_t h5f_OBJ_ALL) hid mbFile) (objTypesToInt objTypes .|. if local then 0 else h5f_OBJ_LOCAL) n (castWrappedPtr objects) + +getFileFreespace :: File -> IO HSize +getFileFreespace (File file_id) = + fmap fromIntegral $ + withErrorWhen (< 0) $ + h5f_get_freespace file_id diff --git a/src/Bindings/HDF5/Link.hs b/src/Bindings/HDF5/Link.hs deleted file mode 100644 --- a/src/Bindings/HDF5/Link.hs +++ /dev/null @@ -1,258 +0,0 @@ -{-# LANGUAGE ForeignFunctionInterface #-} -{- - - h5l_get_info_by_idx [ FAIL ] - h5l_iterate [ OK ] - h5l_register [ FAIL ] - h5l_iterate_by_name [ OK ] - h5l_unpack_elink_val [ FAIL ] - h5l_get_val_by_idx [ FAIL ] - h5l_create_external [ OK ] - h5l_exists [ OK ] - h5l_move [ OK ] - h5l_create_ud [ FAIL ] - h5l_create_hard [ OK ] - h5l_is_registered [ FAIL ] - h5l_get_name_by_idx [ OK ] - h5l_create_soft [ OK ] - h5l_copy [ OK ] - h5l_get_val [ OK ] - h5l_visit [ OK ] - h5l_get_info [ OK ] - h5l_delete_by_idx [ FAIL ] - h5l_visit_by_name [ OK ] - h5l_delete [ OK ] - h5l_unregister [ FAIL ] - --} -module Bindings.HDF5.Link - ( createHardLink - , createSoftLink - , createExternalLink - - , getLinkNameByIdx - - , doesLinkExist - - , moveLink - , copyLink - , deleteLink - - , LinkType(..) - , LinkInfo(..) - , getLinkInfo - - , getSymLinkVal - - , iterateLinks - , iterateLinksByName - - , visitLinks - , visitLinksByName - ) where - -import Bindings.HDF5.Core -import Bindings.HDF5.Datatype.Internal -import Bindings.HDF5.Error -import Bindings.HDF5.Group -import Bindings.HDF5.PropertyList.LAPL -import Bindings.HDF5.PropertyList.LCPL -import Bindings.HDF5.Raw.H5 -import Bindings.HDF5.Raw.H5I -import Bindings.HDF5.Raw.H5L -import Bindings.HDF5.Raw.H5P -import Bindings.HDF5.Raw.Util -import Control.Exception (SomeException, finally, - throwIO, try) -import qualified Data.ByteString as BS -import Data.IORef -import Foreign -import Foreign.C -import Foreign.Ptr.Conventions - -{-# ANN module "HLint: ignore Use camelCase" #-} - -createHardLink :: (Location src, Location dst) => src -> BS.ByteString -> dst -> BS.ByteString -> Maybe LCPL -> Maybe LAPL -> IO () -createHardLink src srcName dst dstName lcpl lapl = - withErrorCheck_ $ - BS.useAsCString srcName $ \csrcName -> - BS.useAsCString dstName $ \cdstName -> - h5l_create_hard (hid src) csrcName (hid dst) cdstName - (maybe h5p_DEFAULT hid lcpl) - (maybe h5p_DEFAULT hid lapl) - -createSoftLink :: Location dst => BS.ByteString -> dst -> BS.ByteString -> Maybe LCPL -> Maybe LAPL -> IO () -createSoftLink srcName dst dstName lcpl lapl = - withErrorCheck_ $ - BS.useAsCString srcName $ \csrcName -> - BS.useAsCString dstName $ \cdstName -> - h5l_create_soft csrcName (hid dst) cdstName - (maybe h5p_DEFAULT hid lcpl) - (maybe h5p_DEFAULT hid lapl) - -createExternalLink :: Location loc => BS.ByteString -> BS.ByteString -> loc -> BS.ByteString -> Maybe LCPL -> Maybe LAPL -> IO () -createExternalLink file obj loc name lcpl lapl = - withErrorCheck_ $ - BS.useAsCString file $ \cfile -> - BS.useAsCString obj $ \cobj -> - BS.useAsCString name $ \cname -> - h5l_create_external cfile cobj (hid loc) cname (maybe h5p_DEFAULT hid lcpl) (maybe h5p_DEFAULT hid lapl) - -getLinkNameByIdx :: Location loc => loc -> BS.ByteString -> IndexType -> IterOrder -> HSize -> Maybe LAPL -> IO BS.ByteString -getLinkNameByIdx loc group indexType order idx lapl = - withOutByteString' $ \cname nameSize -> - BS.useAsCString group $ \cgroup -> - h5l_get_name_by_idx (hid loc) cgroup (indexTypeCode indexType) (iterOrderCode order) (hSize idx) cname nameSize (maybe h5p_DEFAULT hid lapl) - -doesLinkExist :: Location loc => loc -> BS.ByteString -> Maybe LAPL -> IO Bool -doesLinkExist loc name lapl = - htriToBool $ - BS.useAsCString name $ \cname -> - h5l_exists (hid loc) cname (maybe h5p_DEFAULT hid lapl) - -moveLink :: (Location src, Location dst) => src -> BS.ByteString -> dst -> BS.ByteString -> Maybe LCPL -> Maybe LAPL -> IO () -moveLink src srcName dst dstName lcpl lapl = - withErrorCheck_ $ - BS.useAsCString srcName $ \csrcName -> - BS.useAsCString dstName $ \cdstName -> - h5l_move (hid src) csrcName (hid dst) cdstName - (maybe h5p_DEFAULT hid lcpl) - (maybe h5p_DEFAULT hid lapl) - -copyLink :: (Location src, Location dst) => src -> BS.ByteString -> dst -> BS.ByteString -> Maybe LCPL -> Maybe LAPL -> IO () -copyLink src srcName dst dstName lcpl lapl = - withErrorCheck_ $ - BS.useAsCString srcName $ \csrcName -> - BS.useAsCString dstName $ \cdstName -> - h5l_copy (hid src) csrcName (hid dst) cdstName - (maybe h5p_DEFAULT hid lcpl) - (maybe h5p_DEFAULT hid lapl) - -deleteLink :: Location t => t -> BS.ByteString -> Maybe LAPL -> IO () -deleteLink loc name lapl = - withErrorCheck_ $ - BS.useAsCString name $ \cname -> - h5l_delete (hid loc) cname (maybe h5p_DEFAULT hid lapl) - -data LinkType - = External - | Hard - | Soft - | OtherLinkType !H5L_type_t - deriving (Eq, Ord, Read, Show) - -linkTypeFromCode :: H5L_type_t -> LinkType -linkTypeFromCode c - | c == h5l_TYPE_EXTERNAL = External - | c == h5l_TYPE_HARD = Hard - | c == h5l_TYPE_SOFT = Soft - | c >= h5l_TYPE_UD_MIN = OtherLinkType c - | otherwise = error ("Unknown link type: " ++ show c) - - -data LinkInfo = LinkInfo - { linkType :: LinkType - , linkCOrderValid :: Bool - , linkCOrder :: Int64 - , linkCSet :: CSet - , linkAddress :: HAddr - , linkValSize :: CSize - } deriving (Eq, Ord, Read, Show) - -readLinkInfo :: H5L_info_t -> LinkInfo -readLinkInfo i = LinkInfo - { linkType = linkTypeFromCode (h5l_info_t'type i) - , linkCOrderValid = hboolToBool (h5l_info_t'corder_valid i) - , linkCOrder = h5l_info_t'corder i - , linkCSet = cSetFromCode (h5l_info_t'cset i) - , linkAddress = HAddr (h5l_info_t'u'address i) - , linkValSize = h5l_info_t'u'val_size i - } - -getLinkInfo :: Location loc => loc -> BS.ByteString -> Maybe LAPL -> IO LinkInfo -getLinkInfo loc name lapl = - fmap readLinkInfo $ - withOut_ $ \info -> - withErrorCheck_ $ - BS.useAsCString name $ \cname -> - h5l_get_info (hid loc) cname info (maybe h5p_DEFAULT hid lapl) - -getSymLinkVal :: Location loc => loc -> BS.ByteString -> Maybe LAPL -> IO BS.ByteString -getSymLinkVal loc name mb_lapl = - BS.useAsCString name $ \cname -> do - let lapl = maybe h5p_DEFAULT hid mb_lapl - info <- withOut_ $ \info -> - withErrorCheck_ $ - h5l_get_info (hid loc) cname info lapl - - let n = h5l_info_t'u'val_size info - - buf <- mallocBytes (fromIntegral n) - - withErrorCheck_ $ - h5l_get_val (hid loc) cname (OutArray buf) n lapl - -- TODO: this will leak memory if an exception is thrown - - BS.packCStringLen (buf, fromIntegral n) - - -foreign import ccall "wrapper" wrap_H5L_iterate_t - :: (HId_t -> CString -> In H5L_info_t -> InOut a -> IO HErr_t) - -> IO (FunPtr (HId_t -> CString -> In H5L_info_t -> InOut a -> IO HErr_t)) - -with_iterate_t :: (Group -> BS.ByteString -> LinkInfo -> IO HErr_t) - -> (H5L_iterate_t () -> InOut () -> IO HErr_t) - -> IO HErr_t -with_iterate_t op f = do - exception1 <- newIORef Nothing :: IO (IORef (Maybe SomeException)) - - op1 <- wrap_H5L_iterate_t $ \grp name (In link) _opData -> do - name1 <- BS.packCString name - link1 <- peek link - result <- try (op (uncheckedFromHId grp) name1 (readLinkInfo link1)) - case result of - Left exc -> do - writeIORef exception1 (Just exc) - return maxBound - Right x -> return x - - result <- f op1 (InOut nullPtr) `finally` freeHaskellFunPtr op1 - - if result == maxBound - then do - exception2 <- readIORef exception1 - maybe (return result) throwIO exception2 - - else return result - --- TODO : It would be nice if we didn't expose HErr_t in these callback functions. --- Decide whether we want Either or Exceptions. -iterateLinks :: Location t => t -> IndexType -> IterOrder -> Maybe HSize -> (Group -> BS.ByteString -> LinkInfo -> IO HErr_t) -> IO HSize -iterateLinks loc indexType order startIndex op = - fmap HSize $ - withInOut_ (maybe 0 hSize startIndex) $ \ioStartIndex -> - withErrorCheck_ $ - with_iterate_t op $ \iop opData -> - h5l_iterate (hid loc) (indexTypeCode indexType) (iterOrderCode order) ioStartIndex iop opData - -iterateLinksByName :: Location t => t -> BS.ByteString -> IndexType -> IterOrder -> Maybe HSize -> Maybe LAPL -> (Group -> BS.ByteString -> LinkInfo -> IO HErr_t) -> IO HSize -iterateLinksByName loc groupName indexType order startIndex lapl op = - fmap HSize $ - withInOut_ (maybe 0 hSize startIndex) $ \ioStartIndex -> - withErrorCheck_ $ - with_iterate_t op $ \iop opData -> - BS.useAsCString groupName $ \cgroupName -> - h5l_iterate_by_name (hid loc) cgroupName (indexTypeCode indexType) (iterOrderCode order) ioStartIndex iop opData (maybe h5p_DEFAULT hid lapl) - -visitLinks :: Location t => t -> IndexType -> IterOrder -> (Group -> BS.ByteString -> LinkInfo -> IO HErr_t) -> IO () -visitLinks loc indexType order op = - withErrorCheck_ $ - with_iterate_t op $ \iop opData -> - h5l_visit (hid loc) (indexTypeCode indexType) (iterOrderCode order) iop opData - -visitLinksByName :: Location t => t -> BS.ByteString -> IndexType -> IterOrder -> Maybe LAPL -> (Group -> BS.ByteString -> LinkInfo -> IO HErr_t) -> IO () -visitLinksByName loc groupName indexType order lapl op = - withErrorCheck_ $ - with_iterate_t op $ \iop opData -> - BS.useAsCString groupName $ \cgroupName -> - h5l_visit_by_name (hid loc) cgroupName (indexTypeCode indexType) (iterOrderCode order) iop opData (maybe h5p_DEFAULT hid lapl) diff --git a/src/Bindings/HDF5/Link.hsc b/src/Bindings/HDF5/Link.hsc new file mode 100644 --- /dev/null +++ b/src/Bindings/HDF5/Link.hsc @@ -0,0 +1,304 @@ +#include +#include +#include +#if H5_VERSION_GE(1,14,0) +#include +#endif +{-# LANGUAGE ForeignFunctionInterface #-} +{-# LANGUAGE CPP #-} +{- + + h5l_get_info_by_idx [ FAIL ] + h5l_iterate [ OK ] + h5l_register [ FAIL ] + h5l_iterate_by_name [ OK ] + h5l_unpack_elink_val [ FAIL ] + h5l_get_val_by_idx [ FAIL ] + h5l_create_external [ OK ] + h5l_exists [ OK ] + h5l_move [ OK ] + h5l_create_ud [ FAIL ] + h5l_create_hard [ OK ] + h5l_is_registered [ FAIL ] + h5l_get_name_by_idx [ OK ] + h5l_create_soft [ OK ] + h5l_copy [ OK ] + h5l_get_val [ OK ] + h5l_visit [ OK ] + h5l_get_info [ OK ] + h5l_delete_by_idx [ FAIL ] + h5l_visit_by_name [ OK ] + h5l_delete [ OK ] + h5l_unregister [ FAIL ] + +-} +module Bindings.HDF5.Link + ( createHardLink + , createSoftLink + , createExternalLink + + , getLinkNameByIdx + + , doesLinkExist + + , moveLink + , copyLink + , deleteLink + + , LinkType(..) + , LinkInfo(..) + , getLinkInfo + + , getSymLinkVal + + , iterateLinks + , iterateLinksByName + + , visitLinks + , visitLinksByName + ) where + +import Bindings.HDF5.Core +import Bindings.HDF5.Datatype.Internal +import Bindings.HDF5.Error +import Bindings.HDF5.Group +import Bindings.HDF5.PropertyList.LAPL +import Bindings.HDF5.PropertyList.LCPL +import Bindings.HDF5.Raw.H5 +import Bindings.HDF5.Raw.H5I +import Bindings.HDF5.Raw.H5L +import Bindings.HDF5.Raw.H5P +import Bindings.HDF5.Raw.Util +import Control.Exception (SomeException, finally, + throwIO, try) +import qualified Data.ByteString as BS +import Data.IORef +import Foreign +import Foreign.C +import Foreign.Ptr.Conventions + +{-# ANN module "HLint: ignore Use camelCase" #-} + +createHardLink :: (Location src, Location dst) => src -> BS.ByteString -> dst -> BS.ByteString -> Maybe LCPL -> Maybe LAPL -> IO () +createHardLink src srcName dst dstName lcpl lapl = + withErrorCheck_ $ + BS.useAsCString srcName $ \csrcName -> + BS.useAsCString dstName $ \cdstName -> + h5l_create_hard (hid src) csrcName (hid dst) cdstName + (maybe h5p_DEFAULT hid lcpl) + (maybe h5p_DEFAULT hid lapl) + +createSoftLink :: Location dst => BS.ByteString -> dst -> BS.ByteString -> Maybe LCPL -> Maybe LAPL -> IO () +createSoftLink srcName dst dstName lcpl lapl = + withErrorCheck_ $ + BS.useAsCString srcName $ \csrcName -> + BS.useAsCString dstName $ \cdstName -> + h5l_create_soft csrcName (hid dst) cdstName + (maybe h5p_DEFAULT hid lcpl) + (maybe h5p_DEFAULT hid lapl) + +createExternalLink :: Location loc => BS.ByteString -> BS.ByteString -> loc -> BS.ByteString -> Maybe LCPL -> Maybe LAPL -> IO () +createExternalLink file obj loc name lcpl lapl = + withErrorCheck_ $ + BS.useAsCString file $ \cfile -> + BS.useAsCString obj $ \cobj -> + BS.useAsCString name $ \cname -> + h5l_create_external cfile cobj (hid loc) cname (maybe h5p_DEFAULT hid lcpl) (maybe h5p_DEFAULT hid lapl) + +getLinkNameByIdx :: Location loc => loc -> BS.ByteString -> IndexType -> IterOrder -> HSize -> Maybe LAPL -> IO BS.ByteString +getLinkNameByIdx loc group indexType order idx lapl = + withOutByteString' $ \cname nameSize -> + BS.useAsCString group $ \cgroup -> + h5l_get_name_by_idx (hid loc) cgroup (indexTypeCode indexType) (iterOrderCode order) (hSize idx) cname nameSize (maybe h5p_DEFAULT hid lapl) + +doesLinkExist :: Location loc => loc -> BS.ByteString -> Maybe LAPL -> IO Bool +doesLinkExist loc name lapl = + htriToBool $ + BS.useAsCString name $ \cname -> + h5l_exists (hid loc) cname (maybe h5p_DEFAULT hid lapl) + +moveLink :: (Location src, Location dst) => src -> BS.ByteString -> dst -> BS.ByteString -> Maybe LCPL -> Maybe LAPL -> IO () +moveLink src srcName dst dstName lcpl lapl = + withErrorCheck_ $ + BS.useAsCString srcName $ \csrcName -> + BS.useAsCString dstName $ \cdstName -> + h5l_move (hid src) csrcName (hid dst) cdstName + (maybe h5p_DEFAULT hid lcpl) + (maybe h5p_DEFAULT hid lapl) + +copyLink :: (Location src, Location dst) => src -> BS.ByteString -> dst -> BS.ByteString -> Maybe LCPL -> Maybe LAPL -> IO () +copyLink src srcName dst dstName lcpl lapl = + withErrorCheck_ $ + BS.useAsCString srcName $ \csrcName -> + BS.useAsCString dstName $ \cdstName -> + h5l_copy (hid src) csrcName (hid dst) cdstName + (maybe h5p_DEFAULT hid lcpl) + (maybe h5p_DEFAULT hid lapl) + +deleteLink :: Location t => t -> BS.ByteString -> Maybe LAPL -> IO () +deleteLink loc name lapl = + withErrorCheck_ $ + BS.useAsCString name $ \cname -> + h5l_delete (hid loc) cname (maybe h5p_DEFAULT hid lapl) + +data LinkType + = External + | Hard + | Soft + | OtherLinkType !H5L_type_t + deriving (Eq, Ord, Read, Show) + +linkTypeFromCode :: H5L_type_t -> LinkType +linkTypeFromCode c + | c == h5l_TYPE_EXTERNAL = External + | c == h5l_TYPE_HARD = Hard + | c == h5l_TYPE_SOFT = Soft + | c >= h5l_TYPE_UD_MIN = OtherLinkType c + | otherwise = error ("Unknown link type: " ++ show c) + + +data LinkInfo = LinkInfo + { linkType :: LinkType + , linkCOrderValid :: Bool + , linkCOrder :: Int64 + , linkCSet :: CSet + , linkValSize :: CSize + } deriving (Eq, Ord, Read, Show) + +#if H5Fget_info_vers == 1 +readLinkInfo :: H5L_info_t -> LinkInfo +readLinkInfo i = LinkInfo + { linkType = linkTypeFromCode (h5l_info_t'type i) + , linkCOrderValid = hboolToBool (h5l_info_t'corder_valid i) + , linkCOrder = h5l_info_t'corder i + , linkCSet = cSetFromCode (h5l_info_t'cset i) + , linkValSize = h5l_info_t'u'val_size i + } +#elif H5Fget_info_vers == 2 +readLinkInfo :: H5L_info_t -> LinkInfo +readLinkInfo i = LinkInfo + { linkType = linkTypeFromCode (h5l_info2_t'type i) + , linkCOrderValid = hboolToBool (h5l_info2_t'corder_valid i) + , linkCOrder = h5l_info2_t'corder i + , linkCSet = cSetFromCode (h5l_info2_t'cset i) + , linkValSize = h5l_info2_t'u'val_size i + } +#else +#error "unknown info vers" +#endif + +getLinkInfo :: Location loc => loc -> BS.ByteString -> Maybe LAPL -> IO LinkInfo +getLinkInfo loc name lapl = + fmap readLinkInfo $ + withOut_ $ \info -> + withErrorCheck_ $ + BS.useAsCString name $ \cname -> +#if (H5Fget_info_vers == 1) + h5l_get_info (hid loc) cname info (maybe h5p_DEFAULT hid lapl) +#else + h5l_get_info2 (hid loc) cname info (maybe h5p_DEFAULT hid lapl) +#endif + +getSymLinkVal :: Location loc => loc -> BS.ByteString -> Maybe LAPL -> IO BS.ByteString +getSymLinkVal loc name mb_lapl = + BS.useAsCString name $ \cname -> do + let lapl = maybe h5p_DEFAULT hid mb_lapl + info <- withOut_ $ \info -> + withErrorCheck_ $ +#if (H5Fget_info_vers == 1) + h5l_get_info (hid loc) cname info lapl +#else + h5l_get_info2 (hid loc) cname info lapl +#endif + +#if (H5Fget_info_vers == 1) + let n = h5l_info_t'u'val_size info +#else + let n = h5l_info2_t'u'val_size info +#endif + + buf <- mallocBytes (fromIntegral n) + + withErrorCheck_ $ + h5l_get_val (hid loc) cname (OutArray buf) n lapl + -- TODO: this will leak memory if an exception is thrown + + BS.packCStringLen (buf, fromIntegral n) + + +foreign import ccall "wrapper" wrap_H5L_iterate_t + :: (HId_t -> CString -> In H5L_info_t -> InOut a -> IO HErr_t) + -> IO (FunPtr (HId_t -> CString -> In H5L_info_t -> InOut a -> IO HErr_t)) + +with_iterate_t :: (Group -> BS.ByteString -> LinkInfo -> IO HErr_t) + -> (H5L_iterate_t () -> InOut () -> IO HErr_t) + -> IO HErr_t +with_iterate_t op f = do + exception1 <- newIORef Nothing :: IO (IORef (Maybe SomeException)) + + op1 <- wrap_H5L_iterate_t $ \grp name (In link) _opData -> do + name1 <- BS.packCString name + link1 <- peek link + result <- try (op (uncheckedFromHId grp) name1 (readLinkInfo link1)) + case result of + Left exc -> do + writeIORef exception1 (Just exc) + return maxBound + Right x -> return x + + result <- f op1 (InOut nullPtr) `finally` freeHaskellFunPtr op1 + + if result == maxBound + then do + exception2 <- readIORef exception1 + maybe (return result) throwIO exception2 + + else return result + +-- TODO : It would be nice if we didn't expose HErr_t in these callback functions. +-- Decide whether we want Either or Exceptions. +iterateLinks :: Location t => t -> IndexType -> IterOrder -> Maybe HSize -> (Group -> BS.ByteString -> LinkInfo -> IO HErr_t) -> IO HSize +iterateLinks loc indexType order startIndex op = + fmap HSize $ + withInOut_ (maybe 0 hSize startIndex) $ \ioStartIndex -> + withErrorCheck_ $ + with_iterate_t op $ \iop opData -> +#if (H5Fget_info_vers == 1) + h5l_iterate (hid loc) (indexTypeCode indexType) (iterOrderCode order) ioStartIndex iop opData +#else + h5l_iterate2 (hid loc) (indexTypeCode indexType) (iterOrderCode order) ioStartIndex iop opData +#endif + +iterateLinksByName :: Location t => t -> BS.ByteString -> IndexType -> IterOrder -> Maybe HSize -> Maybe LAPL -> (Group -> BS.ByteString -> LinkInfo -> IO HErr_t) -> IO HSize +iterateLinksByName loc groupName indexType order startIndex lapl op = + fmap HSize $ + withInOut_ (maybe 0 hSize startIndex) $ \ioStartIndex -> + withErrorCheck_ $ + with_iterate_t op $ \iop opData -> + BS.useAsCString groupName $ \cgroupName -> +#if (H5Fget_info_vers == 1) + h5l_iterate_by_name (hid loc) cgroupName (indexTypeCode indexType) (iterOrderCode order) ioStartIndex iop opData (maybe h5p_DEFAULT hid lapl) +#else + h5l_iterate_by_name2 (hid loc) cgroupName (indexTypeCode indexType) (iterOrderCode order) ioStartIndex iop opData (maybe h5p_DEFAULT hid lapl) +#endif + +visitLinks :: Location t => t -> IndexType -> IterOrder -> (Group -> BS.ByteString -> LinkInfo -> IO HErr_t) -> IO () +visitLinks loc indexType order op = + withErrorCheck_ $ + with_iterate_t op $ \iop opData -> +#if (H5Fget_info_vers == 1) + h5l_visit (hid loc) (indexTypeCode indexType) (iterOrderCode order) iop opData +#else + h5l_visit2 (hid loc) (indexTypeCode indexType) (iterOrderCode order) iop opData +#endif + +visitLinksByName :: Location t => t -> BS.ByteString -> IndexType -> IterOrder -> Maybe LAPL -> (Group -> BS.ByteString -> LinkInfo -> IO HErr_t) -> IO () +visitLinksByName loc groupName indexType order lapl op = + withErrorCheck_ $ + with_iterate_t op $ \iop opData -> + BS.useAsCString groupName $ \cgroupName -> +#if (H5Fget_info_vers == 1) + h5l_visit_by_name (hid loc) cgroupName (indexTypeCode indexType) (iterOrderCode order) iop opData (maybe h5p_DEFAULT hid lapl) +#else + h5l_visit_by_name2 (hid loc) cgroupName (indexTypeCode indexType) (iterOrderCode order) iop opData (maybe h5p_DEFAULT hid lapl) +#endif diff --git a/src/Bindings/HDF5/Raw/H5E.hsc b/src/Bindings/HDF5/Raw/H5E.hsc --- a/src/Bindings/HDF5/Raw/H5E.hsc +++ b/src/Bindings/HDF5/Raw/H5E.hsc @@ -118,7 +118,9 @@ #cinline H5E_OHDR, -- |Object atom +#if !H5_VERSION_GE(1,8,14) #cinline H5E_ATOM, +#endif -- |Attribute #cinline H5E_ATTR, @@ -284,7 +286,9 @@ #cinline H5E_MOUNT, -- ** Object atom related errors +#if !H5_VERSION_GE(1,8,14) #cinline H5E_BADATOM, +#endif #cinline H5E_BADGROUP, #cinline H5E_CANTREGISTER, #cinline H5E_CANTINC, diff --git a/src/Bindings/HDF5/Raw/H5F.hsc b/src/Bindings/HDF5/Raw/H5F.hsc --- a/src/Bindings/HDF5/Raw/H5F.hsc +++ b/src/Bindings/HDF5/Raw/H5F.hsc @@ -131,44 +131,6 @@ #newtype_const H5F_close_degree_t, H5F_CLOSE_STRONG -#if H5_VERSION_GE(1,10,0) - --- |Current "global" information about file --- (just size info currently) -#starttype H5F_info2_t - --- |Superblock version -#field super.version, CUInt - --- |Superblock size -#field super.super_size, - - --- |Superblock extension size -#field super.super_ext_size, - --- |Version # of file free space management -#field free.version, CUInt - --- |Free space manager metadata size -#field free.meta_size, - --- |Amount of free space in the file -#field free.tot_space, - --- |Version # of shared object header info -#field sohm.version, CUInt - --- |Shared object header message header size -#field sohm.hdr_size, - --- |Shared object header message index & heap size -#field sohm.msgs_info, - -#stoptype - -#endif - #if H5_VERSION_GE(1,8,4) -- |Types of allocation requests. The values larger than 'h5fd_MEM_DEFAULT' @@ -573,8 +535,10 @@ -- #if H5_VERSION_GE(1,10,0) +#if H5Fget_info_vers == 2 -- > herr_t H5Fget_info2(hid_t obj_id, H5F_info2_t *bh_info); -#ccall H5Fget_info2, -> Out H5F_info2_t -> IO +#ccall H5Fget_info2, -> Out H5F_info_t -> IO +#endif -- > herr_t H5Fget_metadata_read_retry_info(hid_t file_id, H5F_retry_info_t *info); #ccall H5Fget_metadata_read_retry_info, -> Out H5F_retry_info_t -> IO @@ -655,7 +619,8 @@ #endif -#if (H5_VERSION_GE(1,10,0) && (H5Fget_info_vers == 1)) || H5_VERSION_LE(1,8,18) +-- #if (H5_VERSION_GE(1,10,0) && (H5Fget_info_vers == 1)) || H5_VERSION_LE(1,8,18) +#if H5Fget_info_vers == 1 -- |Current "global" information about file -- (just size info currently) @@ -672,7 +637,7 @@ #stoptype -#else +#elif H5Fget_info_vers == 2 -- |Current "global" information about file -- (just size info currently) @@ -706,6 +671,12 @@ #field sohm.msgs_info, #stoptype + +type H5F_info2_t = H5F_info_t + +#else + +#error unknown H5Fget_info_vers #endif diff --git a/src/Bindings/HDF5/Raw/H5FD.hsc b/src/Bindings/HDF5/Raw/H5FD.hsc --- a/src/Bindings/HDF5/Raw/H5FD.hsc +++ b/src/Bindings/HDF5/Raw/H5FD.hsc @@ -1,5 +1,8 @@ #include #include +#if H5_VERSION_GE(1,14,0) +#include +#endif -- |The Virtual File Layer as described in documentation. -- This is the greatest common denominator for all types of @@ -350,7 +353,7 @@ #if H5_VERSION_GE(1,10,0) && H5_VERSION_LE(1,10,1) -- |Whether the file is open for SWMR read access -- Information from file open flags, for SWMR access -#field swmr_read, +-- #field swmr_read, #endif -- Space allocation management fields diff --git a/src/Bindings/HDF5/Raw/H5FD/Direct.hsc b/src/Bindings/HDF5/Raw/H5FD/Direct.hsc --- a/src/Bindings/HDF5/Raw/H5FD/Direct.hsc +++ b/src/Bindings/HDF5/Raw/H5FD/Direct.hsc @@ -7,6 +7,9 @@ module Bindings.HDF5.Raw.H5FD.Direct where import Bindings.HDF5.Raw.H5I +#ifdef H5_HAVE_DIRECT +import System.IO.Unsafe(unsafePerformIO) +#endif /* H5_HAVE_DIRECT */ #mangle_ident "H5FD_DIRECT" :: HId_t diff --git a/src/Bindings/HDF5/Raw/H5I.hsc b/src/Bindings/HDF5/Raw/H5I.hsc --- a/src/Bindings/HDF5/Raw/H5I.hsc +++ b/src/Bindings/HDF5/Raw/H5I.hsc @@ -40,9 +40,6 @@ -- |type ID for Attribute objects #newtype_const H5I_type_t, H5I_ATTR --- |type ID for Reference objects -#newtype_const H5I_type_t, H5I_REFERENCE - -- |type ID for virtual file layer #newtype_const H5I_type_t, H5I_VFL diff --git a/src/Bindings/HDF5/Raw/H5L.hsc b/src/Bindings/HDF5/Raw/H5L.hsc --- a/src/Bindings/HDF5/Raw/H5L.hsc +++ b/src/Bindings/HDF5/Raw/H5L.hsc @@ -1,6 +1,9 @@ #include #include - +#include +#if H5_VERSION_GE(1,14,0) +#include +#endif module Bindings.HDF5.Raw.H5L where import Data.Int @@ -14,6 +17,9 @@ import Bindings.HDF5.Raw.H5 import Bindings.HDF5.Raw.H5I import Bindings.HDF5.Raw.H5T +#if H5Fget_info_vers != 1 +import Bindings.HDF5.Raw.H5O +#endif import Foreign.Ptr.Conventions -- |Maximum length of a link's name @@ -60,7 +66,13 @@ #newtype_const H5L_type_t, H5L_TYPE_UD_MIN -- |Information struct for link (for 'h5l_get_info' / 'h5l_get_info_by_idx') +#if H5Fget_info_vers == 1 #starttype H5L_info_t +#elif H5Fget_info_vers == 2 +#starttype H5L_info2_t +#else +#error "unknown info vers" +#endif -- |Type of link #field type, @@ -74,13 +86,22 @@ -- |Character set of link name #field cset, +#if (H5Fget_info_vers == 1) -- |Address hard link points to #union_field u.address, +#else +#union_field u.token, +#endif + + -- |Size of a soft link or UD link value #union_field u.val_size, #stoptype +#if H5Fget_info_vers == 2 +type H5L_info_t = H5L_info2_t +#endif -- /* The H5L_class_t struct can be used to override the behavior of a -- * "user-defined" link class. Users should populate the struct with callback @@ -163,7 +184,11 @@ -- -- > typedef herr_t (*H5L_iterate_t)(hid_t group, const char *name, const H5L_info_t *info, -- > void *op_data); +-- #if (H5Fget_info_vers == 1) type H5L_iterate_t a = FunPtr (HId_t -> CString -> In H5L_info_t -> InOut a -> IO HErr_t) +#if (H5Fget_info_vers != 1) +type H5L_iterate2_t a = H5L_iterate_t a +#endif -- |Callback for external link traversal -- diff --git a/src/Bindings/HDF5/Raw/H5O.hsc b/src/Bindings/HDF5/Raw/H5O.hsc --- a/src/Bindings/HDF5/Raw/H5O.hsc +++ b/src/Bindings/HDF5/Raw/H5O.hsc @@ -155,16 +155,37 @@ #endif +#if H5_VERSION_GE(1,11,0) + +#starttype H5O_token_t + +#field __data, CUChar + +#stoptype + +#endif + -- |Information struct for object -- (for 'h5o_get_info'/ 'h5o_get_info_by_name' / 'h5o_get_info_by_idx') +#if (H5Fget_info_vers == 1) #starttype H5O_info_t +#else +#starttype H5O_info2_t +#endif -- |File number that object is located in #field fileno, CULong +#if (H5Fget_info_vers == 1) -- |Object address in file #field addr, +#endif +-- |Token representing the object +#if H5_VERSION_GE(1,11,0) +#field token, +#endif + -- |Basic object type (group, dataset, etc.) #field type, @@ -188,11 +209,14 @@ #if H5_VERSION_GE(1,8,4) +#if (H5Fget_info_vers == 1) -- |Object header information #field hdr, +#endif #else +#if (H5Fget_info_vers == 1) -- |Version number of header format in file #field hdr.version, CUInt @@ -225,20 +249,30 @@ #endif +#endif + +#if (H5Fget_info_vers == 1) -- |v1/v2 B-tree & local/fractal heap for groups, B-tree for chunked datasets #field meta_size.obj, -- |v2 B-tree & heap for attributes #field meta_size.attr, +#endif + #stoptype -- |Typedef for message creation indexes #newtype H5O_msg_crt_idx_t, Eq, Ord, Read +#if (H5Fget_info_vers == 1) -- |Prototype for 'h5o_visit' / 'h5o_visit_by_name' operator type H5O_iterate_t a = FunPtr (HId_t -> CString -> In H5O_info_t -> InOut a -> IO HErr_t) +#else +-- |Prototype for 'h5o_visit' / 'h5o_visit_by_name' operator +type H5O_iterate2_t a = FunPtr (HId_t -> CString -> In H5O_info2_t -> InOut a -> IO HErr_t) +#endif #newtype H5O_mcdt_search_ret_t @@ -339,7 +373,11 @@ -- Returns non-negative on success, negative on failure. -- -- > herr_t H5Oget_info(hid_t loc_id, H5O_info_t *oinfo); +#if (H5Fget_info_vers == 1) #ccall H5Oget_info, -> Out -> IO +#else +#ccall H5Oget_info, -> Out -> IO +#endif -- |Retrieve information about an object. -- @@ -556,7 +594,11 @@ -- -- > herr_t H5Ovisit(hid_t obj_id, H5_index_t idx_type, H5_iter_order_t order, -- > H5O_iterate_t op, void *op_data); +#if (H5Fget_info_vers == 1) #ccall H5Ovisit, -> -> -> H5O_iterate_t a -> InOut a -> IO +#else +#ccall H5Ovisit, -> -> -> H5O_iterate2_t a -> InOut a -> IO +#endif -- |Recursively visit an object and all the objects reachable -- from it. If the starting object is a group, all the objects diff --git a/src/Bindings/HDF5/Raw/H5S.hsc b/src/Bindings/HDF5/Raw/H5S.hsc --- a/src/Bindings/HDF5/Raw/H5S.hsc +++ b/src/Bindings/HDF5/Raw/H5S.hsc @@ -1,5 +1,6 @@ #include #include +#include module Bindings.HDF5.Raw.H5S where @@ -171,7 +172,14 @@ -- Returns non-negative on success, negative on failure. -- -- > herr_t H5Sencode(hid_t obj_id, void *buf, size_t *nalloc); +#if HDF5get_info_vers == 1 #ccall H5Sencode, -> OutArray CChar -> InOut -> IO +#else +#ccall H5Sencode2, -> OutArray CChar -> InOut -> IO + +h5s_encode :: HId_t -> OutArray CChar -> InOut CSize -> IO HErr_t +h5s_encode = h5s_encode2 +#endif -- |Decode a binary object description of dataspace and -- return a new object handle. diff --git a/src/Bindings/HDF5/Raw/H5T.hsc b/src/Bindings/HDF5/Raw/H5T.hsc --- a/src/Bindings/HDF5/Raw/H5T.hsc +++ b/src/Bindings/HDF5/Raw/H5T.hsc @@ -1,6 +1,9 @@ #include #include +#if H5_VERSION_GE(1,14,0) +#include +#endif module Bindings.HDF5.Raw.H5T where diff --git a/src/Bindings/HDF5/Raw/H5Z.hsc b/src/Bindings/HDF5/Raw/H5Z.hsc --- a/src/Bindings/HDF5/Raw/H5Z.hsc +++ b/src/Bindings/HDF5/Raw/H5Z.hsc @@ -1,6 +1,9 @@ #include #include #include +#if H5_VERSION_GE(1,13,0) +#include +#endif module Bindings.HDF5.Raw.H5Z where