add INPUT-REQUIRED
Used by git-annex-compute-singularity to make addcomputed --fast work. Also, simplified git-annex-compute-singularity; there is no need to hard link the container into place. singularity does not care about the extension of the container, so can just pass it the annex object file.
This commit is contained in:
Joey Hess
parent
bb0bc078fc
commit
0477a8d098
6 changed files with 83 additions and 66 deletions
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@ -206,14 +206,14 @@ addComputed maddaction stagefiles r reproducibleconfig choosebackend destfile fa
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Just v -> isReproducible v
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Nothing -> Remote.Compute.computeReproducible result
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getInputContent :: Bool -> OsPath -> Annex (Key, Maybe (Either Git.Sha OsPath))
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getInputContent fast p = catKeyFile p >>= \case
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Just inputkey -> getInputContent' fast inputkey filedesc
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getInputContent :: Bool -> OsPath -> Bool -> Annex (Key, Maybe (Either Git.Sha OsPath))
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getInputContent fast p required = catKeyFile p >>= \case
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Just inputkey -> getInputContent' fast inputkey required filedesc
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Nothing -> inRepo (Git.fileRef p) >>= \case
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Just fileref -> catObjectMetaData fileref >>= \case
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Just (sha, _, t)
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| t == Git.BlobObject ->
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getInputContent' fast (gitShaKey sha) filedesc
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getInputContent' fast (gitShaKey sha) required filedesc
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| otherwise ->
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badinput $ ", not a git " ++ decodeBS (Git.fmtObjectType t)
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Nothing -> notcheckedin
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@ -223,9 +223,9 @@ getInputContent fast p = catKeyFile p >>= \case
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badinput s = giveup $ "The computation needs an input file " ++ s ++ ": " ++ fromOsPath p
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notcheckedin = badinput "that is not checked into the git repository"
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getInputContent' :: Bool -> Key -> String -> Annex (Key, Maybe (Either Git.Sha OsPath))
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getInputContent' fast inputkey filedesc
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| fast = return (inputkey, Nothing)
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getInputContent' :: Bool -> Key -> Bool -> String -> Annex (Key, Maybe (Either Git.Sha OsPath))
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getInputContent' fast inputkey required filedesc
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| fast && not required = return (inputkey, Nothing)
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| otherwise = case keyGitSha inputkey of
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Nothing -> ifM (inAnnex inputkey)
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( do
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@ -152,14 +152,14 @@ perform o r file origkey origstate = do
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check "not outputting"
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Remote.Compute.computeOutputs origstate state
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getinputcontent program p
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getinputcontent program p required
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| originalOption o =
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case M.lookup p (Remote.Compute.computeInputs origstate) of
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Just inputkey -> getInputContent' False inputkey
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Just inputkey -> getInputContent' False inputkey required
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(fromOsPath p ++ "(key " ++ serializeKey inputkey ++ ")")
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Nothing -> Remote.Compute.computationBehaviorChangeError program
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"requesting a new input file" p
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| otherwise = getInputContent False p
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| otherwise = getInputContent False p required
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destfile outputfile
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| Just outputfile == origfile = Just file
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@ -201,17 +201,19 @@ programField = Accepted "program"
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data ProcessCommand
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= ProcessInput FilePath
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| ProcessOutput FilePath
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| ProcessProgress PercentFloat
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| ProcessReproducible
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| ProcessSandbox
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| ProcessProgress PercentFloat
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| ProcessInputRequired FilePath
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deriving (Show, Eq)
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instance Proto.Receivable ProcessCommand where
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parseCommand "INPUT" = Proto.parse1 ProcessInput
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parseCommand "OUTPUT" = Proto.parse1 ProcessOutput
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parseCommand "PROGRESS" = Proto.parse1 ProcessProgress
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parseCommand "REPRODUCIBLE" = Proto.parse0 ProcessReproducible
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parseCommand "SANDBOX" = Proto.parse0 ProcessSandbox
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parseCommand "PROGRESS" = Proto.parse1 ProcessProgress
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parseCommand "INPUT-REQUIRED" = Proto.parse1 ProcessInputRequired
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parseCommand _ = Proto.parseFail
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newtype PercentFloat = PercentFloat Float
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@ -392,9 +394,10 @@ runComputeProgram
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:: ComputeProgram
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-> ComputeState
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-> ImmutableState
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-> (OsPath -> Annex (Key, Maybe (Either Git.Sha OsPath)))
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-- ^ get input file's content, or Nothing the input file's
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-- content is not available
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-> (OsPath -> Bool -> Annex (Key, Maybe (Either Git.Sha OsPath)))
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-- ^ Get input file's content, or Nothing the input file's
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-- content is not available. True is passed when the input content
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-- is required even for addcomputed --fast.
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-> Maybe (Key, MeterUpdate)
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-- ^ update meter for this key
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-> (ComputeProgramResult -> OsPath -> NominalDiffTime -> Annex v)
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@ -454,37 +457,8 @@ runComputeProgram (ComputeProgram program) state (ImmutableState immutablestate)
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liftIO $ hFlush (stdinHandle p)
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parseoutput p tmpdir subdir result meterfile l = case Proto.parseMessage l of
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Just (ProcessInput f) -> do
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let f' = toOsPath f
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let knowninput = M.member f'
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(computeInputs (computeState result))
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checksafefile tmpdir subdir f' "input"
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checkimmutable knowninput "inputting" f' $ do
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(k, inputcontent) <- getinputcontent f'
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let mkrel a = Just <$>
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(a >>= liftIO . relPathDirToFile subdir)
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mp <- case inputcontent of
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Nothing -> pure Nothing
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Just (Right obj)
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| computeSandbox result ->
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mkrel $ populatesandbox obj tmpdir
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| otherwise ->
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mkrel $ pure obj
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Just (Left gitsha) ->
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mkrel $ populategitsha gitsha tmpdir
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sendresponse p $
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maybe "" fromOsPath mp
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let result' = result
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{ computeInputsUnavailable =
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isNothing mp || computeInputsUnavailable result
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}
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return $ if immutablestate
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then result'
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else modresultstate result' $ \s -> s
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{ computeInputs =
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M.insert f' k
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(computeInputs s)
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}
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Just (ProcessInput f) -> handleinput f False p tmpdir subdir result
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Just (ProcessInputRequired f) -> handleinput f True p tmpdir subdir result
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Just (ProcessOutput f) -> do
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let f' = toOsPath f
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checksafefile tmpdir subdir f' "output"
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@ -525,6 +499,38 @@ runComputeProgram (ComputeProgram program) state (ImmutableState immutablestate)
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Nothing -> giveup $
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program ++ " output an unparseable line: \"" ++ l ++ "\""
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handleinput f required p tmpdir subdir result = do
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let f' = toOsPath f
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let knowninput = M.member f'
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(computeInputs (computeState result))
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checksafefile tmpdir subdir f' "input"
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checkimmutable knowninput "inputting" f' $ do
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(k, inputcontent) <- getinputcontent f' required
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let mkrel a = Just <$>
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(a >>= liftIO . relPathDirToFile subdir)
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mp <- case inputcontent of
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Nothing -> pure Nothing
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Just (Right obj)
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| computeSandbox result ->
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mkrel $ populatesandbox obj tmpdir
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| otherwise ->
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mkrel $ pure obj
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Just (Left gitsha) ->
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mkrel $ populategitsha gitsha tmpdir
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sendresponse p $
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maybe "" fromOsPath mp
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let result' = result
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{ computeInputsUnavailable =
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isNothing mp || computeInputsUnavailable result
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}
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return $ if immutablestate
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then result'
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else modresultstate result' $ \s -> s
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{ computeInputs =
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M.insert f' k
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(computeInputs s)
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}
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modresultstate result f =
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result { computeState = f (computeState result) }
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@ -630,7 +636,7 @@ computeKey rs (ComputeProgram program) k _af dest meterupdate vc =
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(Just (k, p))
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(postcompute keyfile)
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getinputcontent state f =
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getinputcontent state f _required =
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case M.lookup f (computeInputs state) of
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Just inputkey -> case keyGitSha inputkey of
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Nothing ->
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@ -73,12 +73,13 @@ If an input file is not available, the program's stdin will be closed
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without a path being written to it. So when reading from stdin fails,
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the program should exit.
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When `git-annex addcomputed --fast` is being used to add a computation
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to the git-annex repository without actually performing it, the
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response to eaach `INPUT` will be an empty line rather than the path to
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an input file. In that case, the program should proceed with the rest of
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its output to stdout (eg `OUTPUT` and `REPRODUCIBLE`), but should not
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perform any computation.
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When `git-annex addcomputed --fast` is being used to add a computation to
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the git-annex repository without actually performing it, the response to
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each `INPUT` will be an empty line rather than the path to an input file.
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This can also happen when an input file is not available for whatever
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reason. In this case, the program should proceed with the rest of its
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output to stdout (eg `OUTPUT` and `REPRODUCIBLE`), but should not perform
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any computation.
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## output files
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@ -133,6 +134,16 @@ messages that the program can output. All of these are optional.
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that is done by making hard links, but it will fall back to copying annexed
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files if the filesystem does not support hard links.
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* `INPUT-REQUIRED`
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This works the same as `INPUT`, except when `git-annex addcomputed --fast`
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is being used to add a computation to the git-annex repository without
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actually performing it, the input file will be provided as a response
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to this, rather than the empty line provided as a response to `INPUT`.
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If the input file is not available for some reason, an empty line will
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still be provided as a response to this.
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## example
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An example `git-annex-compute-foo` shell script follows:
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@ -78,17 +78,13 @@ else
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echo "SANDBOX"
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read pathtotop
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binddir="$(realpath "$pathtotop")"
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echo "INPUT $pathtotop/$ANNEX_COMPUTE_passthrough"
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read input
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if [ -n "$input" ]; then
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container="./$ANNEX_COMPUTE_passthrough"
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mkdir -p "$(dirname "$container")"
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ln "$(realpath "$input")" "$container"
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else
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echo "Unfortunately, addcomputed --fast cannot be used with git-annex-compute-singularity --passthrough=" >&2
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echo "INPUT-REQUIRED $pathtotop/$ANNEX_COMPUTE_passthrough"
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read container
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if [ -z "$container" ]; then
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echo "Cannot proceed without container $ANNEX_COMPUTE_passthrough" >&2
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exit 1
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fi
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# stdio is passed through to the git-annex-compute- command inside
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# singularity
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# the container
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run_singularity "$@" 2> >( strip_escape 1>&2 )
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fi
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@ -1,13 +1,17 @@
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This is the remainder of my todo list while I was building the
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compute special remote. --[[Joey]]
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* git-annex-compute-singularity with passthrough= cannot be used
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by `git-annex addcomputed --fast` because the singularity image is not
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available to run. Maybe make a varity of INPUT that is provided also
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in --fast mode to solve this?
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* git-annex responds to each INPUT immediately, and flushes stdout.
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This could cause problems if the program is sending several INPUT
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first, before reading responses, as is documented it should do to allow
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for parallel get of the input files.
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* write a tip showing how to use this
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* Support parallel get of input files. The design allows for this,
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but how much parallelism makes sense? Would it be possible to use the
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usual worker pool?
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* Write some simple compute programs so we have something to start with.
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- convert between images eg jpeg to png
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