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.
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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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