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.
Just v -> isReproducible v
Nothing -> Remote.Compute.computeReproducible result
-getInputContent :: Bool -> OsPath -> Annex (Key, Maybe (Either Git.Sha OsPath))
-getInputContent fast p = catKeyFile p >>= \case
- Just inputkey -> getInputContent' fast inputkey filedesc
+getInputContent :: Bool -> OsPath -> Bool -> Annex (Key, Maybe (Either Git.Sha OsPath))
+getInputContent fast p required = catKeyFile p >>= \case
+ Just inputkey -> getInputContent' fast inputkey required filedesc
Nothing -> inRepo (Git.fileRef p) >>= \case
Just fileref -> catObjectMetaData fileref >>= \case
Just (sha, _, t)
| t == Git.BlobObject ->
- getInputContent' fast (gitShaKey sha) filedesc
+ getInputContent' fast (gitShaKey sha) required filedesc
| otherwise ->
badinput $ ", not a git " ++ decodeBS (Git.fmtObjectType t)
Nothing -> notcheckedin
badinput s = giveup $ "The computation needs an input file " ++ s ++ ": " ++ fromOsPath p
notcheckedin = badinput "that is not checked into the git repository"
-getInputContent' :: Bool -> Key -> String -> Annex (Key, Maybe (Either Git.Sha OsPath))
-getInputContent' fast inputkey filedesc
- | fast = return (inputkey, Nothing)
+getInputContent' :: Bool -> Key -> Bool -> String -> Annex (Key, Maybe (Either Git.Sha OsPath))
+getInputContent' fast inputkey required filedesc
+ | fast && not required = return (inputkey, Nothing)
| otherwise = case keyGitSha inputkey of
Nothing -> ifM (inAnnex inputkey)
( do
check "not outputting"
Remote.Compute.computeOutputs origstate state
- getinputcontent program p
+ getinputcontent program p required
| originalOption o =
case M.lookup p (Remote.Compute.computeInputs origstate) of
- Just inputkey -> getInputContent' False inputkey
+ Just inputkey -> getInputContent' False inputkey required
(fromOsPath p ++ "(key " ++ serializeKey inputkey ++ ")")
Nothing -> Remote.Compute.computationBehaviorChangeError program
"requesting a new input file" p
- | otherwise = getInputContent False p
+ | otherwise = getInputContent False p required
destfile outputfile
| Just outputfile == origfile = Just file
data ProcessCommand
= ProcessInput FilePath
| ProcessOutput FilePath
+ | ProcessProgress PercentFloat
| ProcessReproducible
| ProcessSandbox
- | ProcessProgress PercentFloat
+ | ProcessInputRequired FilePath
deriving (Show, Eq)
instance Proto.Receivable ProcessCommand where
parseCommand "INPUT" = Proto.parse1 ProcessInput
parseCommand "OUTPUT" = Proto.parse1 ProcessOutput
+ parseCommand "PROGRESS" = Proto.parse1 ProcessProgress
parseCommand "REPRODUCIBLE" = Proto.parse0 ProcessReproducible
parseCommand "SANDBOX" = Proto.parse0 ProcessSandbox
- parseCommand "PROGRESS" = Proto.parse1 ProcessProgress
+ parseCommand "INPUT-REQUIRED" = Proto.parse1 ProcessInputRequired
parseCommand _ = Proto.parseFail
newtype PercentFloat = PercentFloat Float
:: ComputeProgram
-> ComputeState
-> ImmutableState
- -> (OsPath -> Annex (Key, Maybe (Either Git.Sha OsPath)))
- -- ^ get input file's content, or Nothing the input file's
- -- content is not available
+ -> (OsPath -> Bool -> Annex (Key, Maybe (Either Git.Sha OsPath)))
+ -- ^ Get input file's content, or Nothing the input file's
+ -- content is not available. True is passed when the input content
+ -- is required even for addcomputed --fast.
-> Maybe (Key, MeterUpdate)
-- ^ update meter for this key
-> (ComputeProgramResult -> OsPath -> NominalDiffTime -> Annex v)
liftIO $ hFlush (stdinHandle p)
parseoutput p tmpdir subdir result meterfile l = case Proto.parseMessage l of
- Just (ProcessInput f) -> do
- let f' = toOsPath f
- let knowninput = M.member f'
- (computeInputs (computeState result))
- checksafefile tmpdir subdir f' "input"
- checkimmutable knowninput "inputting" f' $ do
- (k, inputcontent) <- getinputcontent f'
- let mkrel a = Just <$>
- (a >>= liftIO . relPathDirToFile subdir)
- mp <- case inputcontent of
- Nothing -> pure Nothing
- Just (Right obj)
- | computeSandbox result ->
- mkrel $ populatesandbox obj tmpdir
- | otherwise ->
- mkrel $ pure obj
- Just (Left gitsha) ->
- mkrel $ populategitsha gitsha tmpdir
- sendresponse p $
- maybe "" fromOsPath mp
- let result' = result
- { computeInputsUnavailable =
- isNothing mp || computeInputsUnavailable result
- }
- return $ if immutablestate
- then result'
- else modresultstate result' $ \s -> s
- { computeInputs =
- M.insert f' k
- (computeInputs s)
- }
+ Just (ProcessInput f) -> handleinput f False p tmpdir subdir result
+ Just (ProcessInputRequired f) -> handleinput f True p tmpdir subdir result
Just (ProcessOutput f) -> do
let f' = toOsPath f
checksafefile tmpdir subdir f' "output"
Nothing -> giveup $
program ++ " output an unparseable line: \"" ++ l ++ "\""
+ handleinput f required p tmpdir subdir result = do
+ let f' = toOsPath f
+ let knowninput = M.member f'
+ (computeInputs (computeState result))
+ checksafefile tmpdir subdir f' "input"
+ checkimmutable knowninput "inputting" f' $ do
+ (k, inputcontent) <- getinputcontent f' required
+ let mkrel a = Just <$>
+ (a >>= liftIO . relPathDirToFile subdir)
+ mp <- case inputcontent of
+ Nothing -> pure Nothing
+ Just (Right obj)
+ | computeSandbox result ->
+ mkrel $ populatesandbox obj tmpdir
+ | otherwise ->
+ mkrel $ pure obj
+ Just (Left gitsha) ->
+ mkrel $ populategitsha gitsha tmpdir
+ sendresponse p $
+ maybe "" fromOsPath mp
+ let result' = result
+ { computeInputsUnavailable =
+ isNothing mp || computeInputsUnavailable result
+ }
+ return $ if immutablestate
+ then result'
+ else modresultstate result' $ \s -> s
+ { computeInputs =
+ M.insert f' k
+ (computeInputs s)
+ }
+
modresultstate result f =
result { computeState = f (computeState result) }
(Just (k, p))
(postcompute keyfile)
- getinputcontent state f =
+ getinputcontent state f _required =
case M.lookup f (computeInputs state) of
Just inputkey -> case keyGitSha inputkey of
Nothing ->
without a path being written to it. So when reading from stdin fails,
the program should exit.
-When `git-annex addcomputed --fast` is being used to add a computation
-to the git-annex repository without actually performing it, the
-response to eaach `INPUT` will be an empty line rather than the path to
-an input file. In that case, the program should proceed with the rest of
-its output to stdout (eg `OUTPUT` and `REPRODUCIBLE`), but should not
-perform any computation.
+When `git-annex addcomputed --fast` is being used to add a computation to
+the git-annex repository without actually performing it, the response to
+each `INPUT` will be an empty line rather than the path to an input file.
+This can also happen when an input file is not available for whatever
+reason. In this case, the program should proceed with the rest of its
+output to stdout (eg `OUTPUT` and `REPRODUCIBLE`), but should not perform
+any computation.
## output files
that is done by making hard links, but it will fall back to copying annexed
files if the filesystem does not support hard links.
+* `INPUT-REQUIRED`
+
+ This works the same as `INPUT`, except when `git-annex addcomputed --fast`
+ is being used to add a computation to the git-annex repository without
+ actually performing it, the input file will be provided as a response
+ to this, rather than the empty line provided as a response to `INPUT`.
+
+ If the input file is not available for some reason, an empty line will
+ still be provided as a response to this.
+
## example
An example `git-annex-compute-foo` shell script follows:
echo "SANDBOX"
read pathtotop
binddir="$(realpath "$pathtotop")"
- echo "INPUT $pathtotop/$ANNEX_COMPUTE_passthrough"
- read input
- if [ -n "$input" ]; then
- container="./$ANNEX_COMPUTE_passthrough"
- mkdir -p "$(dirname "$container")"
- ln "$(realpath "$input")" "$container"
- else
- echo "Unfortunately, addcomputed --fast cannot be used with git-annex-compute-singularity --passthrough=" >&2
+ echo "INPUT-REQUIRED $pathtotop/$ANNEX_COMPUTE_passthrough"
+ read container
+ if [ -z "$container" ]; then
+ echo "Cannot proceed without container $ANNEX_COMPUTE_passthrough" >&2
exit 1
fi
# stdio is passed through to the git-annex-compute- command inside
- # singularity
+ # the container
run_singularity "$@" 2> >( strip_escape 1>&2 )
fi
This is the remainder of my todo list while I was building the
compute special remote. --[[Joey]]
-* git-annex-compute-singularity with passthrough= cannot be used
- by `git-annex addcomputed --fast` because the singularity image is not
- available to run. Maybe make a varity of INPUT that is provided also
- in --fast mode to solve this?
+* git-annex responds to each INPUT immediately, and flushes stdout.
+ This could cause problems if the program is sending several INPUT
+ first, before reading responses, as is documented it should do to allow
+ for parallel get of the input files.
* write a tip showing how to use this
+* Support parallel get of input files. The design allows for this,
+ but how much parallelism makes sense? Would it be possible to use the
+ usual worker pool?
+
* Write some simple compute programs so we have something to start with.
- convert between images eg jpeg to png
projects / git-annex.git / commitdiff