-- Hoogle documentation, generated by Haddock
-- See Hoogle, http://www.haskell.org/hoogle/


-- | Scientific workflow management system
--   
--   SciFlow is a DSL for building scientific workflows. Workflows built
--   with SciFlow can be run either on desktop computers or in grid
--   computing environments that support DRMAA.
@package SciFlow
@version 0.6.0

module Scientific.Workflow.Main.Options
data CMD
Run :: GlobalOpts -> Int -> Bool -> (Maybe [String]) -> (Maybe String) -> CMD
View :: Bool -> CMD
Cat :: GlobalOpts -> String -> CMD
Write :: GlobalOpts -> String -> FilePath -> CMD
Delete :: GlobalOpts -> String -> CMD
Recover :: GlobalOpts -> FilePath -> CMD
DumpDB :: GlobalOpts -> FilePath -> CMD
Call :: GlobalOpts -> String -> String -> String -> CMD
data GlobalOpts
GlobalOpts :: FilePath -> Maybe [FilePath] -> GlobalOpts
[dbPath] :: GlobalOpts -> FilePath
[configFile] :: GlobalOpts -> Maybe [FilePath]
argsParser :: String -> ParserInfo CMD

module Scientific.Workflow.Internal.DB
openDB :: FilePath -> IO WorkflowDB
closeDB :: WorkflowDB -> IO ()
readData :: DBData r => PID -> WorkflowDB -> IO r
readDataByteString :: PID -> WorkflowDB -> IO ByteString
saveDataByteString :: PID -> ByteString -> WorkflowDB -> IO ()
saveData :: DBData r => PID -> r -> WorkflowDB -> IO ()
updateData :: DBData r => PID -> r -> WorkflowDB -> IO ()
delRecord :: PID -> WorkflowDB -> IO ()
isFinished :: PID -> WorkflowDB -> IO Bool
getKeys :: WorkflowDB -> IO [PID]

-- | An abstract type representing the database used to store states of
--   workflow
newtype WorkflowDB
WorkflowDB :: Connection -> WorkflowDB

-- | <tt>DBData</tt> constraint is used for data serialization.
type DBData a = (FromJSON a, ToJSON a, Serialize a)
serialize :: DBData a => a -> ByteString
deserialize :: DBData a => ByteString -> a
readYaml :: DBData a => ByteString -> a
showYaml :: DBData a => a -> ByteString

module Scientific.Workflow.Internal.Utils
data RemoteOpts config
RemoteOpts :: String -> config -> RemoteOpts config
[extraParams] :: RemoteOpts config -> String
[environment] :: RemoteOpts config -> config
data Log
Running :: Text -> Log
Complete :: Text -> Log
Warn :: Text -> String -> Log
Error :: String -> Log
Exit :: Log
runRemote :: (DBData a, DBData b, ToJSON config) => RemoteOpts config -> Text -> a -> IO b
sendLog :: Maybe Socket -> Log -> IO ()
instance GHC.Show.Show Scientific.Workflow.Internal.Utils.Log
instance GHC.Generics.Generic Scientific.Workflow.Internal.Utils.Log
instance Data.Serialize.Serialize Scientific.Workflow.Internal.Utils.Log

module Scientific.Workflow.Internal.Builder.Types

-- | A computation node.
data Node
Node :: Text -> ExpQ -> Attribute -> Node
[_nodePid] :: Node -> Text
[_nodeFunction] :: Node -> ExpQ
[_nodeAttr] :: Node -> Attribute

-- | Links between computational nodes
data Edge
Edge :: Text -> Text -> EdgeOrd -> Edge
[_edgeFrom] :: Edge -> Text
[_edgeTo] :: Edge -> Text

-- | Order of the edge
[_edgeOrd] :: Edge -> EdgeOrd
type EdgeOrd = Int
type Builder = State ([Node], [Edge])

-- | Node attributes.
data Attribute
Attribute :: Text -> Text -> Maybe Bool -> String -> FunctionConfig -> Attribute

-- | Short description
[_label] :: Attribute -> Text

-- | Long description
[_note] :: Attribute -> Text

-- | Overwrite the global option
[_submitToRemote] :: Attribute -> Maybe Bool

-- | Parameters for to remote execution
[_remoteParam] :: Attribute -> String

-- | Usually not being used directly
[_functionConfig] :: Attribute -> FunctionConfig

-- | The type of node function
data FunctionConfig
FunctionConfig :: ParallelMode -> FunctionType -> FunctionConfig
data ParallelMode

-- | No parallelism.
None :: ParallelMode

-- | Turn input <tt>a</tt> into <tt>[a]</tt> and process them in parallel.
Standard :: Int -> ParallelMode

-- | Assume the input is <tt>ContextData d a</tt>, where <tt>d</tt> is
--   shared and <tt>a</tt> becomes <tt>[a]</tt>.
ShareData :: Int -> ParallelMode
data FunctionType

-- | The function is pure, i.e., <tt>a -&gt; b</tt>.
Pure :: FunctionType

-- | A IO function, i.e., <tt>a -&gt; IO b</tt>.
IOAction :: FunctionType

-- | A function that has access to configuration, i.e., <tt>a -&gt;
--   WorkflowConfig config b</tt>.
Stateful :: FunctionType
submitToRemote :: Lens' Attribute (Maybe Bool)
remoteParam :: Lens' Attribute String
note :: Lens' Attribute Text
label :: Lens' Attribute Text
functionConfig :: Lens' Attribute FunctionConfig
defaultAttribute :: Attribute
type AttributeSetter = State Attribute ()
type DAG = Gr Node EdgeOrd

-- | Objects that can be converted to ExpQ
class ToExpQ a
toExpQ :: ToExpQ a => a -> ExpQ

-- | Data and its environment.
data ContextData context dat
ContextData :: context -> dat -> ContextData context dat
[_context] :: ContextData context dat -> context
[_data] :: ContextData context dat -> dat
instance GHC.Generics.Generic (Scientific.Workflow.Internal.Builder.Types.ContextData context dat)
instance Scientific.Workflow.Internal.Builder.Types.ToExpQ Language.Haskell.TH.Syntax.Name
instance Scientific.Workflow.Internal.Builder.Types.ToExpQ Language.Haskell.TH.Lib.ExpQ
instance (Data.Aeson.Types.FromJSON.FromJSON c, Data.Aeson.Types.FromJSON.FromJSON d) => Data.Aeson.Types.FromJSON.FromJSON (Scientific.Workflow.Internal.Builder.Types.ContextData c d)
instance (Data.Aeson.Types.ToJSON.ToJSON c, Data.Aeson.Types.ToJSON.ToJSON d) => Data.Aeson.Types.ToJSON.ToJSON (Scientific.Workflow.Internal.Builder.Types.ContextData c d)
instance (Data.Serialize.Serialize c, Data.Serialize.Serialize d) => Data.Serialize.Serialize (Scientific.Workflow.Internal.Builder.Types.ContextData c d)
instance Language.Haskell.TH.Syntax.Lift Scientific.Workflow.Internal.Builder.Types.Attribute
instance Language.Haskell.TH.Syntax.Lift Scientific.Workflow.Internal.Builder.Types.FunctionType
instance Language.Haskell.TH.Syntax.Lift Scientific.Workflow.Internal.Builder.Types.ParallelMode
instance Language.Haskell.TH.Syntax.Lift Scientific.Workflow.Internal.Builder.Types.FunctionConfig
instance GHC.Generics.Generic Scientific.Workflow.Internal.Builder.Types.Attribute
instance GHC.Generics.Generic Scientific.Workflow.Internal.Builder.Types.FunctionConfig
instance GHC.Generics.Generic Scientific.Workflow.Internal.Builder.Types.FunctionType
instance GHC.Generics.Generic Scientific.Workflow.Internal.Builder.Types.ParallelMode
instance Data.Serialize.Serialize Scientific.Workflow.Internal.Builder.Types.Attribute
instance Data.Serialize.Serialize Scientific.Workflow.Internal.Builder.Types.FunctionConfig
instance Data.Serialize.Serialize Scientific.Workflow.Internal.Builder.Types.ParallelMode
instance Data.Serialize.Serialize Scientific.Workflow.Internal.Builder.Types.FunctionType

module Scientific.Workflow.Types

-- | A Workflow is a stateful function
data Workflow config
Workflow :: Gr PID Int -> Map Text Attribute -> Processor config () () -> Workflow config
[_worflow_dag] :: Workflow config -> Gr PID Int
[_worflow_pidToAttr] :: Workflow config -> Map Text Attribute
[_workflow] :: Workflow config -> Processor config () ()

-- | The id of a node
type PID = Text

-- | The result of a computation node
data NodeState

-- | The node has been executed
Success :: NodeState

-- | The node failed to finish
Fail :: SomeException -> NodeState

-- | The node will be executed
Scheduled :: NodeState

-- | Indicate the workflow is currently running under special mode
Special :: SpecialMode -> NodeState
data SpecialMode

-- | The node will not be executed
Skip :: SpecialMode

-- | Simply read the saved data from database
FetchData :: SpecialMode

-- | Read the result from the input file and save it to database.
WriteData :: FilePath -> SpecialMode

-- | Read input from the input file and save results to the output file.
--   This is used in remote mode.
EXE :: FilePath -> FilePath -> SpecialMode
type ProcState config = ReaderT WorkflowState (ExceptT (PID, SomeException) (WorkflowConfig config))
data WorkflowState
WorkflowState :: WorkflowDB -> Map PID (MVar NodeState, Attribute) -> MVar () -> Bool -> Maybe Socket -> WorkflowState
[_database] :: WorkflowState -> WorkflowDB
[_procStatus] :: WorkflowState -> Map PID (MVar NodeState, Attribute)

-- | Concurrency controller
[_procParaControl] :: WorkflowState -> MVar ()

-- | Global remote switch
[_remote] :: WorkflowState -> Bool

-- | Server for logging
[_logServer] :: WorkflowState -> Maybe Socket
database :: Lens' WorkflowState WorkflowDB
procStatus :: Lens' WorkflowState (Map PID (MVar NodeState, Attribute))
procParaControl :: Lens' WorkflowState (MVar ())
remote :: Lens' WorkflowState Bool
logServer :: Lens' WorkflowState (Maybe Socket)
type Processor config a b = a -> (ProcState config) b
data RunMode

-- | Run as the master process
Master :: RunMode

-- | Run as a slave process
Slave :: PID -> FilePath -> FilePath -> RunMode

-- | Review the info stored in a node
Review :: PID -> RunMode

-- | Replace the info stored in a node
Replace :: PID -> FilePath -> RunMode

-- | Options
data RunOpt
RunOpt :: FilePath -> Int -> Bool -> RunMode -> [FilePath] -> Maybe [PID] -> Maybe String -> RunOpt
[dbFile] :: RunOpt -> FilePath

-- | number of concurrent processes
[nThread] :: RunOpt -> Int
[runOnRemote] :: RunOpt -> Bool
[runMode] :: RunOpt -> RunMode
[configuration] :: RunOpt -> [FilePath]

-- | Should run only selected nodes
[selected] :: RunOpt -> Maybe [PID]
[logServerAddr] :: RunOpt -> Maybe String
defaultRunOpt :: RunOpt

-- | Auxiliary type for concurrency support.
newtype Parallel config r
Parallel :: (ProcState config) r -> Parallel config r
[runParallel] :: Parallel config r -> (ProcState config) r
type WorkflowConfig config = ReaderT config IO
instance (Language.Haskell.TH.Syntax.Lift a, Language.Haskell.TH.Syntax.Lift b) => Language.Haskell.TH.Syntax.Lift (Data.Graph.Inductive.PatriciaTree.Gr a b)
instance GHC.Base.Functor (Scientific.Workflow.Types.Parallel config)
instance GHC.Base.Applicative (Scientific.Workflow.Types.Parallel config)
instance Data.Serialize.Serialize (Data.Graph.Inductive.PatriciaTree.Gr (Scientific.Workflow.Types.PID, Scientific.Workflow.Internal.Builder.Types.Attribute) GHC.Types.Int)

module Scientific.Workflow.Visualize

-- | Output the computation graph in dot code which can be visualize by
--   Graphviz.
drawWorkflow :: Gr (PID, Attribute) Int -> Text

module Scientific.Workflow.Internal.Builder

-- | Declare an IO computational step.
node :: ToExpQ fun => PID -> fun -> State Attribute () -> Builder ()

-- | Declare a pure computational step.
node' :: ToExpQ fun => PID -> fun -> State Attribute () -> Builder ()

-- | Declare a stateful computational step.
nodeS :: ToExpQ fun => PID -> fun -> State Attribute () -> Builder ()

-- | Declare an IO and parallel computational step. This will turn
--   functions with type "<tt>a -&gt; IO b</tt>" into functions with type
--   "<tt>[a] -&gt; IO [b]</tt>". And <tt>[a]</tt> will be processed in
--   parallel with provided batch size. Note: Currently, parallelism is
--   available only when <tt>"--remote"</tt> flag is on.
nodeP :: ToExpQ fun => Int -> PID -> fun -> State Attribute () -> Builder ()

-- | Same as <tt><a>nodeP</a></tt> but work with pure functions.
nodeP' :: ToExpQ fun => Int -> PID -> fun -> State Attribute () -> Builder ()

-- | Same as <tt><a>nodeP</a></tt> but work with stateful functions.
nodePS :: ToExpQ fun => Int -> PID -> fun -> State Attribute () -> Builder ()

-- | Similar to <tt><a>nodeP</a></tt> but work with inputs that are
--   associated with a shared context. Turn <tt><a>ContextData</a> context
--   a -&gt; <a>IO</a> b</tt> into <tt><a>ContextData</a> context [a] -&gt;
--   <a>IO</a> [b]</tt>.
nodeSharedP :: ToExpQ fun => Int -> PID -> fun -> State Attribute () -> Builder ()
nodeSharedP' :: ToExpQ fun => Int -> PID -> fun -> State Attribute () -> Builder ()
nodeSharedPS :: ToExpQ fun => Int -> PID -> fun -> State Attribute () -> Builder ()

-- | Declare the dependency between nodes. Example:
--   
--   <pre>
--   node' "step1" [| \() -&gt; 1 :: Int |] $ return ()
--   node' "step2" [| \() -&gt; 2 :: Int |] $ return ()
--   node' "step3" [| \(x, y) -&gt; x * y |] $ return ()
--   link ["step1", "step2"] "step3"
--   </pre>
link :: [PID] -> PID -> Builder ()

-- | <tt>(~&gt;) = <a>link</a></tt>.
(~>) :: [PID] -> PID -> Builder ()

-- | "<tt><a>path</a> [a, b, c]</tt>" is equivalent to "<tt><a>link</a> a b
--   &gt;&gt; <a>link</a> b c</tt>"
path :: [PID] -> Builder ()

-- | Add a prefix to IDs of nodes for a given builder, i.e., <tt>id</tt>
--   becomes <tt>prefix_id</tt>.
namespace :: Text -> Builder () -> Builder ()

-- | Build the workflow. This function will first create functions defined
--   in the builder. These pieces will then be assembled to form a function
--   that will execute each individual function in a correct order, named
--   $name$.
buildWorkflow :: String -> Builder () -> Q [Dec]

-- | Build only a part of the workflow that has not been executed. This is
--   used during development for fast compliation.
buildWorkflowPart :: FilePath -> String -> Builder () -> Q [Dec]

-- | Contruct a DAG representing the workflow
mkDAG :: Builder () -> DAG
mkProc :: (DBData a, DBData b, ToJSON config) => PID -> (a -> (ProcState config) b) -> (Processor config a b)

module Scientific.Workflow.Main
defaultMain :: Builder () -> Q [Dec]
defaultMainOpts :: MainOpts
mainWith :: MainOpts -> Builder () -> Q [Dec]
data MainOpts
MainOpts :: Name -> String -> MainOpts

-- | An action to be execute before the workflow. The action should have
--   type: <tt><a>IO</a> () -&gt; <a>IO</a> ()</tt>. e.g., some
--   initialization processes.
[preAction] :: MainOpts -> Name
[programHeader] :: MainOpts -> String
runWorkflow :: (Default config, FromJSON config) => Workflow config -> RunOpt -> IO ()
instance Language.Haskell.TH.Syntax.Lift Scientific.Workflow.Main.MainOpts


-- | SciFlow is a DSL for building scientific workflows. Workflows built
--   with SciFlow can be run either on desktop computers or in grid
--   computing environments that support DRMAA.
--   
--   Features:
--   
--   <ol>
--   <li>Easy to use and safe: Provide a simple and flexible way to design
--   type safe computational pipelines in Haskell.</li>
--   <li>Automatic Checkpointing: The states of intermediate steps are
--   automatically logged, allowing easy restart upon failures.</li>
--   <li>Parallelism and grid computing support.</li>
--   </ol>
--   
--   Example:
--   
--   <pre>
--   import           Control.Lens             ((.=))
--   import           Scientific.Workflow
--   
--   f :: Int -&gt; Int
--   f = (+1)
--   
--   defaultMain $ do
--       nodeS "step0" [| return . const [1..10] :: () -&gt; WorkflowConfig () [Int] |] $ return ()
--       nodeP' 2 "step1" 'f $ note .= "run in parallel with batch size 2"
--       nodeP' 4 "step2" 'f $ note .= "run in parallel with batch size 4"
--       node' "step3" [| \(x, y) -&gt; x ++ y |] $ return ()
--   
--       ["step0"] ~&gt; "step1"
--       ["step0"] ~&gt; "step2"
--       ["step1", "step2"] ~&gt; "step3"
--   </pre>
module Scientific.Workflow
defaultMain :: Builder () -> Q [Dec]
mainWith :: MainOpts -> Builder () -> Q [Dec]
defaultMainOpts :: MainOpts
data MainOpts
MainOpts :: Name -> String -> MainOpts

-- | An action to be execute before the workflow. The action should have
--   type: <tt><a>IO</a> () -&gt; <a>IO</a> ()</tt>. e.g., some
--   initialization processes.
[preAction] :: MainOpts -> Name
[programHeader] :: MainOpts -> String
type Builder = State ([Node], [Edge])

-- | Add a prefix to IDs of nodes for a given builder, i.e., <tt>id</tt>
--   becomes <tt>prefix_id</tt>.
namespace :: Text -> Builder () -> Builder ()

-- | Declare an IO computational step.
node :: ToExpQ fun => PID -> fun -> State Attribute () -> Builder ()

-- | Declare a pure computational step.
node' :: ToExpQ fun => PID -> fun -> State Attribute () -> Builder ()

-- | Declare a stateful computational step.
nodeS :: ToExpQ fun => PID -> fun -> State Attribute () -> Builder ()

-- | Declare an IO and parallel computational step. This will turn
--   functions with type "<tt>a -&gt; IO b</tt>" into functions with type
--   "<tt>[a] -&gt; IO [b]</tt>". And <tt>[a]</tt> will be processed in
--   parallel with provided batch size. Note: Currently, parallelism is
--   available only when <tt>"--remote"</tt> flag is on.
nodeP :: ToExpQ fun => Int -> PID -> fun -> State Attribute () -> Builder ()

-- | Same as <tt><a>nodeP</a></tt> but work with pure functions.
nodeP' :: ToExpQ fun => Int -> PID -> fun -> State Attribute () -> Builder ()

-- | Same as <tt><a>nodeP</a></tt> but work with stateful functions.
nodePS :: ToExpQ fun => Int -> PID -> fun -> State Attribute () -> Builder ()

-- | Similar to <tt><a>nodeP</a></tt> but work with inputs that are
--   associated with a shared context. Turn <tt><a>ContextData</a> context
--   a -&gt; <a>IO</a> b</tt> into <tt><a>ContextData</a> context [a] -&gt;
--   <a>IO</a> [b]</tt>.
nodeSharedP :: ToExpQ fun => Int -> PID -> fun -> State Attribute () -> Builder ()
nodeSharedP' :: ToExpQ fun => Int -> PID -> fun -> State Attribute () -> Builder ()
nodeSharedPS :: ToExpQ fun => Int -> PID -> fun -> State Attribute () -> Builder ()

-- | Declare the dependency between nodes. Example:
--   
--   <pre>
--   node' "step1" [| \() -&gt; 1 :: Int |] $ return ()
--   node' "step2" [| \() -&gt; 2 :: Int |] $ return ()
--   node' "step3" [| \(x, y) -&gt; x * y |] $ return ()
--   link ["step1", "step2"] "step3"
--   </pre>
link :: [PID] -> PID -> Builder ()

-- | <tt>(~&gt;) = <a>link</a></tt>.
(~>) :: [PID] -> PID -> Builder ()

-- | "<tt><a>path</a> [a, b, c]</tt>" is equivalent to "<tt><a>link</a> a b
--   &gt;&gt; <a>link</a> b c</tt>"
path :: [PID] -> Builder ()
label :: Lens' Attribute Text
note :: Lens' Attribute Text
submitToRemote :: Lens' Attribute (Maybe Bool)
remoteParam :: Lens' Attribute String

-- | Data and its environment.
data ContextData context dat
ContextData :: context -> dat -> ContextData context dat
[_context] :: ContextData context dat -> context
[_data] :: ContextData context dat -> dat
type WorkflowConfig config = ReaderT config IO