Scientific.Workflow.Types

Documentation

data Workflow config

A Workflow is a stateful function

Constructors

Workflow

Fields

• _worflow_dag :: Gr PID Int
• _worflow_pidToAttr :: Map Text Attribute
• _workflow :: Processor config () ()

type PID = Text

The id of a node

data NodeState

The result of a computation node

Constructors

Success

The node has been executed

Fail SomeException

The node failed to finish

Scheduled

The node will be executed

Special SpecialMode

Indicate the workflow is currently running under special mode

data SpecialMode

Constructors

Skip

The node will not be executed

FetchData

Simply read the saved data from database

WriteData FilePath

Read the result from the input file and save it to database.

EXE FilePath FilePath

Read input from the input file and save results to the output file. This is used in remote mode.

type ProcState config = ReaderT WorkflowState (ExceptT (PID, SomeException) (WorkflowConfig config))

data WorkflowState

Constructors

WorkflowState

Fields

• _database :: WorkflowDB
• _procStatus :: Map PID (MVar NodeState, Attribute)
• _procParaControl :: MVar ()

  Concurrency controller

• _remote :: Bool

  Global remote switch

• _logServer :: Maybe Socket

  Server for logging

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

Constructors

Master

Run as the master process

Slave PID FilePath FilePath

Run as a slave process

Review PID

Review the info stored in a node

Replace PID FilePath

Replace the info stored in a node

data RunOpt

Options

Constructors

RunOpt

Fields

• dbFile :: FilePath
• nThread :: Int

  number of concurrent processes

• runOnRemote :: Bool
• runMode :: RunMode
• configuration :: [FilePath]
• selected :: Maybe [PID]

  Should run only selected nodes

• logServerAddr :: Maybe String

defaultRunOpt :: RunOpt

newtype Parallel config r

Auxiliary type for concurrency support.

Constructors

Parallel

Fields

• runParallel :: ProcState config r

Instances

Functor (Parallel config)

Methods

fmap :: (a -> b) -> Parallel config a -> Parallel config b

(<$) :: a -> Parallel config b -> Parallel config a

Applicative (Parallel config)

Methods

pure :: a -> Parallel config a

(<*>) :: Parallel config (a -> b) -> Parallel config a -> Parallel config b

liftA2 :: (a -> b -> c) -> Parallel config a -> Parallel config b -> Parallel config c

(*>) :: Parallel config a -> Parallel config b -> Parallel config b

(<*) :: Parallel config a -> Parallel config b -> Parallel config a

type WorkflowConfig config = ReaderT config IO

Orphan instances

(Lift a, Lift b) => Lift (Gr a b)

Methods

lift :: Gr a b -> Q Exp

Serialize (Gr (PID, Attribute) Int)

Methods

put :: Putter (Gr (PID, Attribute) Int)

get :: Get (Gr (PID, Attribute) Int)