Scientific.Workflow.Types

Documentation

newtype WorkflowDB

An abstract type representing the database used to store states of workflow

Constructors

WorkflowDB Connection

data Workflow

A Workflow is a DAG

Constructors

Workflow (Map Text Attribute) (Map String Closure) (Processor () ())

data Closure where

Constructors

Closure :: (DBData a, DBData b) => (a -> IO b) -> Closure

type PID = Text

The id of a node

data NodeResult

The result of a computation node

Constructors

Success

Fail SomeException

Scheduled

type ProcState b = StateT WorkflowState (ExceptT (PID, SomeException) IO) b

data WorkflowState

Constructors

WorkflowState

Fields

• _db :: WorkflowDB
• _procStatus :: Map PID (MVar NodeResult, Attribute)
• _procParaControl :: MVar ()

  concurrency controller

• _remote :: Bool

db :: Lens' WorkflowState WorkflowDB

procStatus :: Lens' WorkflowState (Map PID (MVar NodeResult, Attribute))

procParaControl :: Lens' WorkflowState (MVar ())

remote :: Lens' WorkflowState Bool

type Processor a b = a -> ProcState b

data RunOpt

Constructors

RunOpt

Fields

• database :: FilePath
• nThread :: Int

  number of concurrent processes

• runOnRemote :: Bool

class BatchData a b where

Minimal complete definition

batchFunction

Methods

batchFunction :: (a -> IO b) -> Int -> (a -> [a], [b] -> b)

Instances

((~) * (IsList a b) flag, BatchData' flag a b) => BatchData a b

Methods

batchFunction :: (a -> IO b) -> Int -> (a -> [a], [b] -> b)

class BatchData' flag a b where

Minimal complete definition

batchFunction'

Methods

batchFunction' :: flag -> (a -> IO b) -> Int -> (a -> [a], [b] -> b)

type family IsList a b where ...

Equations

IsList [a] [b] = HTrue

IsList a b = HFalse

class DBData a where

Minimal complete definition

serialize, deserialize, showYaml, readYaml

Methods

serialize :: a -> ByteString

deserialize :: ByteString -> a

showYaml :: a -> ByteString

readYaml :: ByteString -> a

Instances

(FromJSON a, ToJSON a, Serialize a) => DBData a

Methods

serialize :: a -> ByteString

deserialize :: ByteString -> a

showYaml :: a -> ByteString

readYaml :: ByteString -> a

data Attribute

Node attribute

Constructors

Attribute

Fields

• _label :: Text

  short description

• _note :: Text

  long description

• _batch :: Int
• _submitToRemote :: Maybe Bool

  overwrite the global option

type AttributeSetter = State Attribute ()

defaultAttribute :: Attribute

label :: Lens' Attribute Text

note :: Lens' Attribute Text

batch :: Lens' Attribute Int

submitToRemote :: Lens' Attribute (Maybe Bool)