FASTR

FASTR is a framework that helps creating workflows of different tools. The workflows created in FASTR are automatically enhanced with flexible data input/output, execution options (local, cluster, etc) and solid provenance.

We chose to create tools by creating wrappers around executables and connecting everything with Python.

Fastr is open-source (licensed under the Apache 2.0 license) and hosted on gitlab at https://gitlab.com/radiology/infrastructure/fastr

For support, go to https://groups.google.com/d/forum/fastr-users

To get yourself a copy, see the Installation

The official documentation can be found at fastr.readthedocs.io

The Fastr workflow system is presented in the following article:

Hakim Achterberg, Marcel Koek, and Wiro Niessen. “Fastr: a workflow engine for advanced data flows in medical image analysis.” Frontiers in ICT 3 (2016): 15.

Fastr is made possible by contributions from the following people: Hakim Achterberg, Marcel Koek, Adriaan Versteeg, Thomas Phil, Mattias Hansson, Baldur van Lew, Marcel Zwiers, and Coert Metz

FASTR Documentation

• Introduction
  • Philosophy
  • System overview
• Quick start guide
  • Installation
    • Installing via pip
    • Installing from source code
  • Configuration
  • Creating a simple network
    • Creating nodes
    • Creating links
    • Create an image of the Network
  • Running a Network
• User Manual
  • Tools
    • Create your own tool
  • Network
    • Node
    • SourceNode
    • ConstantNode
    • SinkNode
    • Link
  • Data Flow
    • Data flow inside a Node
    • Data flows in a Link
    • Data flows in an Input
    • Broadcasting (matching data of different dimensions)
  • DataTypes
    • Resolving Datatypes
  • Execution
    • Continuing a Network
  • IOPlugins
  • Secrets
  • Debugging
    • Debugging a Fastr tool
    • Debugging an invalid Network
    • Debugging a Network run with errors
    • Asking for help with debugging
  • Naming Convention
  • Provenance
    • W3C Prov
    • Implementation
    • Usage
• Command Line Tools
  • fastr cat
    • Positional Arguments
  • fastr dump
    • Positional Arguments
  • fastr execute
    • Positional Arguments
  • fastr extract_argparse
    • Positional Arguments
  • fastr provenance
    • Positional Arguments
    • Named Arguments
  • fastr pylint
    • Named Arguments
  • fastr report
    • Positional Arguments
    • Named Arguments
  • fastr run
    • Positional Arguments
  • fastr sink
    • Named Arguments
  • fastr source
    • Named Arguments
  • fastr test
    • Sub-commands
  • fastr trace
    • Positional Arguments
    • Named Arguments
  • fastr upgrade
    • Positional Arguments
    • Named Arguments
  • fastr verify
    • Positional Arguments
    • Named Arguments
• Resource File Formats
  • Config file
    • Splitting up config files
    • Example config file
    • Format
    • Configuration fields
  • Tool description
• Plugin Reference
  • CollectorPlugin Reference
    • JsonCollector
    • PathCollector
    • StdoutCollector
  • ExecutionPlugin Reference
    • BlockingExecution
    • DRMAAExecution
    • LinearExecution
    • ProcessPoolExecution
    • RQExecution
    • SlurmExecution
    • StrongrExecution
  • FlowPlugin Reference
    • CrossValidation
  • IOPlugin Reference
    • CommaSeperatedValueFile
    • FileSystem
    • HTTPPlugin
    • NetworkScope
    • Null
    • Reference
    • S3Filesystem
    • VirtualFileSystem
    • VirtualFileSystemRegularExpression
    • VirtualFileSystemValueList
    • XNATStorage
  • Interface Reference
    • FastrInterface
    • FlowInterface
    • NipypeInterface
  • ReportingPlugin Reference
    • ElasticsearchReporter
    • PimReporter
    • SimpleReport
  • Target Reference
    • DockerTarget
    • LocalBinaryTarget
    • MacroTarget
    • SingularityTarget
• Development and Design Documentation
  • Sample flow in Fastr
  • Network Execution
    • SchedulingPlugins
  • Secrets
    • Using secrets
    • Implementing a SecretProvider
• Changelog
  • 3.4.0 - 2024-05-23
    • Added
    • Fixed
    • Changed
  • 3.3.1 - 2022-10-13
    • Added
    • Fixed
  • 3.3.0 - 2021-06-11
    • Added
    • Fixes
  • 3.2.3 - 2020-06-25
    • Fixed
  • 3.2.2 - 2020-06-25
    • Fixed
  • 3.2.1 - 2020-06-22
    • Fixed
  • 3.2.0 - 2020-06-19
    • Changed
  • 3.1.4 - 2020-06-10
    • Added
  • 3.1.3 - 2019-11-28
    • Added
    • Improved
    • Fixed
  • 3.1.2 - 2019-06-18
    • Improved
    • Fixed
  • 3.1.1 - 2019-05-02
    • Fixed
  • 3.1.0 - 2019-05-02
    • Added
    • Fixed
    • Improved
    • Changed
  • 3.0.1 - 2019-03-28
    • Fixed
  • 3.0.0 - 2019-03-05
    • Changed
    • Added
    • Fixed
  • 2.1.2 - 2018-10-24
    • Added
    • Changed
  • 2.1.1 - 2018-06-29
    • Fixed
  • 2.1.0 - 2018-04-13
    • Added
    • Changed
    • Fixed
  • 2.0.1 - 2017-10-19
  • 2.0.0 - 2017-09-28
    • Added
    • Changed
    • Fixed
    • Removed
  • 1.2.2 - 2017-08-24
    • Fixed
  • 1.2.1 - 2017-04-04
    • Added
    • Changed
    • Fixed
  • 1.2.0 - 2017-03-15
    • Added
    • Changed
    • Fixed
  • 1.1.2 - 2016-12-22
    • Fixed
  • 1.1.1 - 2016-12-22
    • Fixed
  • 1.1.0 - 2016-12-08
    • Added
    • Changed
    • Removed
    • Fixed

FASTR User reference

• Fastr User Reference
  • fastr.tools
  • fastr.types
  • fastr.networks
  • api.create_network()
  • api.create_network_copy()
  • Network
    • Network.create_constant()
    • Network.create_link()
    • Network.create_macro()
    • Network.create_node()
    • Network.create_sink()
    • Network.create_source()
    • Network.draw()
    • Network.execute()
    • Network.id
    • Network.load()
    • Network.save()
    • Network.version
  • Link
    • Link.collapse
    • Link.expand
    • Link.id
  • Node
    • Node.id
    • Node.input
    • Node.inputs
    • Node.output
    • Node.outputs
  • Input
    • Input.__lshift__()
    • Input.__rrshift__()
    • Input.append()
    • Input.id
    • Input.input_group
  • Output
    • Output.__getitem__()
    • Output.id

FASTR Developer Module reference

Indices and tables

• Index

• Module Index

• Search Page