Resource File Formats

This chapter describes the various files fastr uses. The function and format of the files is described allowing the user to configure fastr and add DataTypes and Tools.

Config file

Fastr reads the config files from the following locations by default (in order):

  • $FASTRHOME/config.py
  • ~/.fastr/config.py

Reading a new config file change or override settings, making the last config file read have the highest priority. All settings have a default value, making config files and all settings within optional.

Example config file

Here is a minimal config file:

# Enable debugging output
debug = False

# Define the path to the tool definitions
tools_path = ['/path/to/tools',
              '/path/to/other/tools'] + tools_path
types_path = ['/path/to/datatypes',
              '/path/to/other/datatypes'] + types_path


# Specify what your preferred output types are.
preferred_types += ["NiftiImageFileCompressed",
                    "NiftiImageFile"]

# Set the tmp mount
mounts['tmp'] = '/path/to/tmpdir'

Format

The config file is actually a python source file. The next syntax applies to setting configuration values:

# Simple values
float_value = 1.0
int_value = 1
str_value = "Some value"
other_str_value = 'name'.capitalize()

# List-like values
list_value = ['over', 'ride', 'values']
other_list_value.prepend('first')
other_list_value.append('list')

# Dict-like values
dict_value = {'this': 1, 'is': 2, 'fixed': 3}
other_dict_value['added'] = 'this key'

Note

Dictionaries and list always have a default, so you can always append or assign elements to them and do not have to create them in a config file. Best practice is to only edit them unless you really want to block out the earliers config files.

Most operations will be assigning values, but for list and dict values a special wrapper object is used that allows manipulations from the default. This limits the operations allowed.

List values in the config.py have the following supported operators/methods:

  • +, __add__ and __radd__
  • += or __iadd__
  • append
  • prepend
  • extend

Mapping (dict-like) values in the config.py have the following supported operators/methods:

  • update
  • [] or __getitem__, __setitem__ and __delitem__

Configuration fields

This is a table the known config fields on the system:

name type description default
debug bool Flag to enable/disable debugging False
examplesdir str Directory containing the fastr examples $systemdir/examples
execution_plugin str The default execution plugin to use ‘ProcessPoolExecution’
executionscript str Execution script location $systemdir/execution/executionscript.py
filesynchelper_url str Redis url e.g. redis://localhost:6379 ‘’
logdir str Directory where the fastr logs will be placed $userdir/logs
logging_config dict Python logger config {}
loglevel int The log level to use (as int), INFO is 20, WARNING is 30, etc 20
logtype str Type of logging to use ‘default’
mounts dict A dictionary containing all mount points in the VFS system {‘tmp’: ‘$TMPDIR’, ‘home’: ‘~/’, ‘example_data’: ‘$systemdir/examples/data’}
networks_path list Directories to scan for networks [‘$userdir/networks’, ‘$resourcedir/networks’]
pim_host str Host of the PIM server to report to ‘’
plugins_path list Directories to scan for plugins [‘$userdir/plugins’, ‘$resourcedir/plugins’]
preferred_types list A list indicating the order of the preferred types to use. First item is most preferred. []
protected_modules list A list of modules in the environmnet modules that are protected against unloading []
resourcesdir str Directory containing the fastr system resources $systemdir/resources
schemadir str Directory containing the fastr data schemas $systemdir/schemas
source_job_limit int The number of source jobs allowed to run concurrently 0
systemdir str Fastr installation directory ‘/home/docs/checkouts/readthedocs.org/user_builds/fastr/envs/stable/local/lib/python2.7/site-packages/fastr-2.0.1-py2.7.egg/fastr’
tools_path list Directories to scan for tools [‘$userdir/tools’, ‘$resourcedir/tools’]
types_path list Directories to scan for datatypes [‘$userdir/datatypes’, ‘$resourcedir/datatypes’]
userdir str Fastr user configuration directory ~/.fastr
warn_develop bool Warning users on import if this is not a production version of fastr True
web_hostname str The hostname to expose the web app for ‘localhost’
web_port str The port to expose the web app on ‘5000’
web_secret_key str The secret key to use for the flask web app ‘VERYSECRETKEY!’

Tool description

Tools are the building blocks in the fastr network. To add new Tools to fastr, XML/json files containing a Tool definition can be added. These files have the following layout:

Attribute Description
id The id of this Tool (used internally in fastr)
name   The name of the Tool, for human readability
version   The version of the Tool wrapper (not the binary)
url   The url of the Tool wrapper
authors[]   List of authors of the Tools wrapper
name Name of the author
email Email address of the author
url URL of the website of the author
tags tag[] List of tags describing the Tool
command   Description of the underlying command
version Version of the tool that is wrapped
url Website where the tools that is wrapped can be obtained
targets[]   Description of the target binaries/script of this Tool
os OS targeted (windows, linux, macos or * (for any)
arch Architecture targeted 32, 64 or * (for any)
... Extra variables based on the target used, see Targets
description Description of the Tool
license License of the Tool, either full license or a clear name (e.g. LGPL, GPL v2)
authors[]   List of authors of the Tool (not the wrapper!)
name Name of the authors
email Email address of the author
url URL of the website of the author
interface The interface definition see Interfaces
help Help text explaining the use of the Tool
cite Bibtext of the Citation(s) to reference when using this Tool for a publication