Command Line Tools

Fastr is shipped with a number of command line tools to perform common tasks and greatly simplify things such as debugging. The list of command line tools that is included in Fastr:

command description
cat Print information from a job file
dump Dump the contents of a network run tempdir into a zip for remote assistance
execute Execute a fastr job file
extract_argparse Create a stub for a Tool based on a python script using argparse
prov Get PROV information from the result pickle.
run Run a Network from the commandline
test Run the tests of a tool to verify the proper function
trace Trace samples/sinks from a run
verify Print information from a job file
webapp Start the fastr webapp and open in a new browser tab

fastr cat

Extract selected information from the extra job info. The path is the selection of the data to retrieve. Every parts of the path (separated by a /) is seen as the index for the previous object. So for example to get the stdout of a job, you could use ‘fastr cat __fastr_extra_job_info__.json process/stdout’.

usage: fastr cat [-h] __fastr_extra_job_info__.json path

Positional Arguments

 result file to cat
path path of the data to print

fastr dump

Create a dump of a network run directory that contains the most important information for debugging. This includes a serialization of the network, all the job command and result files, the extra job information files and the provenance files. No data files will be included, but note that if jobs get sensitive information passed via the command line this will be included in the job files.

usage: fastr dump [-h] RUNDIR

Positional Arguments

RUNDIR The run directory to dump The file to place the dump in

fastr execute

Execute a job from commandline.

usage: fastr execute [-h] [JOBFILE]

Positional Arguments

JOBFILE File of the job to execute (default ./__fastr_command__.pickle.gz)

fastr extract_argparse

Extract basic information from argparse.

usage: fastr extract_argparse [-h] TOOL.xml

Positional Arguments Python script to inspect
TOOL.xml created Tool stub

fastr prov

Export the provenance information from JSON to other formats or plot the provenance data as a graph.

usage: fastr prov [-h] [-so SYNTAX_OUT_FILE] [-sf SYNTAX_FORMAT] [-i INDENT]
                  [-vo VISUALIZE_OUT_FILE]

Positional Arguments

RESULTFILE File of the job to execute (default ./__fastr_prov__.json)

Named Arguments

-so, --syntax-out-file
 Write the syntax to file.
-sf, --syntax-format

Choices are: [json], provn or xml

Default: “json”

-i, --indent

Indent size of the serialized documents.

Default: 2

-vo, --visualize-out-file
 Visualize the provenance. The most preferred format is svg. You can specify any format pydot supports. Specify the format by postfixing the filename with an extension.

fastr run

Execute a job or network from commandline.

usage: fastr run [-h] NETWORKFILE

Positional Arguments

NETWORKFILE File of the network to execute

fastr test

Run a tests for a fastr resource.

usage: fastr test [-h] {tool,tools,network,networks} ...



Test a single tool

fastr test tool [-h] TOOL
Positional Arguments
TOOL Tool to test or directory with tool reference data


Test all tools known to fastr

fastr test tools [-h]


Test a single network

fastr test network [-h] NETWORK
Positional Arguments
NETWORK The reference data to test the Network


Test all network references inside subdirectories

fastr test networks [-h] [--result RESULT.json] REFERENCE
Positional Arguments
REFERENCE path of the directory containing subdirectories with reference data
Named Arguments
--result Write the results of the test to a JSON file

fastr trace

Fastr trace helps you inspect the staging directory of the Network run and pinpoint the errors.

usage: fastr trace [-h] [--verbose] [--sinks [SINKS [SINKS ...]]]
                   [--samples [SAMPLES [SAMPLES ...]]]

Positional Arguments


result file to cat

Default: “/home/docs/checkouts/”

Named Arguments

--verbose, -v

set verbose output for more details

Default: False

--sinks list results for specified sinks
--samples list result for all samples

fastr verify

Verify fastr resources, at the moment only tool definitionsare supported.

usage: fastr verify [-h] TYPE path

Positional Arguments


Possible choices: tool

Type of resource to verify (e.g. tool)

path path of the resource to verify

fastr webapp

Starts the fastr web client.

usage: fastr webapp [-h] [-d] [-o]

Named Arguments

-d, --debug

Debug mode.

Default: False

-o, --openpage

Open web page after start.

Default: False