Command Line Tools¶
command | description |
---|---|
cat | Print information from a job file |
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 |
testtool | 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 |
cat¶
usage: fastr cat [-h] __fastr_extra_job_info__.json path
Positional Arguments¶
__fastr_extra_job_info__.json | |
result file to cat | |
path | path of the data to print |
execute¶
Execute a job or network from commandline
usage: fastr execute [-h] [JOBFILE]
Positional Arguments¶
JOBFILE | File of the job to execute (default ./__fastr_command__.pickle.gz) |
extract_argparse¶
usage: fastr extract_argparse [-h] SCRIPT.py TOOL.xml
Positional Arguments¶
SCRIPT.py | Python script to inspect |
TOOL.xml | created Tool stub |
prov¶
Get PROV information from the result pickle. When no options are given, the provenance syntax is printed to stdout in PROV-JSON format.
usage: fastr prov [-h] [-so SYNTAX_OUT_FILE] [-sf SYNTAX_FORMAT] [-i INDENT]
[-vo VISUALIZE_OUT_FILE]
[RESULTFILE]
Positional Arguments¶
RESULTFILE | File of the job to execute (default ./__fastr_result__.pickle.gz) |
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. |
run¶
Execute a job or network from commandline
usage: fastr run [-h] NETWORKFILE
Positional Arguments¶
NETWORKFILE | File of the network to execute |
testtool¶
Run the tests for a Tool to check the function
usage: fastr testtool [-h] TOOL
Positional Arguments¶
TOOL | the id of the tool to test |
trace¶
usage: fastr trace [-h] [--verbose] [--sinks [SINKS [SINKS ...]]]
[--nodes [NODES [NODES ...]]]
[--samples [SAMPLES [SAMPLES ...]]]
[__sink_data__.json]
Positional Arguments¶
__sink_data__.json | |
result file to cat Default: “/home/docs/checkouts/readthedocs.org/user_builds/fastr/checkouts/1.2.2/fastr/doc/__sink_data__.json” |
Named Arguments¶
–verbose, -v | path of the data to print Default: False |
–sinks | list results for specified sinks |
–nodes | list results for specified nodes |
–samples | list result for all samples |