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/1.2.1/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 |