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¶
__fastr_extra_job_info__.json | |
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 DUMP.zip
Positional Arguments¶
RUNDIR | The run directory to dump |
DUMP.zip | 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] SCRIPT.py TOOL.xml
Positional Arguments¶
SCRIPT.py | 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]
[RESULTFILE]
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} ...
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 ...]]]
[__sink_data__.json]
Positional Arguments¶
__sink_data__.json | |
result file to cat Default: “/home/docs/checkouts/readthedocs.org/user_builds/fastr/checkouts/2.1.0/fastr/doc/__sink_data__.json” |
Named Arguments¶
--verbose, -v | set verbose output for more details Default: False |
--sinks | list results for specified sinks |
--samples | list result for all samples |