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 |
| provenance | Get PROV information from the result pickle. |
| pylint | Dump the contents of a network run tempdir into a zip for remote assistance |
| run | Run a Network from the commandline |
| sink | Command line access to the IOPlugin sink |
| source | Command line access to the IOPlugin source |
| test | Run the tests of a tool to verify the proper function |
| trace | Trace samples/sinks from a run |
| upgrade | Print information from a job file |
| verify | Verify fastr resources, at the moment only tool definitions are supported. |
| 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 provenance¶
Export the provenance information from JSON to other formats or plot the provenance data as a graph.
usage: fastr provenance [-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 pylint¶
Run pylint in such a way that the output is written to a file
usage: fastr pylint [-h] --output_file PYLINT.OUT
Named Arguments¶
| --output_file | The file to result in |
fastr run¶
Execute a job or network from commandline.
usage: fastr run [-h] NETWORKFILE
Positional Arguments¶
| NETWORKFILE | File of the network to execute |
fastr sink¶
executes an ioplugin
usage: fastr sink [-h] -i INPUT [INPUT ...] -o OUTPUT [OUTPUT ...]
[-d DATATYPE [DATATYPE ...]]
Named Arguments¶
| -i, --input | The url to process (can also be a list) |
| -o, --output | The output urls in vfs scheme (can also be a list and should be the same size as –inurl) |
| -d, --datatype | The datatype of the source/sink data to handle |
fastr source¶
Executes an source command
usage: fastr source [-h] -i INPUT [INPUT ...] -o OUTPUT [-d DATATYPE]
[-s SAMPLE_ID]
Named Arguments¶
| -i, --input | The url to process (can also be a list) |
| -o, --output | The output url in vfs scheme |
| -d, --datatype | The datatype of the source/sink data to handle |
| -s, --sample_id | |
| The sample_id of the source/sink data to handle | |
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/3.0.1/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 |
fastr upgrade¶
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 upgrade [-h] NETWORK.py NEW.py
Positional Arguments¶
| NETWORK.py | Network creation file (in python) to upgrade |
| NEW.py | location of the result file |