Command Line Interface

Usage:

usage: main [-h] [-f SOURCES_FILE] [-s {year,decade}]
            [-v {DEBUG,INFO,WARNING,ERROR,CRITICAL}]

To run the the application using udocker at the Runtime machine you need to provide the following volumes to the container:

• –volume, mount /app/data: Input path with data to skim.

• –volume, mount /app/output: Output path for skimmed results.

• –volume, mount /app/sources.yaml: Configuration file with a data structure description at the input path in YAML format. See ../user_guide/source-file for a configuration example.

Also, in the specific case of udocker, it is needed to specify that the user application should run inside the container:

For example,to run the container using udocker use the following:

$ udocker run \
  --user=application \
  --volume=${PWD}/sources.yaml:/app/sources.yaml \
  --volume=${PWD}/data:/app/data \
  --volume=${PWD}/output:/app/output \
  o3skim --verbosity INFO
...
executing: main
...
2020-08-25 12:42:34,151 - INFO     - Configuration found at: './sources.yaml'
2020-08-25 12:42:34,152 - INFO     - Loading data from './data'
2020-08-25 12:42:34,261 - INFO     - Skimming data to './output'

For the main function description and commands help you can call:

$ udocker run --user=application o3skim --help

As optional arguments, it is possible to indicate:

• -h, –help: show this help message and exit

• -f, –sources_file SOURCES_FILE: Custom sources YAML configuration. (default: ./sources.yaml)

• -s, –split_by {year,decade}: Period time to split output (default: None)

• -v, –verbosity {DEBUG,INFO,WARNING,ERROR,CRITICAL}: Sets the logging level (default: ERROR)

Note that SOURCES_FILE is only modified for development purposes as usually any file from host can be mounted using the container directive ‘–volume’.