IO Module

Functionality

The IO module serves as a communication layer between the user and the pipeline. It standardizes the input through a base class which makes the reasoning about input easier when implementing steps.

Current Adapters

Currently, there are two adapters available. Cli and Dict input.

Adapter	Functionality
DictIo	Configures the step from a provided dict.
CliIo	Configures the step using user input in the console.

Example

Let’s assume we want to add a step to the pipeline and configure it through inputs in the CLI.

from pathlib import Path

from expectmine.io.io.cli_io import CliIo
from expectmine.pipeline.pipeline import Pipeline
from expectmine.pipeline.utils import get_quickstart_config

from expectmine.steps.steps import MZmine3

pipeline = Pipeline(*get_quickstart_config(output_path=Path("output/")))

pipeline.set_input([Path("File1.mzML")])

"""
Here we add the CliIo instance as second argument, the Step is then 
initialized using input from the Cli
"""
pipeline.add_step(MZmine3, CliIo())

Further reading

• IO Base Class
• IO Base Adapter Class
• IO Helper Functions
• Cli IO
• Dict IO