CLI
===

Extract
~~~~~~~
The extract command of MESSES supports turning tabular data into JSON. 
This is done by adding a layer of tags on top of the data. These tags tell 
the extract command how to construct the JSON tables and records. There are features 
for automatically applying tags to untagged data and features for modifying 
the names and values of data. The extract command can also be used to modify already 
JSONized data. There is also support for viewing the data in different ways, such 
as viewing the record lineages. For a more detailed explanation of the options 
with examples as to how they might be used, see the :doc:`tutorial` page.

Usage
-----

.. literalinclude:: ../src/messes/extract/extract.py
    :start-at: Usage:
    :end-before: """
    :language: none
       


Validate
~~~~~~~~
The validate command of MESSES supports validating JSON data. This is done largely 
through utilizing `JSON Schema <https://json-schema.org/understanding-json-schema/>`_ (`jsonschema <https://pypi.org/project/jsonschema/>`_), 
but validation beyond the capabilities of JSON Schema (`jsonschema <https://pypi.org/project/jsonschema/>`_) is also done. By default, 
JSON files are validated against the :doc:`experiment_description_specification`, but this 
can be turned off with options. Users can also provide additional validation in 
the form of their own JSON schema and a :doc:`protocol_dependent_schema`. More details 
and examples for the validate command are in the :doc:`tutorial`.

Usage
-----

.. literalinclude:: ../src/messes/validate/validate.py
    :start-at: Usage:
    :end-before: """
    :language: none



Convert
~~~~~~~
The convert command of MESSES supports converting JSON data to another JSON format 
or another supported format. This is done by using conversion directives, which 
are detailed in the :doc:`conversion_directives` section. Arbitrary JSON to JSON 
conversions are supported through the "generic" command and all supported formats 
are converted using commands that match their namesake. All supported formats are 
detailed in the :doc:`supported_formats` section. More details and examples for 
the convert command are in the :doc:`tutorial`.

Usage
-----

.. literalinclude:: ../src/messes/convert/convert.py
    :start-at: Usage:
    :end-before: """
    :language: none