===========
Quick Start
===========

General
=======
The tool is invoked from the command line using the main script name, ``FAIRLinked``, followed by a command and its specific arguments.

.. code-block:: bash

   FAIRLinked [COMMAND] [OPTIONS]

To see the help message for any command, use the ``-h`` or ``--help`` flag.

.. code-block:: bash

   FAIRLinked filter -h
   FAIRLinked generate-template -help

InterfaceMDS Commands
=====================
These commands are used for interacting with the Materials Data Schema (MDS) ontology.

filter
------
Get terms associated with a certain Domain, Subdomain, or Study Stage.

**Usage**

.. code-block:: bash

   FAIRLinked filter -t <SEARCH_TYPES> -q <QUERY_TERM> [OPTIONS]

**Arguments**

* ``-q, --query_term``: (**Required**) Enter the domain, subdomain, or study stage.
* ``-t, --search_types``: (**Required**) Specifies the search criteria. Choices: ``"Domain"``, ``"SubDomain"``, ``"Study Stage"``.
* ``-op, --ontology_path``: Path to the ontology file. Defaults to ``"default"``.
* ``-te, --ttl_extr``: Specifies whether user wants to save search results. Enter T or F. Defaults to ``"F"``.
* ``-tp, --ttl_path``: If user wants to save search results, provide path to save file. Append file name at the end of the path.

view-domains
------------
Display unique Domains and SubDomains from the ontology.

**Usage**

.. code-block:: bash

   FAIRLinked view-domains

dir-make
-------
View and make directory tree of turtle files based on domains and subdomains.

**Usage**

.. code-block:: bash

   FAIRLinked dir-make

add-terms
---------
Add new terms to an existing ontology file via an interactive session.

**Usage**

.. code-block:: bash

   FAIRLinked add-terms -op <PATH_TO_ONTOLOGY>

term-search
----------
Search for terms by matching term labels using a fuzzy search algorithm.

**Usage**

.. code-block:: bash

   FAIRLinked term-search

RDFTableConversion Commands
===========================
These commands facilitate the conversion of tabular data (CSV) to and from RDF (JSON-LD format).

generate-template
-----------------
Generate a JSON-LD template based on a CSV file.

**Usage**

.. code-block:: bash

   FAIRLinked generate-template -cp <CSV_PATH> -out <OUTPUT_PATH> -lp <LOG_PATH> [OPTIONS]

**Arguments**

* ``-cp, --csv_path``: (**Required**) Path to CSV file.
* ``-out, --output_path``: (**Required**) Path to output JSON-LD file.
* ``-lp, --log_path``: (**Required**) Path to store files that log labels that could/couldn't be matched to a term in MDS-Onto.
* ``-op, --ontology_path``: Path to ontology. To get official MDS-Onto choose 'default'.

serialize-data
---------------
Create a directory of JSON-LDs from a single CSV file.

**Usage**

.. code-block:: bash

   FAIRLinked serialize-data -mdt <TEMPLATE_PATH> -cf <CSV_FILE> -rkc <ROW_KEY_COLS> ...

**Arguments**

* ``-mdt, --metadata_template``: (**Required**) Metadata template (path to JSON file if using CLI).
* ``-cf, --csv_file``: (**Required**) Path to the CSV file containing the data.
* ``-rkc, --row_key_cols``: (**Required**) Comma-separated list of column names used to uniquely identify rows (e.g. col1,col2,col3).
* ``-orc, --orcid``: (**Required**) ORCID identifier of the researcher.
* ``-of, --output_folder``: (**Required**) Directory where JSON-LD files will be saved.
* ``-pc, --prop_col``: Python dictionary literal to define relationships between columns.
* ``-op, --ontology_path``: Path to ontology. Must be provided if 'prop_col' is provided.
* ``-base, --base_uri``: Base URI used to construct subject and object URIs.
* ``-l, --license``: License used, find valid licenses at https://spdx.org/licenses/.

deserialize-data
----------------
Deserialize a directory of JSON-LDs back into a CSV.

**Usage**

.. code-block:: bash

   FAIRLinked deserialize-data -jd <JSONLD_DIRECTORY> -on <OUTPUT_NAME> -od <OUTPUT_DIR>

**Arguments**

* ``-jd, --jsonld_directory``: (**Required**) Directory containing JSON-LD files.
* ``-on, --output_name``: (**Required**) Base name of output files.
* ``-od, --output_dir``: (**Required**) Path to directory to save the outputs.

QBWorkflow Commands
=====================
Commands related to the RDF Data Cube workflow.

data-cube-run
-------------
Start RDF Data Cube Workflow.

**Description**

This command launches an interactive workflow to create richly structured, multidimensional datasets that adhere to the `RDF Data Cube vocabulary <https://www.w3.org/TR/vocab-data-cube/>`_.

**Usage**

.. code-block:: bash

   FAIRLinked data-cube-run