ya2ro

DOI PyPI Project Status: Active: The project has reached a stable, usable state and is being actively developed.

Example

Ya2ro generates Research Objects (ROs) like the following: https://w3id.org/dgarijo/ro/sepln2022. Given a few ROs, ya2ro can also create a landing page: https://oeg-upm.github.io/ya2ro/output/landing_page.html

Requirements

The latest version of ya2ro works in Python 3.10.

Installation

To run ya2ro, please follow the next steps:

Install from PyPI

pip install ya2ro

Install from GitHub

git clone https://github.com/oeg-upm/ya2ro
cd ya2ro
pip install -e .

Installing through Docker

We provide a Dockerfile with ya2ro already installed. To run through Docker, you may build the Dockerfile provided in the repository by running:

docker build -t ya2ro .

Then, to run your image just type:

docker run -it ya2ro /bin/bash

And you will be ready to use ya2ro (see section below). If you want to have access to the results we recommend mounting a volume. For example, the following command will mount the current directory as the out folder in the Docker image:

docker run -it --rm -v $PWD/:/out ya2ro /bin/bash

If you move any files produced by ya2ro into /out, then you will be able to see them in your current directory.

Usage

Configure

Before running ya2ro, you must configure it appropriately. Please add your GitHub personal token in ya2ro properties file. This needed if you want ya2ro to extract your software metadata automatically. The file can be found at:

--> ~/ya2ro/src/ya2ro/resources/properties.yaml <--

Add a line like the following:

# Add here your GitHub personal access token
GITHUB_PERSONAL_ACCESS_TOKEN: xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

ya2ro will work if this is not configured, but is highly recommended to apply this setting, as the GitHub API has restricted access.

Test ya2ro installation

ya2ro --help

If everything goes fine, you should see:

                        ad888888b,
                       d8"     "88
                               a8P
8b       d8 ,adPPYYba,      ,d8P"  8b,dPPYba,  ,adPPYba,
`8b     d8' ""     `Y8    a8P"     88P'   "Y8 a8"     "8a
 `8b   d8'  ,adPPPPP88  a8P'       88         8b       d8
  `8b,d8'   88,    ,88 d8"         88         "8a,   ,a8"
    Y88'    `"8bbdP"Y8 88888888888 88          `"YbbdP"'
    d8'
   d8'
_________________________________________________________

usage: ya2ro [-h] (-i YAML_PATH | -l YA2RO_PREV_OUTPUT) [-o OUTPUT_DIR] [-p PROPERTIES_FILE] [-ns]

Human and machine readable input as a yaml file and create RO-Object in jsonld and/or HTML view. Run 'ya2ro -configure GITHUB_PERSONAL_ACCESS_TOKEN' this the first time to configure ya2ro
properly

options:
  -h, --help            show this help message and exit
  -i YAML_PATH, --input YAML_PATH
                        Path of the required yaml input. Follow the documentation or the example given to see the structure of the file.
  -l YA2RO_PREV_OUTPUT, --landing_page YA2RO_PREV_OUTPUT
                        Path of a previous output folder using the ya2ro tool. This flag will make a landing page to make all the resources accessible.
  -o OUTPUT_DIR, --output_directory OUTPUT_DIR
                        Output directory.
  -p PROPERTIES_FILE, --properties_file PROPERTIES_FILE
                        Properties file name.
  -ns, --no_somef       Disable SOMEF for a faster execution (software cards will not work).

How to use

The first thing to do is create some input for ya2ro. To create valid a yaml you should follow the documentation bellow.

Create a yaml from scratch or use one of the supplied templates. Currently ya2ro supports two formats:

Please find a template for each type under the directory templates. Once you have a valid yaml (project or paper) is time to run ya2ro.

Create machine and human readable content

It is possible to process batches of yamls at the same time, to do that just specify as input a folder with all the yamls inside.

Simple execution

ya2ro -i templates

ya2ro -i templates/project_template.yaml

With optional arguments

ya2ro -input templates --output_directory out --properties_file custom_properties.yaml

ya2ro -i templates -o out -p custom_properties.yaml

Faster execution?

Use the flag –no_somef or -ns for disabling SOMEF which is the most time consuming process.

ya2ro -i templates -ns

WARNING: Software cards will no longer work on github links. Therefore you will need to manually insert the software data in the yaml file.

Create landing page

ya2ro offers the option to create a landing page where all the resources produced are easily accessible. Just indicate the folder where this resources are, for example:

ya2ro -l output

Documentation

Please have a look at our documentation to know which metadata fields are supported by ya2ro.

Funding

This work has been funded by the EELISA European University network (https://eelisa.eu/), by the European Commission within the H2020 Programme in the context of the project RELIANCE under grant agreement no. 101017501 and by the Madrid Government (Comunidad de Madrid-Spain) under the Multiannual Agreement with Universidad Polit ́ecnica de Madrid in the line Support for R&D projects for Beatriz Galindo researchers, in the context of the V PRICIT (Regional Programme of Research and Technological Innovation) and the call Research Grants for Young Investigators from Universidad Politécnica de Madrid.

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