OpenSchemas map2model

This repository will show you how to use map2model, which is a module provided by openschemas python, and a simplified version of the now deprecated Python module derived from the Bioschemas Groups. It will help you to create an OpenSchema intended for submission to schemas.org, with a focus on technology and research software or high performance computing specifications that might not fall cleanly under strictly biological sciences (but support open science).

map2model retrieves properties and schema.org (Marginality, Cardinality and Controlled Vocabularies) using mapping files (in a specifications folder, see an example here) then classifies properties into two groups:

1. Extended properties: Properties that are part of the extended schema.org Type.
2. New properties: Properties that are new to the schema.org vocabulary or are completely new to schema.org.

After classifying the properties, map2model generates Markdown file(s) that can be interpreted by openschemas.github.io

If you want to modify the Flow Chart open the xml file and name it map2model_workflow.png in the doc > img.

Contribute a Specification

Do you want to contribute a specification? Your workflow will look like this:

1. Start with a Template

Fork the template repository and download them to it. You can also see a live example, soec-container that also has content in Github Pages. When you connect your forked repository to CircleCI it will use the schema-builder to generate the files as artifacts or back to github pages. You can use the same schema-builder container to do this locally.

1. Issue a pull request to the specifications repository with your contribution! This means:
   • forking the repository, cloning your fork
   • adding your MySpecification.html file to the _specifications folder
   • opening a pull request for review

We encourage this setup so that each of the specifications is maintained in a modular fashion. You can maintain your specification (and issues / discussion around it) in its own Git repository, to ensure modularity and version control of examples and associated documentation. We would be happy to create for you an openschemas/spec-<NAME> repository here if you want to join the Github organization and get support from the maintainers within!

2. Create your Specification

In the template repository (and here) you will notice tsv files under subfolders of the "specifications" folder. This is where you need to create and download your own files for your new specification! You can create these files easily using Google Sheets. If this is a new specification, you will want to add an entry to [specifications/configuration.yml]. This file tells map2model which specifications exist. Here is an example:

- name: NameOfMySpec
  status: revision
  spec_type: Profile
  use_cases_url:
  version: 0.2.0
  parent_type: CreativeWork

Next, run map2model! As mentioned above, if you use the template this step will be done for you in the continuous integration (and you can stop reading here). If you want to do this natively, on your host, then keep reading.

Map2Model Usage

This usage details native usage of map2model, which isn't reproducible and not the recommended approach! However if you are building software with it, you will need to know this. If not, we recommend first the template and the docker openschemas/schema-builder that packages map2model and is used by the template.

Requirements

These instructions are for local usage.

Before starting, please ensure you have the following installed:

1. Git https://git-scm.com/downloads
2. Python 3 https://www.python.org/downloads/
3. Pip https://pip.pypa.io/en/stable/installing/

Installation

If you want to use the configuration and specification templates provided, first clone the map2model repository:

git clone https://github.com/openschemas/map2model.git
cd map2model

Next, install openschemas, which provides map2model

pip install openschemas

1. Command Line Usage

The Openschemas Python module provides a map2model console script that you can run. For usage, ask it for help"

map2model --help
usage: map2model [-h] [--config CONFIG] [--folder SPECS] [--output OUTFOLDER]
                 [--template TEMPLATE] [--repo REPO]

map2model

optional arguments:
  -h, --help           show this help message and exit
  --config CONFIG      configuration.yml file, defaults to configuration.yml
                       in folder
  --folder SPECS       folder with input specification subfolders
  --output OUTFOLDER   folder to write output specification subfolders
  --template TEMPLATE  template for openschemas.github.io. Should not need
                       change.
  --repo REPO          final repo intended for specifications.
usage: map2model [-h] [--config CONFIG] [--folder SPECS] [--output OUTFOLDER]
                 [--template TEMPLATE] [--repo REPO]

map2model

optional arguments:
  -h, --help           show this help message and exit
  --config CONFIG      configuration.yml file, defaults to configuration.yml
                       in folder
  --folder SPECS       folder with input specification subfolders
  --output OUTFOLDER   folder to write output specification subfolders
  --template TEMPLATE  template for openschemas.github.io. Should not need
                       change.
  --repo REPO          final repo intended for specifications.

See the schema-builder for good examples of these various arguments. Generally, you will want to tell the module where your configuration file, input folder, and output folder are. For example:

map2model --config specifications/configuration.yml --folder specifications --output docs/spec_files

1. Python Usage

You can also interact with the module from within python! This example is provided in run.py

#!/usr/bin/env python3

# This is an example of using map2model, a module provided by
# openschemas-python
# python3 run.py
#
# https://www.github.com/openschemas/openschemas-python
# pip install openschemas
from openschemas.main.map2model import main

# Here is an example to run the parser in python
spec_parser = main(config_yml='specifications/configuration.yml',
                   output='docs/spec_files',
                   folder='specifications')

Again, all you need to do is generate the tsv files and add an entry to the configuration.yml, and we provide a Google Drive sheets template that you can use to do this. Simply export each sheet as .tsv (tab separated values). This means that four files should go into your _NameOfMySpec folder. While your specification is a draft, the name of the folder will start with an underscore (_NameOfMySpec). When you are done, remove the underscore (NameOfMySpec).

When you are finished with your specification, if you run the script here you will generate files in map2model > docs > spec_files. Check that your folder is present!

tree docs/spec_files
├── Container
│   ├── Container.html
│   ├── Container.yml
│   ├── examples
│   │   └── README.md
│   └── README.md
└── DataCatalog
    ├── DataCatalog.html
    ├── DataCatalog.yml
    ├── examples
    │   └── README.md
    └── README.md

If you are generating specifications for contribution, you will next want to open a pull request (PR) to update the specifications repository. Specifically, add the *.html files to the _specifications folder in this repository.