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<div class="section" id="openschemas-map2model">
<h1>OpenSchemas map2model<a class="headerlink" href="#openschemas-map2model" title="Permalink to this headline">¶</a></h1>
<a class="reference external image-reference" href="https://github.com/openschemas/spec-template/raw/master/img/hexagon_square_small.png"><img alt="https://github.com/openschemas/spec-template/raw/master/img/hexagon_square_small.png" src="https://github.com/openschemas/spec-template/raw/master/img/hexagon_square_small.png" /></a>
<p>This version of <strong>map2model</strong> is a simplified version of Python module
derived from the <a class="reference external" href="http://bioschemas.org/groups/">Bioschemas Groups</a>. It will help you
to create an OpenSchema intended for submission to <a class="reference external" href="schemas.org">schemas.org</a>, with
a focus on tech / hpc specifications that might not fall cleanly under strictly
biological sciences, but support open science.</p>
<p><strong>map2model</strong> retrieves properties and schema.org (Marginality, Cardinality and Controlled Vocabularies)
using mapping files (in a specifications folder, see an <a class="reference external" href="https://www.github.com/openschemas/spec-container">example here</a>)
then classifies properties into two groups:</p>
<ol class="arabic simple">
<li><strong>Extended properties:</strong> Properties that are part of the extended schema.org Type.</li>
<li><strong>New properties:</strong> Properties that are new to the schema.org vocabulary or are completely new to schema.org.</li>
</ol>
<p>After classifying the properties, <strong>map2model</strong> generates Markdown file(s)
that can be interpreted by <a class="reference external" href="https://openschemas.github.io">openschemas.github.io</a></p>
<a class="reference external image-reference" href="https://github.com/openschemas/map2model/raw/master/docs/img/map2model_workflow.png"><img alt="map2model workflow" src="https://github.com/openschemas/map2model/raw/master/docs/img/map2model_workflow.png" /></a>
<blockquote>
<div>If you want to modify the Flow Chart open the <a class="reference external" href="docs/img/map2model_workflow.xml">xml file</a> and name it <code class="docutils literal"><span class="pre">map2model_workflow.png</span></code> in the <em>doc > img</em>.</div></blockquote>
<div class="section" id="contribute-a-specification">
<h2>Contribute a Specification<a class="headerlink" href="#contribute-a-specification" title="Permalink to this headline">¶</a></h2>
<p>Do you want to contribute a specification? Your workflow will look like this:</p>
<ol class="arabic simple">
<li>Create your specification easily using <a class="reference external" href="https://docs.google.com/spreadsheets/d/1Ty69GRzc3xuvfpEIRHjfl_9L25MNFfrKXCdwrpxYslo/edit?usp=sharing">Google Sheets</a></li>
<li>Fork the <a class="reference external" href="https://www.github.com/openschemas/spec-template">template repository</a> and download them to it. You can also see a live example, <a class="reference external" href="https://www.github.com/openschemas/spec-container">soec-container</a> that also has content in Github Pages. When you connect your forked repository to CircleCI it will use the <a class="reference external" href="https://www.github.com/openschemas/schema-builder">schema-builder</a> to generate the files as artifacts or back to github pages. You can use the same <code class="docutils literal"><span class="pre">schema-builder</span></code> container to do this locally.</li>
<li>Issue a pull request to the <a class="reference external" href="https://www.github.com/openschemas/specifications">specifications</a> repository with your contribution! This means:<ul>
<li>forking the repository, cloning your fork</li>
<li>adding your <code class="docutils literal"><span class="pre">MySpecification.html</span></code> file to the <code class="docutils literal"><span class="pre">_specifications</span></code> folder</li>
<li>opening a pull request for review</li>
</ul>
</li>
</ol>
<p>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 <code class="docutils literal"><span class="pre">openschemas/spec-<NAME></span></code> repository here if you want to join the Github organization
and get support from the maintainers within!</p>
</div>
<div class="section" id="usage">
<h2>Usage<a class="headerlink" href="#usage" title="Permalink to this headline">¶</a></h2>
<p>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
<a class="reference external" href="https://www.github.com/openschemas/spec-template">template</a> and the docker
<a class="reference external" href="https://www.github.com/openschemas/schema-builder">openschemas/schema-builder</a> that
packages map2model and is used by the template.</p>
<div class="section" id="requirements">
<h3>Requirements<a class="headerlink" href="#requirements" title="Permalink to this headline">¶</a></h3>
<p>These instructions are for local usage.</p>
<p>Before starting, please ensure you have the following installed:</p>
<ol class="arabic simple">
<li>Git <a class="reference external" href="https://git-scm.com/downloads">https://git-scm.com/downloads</a></li>
<li>Python 3 <a class="reference external" href="https://www.python.org/downloads/">https://www.python.org/downloads/</a></li>
<li>Pip <a class="reference external" href="https://pip.pypa.io/en/stable/installing/">https://pip.pypa.io/en/stable/installing/</a></li>
</ol>
</div>
<div class="section" id="executing-map2model">
<h3>Executing map2model<a class="headerlink" href="#executing-map2model" title="Permalink to this headline">¶</a></h3>
<p>Clone the <strong>map2model</strong> repository: <code class="docutils literal"><span class="pre">git</span> <span class="pre">clone</span> <span class="pre">https://github.com/OpenSchemas/map2model.git</span></code></p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>git clone https://github.com/OpenSchemas/map2model.git
<span class="nb">cd</span> map2model
</pre></div>
</div>
<p>Install dependencies</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>python3 -m pip install -r requirements.txt
</pre></div>
</div>
<p>If you want to add a specification, add an entry to [spec2model/configuration.yml]. This file tells map2model which specifications exist. To create a new specification, the section that you need to add includes:</p>
<div class="highlight-guess"><div class="highlight"><pre><span></span>- name: NameOfMySpec
status: revision
spec_type: Profile
use_cases_url:
version: 0.2.0
parent_type: CreativeWork
</pre></div>
</div>
<p>For usage, ask the run.py script:</p>
<div class="highlight-guess"><div class="highlight"><pre><span></span>python3 run.py --help
usage: run.py [-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: run.py [-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.
</pre></div>
</div>
<p>See the <a class="reference external" href="https://www.github.com/openschemas/schema-builder">schema-builder</a> for
good examples of these various arguments.</p>
<p>We provide a <a class="reference external" href="https://docs.google.com/spreadsheets/d/1Ty69GRzc3xuvfpEIRHjfl_9L25MNFfrKXCdwrpxYslo/edit?usp=sharing">Google Drive sheets template</a> that you can use to do this, and simply export each sheet as .tsv (tab separated values). This means that four files should go into your <code class="docutils literal"><span class="pre">_NameOfMySpec</span></code> folder. While your specification is a draft, the name of the folder will start with an underscore (<code class="docutils literal"><span class="pre">_NameOfMySpec</span></code>). When you are done, remove the underscore (<code class="docutils literal"><span class="pre">NameOfMySpec</span></code>).</p>
<p>When you are finished with your spec, run the script to generate files in <em>map2model > docs > spec_files</em>. Check that your folder is present!</p>
<div class="highlight-guess"><div class="highlight"><pre><span></span>tree docs/spec_files
├── Container
│ ├── Container.html
│ ├── Container.yml
│ ├── examples
│ │ └── README.md
│ └── README.md
└── DataCatalog
├── DataCatalog.html
├── DataCatalog.yml
├── examples
│ └── README.md
└── README.md
</pre></div>
</div>
<p>If you are generating specifications for contribution, you will next want to
open a pull request (PR) to update the <a class="reference external" href="https://www.github.com/openschemas/specifications">specifications</a> repository.
Specifically, add the <a href="#id3"><span class="problematic" id="id4">*</span></a>.html files to the <a class="reference external" href="https://github.com/openschemas/specifications/tree/master/_specifications">_specifications folder</a> in this repository.</p>
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