Ideas for modelling reproducible documents in JATS

reproducible-jats.xml

<!-- Executable Cell (e.g. Jupyter) -->
<cell>
<source language="javascript">
<![CDATA[var randomNumbers = []
for (var i = 0; i < length; i++) {
randomNumbers.push(Math.floor(Math.random()*100))
}
return randomNumbers]]>
</source>
<value value-type="array">
  <![CDATA[[1,2,3]]]>
</value>
</cell>

<!-- Reproducible Figure -->
<fig id="F1">
<caption>
  <title>A bar chart</title>
  <p>Figure caption text</p>
</caption>
<cell expr="barchart(randomNumbers)">
  <value value-type="plot-ly">{ plotly: 'specifiction' }</value>
  <value value-type="image/png">path/to/image.png</value>
</cell>
</fig>

<!-- Reproducible Figure -->
<fig id="F1">
<caption>
  <title>A bar chart</title>
  <p>Figure caption text</p>
</caption>
<cell>
  <source language="python">some python code</source>
  <value value-type="image/png">path/to/image.png</value>
</cell>
</fig>

<!-- Reproducible Figure (squeeze into existing JATS) -->
<fig id="F1">
<caption>
  <title>A bar chart</title>
  <p>Figure caption text</p>
</caption>
<alternatives>
  <code executable="yes" specific-use="input" language="javascript">
    barchart(x)
  </code>
  <code specific-use="output" language="jupyter-output">
    {
      "execution_time": 322,
      "value_type": "plot-ly",
      "value": {...}
    }
  </code>
  <!-- static version for existing JATS toolchains -->
  <graphic xlink:href="89f8b53e361f.svg"/>
</alternatives>
</fig>


<!-- code block that generates a string -->
<named-content specific-use="cell">
  <alternatives>
    <code specific-use="input" language="javascript">
      10 + 15
    </code>
    <code specific-use="output" language="jupyter-output">
      {
        "execution_time": 322,
        "value_type": "number",
        "value": 25
      }
    </code>
    <preformat specific-use="output">
      25
    </preformat>
  </alternatives>

</named-content>

<named-content specific-use="cell">
  <alternatives>
    <code specific-use="input" language="javascript">
      barchart(x)
    </code>
    <code specific-use="output" language="jupyter-output">
      {
        "execution_time": 322,
        "value_type": "plot-ly",
        "value": {...}
      }
    </code>
    <graphic xlink:href="89f8b53e361f.svg"/>
  </alternatives>
</named-content>


<!-- Inline Select -->
<!-- Problem: cdata needs to be parsed separately -->
lorem<named-content specific-use="select">
  <alternatives>
    <texual-form>Peanut Butter</textual-form>
    <code specific-use="select-data">
      <![CDATA[
        <select name="calories">
          <option value="30.2" selected="selected">Fortune</option>
          <option value="71.6">Peanut butter</option>
        </select>
      ]]>
    </code>
  </alternatives>
</named-content> ipsum

lorem<named-content specific-use="select">
  <alternatives>
    <texual-form>Peanut Butter</textual-form>
    <code specific-use="select-data">
      <!-- Idea: use processing instructions, which are parsable -->
      <?html 
        <select name="calories">
          <option value="30.2" selected="selected">Fortune</option>
          <option value="71.6">Peanut butter</option>
        </select>
      ?>
    </code>
  </alternatives>
</named-content> ipsum



bla a <select name="calories">
  <option value="30.2" selected="selected">Fortune</option>
  <option value="71.6">Peanut butter</option>
</select> lkajs df

<!-- Input -->
<input type="range" min="1" max="100" step="1" name="num_weeks" value="52"/>




<named-content specific-use="output">
  <alternatives>
    <code specific-use="input" language="javascript">
      calories
    </code>
    <textual-form>234</textual-form>
  </alternatives>
</named-content>



<table-wrap>
  <caption>
  <title>A bar chart</title>
  <p>Figure caption text</p>
  </caption>
</table-wrap>