Link previews: class `.tooltip` collide with Bootstrap's tooltips

[jpfeuffer]

It's just not working. Sorry but I don't know what more to write.
Obviously it's enabled according to the docs in our settings.
Hoverxrefs worked like a charm..

https://pyopenms.readthedocs.io/en/latest/

[humitos]

I quickly check this and it seems the ajax call works fine and the content is added to the DOM. However, it seems there are some CSS in the theme you are using that interferes with the link preview tooltip and makes it to not be shown.

[jpfeuffer]

Thanks a lot! I will check this then and report back.

[jpfeuffer]

So, pydata theme uses bootstrap tooltips. Bootstrap tooltips also use the .tooltip css. Bootstrap uses opacity to show tooltips. Default opacity is 0.

Essentially it looks like the addon is incompatible with bootstrap.

Even if I make the tooltip visible, the contents are completely empty, which is also very different from the behaviour of hoverxref and useless for glossary terms.

vs before on e.g. https://pyopenms.readthedocs.io/en/release-3.4.0/index.html

Overall I am quite disappointed with the new experience as I assumed that an official addon would at least replicate the same features or stability of the former extension.

[humitos]

Thanks for taking the time to investigate this. We should probably use a different class name in our side so it doesn't collide with Boostrap. That should be an easy change.

[humitos]

We had a similar issue with the notification in #413 -- so, we should find a more generic solution to this problem.

[jpfeuffer]

No worries! Thank you for your quick response. Do you have an idea about the contents, too? I read about your (new?) heuristics to generate them but I am wondering how I could make it work for us.

Our main use case is for glossary terms.

The old hoverxref extension nicely displayed the text after potentially many synonymous glossary terms while the new link preview never shows anything, even for unique glossary terms.

The html of the glossary is sth like this:

<main>
...  some divs ...
<article class="bd-article">
  <section id="openms-glossary">
    <h1>OpenMS <span class="highlighted">Glossary</span><a class="headerlink" href="#openms-glossary" title="Permalink to this heading">#</a></h1>
    <p>A <span class="highlighted">glossary</span> of common terms used throughout OpenMS documentation.</p>
    <dl class="simple glossary">
    <dt id="term-C18">C18<a class="headerlink" href="#term-C18" title="Permalink to this term">#</a></dt><dd><p>Octadecyl (C18) is an alkyl radical C(18)H(37) derived from an octadecane by removal of one hydrogen atom.</p>
    </dd>
    <dt id="term-CID">CID<a class="headerlink" href="#term-CID" title="Permalink to this term">#</a></dt><dt id="term-collision-induced-dissociation">collision-induced dissociation<a class="headerlink" href="#term-collision-induced-dissociation" title="Permalink to this term">#</a></dt><dd><p>Collision-induced dissociation is an MS technique to induce fragmentation of selected ions in the gas phase, which are subjected to a subsequent measurement (see <a class="hxr-hoverxref hxr-tooltip reference internal" href="#term-MS2"><span class="xref std std-term">MS2</span></a>).</p>
    </dd>
    <dt id="term-consensus-features">consensus features<a class="headerlink" href="#term-consensus-features" title="Permalink to this term">#</a></dt>
    <dt id="term-consensus-feature">consensus feature<a class="headerlink" href="#term-consensus-feature" title="Permalink to this term">#</a></dt>
    <dd><p>Features from replicate experiments with similar retention times and m/z values are linked and considered a consensus feature.
    A consensus feature contains information on the common retention time and m/z values as well as intensities for each sample.
    OpenMS represents a consensus feature using the class <a class="reference external" href="https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/classOpenMS_1_1ConsensusFeature.html">ConsensusFeature</a>.</p>
    </dd>
    <dt id="term-consensus-maps">consensus maps<a class="headerlink" href="#term-consensus-maps" title="Permalink to this term">#</a></dt><dt id="term-consensus-map">consensus map<a class="headerlink" href="#term-consensus-map" title="Permalink to this term">#</a></dt><dd><p>A consensus map is a collection of <a class="hxr-hoverxref hxr-tooltip reference internal" href="#term-consensus-features"><span class="xref std std-term">consensus features</span></a> identified from mass spectra across replicate experiments,
    usually by combining multiple <a class="hxr-hoverxref hxr-tooltip reference internal" href="#term-feature-maps"><span class="xref std std-term">feature maps</span></a>.
    One consensus map usually contains many consensus features. OpenMS represents a consensus map using
    the class <a class="reference external" href="https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/classOpenMS_1_1ConsensusMap.html">ConsensusMap</a>.</p>
    </dd>
  </section>
</article>

[humitos]

Do you have an idea about the contents, too? I read about your (new?) heuristics to generate them but I am wondering how I could make it work for us.

Yes, the problem is that the addons library is not detecting the documentation tools or theme for some reason. In the console, it appears:

We were not able to detect the documentation tool.
Documentation tool detected: null
Documentation theme detected: null

When passing ?doctool=sphinx to the EmbedAPI endpoint, it returns the correct content: https://pyopenms.readthedocs.io/_/api/v3/embed/?url=https%3A%2F%2Fpyopenms.readthedocs.io%2Fen%2Flatest%2Fuser_guide%2Fglossary.html%23term-Mass-Spectrometry&maincontent=article&doctool=sphinx

This seems to be a different bug. I will take a look.

[humitos]

I opened #667 to fix the tool detection.