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fix: fix bioportal link generation and remove redundant links #2655

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merged 6 commits into from
Nov 25, 2024
Merged

fix: fix bioportal link generation and remove redundant links #2655

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26b93f9
fix: use direct liquid assign expressions and remove redundant biopor…
jsstevenson Nov 25, 2024
acfa350
upcase checks
jsstevenson Nov 25, 2024
870c6fb
revert ontology metadata changes
jsstevenson Nov 25, 2024
c6e650d
don't edit metadata, skip if available
jsstevenson Nov 25, 2024
e623db6
case neutral
jsstevenson Nov 25, 2024
ad13307
that doesn't work
jsstevenson Nov 25, 2024
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41 changes: 38 additions & 3 deletions _layouts/ontology_detail.html
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Original file line number Diff line number Diff line change
Expand Up @@ -70,9 +70,44 @@ <h1>
<a href="http://www.ebi.ac.uk/ols/ontologies/{{page.id}}" class="btn btn-outline-primary" target="_blank" rel="noopener">
OLS
</a>
<a href="https://bioportal.bioontology.org/ontologies/{{ page.id | make_bioportal_id }}" class="btn btn-outline-primary" target="_blank" rel="noopener">
BioPortal
</a>
{% assign skip_bioportal = false %}
{% for browser in page.browsers %}
{% if browser.label == "BioPortal" %}
{% assign skip_bioportal = true %}
{% endif %}
{% endfor %}

{% unless skip_bioportal %}
{% assign bioportal_id = page.id | upcase %}
{% if bioportal_id == 'FBBT' %}
{% assign bioportal_id = 'FB-BT' %}
{% elsif bioportal_id == 'RO' %}
{% assign bioportal_id = 'OBOREL' %}
{% elsif bioportal_id == 'APOLLO_SV' %}
{% assign bioportal_id = 'APOLLO-SV' %}
{% elsif bioportal_id == 'TRANS' %}
{% assign bioportal_id = 'PTRANS' %}
{% elsif bioportal_id == 'WBLS' %}
{% assign bioportal_id = 'WB-LS' %}
{% elsif bioportal_id == 'FBDV' %}
{% assign bioportal_id = 'FB-DV' %}
{% elsif bioportal_id == 'WBBT' %}
{% assign bioportal_id = 'WB-BT' %}
{% elsif bioportal_id == 'WBPHENOTYPE' %}
{% assign bioportal_id = 'WB-PHENOTYPE' %}
{% elsif bioportal_id == 'TO' %}
{% assign bioportal_id = 'PTO' %}
{% elsif bioportal_id == 'FBCV' %}
{% assign bioportal_id = 'FB-CV' %}
{% elsif bioportal_id == 'MOD' %}
{% assign bioportal_id = 'PSIMOD' %}
{% elsif bioportal_id == 'PSO' %}
{% assign bioportal_id = 'PLANTSO' %}
{% endif %}
<a href="https://bioportal.bioontology.org/ontologies/{{ bioportal_id }}" class="btn btn-outline-primary" target="_blank" rel="noopener">
BioPortal
</a>
{% endunless %}
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Wait the way you do it, if a bioportal link is manually set, wont they now see no button at all?

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Don't believe so --

Lines 73 through 78 set a local skip_bioportal variable. If it's false, then lines 80-110 render a BioPortal button, but if it's true, then that's skipped. Regardless, 111-115 render custom buttons for each set of values defined in the ontology's front matter.

OBOFoundry.github.io/_layouts/ontology_detail.html

Lines 111 to 115 in c6e650d

{% for b in page.browsers %}
<a href="{{b.url}}" class="btn btn-outline-primary" target="_blank" rel="noopener">
{{b.label}}
</a>
{% endfor %}

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eg here's my local render of PRO

Screenshot 2024-11-25 at 1 22 17 PM

{% for b in page.browsers %}
<a href="{{b.url}}" class="btn btn-outline-primary" target="_blank" rel="noopener">
{{b.label}}
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28 changes: 0 additions & 28 deletions _plugins/bioportal_identifier.rb
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