From 13620af6f7bc6df13bcc16dc3088da692c820147 Mon Sep 17 00:00:00 2001
From: James Stevenson <james.sharpsteen@gmail.com>
Date: Mon, 25 Nov 2024 13:26:00 -0500
Subject: [PATCH] fix: fix bioportal link generation and remove redundant links
 (#2655)

* fix bioportal button render issues. remove custom liquid filter (unsupported by github actions deployment)
* don't make redundant buttons when ontology already provides link
---
 _layouts/ontology_detail.html    | 41 +++++++++++++++++++++++++++++---
 _plugins/bioportal_identifier.rb | 28 ----------------------
 2 files changed, 38 insertions(+), 31 deletions(-)
 delete mode 100644 _plugins/bioportal_identifier.rb

diff --git a/_layouts/ontology_detail.html b/_layouts/ontology_detail.html
index 8bdc6d2f3..dc00f9666 100644
--- a/_layouts/ontology_detail.html
+++ b/_layouts/ontology_detail.html
@@ -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 %}
         {% for b in page.browsers %}
           <a href="{{b.url}}" class="btn btn-outline-primary" target="_blank" rel="noopener">
             {{b.label}}
diff --git a/_plugins/bioportal_identifier.rb b/_plugins/bioportal_identifier.rb
deleted file mode 100644
index 7c37d23e9..000000000
--- a/_plugins/bioportal_identifier.rb
+++ /dev/null
@@ -1,28 +0,0 @@
-module CustomFilter
-  def make_bioportal_id(obo_id)
-    return obo_id unless obo_id.is_a?(String)
-
-    # ID requirements should be locked down moving forward, so additions to this table
-    # should be rare
-    special_cases = {
-      'fbbt' => 'FB-BT',
-      'ro' => 'OBOREL',
-      'apollo_sv' => 'APOLLO-SV',
-      'trans' => 'PTRANS',
-      'wbls' => 'WB-LS',
-      'fbdv' => 'FB-DV',
-      'wbbt' => 'WB-BT',
-      'wbphenotype' => 'WB-PHENOTYPE',
-      'to' => 'PTO',
-      'fbcv' => 'FB-CV',
-      'mod' => 'PSIMOD',
-      'pso' => 'PLANTSO'
-    }
-
-    return special_cases[obo_id] if special_cases.key? obo_id
-
-    obo_id == obo_id.downcase ? obo_id.upcase : obo_id
-  end
-end
-
-Liquid::Template.register_filter(CustomFilter)