Feature: Add skos features UIs by syphax-bouazzouni · Pull Request #49 · ontoportal/ontoportal_web_ui

syphax-bouazzouni · 2025-07-21T09:30:49Z

Changes

Removed simple tree dependency (ac54662)
Added schemes tab

Added collections tab

Updated concept tab with new Tree

Added the concept collection browser

Added the date history for the concepts

…te list

Copilot

Pull Request Overview

This PR adds comprehensive SKOS (Simple Knowledge Organization System) feature UIs to the ontology portal, including new concept schemes and collections interfaces, updated tree visualization components, and refactored navigation.

Removed simple tree dependency and replaced with custom tree components
Added new schemes and collections tabs with dedicated controllers and views
Updated concept visualization with enhanced tree browser functionality including collection filtering and date-based sorting

Reviewed Changes

Copilot reviewed 56 out of 88 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
mise.toml	Updated Ruby version from 2.7.8 to 3.2 and removed Node.js dependency
config/routes.rb	Added new routes for schemes, collections, instances, and properties with AJAX endpoints
config/locales/en.yml	Added localization strings for schemes, collections, and concept browsers
app/controllers/*	Added new SchemesController and CollectionsController with SKOS functionality
app/views/schemes/*	New HAML templates for schemes tree view and details display
app/views/collections/*	New HAML templates for collections list view and details display
app/views/concepts/*	New templates for concept lists and date-sorted views
app/components/*	New ViewComponent classes for tree visualization and infinite scroll
app/helpers/*	New helper modules for schemes, collections, and URL management
app/javascript/*	Updated JavaScript controllers replacing simple tree with custom implementation

Copilot · 2025-07-21T09:42:40Z

app/views/ontologies/concepts_browsers/_collections_picker.html.haml

@@ -0,0 +1,12 @@
+- if no_collections?
+  = no_collections_alert
+-else


Missing space after dash. Should be '- else' to match HAML syntax convention.

Suggested change

-else

- else

Copilot · 2025-07-21T09:42:41Z

app/javascript/component_controllers/skos_collections_selector.js

+  }
+
+  connect() {
+    console.log(this.element, "connect")


Console.log statement should be removed from production code or replaced with proper logging.

Copilot · 2025-07-21T09:42:41Z

app/helpers/schemes_helper.rb

+    ontology.explore.schemes({ include: 'all',  language: request_lang}, scheme_uri)
+  end
+
+  def get_scheme_label(scheme)


Missing null check for scheme parameter. Should add 'return '' if scheme.nil?' at the beginning of the method.

Copilot · 2025-07-21T09:42:41Z

config/initializers/ontologies_api_client.rb

+  config.federated_portals = $PORTALS_INSTANCES ? $PORTALS_INSTANCES.map{|x| x[:api] && x[:apikey] ? [x[:name].downcase.to_sym, x] : nil }.compact.to_h : {}
 end


Complex ternary operation with nested conditions is hard to read. Consider breaking this into multiple lines or a separate method for better maintainability.

Suggested change

config.federated_portals = $PORTALS_INSTANCES ? $PORTALS_INSTANCES.map{|x| x[:api] && x[:apikey] ? [x[:name].downcase.to_sym, x] : nil }.compact.to_h : {}

end

config.federated_portals = build_federated_portals

end

def build_federated_portals

return {} unless $PORTALS_INSTANCES

$PORTALS_INSTANCES.map do |x|

if x[:api] && x[:apikey]

[x[:name].downcase.to_sym, x]

else

nil

end

end.compact.to_h

end

Copilot · 2025-07-21T09:42:42Z

app/controllers/concepts_controller.rb

-    @delete_mapping_permission = check_delete_mapping_permission(@mappings)
-    update_tab(@ontology, @concept.id)
+  def concepts_to_years_months(concepts)
+    return unless concepts || concepts.nil?


The condition 'unless concepts || concepts.nil?' is logically incorrect. It should be 'return {} if concepts.nil? || concepts.empty?' to properly handle empty/nil cases.

Suggested change

return unless concepts || concepts.nil?

return {} if concepts.nil? || concepts.empty?

Gemfile

Copilot · 2025-07-21T09:42:42Z

app/views/ontologies/concepts_browsers/_jump_to.html.haml

+      'class-search-auto-complete-spinner-src-value': asset_path("spinner.gif")})
+
+  = hidden_field_tag("jump_to_concept_id")
+  - if skos? && false  # disabled for now as no time to test #TODO


Dead code with hardcoded 'false' condition. Either remove this code block or implement proper feature flagging.

Copilot · 2025-07-21T09:42:43Z

app/javascript/controllers/simple_tree_controller.js

+  }
+
+  #onClickTooManyChildrenInit () {
+    jQuery('.too_many_children_override').live('click', (event) => {


jQuery .live() method is deprecated and has been removed in jQuery 3.0. Should use .on() with event delegation instead.

Suggested change

jQuery('.too_many_children_override').live('click', (event) => {

jQuery(this.element).on('click', '.too_many_children_override', (event) => {

syphax-bouazzouni added 8 commits July 21, 2025 11:02

update git ignore

804afeb

Merge remote-tracking branch 'ncbo/master' into feature/add-skos

32a3617

use ontoportal lirmm api client to have skos models

fecb29d

remove simple tree jquery and replace it with HTML and hotwire

ac54662

add schems and collection new code for the view, controllers and routes

b26bea4

update the concepts page to have the new tree, collection list and da…

8ba9731

…te list

Merge remote-tracking branch 'ontoportal/master' into feature/add-skos

1342a7f

remove the reference to simple tree in vendor.js

013553a

syphax-bouazzouni requested review from alexskr, Copilot and mdorf July 21, 2025 09:40

Copilot AI reviewed Jul 21, 2025

View reviewed changes

remove instances tab as requiring the search features

26132f9

alexskr merged commit a97079b into master Jul 25, 2025
2 checks passed

This was referenced Jul 25, 2025

Merge upstream/master into enhanced_skos_support ncbo/bioportal_web_ui#443

Merged

enhanced skos support follow up ncbo/bioportal_web_ui#447

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Feature: Add skos features UIs#49

Feature: Add skos features UIs#49
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syphax-bouazzouni commented Jul 21, 2025 •

edited

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		config.federated_portals = $PORTALS_INSTANCES ? $PORTALS_INSTANCES.map{\|x\| x[:api] && x[:apikey] ? [x[:name].downcase.to_sym, x] : nil }.compact.to_h : {}
		end

-  config.federated_portals = $PORTALS_INSTANCES ? $PORTALS_INSTANCES.map{|x| x[:api] && x[:apikey] ? [x[:name].downcase.to_sym, x] : nil }.compact.to_h : {}
-end
+  config.federated_portals = build_federated_portals
+end
+def build_federated_portals
+  return {} unless $PORTALS_INSTANCES
+  $PORTALS_INSTANCES.map do |x|
+    if x[:api] && x[:apikey]
+      [x[:name].downcase.to_sym, x]
+    else
+      nil
+    end
+  end.compact.to_h
+end

	return unless concepts \|\| concepts.nil?
	return {} if concepts.nil? \|\| concepts.empty?

	jQuery('.too_many_children_override').live('click', (event) => {
	jQuery(this.element).on('click', '.too_many_children_override', (event) => {

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Pull Request Overview

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syphax-bouazzouni commented Jul 21, 2025 •

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