From 031888fd3de5be3cb4c410181a7447f2f206ceb7 Mon Sep 17 00:00:00 2001
From: Alex Skrenchuk <alexskr@stanford.edu>
Date: Sun, 1 Dec 2024 23:01:06 -0800
Subject: [PATCH 1/2] Remove BPIDResolver

Addresses https://github.com/ncbo/bioportal_web_ui/issues/337
---
 app/controllers/application_controller.rb | 28 -----------------------
 app/controllers/concepts_controller.rb    |  9 --------
 app/controllers/notes_controller.rb       |  6 -----
 app/controllers/ontologies_controller.rb  | 14 +-----------
 app/controllers/search_controller.rb      |  3 ---
 app/models/bpid_resolver.rb               |  6 -----
 config/initializers/zeitwerk.rb           |  1 -
 config/routes.rb                          |  2 --
 8 files changed, 1 insertion(+), 68 deletions(-)
 delete mode 100644 app/models/bpid_resolver.rb

diff --git a/app/controllers/application_controller.rb b/app/controllers/application_controller.rb
index 7e1b0acbe..2f7853f03 100644
--- a/app/controllers/application_controller.rb
+++ b/app/controllers/application_controller.rb
@@ -231,34 +231,6 @@ def redirect_to_home # Redirect to Home Page
     redirect_to "/"
   end
 
-  def redirect_new_api(class_view = false)
-    # Hack to make ontologyid and conceptid work in addition to id and ontology params
-    params[:ontology] = params[:ontology].nil? ? params[:ontologyid] : params[:ontology]
-    # Error checking
-    if params[:ontology].nil? || params[:id] && params[:ontology].nil?
-      @error = "Please provide an ontology id or concept id with an ontology id."
-      return
-    end
-    acronym = BPIDResolver.id_to_acronym(params[:ontology])
-    not_found unless acronym
-    if class_view
-      @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(acronym).first
-      @submission = get_ontology_submission_ready(@ontology)
-      concept = get_class(params, @submission).first.to_s
-      redirect_to "/ontologies/#{acronym}?p=classes#{params_string_for_redirect(params, prefix: "&")}", :status => :moved_permanently
-    else
-      redirect_to "/ontologies/#{acronym}#{params_string_for_redirect(params)}", :status => :moved_permanently
-    end
-  end
-
-  def params_cleanup_new_api
-    params = @_params
-    if params[:ontology] && params[:ontology].to_i > 0
-      params[:ontology] = BPIDResolver.id_to_acronym(params[:ontology])
-    end
-
-    params
-  end
 
   def params_string_for_redirect(params, options = {})
     prefix = options[:prefix] || "?"
diff --git a/app/controllers/concepts_controller.rb b/app/controllers/concepts_controller.rb
index 44a4eef34..94478c537 100644
--- a/app/controllers/concepts_controller.rb
+++ b/app/controllers/concepts_controller.rb
@@ -2,7 +2,6 @@
 
 class ConceptsController < ApplicationController
   include MappingsHelper
-  before_action :redirect_new_api, except: [:show, :biomixer]
 
   layout 'ontology'
 
@@ -113,14 +112,6 @@ def biomixer
     render partial: 'biomixer', layout: false
   end
 
-  def redirect_new_api
-    return unless params[:ontology].to_i.positive?
-
-    params_cleanup_new_api
-    redirect_to "#{request.path}#{params_string_for_redirect(params, stop_words: %w[controller action])}",
-                status: :moved_permanently
-  end
-
   private
 
   # Load data for a concept or retrieve a concept's children, depending on the value of the :callback parameter.
diff --git a/app/controllers/notes_controller.rb b/app/controllers/notes_controller.rb
index 875e3138e..8bf72d0c4 100644
--- a/app/controllers/notes_controller.rb
+++ b/app/controllers/notes_controller.rb
@@ -115,12 +115,6 @@ def archive
     end
   end
 
-  def show_concept_list
-    params[:p] = 'classes'
-    params[:t] = 'notes'
-    redirect_new_api
-  end
-
   private
 
   def note_params
diff --git a/app/controllers/ontologies_controller.rb b/app/controllers/ontologies_controller.rb
index 6fc48fa41..60cc259c0 100644
--- a/app/controllers/ontologies_controller.rb
+++ b/app/controllers/ontologies_controller.rb
@@ -245,17 +245,9 @@ def show
       return
     end
 
-    if params[:ontology].to_i > 0
-      acronym = BPIDResolver.id_to_acronym(params[:ontology])
-      if acronym
-        redirect_new_api
-        return
-      end
-    end
-
     # Note: find_by_acronym includes ontology views
     @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology], include: 'all').first
-    not_found if @ontology.nil?
+    not_found if @ontology.nil? || @ontology.errors
 
     # Handle the case where an ontology is converted to summary only. 
     # See: https://github.com/ncbo/bioportal_web_ui/issues/133.
@@ -361,10 +353,6 @@ def update
     end
   end
 
-  def virtual
-    redirect_new_api
-  end
-
   def widgets
     if request.xhr?
       render :partial => 'widgets', :layout => false
diff --git a/app/controllers/search_controller.rb b/app/controllers/search_controller.rb
index 70a235c76..32a3b8279 100644
--- a/app/controllers/search_controller.rb
+++ b/app/controllers/search_controller.rb
@@ -96,9 +96,6 @@ def check_params_ontologies(params)
       else
         params[:ontologies] = [params[:ontologies]]
       end
-      if params[:ontologies].first.to_i > 0
-        params[:ontologies].map! {|o| BPIDResolver.id_to_acronym(o)}
-      end
       params[:ontologies] = params[:ontologies].join(",")
     end
   end
diff --git a/app/models/bpid_resolver.rb b/app/models/bpid_resolver.rb
deleted file mode 100644
index db73b4b7e..000000000
--- a/app/models/bpid_resolver.rb
+++ /dev/null
@@ -1,6 +0,0 @@
-# frozen_string_literal: true
-
-class BPIDResolver
-  # deprecated; see https://github.com/ncbo/bioportal_web_ui/issues/337
-  nil
-end
diff --git a/config/initializers/zeitwerk.rb b/config/initializers/zeitwerk.rb
index 5e278416f..edc750f48 100644
--- a/config/initializers/zeitwerk.rb
+++ b/config/initializers/zeitwerk.rb
@@ -3,7 +3,6 @@
 Rails.autoloaders.each do |autoloader|
   autoloader.inflector = Zeitwerk::Inflector.new
   autoloader.inflector.inflect(
-    'bpid_resolver' => 'BPIDResolver',
     'kgcl' => 'KGCL'
   )
 end
diff --git a/config/routes.rb b/config/routes.rb
index 8377a8c98..6421b1c73 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -65,7 +65,6 @@
   get '/robots.txt' => 'robots#index'
 
   # Ontologies
-  get '/ontologies/virtual/:ontology' => 'ontologies#virtual', :as => :ontology_virtual
   get '/ontologies/success/:id' => 'ontologies#submit_success'
   match '/ontologies/:acronym' => 'ontologies#update', via: [:get, :post]
   match '/ontologies/:acronym/submissions/:id' => 'submissions#update', via: [:get, :post]
@@ -93,7 +92,6 @@
   get '/ajax/json_class' => 'ajax_proxy#json_class'
   get '/ajax/loading_spinner' => 'ajax_proxy#loading_spinner'
   get '/ajax/notes/delete' => 'notes#destroy'
-  get '/ajax/notes/concept_list' => 'notes#show_concept_list'
   get '/ajax/classes/label' => 'concepts#show_label'
   get '/ajax/classes/definition' => 'concepts#show_definition'
   get '/ajax/classes/treeview' => 'concepts#show_tree'

From 13a25c3c299d380d1a0c45a72c6b529afa585deb Mon Sep 17 00:00:00 2001
From: Alex Skrenchuk <alexskr@stanford.edu>
Date: Mon, 2 Dec 2024 09:16:12 -0800
Subject: [PATCH 2/2] Revert change: to be addressed in a separate PR

---
 app/controllers/ontologies_controller.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/controllers/ontologies_controller.rb b/app/controllers/ontologies_controller.rb
index 60cc259c0..05b138c25 100644
--- a/app/controllers/ontologies_controller.rb
+++ b/app/controllers/ontologies_controller.rb
@@ -247,7 +247,7 @@ def show
 
     # Note: find_by_acronym includes ontology views
     @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology], include: 'all').first
-    not_found if @ontology.nil? || @ontology.errors
+    not_found if @ontology.nil?
 
     # Handle the case where an ontology is converted to summary only. 
     # See: https://github.com/ncbo/bioportal_web_ui/issues/133.