From 7149982578010b91fba27712b83d1f096b51b27c Mon Sep 17 00:00:00 2001
From: Jennifer Vendetti <vendetti@stanford.edu>
Date: Mon, 23 Jan 2023 17:22:10 -0800
Subject: [PATCH] Remove defunct marginal notes code

---
 app/assets/javascripts/bioportal.js.erb   |  75 -------------
 app/helpers/application_helper.rb         |  76 -------------
 app/views/margin_notes/_proposal.html.erb |  94 ----------------
 app/views/margin_notes/_show.html.erb     | 127 ----------------------
 app/views/margin_notes/_update.html.erb   |   2 -
 config/routes.rb                          |   2 -
 6 files changed, 376 deletions(-)
 delete mode 100644 app/views/margin_notes/_proposal.html.erb
 delete mode 100644 app/views/margin_notes/_show.html.erb
 delete mode 100644 app/views/margin_notes/_update.html.erb

diff --git a/app/assets/javascripts/bioportal.js.erb b/app/assets/javascripts/bioportal.js.erb
index 39b68a27e..64ff865e2 100644
--- a/app/assets/javascripts/bioportal.js.erb
+++ b/app/assets/javascripts/bioportal.js.erb
@@ -143,40 +143,6 @@ function toggleHide(id,name_to_hide){
 
 }
 
-
-//helper function for demo only
-function newProposal(string){
-  document.getElementById('subject').value="Proposal For Change";
-  document.getElementById('comment').value=string;
-
-  selectBox = document.getElementById('margin_note_note_type');
-  for(var x =0; x<selectBox.options.length;x++){
-    option = selectBox.options[x]
-    if(option.value!=5){
-      option.disabled=true;
-    }
-    if(option.value==5){
-      option.selected=true;
-    }
-  }
-}
-
-  function newNote(){
-    toggleHide("commentForm","forms")
-  }
-
-
-
-
-  function compare(note_id){
-    oldValue = document.getElementById("oldValue").innerHTML;
-    element = document.getElementById("note_value"+note_id)
-    target = document.getElementById("note_text"+note_id)
-    var d = dmp.diff_main(oldValue, element.value);
-      dmp.diff_cleanupSemantic(d);
-      target.innerHTML=dmp.diff_prettyHtml(d)
-  }
-
   function hide(id){
     document.getElementById(id).style.display="none";
   }
@@ -302,47 +268,6 @@ var tabs=null;
 
   }
 
-  function resetNoteForm(uniq){
-    document.getElementById("note_subject"+uniq).value=""
-    document.getElementById("note_comment"+uniq).value=""
-    document.getElementById('noteParent'+uniq).value="";
-  }
-
-
-var myEditor;
-
-
-
-function buildEditor(uniq){
-
-
-
-  var Dom = YAHOO.util.Dom,
-        Event = YAHOO.util.Event;
-
-  myEditor = new YAHOO.widget.SimpleEditor('note_comment'+uniq, {
-    height: '300px',
-    width: '522px',
-    dompath: false //Turns on the bar at the bottom
-});
-myEditor.render();
-}
-
-function saveNote(){
-  myEditor.saveHTML();
-  myEditor.destroy();
-
-}
-
-function destroyEditor(){
-    myEditor.clearEditorDoc();
-    myEditor.destroy();
-
-}
-
-
-
-
 function updateOntologyList(ontology){
     list = document.getElementById("ontologieslist")
     if(ontology.checked){
diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb
index 1292f4fe8..1e93c2aac 100644
--- a/app/helpers/application_helper.rb
+++ b/app/helpers/application_helper.rb
@@ -27,14 +27,6 @@ def isOwner?(id)
     end
   end
 
-  def encode_param(string)
-    return URI.escape(string, Regexp.new("[^#{URI::PATTERN::UNRESERVED}]"))
-  end
-
-  def escape(string)
-    CGI.escape(string)
-  end
-
   def clean(string)
     string = string.gsub("\"",'\'')
     return string.gsub("\n",'')
@@ -45,10 +37,6 @@ def clean_id(string)
     return new_string
   end
 
-  def to_param(string)
-     "#{encode_param(string.gsub(" ","_"))}"
-  end
-
   def get_username(user_id)
     user = LinkedData::Client::Models::User.find(user_id)
     username = user.nil? ? user_id : user.username
@@ -75,70 +63,6 @@ def remove_owl_notation(string)
     end
   end
 
-  def draw_note_tree(notes,key)
-    output = ""
-    draw_note_tree_leaves(notes,0,output,key)
-    return output
-  end
-
-  def draw_note_tree_leaves(notes,level,output,key)
-    for note in notes
-      name="Anonymous"
-      unless note.user.nil?
-        name=note.user.username
-      end
-      headertext=""
-      notetext=""
-      if note.note_type.eql?(5)
-        headertext<< "<div class=\"header\" onclick=\"toggleHide('note_body#{note.id}','');compare('#{note.id}')\">"
-        notetext << " <input type=\"hidden\" id=\"note_value#{note.id}\" value=\"#{note.comment}\">
-                  <span class=\"message\" id=\"note_text#{note.id}\">#{note.comment}</span>"
-      else
-        headertext<< "<div onclick=\"toggleHide('note_body#{note.id}','')\">"
-
-        notetext<< "<span class=\"message\" id=\"note_text#{note.id}\">#{simple_format(note.comment)}</span>"
-      end
-
-
-      output << "
-        <div style=\"clear:both;margin-left:#{level*20}px;\">
-        <div  style=\"float:left;width:100%\">
-          #{headertext}
-              <div>
-                <span class=\"sender\" style=\"float:right\">#{name} at #{note.created_at.strftime('%m/%d/%y %H:%M')}</span>
-                <div class=\"header\"><span class=\"notetype\">#{note.type_label.titleize}:</span> #{note.subject}</div>
-                              <div style=\"clear:both\"></div>
-              </div>
-
-          </div>
-
-          <div name=\"hiddenNote\" id=\"note_body#{note.id}\" >
-          <div class=\"messages\">
-            <div>
-              <div>
-               #{notetext}"
-      if session[:user].nil?
-        output << "<div id=\"insert\"><a href=\"\/login?redirect=/visualize/#{@ontology.to_param}/?conceptid=#{@concept.id}#notes\">Reply</a></div>"
-      else
-        if @modal
-          output << "<div id=\"insert\"><a href=\"#\"  onclick =\"document.getElementById('m_noteParent').value='#{note.id}';document.getElementById('m_note_subject#{key}').value='RE:#{note.subject}';jQuery('#modal_form').html(jQuery('#modal_comment').html());return false;\">Reply</a></div>"
-        else
-          output << "<div id=\"insert\"><a href=\"#TB_inline?height=400&width=600&inlineId=commentForm\" class=\"thickbox\" onclick =\"document.getElementById('noteParent').value='#{note.id}';document.getElementById('note_subject#{key}').value='RE:#{note.subject}';\">Reply</a></div>"
-        end
-      end
-      output << "</div>
-            </div>
-          </div>
-
-          </div>
-        </div>
-        </div>"
-      if(!note.children.nil? && note.children.size>0)
-        draw_note_tree_leaves(note.children,level+1,output,key)
-      end
-    end
-  end
-
   def draw_tree(root, id = nil, type = "Menu")
     if id.nil?
       id = root.children.first.id
diff --git a/app/views/margin_notes/_proposal.html.erb b/app/views/margin_notes/_proposal.html.erb
deleted file mode 100644
index cacd1d0cf..000000000
--- a/app/views/margin_notes/_proposal.html.erb
+++ /dev/null
@@ -1,94 +0,0 @@
-<!-- this is just a quick way to do proposals for the demo -->
-
-<div id="original" style="float:left;width:330px;">
-<fieldset>
-	<legend>Current Value</legend>
-<span id="oldValue"><%=@old_value%></span>
-</fieldset>
-
-</div>
-
-<div style="float:right;">
-
-
-<div id ="notes">
-<%=draw_note_tree(@margin_notes)%>
-</div>
-
-<div id="form" style="display:none;clear:both;">
-<div id="proposalForm" name="forms">
-<%= form_for(:margin_note, :url => margin_notes_path, :update => "notes", :complete => "document.getElementById('form').style.display='none';document.getElementById('buttons').style.display='';", :remote => true) do |f| %>
-	<%=hidden_field 'margin_note', 'concept_id'%>
-	<%unless @ontology.nil?%>
-	<%=hidden_field 'margin_note', 'ontology_id', :value=>@ontology.name%>
-	<%end%>
-	<%=hidden_field 'margin_note', 'mapping_id'%>
-	<%=hidden_field 'margin_note', 'property_name'%>
-<br>
-
-<fieldset>
-	<legend>New Proposal</legend>
-<table width="450px">
-	<tr>
-		<td align="right">Note Type:</td>
-		<td><%=
-                options = MarginNote::NOTE_TYPES                       
-                select('margin_note','note_type',options.invert)
-                %></td>
-	</tr>
-	
-	<tr>
-		<td align="right">Subject:</td><td><%=text_field 'margin_note', 'subject',:size=>70,:id=>'subject'%></td>
-	<tr>
-		<td valign="top"  align="right">Proposed Value:</td><td><%=text_area 'margin_note', 'comment',:rows=>15,:cols=>70, :id=>'comment'%></td>
-	</tr>
-	<tr>
-		<td valign="top"  align="right">Explanation:</td><td><%=text_area_tag 'explanation',"",{:rows=>15,:cols=>70}%></td>
-	</tr>
- 	<tr>
-		<td colspan="2" align="right"><%= submit_tag "Save" ,:class =>"blueButton"%> <%if @modal%><input type="button" value="Close" onclick="Dialog.cancelCallback()" class='blueButton'><%end%></td>
-</table>
-</fieldset>
-</div>
-<%end%>
-
-<div id="commentForm" name="forms">
-	<%= form_for(:margin_note, :url => margin_notes_path, :update => "notes", :complete => "document.getElementById('form').style.display='none';document.getElementById('buttons').style.display='';", :remote => true) do |f| %>
-	<%=hidden_field 'margin_note', 'concept_id'%>
-	<%unless @ontology.nil?%>
-	<%=hidden_field 'margin_note', 'ontology_id', :value=>@ontology.id%>
-	<%end%>
-	<%=hidden_field 'margin_note', 'mapping_id'%>
-	<%=hidden_field 'margin_note', 'parent_id', :id=>'noteParent'%>
-	<%=hidden_field 'margin_note', 'property_name'%>
-<br>
-<fieldset>
-	<legend>New Note</legend>
-<table width="450px">
-	<tr>
-		<td align="right">Note Type:</td>
-		<td><%=
-                options = MarginNote::NOTE_TYPES                       
-                select('margin_note','note_type',options.invert)
-                %></td>
-	</tr>
-	
-	<tr>
-		<td align="right">Subject:</td><td><%=text_field 'margin_note', 'subject',:size=>70%></td>
-	<tr>
-		<td valign="top"  align="right">Note:</td><td><%=text_area 'margin_note', 'comment',:rows=>15,:cols=>70%></td>
-	</tr>
- 	<tr>
-		<td colspan="2" align="right"><%= submit_tag "Save" ,:class =>"blueButton"%> <%if @modal%><input type="button" value="Close" onclick="Dialog.cancelCallback()" class='blueButton'><%end%></td>
-</table>
-</fieldset>
-</div>
-<% end %>
-</div>
-<div id="buttons" style="clear:both;">
-<input type="button" class ="blueButton" value="New Proposal" onclick ="newProposal('<%="#{@old_value}" %>');toggleHide('proposalForm','forms');toggleHide('form','');toggleHide('buttons','');document.getElementById('noteParent').value='';"> 
-<%if @modal%><input type="button" value="Close" onclick="Dialog.cancelCallback()" class='blueButton'><%end%>
-</div>
-</div>
-
-
diff --git a/app/views/margin_notes/_show.html.erb b/app/views/margin_notes/_show.html.erb
deleted file mode 100644
index c30e2a084..000000000
--- a/app/views/margin_notes/_show.html.erb
+++ /dev/null
@@ -1,127 +0,0 @@
-
-
-<%
-uniq = Time.now.to_i
-javascripts = "resetNoteForm(#{uniq});"
- unless @concept.nil?
-	javascripts << "refreshCache('#{@concept.id}');"
- end
-
-%>
-
-<%# to keep IDs from gettin mixed up%>
-<%if @modal%>
-<div id="modal_notes">
-<%else%>
-<div id ="margin_notes">
-<%end%>
-
-	<%if @margin_notes.size<1%>	
-		<h1>There are currently no notes.</h1>
-	<%end%>
-<%=draw_note_tree(@margin_notes,uniq)%>
-</div>
-
-
-
-
-<div id="buttons" style="clear:both;">
-<%if session[:user].nil? %>
-	<br>
-		<a href="/login?redirect=/visualize/<%=@ontology.to_param%>/?conceptid=<%=@concept.id%>#notes">New Note</a>
-<%else%>
-<br>
-<%if @modal%>
-<input title="Add Note" type="button" value="New Note" onclick="jQuery('#modal_form').html(jQuery('#modal_comment').html());"/>  
-<div id="modal_form"></div>
-<%else%>
-<input alt="#TB_inline?height=400&width=600&inlineId=commentForm" title="Add Note" class="thickbox" type="button" value="New Note" />  
-<%end%>
-
-<!--	<input type="button" class ="blueButton" value="New Thread" onclick ="buildEditor('<%=uniq%>');toggleHide('form','');toggleHide('buttons','');document.getElementById('noteParent').value='';">  -->
-<%end%>
-</div>
-
-<div style="display:none;">
-<%# need seperate forms for if its a modal window%>
-<% if @modal%>
-<div id="modal_comment" name="forms">	
-<%= form_for(:margin_note, :url => margin_notes_path,:html=>{:onsubmit=>"ajaxForm(this,'#modal_notes',function(){jQuery('#modal_form').html('');});return false;"}) do |f| %>
-	<%=hidden_field 'margin_note', 'concept_id'%>
-	<%unless @ontology.nil?%>
-		<%=hidden_field 'margin_note', 'ontology_version_id', :value=>@ontology.id%>
-		<%=hidden_field 'margin_note', 'ontology_id', :value=>@ontology.ontologyId%>
-	<%end%>
-	<%=hidden_field 'margin_note', 'mapping_id'%>
-	<%=hidden_field 'margin_note', 'parent_id', :id=>'m_noteParent'%>
-	<%=hidden_field_tag 'key', uniq%>
-
-<fieldset>
-	<legend>New Note</legend>
-<table class="form">
-	<tr>
-		<th>Note Type:</th>
-		<td class="top"><%=
-                options = MarginNote::NOTE_TYPES                       
-                select('margin_note','note_type',options.invert,:id=>'note_type')
-                %></td>
-	</tr>
-	<tr>
-		<th>Subject:</th><td><%=text_field 'margin_note', 'subject',:size=>70,:id=>"m_note_subject#{uniq}",:maxlength=>100%></td>
-	<tr>
-		<th>Note:</th><td><%=text_area 'margin_note' ,'comment',:cols=>70,:rows=>10, :id=>"note_comment#{uniq}"%>
-			</td>
-	</tr>
- 	<tr>
-		<td colspan="2" align="right">			
-				<%= submit_tag "Save" ,:class =>"blueButton"%> | 
-
-				<input class="blueButton" type="button" value="Cancel" onclick="tb_remove()"> 			
-	<!--							<input class="blueButton" type="button" value="Cancel" onclick="resetNoteForm(<%="#{uniq}"%>);toggleHide('form','');toggleHide('buttons','');destroyEditor();"> 			-->
-			 <%if @modal%>| <input type="button" value="Close" onclick="tb_remove()" class='blueButton'><%end%></td>
-</table>
-</fieldset>
-<% end %>
-</div>
-<%else%>
-<div id="commentForm" name="forms">	
-<%= form_for(:margin_note, :url => margin_notes_path,:html=>{:onsubmit=>"ajaxForm(this,'#notes',tb_remove());return false;"}) do |f| %>
-	<%=hidden_field 'margin_note', 'concept_id'%>
-	<%unless @ontology.nil?%>
-		<%=hidden_field 'margin_note', 'ontology_version_id', :value=>@ontology.id%>
-		<%=hidden_field 'margin_note', 'ontology_id', :value=>@ontology.ontologyId%>
-	<%end%>
-	<%=hidden_field 'margin_note', 'mapping_id'%>
-	<%=hidden_field 'margin_note', 'parent_id', :id=>'noteParent'%>
-	<%=hidden_field_tag 'key', uniq%>
-
-<fieldset>
-	<legend>New Note</legend>
-<table class="form">
-	<tr>
-		<th>Note Type:</th>
-		<td class="top"><%=
-                options = MarginNote::NOTE_TYPES                       
-                select('margin_note','note_type',options.invert,:id=>'note_type')
-                %></td>
-	</tr>
-	<tr>
-		<th>Subject:</th><td><%=text_field 'margin_note', 'subject',:size=>70,:id=>"note_subject#{uniq}",:maxlength=>100%></td>
-	<tr>
-		<th>Note:</th><td><%=text_area 'margin_note' ,'comment',:cols=>70,:rows=>10, :id=>"note_comment#{uniq}"%>
-			</td>
-	</tr>
- 	<tr>
-		<td colspan="2" align="right">			
-				<%= submit_tag "Save" ,:class =>"blueButton"%> | 
-
-				<input class="blueButton" type="button" value="Cancel" onclick="tb_remove()"> 			
-	<!--							<input class="blueButton" type="button" value="Cancel" onclick="resetNoteForm(<%="#{uniq}"%>);toggleHide('form','');toggleHide('buttons','');destroyEditor();"> 			-->
-			 <%if @modal%>| <input type="button" value="Close" onclick="tb_remove()" class='blueButton'><%end%></td>
-</table>
-</fieldset>
-<% end %>
-</div>
-<%end%>
-</div>
-
diff --git a/app/views/margin_notes/_update.html.erb b/app/views/margin_notes/_update.html.erb
deleted file mode 100644
index 46ef7556b..000000000
--- a/app/views/margin_notes/_update.html.erb
+++ /dev/null
@@ -1,2 +0,0 @@
-
-<%=draw_note_tree(@margin_notes,@key)%>
diff --git a/config/routes.rb b/config/routes.rb
index cdb4ffc7c..9c1849f5f 100644
--- a/config/routes.rb
+++ b/config/routes.rb
@@ -16,8 +16,6 @@
 
   resources :mappings
 
-  resources :margin_notes
-
   resources :concepts
 
   resources :ontologies do