Merge staging for release

Gemfile

@@ -40,7 +40,7 @@ gem 'rack-mini-profiler'
 gem 'rails_autolink'
 gem 'rdoc'
 gem 'recaptcha', '~> 5.2'
-gem 'rest-client', '~> 1.8.0'
+gem 'rest-client'
 gem 'stackprof', require: false
 gem 'thin'
 gem 'will_paginate', '~> 3.0'

Gemfile.lock

@@ -62,13 +62,13 @@ GEM
       sshkit (>= 1.6.1, != 1.7.0)
     arel (9.0.0)
     ast (2.4.1)
-    autoprefixer-rails (9.8.6.3)
+    autoprefixer-rails (10.0.1.0)
       execjs
     bootstrap (4.1.3)
       autoprefixer-rails (>= 6.0.3)
       popper_js (>= 1.12.9, < 2)
       sass (>= 3.5.2)
-    brakeman (4.9.0)
+    brakeman (4.10.0)
     builder (3.2.4)
     capistrano (3.14.1)
       airbrussh (>= 1.0.0)
@@ -101,7 +101,7 @@ GEM
     crass (1.0.6)
     cube-ruby (0.0.3)
     daemons (1.3.1)
-    dalli (2.7.10)
+    dalli (2.7.11)
     diff-lcs (1.4.4)
     domain_name (0.5.20190701)
       unf (>= 0.0.5, < 1.0.0)
@@ -116,14 +116,15 @@ GEM
     flamegraph (0.9.5)
     globalid (0.4.2)
       activesupport (>= 4.2.0)
-    haml (5.1.2)
+    haml (5.2.0)
       temple (>= 0.8.0)
       tilt
     html2haml (2.2.0)
       erubis (~> 2.7.0)
       haml (>= 4.0, < 6)
       nokogiri (>= 1.6.0)
       ruby_parser (~> 3.5)
+    http-accept (1.7.0)
     http-cookie (1.0.3)
       domain_name (~> 0.5)
     i18n (1.8.5)
@@ -148,7 +149,9 @@ GEM
     marcel (0.3.3)
       mimemagic (~> 0.3.2)
     method_source (1.0.0)
-    mime-types (2.99.3)
+    mime-types (3.3.1)
+      mime-types-data (~> 3.2015)
+    mime-types-data (3.2020.0512)
     mimemagic (0.3.5)
     mini_mime (1.0.2)
     mini_portile2 (2.4.0)
@@ -160,22 +163,22 @@ GEM
       net-ssh (>= 2.6.5, < 7.0.0)
     net-ssh (6.1.0)
     netrc (0.11.0)
-    newrelic_rpm (6.12.0.367)
-    nio4r (2.5.2)
+    newrelic_rpm (6.13.1)
+    nio4r (2.5.4)
     nokogiri (1.10.10)
       mini_portile2 (~> 2.4.0)
-    oj (3.10.13)
+    oj (3.10.14)
     open_uri_redirections (0.2.1)
     parallel (1.19.2)
-    parser (2.7.1.4)
+    parser (2.7.2.0)
       ast (~> 2.4.1)
     popper_js (1.16.0)
     pry (0.13.1)
       coderay (~> 1.1)
       method_source (~> 1.0)
     public_suffix (4.0.6)
     rack (2.2.3)
-    rack-mini-profiler (2.0.4)
+    rack-mini-profiler (2.1.0)
       rack (>= 1.2.0)
     rack-test (1.1.0)
       rack (>= 1.0, < 3)
@@ -213,13 +216,14 @@ GEM
     rdoc (6.2.1)
     recaptcha (5.5.0)
       json
-    regexp_parser (1.7.1)
-    rest-client (1.8.0)
+    regexp_parser (1.8.2)
+    rest-client (2.1.0)
+      http-accept (>= 1.7.0, < 2.0)
       http-cookie (>= 1.0.2, < 2.0)
-      mime-types (>= 1.16, < 3.0)
-      netrc (~> 0.7)
+      mime-types (>= 1.16, < 4.0)
+      netrc (~> 0.8)
     rexml (3.2.4)
-    rspec-core (3.9.2)
+    rspec-core (3.9.3)
       rspec-support (~> 3.9.3)
     rspec-expectations (3.9.2)
       diff-lcs (>= 1.2.0, < 2.0)
@@ -236,17 +240,17 @@ GEM
       rspec-mocks (~> 3.9)
       rspec-support (~> 3.9)
     rspec-support (3.9.3)
-    rubocop (0.90.0)
+    rubocop (0.93.1)
       parallel (~> 1.10)
-      parser (>= 2.7.1.1)
+      parser (>= 2.7.1.5)
       rainbow (>= 2.2.2, < 4.0)
-      regexp_parser (>= 1.7)
+      regexp_parser (>= 1.8)
       rexml
-      rubocop-ast (>= 0.3.0, < 1.0)
+      rubocop-ast (>= 0.6.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 1.4.0, < 2.0)
-    rubocop-ast (0.3.0)
-      parser (>= 2.7.1.4)
+    rubocop-ast (0.8.0)
+      parser (>= 2.7.1.5)
     ruby-progressbar (1.10.1)
     ruby_parser (3.15.0)
       sexp_processor (~> 4.9)
@@ -267,7 +271,7 @@ GEM
     sprockets (3.7.2)
       concurrent-ruby (~> 1.0)
       rack (> 1, < 3)
-    sprockets-rails (3.2.1)
+    sprockets-rails (3.2.2)
       actionpack (>= 4.0)
       activesupport (>= 4.0)
       sprockets (>= 3.0.0)
@@ -335,7 +339,7 @@ DEPENDENCIES
   rails_autolink
   rdoc
   recaptcha (~> 5.2)
-  rest-client (~> 1.8.0)
+  rest-client
   rspec-rails
   rubocop
   sass-rails (~> 5.0)

app/assets/javascripts/bp_ontolobridge.js

@@ -12,6 +12,109 @@ function bindCancelRequestTermClick() {
   });
 }
 
+function bindNewTermInstructionsClick() {
+  jQuery("#new_term_instructions").live("click", function() {
+    jQuery(this).trumbowyg({
+      btns: [
+        ['viewHTML'],
+        ['undo', 'redo'], // Only supported in Blink browsers
+        ['formatting'],
+        ['strong', 'em', 'del'],
+        ['superscript', 'subscript'],
+        ['link'],
+        ['insertImage'],
+        ['justifyLeft', 'justifyCenter', 'justifyRight', 'justifyFull'],
+        ['unorderedList', 'orderedList'],
+        ['horizontalRule'],
+        ['removeformat'],
+        ['fullscreen']
+      ]
+    });
+    jQuery("#new_term_instructions_submit").show();
+    jQuery("#new_term_instructions_cancel").show();
+  });
+}
+
+function bindNewTermInstructionsSubmit() {
+  jQuery("#new_term_instructions_submit").live("click", function() {
+    saveNewTermInstructions();
+  });
+}
+
+function bindNewTermInstructionsCancel() {
+  jQuery("#new_term_instructions_cancel").live("click", function() {
+    var oldVal = jQuery("#new_term_instructions_old").val().trim();
+    var curVal = jQuery('#new_term_instructions').html().trim();
+
+    if (oldVal != curVal) {
+      if (confirm('Are you sure you want to discard your changes?')) {
+        jQuery('#new_term_instructions').trumbowyg('destroy');
+        jQuery('#new_term_instructions').html(oldVal);
+        hideButtons();
+      }
+    } else {
+      jQuery('#new_term_instructions').trumbowyg('destroy');
+      hideButtons();
+    }
+  });
+}
+
+function preventNewTermInstructionsFormSubmit() {
+  jQuery("#new_term_instructions_form").submit(function(e) {
+    e.preventDefault(e);
+  });
+}
+
+function clearProgressMessage() {
+  jQuery("#progress_message").hide();
+  jQuery("#progress_message").html("");
+};
+
+function showProgressMessage() {
+  clearProgressMessage();
+  var msg = "Saving...";
+  jQuery("#progress_message").text(msg).html();
+  jQuery("#progress_message").show();
+}
+
+function saveNewTermInstructions() {
+  var params = jQuery('#new_term_instructions_form').serialize();
+  var newInstructions = jQuery('#new_term_instructions').html().trim();
+  params += '&new_term_instructions=' + newInstructions;
+  showProgressMessage();
+
+  jQuery.ajax({
+    type: "POST",
+    url: "/ontolobridge/save_new_term_instructions",
+    dataType: "json",
+    data: params,
+    success: function(data) {
+      var status = data[1];
+
+      if (status && status >= 400 || data[0]['error'].length) {
+        showStatusMessages('', data[0]['error']);
+      } else {
+        jQuery('#new_term_instructions').trumbowyg('destroy');
+        jQuery("#new_term_instructions_old").val(newInstructions);
+        showStatusMessages(data[0]["success"], '');
+        setTimeout(function() { clearStatusMessages(); }, 5000);
+      }
+    },
+    error: function(request, textStatus, errorThrown) {
+      showStatusMessages('', errorThrown);
+    },
+    complete: function(request, textStatus) {
+      clearProgressMessage();
+      hideButtons();
+    }
+  });
+}
+
+function hideButtons() {
+  jQuery("#new_term_instructions_submit").hide();
+  jQuery("#new_term_instructions_cancel").hide();
+}
+
 function bindRequestTermSaveClick() {
   var success = "";
   var error = "";
@@ -33,7 +136,7 @@ function bindRequestTermSaveClick() {
       var status = data[1];
 
       if (status && status >= 400) {
-        showStatusMessages(null, data[0]["error"]);
+        showStatusMessages('', data[0]["error"]);
       } else {
         var msg = "<strong>A new term request has been submitted successfully:</strong><br/><br/>";
         var button = jQuery(".request_term_form_div .save");
@@ -42,7 +145,6 @@ function bindRequestTermSaveClick() {
         for (var i in data[0]) {
           msg += i + ": " + data[0][i] + "<br/>";
         }
-
         showStatusMessages(msg, error);
       }
     },
@@ -59,7 +161,6 @@ function removeRequestTermBox(button) {
 
 function addRequestTermBox(id, type, button) {
   clearStatusMessages();
-
   var formContainer = jQuery(button).parents(".notes_list_container").children(".request_term_form_div");
   requestTermFields(id, formContainer);
   formContainer.show();
@@ -86,17 +187,17 @@ function showStatusMessages(success, error) {
 
 function requestTermButtons() {
   var button_submit = jQuery("<button>")
+    .attr("class", "btn")
     .attr("type", "submit")
     .attr("onclick", "")
     .addClass("save")
-    .css("margin-right", "20px")
-    .css("padding", "2px 8px")
+    .css("margin-right", "5px")
     .html("Submit");
   var button_cancel = jQuery("<button>")
+    .attr("class", "btn")
     .attr("type", "button")
     .attr("onclick", "")
     .addClass("cancel")
-    .css("padding", "2px 8px")
     .html("Cancel");
   return button_submit.add(button_cancel);
 }
@@ -128,7 +229,6 @@ function appendTextArea(id, placeholder, div, isRequired, invalidMessage) {
     txtArea.prop('required', true);
     txtArea.attr("class", "req");
   }
-
   div.append(txtArea);
   div.append("<br/>");
 }
@@ -159,7 +259,6 @@ function appendField(id, text, div, isRequired, invalidMessage) {
     ipt.prop('required', true);
     ipt.attr("class", "req");
   }
-
   div.append(ipt);
   div.append("<br/>");
 }
@@ -195,4 +294,9 @@ jQuery(document).ready(function() {
   clearStatusMessages();
   bindAddRequestTermClick();
   bindCancelRequestTermClick();
+
+  preventNewTermInstructionsFormSubmit();
+  bindNewTermInstructionsSubmit();
+  bindNewTermInstructionsCancel();
+  bindNewTermInstructionsClick();
 });

app/assets/javascripts/vendor.js

@@ -35,4 +35,5 @@
 //= require Chart.min
 //= require select2 
 //= require jquery.readyselector
+//= require trumbowyg
 

app/assets/stylesheets/application.css.scss

@@ -19,6 +19,7 @@
  *= require jquery.tooltip
  *= require thickbox
  *= require select2
+ *= require trumbowyg
  *
  */
 

app/assets/stylesheets/ontolobridge.scss

@@ -27,3 +27,9 @@ input.req,
 textarea.req {
   border-color: darksalmon !important;
 }
+
+blockquote {
+  padding: 0 1em;
+  color: #6a737d;
+  border-left: .25em solid #dfe2e5;
+}

app/controllers/concepts_controller.rb

@@ -16,6 +16,8 @@ def show
 
     # Note that find_by_acronym includes views by default
     @ontology = LinkedData::Client::Models::Ontology.find_by_acronym(params[:ontology]).first
+    @ob_instructions = helpers.ontolobridge_instructions_template(@ontology)
+
     if request.xhr?
       display = params[:callback].eql?('load') ? {full: true} : {display: "prefLabel"}
       @concept = @ontology.explore.single_class(display, params[:id])

app/controllers/ontolobridge_controller.rb

@@ -41,4 +41,23 @@ def request_term
     render json: [response, code], status: code
   end
 
+  def save_new_term_instructions
+    code = 200
+    response = {error: '', success: ''}
+    response[:success] = "New term request instructions for #{params['acronym']} saved"
+    ont_data = Ontology.find_by(acronym: params['acronym'])
+    ont_data ||= Ontology.new
+    ont_data.acronym = params['acronym']
+    ont_data.new_term_instructions = params['new_term_instructions']
+
+    begin
+      ont_data.save
+    rescue Exception => e
+      code = 500
+      response[:error] = "Unable to save new term instructions for #{params['acronym']} due to a server error"
+    end
+    sleep(1)
+    render json: [response, code], status: code
+  end
+
 end

app/controllers/ontologies_controller.rb

@@ -289,6 +289,8 @@ def show
       end
     end
 
+    @ob_instructions = helpers.ontolobridge_instructions_template(@ontology)
+
     # Retrieve submissions in descending submissionId order (should be reverse chronological order)
     @submissions = @ontology.explore.submissions.sort {|a,b| b.submissionId.to_i <=> a.submissionId.to_i } || []
     LOG.add :error, "No submissions for ontology: #{@ontology.id}" if @submissions.empty?