From a60be0dc24d35d87a6a67cd8caad26cbea658996 Mon Sep 17 00:00:00 2001 From: Jennifer Vendetti Date: Wed, 11 Sep 2024 10:10:43 -0700 Subject: [PATCH 1/4] Account for https in class IDs Resolves #326 --- app/helpers/application_helper.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb index d8d9d028b..c57b32dfd 100644 --- a/app/helpers/application_helper.rb +++ b/app/helpers/application_helper.rb @@ -357,7 +357,7 @@ def get_link_for_cls_ajax(cls_id, ont_acronym, target=nil) else target = " target='#{target}' " end - if cls_id.start_with? 'http://' + if cls_id.start_with?('http://', 'https://') href_cls = " href='#{bp_class_link(cls_id, ont_acronym)}' " data_cls = " data-cls='#{cls_id}' " data_ont = " data-ont='#{ont_acronym}' " From 2397bdc182f9004194d0e791ce268a85b03fd673 Mon Sep 17 00:00:00 2001 From: Jennifer Vendetti Date: Wed, 11 Sep 2024 10:16:18 -0700 Subject: [PATCH 2/4] Removed unused method --- app/helpers/application_helper.rb | 8 -------- 1 file changed, 8 deletions(-) diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb index c57b32dfd..0cc0d96de 100644 --- a/app/helpers/application_helper.rb +++ b/app/helpers/application_helper.rb @@ -136,14 +136,6 @@ def help_icon(link, html_attribs = {}) BLOCK end - def anonymous_user - # - # TODO: Fix and failures from removing 'DataAccess' call here. - # - #user = DataAccess.getUser($ANONYMOUS_USER) - user ||= User.new({"id" => 0}) - end - def render_advanced_picker(custom_ontologies = nil, selected_ontologies = [], align_to_dom_id = nil) selected_ontologies ||= [] init_ontology_picker(custom_ontologies, selected_ontologies) From ccc28341345b80242e46f827b88f9f80accd0164 Mon Sep 17 00:00:00 2001 From: Jennifer Vendetti Date: Thu, 12 Sep 2024 17:51:39 -0700 Subject: [PATCH 3/4] Remove unused partials --- app/views/search/_concept_preview.html.erb | 17 ------ app/views/search/_concepts.html.erb | 22 ------- app/views/search/_results.html.erb | 69 ---------------------- 3 files changed, 108 deletions(-) delete mode 100644 app/views/search/_concept_preview.html.erb delete mode 100644 app/views/search/_concepts.html.erb delete mode 100644 app/views/search/_results.html.erb diff --git a/app/views/search/_concept_preview.html.erb b/app/views/search/_concept_preview.html.erb deleted file mode 100644 index 5d8cdc1fe..000000000 --- a/app/views/search/_concept_preview.html.erb +++ /dev/null @@ -1,17 +0,0 @@ -
-Preview of <%=link_to "#{@concept.label_html},#{@concept.id}",uri_url(:ontology=>@ontology,:conceptid=>@concept.id),:target=>"_new"%> - -
- - -<%@concept.properties.each_pair{|key,value| %> - - - - - -<% } %> - -
<%="#{remove_owl_notation(key)}:"%><%="#{value}"%>
- -
\ No newline at end of file diff --git a/app/views/search/_concepts.html.erb b/app/views/search/_concepts.html.erb deleted file mode 100644 index b0593ccee..000000000 --- a/app/views/search/_concepts.html.erb +++ /dev/null @@ -1,22 +0,0 @@ -<%if @concepts.size > 0%> -
-
- -
- -
- -
Comment
<%=text_area(:mapping, :comment, :size => "30x10")%>
-
- -
- <%= select("mapping", "directionality", { "Bidirectional" => "bidirectional", "Unidirectional" => "unidirectional" })%>

- <%= submit_tag "Create", :class=>'blueButton'%>    -
-<%else%> -

No Results Found

-<%end%> \ No newline at end of file diff --git a/app/views/search/_results.html.erb b/app/views/search/_results.html.erb deleted file mode 100644 index 314707ad3..000000000 --- a/app/views/search/_results.html.erb +++ /dev/null @@ -1,69 +0,0 @@ - -<%if @results.size > 0%> - - <%if params[:page].to_i > 1 %> - << Previous Page - - <%end%> - Page <%=params[:page] || 1%> of <%=@pages%> - <%if !params[:page].to_i.eql?(@pages.to_i)%> - Next Page >> - - <%end%> - - - - - - - - - - - - - - <%for result in @results%> - <%begin - #catch exceptions and dont draw row - row = " - - - - "%> - <%=row%> - <%rescue - end - %> - <%end%> - - - - - -
- <%if params[:page].to_i >1 %> << Previous Page <%end%> Page <%=params[:page] || 1%> of <%=@pages%> <%if !params[:page].to_i.eql?(@pages.to_i)%> Next Page >><%end%> -
Class NameFound InOntology
#{link_to highlight(result[:contents],@keyword), uri_url(:ontology => result[:ontologyVersionId], :conceptid => result[:conceptIdShort]), :onclick => "YAHOO.tabwait.container.wait.show();"}#{result[:recordType].titleize.gsub("Record Type","")}#{link_to result[:ontologyDisplayLabel], ontology_path(:id=>result[:ontologyVersionId])}
- <%if params[:page].to_i >1 %> << Previous Page <%end%> Page <%=params[:page] || 1%> of <%=@pages%> <%if !params[:page].to_i.eql?(@pages.to_i)%> Next Page >><%end%> -
-<%else%> -

No Results Found

-<%end%> From 918eff166f77000a08cd5d438141f11b9822cdd2 Mon Sep 17 00:00:00 2001 From: Jennifer Vendetti Date: Tue, 17 Sep 2024 14:17:31 -0700 Subject: [PATCH 4/4] Fix 163 RuboCop warnings Also removes three unused methods: isOwner?, truncate_with_more, and help_icon. --- app/helpers/application_helper.rb | 203 ++++++++++-------------------- 1 file changed, 66 insertions(+), 137 deletions(-) diff --git a/app/helpers/application_helper.rb b/app/helpers/application_helper.rb index 0cc0d96de..12ec47cfe 100644 --- a/app/helpers/application_helper.rb +++ b/app/helpers/application_helper.rb @@ -1,40 +1,23 @@ -# Methods added to this helper will be available to all templates in the application. - require 'uri' require 'cgi' require 'digest/sha1' -require 'pry' # used in a rescue module ApplicationHelper - def get_apikey unless session[:user].nil? - return session[:user].apikey + session[:user].apikey else - return LinkedData::Client.settings.apikey - end - end - - def isOwner?(id) - unless session[:user].nil? - if session[:user].admin? - return true - elsif session[:user].id.eql?(id) - return true - else - return false - end + LinkedData::Client.settings.apikey end end def clean(string) - string = string.gsub("\"",'\'') - return string.gsub("\n",'') + string = string.gsub("\"", '\'') + string.gsub("\n", '') end def clean_id(string) - new_string = string.gsub(":","").gsub("-","_").gsub(".","_") - return new_string + string.gsub(':', '').gsub('-', '_').gsub('.', '_') end def get_username(user_id) @@ -47,50 +30,31 @@ def current_user_admin? def remove_owl_notation(string) # TODO_REV: No OWL notation, but should we modify the IRI? - return string - - unless string.nil? - strings = string.split(":") - if strings.size<2 - #return string.titleize - return string - else - #return strings[1].titleize - return strings[1] - end - end + string end - def draw_tree(root, id = nil, type = "Menu", submission) + def draw_tree(root, id = nil, type = 'Menu', submission) if id.nil? id = root.children.first.id end # TODO: handle tree view for obsolete classes, e.g. 'http://purl.obolibrary.org/obo/GO_0030400' - raw build_tree(root, "", id, submission) # returns a string, representing nested list items + raw build_tree(root, '', id, submission) # returns a string, representing nested list items end def build_tree(node, string, id, submission) - if node.children.nil? || node.children.length < 1 - return string # unchanged + if node.children.nil? || node.children.empty? + return string end - node.children.sort! {|a,b| (a.prefLabel || a.id).downcase <=> (b.prefLabel || b.id).downcase} - for child in node.children - if child.id.eql?(id) - active_style="class='active'" - else - active_style = "" - end - if child.expanded? - open = "class='open'" - else - open = "" - end + node.children.sort! { |a, b| (a.prefLabel || a.id).downcase <=> (b.prefLabel || b.id).downcase } + node.children.each do |child| + active_style = child.id.eql?(id) ? "class='active'" : '' + open = child.expanded? ? "class='open'" : '' # This fake root will be present at the root of "flat" ontologies, we need to keep the id intact - li_id = child.id.eql?("bp_fake_root") ? "bp_fake_root" : short_uuid + li_id = child.id.eql?('bp_fake_root') ? 'bp_fake_root' : short_uuid - if child.id.eql?("bp_fake_root") + if child.id.eql?('bp_fake_root') string << "
  • #{child.prefLabel}
    • " else icons = child.relation_icon(node) @@ -99,11 +63,11 @@ def build_tree(node, string, id, submission) if child.hasChildren && !child.expanded? string << "" elsif child.expanded? - string << "
      " + string << '
        ' build_tree(child, string, id, submission) - string << "
      " + string << '
    ' end - string << "" + string << '' end end @@ -111,11 +75,11 @@ def build_tree(node, string, id, submission) end def loading_spinner(padding = false, include_text = true) - loading_text = include_text ? " loading..." : "" + loading_text = include_text ? ' loading...' : '' if padding - raw('
    ' + image_tag("spinners/spinner_000000_16px.gif", style: "vertical-align: text-bottom;") + loading_text + '
    ') + raw('
    ' + image_tag('spinners/spinner_000000_16px.gif', style: 'vertical-align: text-bottom;') + loading_text + '
    ') else - raw(image_tag("spinners/spinner_000000_16px.gif", style: "vertical-align: text-bottom;") + loading_text) + raw(image_tag('spinners/spinner_000000_16px.gif', style: 'vertical-align: text-bottom;') + loading_text) end end @@ -125,22 +89,11 @@ def short_uuid rand(36**8).to_s(36) end - def help_icon(link, html_attribs = {}) - html_attribs["title"] ||= "Help" - attribs = [] - html_attribs.each {|k,v| attribs << "#{k.to_s}='#{v}'"} - return <<-BLOCK - - - - BLOCK - end - def render_advanced_picker(custom_ontologies = nil, selected_ontologies = [], align_to_dom_id = nil) selected_ontologies ||= [] init_ontology_picker(custom_ontologies, selected_ontologies) - render :partial => "shared/ontology_picker_advanced", :locals => { - :custom_ontologies => custom_ontologies, :selected_ontologies => selected_ontologies, :align_to_dom_id => align_to_dom_id + render partial: 'shared/ontology_picker_advanced', locals: { + custom_ontologies: custom_ontologies, selected_ontologies: selected_ontologies, align_to_dom_id: align_to_dom_id } end @@ -159,69 +112,63 @@ def init_ontology_picker_single end def get_ontologies_data(ontologies = nil) - ontologies ||= LinkedData::Client::Models::Ontology.all(include: "acronym,name") + ontologies ||= LinkedData::Client::Models::Ontology.all(include: 'acronym,name') @onts_for_select = [] @onts_acronym_map = {} @onts_uri2acronym_map = {} ontologies.each do |ont| - # TODO: ontologies parameter may be a list of ontology models (not ontology submission models): - # ont.acronym instead of ont.ontology.acronym - # ont.name instead of ont.ontology.name - # ont.id instead of ont.ontology.id - # TODO: annotator passes in 'custom_ontologies' to the ontologies parameter. - next if ( ont.acronym.nil? or ont.acronym.empty? ) + next if ont.acronym.blank? + acronym = ont.acronym name = ont.name - #id = ont.id # ontology URI - abbreviation = acronym.empty? ? "" : "(#{acronym})" + abbreviation = acronym.empty? ? '' : "(#{acronym})" ont_label = "#{name.strip} #{abbreviation}" - #@onts_for_select << [ont_label, id] # using the URI crashes the UI checkbox selection behavior. @onts_for_select << [ont_label, acronym] @onts_acronym_map[ont_label] = acronym - @onts_uri2acronym_map[ont.id] = acronym # required in ontologies_to_acronyms + @onts_uri2acronym_map[ont.id] = acronym end - @onts_for_select.sort! { |a,b| a[0].downcase <=> b[0].downcase } + @onts_for_select.sort! { |a, b| a[0].downcase <=> b[0].downcase } @onts_for_js = @onts_acronym_map.to_json end def categories_for_select - # This method is called in the search index page. get_ontologies_data get_categories_data - return @categories_for_select + @categories_for_select end def get_categories_data @categories_for_select = [] @categories_map = {} - categories = LinkedData::Client::Models::Category.all(include: "name,ontologies") + categories = LinkedData::Client::Models::Category.all(include: 'name,ontologies') categories.each do |c| - @categories_for_select << [ c.name, c.id ] - @categories_map[c.id] = ontologies_to_acronyms(c.ontologies) # c.ontologies is a list of URIs + @categories_for_select << [c.name, c.id] + @categories_map[c.id] = ontologies_to_acronyms(c.ontologies) end - @categories_for_select.sort! { |a,b| a[0].downcase <=> b[0].downcase } + @categories_for_select.sort! { |a, b| a[0].downcase <=> b[0].downcase } @categories_for_js = @categories_map.to_json end def get_groups_data @groups_map = {} @groups_for_select = [] - groups = LinkedData::Client::Models::Group.all(include: "acronym,name,ontologies") + groups = LinkedData::Client::Models::Group.all(include: 'acronym,name,ontologies') groups.each do |g| - next if ( g.acronym.nil? or g.acronym.empty? ) - @groups_for_select << [ g.name + " (#{g.acronym})", g.acronym ] - @groups_map[g.acronym] = ontologies_to_acronyms(g.ontologies) # g.ontologies is a list of URIs + next if g.acronym.blank? + + @groups_for_select << [g.name + " (#{g.acronym})", g.acronym] + @groups_map[g.acronym] = ontologies_to_acronyms(g.ontologies) end - @groups_for_select.sort! { |a,b| a[0].downcase <=> b[0].downcase } + @groups_for_select.sort! { |a, b| a[0].downcase <=> b[0].downcase } @groups_for_js = @groups_map.to_json end def ontologies_to_acronyms(ontologyIDs) acronyms = [] ontologyIDs.each do |id| - acronyms << @onts_uri2acronym_map[id] # hash generated in get_ontologies_data + acronyms << @onts_uri2acronym_map[id] end - return acronyms.compact # remove nil values from any failures to convert ontology URI to acronym + acronyms.compact end def at_slice? @@ -229,7 +176,7 @@ def at_slice? end def link_last_part(url) - return "" if url.nil? + return '' if url.nil? if url.include?('#') url.split('#').last @@ -238,24 +185,13 @@ def link_last_part(url) end end - def truncate_with_more(text, options = {}) - length ||= options[:length] ||= 30 - trailing_text ||= options[:trailing_text] ||= " ... " - link_more ||= options[:link_more] ||= "[more]" - link_less ||= options[:link_less] ||= "[less]" - more_text = " #{link_more}#{text} #{link_less}" - more = text.length > length ? more_text : "" - output = "#{truncate(text, :length => length, :omission => trailing_text)}" + more + "" - end - def subscribe_ontology_button(ontology_id, user = nil) user = session[:user] if user.nil? if user.nil? - # subscribe button must redirect to login return sanitize("") end - # Init subscribe button parameters. - sub_text = "Subscribe" + + sub_text = 'Subscribe' params = "data-bp_ontology_id='#{ontology_id}' data-bp_is_subbed='false' data-bp_user_id='#{user.id}'" begin # Try to create an intelligent subscribe button. @@ -264,17 +200,15 @@ def subscribe_ontology_button(ontology_id, user = nil) else ont = LinkedData::Client::Models::Ontology.find_by_acronym(ontology_id).first end - subscribed = subscribed_to_ontology?(ont.acronym, user) # application_helper - sub_text = subscribed ? "Unsubscribe" : "Subscribe" + subscribed = subscribed_to_ontology?(ont.acronym, user) + sub_text = subscribed ? 'Unsubscribe' : 'Subscribe' params = "data-bp_ontology_id='#{ont.acronym}' data-bp_is_subbed='#{subscribed}' data-bp_user_id='#{user.id}'" rescue # pass, fallback init done above begin block to scope parameters beyond the begin/rescue block end - # TODO: modify/copy CSS for notes_sub_error => subscribe_error - # TODO: modify/copy CSS for subscribe_to_notes => subscribe_to_ontology spinner = '' error = "" - return " #{spinner} #{error}" + " #{spinner} #{error}" end def subscribed_to_ontology?(ontology_acronym, user) @@ -297,10 +231,11 @@ def ontolobridge_instructions_template(ontology) # http://stackoverflow.com/questions/1293573/rails-smart-text-truncation def smart_truncate(s, opts = {}) - opts = {:words => 20}.merge(opts) + opts = { words: 20 }.merge(opts) if opts[:sentences] - return s.split(/\.(\s|$)+/)[0, opts[:sentences]].map{|s| s.strip}.join('. ') + '. ...' + return s.split(/\.(\s|$)+/)[0, opts[:sentences]].map { |s| s.strip }.join('. ') + '. ...' end + a = s.split(/\s/) # or /[ ]+/ to only split on spaces n = opts[:words] a[0...n].join(' ') + (a.size > n ? '...' : '') @@ -311,11 +246,9 @@ def smart_truncate(s, opts = {}) # => '06/27/2010' def xmldatetime_to_date(xml_date_time_str) require 'date' - d = DateTime.xmlschema( xml_date_time_str ).to_date + d = DateTime.xmlschema(xml_date_time_str).to_date # Return conventional US date format: - return sprintf("%02d/%02d/%4d", d.month, d.day, d.year) - # Or return "yyyy/mm/dd" format with: - #return DateTime.xmlschema( xml_date_time_str ).to_date.to_s + sprintf("%02d/%02d/%4d", d.month, d.day, d.year) end def flash_class(level) @@ -329,41 +262,37 @@ def flash_class(level) bootstrap_alert_class[level] end - ###BEGIN ruby equivalent of JS code in bp_ajax_controller. - ###Note: this code is used in concepts/_details partial. + # NOTE: The following 4 methods (bp_ont_link, bp_class_link, get_link_for_cls_ajax, get_link_for_ont_ajax) are + # the Ruby equivalent of JS code in bp_ajax_controller.js and are used in the concepts/_details partial. def bp_ont_link(ont_acronym) - return "/ontologies/#{ont_acronym}" + "/ontologies/#{ont_acronym}" end def bp_class_link(cls_id, ont_acronym) ontology_path(id: ont_acronym, p: 'classes', conceptid: cls_id) end - def get_link_for_cls_ajax(cls_id, ont_acronym, target=nil) - # Note: bp_ajax_controller.ajax_process_cls will try to resolve class labels. + def get_link_for_cls_ajax(cls_id, ont_acronym, target = nil) + # NOTE: bp_ajax_controller.ajax_process_cls will try to resolve class labels. # Uses 'http' as a more generic attempt to resolve class labels than .include? ont_acronym; the # bp_ajax_controller.ajax_process_cls will try to resolve class labels and # otherwise remove the UNIQUE_SPLIT_STR and the ont_acronym. - if target.nil? - target = "" - else - target = " target='#{target}' " - end + target = target.nil? ? '' : " target='#{target}' " + if cls_id.start_with?('http://', 'https://') href_cls = " href='#{bp_class_link(cls_id, ont_acronym)}' " data_cls = " data-cls='#{cls_id}' " data_ont = " data-ont='#{ont_acronym}' " - return "#{cls_id}" + "#{cls_id}" else - return auto_link(cls_id, :all, :target => '_blank') + auto_link(cls_id, :all, target: '_blank') end end + def get_link_for_ont_ajax(ont_acronym) - # ajax call will replace the acronym with an ontology name (triggered by class='ont4ajax') + # Ajax call will replace the acronym with an ontology name (triggered by class='ont4ajax') href_ont = " href='#{bp_ont_link(ont_acronym)}' " data_ont = " data-ont='#{ont_acronym}' " - return "#{ont_acronym}" + "#{ont_acronym}" end - ###END ruby equivalent of JS code in bp_ajax_controller. - end