changes to make it easier to deplay LatticeGrid

app/controllers/graphs_controller.rb

@@ -2,12 +2,12 @@ class GraphsController < ApplicationController
   caches_page :show_org, :show_member, :member_nodes, :org_nodes
 
   def index
-    redirect_to show_org_graph_url(1)
+    redirect_to show_org_graph_path(1)
   end
 
   def show_org
     if params[:id].blank? then
-      redirect_to show_org_graph_url(1)
+      redirect_to show_org_graph_path(1)
     end
   end
 
@@ -17,7 +17,7 @@ def show_member
        params[:id]=params[:id]+'.'+params[:format]
      end
    else 
-     redirect_to show_org_graph_url(1)
+     redirect_to show_org_graph_path(1)
    end 
   end 
 

app/controllers/investigators_controller.rb

@@ -1,8 +1,7 @@
 class InvestigatorsController < ApplicationController
   caches_page :show, :full_show, :list_all, :tag_cloud_side, :tag_cloud, :show_all_tags
   helper :sparklines
-  require 'net/ldap'
-  require 'ldap_utilities' #specific methods
+  require 'ldap_utilities' #specific ldap methods
 
   skip_before_filter  :find_last_load_date, :only => [:tag_cloud_side, :tag_cloud]
   skip_before_filter  :handle_year, :only => [:tag_cloud_side, :tag_cloud]
@@ -11,7 +10,7 @@ class InvestigatorsController < ApplicationController
   skip_before_filter  :define_keywords, :only => [:tag_cloud_side, :tag_cloud]
 
   def index
-    redirect_to( year_list_abstracts_url )
+    redirect_to( year_list_abstracts_path )
   end
   def list_all
     @investigators = Investigator.find(:all, :include=>[:home_department,:appointments], :conditions => ['investigators.end_date is null or investigators.end_date >= :now', {:now => Date.today }], :order => "last_name, first_name")   
@@ -23,7 +22,7 @@ def list_all
   end
   def full_show
     if params[:id].nil? then
-      redirect_to( year_list_abstracts_url )
+      redirect_to( year_list_abstracts_path )
     elsif !params[:page].nil? then
       params.delete(:page)
       redirect_to params
@@ -38,7 +37,7 @@ def full_show
   end
   def show 
     if params[:id].nil? then
-      redirect_to( year_list_abstracts_url)
+      redirect_to( year_list_abstracts_path)
     elsif params[:page].nil? then
       params[:page]="1"
       redirect_to params
@@ -53,7 +52,7 @@ def show
 
   def show_all_tags
     if params[:id].nil? then
-      redirect_to( year_list_abstracts_url)
+      redirect_to( year_list_abstracts_path)
     elsif params[:page].nil? then
       params[:page]="1"
       redirect_to params
@@ -100,8 +99,12 @@ def handle_member_name
         params[:name] =  @investigator.first_name + " " + @investigator.last_name
         begin
           pi_data = GetLDAPentry(@investigator.username)
-           ldap_rec=CleanPIfromLDAP(pi_data)
-           @investigator=MergePIrecords(@investigator,ldap_rec)
+          if pi_data.nil?
+            logger.warn("Probable error reaching the LDAP server in GetLDAPentry: GetLDAPentry returned null for #{params[:name]} using netid #{@investigator.username}.")
+          else
+            ldap_rec=CleanPIfromLDAP(pi_data)
+            @investigator=MergePIrecords(@investigator,ldap_rec)
+          end
          rescue Exception => error
           logger.error("Probable error reaching the LDAP server in GetLDAPentry: #{error.message}")
         end

app/helpers/application_helper.rb

@@ -1,14 +1,8 @@
 # Methods added to this helper will be available to all templates in the application.
 module ApplicationHelper
   include TagsHelper
-
-  def menu_head_abbreviation
-    "Feinberg"
-  end
-  def title_abbreviation
-    "Feinberg"
-  end
-
+  require 'config'
+
   def build_menu(nodes, org_type=nil, &block)
     out="<ul>"
 		for unit in nodes
@@ -74,12 +68,12 @@ def setInvestigatorClass(citation,investigator)
     end
   end
 
-	def link_to_coauthors(coauthors, delimiter=", ")
-	  coauthors.collect{|coauthor| link_to( coauthor.colleague.name, 
-		show_investigator_path(:id=>coauthor.colleague.username, :page=>1), # can't use this form for usernames including non-ascii characters
-		  :title => " #{coauthor.colleague.total_pubs} pubs, "+(coauthor.colleague.num_intraunit_collaborators+coauthor.colleague.num_extraunit_collaborators).to_s+" collaborators")}.join(delimiter)
-	end
-	
+  def link_to_coauthors(coauthors, delimiter=", ")
+    coauthors.collect{|coauthor| link_to( coauthor.colleague.name, 
+      show_investigator_path(:id=>coauthor.colleague.username, :page=>1), # can't use this form for usernames including non-ascii characters
+        :title => " #{coauthor.colleague.total_pubs} pubs, "+(coauthor.colleague.num_intraunit_collaborators+coauthor.colleague.num_extraunit_collaborators).to_s+" collaborators")}.join(delimiter)
+  end
+
   def link_to_collaborators(collaborators, delimiter=", ")
     collaborators.collect{|investigator| link_to( investigator.name, 
       show_investigator_path(:id=>investigator.username, :page=>1), # can't use this form for usernames including non-ascii characters
@@ -186,4 +180,24 @@ def link_to_units(appointments, delimiter="<br/>")
           link_to( appointment.name, show_investigators_org_path(appointment.id), 
           :title => "Show investigators in #{appointment.name}")}.join(delimiter)
   end
+
+  def handle_tr_format(title, object, re="", replacement="")
+    return "" if object.blank?
+    if re.blank?
+      string=object.to_s
+    else
+      string=object.gsub(re,replacement)
+    end
+		output = "<tr><th>#{title}</th>"
+		output += "<td><span id='#{title}'>#{string}</span></td>"
+		output += "</tr>"
+		return output
+	end
+
+	def email_link(email)
+	  return "" if email.blank?
+	  return mail_to(email, email.split("@").join(" at "), 
+          		:subject => email_subject(),
+          		:encode => "javascript") 
+  end
 end

app/models/journal.rb

@@ -24,9 +24,9 @@ def self.publication_record( year, sortby )
 
   def self.high_impact( )
     sortby = "article_influence_score DESC" 
-    conditions = "article_influence_score > 0.001"
+    conditions = "impact_factor >= 5.0"
     # sortby should be one of impact_factor DESC, count_all DESC, journals.journal_abbreviation
-    find(:all, :limit=>25,
+    find(:all,
       :select => "score_year, impact_factor, journal_abbreviation, issn, total_cites, impact_factor_five_year, immediacy_index, total_articles, eigenfactor_score, article_influence_score",
    		:conditions => conditions, 
       :order => "score_year DESC, #{sortby}" )

app/views/abstracts/ccsg.rhtml

@@ -30,10 +30,10 @@
 
 	<div id="impact_factor">
 		<h2>Impact Factor and Eigenvalues Analysis</h2>
-		<h2><%= link_to "List High Impact Journals", high_impact_url %></h2>
+		<h2><%= link_to "List High Impact Journals", high_impact_path %></h2>
 		<h2>Click on the year to run the analysis</h2>
 		<% @year_array.each do |year| %>
-			<h3><%= link_to year, impact_factor_url(year, '') %></h3>
+			<h3><%= link_to year, impact_factor_path(year, '') %></h3>
 		<% end %>
 	</div>
 </div>

app/views/abstracts/year_list.rhtml

@@ -8,7 +8,7 @@
 	<h3><%= "MeSH cloud from publications for the year #{@year}" %></h3>
 	<div id="tag_cloud"></div>
 	<script language="javascript">
-	<%= remote_function(:url => tag_cloud_by_year_abstract_url( @year ), :method => :get, :before => "Element.show('spinner')", :complete => "Element.hide('spinner')" ) %> 
+	<%= remote_function(:url => tag_cloud_by_year_abstract_path( @year ), :method => :get, :before => "Element.show('spinner')", :complete => "Element.hide('spinner')" ) %> 
 	</script>
 	<br/>
 	<% end %>

app/views/investigators/_all_tags.html.erb

@@ -2,7 +2,7 @@
 <h3>MeSH cloud from publications for <i><%= investigator.name %></i></h3>
 <div id="tag_cloud"></div>
 <script language="javascript">
-<%= remote_function(:url => tag_cloud_investigator_url(investigator.id), :method => :get, :before => "Element.show('spinner')", 
+<%= remote_function(:url => tag_cloud_investigator_path(investigator.id), :method => :get, :before => "Element.show('spinner')", 
 :complete => "Element.hide('spinner')" ) %> 
 </script>
 <br/>

app/views/investigators/list_all.html.erb

@@ -41,9 +41,7 @@
 			<%= investigator.first_name %>
 		</td>
 		<td class="list-left">
-			<%= mail_to(investigator.email, investigator.email.split("@").join(" at "), 
-				:subject => "Contact from the Feinberg Publications site",
-				:encode => "javascript") if ! investigator.email.blank? %>
+			<%= email_link(investigator.email) %>
 		</td>
 		<td class="list-left">
 			<%= investigator.home_department.abbreviation %>

app/views/investigators/show.html.erb

@@ -44,7 +44,7 @@
 		<h3>Keywords (MeSH):</h3>
 		<div id="tag_cloud_side"></div>
 		<script language="javascript">
-		<%= remote_function(:url => tag_cloud_side_investigator_url( @investigator.id), :method => :get, :before => "Element.show('spinner')", 
+		<%= remote_function(:url => tag_cloud_side_investigator_path( @investigator.id), :method => :get, :before => "Element.show('spinner')", 
 		:complete => "Element.hide('spinner')" ) %> 
 		</script>
 		<% end %>

app/views/layouts/application.html.erb

@@ -3,20 +3,15 @@
 
 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
 <head>
-	<meta http-equiv="content-type" content="text/html;charset=UTF-8" />
-	<title>Feinberg Faculty Publications: <%= controller.action_name %></title>
+  <meta http-equiv="content-type" content="text/html;charset=UTF-8" />
+  <title>RHLCCC Faculty Publications: <%= controller.action_name %></title>
 	<%= javascript_include_tag :defaults, 'FusionCharts', 'ddsmoothmenu', 'jquery.min' %> 
 	<%= stylesheet_link_tag 'publications','ddsmoothmenu', 'ddsmoothmenu-v'   %>
 	<%= render :partial => "shared/menu_scripts", :locals => { :menu_nodes => @menu_nodes } %>
 	<script>
      jQuery.noConflict();
      // Use jQuery via jQuery(...)
     </script>
-	<style type="text/css">
-	#search {
-	  	background: url(<%= image_path("titlebar.jpg") %>) ;
-	}
-	</style>
 </head>
 <body>
 
@@ -30,9 +25,9 @@
     </div>
 <% end %>
 <div id="main" class="autoclear">
-	<div id="banner"><a href="http://www.nucats.northwestern.edu" ><%= image_tag "pageheader.jpg", options={:alt=>"The Northwestern University Clinical and Translational Sciences Institute"} %></a></div>
+	<div id="banner"><a href="http://www.cancer.northwestern.edu" ><%= image_tag "pageheader.jpg", options={:alt=>"The Robert H. Lurie Comprehensive Cancer Center of Northwestern University"} %></a></div>
 	<div id="results" class="notice"><%= flash[:notice] %> 	<%= image_tag 'loading.gif', :id=>'spinner', :style=>"display:none; float:right;" %> </div>
-	<div id="title">Feinberg Publications and Abstracts Site  </div>
+	<div id="title">Cancer Center Member Publications and Abstracts Site</div>
 	<div id="search">
 		<% form_for :keywords, :url => {:controller => 'abstracts', :action => "search"}  do |form| %> 
 		 	<%= form.text_field :keywords, :size => 20 %> Search
@@ -48,6 +43,11 @@
 			<%= link_to( image_tag( 'lattice_grid_med.gif', :size => "60x60" ), "http://wiki.bioinformatics.northwestern.edu/index.php/LatticeGrid") %> <br/>
 			Powered by <%= link_to( "LatticeGrid", "http://wiki.bioinformatics.northwestern.edu/index.php/LatticeGrid") %> 
 		</div>
+		<br/>
+		<div id="nubic">
+			<%= link_to( image_tag( 'nubic-logo.gif', :size => "167x55" ), "http://www.nucats.northwestern.edu/centers/nubic/index.html") %> 
+		 	<%= link_to( "Sponsored by NUBIC", "http://www.nucats.northwestern.edu/centers/nubic/index.html") %>
+		</div>
 		<p></p>
 	</div> <!-- end of side -->
 	<div id="maincontent">