Merge branch 'rest_api_revision'

app/controllers/annotator_controller.rb

@@ -50,29 +50,41 @@ def create
     #annotations = LinkedData::Client::HTTP.get(query)
     LOG.add :debug, "Retrieved #{annotations.length} annotations: #{Time.now - start}s"
     massage_annotated_classes(annotations, options) unless annotations.empty?
+    # Trying to generate highlighted match context in controller.  More
+    # overhead on controller and more data transfer to the client.
+    # This is handled in bp_annotator.js, to move the processing load onto
+    # the client side in JS.  (TODO: evaluate if JS handles UTF8.)
+    #annotations.each do |a|
+    #  #annotation = a['annotations'].first
+    #  #=> {"from"=>1, "to"=>8, "matchType"=>"PREF", "text"=>"MELANOMA"}
+    #  a['annotations'].each do |annotation|
+    #    position = [annotation['from'], annotation['to']]
+    #    context = highlight_and_get_context(text_to_annotate, position)
+    #    annotation['context'] = context
+    #  end
+    #end
     render :json => annotations
   end
 
 
 private
 
-
-  # TODO: Use this method to highlight matched classes in the annotation text.  Currently done in JS on the client.
-  def highlight_and_get_context(text, position, words_to_keep = 4)
-    # Process the highlighted text
-    highlight = ["<span style='color: #006600; padding: 2px 0; font-weight: bold;'>", "", "</span>"]
-    highlight[1] = text.utf8_slice(position[0] - 1, position[1] - position[0] + 1)
-    # Use scan to split the text on spaces while keeping the spaces
-    scan_filter = Regexp.new(/[ ]+?[-\?'"\+\.,]+\w+|[ ]+?[-\?'"\+\.,]+\w+[-\?'"\+\.,]|\w+[-\?'"\+\.,]+|[ ]+?\w+/)
-    before = text.utf8_slice(0, position[0] - 1).match(/(\s+\S+|\S+\s+){0,4}$/).to_s
-    after = text.utf8_slice(position[1], ActiveSupport::Multibyte::Chars.new(text).length - position[1]).match(/^(\S+\s+\S+|\s+\S+|\S+\s+){0,4}/).to_s
-    # The process above will not keep a space right before the highlighted word, so let's keep it here if needed
-    # 32 is the character code for space
-    kept_space = text.utf8_slice(position[0] - 2) == " " ? " " : ""
-    # Put it all together
-    [before, kept_space, highlight.join, after].join
-  end
-
+  ## This method can be used to highlight matched classes in the annotation text.  Currently done in JS on the client.
+  #def highlight_and_get_context(text, position, words_to_keep = 4)
+  #  # Process the highlighted text
+  #  #highlight = ["<span style='color: #006600; padding: 2px 0; font-weight: bold;'>", "", "</span>"]
+  #  highlight = ["<span class='annotator_context_highlight'>", "", "</span>"]
+  #  highlight[1] = text.utf8_slice(position[0] - 1, position[1] - position[0] + 1)
+  #  # Use scan to split the text on spaces while keeping the spaces
+  #  #scan_filter = Regexp.new(/[ ]+?[-\?'"\+\.,]+\w+|[ ]+?[-\?'"\+\.,]+\w+[-\?'"\+\.,]|\w+[-\?'"\+\.,]+|[ ]+?\w+/)
+  #  before = text.utf8_slice(0, position[0] - 1).match(/(\s+\S+|\S+\s+){0,4}$/).to_s
+  #  after = text.utf8_slice(position[1], ActiveSupport::Multibyte::Chars.new(text).length - position[1]).match(/^(\S+\s+\S+|\s+\S+|\S+\s+){0,4}/).to_s
+  #  # The process above will not keep a space right before the highlighted word, so let's keep it here if needed
+  #  # 32 is the character code for space
+  #  kept_space = text.utf8_slice(position[0] - 2) == " " ? " " : ""
+  #  # Put it all together
+  #  [before, kept_space, highlight.join, after].join
+  #end
 
 end
 

app/controllers/ontologies_controller.rb

@@ -228,16 +228,16 @@ def show
         redirect_to "/ontologies/#{params[:ontology]}#{params_string_for_redirect(params)}", :status => :moved_permanently
         return
       when "classes"
-        self.classes
+        self.classes rescue self.summary
         return
       when "mappings"
-        self.mappings
+        self.mappings rescue self.summary
         return
       when "notes"
-        self.notes
+        self.notes rescue self.summary
         return
       when "widgets"
-        self.widgets
+        self.widgets rescue self.summary
         return
       when "summary"
         self.summary

app/helpers/ontologies_helper.rb

@@ -143,7 +143,7 @@ def count_links(ont_acronym, page_name='summary', count=0)
   end
 
   def classes_link(ontology, count)
-    count = 0 if ontology.summaryOnly
+    return "0" if (ontology.summaryOnly || count.nil? || count == 0)
     return count_links(ontology.ontology.acronym, 'classes', count)
   end
 
@@ -164,7 +164,7 @@ def download_link(submission)
   end
 
   def mappings_link(ontology, count)
-    count = 0 if ontology.summaryOnly
+    return "0" if (ontology.summaryOnly || count.nil? || count == 0)
     return count_links(ontology.ontology.acronym, 'mappings', count)
   end
 
@@ -215,10 +215,9 @@ def submission_status2string(sub)
   # Link for private/public/licensed ontologies
   def visibility_link(ontology)
     ont_url = "/ontologies/#{ontology.acronym}"  # 'ontology' is NOT a submission here
-    page_name = 'classes'  # default ontology page view for visibility link
+    page_name = 'summary'  # default ontology page view for visibility link
     link_name = 'Public'   # default ontology visibility
     if ontology.summaryOnly
-      page_name = 'summary'
       link_name = 'Summary Only'
     elsif ontology.private?
       link_name = 'Private'

app/views/home/index.html.haml

@@ -165,7 +165,7 @@
     \  
     %a{:href => "#", :onclick => "close_message(); return false;", :style => "font-size: small; color: darkGray;"} [close]
 %div{:style => "padding:10px;margin:10px;"}
-  = t('home.intro').nil? || t('home.intro').empty? ? "<span style='font-size:2em'><b>Welcome to BioPortal!</b></span> For help using #{$SITE}, click on this icon: #{help_icon("/help#Home_Page")}" : t('home.intro')
+  = t('home.intro').nil? || t('home.intro').empty? ? "<span style='font-size:1.5em'><b>Welcome to BioPortal!</b> For help using #{$SITE}, click on this icon: #{help_icon("/help#Home_Page")}</span>" : t('home.intro')
 %table{:width => "100%"}
   %tr
     %td{:valign => "top", :width => "33%"}

app/views/ontologies/_details.html.haml

@@ -10,20 +10,34 @@
       %tr
         %th Visibility
         %td= strip_links(visibility_link(@ontology))
+
       - if !$PURL_ENABLED.nil? && $PURL_ENABLED && [email protected]
         %tr
           %th
-            = $SITE
-            PURL
+            = "#{$SITE} PURL".strip
           %td
             = auto_link(@ontology.purl, :all, :target => "_blank")
+
       - if @ontology.viewing_restricted?
         %tr
           %th
             Viewing Restriction
           %td
             = @ontology.viewingRestriction.capitalize
 
+      - if @ontology.respond_to?('viewOf')
+        - unless @ontology.viewOf.nil?
+          %tr
+            %th
+              View of Ontology
+            %td
+              - ont_parent_acronym = @ontology.viewOf.split('/').last
+              - if !$PURL_ENABLED.nil? && $PURL_ENABLED
+                - ont_url = @ontology.purl.sub(@ontology.acronym, ont_parent_acronym)
+              - else
+                - ont_url = @ontology.links['ui'].sub(@ontology.acronym, ont_parent_acronym)
+              = auto_link(ont_url, :all, :target => "_blank")
+
       -# Get the latest submission (not necessarily the latest ready submission).
       - sub = @submission_latest
       - unless sub.nil? || (sub.respond_to?(:status) && sub.status == 404)

public/javascripts/bp_annotator.js

@@ -456,12 +456,13 @@ function get_annotation_rows(annotation, text) {
   var match_span = '<span style="color: rgb(153,153,153);">';
   var match_markup_span = '<span style="color: rgb(35, 73, 121); font-weight: bold; padding: 2px 0px;">';
   jQuery.each(annotation.annotations, function (i, a) {
-
-    // TODO: consider string truncation around the annotation markups.
-
     text_match = text.substring(a.from - 1, a.to);
     text_prefix = text.substring(0, a.from - 1);
     text_suffix = text.substring(a.to);
+    // remove everything prior to the preceding three words (using space delimiters):
+    text_prefix = text_prefix.replace(/.* ((?:[^ ]* ){2}[^ ]*$)/, "... $1");
+    // remove the fourth space and everything following it:
+    text_suffix = text_suffix.replace(/^((?:[^ ]* ){3}[^ ]*) [\S\s]*/, "$1 ...");
     text_markup = match_markup_span + text_match + "</span>";
     text_markup = match_span + text_prefix + text_markup + text_suffix + "</span>";
     //console.log('text markup: ' + text_markup);