sequenceserver 1.0.2 → 1.0.3

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -32,6 +32,14 @@ cd sequenceserver
 gem install bundler && bundle
 ```
 
+We use Capybara with WebKit driver for functional testing. If the above step
+fails, install `qt` (On Mac: `brew install qt`) and run `bundle` again.
+
+If you are deploying SequenceServer from git (not advised) you can skip
+installing development dependencies (and `qt`) by running
+
+    bundle install --without=development
+
 ###### Node
 ```
 npm install

data/lib/sequenceserver/blast/hsp.rb

@@ -29,8 +29,8 @@ module SequenceServer
       #
       def stats
         {
-          'Score'      => [bit_score, score],
-          'E value'    => evalue,
+          'Score'      => [in_twodecimal(bit_score), score],
+          'E value'    => in_scientific_or_twodecimal(evalue),
           'Identities' => [in_fraction(identity,   length),
                            in_percentage(identity, length)],
           'Gaps'       => [in_fraction(gaps,   length),
@@ -148,7 +148,7 @@ module SequenceServer
 
       ## We define stats in terms of the following functions. ##
 
-      # Return fractional representation as String.
+      # Returns fractional representation as String.
       #
       # NOTE:
       #   Rational class reduces the fraction so we can't use that.
@@ -156,10 +156,22 @@ module SequenceServer
         "#{num}/#{den}"
       end
 
-      # Return percentage as Float.
+      # Returns percentage as Float-String formatted to two decimal places.
       def in_percentage(num, den)
         format '%.2f', (num * 100.0 / den)
       end
+
+      # Returns given Float as String formatted to two decimal places.
+      def in_twodecimal(num)
+        format '%.2f', num
+      end
+
+      # Formats the given number as "1e-3" if the number is less than 1 or
+      # greater than 10.
+      def in_scientific_or_twodecimal(num)
+        return in_twodecimal(num) if num >= 1 && num < 10
+        format '%.2e', num.to_f
+      end
     end
 
     class HSP

data/lib/sequenceserver/database.rb

@@ -106,16 +106,22 @@ module SequenceServer
           out.each_line do |line|
             name = line.split('	')[0]
             next if multipart_database_name?(name)
-            self << Database.new(*line.split('	'))
+            begin
+              self << Database.new(*line.split('	'))
+            rescue NoMethodError => e
+              err << "BLAST Database error:\n#{e}\n#{line}"
+            end
           end
+          throw_scan_error(cmd, out, err, $CHILD_STATUS)
         end
       end
 
       def throw_scan_error(cmd, out, err, child_status)
         errpat = /BLAST Database error/
+        if !child_status.success? || err.match(errpat)
+          fail BLAST_DATABASE_ERROR.new(cmd, err)
+        end
         fail NO_BLAST_DATABASE_FOUND, config[:database_dir] if out.empty?
-        fail BLAST_DATABASE_ERROR.new(cmd, err) if !child_status.success? ||
-                                                   err.match(errpat)
       end
 
       # Recursively scan `database_dir` for un-formatted FASTA and format them

data/lib/sequenceserver/routes.rb

@@ -19,16 +19,12 @@ module SequenceServer
       # Make it a policy to dump to 'rack.errors' any exception raised by the
       # app so that error handlers don't have to do it themselves. But for it
       # to always work, Exceptions defined by us should not respond to `code`
-      # or http_status` methods. Error blocks errors must explicitly set http
+      # or `http_status` methods. Error blocks must explicitly set http
       # status, if needed, by calling `status` method.
-      # method.
       enable :dump_errors
 
       # We don't want Sinatra do setup any loggers for us. We will use our own.
       set :logging, nil
-
-      # Public, and views directory will be found here.
-      set :root,    lambda { SequenceServer.root }
     end
 
     # See
@@ -39,6 +35,21 @@ module SequenceServer
       mime_type :tsv,   'text/tsv'
     end
 
+    configure do
+      # Public, and views directory will be found here.
+      set :root, lambda { SequenceServer.root }
+
+      # Allow :frame_options to be configured for Rack::Protection.
+      #
+      # By default _any website_ can embed SequenceServer in an iframe. To
+      # change this, set `:frame_options` config to :deny, :sameorigin, or
+      # 'ALLOW-FROM uri'.
+      set :protection, lambda {
+        frame_options = SequenceServer.config[:frame_options]
+        frame_options && {:frame_options => frame_options}
+      }
+    end
+
     configure :production do
       set :public_folder,
           lambda { File.join SequenceServer.root, 'public', 'dist' }
@@ -67,20 +78,19 @@ target="#{target}">)
       # Prettify given data.
       def prettify(data)
         return prettify_tuple(data) if tuple? data
-        return prettify_float(data) if data.is_a? Float
+        return prettify_float(data) if float? data
         data
       end
 
-      # Formats float as "a.bcd" or "a x b^c". The latter if float is
+      # Formats float as "a.bc" or "a x b^c". The latter if float is in
       # scientific notation. Former otherwise.
-      def prettify_float(float)
-        float.to_s.sub(/(\d*\.\d*)e?([+-]\d*)?/) do
-          base  = Regexp.last_match[1]
-          power = Regexp.last_match[2]
-          s = format '%.2f', base
-          s << " &times; 10<sup>#{power}</sup>" if power
-          s
-        end
+      def prettify_float(data)
+        data.to_s.match(/(\d+\.\d+)e?([+-]\d+)?/)
+        base  = Regexp.last_match[1]
+        power = Regexp.last_match[2]
+        s = format '%.2f', base
+        s << " &times; 10<sup>#{power}</sup>" if power
+        s
       end
 
       # Formats an array of two elements as "first (last)".
@@ -90,7 +100,12 @@ target="#{target}">)
 
       # Is the given value a tuple? (array of length two).
       def tuple?(data)
-        return true if data.is_a?(Array) && data.length == 2
+        data.is_a?(Array) && data.length == 2
+      end
+
+      def float?(data)
+        data.is_a?(Float) ||
+          (data.is_a?(String) && data =~ /(\d+\.\d+)e?([+-]\d+)?/)
       end
     end
 

data/lib/sequenceserver/version.rb

@@ -1,4 +1,4 @@
 # Define version number.
 module SequenceServer
-  VERSION = '1.0.2'
+  VERSION = '1.0.3'
 end

data/views/result.erb

@@ -48,8 +48,8 @@
                 <tr>
                   <td class="text-left"><%= h + 1 %>.</td>
                   <td> <a href="<%="#Query_#{query.number}_hit_#{hit.number}"%>"><%= "#{hit.id}" %></a> </td>
-                  <td class="text-right"><%= prettify_float hit.score  %></td>
-                  <td class="text-right"><%= prettify_float hit.evalue %></td>
+                  <td class="text-right"><%= prettify hit.score  %></td>
+                  <td class="text-right"><%= prettify hit.evalue %></td>
                 </tr>
               <% end %>
               </tbody>

data/views/search.erb

@@ -285,8 +285,13 @@
             "Custom BLAST web interface by SequenceServer.",
             "SequenceServer: Local BLAST with bespoke html interface.",
             "Set up custom BLAST interface with SequenceServer.",
-            "Easy BLASTing with SequenceServer."
-          ][rand(4)]
+            "Easy BLASTing with SequenceServer.",
+            "Run BLAST locally with Sequenceserver.",
+            "BLAST against a custom, local database with SequenceServer.",
+            "Run BLAST locally on Mac OSX with SequenceServer.",
+            "Run BLAST locally on Ubuntu with SequenceServer.",
+            "Run BLAST locally on Linux with SequenceServer."
+          ][rand(9)]
         %>
       </a>
       <a

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: sequenceserver
 version: !ruby/object:Gem::Version
-  version: 1.0.2
+  version: 1.0.3
 platform: ruby
 authors:
 - Anurag Priyam
@@ -11,7 +11,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-03-23 00:00:00.000000000 Z
+date: 2015-05-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: sinatra