quorum 0.6.0 → 0.7.0

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    quorum (0.6.0)
+    quorum (0.7.0)
       bio-blastxmlparser (~> 1.1.0)
       jquery-rails
       net-ssh (~> 2.3.0)
@@ -69,7 +69,7 @@ GEM
       selenium-webdriver (>= 0.1.3)
     jasmine-core (1.2.0)
     journey (1.0.4)
-    jquery-rails (2.1.2)
+    jquery-rails (2.1.3)
       railties (>= 3.1.0, < 5.0)
       thor (~> 0.14)
     json (1.7.5)
@@ -93,7 +93,7 @@ GEM
       rack
     rack-ssl (1.3.2)
       rack
-    rack-test (0.6.1)
+    rack-test (0.6.2)
       rack (>= 1.0)
     rails (3.2.8)
       actionmailer (= 3.2.8)

data/HISTORY.md

@@ -1,3 +1,9 @@
+## 0.7.0 (2012-10-02)
+
+* Fixed empty blast report bug. https://github.com/ncgr/quorum/issues/6
+* Added max_sequence_size to quorum_settings.yml to allow user to specify
+  max input sequence size in bytes. Defaults to 50 KB.
+
 ## 0.6.0 (2012-09-21)
 
 * Renamed blast report max_score to max_target_seqs to match NCBI Blast

data/app/models/quorum/job.rb

@@ -31,7 +31,7 @@ module Quorum
 
     validates_associated :blastn_job, :blastx_job, :tblastn_job, :blastp_job
 
-    validate :filter_input_sequences, :algorithm_selected
+    validate :filter_input_sequences, :algorithm_selected, :sequence_size
 
     #
     # Fetch Blast hit_id, hit_display_id, queue Resque worker and
@@ -136,6 +136,21 @@ module Quorum
       end
     end
 
+    #
+    # Validate input sequence size.
+    #
+    # Defaults to 50 KB. See lib/quorum.rb.
+    #
+    def sequence_size
+      if self.sequence.size > Quorum.max_sequence_size
+        errors.add(
+          :sequence,
+          " - Input sequence size too large. " <<
+          "Max size: #{Quorum.max_sequence_size / 1024} KB"
+        )
+      end
+    end
+
     #
     # Queue Resque workers.
     #

data/lib/generators/templates/blast.rb

@@ -318,12 +318,7 @@ module Quorum
             @tmp_files
           )
         end
-        @logger.log(
-          "NCBI Blast",
-          "#{@algorithm} report empty.",
-          0,
-          @tmp_files
-        )
+        @logger.log("NCBI Blast", "#{@algorithm} report empty.")
       end
 
       #

data/lib/generators/templates/quorum_initializer.rb

@@ -10,13 +10,22 @@ settings = YAML.load_file(
 
 ## Sub %{RAILS_ROOT} ##
 settings.keys.each do |k|
-  settings[k.to_s].each_value do |v|
-    if v.kind_of?(String)
-      v.to_s.gsub!('%{RAILS_ROOT}', ::Rails.root.to_s)
+  if settings[k.to_s].respond_to?(:each_value)
+    settings[k.to_s].each_value do |v|
+      if v.kind_of?(String)
+        v.to_s.gsub!('%{RAILS_ROOT}', ::Rails.root.to_s)
+      end
+    end
+  else
+    if settings[k.to_s].kind_of?(String)
+      settings[k.to_s].gsub!('%{RAILS_ROOT}', ::Rails.root.to_s)
     end
   end
 end
 
+## Quorum General Settings ##
+Quorum.max_sequence_size = settings['max_sequence_size']
+
 blast = settings['blast']
 
 ## Quorum Blast Settings ##
@@ -33,4 +42,3 @@ Quorum.blastp            = blast['blastp']
 Quorum.blastn            = blast['blastn']
 Quorum.blastx            = blast['blastx']
 Quorum.blast_threads     = blast['blast_threads']
-

data/lib/generators/templates/quorum_settings.yml

@@ -3,6 +3,9 @@
 # ==> General
 # Quorum initializer safely substitutes %{RAILS_ROOT} with ::Rails.root.to_s.
 #
+# max_sequence_size: Max input sequence size in bytes.
+#   Defaults to 51200 (50 KB).
+#
 # ==> NCBI BLAST+ Settings
 # blast:
 #   remote: true to execute script on remote machine via
@@ -64,6 +67,7 @@
 #     Defaults to 1.
 
 development:
+  max_sequence_size:
   blast:
     remote: false
     ssh_host:
@@ -95,6 +99,7 @@ development:
     blast_threads:
 
 test:
+  max_sequence_size:
   blast:
     remote: false
     ssh_host:
@@ -126,6 +131,7 @@ test:
     blast_threads:
 
 production:
+  max_sequence_size:
   blast:
     remote: true
     ssh_host:

data/lib/quorum/version.rb

@@ -1,3 +1,3 @@
 module Quorum
-  VERSION = "0.6.0"
+  VERSION = "0.7.0"
 end

data/lib/quorum.rb

@@ -11,17 +11,25 @@ require "workers/quorum"
 module Quorum
 
   ## Supported Algorithms ##
-  BLAST_ALGORITHMS = ["blastn", "blastx", "blastp", "tblastn"]
+  BLAST_ALGORITHMS = ["blastn", "blastx", "blastp", "tblastn"].freeze
 
-  mattr_accessor :blast_remote, :blast_ssh_host, :blast_ssh_user,
-    :blast_ssh_options, :blast_bin, :blast_log_dir, :blast_tmp_dir,
-    :blast_db, :tblastn, :blastp, :blastn, :blastx, :blast_threads
+  mattr_accessor :max_sequence_size, :blast_remote, :blast_ssh_host,
+                 :blast_ssh_user, :blast_ssh_options, :blast_bin,
+                 :blast_log_dir, :blast_tmp_dir, :blast_db, :tblastn,
+                 :blastp, :blastn, :blastx, :blast_threads
 
   ## Deprecated ##
   mattr_accessor :blast_script
 
   class << self
 
+    ## General ##
+
+    # Max input sequence size.
+    def max_sequence_size
+      @@max_sequence_size || 50.kilobytes
+    end
+
     ## Blast ##
 
     # Execute remotely.

data/spec/config/quorum_settings.yml

@@ -1,4 +1,5 @@
 development:
+  max_sequence_size:
   blast:
     remote: false
     ssh_host:
@@ -19,6 +20,7 @@ development:
     blast_threads: 4
 
 test:
+  max_sequence_size:
   blast:
     remote: false
     ssh_host:
@@ -39,6 +41,7 @@ test:
     blast_threads:
 
 production:
+  max_sequence_size:
   blast:
     remote: true
     ssh_host:

data/spec/models/job_spec.rb

@@ -12,6 +12,22 @@ describe Quorum::Job do
     @job.should have(1).error_on(:algorithm)
   end
 
+  it "fails validation when input sequence size is too large" do
+    @job.sequence = ">header\n" << "a" * 51200
+    @job.build_blastn_job
+    @job.blastn_job.queue = true
+    @job.should have(1).errors_on(:sequence)
+  end
+
+  it "fails validation with invalid sequence data" do
+    @job.sequence = File.open(
+      File.expand_path("../../data/seqs_not_fa.txt", __FILE__)
+    ).read
+    @job.build_blastn_job
+    @job.blastn_job.queue = true
+    @job.should have(1).errors_on(:sequence)
+  end
+
   it "passes validation with algorithm and valid sequence data" do
     @job.sequence = File.open(
       File.expand_path("../../data/nucl_prot_seqs.txt", __FILE__)

data/spec/templates/blast_spec.rb

@@ -149,7 +149,7 @@ describe "Quorum::SearchTools::Blast" do
       blast = Quorum::SearchTools::Blast.new(@args)
       expect {
         blast.execute_blast
-      }.to raise_error
+      }.to_not raise_error
 
       Dir.glob(
         File.join(@args[:tmp_directory], "*")

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: quorum
 version: !ruby/object:Gem::Version
-  version: 0.6.0
+  version: 0.7.0
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-09-21 00:00:00.000000000 Z
+date: 2012-10-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -402,7 +402,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -238619027488195291
+      hash: 376462079150931508
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -411,7 +411,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -238619027488195291
+      hash: 376462079150931508
 requirements: []
 rubyforge_project: 
 rubygems_version: 1.8.24