quorum 0.7.1 → 0.8.0

data/.rspec

@@ -1 +1,2 @@
 --colour
+--profile

data/.travis.yml

@@ -5,6 +5,9 @@ rvm:
 gemfile:
   - gemfiles/Gemfile.rails-3.1.x
   - gemfiles/Gemfile.rails-3.2.x
+env:
+  - DB=mysql
+  - DB=postgresql
 before_install:
   - sudo apt-get update
   - sudo apt-get install ncbi-blast+ emboss
@@ -12,7 +15,8 @@ before_script:
   - "export DISPLAY=:99.0"
   - "sh -e /etc/init.d/xvfb start"
   - bundle install
-  - mysql -e "create database quorum_test;"
+  - sh -c "if [ '$DB' = 'mysql' ]; then mysql -e 'create database quorum_test;'; fi"
+  - sh -c "if [ '$DB' = 'postgresql' ]; then psql -c 'create database quorum_test;' -U postgres; fi"
 script: "rake travis:spec"
 notifications:
   email:

data/Gemfile

@@ -2,6 +2,8 @@ source "http://rubygems.org"
 
 gemspec
 
-group :test do
-  gem 'rake', '~> 0.9.2'
+group :development, :test do
+  gem 'rake', '~> 10.0.0'
+  gem 'thin'
+  gem 'debugger'
 end

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    quorum (0.7.1)
+    quorum (0.8.0)
       bio-blastxmlparser (~> 1.1.0)
       jquery-rails
       net-ssh (~> 2.3.0)
@@ -12,34 +12,33 @@ PATH
 GEM
   remote: http://rubygems.org/
   specs:
-    actionmailer (3.2.8)
-      actionpack (= 3.2.8)
+    actionmailer (3.2.9)
+      actionpack (= 3.2.9)
       mail (~> 2.4.4)
-    actionpack (3.2.8)
-      activemodel (= 3.2.8)
-      activesupport (= 3.2.8)
+    actionpack (3.2.9)
+      activemodel (= 3.2.9)
+      activesupport (= 3.2.9)
       builder (~> 3.0.0)
       erubis (~> 2.7.0)
       journey (~> 1.0.4)
       rack (~> 1.4.0)
       rack-cache (~> 1.2)
       rack-test (~> 0.6.1)
-      sprockets (~> 2.1.3)
-    activemodel (3.2.8)
-      activesupport (= 3.2.8)
+      sprockets (~> 2.2.1)
+    activemodel (3.2.9)
+      activesupport (= 3.2.9)
       builder (~> 3.0.0)
-    activerecord (3.2.8)
-      activemodel (= 3.2.8)
-      activesupport (= 3.2.8)
+    activerecord (3.2.9)
+      activemodel (= 3.2.9)
+      activesupport (= 3.2.9)
       arel (~> 3.0.2)
       tzinfo (~> 0.3.29)
-    activeresource (3.2.8)
-      activemodel (= 3.2.8)
-      activesupport (= 3.2.8)
-    activesupport (3.2.8)
+    activeresource (3.2.9)
+      activemodel (= 3.2.9)
+      activesupport (= 3.2.9)
+    activesupport (3.2.9)
       i18n (~> 0.6)
       multi_json (~> 1.0)
-    addressable (2.3.2)
     arel (3.0.2)
     bio-blastxmlparser (1.1.0)
       bio-logger (>= 1.0.0)
@@ -56,10 +55,20 @@ GEM
       xpath (~> 0.1.4)
     childprocess (0.3.6)
       ffi (~> 1.0, >= 1.0.6)
+    columnize (0.3.6)
+    daemons (1.1.9)
     database_cleaner (0.9.1)
+    debugger (1.2.2)
+      columnize (>= 0.3.1)
+      debugger-linecache (~> 1.1.1)
+      debugger-ruby_core_source (~> 1.1.5)
+    debugger-linecache (1.1.2)
+      debugger-ruby_core_source (>= 1.1.1)
+    debugger-ruby_core_source (1.1.5)
     diff-lcs (1.1.3)
     erubis (2.7.0)
-    ffi (1.1.5)
+    eventmachine (1.0.0)
+    ffi (1.2.0)
     hike (1.2.1)
     i18n (0.6.1)
     jasmine (1.2.1)
@@ -67,14 +76,14 @@ GEM
       rack (~> 1.0)
       rspec (>= 1.3.1)
       selenium-webdriver (>= 0.1.3)
-    jasmine-core (1.2.0)
+    jasmine-core (1.3.0)
     journey (1.0.4)
-    jquery-rails (2.1.3)
-      railties (>= 3.1.0, < 5.0)
-      thor (~> 0.14)
+    jquery-rails (2.1.4)
+      railties (>= 3.0, < 5.0)
+      thor (>= 0.14, < 2.0)
     json (1.7.5)
-    libwebsocket (0.1.5)
-      addressable
+    libwebsocket (0.1.6.1)
+      websocket
     log4r (1.1.10)
     mail (2.4.4)
       i18n (>= 0.4.0)
@@ -85,6 +94,7 @@ GEM
     mysql2 (0.3.11)
     net-ssh (2.3.0)
     nokogiri (1.5.5)
+    pg (0.14.1)
     polyglot (0.3.3)
     rack (1.4.1)
     rack-cache (1.2)
@@ -95,22 +105,22 @@ GEM
       rack
     rack-test (0.6.2)
       rack (>= 1.0)
-    rails (3.2.8)
-      actionmailer (= 3.2.8)
-      actionpack (= 3.2.8)
-      activerecord (= 3.2.8)
-      activeresource (= 3.2.8)
-      activesupport (= 3.2.8)
+    rails (3.2.9)
+      actionmailer (= 3.2.9)
+      actionpack (= 3.2.9)
+      activerecord (= 3.2.9)
+      activeresource (= 3.2.9)
+      activesupport (= 3.2.9)
       bundler (~> 1.0)
-      railties (= 3.2.8)
-    railties (3.2.8)
-      actionpack (= 3.2.8)
-      activesupport (= 3.2.8)
+      railties (= 3.2.9)
+    railties (3.2.9)
+      actionpack (= 3.2.9)
+      activesupport (= 3.2.9)
       rack-ssl (~> 1.3.2)
       rake (>= 0.8.7)
       rdoc (~> 3.4)
       thor (>= 0.14.6, < 2.0)
-    rake (0.9.2.2)
+    rake (10.0.2)
     rdoc (3.12)
       json (~> 1.4)
     redis (2.2.2)
@@ -126,22 +136,24 @@ GEM
     resque-result (1.0.1)
       resque (~> 1.9)
       resque-meta (~> 1.0)
-    resque_spec (0.12.5)
+    resque_spec (0.12.6)
       resque (>= 1.19.0)
       rspec (>= 2.5.0)
-    rspec (2.11.0)
-      rspec-core (~> 2.11.0)
-      rspec-expectations (~> 2.11.0)
-      rspec-mocks (~> 2.11.0)
-    rspec-core (2.11.1)
-    rspec-expectations (2.11.3)
+    rspec (2.12.0)
+      rspec-core (~> 2.12.0)
+      rspec-expectations (~> 2.12.0)
+      rspec-mocks (~> 2.12.0)
+    rspec-core (2.12.0)
+    rspec-expectations (2.12.0)
       diff-lcs (~> 1.1.3)
-    rspec-mocks (2.11.3)
-    rspec-rails (2.11.4)
+    rspec-mocks (2.12.0)
+    rspec-rails (2.12.0)
       actionpack (>= 3.0)
       activesupport (>= 3.0)
       railties (>= 3.0)
-      rspec (~> 2.11.0)
+      rspec-core (~> 2.12.0)
+      rspec-expectations (~> 2.12.0)
+      rspec-mocks (~> 2.12.0)
     rubyzip (0.9.9)
     selenium-webdriver (2.26.0)
       childprocess (>= 0.2.5)
@@ -152,10 +164,15 @@ GEM
       rack (~> 1.3, >= 1.3.6)
       rack-protection (~> 1.2)
       tilt (~> 1.3, >= 1.3.3)
-    sprockets (2.1.3)
+    sprockets (2.2.2)
       hike (~> 1.2)
+      multi_json (~> 1.0)
       rack (~> 1.0)
       tilt (~> 1.1, != 1.3.0)
+    thin (1.5.0)
+      daemons (>= 1.0.9)
+      eventmachine (>= 0.12.6)
+      rack (>= 1.0.0)
     thor (0.16.0)
     tilt (1.3.3)
     treetop (1.4.12)
@@ -164,6 +181,7 @@ GEM
     tzinfo (0.3.35)
     vegas (0.1.11)
       rack (>= 1.0.0)
+    websocket (1.0.4)
     xpath (0.1.4)
       nokogiri (~> 1.3)
 
@@ -173,9 +191,12 @@ PLATFORMS
 DEPENDENCIES
   capybara (~> 1.1)
   database_cleaner (~> 0.8)
+  debugger
   jasmine (~> 1.2)
   mysql2 (~> 0.3.11)
+  pg (~> 0.14.1)
   quorum!
-  rake (~> 0.9.2)
+  rake (~> 10.0.0)
   resque_spec (~> 0.12)
   rspec-rails (~> 2.11)
+  thin

data/HISTORY.md

@@ -1,3 +1,12 @@
+## 0.8.0 (2012-11-30)
+
+* Major refactoring and bug fixes.
+* Merged feature branch data_export. Search results are available as .txt (tab
+  delimited), .gff (GFF3) and JSONi (default).
+* Shortened search url to /quorum/jobs/:id/search?algo=[ie: blastn]
+* Search returns [{ enqueued: false }] if algorithm was not enqueued.
+* Upgrading? Install migrations and run generators.
+
 ## 0.7.1 (2012-11-07)
 
 * Added quorum:delete_jobs rake task.

data/README.rdoc

@@ -1,4 +1,4 @@
-= Quorum {<img src="https://secure.travis-ci.org/ncgr/quorum.png?branch=master"alt="Build Status" />}[http://travis-ci.org/ncgr/quorum]
+= Quorum {<img src="https://secure.travis-ci.org/ncgr/quorum.png?branch=master" alt="Build Status" />}[http://travis-ci.org/ncgr/quorum]
 
 A flexible bioinformatics search tool.
 

data/app/assets/javascripts/quorum/quorum.js

@@ -18,7 +18,7 @@ QUORUM.algorithms = ["blastn", "blastx", "tblastn", "blastp"];
 QUORUM.pollResults = function(callback, callback_obj, interval, algos) {
 
   var self = this,
-      url = document.URL + '/get_quorum_search_results.json',
+      url = document.URL + '/search',
       interval = interval || 5000,
       algos = algos || self.algorithms,
       error = false,
@@ -97,7 +97,7 @@ QUORUM.pollResults = function(callback, callback_obj, interval, algos) {
 QUORUM.viewDetailedReport = function(focus_id, query, algo) {
 
   var self = this,
-      url = document.URL + '/get_quorum_search_results.json';
+      url = document.URL + '/search';
 
   // Create the modal box.
   $('#detailed_report_dialog').html(
@@ -327,7 +327,7 @@ QUORUM.displayHspLinks = function(focus, group, data) {
 QUORUM.downloadSequence = function(algo_id, algo, el) {
 
   var self = this,
-      url = document.URL + '/get_quorum_blast_hit_sequence.json';
+      url = document.URL + '/get_blast_hit_sequence';
 
   $(el).html('Fetching sequence...');
 
@@ -357,7 +357,7 @@ QUORUM.downloadSequence = function(algo_id, algo, el) {
 QUORUM.getSequenceFile = function(meta_id, el) {
 
   var self = this,
-      url = document.URL + '/send_quorum_blast_hit_sequence?meta_id=' + meta_id,
+      url = document.URL + '/send_blast_hit_sequence?meta_id=' + meta_id,
       timeoutId = 0;
 
   function downloadFile(data) {

data/app/controllers/quorum/application_controller.rb

@@ -1,5 +1,6 @@
 module Quorum
   class ApplicationController < ActionController::Base
     include Quorum::Helpers
+    include Quorum::Sequence::SendSequence
   end
 end

data/app/controllers/quorum/jobs_controller.rb

@@ -1,7 +1,7 @@
 module Quorum
   class JobsController < ApplicationController
 
-    respond_to :html, :json
+    respond_to :html, :json, :gff, :txt
     before_filter :set_blast_dbs, :only => [:new, :create]
 
     def index
@@ -9,31 +9,16 @@ module Quorum
     end
 
     def new
-      @job = Job.new
-      @job.build_blastn_job
-      @job.build_blastx_job
-      @job.build_tblastn_job
-      @job.build_blastp_job
+      build_blast_jobs
     end
 
     def create
-      if params[:job][:sequence_file]
-        file = params[:job][:sequence_file].read
-        params[:job].delete(:sequence_file)
-      end
-
+      read_sequence_file
       @job = Job.new(params[:job])
-
-      if file
-        @job.sequence = ""
-        @job.sequence << file
-      end
+      set_sequence
 
       unless @job.save
-        @job.build_blastn_job  if @job.blastn_job.nil?
-        @job.build_blastx_job  if @job.blastx_job.nil?
-        @job.build_tblastn_job if @job.tblastn_job.nil?
-        @job.build_blastp_job  if @job.blastp_job.nil?
+        build_blast_jobs
         render :action => "new"
         return
       end
@@ -50,56 +35,36 @@ module Quorum
     end
 
     #
-    # Returns Resque worker results.
-    #
-    def get_quorum_search_results
-      json = [{ :results => false }].to_json
-
-      if Quorum::BLAST_ALGORITHMS.include?(params[:algo])
-        queued = "#{params[:algo]}_job".to_sym
-        report = "#{params[:algo]}_job_reports".to_sym
-
-        begin
-          job = Job.find(params[:id])
-        rescue ActiveRecord::RecordNotFound => e
-          json
-        else
-          if job.method(queued).call.present?
-            if job.method(report).call.present?
-              if params[:query]
-                json = job.method(report).call.by_query(params[:query]).default_order
-              else
-                json = job.method(report).call.default_order
-              end
-            else
-              json = []
-            end
-          end
-        end
+    # Returns Quorum's search results.
+    #
+    # This method should be used to gather Resque worker results, or user
+    # supplied query params.
+    #
+    def search
+      data = Job.search(params)
+
+      # Respond with :json, :txt (tab delimited Blast results), or GFF3.
+      respond_with data.flatten!(1) do |format|
+        format.json {
+          render :json => Quorum::JobSerializer.as_json(data)
+        }
+        format.gff {
+          render :text => Quorum::JobSerializer.as_gff(data)
+        }
+        format.txt {
+          render :text => Quorum::JobSerializer.as_txt(data)
+        }
       end
-
-      respond_with json
     end
 
     #
-    # Find hit sequence, queue worker and return worker meta_id
-    # for lookup.
-    #
-    def get_quorum_blast_hit_sequence
-      if Quorum::BLAST_ALGORITHMS.include?(params[:algo])
-        begin
-          job = Job.find(params[:id])
-        rescue ActiveRecord::RecordNotFound => e
-          logger.error e.message
-        else
-          data = job.fetch_quorum_blast_sequence(
-            params[:algo], params[:algo_id]
-          )
-          json = [{ :meta_id => data.meta_id }]
-        end
-      end
-
-      respond_with json || []
+    # Find hit sequence and return worker meta_id for lookup. If the method
+    # returns [], try again.
+    #
+    def get_blast_hit_sequence
+      fetch_data = Job.set_blast_hit_sequence_lookup_values(params)
+      data       = Quorum::JobQueueService.queue_fetch_worker(fetch_data)
+      respond_with data || []
     end
 
     #
@@ -108,25 +73,24 @@ module Quorum
     #
     # See lib/generators/templates/blast_db.rb for more info.
     #
-    def send_quorum_blast_hit_sequence
+    def send_blast_hit_sequence
       data = Workers::System.get_meta(params[:meta_id])
-      if data.succeeded?
-        if data.result.downcase.include?("error")
-          render :text => data.result
-          return
-        else
-          send_data data.result,
-            :filename    => "#{params[:meta_id]}.fa",
-            :type        => "text/plain",
-            :disposition => "attachment"
-          return
-        end
-      end
-      render :text => ""
+      sequence(data)
     end
 
     private
 
+    #
+    # Create new Job and build associations.
+    #
+    def build_blast_jobs
+      @job ||= Job.new
+      @job.build_blastn_job  if @job.blastn_job.nil?
+      @job.build_blastx_job  if @job.blastx_job.nil?
+      @job.build_tblastn_job if @job.tblastn_job.nil?
+      @job.build_blastp_job  if @job.blastp_job.nil?
+    end
+
     #
     # Blast Database options for select.
     #
@@ -139,5 +103,26 @@ module Quorum
       }
     end
 
+    #
+    # Read and remove uploaded sequence file from params.
+    #
+    def read_sequence_file
+      if params[:job][:sequence_file]
+        @file = params[:job][:sequence_file].read
+        params[:job].delete(:sequence_file)
+      end
+    end
+
+    #
+    # Set uploaded sequence file.
+    #
+    def set_sequence
+      if @file
+        @job.sequence = ""
+        @job.sequence << @file
+      end
+      @file = nil
+    end
+
   end
 end

data/app/models/quorum/blastn_job.rb

@@ -17,7 +17,7 @@ module Quorum
       :blast_dbs
 
     validates_format_of :expectation,
-      :with        => /^[+-]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$/,
+      :with        => /\A[+-]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?\z/,
       :message     => " - Valid formats (12, 32.05, 43e-123)",
       :allow_blank => true
     validates_numericality_of :max_target_seqs,

data/app/models/quorum/blastn_job_report.rb

@@ -1,7 +1,10 @@
 module Quorum
   class BlastnJobReport < ActiveRecord::Base
+
+    extend Quorum::JobReportSearcher
+
     belongs_to :blastn_job
     scope :default_order, order("query ASC, bit_score DESC")
-    scope :by_query, lambda { |query| where("query = ?", query) }
+
   end
 end

data/app/models/quorum/blastp_job.rb

@@ -17,7 +17,7 @@ module Quorum
       :blast_dbs
 
     validates_format_of :expectation,
-      :with        => /^[+-]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$/,
+      :with        => /\A[+-]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?\z/,
       :message     => " - Valid formats (12, 32.05, 43e-123)",
       :allow_blank => true
     validates_numericality_of :max_target_seqs,

data/app/models/quorum/blastp_job_report.rb

@@ -1,7 +1,10 @@
 module Quorum
   class BlastpJobReport < ActiveRecord::Base
+
+    extend Quorum::JobReportSearcher
+
     belongs_to :blastp_job
     scope :default_order, order("query ASC, bit_score DESC")
-    scope :by_query, lambda { |query| where("query = ?", query) }
+
   end
 end

data/app/models/quorum/blastx_job.rb

@@ -17,7 +17,7 @@ module Quorum
       :blast_dbs
 
     validates_format_of :expectation,
-      :with        => /^[+-]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$/,
+      :with        => /\A[+-]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?\z/,
       :message     => " - Valid formats (12, 32.05, 43e-123)",
       :allow_blank => true
     validates_numericality_of :max_target_seqs,

data/app/models/quorum/blastx_job_report.rb

@@ -1,7 +1,10 @@
 module Quorum
   class BlastxJobReport < ActiveRecord::Base
+
+    extend Quorum::JobReportSearcher
+
     belongs_to :blastx_job
     scope :default_order, order("query ASC, bit_score DESC")
-    scope :by_query, lambda { |query| where("query = ?", query) }
+
   end
 end