Refactoring

* Removed lib/quorum/data_export.rb - replaced by job_serializer.rb
* Added Quorum::JobData object for data export.
* Added Quorum::JobQueueObserver and Service.
* Fixed rake task bug.
* Shortened job query urls.
* Disabled all observers in specs. Enable when needed.
* Created JobFetchData object to contain fetch blast sequence data.
* Moved send blast sequence to sequence module.
* Update README.rdoc
* Updated *.js and specs for refactoring.

Renamed routes.

* Renamed job controller route search_results => search.
* Added default format values for json results.
* Updated js ajax calls.

Added LSS information to comments in show view.

Print "Not enqueued" if algorithm wasn't enqueued.

Removed deprecated attributes.

.rspec

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

Gemfile

@@ -3,5 +3,5 @@ source "http://rubygems.org"
 gemspec
 
 group :test do
-  gem 'rake', '~> 0.9.2'
+  gem 'rake', '~> 10.0.0'
 end

README.rdoc

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

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) {

app/controllers/quorum/application_controller.rb

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

app/controllers/quorum/jobs_controller.rb

@@ -9,31 +9,16 @@ def index
     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
@@ -55,76 +40,31 @@ def show
     # This method should be used to gather Resque worker results, or user
     # supplied query params.
     #
-    def get_quorum_search_results
-      empty        = [{ :results => false }]
-      not_enqueued = { :enqueued => false }.merge(empty[0])
-      data         = []
-
-      # Allow for multiple algos and search params.
-      # Ex: /quorum/jobs/:id/get_quorum_search_results.json?algo=blastn,blastp
-      if params[:algo]
-        params[:algo].split(",").each do |a|
-          if Quorum::BLAST_ALGORITHMS.include?(a)
-            queued = "#{a}_job".to_sym
-            report = "#{a}_job_reports".to_sym
-
-            begin
-              job = Job.find(params[:id])
-            rescue ActiveRecord::RecordNotFound => e
-              logger.error e.message
-            else
-              if job.method(queued).call.present?
-                if job.method(report).call.present?
-                  data << job.method(report).call.search(params).default_order
-                else
-                  data = []
-                end
-              else
-                data << not_enqueued
-              end
-            end
-          end
-        end
-      else
-        data << empty
-      end
-
-      # Flatten the array of arrays if necessary.
-      data.flatten!(1)
+    def search
+      data = Job.search(params)
 
       # Respond with :json, :txt (tab delimited Blast results), or GFF3.
-      respond_with data do |format|
+      respond_with data.flatten!(1) do |format|
         format.json {
-          render :json => data
+          render :json => Quorum::JobSerializer.as_json(data)
         }
         format.gff {
-          render :text => to_gff(data)
+          render :text => Quorum::JobSerializer.as_gff(data)
         }
         format.txt {
-          render :text => to_txt(data)
+          render :text => Quorum::JobSerializer.as_txt(data)
         }
       end
     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
 
     #
@@ -133,25 +73,24 @@ def get_quorum_blast_hit_sequence
     #
     # 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.
     #
@@ -164,5 +103,26 @@ def set_blast_dbs
       }
     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

app/models/quorum/job.rb

@@ -3,8 +3,6 @@ class Job < ActiveRecord::Base
 
     include Quorum::Sequence
 
-    after_save :queue_workers
-
     has_one :blastn_job, :dependent => :destroy
     has_many :blastn_job_reports, :through => :blastn_job,
       :dependent => :destroy
@@ -34,33 +32,72 @@ class Job < ActiveRecord::Base
     validate :filter_input_sequences, :algorithm_selected, :sequence_size
 
     #
-    # Fetch Blast hit_id, hit_display_id, queue Resque worker and
-    # return worker's meta_id.
+    # Return search results (Resque worker results).
     #
-    def fetch_quorum_blast_sequence(algo, algo_id)
-      job         = "#{algo}_job".to_sym
-      job_reports = "#{algo}_job_reports".to_sym
-
-      blast_dbs = self.method(job).call.blast_dbs
-
-      job_report = self.method(job_reports).call.where(
-        "quorum_#{algo}_job_reports.id = ?", algo_id
-      ).first
-
-      hit_id          = job_report.hit_id
-      hit_display_id  = job_report.hit_display_id
-
-      cmd = Workers::System.create_blast_fetch_command(
-        blast_dbs, hit_id, hit_display_id, algo
-      )
+    def self.search(params)
+      data = JobData.new
+
+      # Allow for multiple algos and search params.
+      # Ex: /quorum/jobs/:id/search?algo=blastn,blastp
+      if params[:algo]
+        params[:algo].split(",").each do |a|
+          if Quorum::BLAST_ALGORITHMS.include?(a)
+            enqueued = "#{a}_job".to_sym
+            report   = "#{a}_job_reports".to_sym
+            begin
+              job = Job.find(params[:id])
+            rescue ActiveRecord::RecordNotFound => e
+              logger.error e.message
+            else
+              if job.try(enqueued).present?
+                if job.try(report).present?
+                  data.results << job.try(report).search(params).default_order
+                else
+                  data = JobData.new
+                end
+              else
+                data.not_enqueued
+              end
+            end
+          end
+        end
+      else
+        data.no_results
+      end
 
-      data = Workers::System.enqueue(
-        cmd, Quorum.blast_remote,
-        Quorum.blast_ssh_host, Quorum.blast_ssh_user,
-        Quorum.blast_ssh_options, true
-      )
+      data.results
+    end
 
-      Workers::System.get_meta(data.meta_id)
+    #
+    # Fetch Blast hit_id, hit_display_id, queue Resque worker and
+    # return worker's meta_id.
+    #
+    def self.set_blast_hit_sequence_lookup_values(params)
+      fetch_data   = JobFetchData.new
+      algo         = params[:algo]
+      algo_id      = params[:algo_id]
+
+      if Quorum::BLAST_ALGORITHMS.include?(algo)
+        fetch_data.algo = algo
+        begin
+          job = Job.find(params[:id])
+        rescue ActiveRecord::RecordNotFound => e
+          logger.error e.message
+        else
+          algo_job         = "#{algo}_job".to_sym
+          algo_job_reports = "#{algo}_job_reports".to_sym
+
+          fetch_data.blast_dbs = job.try(algo_job).blast_dbs
+
+          job_report = job.try(algo_job_reports).where(
+            "quorum_#{algo}_job_reports.id = ?", algo_id
+          ).first
+
+          fetch_data.hit_id          = job_report.hit_id
+          fetch_data.hit_display_id  = job_report.hit_display_id
+        end
+      end
+      fetch_data
     end
 
     #
@@ -164,34 +201,5 @@ def sequence_size
       end
     end
 
-    #
-    # Queue Resque workers.
-    #
-    def queue_workers
-      jobs = []
-      if self.blastn_job && self.blastn_job.queue
-        jobs << Workers::System.create_search_command("blastn", self.id)
-      end
-      if self.blastx_job && self.blastx_job.queue
-        jobs << Workers::System.create_search_command("blastx", self.id)
-      end
-      if self.tblastn_job && self.tblastn_job.queue
-        jobs << Workers::System.create_search_command("tblastn", self.id)
-      end
-      if self.blastp_job && self.blastp_job.queue
-        jobs << Workers::System.create_search_command("blastp", self.id)
-      end
-
-      unless jobs.blank?
-        jobs.each do |j|
-          Workers::System.enqueue(
-            j, Quorum.blast_remote,
-            Quorum.blast_ssh_host, Quorum.blast_ssh_user,
-            Quorum.blast_ssh_options
-          )
-        end
-      end
-    end
-
   end
 end