quorum 0.7.0 → 0.7.1

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    quorum (0.7.0)
+    quorum (0.7.1)
       bio-blastxmlparser (~> 1.1.0)
       jquery-rails
       net-ssh (~> 2.3.0)
@@ -46,17 +46,17 @@ GEM
       nokogiri (>= 1.5.0)
     bio-logger (1.0.1)
       log4r (>= 1.1.9)
-    builder (3.0.3)
-    capybara (1.1.2)
+    builder (3.0.4)
+    capybara (1.1.3)
       mime-types (>= 1.16)
       nokogiri (>= 1.3.3)
       rack (>= 1.0.0)
       rack-test (>= 0.5.4)
       selenium-webdriver (~> 2.0)
       xpath (~> 0.1.4)
-    childprocess (0.3.5)
+    childprocess (0.3.6)
       ffi (~> 1.0, >= 1.0.6)
-    database_cleaner (0.8.0)
+    database_cleaner (0.9.1)
     diff-lcs (1.1.3)
     erubis (2.7.0)
     ffi (1.1.5)
@@ -81,7 +81,7 @@ GEM
       mime-types (~> 1.16)
       treetop (~> 1.4.8)
     mime-types (1.19)
-    multi_json (1.3.6)
+    multi_json (1.3.7)
     mysql2 (0.3.11)
     net-ssh (2.3.0)
     nokogiri (1.5.5)
@@ -126,7 +126,7 @@ GEM
     resque-result (1.0.1)
       resque (~> 1.9)
       resque-meta (~> 1.0)
-    resque_spec (0.12.3)
+    resque_spec (0.12.5)
       resque (>= 1.19.0)
       rspec (>= 2.5.0)
     rspec (2.11.0)
@@ -137,13 +137,13 @@ GEM
     rspec-expectations (2.11.3)
       diff-lcs (~> 1.1.3)
     rspec-mocks (2.11.3)
-    rspec-rails (2.11.0)
+    rspec-rails (2.11.4)
       actionpack (>= 3.0)
       activesupport (>= 3.0)
       railties (>= 3.0)
       rspec (~> 2.11.0)
     rubyzip (0.9.9)
-    selenium-webdriver (2.25.0)
+    selenium-webdriver (2.26.0)
       childprocess (>= 0.2.5)
       libwebsocket (~> 0.1.3)
       multi_json (~> 1.0)
@@ -158,10 +158,10 @@ GEM
       tilt (~> 1.1, != 1.3.0)
     thor (0.16.0)
     tilt (1.3.3)
-    treetop (1.4.10)
+    treetop (1.4.12)
       polyglot
       polyglot (>= 0.3.1)
-    tzinfo (0.3.33)
+    tzinfo (0.3.35)
     vegas (0.1.11)
       rack (>= 1.0.0)
     xpath (0.1.4)

data/HISTORY.md

@@ -1,3 +1,8 @@
+## 0.7.1 (2012-11-07)
+
+* Added quorum:delete_jobs rake task.
+* Bug fixes.
+
 ## 0.7.0 (2012-10-02)
 
 * Fixed empty blast report bug. https://github.com/ncgr/quorum/issues/6

data/README.rdoc

@@ -316,6 +316,9 @@ Override Quorum's views and specify your own JavaScript callback function!
 
 See "app/views/quorum/show.html.erb" for more details.
 
+For an example using d3.js (https://github.com/mbostock/d3) see:
+https://github.com/ncgr/lis_sequence_search
+
 === Redis
 
 For detailed Redis installation instructions, follow the links below.

data/app/controllers/quorum/jobs_controller.rb

@@ -53,9 +53,7 @@ module Quorum
     # Returns Resque worker results.
     #
     def get_quorum_search_results
-      empty = [{ :results => false }].to_json
-
-      json = empty
+      json = [{ :results => false }].to_json
 
       if Quorum::BLAST_ALGORITHMS.include?(params[:algo])
         queued = "#{params[:algo]}_job".to_sym
@@ -64,7 +62,7 @@ module Quorum
         begin
           job = Job.find(params[:id])
         rescue ActiveRecord::RecordNotFound => e
-          json = empty
+          json
         else
           if job.method(queued).call.present?
             if job.method(report).call.present?
@@ -88,8 +86,6 @@ module Quorum
     # for lookup.
     #
     def get_quorum_blast_hit_sequence
-      json = []
-
       if Quorum::BLAST_ALGORITHMS.include?(params[:algo])
         begin
           job = Job.find(params[:id])
@@ -103,7 +99,7 @@ module Quorum
         end
       end
 
-      respond_with json
+      respond_with json || []
     end
 
     #

data/app/models/quorum/job.rb

@@ -38,19 +38,21 @@ module Quorum
     # return worker's meta_id.
     #
     def fetch_quorum_blast_sequence(algo, algo_id)
-      job    = "#{algo}_job".to_sym
-      report = "#{algo}_job_reports".to_sym
+      job         = "#{algo}_job".to_sym
+      job_reports = "#{algo}_job_reports".to_sym
 
       blast_dbs = self.method(job).call.blast_dbs
 
-      job_report = self.method(report).call.where(
+      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 = create_blast_fetch_command(blast_dbs, hit_id, hit_display_id, algo)
+      cmd = Workers::System.create_blast_fetch_command(
+        blast_dbs, hit_id, hit_display_id, algo
+      )
 
       data = Workers::System.enqueue(
         cmd, Quorum.blast_remote,
@@ -61,6 +63,17 @@ module Quorum
       Workers::System.get_meta(data.meta_id)
     end
 
+    #
+    # Delete submitted jobs.
+    #
+    def self.delete_jobs(time = 1.week)
+      if time.is_a?(String)
+        time = time.split.inject { |count, unit| count.to_i.send(unit) }
+      end
+
+      self.where("created_at < '#{time.ago.to_s(:db)}'").destroy_all
+    end
+
     private
 
     #
@@ -157,16 +170,16 @@ module Quorum
     def queue_workers
       jobs = []
       if self.blastn_job && self.blastn_job.queue
-        jobs << create_search_command("blastn")
+        jobs << Workers::System.create_search_command("blastn", self.id)
       end
       if self.blastx_job && self.blastx_job.queue
-        jobs << create_search_command("blastx")
+        jobs << Workers::System.create_search_command("blastx", self.id)
       end
       if self.tblastn_job && self.tblastn_job.queue
-        jobs << create_search_command("tblastn")
+        jobs << Workers::System.create_search_command("tblastn", self.id)
       end
       if self.blastp_job && self.blastp_job.queue
-        jobs << create_search_command("blastp")
+        jobs << Workers::System.create_search_command("blastp", self.id)
       end
 
       unless jobs.blank?
@@ -180,43 +193,5 @@ module Quorum
       end
     end
 
-    #
-    # Create fetch command based on config/quorum_settings.yml
-    #
-    def create_blast_fetch_command(db_names, hit_id, hit_display_id, algo)
-      # System command
-      cmd = ""
-
-      fetch = File.join(Quorum.blast_bin, "fetch")
-      cmd << "#{fetch} -f blastdbcmd -l #{Quorum.blast_log_dir} " <<
-        "-m #{Quorum.blast_tmp_dir} -d #{Quorum.blast_db} " <<
-        "-n '#{db_names}' -b '#{hit_id}' -s '#{hit_display_id}' " <<
-        "-a #{algo}"
-    end
-
-    #
-    # Create search command based on config/quorum_settings.yml
-    #
-    def create_search_command(algorithm)
-      # System command
-      cmd = ""
-
-      if Quorum::BLAST_ALGORITHMS.include?(algorithm)
-        search = File.join(Quorum.blast_bin, "search")
-        cmd << "#{search} -l #{Quorum.blast_log_dir} " <<
-          "-m #{Quorum.blast_tmp_dir} -b #{Quorum.blast_db} " <<
-          "-t #{Quorum.blast_threads} "
-      else
-        return cmd
-      end
-
-      cmd << "-s #{algorithm} -i #{self.id} " <<
-        "-d #{ActiveRecord::Base.configurations[::Rails.env.to_s]['database']} " <<
-        "-a #{ActiveRecord::Base.configurations[::Rails.env.to_s]['adapter']} " <<
-        "-k #{ActiveRecord::Base.configurations[::Rails.env.to_s]['host']} " <<
-        "-u #{ActiveRecord::Base.configurations[::Rails.env.to_s]['username']} " <<
-        "-p '#{ActiveRecord::Base.configurations[::Rails.env.to_s]['password']}' "
-    end
-
   end
 end

data/app/views/quorum/jobs/form/_blastp_form.html.erb

@@ -58,8 +58,8 @@
           <%=
             n.select :gap_opening_extension,
               options_for_select(
-                @job.blastn_job.gap_opening_extension_values,
-                @job.blastn_job.gap_opening_extension
+                @job.blastp_job.gap_opening_extension_values,
+                @job.blastp_job.gap_opening_extension
             )
           %>
         </td>

data/app/views/quorum/jobs/form/_blastx_form.html.erb

@@ -58,8 +58,8 @@
           <%=
             n.select :gap_opening_extension,
               options_for_select(
-                @job.blastn_job.gap_opening_extension_values,
-                @job.blastn_job.gap_opening_extension
+                @job.blastx_job.gap_opening_extension_values,
+                @job.blastx_job.gap_opening_extension
             )
           %>
         </td>

data/app/views/quorum/jobs/form/_tblastn_form.html.erb

@@ -58,8 +58,8 @@
           <%=
             n.select :gap_opening_extension,
               options_for_select(
-                @job.blastn_job.gap_opening_extension_values,
-                @job.blastn_job.gap_opening_extension
+                @job.tblastn_job.gap_opening_extension_values,
+                @job.tblastn_job.gap_opening_extension
             )
           %>
         </td>

data/lib/quorum/version.rb

@@ -1,3 +1,3 @@
 module Quorum
-  VERSION = "0.7.0"
+  VERSION = "0.7.1"
 end

data/lib/quorum.rb

@@ -6,7 +6,7 @@ require "resque"
 require "resque/server"
 require "resque-result"
 require "net/ssh"
-require "workers/quorum"
+require "workers/system"
 
 module Quorum
 

data/lib/tasks/{quorum_tasks.rake → quorum_blastdb_build.rake}

@@ -1,5 +1,5 @@
 #
-# Quourm Rake Tasks
+# Quourm Build Blast DBs
 #
 
 $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), 'blastdb'))

data/lib/tasks/quorum_delete_jobs.rake

@@ -0,0 +1,11 @@
+#
+# Remove submitted jobs
+#
+
+namespace :quorum do
+  desc "Remove submitted jobs (options: TIME=\"6 weeks\" -- Default 1 week)."
+  task :delete_jobs => :environment do
+    time = ENV['TIME'] || '1 week'
+    puts "Jobs deleted: #{Quorum::Job.delete_jobs(time).count}"
+  end
+end

data/lib/workers/system.rb

@@ -0,0 +1,116 @@
+module Workers
+  class System
+
+    extend Resque::Plugins::Result
+
+    @queue = :system_queue
+
+    #
+    # Resque worker method.
+    #
+    def self.perform(meta_id, cmd, remote, ssh_host, ssh_user, ssh_options = {}, stdout = false)
+      @meta_id     = meta_id
+      @cmd         = cmd
+      @remote      = remote
+      @ssh_host    = ssh_host
+      @ssh_user    = ssh_user
+      @ssh_options = ssh_options
+      @stdout      = stdout
+      @exit_status = 1
+      @out         = ""
+
+      self.set_ssh_options
+
+      if remote
+        self.execute_ssh
+      else
+        @out         = `#{@cmd}`
+        @exit_status = $?.exitstatus
+      end
+
+      if @exit_status > 0
+        raise "Worker failed :'(. See quorum/log/quorum.log for more information."
+      end
+
+      @out if stdout
+    end
+
+    #
+    # Convert each key in ssh_options to a symbol.
+    #
+    def self.set_ssh_options
+      unless @ssh_options.empty?
+        @ssh_options = @ssh_options.inject({}) do |memo, (k, v)|
+          memo[k.to_sym] = v
+        memo
+        end
+      end
+    end
+
+    #
+    # Execute command on remote machine.
+    #
+    def self.execute_ssh
+      Net::SSH.start(@ssh_host, @ssh_user, @ssh_options) do |ssh|
+        ssh.open_channel do |ch|
+          ch.exec(cmd) do |ch, success|
+            if success
+              # Capture STDOUT from ch.exec()
+              if @stdout
+                ch.on_data do |ch, data|
+                  @out = data
+                end
+              end
+              # Read the exit status of the remote process.
+              ch.on_request("exit-status") do |ch, data|
+                @exit_status = data.read_long
+              end
+            else
+              Rails.logger.warn "Channel Net::SSH exec() failed. :'("
+            end
+          end
+        end
+        ssh.loop
+      end
+    end
+
+    #
+    # Create fetch command based on config/quorum_settings.yml
+    #
+    def self.create_blast_fetch_command(db_names, hit_id, hit_display_id, algo)
+      # System command
+      cmd = ""
+
+      fetch = File.join(Quorum.blast_bin, "fetch")
+      cmd << "#{fetch} -f blastdbcmd -l #{Quorum.blast_log_dir} " <<
+        "-m #{Quorum.blast_tmp_dir} -d #{Quorum.blast_db} " <<
+        "-n '#{db_names}' -b '#{hit_id}' -s '#{hit_display_id}' " <<
+        "-a #{algo}"
+    end
+
+    #
+    # Create search command based on config/quorum_settings.yml
+    #
+    def self.create_search_command(algo, id)
+      # System command
+      cmd = ""
+
+      if Quorum::BLAST_ALGORITHMS.include?(algo)
+        search = File.join(Quorum.blast_bin, "search")
+        cmd << "#{search} -l #{Quorum.blast_log_dir} " <<
+          "-m #{Quorum.blast_tmp_dir} -b #{Quorum.blast_db} " <<
+          "-t #{Quorum.blast_threads} "
+      else
+        return cmd
+      end
+
+      cmd << "-s #{algo} -i #{id} " <<
+        "-d #{ActiveRecord::Base.configurations[::Rails.env.to_s]['database']} " <<
+        "-a #{ActiveRecord::Base.configurations[::Rails.env.to_s]['adapter']} " <<
+        "-k #{ActiveRecord::Base.configurations[::Rails.env.to_s]['host']} " <<
+        "-u #{ActiveRecord::Base.configurations[::Rails.env.to_s]['username']} " <<
+        "-p '#{ActiveRecord::Base.configurations[::Rails.env.to_s]['password']}' "
+    end
+
+  end
+end

data/spec/models/job_spec.rb

@@ -38,6 +38,24 @@ describe Quorum::Job do
     @job.should have(0).errors_on(:algorithm)
   end
 
+  it "deletes submitted jobs" do
+    1.upto(5) do |i|
+      job = Quorum::Job.new()
+      job.sequence = File.open(
+        File.expand_path("../../data/nucl_prot_seqs.txt", __FILE__)
+      ).read
+
+      job.build_blastn_job
+      job.blastn_job.queue     = true
+      job.blastn_job.blast_dbs = ["test"]
+
+      job.created_at = i.weeks.ago
+      job.save!
+    end
+    Quorum::Job.delete_jobs("25 days").count.should eq(2)
+    Quorum::BlastnJob.count.should eq(3)
+  end
+
   it "queues workers after save" do
     @job.sequence = File.open(
       File.expand_path("../../data/nucl_prot_seqs.txt", __FILE__)

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: quorum
 version: !ruby/object:Gem::Version
-  version: 0.7.0
+  version: 0.7.1
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-10-02 00:00:00.000000000 Z
+date: 2012-11-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -303,9 +303,10 @@ files:
 - lib/tasks/blastdb/README
 - lib/tasks/blastdb/build_blast_db.rb
 - lib/tasks/jasmine.rake
+- lib/tasks/quorum_blastdb_build.rake
+- lib/tasks/quorum_delete_jobs.rake
 - lib/tasks/quorum_resque.rake
-- lib/tasks/quorum_tasks.rake
-- lib/workers/quorum.rb
+- lib/workers/system.rb
 - quorum.gemspec
 - script/rails
 - spec/config/quorum_settings.yml
@@ -402,7 +403,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 376462079150931508
+      hash: 1003819355082357991
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -411,7 +412,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 376462079150931508
+      hash: 1003819355082357991
 requirements: []
 rubyforge_project: 
 rubygems_version: 1.8.24

data/lib/workers/quorum.rb

@@ -1,55 +0,0 @@
-module Workers
-  class System
-    extend Resque::Plugins::Result
-
-    @queue = :system_queue
-
-    #
-    # Resque worker method.
-    #
-    def self.perform(meta_id, cmd, remote, ssh_host, ssh_user, ssh_options = {}, stdout = false)
-      unless ssh_options.empty?
-        # Convert each key in ssh_options to a symbol.
-        ssh_options = ssh_options.inject({}) do |memo, (k, v)|
-          memo[k.to_sym] = v
-        memo
-        end
-      end
-
-      exit_status = 1
-      out         = ""
-
-      if remote
-        # Execute command on remote machine.
-        Net::SSH.start(ssh_host, ssh_user, ssh_options) do |ssh|
-          ssh.open_channel do |ch|
-            ch.exec(cmd) do |ch, success|
-              if success
-                # Capture STDOUT from ch.exec()
-                if stdout
-                  ch.on_data do |ch, data|
-                    out = data
-                  end
-                end
-                # Read the exit status of the remote process.
-                ch.on_request("exit-status") do |ch, data|
-                  exit_status = data.read_long
-                end
-              else
-                Rails.logger.warn "Channel Net::SSH exec() failed. :'("
-              end
-            end
-          end
-          ssh.loop
-        end
-      else
-        out         = `#{cmd}`
-        exit_status = $?.exitstatus
-      end
-      if exit_status > 0
-        raise "Worker failed :'(. See quorum/log/quorum.log for more information."
-      end
-      out if stdout
-    end
-  end
-end