quorum 0.7.1 → 0.8.0

data/spec/javascripts/helpers/jasmine-jquery.js

@@ -81,7 +81,7 @@ jasmine.Fixtures.prototype.createContainer_ = function(html) {
   jQuery('body').append(container);
 };
 
-jasmine.Fixtures.prototype.getFixtureHtml_ = function(url) {  
+jasmine.Fixtures.prototype.getFixtureHtml_ = function(url) {
   if (typeof this.fixturesCache_[url] == 'undefined') {
     this.loadFixtureIntoCache_(url);
   }
@@ -223,7 +223,7 @@ jasmine.JQuery.matchersClass = {};
       var events = this.actual.data("events");
       return events && events[eventName].length > 0;
     },
-    
+
     // tests the existence of a specific event binding + handler
     toHandleWith: function(eventName, eventHandler) {
       var stack = this.actual.data("events")[eventName];

data/spec/lib/tasks/travis.rake

@@ -95,10 +95,15 @@ namespace :travis do
   task :create_db_config do
     config = File.expand_path("../../../dummy/config", __FILE__)
     File.open(File.join(config, "database.yml"), "w+") do |file|
-      file.puts "\ntest:\n  adapter: mysql2\n  encoding: utf8\n" <<
-      "  reconnect: false\n  database: quorum_test\n" <<
-      "  pool: 5\n  username: root\n  password:\n" <<
-      "  host: localhost\n"
+      file.puts "\nmysql: &mysql\n  adapter: mysql2\n" <<
+      "  database: quorum_test\n  username: root\n"
+      file.puts "\npostgresql: &postgresql\n  adapter: postgresql\n" <<
+      "  database: quorum_test\n  username: postgres\n" <<
+      "  min_messages: ERROR\n"
+      file.puts "\ndefaults: &defaults\n  pool: 5\n" <<
+      "  timeout: 5000\n  host: localhost\n" <<
+      "  <<: *<%= ENV['DB'] %>\n"
+      file.puts "\ntest:\n  <<: *defaults"
     end
   end
 

data/spec/models/blastn_job_report_spec.rb

@@ -2,12 +2,16 @@ require 'spec_helper'
 
 describe Quorum::BlastnJobReport do
 
+  before(:all) do
+    @blastn = Quorum::BlastnJobReport
+  end
+
   it "should respond to default_order" do
-    Quorum::BlastnJobReport.methods.should include(:default_order)
+    @blastn.respond_to?(:default_order).should be_true
   end
 
-  it "should respond to by_query" do
-    Quorum::BlastnJobReport.methods.should include(:by_query)
+  it "should be searchable" do
+    @blastn.respond_to?(:search).should be_true
   end
 
 end

data/spec/models/blastp_job_report_spec.rb

@@ -2,12 +2,17 @@ require 'spec_helper'
 
 describe Quorum::BlastpJobReport do
 
+  before(:all) do
+    @blastp = Quorum::BlastpJobReport
+  end
+
   it "should respond to default_order" do
-    Quorum::BlastpJobReport.methods.should include(:default_order)
+    @blastp.respond_to?(:default_order).should be_true
   end
 
-  it "should respond to by_query" do
-    Quorum::BlastpJobReport.methods.should include(:by_query)
+  it "should be searchable" do
+    @blastp.respond_to?(:search).should be_true
   end
 
 end
+

data/spec/models/blastx_job_report_spec.rb

@@ -2,12 +2,17 @@ require 'spec_helper'
 
 describe Quorum::BlastxJobReport do
 
-  it "should respond to default_order" do
-    Quorum::BlastxJobReport.methods.should include(:default_order)
+  before(:all) do
+    @blastx = Quorum::BlastxJobReport
   end
 
   it "should respond to default_order" do
-    Quorum::BlastxJobReport.methods.should include(:by_query)
+    @blastx.respond_to?(:default_order).should be_true
+  end
+
+  it "should be searchable" do
+    @blastx.respond_to?(:search).should be_true
   end
 
 end
+

data/spec/models/job_data_spec.rb

@@ -0,0 +1,21 @@
+require 'spec_helper'
+
+describe Quorum::JobData do
+
+  before(:each) do
+    @data = Quorum::JobData.new()
+  end
+
+  it "#results stores data in an array" do
+    @data.results.should be_a(Array)
+  end
+
+  it "#no_results returns a hash { results: false }" do
+    @data.no_results.should eq([{ results: false }])
+  end
+
+  it "#not_enqueued returns a hash { results: false, enqueued: false }" do
+    @data.not_enqueued.should eq([{ results: false, enqueued: false }])
+  end
+
+end

data/spec/models/job_fetch_data_spec.rb

@@ -0,0 +1,25 @@
+require 'spec_helper'
+
+describe Quorum::JobFetchData do
+
+  before(:each) do
+    @fetch = Quorum::JobFetchData.new
+  end
+
+  it "validates presence of attributes" do
+    @fetch.should have(1).error_on(:algo)
+    @fetch.should have(1).error_on(:blast_dbs)
+    @fetch.should have(1).error_on(:hit_id)
+    @fetch.should have(1).error_on(:hit_display_id)
+    @fetch.valid?.should be_false
+  end
+
+  it "passes validation when attrs are set" do
+    @fetch.algo           = "foo"
+    @fetch.blast_dbs      = "foo"
+    @fetch.hit_id         = "foo"
+    @fetch.hit_display_id = "foo"
+    @fetch.valid?.should be_true
+  end
+
+end

data/spec/models/job_queue_observer_spec.rb

@@ -0,0 +1,18 @@
+require 'spec_helper'
+
+describe Quorum::JobQueueObserver do
+
+  it "should queue workers after create" do
+    job = Quorum::Job.new()
+    job.sequence = ">test\n" + "a" * 50
+    job.build_blastn_job
+    job.blastn_job.queue     = true
+    job.blastn_job.blast_dbs = ["test"]
+
+    obs = Quorum::JobQueueObserver.instance
+
+    Quorum::JobQueueService.should_receive(:queue_search_workers).with(job)
+    obs.after_create(job)
+  end
+
+end

data/spec/models/job_queue_service_spec.rb

@@ -0,0 +1,49 @@
+require 'spec_helper'
+
+describe Quorum::JobQueueService do
+
+  before(:each) do
+    ResqueSpec.reset!
+  end
+
+  describe "Job Queue" do
+
+    before(:each) do
+      @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 = ["db"]
+      @job.save!
+    end
+
+    it "enqueues job after save" do
+      Quorum::JobQueueService.queue_search_workers(@job)
+      Workers::System.should have_queue_size_of(1)
+    end
+
+  end
+
+  describe "Fetch Queue" do
+
+    before(:each) do
+      @fetch = Quorum::JobFetchData.new
+      @fetch.algo           = "foo"
+      @fetch.blast_dbs      = "foo"
+      @fetch.hit_id         = "foo"
+      @fetch.hit_display_id = "foo"
+    end
+
+    it "enqueues valid blast fetch and returns meta_id" do
+      f = Quorum::JobQueueService.queue_fetch_worker(@fetch)
+      Workers::System.should have_queue_size_of(1)
+      f.should have(1).items
+      f[0].keys.should eq([:meta_id])
+      f[0].values.should_not be_empty
+    end
+
+  end
+
+end

data/spec/models/job_report_searcher_spec.rb

@@ -0,0 +1,47 @@
+require 'spec_helper'
+
+describe Quorum::JobReportSearcher do
+
+  include Quorum::JobReportSearcher
+
+  before(:each) do
+    @algo  = "blastn"
+    blastn = Quorum::BlastnJobReport
+    2.times do
+      blastn.create!({
+        :query => "test",
+        :hit_display_id => "foo",
+        :identity => 0,
+        :align_len => 0,
+        :query_from => 10,
+        :query_to => 100,
+        :hit_from => 900,
+        :hit_to => 1000,
+        :evalue => "1e-100",
+        :bit_score => 1000,
+        :results => true,
+        :blastn_job_id => 1
+      })
+    end
+  end
+
+  it "makes job reports searchable" do
+    p = { :id => 1, :blastn_id => "1,2", :query => "test" }
+    search(@algo, p).count.should eq(2)
+
+    p = { :id => 1, :blastn_id => "2", :query => "test" }
+    search(@algo, p).count.should eq(1)
+
+    p = { :id => 1, :blastn_id => "1,2", :query => nil }
+    search(@algo, p).count.should eq(2)
+
+    p = { :id => 1, :blastn_id => nil, :query => "test" }
+    search(@algo, p).count.should eq(2)
+
+    p = { :id => 1 }
+    search(@algo, p).count.should eq(2)
+
+    search(@algo, {}).count.should eq(0)
+  end
+
+end

data/spec/models/job_serializer_spec.rb

@@ -0,0 +1,60 @@
+require 'spec_helper'
+
+describe "Quorum::JobSerializer" do
+
+  include Quorum::JobSerializer
+  before(:each) do
+    @blastn = Quorum::BlastnJobReport
+    2.times do
+      @blastn.create!({
+        :query => "test",
+        :hit_display_id => "foo",
+        :identity => 0,
+        :align_len => 0,
+        :pct_identity => 100.0,
+        :query_from => 10,
+        :query_to => 100,
+        :hit_from => 900,
+        :hit_to => 1000,
+        :evalue => "1e-100",
+        :bit_score => 1000,
+        :results => true
+      })
+    end
+  end
+
+  describe "#as_json" do
+    it "returns error messages as json when present" do
+      Quorum::JobSerializer.as_json(Quorum::Job.create({})).should have_key(:errors)
+    end
+
+    it "returns object as json" do
+      Quorum::JobSerializer.as_json(@blastn.first).should eq(@blastn.first.as_json)
+    end
+  end
+
+  describe "#as_txt" do
+    it "returns a tab delimited string of Blast results" do
+      Quorum::JobSerializer.as_txt(@blastn.all).match(/[\w\d\W\t\n]*/).should be_true
+    end
+  end
+
+  describe "#as_gff" do
+    it "returns a gff string of Blast results" do
+      Quorum::JobSerializer.as_gff(@blastn.all).match(/##gff-version 3\n\.*/).should be_true
+      # Strand should be +
+      Quorum::JobSerializer.as_gff(@blastn.all).include?("+").should be_true
+    end
+  end
+
+  describe "#format_hit_start_stop" do
+    it "returns original params when start < stop" do
+      Quorum::JobSerializer.format_hit_start_stop(10, 12).should eq([10,12])
+    end
+
+    it "returns params in acending order when start > stop" do
+      Quorum::JobSerializer.format_hit_start_stop(12, 10).should eq([10,12])
+    end
+  end
+
+end

data/spec/models/job_spec.rb

@@ -4,7 +4,6 @@ describe Quorum::Job do
 
   before(:each) do
     @job = Quorum::Job.new()
-    ResqueSpec.reset!
   end
 
   it "fails validation without params" do
@@ -38,7 +37,7 @@ describe Quorum::Job do
     @job.should have(0).errors_on(:algorithm)
   end
 
-  it "deletes submitted jobs" do
+  it "deletes completed jobs" do
     1.upto(5) do |i|
       job = Quorum::Job.new()
       job.sequence = File.open(
@@ -56,18 +55,4 @@ describe Quorum::Job do
     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__)
-    ).read
-
-    @job.build_blastn_job
-    @job.blastn_job.queue     = true
-    @job.blastn_job.blast_dbs = ["test_1", "test_2"]
-
-    @job.save!
-
-    Workers::System.should have_queue_size_of(1)
-  end
-
 end

data/spec/models/tblastn_job_report_spec.rb

@@ -2,12 +2,17 @@ require 'spec_helper'
 
 describe Quorum::TblastnJobReport do
 
-  it "should respond to default_order" do
-    Quorum::TblastnJobReport.methods.should include(:default_order)
+  before(:all) do
+    @tblastn = Quorum::TblastnJobReport
   end
 
   it "should respond to default_order" do
-    Quorum::TblastnJobReport.methods.should include(:by_query)
+    @tblastn.respond_to?(:default_order).should be_true
+  end
+
+  it "should be searchable" do
+    @tblastn.respond_to?(:search).should be_true
   end
 
 end
+

data/spec/quorum/quorum_sequence_spec.rb

@@ -4,6 +4,7 @@ require 'quorum/sequence'
 include Quorum::Sequence
 
 describe "Quorum::Sequence" do
+
   describe "#create_hash" do
     it "creates a MD5.hexdigest of a sequence" do
       sequence = File.open(
@@ -89,4 +90,5 @@ describe "Quorum::Sequence" do
       discover_input_sequence_type(sequence).should eq("amino_acid")
     end
   end
+
 end

data/spec/requests/jobs_spec.rb

@@ -54,6 +54,7 @@ describe "Jobs" do
       Capybara.current_driver    = :selenium
     end
     before(:each) do
+      ActiveRecord::Base.observers.enable Quorum::JobQueueObserver
       ResqueSpec.reset!
       ResqueSpec.inline = true
     end
@@ -135,7 +136,7 @@ describe "Jobs" do
         page.should have_content("hseq")
 
         # Download sequence
-        find("p.small a#download_sequence_2").click
+        find("p.small a.download_sequence").click
         page.should have_content("Fetching sequence...")
         page.should have_content("Sequence Downloaded Successfully")
 
@@ -150,33 +151,41 @@ describe "Jobs" do
     end
     after(:all) do
       Capybara.use_default_driver
+      ActiveRecord::Base.observers.disable :all
     end
   end
 
   describe "GET /quorum/jobs/id" do
     it "displays notice and renders form with invalid id" do
-      visit job_path('12893479812347912')
+      visit job_path('12893')
       page.should have_content("The data you requested is unavailable. Please check your URL and try again.")
       current_path.should eq(new_job_path)
     end
   end
 
-  describe "GET /quorum/jobs/id/get_quorum_search_results" do
+  describe "GET /quorum/jobs/id/search" do
     it "renders JSON results => false with invalid id" do
-      visit "/quorum/jobs/23542352345/get_quorum_search_results.json"
+      visit "/quorum/jobs/23542/search.json"
       page.should have_content("[{\"results\":false}]")
     end
   end
 
-  describe "GET /quorum/jobs/id/get_quorum_blast_hit_sequence" do
+  describe "GET /quorum/jobs/id/get_blast_hit_sequence" do
     it "renders empty JSON with invalid id" do
-      visit "/quorum/jobs/23542352345/get_quorum_blast_hit_sequence.json"
+      visit "/quorum/jobs/23542/get_blast_hit_sequence.json"
       page.should have_content("[]")
     end
 
     it "renders empty JSON with invalid id and valid params" do
-      visit "/quorum/jobs/23542352345/get_quorum_blast_hit_sequence.json?algo=blastn"
+      visit "/quorum/jobs/23542/get_blast_hit_sequence.json?algo=blastn"
       page.should have_content("[]")
     end
   end
+
+  describe "GET /quorum/jobs/id/send_blast_hit_sequence" do
+    it "renders empty text on error" do
+      visit "/quorum/jobs/23423/send_blast_hit_sequence?meta_id=1231"
+      page.should_not have_content(" ")
+    end
+  end
 end

data/spec/spec_helper.rb

@@ -25,6 +25,8 @@ RSpec.configure do |config|
   config.filter_run :focus => true
   config.run_all_when_everything_filtered = true
 
+  ActiveRecord::Base.observers.disable :all
+
   ## DatabaseCleaner ##
   DatabaseCleaner.logger = Rails.logger
   config.before(:suite) do

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: quorum
 version: !ruby/object:Gem::Version
-  version: 0.7.1
+  version: 0.8.0
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-11-07 00:00:00.000000000 Z
+date: 2012-11-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -123,6 +123,22 @@ dependencies:
     - - ~>
       - !ruby/object:Gem::Version
         version: 0.3.11
+- !ruby/object:Gem::Dependency
+  name: pg
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.14.1
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.14.1
 - !ruby/object:Gem::Dependency
   name: rspec-rails
   requirement: !ruby/object:Gem::Requirement
@@ -255,6 +271,12 @@ files:
 - app/models/quorum/blastx_job.rb
 - app/models/quorum/blastx_job_report.rb
 - app/models/quorum/job.rb
+- app/models/quorum/job_data.rb
+- app/models/quorum/job_fetch_data.rb
+- app/models/quorum/job_queue_observer.rb
+- app/models/quorum/job_queue_service.rb
+- app/models/quorum/job_report_searcher.rb
+- app/models/quorum/job_serializer.rb
 - app/models/quorum/tblastn_job.rb
 - app/models/quorum/tblastn_job_report.rb
 - app/views/layouts/quorum/application.html.erb
@@ -267,6 +289,7 @@ files:
 - app/views/quorum/jobs/templates/_blast_detailed_report_template.html.erb
 - app/views/quorum/jobs/templates/_blast_template.html.erb
 - app/views/shared/_error_messages.html.erb
+- config/initializers/mime_types.rb
 - config/locales/en.yml
 - config/routes.rb
 - db/migrate/20111031204518_create_jobs.rb
@@ -280,8 +303,10 @@ files:
 - db/migrate/20111031204941_create_tblastn_job_reports.rb
 - db/migrate/20120109232446_add_hit_display_id_to_blast_reports.rb
 - db/migrate/20120807202555_add_gaps_to_blast_reports.rb
+- db/migrate/20120809155712_add_percent_identity_to_blast_reports.rb
 - db/migrate/20120910175911_change_hsp_group_column_type.rb
 - db/migrate/20120918205556_rename_max_score_column.rb
+- db/migrate/20120921182416_add_mismatch_to_blast_reports.rb
 - lib/generators/quorum/images_generator.rb
 - lib/generators/quorum/install_generator.rb
 - lib/generators/quorum/styles_generator.rb
@@ -329,7 +354,6 @@ files:
 - spec/dummy/app/helpers/application_helper.rb
 - spec/dummy/app/mailers/.gitkeep
 - spec/dummy/app/models/.gitkeep
-- spec/dummy/app/models/blast.rb
 - spec/dummy/app/views/layouts/application.html.erb
 - spec/dummy/config.ru
 - spec/dummy/config/application.rb
@@ -358,12 +382,12 @@ files:
 - spec/javascripts/fixtures/quorum_search_form.html
 - spec/javascripts/fixtures/quorum_tabs.html
 - spec/javascripts/helpers/jasmine-jquery.js
-- spec/javascripts/jobs_spec.js
 - spec/javascripts/jquery/jquery-ui.min.js
 - spec/javascripts/jquery/jquery.min.js
 - spec/javascripts/jquery/jquery_ujs.js
-- spec/javascripts/quorum_spec.js
-- spec/javascripts/string_spec.js
+- spec/javascripts/suites/jobs_spec.js
+- spec/javascripts/suites/quorum_spec.js
+- spec/javascripts/suites/string_spec.js
 - spec/javascripts/support/jasmine.yml
 - spec/javascripts/support/jasmine_config.rb
 - spec/javascripts/support/jasmine_runner.rb
@@ -374,6 +398,12 @@ files:
 - spec/models/blastp_job_spec.rb
 - spec/models/blastx_job_report_spec.rb
 - spec/models/blastx_job_spec.rb
+- spec/models/job_data_spec.rb
+- spec/models/job_fetch_data_spec.rb
+- spec/models/job_queue_observer_spec.rb
+- spec/models/job_queue_service_spec.rb
+- spec/models/job_report_searcher_spec.rb
+- spec/models/job_serializer_spec.rb
 - spec/models/job_spec.rb
 - spec/models/tblastn_job_report_spec.rb
 - spec/models/tblastn_job_spec.rb
@@ -403,7 +433,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 1003819355082357991
+      hash: -3863476940221336517
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -412,7 +442,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 1003819355082357991
+      hash: -3863476940221336517
 requirements: []
 rubyforge_project: 
 rubygems_version: 1.8.24

data/spec/dummy/app/models/blast.rb

@@ -1,2 +0,0 @@
-class Blast < ActiveRecord::Base
-end