quorum 0.8.1 → 0.8.2

data/.gitignore

@@ -6,3 +6,4 @@ spec/dummy/log/*.log
 spec/dummy/tmp/*
 spec/dummy/config/database.yml
 spec/dummy/quorum/
+Gemfile.lock

data/HISTORY.md

@@ -1,3 +1,8 @@
+## 0.8.2 (2013-2-07)
+
+* Namespace change for bio-blastxmlparser v1.1.1
+* Upgrading? Run generators.
+
 ## 0.8.1 (2012-12-06)
 
 * SSH bug fix.

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] {<img src="https://gemnasium.com/ncgr/quorum.png" alt="Dependency Status" />}[https://gemnasium.com/ncgr/quorum]
 
 A flexible bioinformatics search tool.
 

data/lib/generators/templates/blast.rb

@@ -330,7 +330,7 @@ module Quorum
         @results = false # Did the xml contain results?
 
         if File.size(@out) > 0
-          report = Bio::Blast::XmlIterator.new(@out)
+          report = Bio::BlastXMLParser::XmlIterator.new(@out)
           report.to_enum.each do |iteration|
 
             @data = {}

data/lib/quorum/version.rb

@@ -1,3 +1,3 @@
 module Quorum
-  VERSION = "0.8.1"
+  VERSION = "0.8.2"
 end

data/quorum.gemspec

@@ -20,7 +20,7 @@ Gem::Specification.new do |s|
   s.add_dependency "net-ssh", "~> 2.3.0"
   s.add_dependency "resque", "~> 1.20.0"
   s.add_dependency "resque-result", "~> 1.0.1"
-  s.add_dependency "bio-blastxmlparser", "~> 1.1.0"
+  s.add_dependency "bio-blastxmlparser", "~> 1.1.1"
 
   s.add_development_dependency "mysql2", "~> 0.3.11"
   s.add_development_dependency "pg", "~> 0.14.1"

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: quorum
 version: !ruby/object:Gem::Version
-  version: 0.8.1
+  version: 0.8.2
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-12-06 00:00:00.000000000 Z
+date: 2013-02-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rails
@@ -98,7 +98,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.1.0
+        version: 1.1.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -106,7 +106,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.1.0
+        version: 1.1.1
 - !ruby/object:Gem::Dependency
   name: mysql2
   requirement: !ruby/object:Gem::Requirement
@@ -230,7 +230,6 @@ files:
 - .rspec
 - .travis.yml
 - Gemfile
-- Gemfile.lock
 - HISTORY.md
 - MIT-LICENSE
 - README.rdoc
@@ -273,12 +272,12 @@ files:
 - 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/observers/quorum/job_queue_observer.rb
 - app/views/layouts/quorum/application.html.erb
 - app/views/quorum/jobs/form/_blastn_form.html.erb
 - app/views/quorum/jobs/form/_blastp_form.html.erb
@@ -433,7 +432,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 2115123913404319690
+      hash: -4222826157838690648
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -442,10 +441,10 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 2115123913404319690
+      hash: -4222826157838690648
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.24
+rubygems_version: 1.8.25
 signing_key: 
 specification_version: 3
 summary: Flexible bioinformatics search tool.

data/Gemfile.lock

@@ -1,204 +0,0 @@
-PATH
-  remote: .
-  specs:
-    quorum (0.8.1)
-      bio-blastxmlparser (~> 1.1.0)
-      jquery-rails
-      net-ssh (~> 2.3.0)
-      rails (~> 3.1)
-      resque (~> 1.20.0)
-      resque-result (~> 1.0.1)
-
-GEM
-  remote: http://rubygems.org/
-  specs:
-    actionmailer (3.2.9)
-      actionpack (= 3.2.9)
-      mail (~> 2.4.4)
-    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 (~> 2.2.1)
-    activemodel (3.2.9)
-      activesupport (= 3.2.9)
-      builder (~> 3.0.0)
-    activerecord (3.2.9)
-      activemodel (= 3.2.9)
-      activesupport (= 3.2.9)
-      arel (~> 3.0.2)
-      tzinfo (~> 0.3.29)
-    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)
-      nokogiri (>= 1.5.0)
-    bio-logger (1.0.1)
-      log4r (>= 1.1.9)
-    builder (3.0.4)
-    capybara (1.1.4)
-      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 (0.3.6)
-      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)
-    eventmachine (1.0.0)
-    ffi (1.2.0)
-    hike (1.2.1)
-    i18n (0.6.1)
-    jasmine (1.3.1)
-      jasmine-core (~> 1.3.1)
-      rack (~> 1.0)
-      rspec (>= 1.3.1)
-      selenium-webdriver (>= 0.1.3)
-    jasmine-core (1.3.1)
-    journey (1.0.4)
-    jquery-rails (2.1.4)
-      railties (>= 3.0, < 5.0)
-      thor (>= 0.14, < 2.0)
-    json (1.7.5)
-    libwebsocket (0.1.7.1)
-      addressable
-      websocket
-    log4r (1.1.10)
-    mail (2.4.4)
-      i18n (>= 0.4.0)
-      mime-types (~> 1.16)
-      treetop (~> 1.4.8)
-    mime-types (1.19)
-    multi_json (1.4.0)
-    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)
-      rack (>= 0.4)
-    rack-protection (1.2.0)
-      rack
-    rack-ssl (1.3.2)
-      rack
-    rack-test (0.6.2)
-      rack (>= 1.0)
-    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 (= 3.2.9)
-    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 (10.0.2)
-    rdoc (3.12)
-      json (~> 1.4)
-    redis (2.2.2)
-    redis-namespace (1.0.3)
-      redis (< 3.0.0)
-    resque (1.20.0)
-      multi_json (~> 1.0)
-      redis-namespace (~> 1.0.2)
-      sinatra (>= 0.9.2)
-      vegas (~> 0.1.2)
-    resque-meta (1.0.3)
-      resque (~> 1.8)
-    resque-result (1.0.1)
-      resque (~> 1.9)
-      resque-meta (~> 1.0)
-    resque_spec (0.12.7)
-      resque (>= 1.19.0)
-      rspec (>= 2.5.0)
-    rspec (2.12.0)
-      rspec-core (~> 2.12.0)
-      rspec-expectations (~> 2.12.0)
-      rspec-mocks (~> 2.12.0)
-    rspec-core (2.12.1)
-    rspec-expectations (2.12.0)
-      diff-lcs (~> 1.1.3)
-    rspec-mocks (2.12.0)
-    rspec-rails (2.12.0)
-      actionpack (>= 3.0)
-      activesupport (>= 3.0)
-      railties (>= 3.0)
-      rspec-core (~> 2.12.0)
-      rspec-expectations (~> 2.12.0)
-      rspec-mocks (~> 2.12.0)
-    rubyzip (0.9.9)
-    selenium-webdriver (2.27.0)
-      childprocess (>= 0.2.5)
-      libwebsocket (~> 0.1.3)
-      multi_json (~> 1.0)
-      rubyzip
-    sinatra (1.3.3)
-      rack (~> 1.3, >= 1.3.6)
-      rack-protection (~> 1.2)
-      tilt (~> 1.3, >= 1.3.3)
-    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)
-      polyglot
-      polyglot (>= 0.3.1)
-    tzinfo (0.3.35)
-    vegas (0.1.11)
-      rack (>= 1.0.0)
-    websocket (1.0.4)
-    xpath (0.1.4)
-      nokogiri (~> 1.3)
-
-PLATFORMS
-  ruby
-
-DEPENDENCIES
-  capybara (~> 1.1)
-  database_cleaner (~> 0.8)
-  debugger
-  jasmine (~> 1.2)
-  mysql2 (~> 0.3.11)
-  pg (~> 0.14.1)
-  quorum!
-  rake (~> 10.0.0)
-  resque_spec (~> 0.12)
-  rspec-rails (~> 2.11)
-  thin