genome-pipeline 0.0.1 → 0.0.2

data/spec/pipeline_spec.rb

@@ -2,8 +2,36 @@ require 'spec_helper'
 
 describe Genome::Pipeline do
 
+  let(:genome) { Genome::Genome.new File.open('spec/data/genome.fasta') }
+  let(:pipeline) { Genome::Pipeline.new(Genome::Pipeline::DummyFilter) }
+
+  let(:test_filter) do
+    class TestFilter < Genome::Pipeline::Filter
+      def transform
+        @genome.features << 'a dummy feature'
+      end
+    end
+    return TestFilter
+  end
+
   it 'exists' do
     expect(Genome::Pipeline).to_not eq(nil)
   end
 
+  it 'can perform transformations on a Genome' do
+    expect { pipeline.run(genome) }.not_to raise_error
+    expect(pipeline.run(genome)).to be_a(Genome::Genome)
+  end
+
+  # this belongs in filter_spec
+  it '.run should copy the original genome' do
+    expect(pipeline.run(genome).object_id).not_to eq(genome.object_id)
+  end
+
+  # this belongs in filter_spec
+  it '.run should not alter original features' do
+    test_filter.new(genome).transform
+    expect(genome.features.size).to eq(0)
+  end
+
 end

data/spec/prodigal_filter_spec.rb

@@ -12,7 +12,10 @@ describe Genome::Pipeline::ProdigalFilter do
   end
 
   it '.transform' do
-    expect(filter.transform).to be_a(Genome::Genome)
+    filtered_genome = filter.transform
+    expect(filtered_genome).to be_a(Genome::Genome)
+    expect(filtered_genome.features).not_to eq(nil)
+    expect(filtered_genome.features.size).not_to eq(0)
   end
 
 end

data.tar.gz.sig

@@ -0,0 +1,2 @@
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metadata

@@ -1,15 +1,42 @@
 --- !ruby/object:Gem::Specification
 name: genome-pipeline
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.0.2
   prerelease: 
 platform: ruby
 authors:
 - Austin G. Davis-Richardson
 autorequire: 
 bindir: bin
-cert_chain: []
-date: 2014-09-20 00:00:00.000000000 Z
+cert_chain:
+- !binary |-
+  LS0tLS1CRUdJTiBDRVJUSUZJQ0FURS0tLS0tCk1JSURJRENDQWdpZ0F3SUJB
+  Z0lCQURBTkJna3Foa2lHOXcwQkFRVUZBREEyTVFvd0NBWURWUVFEREFGZk1S
+  UXcKRWdZS0NaSW1pWlB5TEdRQkdSWUVZV2RrY2pFU01CQUdDZ21TSm9tVDhp
+  eGtBUmtXQW1Odk1CNFhEVEUwTURjdwpPVEU1TURjMU1Wb1hEVEUxTURjd09U
+  RTVNRGMxTVZvd05qRUtNQWdHQTFVRUF3d0JYekVVTUJJR0NnbVNKb21UCjhp
+  eGtBUmtXQkdGblpISXhFakFRQmdvSmtpYUprL0lzWkFFWkZnSmpiekNDQVNJ
+  d0RRWUpLb1pJaHZjTkFRRUIKQlFBRGdnRVBBRENDQVFvQ2dnRUJBTmNKVDhm
+  dEkyZXg0Y0NKR0JUZXhvckJvUVR5VkU1WmFtZGk1MS96UE5nVQoxZXc1OWl6
+  WUd2OC9Kak1wVXlURmRGYno4bDdybHllRXNzb3o1WWY2Z2NreGwrbmxtaUJ4
+  dklMS3U4VzJaanlGCmEzeW1DYnllaHIvMWkrR1BvelpGeVZLZElFSUhMYWdB
+  V2VqNE1kMkZzUURLd21hQS8rNXNTcXUxYjgwUjY3NWUKQWU5bzVHNzZHbmlO
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+  NDl5TE9iLwpmWktuUmE2SVpDTCtEdVhVVmlOVGlwUHVPTHZuVVNQVHpmbm53
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+  RlRJQzB3Q3dZRFZSMFBCQVFEQWdTdwpNQTBHQ1NxR1NJYjNEUUVCQlFVQUE0
+  SUJBUUN1VTlUQTdoU1FEN2R5dFdMWWZROFM0dUhyZVNkY2E0UFJrc3hICjM2
+  aXk4U3BteW5LSWg4M1V4Wkg5TnI4eFgza1ZuSFg5c0ZZcVVleVFZckxzb2cr
+  ZXR3d0Q1MUMrdGFNUlV6WVUKeTJJQ01YR2w5VTl1L2xlY0tqL2tDT0pFOGJE
+  aGJWRDlhZG0rWktWcUFvcTBER2xKSTR4YXJJeHd6RENWWnIzdgo0M0xESzZv
+  dVp0N3B0NVRaM3daYkJzU1lYY0M0TlZRSHJ4Yis2WWFrVUxreVVGbDZMZDJw
+  NklEOTdoVE9BSGQyCmI5UlMzK1AwcFJ6UXlvMm9zUVRuT3VwM1pBbGZxdEc5
+  MEYvbTVtU0l2V2VKUUJ3Y1psZDlYMkN2Si9EZ1NmdlgKaEFybEFiejhqSWla
+  NUZoSGVjUVZRNlEwc0Rsak5kRmg1TjZTUXA5YWZZZkowRGxiCi0tLS0tRU5E
+  IENFUlRJRklDQVRFLS0tLS0K
+date: 2014-09-22 00:00:00.000000000 Z
 dependencies: []
 description: Genome processing filters and utilities
 email:
@@ -18,15 +45,18 @@ executables: []
 extensions: []
 extra_rdoc_files: []
 files:
+- .gitignore
 - Gemfile
 - Gemfile.lock
 - Rakefile
+- certs/audy.cert
 - genome-pipeline.gemspec
 - installation.md
 - lib/genome/genome.rb
 - lib/genome/genome/feature.rb
 - lib/genome/genome/genome.rb
 - lib/genome/pipeline.rb
+- lib/genome/pipeline/dummy_filter.rb
 - lib/genome/pipeline/filter.rb
 - lib/genome/pipeline/pipeline.rb
 - lib/genome/pipeline/prodigal_filter.rb
@@ -58,6 +88,9 @@ required_ruby_version: !ruby/object:Gem::Requirement
   - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
+      segments:
+      - 0
+      hash: 1582478238090731680
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
@@ -71,3 +104,4 @@ signing_key:
 specification_version: 3
 summary: Helpers for processing genomes through a chain of annotation filters
 test_files: []
+has_rdoc: 

metadata.gz.sig

@@ -0,0 +1,4 @@
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