sushi_fabric 0.5.4 → 0.5.5

data/.rspec

@@ -0,0 +1,2 @@
+--color
+--require spec_helper

data/lib/sushi_fabric/sushiApp.rb

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20160303-093810'
+# Version = '20160303-160844'
 
 require 'csv'
 require 'fileutils'
@@ -363,6 +363,7 @@ set -o pipefail
 #### SET THE STAGE
 SCRATCH_DIR=#{@scratch_dir}
 GSTORE_DIR=#{@gstore_dir}
+INPUT_DATASET=#{@input_dataset_tsv_path}
 echo "Job runs on `hostname`"
 echo "at $SCRATCH_DIR"
 mkdir $SCRATCH_DIR || exit 1

data/lib/sushi_fabric/version.rb

@@ -1,3 +1,3 @@
 module SushiFabric
-  VERSION = "0.5.4"
+  VERSION = "0.5.5"
 end

data/spec/spec_helper.rb

@@ -0,0 +1,96 @@
+# This file was generated by the `rspec --init` command. Conventionally, all
+# specs live under a `spec` directory, which RSpec adds to the `$LOAD_PATH`.
+# The generated `.rspec` file contains `--require spec_helper` which will cause
+# this file to always be loaded, without a need to explicitly require it in any
+# files.
+#
+# Given that it is always loaded, you are encouraged to keep this file as
+# light-weight as possible. Requiring heavyweight dependencies from this file
+# will add to the boot time of your test suite on EVERY test run, even for an
+# individual file that may not need all of that loaded. Instead, consider making
+# a separate helper file that requires the additional dependencies and performs
+# the additional setup, and require it from the spec files that actually need
+# it.
+#
+# The `.rspec` file also contains a few flags that are not defaults but that
+# users commonly want.
+#
+# See http://rubydoc.info/gems/rspec-core/RSpec/Core/Configuration
+RSpec.configure do |config|
+  # rspec-expectations config goes here. You can use an alternate
+  # assertion/expectation library such as wrong or the stdlib/minitest
+  # assertions if you prefer.
+  config.expect_with :rspec do |expectations|
+    # This option will default to `true` in RSpec 4. It makes the `description`
+    # and `failure_message` of custom matchers include text for helper methods
+    # defined using `chain`, e.g.:
+    #     be_bigger_than(2).and_smaller_than(4).description
+    #     # => "be bigger than 2 and smaller than 4"
+    # ...rather than:
+    #     # => "be bigger than 2"
+    expectations.include_chain_clauses_in_custom_matcher_descriptions = true
+  end
+
+  # rspec-mocks config goes here. You can use an alternate test double
+  # library (such as bogus or mocha) by changing the `mock_with` option here.
+  config.mock_with :rspec do |mocks|
+    # Prevents you from mocking or stubbing a method that does not exist on
+    # a real object. This is generally recommended, and will default to
+    # `true` in RSpec 4.
+    mocks.verify_partial_doubles = true
+  end
+
+# The settings below are suggested to provide a good initial experience
+# with RSpec, but feel free to customize to your heart's content.
+=begin
+  # These two settings work together to allow you to limit a spec run
+  # to individual examples or groups you care about by tagging them with
+  # `:focus` metadata. When nothing is tagged with `:focus`, all examples
+  # get run.
+  config.filter_run :focus
+  config.run_all_when_everything_filtered = true
+
+  # Allows RSpec to persist some state between runs in order to support
+  # the `--only-failures` and `--next-failure` CLI options. We recommend
+  # you configure your source control system to ignore this file.
+  config.example_status_persistence_file_path = "spec/examples.txt"
+
+  # Limits the available syntax to the non-monkey patched syntax that is
+  # recommended. For more details, see:
+  #   - http://rspec.info/blog/2012/06/rspecs-new-expectation-syntax/
+  #   - http://www.teaisaweso.me/blog/2013/05/27/rspecs-new-message-expectation-syntax/
+  #   - http://rspec.info/blog/2014/05/notable-changes-in-rspec-3/#zero-monkey-patching-mode
+  config.disable_monkey_patching!
+
+  # This setting enables warnings. It's recommended, but in some cases may
+  # be too noisy due to issues in dependencies.
+  config.warnings = true
+
+  # Many RSpec users commonly either run the entire suite or an individual
+  # file, and it's useful to allow more verbose output when running an
+  # individual spec file.
+  if config.files_to_run.one?
+    # Use the documentation formatter for detailed output,
+    # unless a formatter has already been configured
+    # (e.g. via a command-line flag).
+    config.default_formatter = 'doc'
+  end
+
+  # Print the 10 slowest examples and example groups at the
+  # end of the spec run, to help surface which specs are running
+  # particularly slow.
+  config.profile_examples = 10
+
+  # Run specs in random order to surface order dependencies. If you find an
+  # order dependency and want to debug it, you can fix the order by providing
+  # the seed, which is printed after each run.
+  #     --seed 1234
+  config.order = :random
+
+  # Seed global randomization in this process using the `--seed` CLI option.
+  # Setting this allows you to use `--seed` to deterministically reproduce
+  # test failures related to randomization by passing the same `--seed` value
+  # as the one that triggered the failure.
+  Kernel.srand config.seed
+=end
+end

data/spec/sushi_app_spec.rb

@@ -0,0 +1,24 @@
+#!/usr/bin/env ruby
+# encoding: utf-8
+
+require './lib/sushi_fabric/sushiApp'
+
+include SushiFabric
+describe SushiApp do
+  subject(:sushi_app) {SushiApp.new}
+  context 'when new' do
+    it {is_expected.to be_an_instance_of SushiApp} 
+  end 
+  describe "#job_header" do
+    subject{sushi_app.job_header}
+    let(:dataset) {{'Name' => 'Name'}}
+    let(:out) {double('out')}
+    before do
+      allow(out).to receive_messages(:print => nil)
+      sushi_app.instance_variable_set(:@out, out)
+      sushi_app.instance_variable_set(:@scratch_result_dir, 'scratch_result_dir')
+      sushi_app.instance_variable_set(:@dataset, dataset)
+    end
+    it {is_expected.to be_nil}
+  end 
+end

metadata

@@ -2,7 +2,7 @@
 name: sushi_fabric
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: 0.5.4
+  version: 0.5.5
 platform: ruby
 authors: 
 - Functional Genomics Center Zurich
@@ -45,6 +45,7 @@ extra_rdoc_files: []
 
 files: 
 - .gitignore
+- .rspec
 - Gemfile
 - LICENSE.txt
 - README.md
@@ -58,6 +59,8 @@ files:
 - sample/WordCountApp.rb
 - sample/sample_dataset.tsv
 - sample/sample_parameterset.tsv
+- spec/spec_helper.rb
+- spec/sushi_app_spec.rb
 - sushi_fabric.gemspec
 homepage: ""
 licenses: 
@@ -86,5 +89,6 @@ rubygems_version: 1.8.23
 signing_key: 
 specification_version: 3
 summary: workflow manager client.
-test_files: []
-
+test_files: 
+- spec/spec_helper.rb
+- spec/sushi_app_spec.rb