bsi-pipeline 0.0.1

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 0fa6863806c23dccbf29d3a2084e673d53d1a666
+  data.tar.gz: d2cb13ddf0cafa07bfa4b5a91b9f7b9395e7e9b5
+SHA512:
+  metadata.gz: 1221f0e7c45e2ea7e97995f4943e9b133ee5786e2d905ba3ca90cf30061806c95f699a67bfdbd379651bba86830e85961c453bd2f4b644525ca4fef8872e120e
+  data.tar.gz: e9d4a21396e09d1ff348da06cb0ef44c02c826047f13ca4cee6f6a1b95900d5058631593ec5d9f0969f81cec2a5414082402f4919b218a714a83499b4c190128

data/.gitignore

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+*.gem
+*.rbc
+*.swp
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp
+*.bundle
+*.so
+*.o
+*.a
+mkmf.log

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in bsi-pipeline.gemspec
+gemspec

data/Guardfile

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+guard 'rspec' do
+  # watch /lib/ files
+  watch(%r{^lib/(.+).rb$}) do |m|
+    "spec/#{m[1]}_spec.rb"
+  end
+
+  # watch /spec/ files
+  watch(%r{^spec/(.+).rb$}) do |m|
+    "spec/#{m[1]}.rb"
+  end
+end

data/LICENSE.txt

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+Copyright (c) 2014 Elijah Christensen
+
+MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+# Bsi::Pipeline
+
+TODO: Write a gem description
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'bsi-pipeline'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install bsi-pipeline
+
+## Usage
+
+TODO: Write usage instructions here
+
+## Contributing
+
+1. Fork it ( https://github.com/[my-github-username]/bsi-pipeline/fork )
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create a new Pull Request

data/Rakefile

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+require "rspec/core/rake_task"
+require "bundler/gem_tasks"
+
+RSpec::Core::RakeTask.new(:spec) do |task|
+  task.rspec_opts = ['--color', '--format', 'documentation']
+end
+
+task :default => :spec

data/bsi-pipeline.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'bsi-pipeline/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "bsi-pipeline"
+  spec.version       = Bsi::Pipeline::VERSION
+  spec.authors       = ["Elijah Christensen"]
+  spec.email         = ["ejd.christensen@gmail.com"]
+  spec.summary       = %q{plugin for pipeline that provides importers and models for migrating data to bsi}
+  spec.description   = spec.summary
+  spec.homepage      = ""
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files -z`.split("\x0")
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+  spec.add_development_dependency "bundler", "~> 1.6"
+  spec.add_development_dependency "rake"
+  spec.add_development_dependency "rspec"
+  spec.add_development_dependency "rspec-nc"
+  spec.add_development_dependency "guard"
+  spec.add_development_dependency "guard-rspec"
+  spec.add_development_dependency "terminal-notifier-guard"
+  spec.add_development_dependency "pry"
+  spec.add_development_dependency "pry-remote"
+  spec.add_development_dependency "pry-nav"
+  spec.add_development_dependency "coveralls"
+  spec.add_development_dependency "factory_girl"
+
+  spec.add_runtime_dependency     "etl-pipeline"
+  spec.add_runtime_dependency     "rbc"
+end

data/lib/bsi-pipeline/importer.rb

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+module Pipeline
+  module BSI
+
+    module Importer
+
+      class DataEntryBatch
+        attr_accessor :type, :properties, :id, :specimens, :client
+        def initialize(client, batch_type, batch_properties)
+          @type       = batch_type
+          @properties = batch_properties
+          @bsi        = client
+          @id         = @bsi.batch.create(batch_type, batch_properties)
+        end
+      end
+
+      class AddBatch < DataEntryBatch
+        attr_accessor :seminal_parents
+
+        def initialize(client, batch_properties)
+          super client, 'A', batch_properties
+        end
+
+        def type
+          'Add'
+        end
+
+        def add_specimens(specimens)
+          @specimens = specimens
+          format
+          @bsi.batch.addVials( @id, specimens.map{ |s| s.to_bfh } )
+          nil
+        end
+
+        def format
+          # Find out how many seminal parents there are
+          num_seminal_parents = @specimens.select{|s| ['N/A', ''].include?( s.parent_id.to_s )}.length
+
+          fails = 0
+          begin
+          # Reserve Sample ID's for all the seminal parent's
+          # Returns and array of strings with both the sampleID and the sequence number in the format: AAA000000 0000
+            # Only keep first 6 characters which represent the sample id's (remove the sequence suffix)
+            @seminal_parents = @bsi.batch.reserveAvailableBsiIds( @id, 'LAA000000', num_seminal_parents ).map{|i| i[0..-6]} if num_seminal_parents > 0
+          # Not sure why I've been getting this error periodically, but it happens
+          rescue NoMethodError
+            fails += 1
+            retry if fails < 3
+          end
+        end
+
+        def perform_edit_checks
+        end
+
+        def commit
+          @bsi.batch.commit(@id)
+        end
+      end
+
+      class SpecimenImporter < Pipeline::Importer::Base
+        attr_accessor :specimens, :batches, :batch_delimiter
+
+        def initialize(key, options={})
+          @bsi              = RBC.new(key)
+          @specimens        = specimens
+          @batches          = Array.new
+        end
+
+        def import(all_specimens, options={})
+          @specimens = all_specimens
+          subject_ids = @specimens.map{|e| e.subject_id}.uniq
+
+          subject_ids.each_with_index do |sid, i|
+            # Filter by subject_id
+            subset = @specimens.select{|e| e.subject_id == sid}
+
+            batch_properties = {
+              'batch.description' => "Subject: #{sid}"
+            }
+
+            @batch = AddBatch.new(@bsi, batch_properties)
+            @batch.add_specimens(subset)
+            @batch.commit if options['commit']
+
+            @batches << @batch
+          end
+
+          @bsi.common.logoff
+        end
+
+      end
+
+      class Subject < Pipeline::Importer::Base
+      end
+    end
+
+  end
+end

data/lib/bsi-pipeline/models.rb

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+require 'etl-pipeline'
+require 'yaml'
+
+module Pipeline
+  module BSI
+    module Models
+      class Specimen < Pipeline::Model::Base
+        attr_accessor :seminal_parent
+        REQUIRED_ATTRIBUTES = %w(study_id subject_id specimen_type date_drawn date_received label_status billing_method thaws).map{|v| v.to_sym}
+        BFH_MAP = {
+          :study_id               => 'vial.study_id',
+          :specimen_type          => 'vial.mat_type',
+          :current_label          => 'vial.current_label',
+          :parent_id              => 'vial.parent_id',
+          :measurement            => 'vial.volume',
+          :measurement_est        => 'vial.volume_est',
+          :measurement_unit       => 'vial.volume_unit',
+          :stain_type             => 'vial.field_268',
+          :block_status           => 'vial.field_266',
+          :biobank                => 'vial.field_269',
+          :grade                  => 'vial.field_271',
+          :room                   => 'location.room',
+          :building               => 'location.building',
+          :freezer                => 'location.freezer',
+          :shelf                  => 'location.shelf',
+          :rack                   => 'location.rack',
+          :box                    => 'location.box',
+          :row                    => 'vial_location.row',
+          :col                    => 'vial_location.col',
+          :sample_id              => 'sample.sample_id',
+          :appointment_time       => 'sample.appointment_time',
+          :center                 => 'sample.center',
+          :data_manager           => 'sample.data_manager',
+          :date_drawn             => 'sample.date_drawn',
+          :cra                    => 'sample.cra',
+          :kit_id                 => 'sample.kit_id',
+          :pickup_location        => 'sample.pickup_location',
+          :subject_id             => 'sample.subject_id',
+          :surgeon                => 'sample.surgeon',
+          :referring_physician    => 'sample.field_273',
+          :surgical_case_number   => 'sample.surgical_case_number',
+          :surgical_case_part     => 'sample.field_267',
+          :telephone              => 'sample.telephone',
+          :timepoint              => 'sample.time_point',
+          :sample_modifiers       => 'sample.sample_modifiers'
+        }
+
+        vial_props = (BFH_MAP.keys+REQUIRED_ATTRIBUTES).uniq
+        begin
+          vial_props = YAML::load(File.open(File.join(File.dirname(__FILE__), 'vial_props.yaml'))).map{|v| v.to_sym}
+        rescue Errno::ENOENT
+        end
+
+        (vial_props-BFH_MAP.keys+[:specimen_code]).each{|attr_string| attr_accessor attr_string.to_sym}
+        BFH_MAP.keys.each{ |attr| attr_accessor attr }
+
+        # Define Defaults
+        def initialize(bfh={})
+
+          unless bfh.empty?
+            self.seminal_parent = true
+            bfh.keys.each do |bfh_key|
+              if BFH_MAP.has_value?(bfh_key)
+                instance_eval("self.#{BFH_MAP.key(bfh_key)} = '#{bfh[bfh_key]}'")
+              else
+                instance_eval("self.#{bfh_key.gsub(/vial\./, '')} = '#{bfh[bfh_key]}'")
+              end
+            end
+
+          else
+            self.thaws = '0'
+          end
+
+        end
+
+        def bsi_id()
+          "#{self.sample_id} #{self.seq_num}"
+        end
+
+        def seminal_parent?
+          return seminal_parent
+        end
+
+        def to_bfh
+          bfh = Hash.new
+          # Add 1-1 matches/translations
+          formatted_attributes.each do |k,v|
+            if BFH_MAP.has_key?(k)
+              bfh[BFH_MAP[k]] = v
+            else
+              bfh["vial.#{k}"] = v
+            end
+          end
+          bfh
+        end
+
+        def valid?
+          incomplete_attrs = REQUIRED_ATTRIBUTES.find{|v| send(v).nil?}.nil?
+        end
+
+        def missing_attrs
+          REQUIRED_ATTRIBUTES.find_all{|a| send(a).nil?}
+        end
+      end # class Specimen < Pipeline::Model::Base
+
+      class Subject < Pipeline::Model::Base
+      end
+    end
+  end
+end

data/lib/bsi-pipeline/version.rb

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+module Bsi
+  module Pipeline
+    VERSION = "0.0.1"
+  end
+end

data/lib/bsi-pipeline.rb

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+require "bsi-pipeline/version"
+require 'bsi-pipeline/models'
+require 'bsi-pipeline/importer'
+require 'rbc'
+
+module Pipeline
+  module BSI
+    class Pipe
+      def initialize(key, options={})
+        @key = key
+        @options = options
+        @bsi = RBC.new( key, options.merge!( {:debug => true} ) )
+      end
+    end
+
+    include Pipeline::BSI::Models
+    include Pipeline::BSI::Importer
+
+  end # module BSI
+end # module Pipeline

data/spec/add_batch_spec.rb

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+require'spec_helper'
+
+describe AddBatch do
+  before :all do
+    @bsi = RBC.new(
+      { :user     => 'ecog_bot',
+        :pass     => ENV['ECOG_BOT_PASS'],
+        :server   => 'PCF',
+        :url      => 'https://websvc-mirror.bsisystems.com:2271/bsi/xmlrpc'
+    },
+    {
+      :debug => false,
+      :stealth => false
+    }
+    )
+
+    batch_description = {
+      'batch.description' => 'My Batch Description'
+    }
+
+    @batch = AddBatch.new @bsi, batch_description
+  end
+
+  describe '#new' do
+    it 'takes 2 parameters and returns an AddBatch object' do
+      expect(@batch).to be_instance_of AddBatch
+    end
+  end
+
+  describe '#id' do
+    it "returns batch id string for the created batch" do
+      expect(@batch.id).not_to be_nil
+      expect(@batch.id).to be_instance_of String
+    end
+  end
+
+  describe '#type' do
+    it "returns Add (the correct type)" do
+      expect(@batch.type).to eq('Add')
+    end
+  end
+
+  describe '#specimens' do
+    context 'before specimens added' do
+    end
+
+    context 'after specimens added' do
+      before :each do
+        test_specimens = build_list(:specimen, 10)
+        @batch.add_specimens(test_specimens)
+      end
+
+      it 'returns array of Pipeline::BSI::Models::Specimen objects' do
+      end
+    end
+  end
+
+  describe '#properties' do
+    it "returns correct properties hash" do
+      expect(@batch.properties).to be_instance_of Hash
+      expect(@batch.properties).to include('batch.description')
+    end
+  end
+
+  describe '#add_specimens' do
+    it 'takes an array of Pipeline::BSI::Models::Specimen objects and adds them to the batch'
+  end
+
+  describe '#perform_edit_checks' do
+    it 'runs the built in edit check functionality of BSI to check for errors in the Add Batch'
+  end
+
+  describe '#commit' do
+    it 'commits specimens in the batch to the BSI database if all edit checks pass'
+  end
+
+  after :all do
+    @bsi.common.logoff
+  end
+end

data/spec/bsi_pipeline_spec.rb

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+require 'spec_helper'

data/spec/factories/specimen.rb

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+require 'spec_helper'
+
+FactoryGirl.define do
+  sequence :current_label do |n|
+    sprintf '%05d', n
+  end
+
+  factory :specimen, class: Specimen do
+    study_id        "STUDY1"
+    subject_id      "12345"
+    specimen_type   "WB"
+    current_label
+    billing_method  "Direct Billing"
+    date_drawn      "06/14/2013 00:00"
+    date_received   "06/14/2013 05:00"
+    label_status    "Barcoded"
+    thaws           '0'
+
+    # Generic Fluid Specimen
+    trait :fluid do
+      specimen_type "WB"
+    end
+
+    # Generic Slide Specimen
+    trait :slide do
+      specimen_type "SLDTS"
+      stain_type    "H&E"
+    end
+
+    factory :slide_specimen, traits: [:slide]
+  end
+end

data/spec/importer_spec.rb

@@ -0,0 +1,31 @@
+require 'spec_helper'
+
+describe SpecimenImporter do
+  before :each do
+      key = {
+        :user     => 'ecog_bot',
+        :pass     => ENV['ECOG_BOT_PASS'],
+        :server   => 'PCF',
+        :url      => 'https://websvc-mirror.bsisystems.com:2271/bsi/xmlrpc'
+      }
+    @importer = SpecimenImporter.new(key)
+
+  end
+
+  describe '#new' do
+  end
+
+  describe '#import' do
+    context '25 slides' do
+      before :example do
+        @specimens = build_list(:slide_specimen, 25)
+        @importer.import(@specimens)
+      end
+
+      it 'stores all the specimens as an attribute' do
+        expect(@importer.specimens).to be_instance_of Array
+      end
+    end
+
+  end
+end

data/spec/models_spec.rb

@@ -0,0 +1,8 @@
+require 'spec_helper'
+
+describe Specimen do
+  before :all do
+    @specimen = build(:specimen)
+  end
+
+end

data/spec/spec_helper.rb

@@ -0,0 +1,25 @@
+require 'coveralls'
+Coveralls.wear!
+
+require 'pry'
+require 'rbc'
+require 'bsi-pipeline'
+require 'bsi-pipeline/importer'
+require 'bsi-pipeline/models'
+require 'bsi-pipeline/version'
+require 'factory_girl'
+include Pipeline::BSI::Importer
+include Pipeline::BSI::Models
+
+RSpec.configure do |config|
+  config.expect_with :rspec
+
+  config.include FactoryGirl::Syntax::Methods
+
+  config.before(:suite) do
+    FactoryGirl.lint
+  end
+
+  FactoryGirl.definition_file_paths = %w{./factories ./test/factories ./spec/factories}
+  FactoryGirl.find_definitions
+end

data/spec/support/factory_girl.rb

@@ -0,0 +1,13 @@
+RSpec.configure do |config|
+  config.include FactoryGirl::Syntax::Methods
+
+  config.before(:suite) do
+    begin
+      DatabaseCleaner.start
+      FactoryGirl.lint
+    ensure
+      DatabaseCleaner.clean
+    end
+  end
+end
+

metadata

@@ -0,0 +1,269 @@
+--- !ruby/object:Gem::Specification
+name: bsi-pipeline
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- Elijah Christensen
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-07-23 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.6'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.6'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rspec-nc
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: guard
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: guard-rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: terminal-notifier-guard
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: pry
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: pry-remote
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: pry-nav
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: coveralls
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: factory_girl
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: etl-pipeline
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rbc
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+description: plugin for pipeline that provides importers and models for migrating
+  data to bsi
+email:
+- ejd.christensen@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- .coveralls.yml
+- .gitignore
+- .travis.yml
+- Gemfile
+- Guardfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- bsi-pipeline.gemspec
+- lib/bsi-pipeline.rb
+- lib/bsi-pipeline/importer.rb
+- lib/bsi-pipeline/models.rb
+- lib/bsi-pipeline/version.rb
+- spec/add_batch_spec.rb
+- spec/bsi_pipeline_spec.rb
+- spec/factories/specimen.rb
+- spec/importer_spec.rb
+- spec/models_spec.rb
+- spec/spec_helper.rb
+- spec/support/factory_girl.rb
+homepage: ''
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.3.0
+signing_key: 
+specification_version: 4
+summary: plugin for pipeline that provides importers and models for migrating data
+  to bsi
+test_files:
+- spec/add_batch_spec.rb
+- spec/bsi_pipeline_spec.rb
+- spec/factories/specimen.rb
+- spec/importer_spec.rb
+- spec/models_spec.rb
+- spec/spec_helper.rb
+- spec/support/factory_girl.rb