ncs_mdes_warehouse 0.1.0 → 0.1.1

data/CHANGELOG.md

@@ -1,6 +1,27 @@
 NCS Navigator MDES Warehouse History
 ====================================
 
+0.1.1
+-----
+
+- Disable DataMapper's identity map during ETL. It caches created
+  records in memory without limit, so it brings the system to a crawl
+  when loading hundreds of thousands of records.
+
+- Wrap each transformer in a transaction during ETL, and turn off
+  synchronous commits. This combination (not tried separately) gives
+  around a 10% speed boost.
+
+- Loosen gem dependencies for compatibility with Rails 3.0.
+
+- Add `Transformers::SamplingUnits` for generating PSU, SSU, and TSU
+  records from the runtime configuration. (#1602)
+
+- Changed default log path to `/var/log/nubic/ncs/warehouse`. This is
+  parallel with the default configuration paths under `/etc`. (#1605)
+
+- Improve error messages in `VdrXml.from_most_recent_file`. (#1604)
+
 0.1.0
 -----
 

data/lib/ncs_navigator/warehouse/cli.rb

@@ -43,7 +43,8 @@ module NcsNavigator::Warehouse
     desc 'clone-working', 'Copies the contents of the working database to the reporting database'
     def clone_working
       db = DatabaseInitializer.new(configuration)
-      db.clone_working_to_reporting
+      db.set_up_repository(:both)
+      db.clone_working_to_reporting or exit(1)
     end
 
     desc 'emit-xml [FILENAME]', 'Generates the VDR submission XML'
@@ -74,7 +75,7 @@ DESC
 
       success = TransformLoad.new(configuration).run
       if success || options['force']
-        db.clone_working_to_reporting
+        db.clone_working_to_reporting or exit(1)
       else
         configuration.shell.say_line "There were errors during ETL. Reporting database not updated."
         configuration.shell.say_line "See the log and the database table wh_transform_error for more details."

data/lib/ncs_navigator/warehouse/configuration.rb

@@ -269,7 +269,7 @@ module NcsNavigator::Warehouse
     #
     # @return [Pathname]
     def log_file
-      @log_directory ||= Pathname.new("/var/log/ncs/warehouse/#{env}.log")
+      @log_directory ||= Pathname.new("/var/log/nubic/ncs/warehouse/#{env}.log")
     end
 
     ##

data/lib/ncs_navigator/warehouse/database_initializer.rb

@@ -80,11 +80,7 @@ module NcsNavigator::Warehouse
     #
     # @return [void]
     def replace_schema
-      shell.say "Dropping everything"
-      log.info "Dropping everything in working schema"
-      ::DataMapper.repository(:mdes_warehouse_working).adapter.
-        execute("DROP OWNED BY #{params(:working)['username']}")
-      shell.clear_line_then_say "Dropped everything in working schema.\n"
+      drop_all(:working)
 
       shell.say "Loading MDES models..."
       log.info "Initializing schema for MDES #{configuration.mdes.specification_version}"
@@ -98,11 +94,23 @@ module NcsNavigator::Warehouse
         "Added #{configuration.models_module.mdes_order.size} MDES tables.\n")
     end
 
+    def drop_all(which)
+      shell.say "Dropping everything in #{which} schema"
+      log.info "Dropping everything in #{which} schema"
+      ::DataMapper.repository(:"mdes_warehouse_#{which}").adapter.
+        execute("DROP OWNED BY #{params(which)['username']}")
+      shell.clear_line_then_say "Dropped everything in #{which} schema.\n"
+    end
+    private :drop_all
+
     ##
     # Replaces the reporting database with a clone of the working
     # database. This method relies on the command line `pg_dump` and
-    # `pg_restore` commands.
+    # `pg_restore` commands. In addition, you must also have
+    # previously called {#set_up_repository} with `:both` as the
+    # argument.
     #
+    # @return [true,false] whether the clone succeeded.
     # @see Configuration#pg_bin_path
     def clone_working_to_reporting
       PostgreSQL::Pgpass.new.tap do |pgpass|
@@ -121,16 +129,24 @@ module NcsNavigator::Warehouse
         configuration.pg_bin('pg_restore'),
         pg_params(params(:reporting)),
         '--schema', 'public',
-        '--clean',
         '--dbname', params(:reporting)['database']
       ].flatten
 
+      drop_all(:reporting)
+
       command = "#{escape_cmd dump_cmd} | #{escape_cmd restore_cmd}"
+      shell.say 'Cloning working schema into reporting schema...'
       log.info('Cloning working schema into reporting schema')
       log.debug("Clone command: #{command.inspect}")
       unless system(command)
-        configuration.shell.say_line "Clone from working to reporting failed. See above for detail."
-        exit 1
+        shell.clear_line_then_say(
+          "Clone from working to reporting failed. See above for detail.\n")
+        log.error('Clone failed.')
+        return false
+      else
+        shell.clear_line_then_say("Clone from working to reporting successful.\n")
+        log.info('Clone succeeded.')
+        return true
       end
     end
 

data/lib/ncs_navigator/warehouse/transform_load.rb

@@ -18,13 +18,23 @@ module NcsNavigator::Warehouse
     def run
       position = 0
       @statuses = configuration.transformers.collect do |transformer|
-        ::DataMapper.repository(:mdes_warehouse_working) do
+        ::DataMapper.repository(:mdes_warehouse_working) do |repo|
+          # redefine identity map as a no-op so it doesn't cache
+          # anything. TODO: provide a patch to DataMapper that makes
+          # something like this an option.
+          def repo.identity_map(model); {}; end
+
           build_status_for(transformer, position).tap do |status|
-            begin
-              transformer.transform(status)
-            rescue => e
-              shell.say_line("\nTransform failed. (See log for more detail.)")
-              status.add_error("Transform failed. #{e.class}: #{e}.")
+            TransformStatus.transaction do
+              if repo.adapter.to_s =~ /Postgres/
+                repo.adapter.execute("SET LOCAL synchronous_commit TO OFF")
+              end
+              begin
+                transformer.transform(status)
+              rescue => e
+                shell.say_line("\nTransform failed. (See log for more detail.)")
+                status.add_error("Transform failed. #{e.class}: #{e}.")
+              end
             end
             status.end_time = Time.now
             unless status.save

data/lib/ncs_navigator/warehouse/transformers.rb

@@ -13,6 +13,7 @@ module NcsNavigator::Warehouse
   module Transformers
     autoload :Database,        'ncs_navigator/warehouse/transformers/database'
     autoload :EnumTransformer, 'ncs_navigator/warehouse/transformers/enum_transformer'
+    autoload :SamplingUnits,   'ncs_navigator/warehouse/transformers/sampling_units'
     autoload :VdrXml,          'ncs_navigator/warehouse/transformers/vdr_xml'
   end
 end

data/lib/ncs_navigator/warehouse/transformers/database.rb

@@ -287,13 +287,12 @@ module NcsNavigator::Warehouse::Transformers
       #
       # @return [void]
       def produce_one_for_one(name, model, options={})
-        options[:on_unused] ||= on_unused_columns
         options[:column_map] =
           (options[:column_map] || {}).inject({}) { |h, (k, v)| h[k.to_s] = v.to_s; h }
-        options[:ignored_columns] =
-          (options[:ignored_columns] || []).collect(&:to_s) + ignored_columns
+        options[:ignored_columns] = (options[:ignored_columns] || []).collect(&:to_s)
 
-        record_producers << OneForOneProducer.new(name, options.delete(:query), model, options)
+        record_producers <<
+          OneForOneProducer.new(name, options.delete(:query), model, self, options)
       end
     end
 
@@ -308,11 +307,12 @@ module NcsNavigator::Warehouse::Transformers
     ##
     # The class encapsulating one call to {DSL#produce_one_for_one}
     class OneForOneProducer < RecordProducer
-      attr_reader :model, :options
+      attr_reader :model, :options, :dsl_host
 
-      def initialize(name, query, model, options)
+      def initialize(name, query, model, dsl_host, options)
         super(name, query, self)
         @model = model
+        @dsl_host = dsl_host
         @options = options
       end
 
@@ -321,9 +321,9 @@ module NcsNavigator::Warehouse::Transformers
       # row as mapped by {#column_map}.
       def convert_row(row)
         col_map = column_map(row.members)
-        unused = row.members.collect(&:to_s) - col_map.keys - options[:ignored_columns]
+        unused = row.members.collect(&:to_s) - col_map.keys - ignored_columns
 
-        if options[:on_unused] == :fail && !unused.empty?
+        if on_unused == :fail && !unused.empty?
           raise UnusedColumnsForModelError.new(unused)
         end
         model.new(
@@ -374,6 +374,16 @@ module NcsNavigator::Warehouse::Transformers
         end
       end
       private :prefixed_property_name
+
+      def on_unused
+        options[:on_unused] || dsl_host.on_unused_columns
+      end
+      private :on_unused
+
+      def ignored_columns
+        options[:ignored_columns] + dsl_host.ignored_columns
+      end
+      private :ignored_columns
     end
 
     ##

data/lib/ncs_navigator/warehouse/transformers/sampling_units.rb

@@ -0,0 +1,96 @@
+require 'ncs_navigator/warehouse'
+
+require 'forwardable'
+
+module NcsNavigator::Warehouse::Transformers
+  ##
+  # An enumerator that yields the sampling unit records implied by the
+  # current `NcsNavigator::Configuration`.
+  #
+  # @see Configuration#navigator
+  class SamplingUnits
+    include Enumerable
+    extend Forwardable
+
+    attr_reader :configuration
+    def_delegators :configuration, :shell, :log
+
+    def self.create_transformer(config)
+      EnumTransformer.new(config, new(config))
+    end
+
+    def initialize(config)
+      @configuration = config
+    end
+
+    def each
+      log.info("Generating MDES records for sampling units.")
+
+      shell_describe('PSU', configuration.navigator.psus.size)
+      configuration.navigator.psus.each do |nav_psu|
+        yield create_psu(nav_psu)
+      end
+
+      shell_describe('SSU', configuration.navigator.ssus.size)
+      configuration.navigator.ssus.each do |nav_ssu|
+        yield create_ssu(nav_ssu)
+      end
+
+      tsus = configuration.navigator.ssus.collect { |nav_ssu| nav_ssu.tsus }.flatten
+      shell_describe('TSU', tsus.size)
+      tsus.each do |nav_tsu|
+        yield create_tsu(nav_tsu)
+      end
+
+      log.info("All sampling unit records generated.")
+      shell.clear_line_then_say("All sampling unit records generated.\n")
+    end
+
+    private
+
+    def shell_describe(what, count)
+      plural = ('s' if count != 1)
+      shell.clear_line_then_say("Generating MDES record#{plural} for #{count} #{what}#{plural}")
+    end
+
+    def psu_model
+      configuration.models_module.const_get(:Psu)
+    end
+
+    def create_psu(nav_psu)
+      psu_model.new(
+        :psu_id => nav_psu.id,
+        :sc_id => configuration.navigator.sc_id,
+        :recruit_type => configuration.navigator.recruitment_type_id,
+        :psu_name => configuration.mdes.types.detect { |t| t.name == 'psu_cl1' }.code_list.
+          detect { |code| code.value == nav_psu.id }.label
+      )
+    end
+
+    def ssu_model
+      configuration.models_module.const_get(:Ssu)
+    end
+
+    def create_ssu(nav_ssu)
+      ssu_model.new(
+        :ssu_id => nav_ssu.id,
+        :ssu_name => nav_ssu.name,
+        :psu_id => nav_ssu.psu.id,
+        :sc_id => configuration.navigator.sc_id
+      )
+    end
+
+    def tsu_model
+      configuration.models_module.const_get(:Tsu)
+    end
+
+    def create_tsu(nav_tsu)
+      tsu_model.new(
+        :tsu_id => nav_tsu.id,
+        :tsu_name => nav_tsu.name,
+        :psu_id => nav_tsu.ssu.psu.id,
+        :sc_id => configuration.navigator.sc_id
+      )
+    end
+  end
+end

data/lib/ncs_navigator/warehouse/transformers/vdr_xml.rb

@@ -13,12 +13,24 @@ module NcsNavigator::Warehouse::Transformers
       end
 
       ##
+      # @param config [Configuration] the configuration for the
+      #   warehouse.
+      # @param list [String,Array<String>] the files to consider. This
+      #   may be either a glob or an explicit list of files.
+      #
       # @return [#transform] a transformer for the most recently
       #   modified VDR XML file from the given list of files.
       def from_most_recent_file(config, list)
+        files =
+          if String === list
+            Dir[list].tap { |a| fail "Glob #{list} does not match any files." if a.empty? }
+          else
+            list.tap { |a| fail "The file list is empty." if a.empty? }
+          end
+
         from_file(
           config,
-          list.collect { |fn| [fn, File.stat(fn).mtime] }.
+          files.collect { |fn| [fn, File.stat(fn).mtime] }.
             sort_by { |fn, mtime| mtime }.reverse.first.first)
       end
     end

data/lib/ncs_navigator/warehouse/version.rb

@@ -1,5 +1,5 @@
 module NcsNavigator
   module Warehouse
-    VERSION = '0.1.0'
+    VERSION = '0.1.1'
   end
 end

data/ncs_mdes_warehouse.gemspec

@@ -16,16 +16,16 @@ Gem::Specification.new do |s|
   s.require_paths = ["lib", "generated_models"]
 
   s.add_dependency 'ncs_mdes', '~> 0.4', '>= 0.4.2'
-  s.add_dependency 'ncs_navigator_configuration', '~> 0.1'
+  s.add_dependency 'ncs_navigator_configuration', '~> 0.2'
 
   s.add_dependency 'activesupport', '~> 3.0'
-  s.add_dependency 'i18n', '~> 0.6' # required by activesupport
+  s.add_dependency 'i18n', '~> 0.4' # required by activesupport
 
   s.add_dependency 'thor', '~> 0.14.6'
   s.add_dependency 'rubyzip', '~> 0.9.4'
 
   s.add_dependency 'nokogiri', '~> 1.5.0'
-  s.add_dependency 'builder', '~> 3.0'
+  s.add_dependency 'builder', '>= 2.1.2'
 
   s.add_dependency 'data_mapper', '~> 1.2.0'
   s.add_dependency 'bcdatabase', '~> 1.1'

data/spec/navigator.ini

@@ -1,5 +1,6 @@
 [Study Center]
-sc_id = "2000042"
+sc_id = "20000029"
+recruitment_type_id = "3"
 sampling_units_file = "test_samples.csv"
 
 [Staff Portal]

data/spec/ncs_navigator/warehouse/configuration_spec.rb

@@ -157,8 +157,8 @@ module NcsNavigator::Warehouse
       end
 
       describe 'by default' do
-        it 'is /var/log/ncs/warehouse/{env_name}.log' do
-          config.log_file.to_s.should == '/var/log/ncs/warehouse/the_moon.log'
+        it 'is /var/log/nubic/ncs/warehouse/{env_name}.log' do
+          config.log_file.to_s.should == '/var/log/nubic/ncs/warehouse/the_moon.log'
         end
 
         it 'is a Pathname' do
@@ -187,7 +187,7 @@ module NcsNavigator::Warehouse
           end
 
           it 'reverts to the default' do
-            config.log_file.to_s.should == '/var/log/ncs/warehouse/the_moon.log'
+            config.log_file.to_s.should == '/var/log/nubic/ncs/warehouse/the_moon.log'
           end
         end
 

data/spec/ncs_navigator/warehouse/transform_load_spec.rb

@@ -137,6 +137,23 @@ module NcsNavigator::Warehouse
 
         it 'sends on failure'
       end
+
+      # This is a crappy test; it would be better if it could be done
+      # another way. Unfortunately, it doesn't look like DataMapper
+      # exposes information to allow another way to check this.
+      it "defeats DataMapper's caching" do
+        seen_maps = []
+        identity_map_tracker_transformer = BlockTransformer.new { |s|
+          seen_maps << ::DataMapper::Repository.context.first.instance_eval { @identity_maps }
+        }
+        config.add_transformer(identity_map_tracker_transformer)
+        config.add_transformer(identity_map_tracker_transformer)
+
+        loader.run
+        loader.statuses.collect { |s| s.transform_errors }.flatten.should == []
+
+        seen_maps.should == [{}, {}]
+      end
     end
 
     class ::BlockTransformer

data/spec/ncs_navigator/warehouse/transformers/database_spec.rb

@@ -304,14 +304,15 @@ module NcsNavigator::Warehouse::Transformers
 
           describe 'when #on_unused_columns is set to :fail' do
             let(:cls) {
-              sample_class do
-                on_unused_columns :fail
+              sample_class.tap do |c|
+                c.on_unused_columns :fail
+                c.produce_one_for_one(:addresses, address_model, options)
               end
             }
 
             it 'fails appropriately' do
               begin
-                model_row(:address_type => '-5', :address_length => '6')
+                producer.call(make_row :address_type => '-5', :address_length => '6')
                 fail "Exception not thrown"
               rescue Database::UnusedColumnsForModelError => e
                 e.unused.should == %w(address_length)
@@ -320,7 +321,13 @@ module NcsNavigator::Warehouse::Transformers
 
             it 'does not fail if the global setting is overridden' do
               options[:on_unused] = :ignore
-              lambda { model_row(:address_type => '-5', :address_length => '6') }.
+              lambda { producer.call(make_row :address_type => '-5', :address_length => '6') }.
+                should_not raise_error
+            end
+
+            it 'can be ignored by modifying the global setting' do
+              cls.on_unused_columns :ignore
+              lambda { producer.call(make_row :address_type => '-5', :address_length => '6') }.
                 should_not raise_error
             end
           end

data/spec/ncs_navigator/warehouse/transformers/sampling_units_spec.rb

@@ -0,0 +1,103 @@
+require File.expand_path('../../../../spec_helper', __FILE__)
+
+module NcsNavigator::Warehouse::Transformers
+  describe SamplingUnits, :use_mdes, :slow do
+    subject { SamplingUnits.new(spec_config) }
+
+    let(:test_sc_id) { '20000029' }
+    let(:test_psu_id) { '20000030' }
+
+    describe '.create_transformer' do
+      it 'creates a transformer' do
+        SamplingUnits.create_transformer(spec_config).should respond_to(:transform)
+      end
+    end
+
+    it 'yields everything in MDES order' do
+      subject.to_a.collect { |i| i.class.to_s.demodulize }.should == %w(Psu Ssu Ssu Tsu)
+    end
+
+    describe 'emitted PSU' do
+      let(:psu_model) { spec_config.models_module.const_get(:Psu) }
+      let(:psu) { subject.to_a.detect { |emitted| emitted.is_a?(psu_model) } }
+
+      it 'exists' do
+        psu.should_not be_nil
+      end
+
+      it 'has the study center ID from the configuration' do
+        psu.sc_id.should == test_sc_id
+      end
+
+      it 'has the correct ID' do
+        psu.psu_id.should == test_psu_id
+      end
+
+      it 'has the name derived from the MDES' do
+        psu.psu_name.should == 'Cook County, IL (Wave 1)'
+      end
+
+      it 'uses the recruitment type from the configuration' do
+        psu.recruit_type.should == '3'
+      end
+    end
+
+    describe 'emitted SSU set' do
+      let(:ssu_model) { spec_config.models_module.const_get(:Ssu) }
+      let(:ssus) { subject.to_a.select { |emitted| emitted.is_a?(ssu_model) } }
+
+      it 'includes all the SSUs from the configuration' do
+        ssus.collect(&:ssu_id).sort.should == %w(24 42)
+      end
+
+      describe 'an exemplar' do
+        let(:ssu) { ssus.detect { |s| s.ssu_id == '42' } }
+
+        it 'has the name' do
+          ssu.ssu_name.should == 'UPT-42'
+        end
+
+        it 'has the ID' do
+          ssu.ssu_id.should == '42'
+        end
+
+        it 'has the SC ID' do
+          ssu.sc_id.should == '20000029'
+        end
+
+        it 'has the PSU ID' do
+          ssu.psu_id.should == test_psu_id
+        end
+      end
+    end
+
+    describe 'emitted TSU set' do
+      let(:tsu_model) { spec_config.models_module.const_get(:Tsu) }
+      let(:tsus) { subject.to_a.select { |emitted| emitted.is_a?(tsu_model) } }
+
+      it 'includes all the TSUs from the configuration' do
+        tsus.collect(&:tsu_id).sort.should == %w(42-3)
+      end
+
+      describe 'an exemplar' do
+        let(:tsu) { tsus.detect { |s| s.tsu_id == '42-3' } }
+
+        it 'has the name' do
+          tsu.tsu_name.should == 'UPT-42X'
+        end
+
+        it 'has the ID' do
+          tsu.tsu_id.should == '42-3'
+        end
+
+        it 'has the SC ID' do
+          tsu.sc_id.should == '20000029'
+        end
+
+        it 'has the PSU ID' do
+          tsu.psu_id.should == test_psu_id
+        end
+      end
+    end
+  end
+end

data/spec/ncs_navigator/warehouse/transformers/vdr_xml_spec.rb

@@ -27,7 +27,7 @@ module NcsNavigator::Warehouse::Transformers
 
     describe '.from_most_recent_file' do
       let(:path) { tmpdir('contractor-files') }
-      subject { VdrXml.from_most_recent_file(config, Dir[File.join(path, '*')]) }
+      subject { VdrXml.from_most_recent_file(config, list_or_glob) }
 
       before do
         system("touch -t 02030405 '#{path}/a'")
@@ -35,11 +35,41 @@ module NcsNavigator::Warehouse::Transformers
         system("touch -t 02020405 '#{path}/c'")
       end
 
-      it 'uses the most recent filename from the list' do
-        subject.enum.filename.should == File.join(path, 'b')
+      describe 'with a file list' do
+        let(:list_or_glob) { Dir[File.join(path, '*')] }
+
+        it 'uses the most recent filename from the list' do
+          subject.enum.filename.should == File.join(path, 'b')
+        end
+
+        include_examples 'a VDR transformer'
+
+        describe 'that is empty' do
+          let(:list_or_glob) { [] }
+
+          it 'fails' do
+            lambda { subject }.should raise_error /The file list is empty./
+          end
+        end
       end
 
-      include_examples 'a VDR transformer'
+      describe 'with a glob' do
+        let(:list_or_glob) { File.join(path, '*') }
+
+        it 'uses the most recent filename matched by the glob' do
+          subject.enum.filename.should == File.join(path, 'b')
+        end
+
+        include_examples 'a VDR transformer'
+
+        describe 'when the glob does not match anything' do
+          let(:list_or_glob) { File.join(path, 'z*') }
+
+          it 'fails' do
+            lambda { subject }.should raise_error %r{Glob .*?./z\* does not match any files}
+          end
+        end
+      end
     end
   end
 end

data/spec/ncs_navigator/warehouse/xml_emitter_spec.rb

@@ -23,11 +23,11 @@ module NcsNavigator::Warehouse
     # Most of the details of the XML are tested on the MdesModel mixin
     describe 'the generated XML', :slow do
       it 'includes the SC from the configuration' do
-        xml.xpath('//sc_id').text.should == '2000042'
+        xml.xpath('//sc_id').text.should == '20000029'
       end
 
       it 'includes the PSU from the configuration' do
-        xml.xpath('//psu_id').text.should == '2000423'
+        xml.xpath('//psu_id').text.should == '20000030'
       end
 
       it 'includes the appropriate specification version' do

data/spec/test_samples.csv

@@ -1,2 +1,3 @@
 PSU_ID, AREA, SSU_ID, SSU_NAME, TSU_ID, TSU_NAME
-2000423, Uptown, 42, UPT-42, 42-3, UPT-42X
+20000030, Uptown, 42, UPT-42, 42-3, UPT-42X
+20000030, Downtown, 24, DT-24

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: ncs_mdes_warehouse
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.1.1
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-11-14 00:00:00.000000000Z
+date: 2011-11-18 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ncs_mdes
-  requirement: &2154732560 !ruby/object:Gem::Requirement
+  requirement: &2156621720 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -24,21 +24,21 @@ dependencies:
         version: 0.4.2
   type: :runtime
   prerelease: false
-  version_requirements: *2154732560
+  version_requirements: *2156621720
 - !ruby/object:Gem::Dependency
   name: ncs_navigator_configuration
-  requirement: &2154731640 !ruby/object:Gem::Requirement
+  requirement: &2156620240 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '0.1'
+        version: '0.2'
   type: :runtime
   prerelease: false
-  version_requirements: *2154731640
+  version_requirements: *2156620240
 - !ruby/object:Gem::Dependency
   name: activesupport
-  requirement: &2154731040 !ruby/object:Gem::Requirement
+  requirement: &2156614960 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -46,21 +46,21 @@ dependencies:
         version: '3.0'
   type: :runtime
   prerelease: false
-  version_requirements: *2154731040
+  version_requirements: *2156614960
 - !ruby/object:Gem::Dependency
   name: i18n
-  requirement: &2154730440 !ruby/object:Gem::Requirement
+  requirement: &2156613720 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: '0.6'
+        version: '0.4'
   type: :runtime
   prerelease: false
-  version_requirements: *2154730440
+  version_requirements: *2156613720
 - !ruby/object:Gem::Dependency
   name: thor
-  requirement: &2154729880 !ruby/object:Gem::Requirement
+  requirement: &2156612920 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -68,10 +68,10 @@ dependencies:
         version: 0.14.6
   type: :runtime
   prerelease: false
-  version_requirements: *2154729880
+  version_requirements: *2156612920
 - !ruby/object:Gem::Dependency
   name: rubyzip
-  requirement: &2154729320 !ruby/object:Gem::Requirement
+  requirement: &2156612060 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -79,10 +79,10 @@ dependencies:
         version: 0.9.4
   type: :runtime
   prerelease: false
-  version_requirements: *2154729320
+  version_requirements: *2156612060
 - !ruby/object:Gem::Dependency
   name: nokogiri
-  requirement: &2154728700 !ruby/object:Gem::Requirement
+  requirement: &2156611040 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -90,21 +90,21 @@ dependencies:
         version: 1.5.0
   type: :runtime
   prerelease: false
-  version_requirements: *2154728700
+  version_requirements: *2156611040
 - !ruby/object:Gem::Dependency
   name: builder
-  requirement: &2154728100 !ruby/object:Gem::Requirement
+  requirement: &2156609980 !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ~>
+    - - ! '>='
       - !ruby/object:Gem::Version
-        version: '3.0'
+        version: 2.1.2
   type: :runtime
   prerelease: false
-  version_requirements: *2154728100
+  version_requirements: *2156609980
 - !ruby/object:Gem::Dependency
   name: data_mapper
-  requirement: &2154727600 !ruby/object:Gem::Requirement
+  requirement: &2156609220 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -112,10 +112,10 @@ dependencies:
         version: 1.2.0
   type: :runtime
   prerelease: false
-  version_requirements: *2154727600
+  version_requirements: *2156609220
 - !ruby/object:Gem::Dependency
   name: bcdatabase
-  requirement: &2154726800 !ruby/object:Gem::Requirement
+  requirement: &2156608360 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -123,10 +123,10 @@ dependencies:
         version: '1.1'
   type: :runtime
   prerelease: false
-  version_requirements: *2154726800
+  version_requirements: *2156608360
 - !ruby/object:Gem::Dependency
   name: dm-postgres-adapter
-  requirement: &2154709640 !ruby/object:Gem::Requirement
+  requirement: &2156607420 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -134,10 +134,10 @@ dependencies:
         version: 1.2.0
   type: :runtime
   prerelease: false
-  version_requirements: *2154709640
+  version_requirements: *2156607420
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &2154709020 !ruby/object:Gem::Requirement
+  requirement: &2156606300 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -145,10 +145,10 @@ dependencies:
         version: '2.6'
   type: :development
   prerelease: false
-  version_requirements: *2154709020
+  version_requirements: *2156606300
 - !ruby/object:Gem::Dependency
   name: rake
-  requirement: &2154708560 !ruby/object:Gem::Requirement
+  requirement: &2156604880 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -156,10 +156,10 @@ dependencies:
         version: 0.9.2
   type: :development
   prerelease: false
-  version_requirements: *2154708560
+  version_requirements: *2156604880
 - !ruby/object:Gem::Dependency
   name: yard
-  requirement: &2154707960 !ruby/object:Gem::Requirement
+  requirement: &2156603540 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -167,10 +167,10 @@ dependencies:
         version: 0.7.2
   type: :development
   prerelease: false
-  version_requirements: *2154707960
+  version_requirements: *2156603540
 - !ruby/object:Gem::Dependency
   name: ci_reporter
-  requirement: &2154707300 !ruby/object:Gem::Requirement
+  requirement: &2156602740 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -178,10 +178,10 @@ dependencies:
         version: 1.6.5
   type: :development
   prerelease: false
-  version_requirements: *2154707300
+  version_requirements: *2156602740
 - !ruby/object:Gem::Dependency
   name: fakefs
-  requirement: &2154706660 !ruby/object:Gem::Requirement
+  requirement: &2156601440 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -189,7 +189,7 @@ dependencies:
         version: 0.4.0
   type: :development
   prerelease: false
-  version_requirements: *2154706660
+  version_requirements: *2156601440
 description: 
 email:
 - r-sutphin@northwestern.edu
@@ -493,6 +493,7 @@ files:
 - lib/ncs_navigator/warehouse/transformers.rb
 - lib/ncs_navigator/warehouse/transformers/database.rb
 - lib/ncs_navigator/warehouse/transformers/enum_transformer.rb
+- lib/ncs_navigator/warehouse/transformers/sampling_units.rb
 - lib/ncs_navigator/warehouse/transformers/vdr_xml.rb
 - lib/ncs_navigator/warehouse/transformers/vdr_xml/reader.rb
 - lib/ncs_navigator/warehouse/updating_shell.rb
@@ -512,6 +513,7 @@ files:
 - spec/ncs_navigator/warehouse/transform_load_spec.rb
 - spec/ncs_navigator/warehouse/transformers/database_spec.rb
 - spec/ncs_navigator/warehouse/transformers/enum_transformer_spec.rb
+- spec/ncs_navigator/warehouse/transformers/sampling_units_spec.rb
 - spec/ncs_navigator/warehouse/transformers/vdr_xml/made_up_vdr_xml.xml
 - spec/ncs_navigator/warehouse/transformers/vdr_xml/reader_spec.rb
 - spec/ncs_navigator/warehouse/transformers/vdr_xml_spec.rb
@@ -532,18 +534,12 @@ required_ruby_version: !ruby/object:Gem::Requirement
   - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
-      segments:
-      - 0
-      hash: -4006681032861892905
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:
   - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
-      segments:
-      - 0
-      hash: -4006681032861892905
 requirements: []
 rubyforge_project: 
 rubygems_version: 1.8.10
@@ -564,6 +560,7 @@ test_files:
 - spec/ncs_navigator/warehouse/transform_load_spec.rb
 - spec/ncs_navigator/warehouse/transformers/database_spec.rb
 - spec/ncs_navigator/warehouse/transformers/enum_transformer_spec.rb
+- spec/ncs_navigator/warehouse/transformers/sampling_units_spec.rb
 - spec/ncs_navigator/warehouse/transformers/vdr_xml/made_up_vdr_xml.xml
 - spec/ncs_navigator/warehouse/transformers/vdr_xml/reader_spec.rb
 - spec/ncs_navigator/warehouse/transformers/vdr_xml_spec.rb