ncs_mdes_warehouse 0.3.1 → 0.3.2

data/CHANGELOG.md

@@ -1,6 +1,17 @@
 NCS Navigator MDES Warehouse History
 ====================================
 
+0.3.2
+-----
+
+- Correct VDR XML reader for the case where an MDES table that
+  contains a variable with the same name as the table. (#1695)
+- Include the Study Center record in the instances created from the
+  `SamplingUnits` transformer. (#1690)
+- Change the default compare level to 3. It turns out that the full
+  compare is not that slow, so there's no reason to default it to 1.
+  (#1691)
+
 0.3.1
 -----
 

data/lib/ncs_navigator/warehouse/cli.rb

@@ -114,7 +114,7 @@ DESC
       :desc => 'The configuration file for warehouse A. The environment default will be used if not specified.'
     method_option 'warehouse-b', :type => :string, :required => true, :aliases => %w(-b),
       :desc => 'The configuration file for warehouse B.'
-    method_option 'level', :type => :numeric, :default => 1,
+    method_option 'level', :type => :numeric, :default => 3,
       :desc => 'The level of detail for the comparison.'
     def compare
       if options['warehouse-a']

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

@@ -26,6 +26,9 @@ module NcsNavigator::Warehouse::Transformers
     def each
       log.info("Generating MDES records for sampling units.")
 
+      shell_describe('Study Center', 1)
+      yield create_study_center
+
       shell_describe('PSU', configuration.navigator.psus.size)
       configuration.navigator.psus.each do |nav_psu|
         yield create_psu(nav_psu)
@@ -42,8 +45,8 @@ module NcsNavigator::Warehouse::Transformers
         yield create_tsu(nav_tsu)
       end
 
-      log.info("All sampling unit records generated.")
-      shell.clear_line_then_say("All sampling unit records generated.\n")
+      log.info("Sampling unit records complete.")
+      shell.clear_line_then_say("Sampling unit records complete.\n")
     end
 
     private
@@ -53,26 +56,33 @@ module NcsNavigator::Warehouse::Transformers
       shell.clear_line_then_say("Generating MDES record#{plural} for #{count} #{what}#{plural}")
     end
 
-    def psu_model
-      configuration.models_module.const_get(:Psu)
+    def code_label(type_name, value)
+      configuration.mdes.types.detect { |t| t.name == type_name }.code_list.
+        detect { |code| code.value == value }.label
+    end
+
+    def model(name)
+      configuration.models_module.const_get(name)
+    end
+
+    def create_study_center
+      model(:StudyCenter).new(
+        :sc_id => configuration.navigator.sc_id,
+        :sc_name => code_label('study_center_cl1', configuration.navigator.sc_id)
+      )
     end
 
     def create_psu(nav_psu)
-      psu_model.new(
+      model(:Psu).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
+        :psu_name => code_label('psu_cl1', nav_psu.id)
       )
     end
 
-    def ssu_model
-      configuration.models_module.const_get(:Ssu)
-    end
-
     def create_ssu(nav_ssu)
-      ssu_model.new(
+      model(:Ssu).new(
         :ssu_id => nav_ssu.id,
         :ssu_name => nav_ssu.name,
         :psu_id => nav_ssu.psu.id,
@@ -80,12 +90,8 @@ module NcsNavigator::Warehouse::Transformers
       )
     end
 
-    def tsu_model
-      configuration.models_module.const_get(:Tsu)
-    end
-
     def create_tsu(nav_tsu)
-      tsu_model.new(
+      model(:Tsu).new(
         :tsu_id => nav_tsu.id,
         :tsu_name => nav_tsu.name,
         :psu_id => nav_tsu.ssu.psu.id,

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

@@ -67,7 +67,7 @@ class NcsNavigator::Warehouse::Transformers::VdrXml
       if node.local_name == 'transmission_tables'
         @in_table_section = is_open
       elsif @current_model_class
-        if node.local_name == @current_model_class.mdes_table_name
+        if !is_open && node.local_name == @current_model_class.mdes_table_name
           # on the way out of this record
           yield build_current_instance
           @current_model_class = nil

data/lib/ncs_navigator/warehouse/version.rb

@@ -1,5 +1,5 @@
 module NcsNavigator
   module Warehouse
-    VERSION = '0.3.1'
+    VERSION = '0.3.2'
   end
 end

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

@@ -14,7 +14,28 @@ module NcsNavigator::Warehouse::Transformers
     end
 
     it 'yields everything in MDES order' do
-      subject.to_a.collect { |i| i.class.to_s.demodulize }.should == %w(Psu Ssu Ssu Tsu)
+      subject.to_a.collect { |i| i.class.to_s.demodulize }.should == %w(StudyCenter Psu Ssu Ssu Tsu)
+    end
+
+    describe 'emitted Study Center' do
+      let(:sc_model) { spec_config.models_module.const_get(:StudyCenter) }
+      let(:sc) { subject.to_a.detect { |emitted| emitted.is_a?(sc_model) } }
+
+      it 'exists' do
+        sc.should_not be_nil
+      end
+
+      it 'has the study center ID from the configuration' do
+        sc.sc_id.should == test_sc_id
+      end
+
+      it 'has the name from the MDES' do
+        sc.sc_name.should == 'Northwestern University'
+      end
+
+      it 'has no comments' do
+        sc.comments.should be_nil
+      end
     end
 
     describe 'emitted PSU' do

data/spec/ncs_navigator/warehouse/transformers/vdr_xml/made_up_vdr_xml.xml

@@ -13,6 +13,7 @@
       <comments>NA</comments>
       <transaction_type>NA</transaction_type>
     </study_center>
+
     <psu>
       <sc_id>20000029</sc_id>
       <psu_id>20000030</psu_id>
@@ -20,6 +21,7 @@
       <recruit_type>3</recruit_type>
       <transaction_type>NA</transaction_type>
     </psu>
+
     <ssu>
       <sc_id>20000029</sc_id>
       <psu_id>20000030</psu_id>
@@ -27,6 +29,7 @@
       <ssu_name>The unluckiest SSU</ssu_name>
       <transaction_type>NA</transaction_type>
     </ssu>
+
     <listing_unit>
       <psu_id>20000030</psu_id>
       <list_id>100</list_id>
@@ -37,6 +40,7 @@
       <list_comment>NA</list_comment>
       <transaction_type>NA</transaction_type>
     </listing_unit>
+
     <person>
       <psu_id>20000030</psu_id>
       <person_id>74</person_id>
@@ -72,6 +76,7 @@
       <person_comment>NA</person_comment>
       <transaction_type xsi:nil="true"/>
     </person>
+
     <link_contact>
       <psu_id>20000030</psu_id>
       <contact_link_id>36</contact_link_id>
@@ -83,5 +88,29 @@
       <provider_id>-7</provider_id>
       <transaction_type>NA</transaction_type>
     </link_contact>
+
+    <email>
+      <psu_id>20000030</psu_id>
+      <email_id>18</email_id>
+      <person_id>74</person_id>
+      <institute_id></institute_id>
+      <provider_id></provider_id>
+      <email>jo@example.net</email>
+      <email_rank>1</email_rank>
+      <email_rank_oth>-7</email_rank_oth>
+      <email_info_source>1</email_info_source>
+      <email_info_source_oth>-7</email_info_source_oth>
+      <email_info_date>2011-03-31</email_info_date>
+      <email_info_update>9777-97-97</email_info_update>
+      <email_type>1</email_type>
+      <email_type_oth>-7</email_type_oth>
+      <email_share>2</email_share>
+      <email_active>1</email_active>
+      <email_comment>NA</email_comment>
+      <email_start_date>9666-96-96</email_start_date>
+      <email_end_date>9666-96-96</email_end_date>
+      <transaction_type xsi:nil="true"/>
+   </email>
+
   </ncs:transmission_tables>
 </ncs:recruitment_substudy_transmission_envelope>

data/spec/ncs_navigator/warehouse/transformers/vdr_xml/reader_spec.rb

@@ -9,17 +9,18 @@ class NcsNavigator::Warehouse::Transformers::VdrXml
       let(:person)       { reader.detect { |rec| rec.class.name =~ /Person$/ } }
       let(:link_contact) { reader.detect { |rec| rec.class.name =~ /LinkContact$/ } }
       let(:listing_unit) { reader.detect { |rec| rec.class.name =~ /ListingUnit$/ } }
+      let(:email)        { reader.detect { |rec| rec.class.name =~ /Email$/ } }
 
       it 'verifies the PSU matches the configuration'
       it 'verifies the specification version matches the runtime MDES version'
 
       it 'yields all records' do
-        reader.to_a.size.should == 6
+        reader.to_a.size.should == 7
       end
 
       it 'yields the records using their model classes' do
         reader.collect { |rec| rec.class.name.demodulize }.should ==
-          %w(StudyCenter Psu Ssu ListingUnit Person LinkContact)
+          %w(StudyCenter Psu Ssu ListingUnit Person LinkContact Email)
       end
 
       it 'reads variable values' do
@@ -43,6 +44,10 @@ class NcsNavigator::Warehouse::Transformers::VdrXml
           person.last_name.should == ''
         end
       end
+
+      it 'handles table-named variables' do
+        email.email.should == 'jo@example.net'
+      end
     end
   end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: ncs_mdes_warehouse
 version: !ruby/object:Gem::Version
-  version: 0.3.1
+  version: 0.3.2
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-12-18 00:00:00.000000000Z
+date: 2012-01-03 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ncs_mdes
-  requirement: &2152342040 !ruby/object:Gem::Requirement
+  requirement: &2152198740 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -21,10 +21,10 @@ dependencies:
         version: '0.5'
   type: :runtime
   prerelease: false
-  version_requirements: *2152342040
+  version_requirements: *2152198740
 - !ruby/object:Gem::Dependency
   name: ncs_navigator_configuration
-  requirement: &2152341040 !ruby/object:Gem::Requirement
+  requirement: &2152197440 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -32,10 +32,10 @@ dependencies:
         version: '0.2'
   type: :runtime
   prerelease: false
-  version_requirements: *2152341040
+  version_requirements: *2152197440
 - !ruby/object:Gem::Dependency
   name: activesupport
-  requirement: &2152340160 !ruby/object:Gem::Requirement
+  requirement: &2152196400 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -43,10 +43,10 @@ dependencies:
         version: '3.0'
   type: :runtime
   prerelease: false
-  version_requirements: *2152340160
+  version_requirements: *2152196400
 - !ruby/object:Gem::Dependency
   name: i18n
-  requirement: &2152339140 !ruby/object:Gem::Requirement
+  requirement: &2152195520 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -54,10 +54,10 @@ dependencies:
         version: '0.4'
   type: :runtime
   prerelease: false
-  version_requirements: *2152339140
+  version_requirements: *2152195520
 - !ruby/object:Gem::Dependency
   name: thor
-  requirement: &2152338380 !ruby/object:Gem::Requirement
+  requirement: &2152194580 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -65,10 +65,10 @@ dependencies:
         version: 0.14.6
   type: :runtime
   prerelease: false
-  version_requirements: *2152338380
+  version_requirements: *2152194580
 - !ruby/object:Gem::Dependency
   name: rubyzip
-  requirement: &2152337400 !ruby/object:Gem::Requirement
+  requirement: &2152193540 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -76,10 +76,10 @@ dependencies:
         version: 0.9.4
   type: :runtime
   prerelease: false
-  version_requirements: *2152337400
+  version_requirements: *2152193540
 - !ruby/object:Gem::Dependency
   name: childprocess
-  requirement: &2152324540 !ruby/object:Gem::Requirement
+  requirement: &2152192480 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -87,10 +87,10 @@ dependencies:
         version: 0.2.3
   type: :runtime
   prerelease: false
-  version_requirements: *2152324540
+  version_requirements: *2152192480
 - !ruby/object:Gem::Dependency
   name: json
-  requirement: &2152323420 !ruby/object:Gem::Requirement
+  requirement: &2152191600 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -98,10 +98,10 @@ dependencies:
         version: '1.6'
   type: :runtime
   prerelease: false
-  version_requirements: *2152323420
+  version_requirements: *2152191600
 - !ruby/object:Gem::Dependency
   name: nokogiri
-  requirement: &2152322540 !ruby/object:Gem::Requirement
+  requirement: &2152190680 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -109,10 +109,10 @@ dependencies:
         version: 1.5.0
   type: :runtime
   prerelease: false
-  version_requirements: *2152322540
+  version_requirements: *2152190680
 - !ruby/object:Gem::Dependency
   name: builder
-  requirement: &2152321160 !ruby/object:Gem::Requirement
+  requirement: &2152189820 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -120,10 +120,10 @@ dependencies:
         version: 2.1.2
   type: :runtime
   prerelease: false
-  version_requirements: *2152321160
+  version_requirements: *2152189820
 - !ruby/object:Gem::Dependency
   name: dm-core
-  requirement: &2152319660 !ruby/object:Gem::Requirement
+  requirement: &2152188600 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -131,10 +131,10 @@ dependencies:
         version: 1.2.0
   type: :runtime
   prerelease: false
-  version_requirements: *2152319660
+  version_requirements: *2152188600
 - !ruby/object:Gem::Dependency
   name: dm-constraints
-  requirement: &2152318920 !ruby/object:Gem::Requirement
+  requirement: &2152187620 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -142,10 +142,10 @@ dependencies:
         version: 1.2.0
   type: :runtime
   prerelease: false
-  version_requirements: *2152318920
+  version_requirements: *2152187620
 - !ruby/object:Gem::Dependency
   name: dm-migrations
-  requirement: &2152318060 !ruby/object:Gem::Requirement
+  requirement: &2152186720 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -153,10 +153,10 @@ dependencies:
         version: 1.2.0
   type: :runtime
   prerelease: false
-  version_requirements: *2152318060
+  version_requirements: *2152186720
 - !ruby/object:Gem::Dependency
   name: dm-transactions
-  requirement: &2152313080 !ruby/object:Gem::Requirement
+  requirement: &2152185700 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -164,10 +164,10 @@ dependencies:
         version: 1.2.0
   type: :runtime
   prerelease: false
-  version_requirements: *2152313080
+  version_requirements: *2152185700
 - !ruby/object:Gem::Dependency
   name: dm-validations
-  requirement: &2152311340 !ruby/object:Gem::Requirement
+  requirement: &2152184580 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -175,10 +175,10 @@ dependencies:
         version: 1.2.0
   type: :runtime
   prerelease: false
-  version_requirements: *2152311340
+  version_requirements: *2152184580
 - !ruby/object:Gem::Dependency
   name: dm-types
-  requirement: &2152309800 !ruby/object:Gem::Requirement
+  requirement: &2152183640 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -186,10 +186,10 @@ dependencies:
         version: 1.2.0
   type: :runtime
   prerelease: false
-  version_requirements: *2152309800
+  version_requirements: *2152183640
 - !ruby/object:Gem::Dependency
   name: dm-aggregates
-  requirement: &2152307500 !ruby/object:Gem::Requirement
+  requirement: &2152182340 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -197,10 +197,10 @@ dependencies:
         version: 1.2.0
   type: :runtime
   prerelease: false
-  version_requirements: *2152307500
+  version_requirements: *2152182340
 - !ruby/object:Gem::Dependency
   name: dm-postgres-adapter
-  requirement: &2152306340 !ruby/object:Gem::Requirement
+  requirement: &2152181640 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -208,10 +208,10 @@ dependencies:
         version: 1.2.0
   type: :runtime
   prerelease: false
-  version_requirements: *2152306340
+  version_requirements: *2152181640
 - !ruby/object:Gem::Dependency
   name: bcdatabase
-  requirement: &2152305760 !ruby/object:Gem::Requirement
+  requirement: &2152180900 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -219,10 +219,10 @@ dependencies:
         version: '1.1'
   type: :runtime
   prerelease: false
-  version_requirements: *2152305760
+  version_requirements: *2152180900
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &2152297240 !ruby/object:Gem::Requirement
+  requirement: &2152180100 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -230,10 +230,10 @@ dependencies:
         version: '2.6'
   type: :development
   prerelease: false
-  version_requirements: *2152297240
+  version_requirements: *2152180100
 - !ruby/object:Gem::Dependency
   name: rake
-  requirement: &2152295720 !ruby/object:Gem::Requirement
+  requirement: &2152179300 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -241,10 +241,10 @@ dependencies:
         version: 0.9.2
   type: :development
   prerelease: false
-  version_requirements: *2152295720
+  version_requirements: *2152179300
 - !ruby/object:Gem::Dependency
   name: yard
-  requirement: &2152294060 !ruby/object:Gem::Requirement
+  requirement: &2152178340 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -252,10 +252,10 @@ dependencies:
         version: 0.7.2
   type: :development
   prerelease: false
-  version_requirements: *2152294060
+  version_requirements: *2152178340
 - !ruby/object:Gem::Dependency
   name: ci_reporter
-  requirement: &2152292580 !ruby/object:Gem::Requirement
+  requirement: &2152177500 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - =
@@ -263,10 +263,10 @@ dependencies:
         version: 1.6.6
   type: :development
   prerelease: false
-  version_requirements: *2152292580
+  version_requirements: *2152177500
 - !ruby/object:Gem::Dependency
   name: fakefs
-  requirement: &2152291240 !ruby/object:Gem::Requirement
+  requirement: &2152176600 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -274,7 +274,7 @@ dependencies:
         version: 0.4.0
   type: :development
   prerelease: false
-  version_requirements: *2152291240
+  version_requirements: *2152176600
 description: 
 email:
 - r-sutphin@northwestern.edu