ncs_mdes 0.4.2 → 0.5.0

data/CHANGELOG.md

@@ -1,6 +1,15 @@
 NCS Navigator MDES Module history
 =================================
 
+0.5.0
+-----
+
+- Add `instrument_table?` and `operational_table?` to heuristically
+  flag tables as one or the other.
+- Fix reference definition for `spec_blood.equip_id`. According to the
+  corresponding instrument, it is not a reference to `spec_equipment`,
+  but rather a manually-filled field.
+
 0.4.2
 -----
 

data/Rakefile

@@ -13,3 +13,36 @@ namespace :ci do
   desc "Run specs for CI"
   task :spec => ['ci:setup:rspec', 'rake:spec']
 end
+
+task :library do
+  $LOAD_PATH << File.expand_path('../lib', __FILE__)
+  require 'ncs_navigator/mdes'
+end
+
+desc 'Generate a dot-formatted graph of the FK relationships in an MDE spec'
+task :fk_dot => :library do
+  fail 'Please specify the MDES version with MDES="X.Y"' unless ENV['MDES']
+  spec = NcsNavigator::Mdes(ENV['MDES'])
+
+  filename = "foreign_keys-MDES_#{spec.specification_version}.dot"
+  $stdout.write "Writing DOT graph to #{filename}..."
+
+  File.open(filename, 'w') do |f|
+    f.puts "digraph mdes_fks {"
+    spec.transmission_tables.each do |t1|
+      shape = if t1.primary_instrument_table?
+                'diamond'
+              elsif t1.instrument_table?
+                'rect'
+              else
+                'oval'
+              end
+      f.puts "  #{t1.name} [shape=#{shape}];"
+      t1.variables.collect(&:table_reference).compact.each do |t2|
+        f.puts "  #{t1.name} -> #{t2.name};"
+      end
+    end
+    f.puts "}"
+  end
+  $stdout.puts "done."
+end

data/ci-exec.sh

@@ -1,6 +1,6 @@
 #!/bin/bash -xe
 
-BUNDLER_VERSION=1.0.18
+BUNDLER_VERSION=1.1.rc
 GEMSET=ncs_mdes
 
 if [ -z $CI_RUBY ]; then
@@ -38,6 +38,6 @@ if [ $? -ne 0 ]; then
 fi
 set -e
 
-bundle update
+bundle _${BUNDLER_VERSION}_ update
 
-bundle exec rake ci:spec --trace
+bundle _${BUNDLER_VERSION}_ exec rake ci:spec --trace

data/documents/2.0/heuristic_overrides.yml

@@ -338,7 +338,9 @@ foreign_keys:
     six_mth_saq_id: six_mth_saq_2
 
   spec_blood:
-    equip_id: spec_equipment
+    # According to the corresponding instrument, equip_id is manually entered and
+    # not a reference to another table.
+    equip_id: false
 
   spec_receipt:
     # Insufficient info to determine what this is supposed to link to

data/lib/ncs_navigator/mdes/transmission_table.rb

@@ -49,5 +49,66 @@ module NcsNavigator::Mdes
     def inspect
       "\#<#{self.class} name=#{name.inspect}>"
     end
+
+    ##
+    # Is this a primary instrument table (i.e., is this the table for
+    # an instrument that stores all single-valued responses for one
+    # execution of that instrument and to which all other instrument
+    # tables for that instrument refer [directly or indirectly])?
+    #
+    # @return [true,false]
+    def primary_instrument_table?
+      self.name != 'instrument' && variables.any? { |v| v.name == 'instrument_version' }
+    end
+
+    ##
+    # Is this an instrument table (i.e., a table for storing results
+    # from an instrument)? Every table is either an instrument table
+    # or an operational table (never both).
+    #
+    # This is not explicitly derivable from the MDES, so this method
+    # (and the related methods {#operational_table?} and
+    # {#primary_instrument_table?}) use this heuristic:
+    #
+    #   * If this table contains a variable named `instrument_version`
+    #     and is not the `instrument` table itself, it is a primary
+    #     instrument table (and so is an instrument table).
+    #   * If this table is not a primary instrument table, but one of
+    #     its {#variables} {Variable#table_reference references} a table
+    #     that is a primary instrument table, then this is an instrument
+    #     table.
+    #   * Similarly, if one of this table's variables references a table
+    #     which is an instrument table according to the second
+    #     definition, then this table is an instrument table as
+    #     well. This continues for any depth of reference.
+    #
+    # If none of these conditions are met, then this table is an
+    # operational table.
+    #
+    # @return [true,false]
+    def instrument_table?
+      instrument_table_predicate_with_stack([])
+    end
+
+    ##
+    # @private # exposed for recursion in siblings
+    def instrument_table_predicate_with_stack(stack)
+      return false if stack.include?(self)
+      primary_instrument_table? || variables.any? { |v|
+        v.table_reference && v.table_reference.instrument_table_predicate_with_stack(stack + [self])
+      }
+    end
+
+    ##
+    # Is this an operational table (i.e., a table for storing
+    # operational data about a participant, household, staff member,
+    # or other study management concept)? Every table is either an
+    # operational table or an instrument table (never both).
+    #
+    # @see #instrument_table?
+    # @return [true,false]
+    def operational_table?
+      !instrument_table?
+    end
   end
 end

data/lib/ncs_navigator/mdes/version.rb

@@ -1,5 +1,5 @@
 module NcsNavigator
   module Mdes
-    VERSION = "0.4.2"
+    VERSION = '0.5.0'
   end
 end

data/ncs_mdes.gemspec

@@ -21,7 +21,7 @@ National Children's Study's Master Data Element Specification.
 
   s.add_dependency 'nokogiri', '~> 1.4'
 
-  s.add_development_dependency 'rspec', '~> 2.6'
+  s.add_development_dependency 'rspec', '~> 2.6.0' # Can't use 2.7.0 due to #477
   s.add_development_dependency 'rake', '~> 0.9.2'
   s.add_development_dependency 'yard', '~> 0.7.2'
   s.add_development_dependency 'ci_reporter', '~> 1.6'

data/spec/ncs_navigator/mdes/specification_spec.rb

@@ -41,6 +41,12 @@ module NcsNavigator::Mdes
             table.variables.collect { |v| v.type }.select { |t| t.reference? }
           }.flatten.collect { |t| t.name }.select { |n| n =~ /^ncs:/ }.should == []
         end
+
+        it 'can determine if each table is instrument or operational' do
+          tables.each do |table|
+            lambda { table.instrument_table? }.should_not raise_error
+          end
+        end
       end
 
       context 'in version 1.2' do

data/spec/ncs_navigator/mdes/transmission_table_spec.rb

@@ -85,5 +85,99 @@ XSD
         subject['quux'].should be_nil
       end
     end
+
+    describe 'instrument table detection' do
+      def table_with_variables(table_name, *variables)
+        TransmissionTable.new(table_name).tap { |t|
+          t.variables = variables.collect { |vn| Variable.new(vn) }
+        }
+      end
+
+      let(:event) { table_with_variables('event', 'event_id') }
+      let(:instrument) { table_with_variables('instrument', 'instrument_id', 'instrument_version') }
+
+      let(:spec_blood) {
+        table_with_variables('spec_blood', 'spec_blood_id',
+          'instrument_id', 'instrument_type', 'instrument_version')
+      }
+      let(:spec_blood_tube) {
+        table_with_variables('spec_blood_tube', 'spec_blood_tube_id', 'spec_blood_id').tap do |t|
+          t.variables.detect { |v| v.name == 'spec_blood_id' }.table_reference = spec_blood
+        end
+      }
+      let(:spec_blood_tube_comments) {
+        table_with_variables(
+          'spec_blood_tube_comments',
+          'spec_blood_tube_comments_id', 'spec_blood_tube_id'
+        ).tap do |t|
+          t.variables.detect { |v| v.name == 'spec_blood_tube_id' }.
+            table_reference = spec_blood_tube
+        end
+      }
+
+      describe '#instrument_table?' do
+        it 'does not consider tables without instrument_version to be instrument tables' do
+          event.should_not be_instrument_table
+        end
+
+        it 'does not consider the instrument operational table to be an instrument table' do
+          instrument.should_not be_instrument_table
+        end
+
+        it 'considers primary instrument tables to be instrument tables' do
+          spec_blood.should be_instrument_table
+        end
+
+        it 'considers secondary instrument tables to be instrument tables' do
+          spec_blood_tube.should be_instrument_table
+        end
+
+        it 'considers tertiary instrument tables to be instrument tables' do
+          spec_blood_tube_comments.should be_instrument_table
+        end
+
+        it 'does not consider circularly referring tables to be instrument tables' do
+          person = table_with_variables('person', 'new_address_id')
+          address = table_with_variables('address', 'person_id')
+          address.variables.first.table_reference = person
+          person.variables.first.table_reference = address
+
+          address.should_not be_instrument_table
+          person.should_not be_instrument_table
+        end
+      end
+
+      describe '#primary_instrument_table?' do
+        it 'does not consider tables without instrument_version to be a primary instrument table' do
+          event.should_not be_primary_instrument_table
+        end
+
+        it 'does not consider the instrument operational table to be a primary instrument table' do
+          instrument.should_not be_primary_instrument_table
+        end
+
+        it 'considers primary instrument tables to be primary instrument tables' do
+          spec_blood.should be_primary_instrument_table
+        end
+
+        it 'does not consider secondary instrument tables to be primary instrument tables' do
+          spec_blood_tube.should_not be_primary_instrument_table
+        end
+
+        it 'does not consider tertiary instrument tables to be primary instrument tables' do
+          spec_blood_tube_comments.should_not be_primary_instrument_table
+        end
+      end
+
+      describe '#operational_table?' do
+        it 'is the opposite of instrument_table?' do
+          [
+            event, instrument, spec_blood, spec_blood_tube, spec_blood_tube_comments
+          ].each do |table|
+            table.instrument_table?.should == !table.operational_table?
+          end
+        end
+      end
+    end
   end
 end

metadata

@@ -1,85 +1,115 @@
---- !ruby/object:Gem::Specification
+--- !ruby/object:Gem::Specification 
 name: ncs_mdes
-version: !ruby/object:Gem::Version
-  version: 0.4.2
-  prerelease: 
+version: !ruby/object:Gem::Version 
+  hash: 11
+  prerelease: false
+  segments: 
+  - 0
+  - 5
+  - 0
+  version: 0.5.0
 platform: ruby
-authors:
+authors: 
 - Rhett Sutphin
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-09-09 00:00:00.000000000Z
-dependencies:
-- !ruby/object:Gem::Dependency
+
+date: 2011-11-29 00:00:00 -06:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
   name: nokogiri
-  requirement: &2152825220 !ruby/object:Gem::Requirement
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
     none: false
-    requirements:
+    requirements: 
     - - ~>
-      - !ruby/object:Gem::Version
-        version: '1.4'
+      - !ruby/object:Gem::Version 
+        hash: 7
+        segments: 
+        - 1
+        - 4
+        version: "1.4"
   type: :runtime
-  prerelease: false
-  version_requirements: *2152825220
-- !ruby/object:Gem::Dependency
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
   name: rspec
-  requirement: &2152824560 !ruby/object:Gem::Requirement
+  prerelease: false
+  requirement: &id002 !ruby/object:Gem::Requirement 
     none: false
-    requirements:
+    requirements: 
     - - ~>
-      - !ruby/object:Gem::Version
-        version: '2.6'
+      - !ruby/object:Gem::Version 
+        hash: 23
+        segments: 
+        - 2
+        - 6
+        - 0
+        version: 2.6.0
   type: :development
-  prerelease: false
-  version_requirements: *2152824560
-- !ruby/object:Gem::Dependency
+  version_requirements: *id002
+- !ruby/object:Gem::Dependency 
   name: rake
-  requirement: &2152823680 !ruby/object:Gem::Requirement
+  prerelease: false
+  requirement: &id003 !ruby/object:Gem::Requirement 
     none: false
-    requirements:
+    requirements: 
     - - ~>
-      - !ruby/object:Gem::Version
+      - !ruby/object:Gem::Version 
+        hash: 63
+        segments: 
+        - 0
+        - 9
+        - 2
         version: 0.9.2
   type: :development
-  prerelease: false
-  version_requirements: *2152823680
-- !ruby/object:Gem::Dependency
+  version_requirements: *id003
+- !ruby/object:Gem::Dependency 
   name: yard
-  requirement: &2152822920 !ruby/object:Gem::Requirement
+  prerelease: false
+  requirement: &id004 !ruby/object:Gem::Requirement 
     none: false
-    requirements:
+    requirements: 
     - - ~>
-      - !ruby/object:Gem::Version
+      - !ruby/object:Gem::Version 
+        hash: 7
+        segments: 
+        - 0
+        - 7
+        - 2
         version: 0.7.2
   type: :development
-  prerelease: false
-  version_requirements: *2152822920
-- !ruby/object:Gem::Dependency
+  version_requirements: *id004
+- !ruby/object:Gem::Dependency 
   name: ci_reporter
-  requirement: &2152822260 !ruby/object:Gem::Requirement
+  prerelease: false
+  requirement: &id005 !ruby/object:Gem::Requirement 
     none: false
-    requirements:
+    requirements: 
     - - ~>
-      - !ruby/object:Gem::Version
-        version: '1.6'
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 1
+        - 6
+        version: "1.6"
   type: :development
-  prerelease: false
-  version_requirements: *2152822260
-description: ! '
-
+  version_requirements: *id005
+description: |
+  
   Provides a consistent ruby interface to the project metainformation in the
+  National Children's Study's Master Data Element Specification.
 
-  National Children''s Study''s Master Data Element Specification.
-
-'
-email:
+email: 
 - r-sutphin@northwestern.edu
-executables:
+executables: 
 - mdes-console
 extensions: []
+
 extra_rdoc_files: []
-files:
+
+files: 
 - .gitignore
 - .rvmrc
 - .yardopts
@@ -111,37 +141,41 @@ files:
 - spec/ncs_navigator/mdes/version_spec.rb
 - spec/ncs_navigator/mdes_spec.rb
 - spec/spec_helper.rb
-homepage: ''
+has_rdoc: true
+homepage: ""
 licenses: []
+
 post_install_message: 
 rdoc_options: []
-require_paths:
+
+require_paths: 
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement
+required_ruby_version: !ruby/object:Gem::Requirement 
   none: false
-  requirements:
-  - - ! '>='
-    - !ruby/object:Gem::Version
-      version: '0'
-      segments:
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
       - 0
-      hash: 1899662951154371602
-required_rubygems_version: !ruby/object:Gem::Requirement
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
   none: false
-  requirements:
-  - - ! '>='
-    - !ruby/object:Gem::Version
-      version: '0'
-      segments:
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
       - 0
-      hash: 1899662951154371602
+      version: "0"
 requirements: []
+
 rubyforge_project: 
-rubygems_version: 1.8.6
+rubygems_version: 1.3.7
 signing_key: 
 specification_version: 3
 summary: A ruby API for various versions of the NCS MDES.
-test_files:
+test_files: 
 - spec/ncs_navigator/mdes/source_documents_spec.rb
 - spec/ncs_navigator/mdes/specification_spec.rb
 - spec/ncs_navigator/mdes/transmission_table_spec.rb