health-data-standards 3.5.3 → 3.6.1

data/lib/health-data-standards/import/cda/section_importer.rb

@@ -45,7 +45,7 @@ module HealthDataStandards
           extract_codes(entry_element, entry)
           extract_dates(entry_element, entry)
           if @value_xpath
-            extract_value(entry_element, entry)
+            extract_values(entry_element, entry)
           end
           entry.description = entry_element.at_xpath("./cda:text").try("text")
           if @status_xpath
@@ -100,21 +100,26 @@ module HealthDataStandards
 
         def extract_dates(parent_element, entry, element_name="effectiveTime")
           if parent_element.at_xpath("cda:#{element_name}/@value")
-            entry.time = HL7Helper.timestamp_to_integer(parent_element.at_xpath("cda:#{element_name}")['value'])
+            entry[:time] = HL7Helper.timestamp_to_integer(parent_element.at_xpath("cda:#{element_name}")['value'])
           end
           if parent_element.at_xpath("cda:#{element_name}/cda:low")
-            entry.start_time = HL7Helper.timestamp_to_integer(parent_element.at_xpath("cda:#{element_name}/cda:low")['value'])
+            entry[:start_time] = HL7Helper.timestamp_to_integer(parent_element.at_xpath("cda:#{element_name}/cda:low")['value'])
           end
           if parent_element.at_xpath("cda:#{element_name}/cda:high")
-            entry.end_time = HL7Helper.timestamp_to_integer(parent_element.at_xpath("cda:#{element_name}/cda:high")['value'])
+            entry[:end_time] = HL7Helper.timestamp_to_integer(parent_element.at_xpath("cda:#{element_name}/cda:high")['value'])
           end
           if parent_element.at_xpath("cda:#{element_name}/cda:center")
-            entry.time = HL7Helper.timestamp_to_integer(parent_element.at_xpath("cda:#{element_name}/cda:center")['value'])
+            entry[:time] = HL7Helper.timestamp_to_integer(parent_element.at_xpath("cda:#{element_name}/cda:center")['value'])
           end
         end
 
-        def extract_value(parent_element, entry)
-          value_element = parent_element.at_xpath(@value_xpath)
+        def extract_values(parent_element, entry)
+          parent_element.xpath(@value_xpath).each do |elem|
+            extract_value(parent_element, elem, entry)
+          end
+        end
+
+        def extract_value(parent_element, value_element, entry)
           if value_element
             value = value_element['value']
             if value.present?
@@ -123,6 +128,7 @@ module HealthDataStandards
             elsif value_element['code'].present?
               crv = CodedResultValue.new
               add_code_if_present(value_element, crv)
+              extract_dates(parent_element, crv)
               entry.values << crv
             else
               value = value_element.text

data/lib/health-data-standards/models/cqm/aggregate_objects.rb

@@ -79,7 +79,11 @@ module HealthDataStandards
       attr_accessor :populations
       def performance_rate
         numerator_count.to_f / 
-          (denominator_count - denominator_exclusions_count - denominator_exceptions_count)
+          (performance_rate_denominator)
+      end
+
+      def performance_rate_denominator
+        denominator_count - denominator_exclusions_count - denominator_exceptions_count
       end
 
       def is_cv?

data/lib/health-data-standards/models/cqm/bundle.rb

@@ -19,6 +19,8 @@ module HealthDataStandards
 
       validates_presence_of :version
 
+      has_many :value_sets, class_name: "HealthDataStandards::SVS::ValueSet", inverse_of: :bundle
+
       scope :active, -> {where(active: true)}
 
       def self.latest_bundle_id
@@ -33,9 +35,9 @@ module HealthDataStandards
         Record.where(bundle_id: self._id, test_id: nil).order_by([["last", :asc]])
       end
 
-      def value_sets
-        HealthDataStandards::SVS::ValueSet.in(bundle_id: self.id)
-      end
+      # def value_sets
+      #   HealthDataStandards::SVS::ValueSet.in(bundle_id: self.id)
+      # end
 
       def delete
         self.measures.destroy

data/lib/health-data-standards/models/cqm/measure.rb

@@ -47,7 +47,7 @@ module HealthDataStandards
       index category: 1
       index sub_id: 1
       index _id: 1, sub_id: 1
-      index bundle_id: 1
+      index({bundle_id: 1, hqmf_id: 1, sub_id: 1})
 
       validates_presence_of :id
       validates_presence_of :name

data/lib/health-data-standards/models/entry.rb

@@ -9,7 +9,7 @@ class Entry
   embedded_in :record
   embeds_one :cda_identifier, class_name: "CDAIdentifier", as: :cda_identifiable
   embeds_many :values, class_name: "ResultValue"
-  
+  embeds_many :references
   field :description, type: String
   field :specifics, type: String
   field :time, type: Integer
@@ -27,6 +27,10 @@ class Entry
   attr_protected :created_at
   attr_protected :updated_at
   
+  def add_reference(entry, type)
+    references.build(type: type, referenced_type: entry.class, referenced_id: entry.id)
+  end
+
   def times_to_s(nil_string='UNK')
     if start_time.present? || end_time.present?
       start_string = start_time ? Entry.time_to_s(start_time) : nil_string

data/lib/health-data-standards/models/record.rb

@@ -25,6 +25,9 @@ class Record
                                                                                     # HITSP C32
 
   index "last" => 1
+  index medical_record_number: 1
+  index test_id: 1
+  index bundle_id: 1
   embeds_many :allergies
   embeds_many :care_goals, class_name: "Entry" # This can be any number of different entry types
   embeds_many :conditions
@@ -103,6 +106,9 @@ class Record
   # based on clinical content
   def dedup_section_ignoring_content!(section)
     unique_entries = self.send(section).uniq do |entry|
+      entry.references.each do |ref|
+        ref.resolve_referenced_id
+      end
       entry.identifier
     end
     self.send("#{section}=", unique_entries)
@@ -110,12 +116,16 @@ class Record
   def dedup_section_merging_codes_and_values!(section)
     unique_entries = {}
     self.send(section).each do |entry|
+      entry.references.each do |ref|
+        ref.resolve_referenced_id
+      end
       if unique_entries[entry.identifier]
         unique_entries[entry.identifier].codes = unique_entries[entry.identifier].codes.deep_merge(entry.codes){ |key, old, new| Array.wrap(old) + Array.wrap(new) }
         unique_entries[entry.identifier].values.concat(entry.values)
       else
         unique_entries[entry.identifier] = entry
       end
+      
     end
     self.send("#{section}=", unique_entries.values)
   end

data/lib/health-data-standards/models/reference.rb

@@ -0,0 +1,23 @@
+class Reference
+  include Mongoid::Document
+  include Mongoid::Attributes::Dynamic
+  embedded_in :entry
+  field :type, type: String
+  field :referenced_type, type: String
+  field :referenced_id
+
+  def resolve_reference
+    entry.record.entries.find do |e|
+      e.class.to_s == referenced_type &&
+      e.identifier.to_s == referenced_id.to_s
+    end
+  end
+
+  def resolve_referenced_id
+    resolved_reference = entry.record.entries.find do |e|
+      e.class.to_s == referenced_type &&
+      e.identifier == referenced_id
+    end
+    self.referenced_id = resolved_reference.id.to_s
+  end
+end

data/lib/health-data-standards/models/svs/value_set.rb

@@ -1,12 +1,13 @@
 module HealthDataStandards
   module SVS
     class ValueSet
-
       include Mongoid::Document
-      include Mongoid::Attributes::Dynamic
       field :oid, type: String
       field :display_name, type: String
       field :version, type: String
+      field :user_id, type: String # Eventually we need to delete this from bundles when exporting
+
+      belongs_to :bundle, class_name: "HealthDataStandards::CQM::Bundle", inverse_of: :value_sets
 
       index({oid: 1})
       index({display_name: 1})
@@ -43,7 +44,7 @@ module HealthDataStandards
             code_system_name = HealthDataStandards::Util::CodeSystemHelper::CODE_SYSTEMS[con["codeSystem"]] || con["codeSystemName"]
             Concept.new(code: con["code"], 
                         code_system_name: code_system_name,
-                        code_system_version: con["code_system_version"],
+                        code_system_version: con["codeSystemVersion"],
                         display_name: con["displayName"], code_system: con["codeSystem"])
           end
           vs.concepts = concepts

data/lib/health-data-standards/railtie.rb

@@ -4,7 +4,7 @@ module HealthDataStandards
       HealthDataStandards.logger = Rails.logger
     end
     rake_tasks do
-      Dir[File.join(File.dirname(__FILE__),'tasks/*.rake')].each { |f| load f }
+      require_relative "tasks"
     end
 
   end

data/lib/health-data-standards/tasks.rb

@@ -0,0 +1 @@
+Dir[File.join(File.dirname(__FILE__),'tasks/*.rake')].each { |f| load f }

data/lib/health-data-standards/tasks/bundle.rake

@@ -1,4 +1,6 @@
 require 'health-data-standards'
+require 'highline/import'
+require 'open-uri'
 
 db_name = ENV['DB_NAME'] || 'test'
 
@@ -20,6 +22,86 @@ namespace :bundle do
 
   end
 
+  desc %{ Download measure/test deck bundle.
+    options
+    nlm_user    - the nlm username to authenticate to the server - will prompt is not supplied
+    nlm_passwd  - the nlm password for authenticating to the server - will prompt if not supplied
+    version     - the version of the bundle to download. This will default to the version
+
+   example usage:
+    rake bundle:download nlm_name=username nlm_passwd=password version=2.1.0-latest
+  }
+  task :download => :environment do
+    nlm_user = ENV["nlm_user"]
+    nlm_passwd = ENV["nlm_pass"]
+    measures_dir = File.join(Dir.pwd, "bundles")
+
+    while nlm_user.nil? || nlm_user == ""
+      nlm_user = ask("NLM Username?: "){ |q| q.readline = true }
+    end
+
+    while nlm_passwd.nil? || nlm_passwd == ""
+      nlm_passwd = ask("NLM Password?: "){ |q| q.echo = false
+					       q.readline = true }
+    end
+
+    bundle_version = ENV["version"] || "latest"
+    @bundle_name = "bundle-#{bundle_version}.zip"
+
+    puts "Downloading and saving #{@bundle_name} to #{measures_dir}"
+    # Pull down the list of bundles and download the version we're looking for
+    bundle_uri = "https://demo.projectcypress.org/bundles/#{@bundle_name}"
+    bundle = nil
+
+    tries = 0
+    max_tries = 10
+    last_error = nil
+    while bundle.nil? && tries < max_tries do
+      tries = tries + 1
+      begin
+	bundle = open(bundle_uri, :proxy => ENV["http_proxy"],:http_basic_authentication=>[nlm_user, nlm_passwd] )
+      rescue OpenURI::HTTPError => oe
+	last_error = oe
+	if oe.message == "401 Unauthorized"
+	  puts "Please check your credentials and try again"
+	  break
+	end
+      rescue => e
+	last_error = e
+	sleep 0.5
+      end
+    end
+
+    if bundle.nil?
+       puts "An error occured while downloading the bundle"
+      raise last_error if last_error
+    end
+    # Save the bundle to the measures directory
+    FileUtils.mkdir_p measures_dir
+    FileUtils.mv(bundle.path, File.join(measures_dir, @bundle_name))
+
+  end
+
+  desc %{ Download and install the measure/test deck bundle.  This is essientally delegating to the bundle_download and bundle:import tasks
+    options
+    nlm_user    - the nlm username to authenticate to the server - will prompt is not supplied
+    nlm_passwd  - the nlm password for authenticating to the server - will prompt if not supplied
+    version     - the version of the bundle to download. This will default to the version
+    delete_existing - delete any existing bundles with the same version and reinstall - default is false - will cause error if same version already exists
+    update_measures - update any existing measures with the same hqmf_id to those contained in this bundle.
+		      Will only work for bundle versions greater than that of the installed version - default is false
+    type -  type of measures to be installed from bundle. A bundle may have measures of different types such as ep or eh.  This will constrain the types installed, defautl is all types
+   example usage:
+    rake budnle:download_and_install nlm_name=username nlm_passwd=password version=2.1.0-latest  type=ep
+  }
+  task :download_and_install => [:download] do
+    de = ENV['delete_existing'] || false
+    um = ENV['update_measures'] || false
+    puts "Importing bundle #{@bundle_name} delete_existing: #{de}  update_measures: #{um} type: #{ENV['type'] || 'ALL'}"
+    task("bundle:import").invoke("bundles/#{@bundle_name}",de, um , ENV['type'], 'true')
+  end
+
+
 
   desc 'List bundles'
   task :list  => [:environment] do
@@ -30,7 +112,7 @@ namespace :bundle do
 
 
   desc 'Import a quality bundle into the database.'
-  task :import, [:bundle_path,  :delete_existing,  :update_measures, :type, :create_indexes, :exclude_results] => [:environment] do |task, args|
+  task :import, [:bundle_path,  :delete_existing,  :update_measures, :type, :create_indexes, :exclude_results] => :environment do |task, args|
     raise "The path to the measures zip file must be specified" unless args.bundle_path
     options = {:delete_existing => (args.delete_existing == "true"),
     					 :type => args.type,
@@ -48,7 +130,7 @@ namespace :bundle do
               value_sets: bundle_contents.value_sets.count}
 
     if (args.create_indexes != 'false')
-      ::Rails.application.eager_load!
+      ::Rails.application.eager_load! if defined? Rails
       ::Mongoid::Tasks::Database.create_indexes
     end
 

data/lib/health-data-standards/util/vs_api.rb

@@ -2,7 +2,10 @@ require 'rest_client'
 require 'uri'
 module HealthDataStandards
   module Util
-		class VSApi			
+  	class VSNotFoundError < StandardError
+  	end
+
+		class VSApi
 			attr_accessor :api_url, :ticket_url, :username, :password
 
 			def initialize(ticket_url, api_url, username, password)
@@ -12,7 +15,7 @@ module HealthDataStandards
 				@password = password
 			end
 
-			def get_valueset(oid, effective_date=nil, include_draft=false, &block)
+      def get_valueset(oid, effective_date=nil, include_draft=false, &block)
 				params = {id: oid, ticket: get_ticket}
 				params[:effectiveDate] = effective_date if effective_date
 				params[:includeDraft] = 'yes' if include_draft
@@ -23,24 +26,54 @@ module HealthDataStandards
 
 			def process_valuesets(oids, effective_date=nil, &block)
 				oids.each do |oid|
-		     		vs = get_valueset(oid,effective_date)
-		     		yield oid,vs
+		    	vs = get_valueset(oid,effective_date)
+		    	yield oid,vs
 				end
 			end
 
 			def proxy_ticket
-			 	@proxy_ticket ||= get_proxy_ticket
+			  @proxy_ticket ||= get_proxy_ticket
 			end
 
 			def get_proxy_ticket
 				# the content type is set and the body is a string becuase the NLM service does not support urlencoded content and
 				# throws an error on that contnet type
-				 RestClient.post ticket_url, {username: username, password: password}
+				RestClient.post ticket_url, {username: username, password: password}
 			end
-			
+
 			def get_ticket
 			  RestClient.post "#{ticket_url}/#{proxy_ticket}", {service: "http://umlsks.nlm.nih.gov"}
 		  end
 		end
+
+    class VSApiV2 < VSApi
+      def initialize(ticket_url, api_url, username, password)
+        super(ticket_url, api_url, username, password)
+      end
+
+      def get_valueset(oid, options = {}, &block)
+        version = options.fetch(:version, nil)
+        include_draft = options.fetch(:include_draft, false)
+				params = {id: oid, ticket: get_ticket}
+				params[:version] = version if version
+				params[:includeDraft] = 'yes' if include_draft
+				begin
+					vs = RestClient.get api_url, {:params=>params}
+				rescue RestClient::ResourceNotFound
+					raise VSNotFoundError, "No ValueSet found for oid '#{oid}'"
+				end
+				yield oid,vs if block_given?
+				vs
+			end
+
+      def process_valuesets(oids, options = {}, &block)
+        version = options.fetch(:version, nil)
+        include_draft = options.fetch(:include_draft, false)
+				oids.each do |oid|
+	        vs = get_valueset(oid, version: version, include_draft: include_draft)
+	    	  yield oid,vs
+				end
+			end
+    end
   end
 end

data/lib/health-data-standards/validate/base_validator.rb

@@ -0,0 +1,23 @@
+module HealthDataStandards
+  module Validate
+    module BaseValidator
+
+      def build_error(msg, loc, file_name)
+        ValidationError.new(message: msg, location: loc, file_name: file_name, validator: @name)
+      end
+
+      def get_document(input)
+        doc = case input
+        when File
+          input.read
+        when Nokogiri::XML::Document
+          return input
+        else
+          input
+        end
+        Nokogiri::XML(doc.to_s) { |conf| conf.strict.nonet.noblanks } #grumble, grumble nokogiri java @SS 
+      end
+    end
+
+  end
+end

data/lib/health-data-standards/validate/data_validator.rb

@@ -0,0 +1,85 @@
+module HealthDataStandards
+  module Validate
+    class DataValidator
+      include BaseValidator
+
+      HL7_QRDA_OIDS = ["2.16.840.1.113883.3.221.5",
+                       "2.16.840.1.113883.3.88.12.3221.8.7",
+                       "2.16.840.1.113883.3.88.12.3221.8.9",
+                       "2.16.840.1.113883.1.11.12839",
+                       "2.16.840.1.113883.3.88.12.3221.8.11",
+                       "2.16.840.1.113883.3.88.12.3221.6.2",
+                       "2.16.840.1.113883.11.20.9.40",
+                       "2.16.840.1.113883.11.20.9.23",
+                       "2.16.840.1.113883.3.88.12.3221.7.4",
+                       "2.16.840.1.113883.11.20.9.18",
+                       "2.16.840.1.113883.11.20.9.22",
+                       "2.16.840.1.113883.1.11.16866",
+                       "2.16.840.1.113883.1.11.20275",
+                       "2.16.840.1.113883.11.20.9.34",
+                       "2.16.840.1.113883.3.88.12.3221.7.2",
+                       "2.16.840.1.113883.3.88.12.80.17",
+                       "2.16.840.1.113883.3.88.12.80.22",
+                       "2.16.840.1.113883.3.88.12.80.64",
+                       "2.16.840.1.113883.3.88.12.3221.6.8",
+                       "2.16.840.1.113883.1.11.78",
+                       "2.16.840.1.113883.11.20.9.25",
+                       "2.16.840.1.113883.11.20.9.39",
+                       "2.16.840.1.113883.3.88.12.80.32",
+                       "2.16.840.1.113883.11.20.9.21",
+                       "2.16.840.1.113883.3.88.12.80.68",
+                       "2.16.840.1.113883.1.11.20.12",
+                       "2.16.840.1.113883.11.20.9.24",
+                       "2.16.840.1.113883.11.20.9.41",
+                       "2.16.840.1.113883.1.11.16926",
+                       "2.16.840.1.113883.1.11.12212",
+                       "2.16.840.1.113883.1.11.19185",
+                       "2.16.840.1.113883.1.11.14914",
+                       "2.16.840.1.114222.4.11.837",
+                       "2.16.840.1.113883.1.11.19563",
+                       "2.16.840.1.113883.1.11.11526",
+                       "2.16.840.1.113883.11.20.9.20",
+                       "2.16.840.1.113883.3.88.12.80.2",
+                       "2.16.840.1.113883.3.88.12.80.63",
+                       "2.16.840.1.113883.1.11.12249",
+                       "2.16.840.1.113883.1.11.1",
+                       "2.16.840.1.113883.1.11.12199",
+                       "2.16.840.1.113883.11.20.9.33",
+                       "2.16.840.1.114222.4.11.1066",
+                       "2.16.840.1.113883.1.11.19579"]
+
+      def initialize(bundle, measure_ids)
+        @bundle = bundle
+        measures = @bundle.measures.in(hqmf_id: measure_ids)
+
+        @oids = measures.collect{|m| m.oids}.flatten.uniq + HL7_QRDA_OIDS
+      end
+
+      def validate(file, options={})
+        doc = get_document(file)
+
+        doc.xpath("//*[@sdtc:valueSet]").inject([]) do |errors, node|
+          oid = node.at_xpath("@sdtc:valueSet")
+          vs = @bundle.value_sets.where({"oid" => oid}).first
+          code = node.at_xpath("@code")
+          code_system = node.at_xpath("@codeSystem")
+          null_flavor = node.at_xpath("@nullFlavor")
+          if !vs
+            errors << build_error("The valueset #{oid} declared in the document cannot be found", node.path, options[:file_name])
+          elsif !@oids.include?(oid.value)
+            errors << build_error("File appears to contain data criteria outside that required by the measures. Valuesets in file not in measures tested #{oid}'",
+                        node.path, options[:file_name])
+          elsif vs.concepts.where({"code" => code, "code_system"=>code_system}).count() == 0
+            if !null_flavor
+              errors << build_error("The code #{code} in codeSystem #{code_system} cannot be found in the declared valueset #{oid}",
+                node.path, options[:file_name])
+            end
+          end
+          errors
+        end
+      end
+
+    end
+  end
+  
+end