health-data-standards 3.4.6 → 3.5.0

data/Gemfile

@@ -16,8 +16,8 @@ group :test do
   gem 'simplecov', :require => false
   gem 'webmock'
 
-  gem "minitest", "~> 4.0"
-  gem 'turn', :require => false
+  gem "minitest", "~> 5.3"
+  gem 'minitest-reporters'
   gem 'awesome_print', :require => 'ap'
 
 end

data/README.md

@@ -25,6 +25,10 @@ Please try to follow the [GitHub Coding Style Guides](https://github.com/stylegu
 Change Log
 ==========
 
+4.0.0 - Not yet released
+
+* Upgrading to mongoid 4
+
 3.4.6 - May 15, 2014
 
 * QRDA Cat I export now exports medical record number if present

data/lib/health-data-standards.rb

@@ -9,6 +9,7 @@ require 'nokogiri'
 require 'ostruct'
 require 'log4r'
 require 'memoist'
+require 'protected_attributes'
 
 # Freedom patches
 require_relative 'health-data-standards/ext/symbol'

data/lib/health-data-standards/export/cat_1.rb

@@ -9,10 +9,10 @@ module HealthDataStandards
       end
 
       @@vs_map = nil
-      def export(patient, measures, start_date, end_date)
-        @rendering_context.render(:template => 'show', :locals => {:patient => patient, :measures => measures, 
-                                                :start_date => start_date, :end_date => end_date})
+      def export(patient, measures, start_date, end_date, header=nil)
+        @rendering_context.render(:template => 'show', :locals => {:patient => patient, :measures => measures,
+                                                :start_date => start_date, :end_date => end_date, :header => header})
       end
     end
   end
-end
+end

data/lib/health-data-standards/export/helper/scooped_view_helper.rb

@@ -12,7 +12,7 @@ module HealthDataStandards
             bundle_id_to_use = bundle_id
           else
             latest_bundle_id = HealthDataStandards::CQM::Bundle.latest_bundle_id
-            bundle_id_to_use = Moped::BSON::ObjectId.from_string(latest_bundle_id) if latest_bundle_id
+            bundle_id_to_use = BSON::ObjectId.from_string(latest_bundle_id) if latest_bundle_id
           end
           VS_MAP[bundle_id_to_use] ||= Hash[ValueSet.where({bundle_id: bundle_id_to_use}).map{ |p| [p.oid, p.code_set_map] }]
         end
@@ -24,13 +24,13 @@ module HealthDataStandards
           all_data_criteria = measures.map {|measure| measure.all_data_criteria}.flatten
           mapped_data_criteria = {}
           all_data_criteria.each do |data_criteria|
-            data_criteria_oid = HQMFTemplateHelper.template_id_by_definition_and_status(data_criteria.definition, 
+            data_criteria_oid = HQMFTemplateHelper.template_id_by_definition_and_status(data_criteria.definition,
                                                                               (data_criteria.status || ""),
                                                                               data_criteria.negation)
             value_set_oid = data_criteria.code_list_id
             dc = {'data_criteria_oid' => data_criteria_oid, 'value_set_oid' => value_set_oid}
             mapping = mapped_data_criteria[dc] ||= {'result_oids' => [], 'field_oids' =>{}, 'data_criteria' => data_criteria}
-            
+
             if data_criteria.field_values
               data_criteria.field_values.each_pair do |field,descr|
                 if descr && descr.type == "CD"
@@ -53,7 +53,7 @@ module HealthDataStandards
         def entry_matches_criteria(entry, data_criteria_info_list)
           data_criteria_info_list.each do |data_criteria_info|
             data_criteria = data_criteria_info['data_criteria']
-            data_criteria_oid = HQMFTemplateHelper.template_id_by_definition_and_status(data_criteria.definition, 
+            data_criteria_oid = HQMFTemplateHelper.template_id_by_definition_and_status(data_criteria.definition,
                                                                                         data_criteria.status || '',
                                                                                         data_criteria.negation)
             if entry.respond_to?(:oid) && (entry.oid == data_criteria_oid)
@@ -67,13 +67,13 @@ module HealthDataStandards
               end
             end
           end
-          
+
           false
         end
-        
+
         # Find all of the entries on a patient that match the given data criteria
         def entries_for_data_criteria(data_criteria, patient)
-          data_criteria_oid = HQMFTemplateHelper.template_id_by_definition_and_status(data_criteria.definition, 
+          data_criteria_oid = HQMFTemplateHelper.template_id_by_definition_and_status(data_criteria.definition,
                                                                                       data_criteria.status || '',
                                                                                        data_criteria.negation)
           HealthDataStandards.logger.warn("Looking for dc [#{data_criteria_oid}]")
@@ -90,21 +90,21 @@ module HealthDataStandards
             entries.concat patient.entries_for_oid(data_criteria_oid)
 
               case data_criteria_oid
-              when '2.16.840.1.113883.3.560.1.5' 
+              when '2.16.840.1.113883.3.560.1.5'
                 #special case handling for Lab Test: Performed being implicitly available through a Lab Test: Result
                 entries.concat patient.entries_for_oid('2.16.840.1.113883.3.560.1.12')
               when '2.16.840.1.113883.3.560.1.12'
-                entries.concat patient.entries_for_oid('2.16.840.1.113883.3.560.1.5')  
-              when '2.16.840.1.113883.3.560.1.6' 
+                entries.concat patient.entries_for_oid('2.16.840.1.113883.3.560.1.5')
+              when '2.16.840.1.113883.3.560.1.6'
                  entries.concat patient.entries_for_oid('2.16.840.1.113883.3.560.1.63')
-              when  '2.16.840.1.113883.3.560.1.63' 
+              when  '2.16.840.1.113883.3.560.1.63'
                  entries.concat patient.entries_for_oid('2.16.840.1.113883.3.560.1.6')
-              when '2.16.840.1.113883.3.560.1.3' 
+              when '2.16.840.1.113883.3.560.1.3'
                  entries.concat patient.entries_for_oid('2.16.840.1.113883.3.560.1.11')
-              when  '2.16.840.1.113883.3.560.1.11' 
+              when  '2.16.840.1.113883.3.560.1.11'
                  entries.concat patient.entries_for_oid('2.16.840.1.113883.3.560.1.3')
               end
- 
+
             codes = (value_set_map(patient["bundle_id"])[data_criteria.code_list_id] || [])
             if codes.empty?
               HealthDataStandards.logger.warn("No codes for #{data_criteria.code_list_id}")
@@ -129,7 +129,7 @@ module HealthDataStandards
 
         def handle_clinical_trial_participant(patient)
           if patient.clinical_trial_participant
-            [{dummy_entry: true}]
+            [Entry.new]
           else
             []
           end
@@ -149,4 +149,4 @@ module HealthDataStandards
       end
     end
   end
-end
+end

data/lib/health-data-standards/export/qrda/hqmf-qrda-oids.json

@@ -611,6 +611,12 @@
     "qrda_name": "Communication from Provider to Provider",
     "qrda_oid": "2.16.840.1.113883.10.20.24.3.4"
   },
+  {
+    "hqmf_name": "Communication: From Patient to Provider not done",
+    "hqmf_oid": "2.16.840.1.113883.3.560.1.130",
+    "qrda_name": "Communication from Patient to Provider",
+    "qrda_oid": "2.16.840.1.113883.10.20.24.3.2"
+  },
   {
     "hqmf_name": "Risk Category Assessment not done",
     "hqmf_oid": "2.16.840.1.113883.3.560.1.121",

data/lib/health-data-standards/export/view_helper.rb

@@ -66,6 +66,7 @@ module HealthDataStandards
       end
       
       def convert_field_to_hash(field, codes)
+        codes = codes[0] if codes.is_a? Array
         if (codes.is_a? Hash)
           clean_hash = {}
           
@@ -96,7 +97,13 @@ module HealthDataStandards
           elsif codes['scalar']
             return "#{codes['scalar']} #{codes['units']}"
           else
-            return codes.map {|hashcode_set, hashcodes| "#{hashcode_set}: #{(hashcodes.respond_to? :join) ? hashcodes.join(', ') : hashcodes.to_s}"}.join(' ')
+            return codes.map do |hashcode_set, hashcodes| 
+              if hashcodes.is_a? Hash
+                "#{hashcode_set}: #{convert_field_to_hash(hashcode_set, hashcodes)}"
+              else
+                "#{hashcode_set}: #{(hashcodes.respond_to? :join) ? hashcodes.join(', ') : hashcodes.to_s}"
+              end
+            end.join(' ')
           end
             
           clean_hash

data/lib/health-data-standards/import/bulk_record_importer.rb

@@ -10,20 +10,44 @@ module HealthDataStandards
            BulkRecordImporter.import_file(file,File.new(file).read,failed_dir)
         end
       end
-      
-      def self.import_archive(file, failed_dir=nil) 
-        begin 
+
+      def self.import_archive(file, failed_dir=nil)
+        begin
         failed_dir ||=File.join(File.dirname(file))
+
+        patient_id_list = nil
+
         Zip::ZipFile.open(file.path) do |zipfile|
           zipfile.entries.each do |entry|
+            if entry.name
+              if entry.name.split("/").last == "patient_manifest.txt"
+                patient_id_list = zipfile.read(entry.name)
+                next
+              end
+            end
             next if entry.directory?
             data = zipfile.read(entry.name)
             BulkRecordImporter.import_file(entry.name,data,failed_dir)
           end
         end
+
+        missing_patients = []
+
+        #if there was a patient manifest, theres a patient id list we need to load
+        if patient_id_list
+          patient_id_list.split("\n").each do |id|
+            patient = Record.where(:medical_record_number => id).first
+            if patient == nil
+              missing_patients << id
+            end
+          end
+        end
+
+        missing_patients
+
       rescue
         FileUtils.mkdir_p(failed_dir)
-        File.cp(file,File.join(failed_dir,file))
+        FileUtils.cp(file,File.join(failed_dir,File.basename(file)))
         File.open(File.join(failed_dir,"#{file}.error")) do |f|
           f.puts($!.message)
           f.puts($!.backtrace)
@@ -54,15 +78,22 @@ module HealthDataStandards
 
       def self.import_json(data,provider_map = {})
         json = JSON.parse(data,:max_nesting=>100)
-        Record.update_or_create(Record.new(json))
+        record = Record.update_or_create(Record.new(json))
+        providers = record.provider_performances
+        providers.each do |prov|
+          prov.provider.ancestors.each do |ancestor|
+            record.provider_performances.push(ProviderPerformance.new(start_date: prov.start_date, end_date: prov.end_date, provider: ancestor))
+          end
+        end
+        record.save!
       end
-      
+
       def self.import(xml_data, provider_map = {})
         doc = Nokogiri::XML(xml_data)
-        
+
         providers = []
         root_element_name = doc.root.name
-        
+
         if root_element_name == 'ClinicalDocument'
           doc.root.add_namespace_definition('cda', 'urn:hl7-org:v3')
           doc.root.add_namespace_definition('sdtc', 'urn:hl7-org:sdtc')
@@ -77,9 +108,11 @@ module HealthDataStandards
             STDERR.puts("Unable to determinate document template/type of CDA document")
             return {status: 'error', message: "Document templateId does not identify it as a C32 or CCDA", status_code: 400}
           end
-          
+
+          record = Record.update_or_create(patient_data)
+
           begin
-            providers = CDA::ProviderImporter.instance.extract_providers(doc)
+            providers = CDA::ProviderImporter.instance.extract_providers(doc, record)
           rescue Exception => e
             STDERR.puts "error extracting providers"
           end
@@ -87,11 +120,10 @@ module HealthDataStandards
           return {status: 'error', message: 'Unknown XML Format', status_code: 400}
         end
 
-        record = Record.update_or_create(patient_data)
         record.provider_performances = providers
-        providers.each do |prov| 
+        providers.each do |prov|
           prov.provider.ancestors.each do |ancestor|
-            record.provider_performances.push(ProviderPerformance.new(start_date: prov.start_date, end_date: prov.end_date, provider: ancestor))  
+            record.provider_performances.push(ProviderPerformance.new(start_date: prov.start_date, end_date: prov.end_date, provider: ancestor))
           end
         end
         record.save

data/lib/health-data-standards/import/bundle/importer.rb

@@ -75,7 +75,7 @@ module HealthDataStandards
           Mongoid.default_session['system.js'].find('_id' => name).upsert(
             {
               "_id" => name,
-              "value" => Moped::BSON::Code.new(fn)
+              "value" => BSON::Code.new(fn)
             }
           )
         end
@@ -140,14 +140,12 @@ module HealthDataStandards
 
         def self.unpack_and_store_valuesets(zip, bundle)
           entries = zip.glob(SOURCE_ROOTS[:valuesets])
-          bulk = []
           entries.each_with_index do |entry, index|
             vs = HealthDataStandards::SVS::ValueSet.new(unpack_json(entry))
             vs['bundle_id'] = bundle.id
-            bulk << vs
+            HealthDataStandards::SVS::ValueSet.collection.insert(vs.as_document)
             report_progress('Value Sets', (index*100/entries.length)) if index%10 == 0
           end
-          HealthDataStandards::SVS::ValueSet.collection.insert(bulk.map {|vs| vs.as_document})
           puts "\rLoading: Value Sets Complete          "
         end
 

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

@@ -18,11 +18,11 @@ module HealthDataStandards
         # @param [Nokogiri::XML::Document] doc It is expected that the root node of this document
         #        will have the "cda" namespace registered to "urn:hl7-org:v3"
         # @return [Array] an array of providers found in the document
-        def extract_providers(doc)
+        def extract_providers(doc, patient=nil)
           performers = doc.xpath("//cda:documentationOf/cda:serviceEvent/cda:performer")
           performers.map do |performer|
             provider_perf = extract_provider_data(performer, true)
-            ProviderPerformance.new(start_date: provider_perf.delete(:start), end_date: provider_perf.delete(:end), provider: find_or_create_provider(provider_perf))
+            ProviderPerformance.new(start_date: provider_perf.delete(:start), end_date: provider_perf.delete(:end), provider: find_or_create_provider(provider_perf, patient))
           end
         end
 

data/lib/health-data-standards/import/green_c32/section_importer.rb

@@ -36,7 +36,7 @@ module HealthDataStandards
             codes.merge!(build_code(trans))
           end
           
-          entry.send("#{attribute}=", codes)
+          entry.write_attribute(attribute, codes)
         end
         
         def extract_description(element, entry)
@@ -71,7 +71,7 @@ module HealthDataStandards
           
           return unless datetime && datetime['value']
           
-          entry.send("#{attribute}=", Time.parse(datetime['value']).utc.to_i)
+          entry.write_attribute(attribute, Time.parse(datetime['value']).utc.to_i)
         end
         
         def extract_interval(element, entry, element_name="effectiveTime")

data/lib/health-data-standards/import/provider_import_utils.rb

@@ -5,7 +5,7 @@ module ProviderImportUtils
     find_or_create_provider(provider_data)
   end
 
-  def find_or_create_provider(provider_hash)
+  def find_or_create_provider(provider_hash, patient=nil)
     provider = Provider.by_npi(provider_hash[:npi]).first if provider_hash[:npi] && !provider_hash[:npi].empty?
     unless provider
       if provider_hash[:npi]
@@ -22,7 +22,7 @@ module ProviderImportUtils
                             :family_name=> provider_hash[:family_name],
                             :specialty => provider_hash[:specialty]}
         provider ||= Provider.where(provider_query).first
-        provider ||= Provider.resolve_provider(provider_hash)
+        provider ||= Provider.resolve_provider(provider_hash, patient)
         provider ||= Provider.create(provider_hash)
       end
     end

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

@@ -1,5 +1,6 @@
 class CDAIdentifier
   include Mongoid::Document
+  include Mongoid::Attributes::Dynamic
 
   field :root, type: String
   field :extension, type: String

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

@@ -4,11 +4,14 @@ module HealthDataStandards
     class Bundle
       include Mongoid::Document
       include Mongoid::Timestamps
+      include Mongoid::Attributes::Dynamic
       store_in collection: 'bundles'
       field :title, type: String
+      field :name, type: String
       field :version, type: String
       field :license, type: String
       field :extensions, type: Array
+      field :measures, type: Array
       field :effective_date
       field :measure_period_start
       field :records, type: Array
@@ -16,7 +19,7 @@ module HealthDataStandards
 
       validates_presence_of :version
 
-      scope :active, where(active: true)
+      scope :active, -> {where(active: true)}
 
       def self.latest_bundle_id
         desc(:exported).first.try(:_id)

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

@@ -7,9 +7,12 @@ module HealthDataStandards
       MSRPOPL = 'MSRPOPL'
 
       store_in collection: 'measures'
-      field :id, type: String
+      field :id, as: :id, type: String
       field :sub_id, type: String
+      field :cms_id, type: String
       field :name, type: String
+      field :title, type: String
+      field :description, type: String
       field :subtitle, type: String
       field :short_subtitle, type: String
       field :hqmf_id, type: String
@@ -29,12 +32,15 @@ module HealthDataStandards
       field :populations, type: Array
       field :preconditions, type: Hash
       field :hqmf_document, type: Hash
-
+      field :map_fn, type: String
+      field :continuous_variable, type: Boolean
+      field :episode_of_care, type: Boolean
+      field :aggregator, type: String
       embeds_many :prefilters
 
       scope :top_level_by_type , ->(type){where({"type"=> type}).any_of({"sub_id" => nil}, {"sub_id" => "a"})}
-      scope :top_level , any_of({"sub_id" => nil}, {"sub_id" => "a"})
-      scope :order_by_id_sub_id, order_by([["id", :asc],["sub_id", :asc]])
+      scope :top_level , ->{any_of({"sub_id" => nil}, {"sub_id" => "a"})}
+      scope :order_by_id_sub_id, ->{order_by([["id", :asc],["sub_id", :asc]])}
 
       index oids: 1
       index hqmf_id: 1
@@ -46,28 +52,37 @@ module HealthDataStandards
       validates_presence_of :id
       validates_presence_of :name
 
-      def self.categories
+      def self.categories(measure_properties = [])
+        measure_properties = Array(measure_properties).map(&:to_s) | %w(
+          name description nqf_id cms_id hqmf_id continuous_variable episode_of_care
+        )
         pipeline = []
-        pipeline << {'$group' => {_id: "$id",
-                                  name: {"$first" => "$name"},
-                                  description: {"$first" => "$description"},
-                                  subs: {'$push' => {"sub_id" => "$sub_id", "short_subtitle" => "$short_subtitle"}},
-                                  sub_ids: {'$push' => "$sub_id"},
-                                  nqf_id: {"$first" => "$nqf_id"},
-                                  cms_id: {"$first" => "$cms_id"},
-                                  continuous_variable: {"$first" => "$continuous_variable"},
-                                  category: {'$first' => "$category"}}}
-
-        pipeline << {'$group' => {_id: "$category",
-                                  measures: {'$push' => {"id" => "$_id",
-                                             'name' => "$name",
-                                             'description' => "$description",
-                                             'subs' => "$subs",
-                                             'sub_ids' => "$sub_ids",
-                                             'nqf_id' => "$nqf_id",
-                                             'cms_id' => "$cms_id",
-                                             'continuous_variable' => "$continuous_variable"
-                                            }}}}
+
+        pipeline << {'$group' =>  measure_properties.inject({
+                                    '_id' => "$id",
+                                    'subs' => {'$push' => {"sub_id" => "$sub_id", "short_subtitle" => "$short_subtitle"}},
+                                    'sub_ids' => {'$push' => "$sub_id"},
+                                    'category' => {'$first' => "$category"}
+                                  }) do |h, prop|
+                                    h[prop] = {"$first" => "$#{prop}"}
+                                    h
+                                  end
+                    }
+
+        pipeline << {'$group' => {
+                      _id: "$category",
+                      measures: {
+                        '$push' =>  measure_properties.inject({
+                                      'id' => "$_id",
+                                      'hqmf_id' => "$_id",
+                                      'subs' => "$subs",
+                                      'sub_ids' => "$sub_ids"
+                                    }) do |h, prop|
+                                      h[prop] = "$#{prop}"
+                                      h
+                                    end
+                      }
+                    }}
 
         pipeline << {'$project' => {'category' => '$_id', 'measures' => 1, '_id' => 0}}