test-patient-generator 1.1.2 → 1.2.0

data/Gemfile

@@ -3,11 +3,10 @@ source "http://rubygems.org"
 gemspec
 
 gem 'rake'
-
 group :test do
   gem 'simplecov'
   gem 'turn'
   gem 'pry'
   gem 'pry-nav'
   gem 'pry-stack_explorer'
-end
+end

data/lib/test-patient-generator.rb

@@ -1,6 +1,5 @@
 require 'hqmf-parser'
 require 'health-data-standards'
-require 'qrda_generator'
 
 require_relative 'tpg/ext/coded'
 require_relative 'tpg/ext/data_criteria'

data/lib/tpg/ext/coded.rb

@@ -9,8 +9,8 @@ module HQMF
     def self.select_codes(oid, value_sets)
       value_sets = HQMF::Coded.select_value_sets(oid, value_sets)
       code_sets = {}
-      value_sets["code_sets"].each do |value_set|
-        code_sets[value_set["code_set"]] = [value_set["codes"].first]
+      value_sets["concepts"].each do |concept|
+        code_sets[concept["code_system_name"]] ||= [concept["code"]]
       end
       code_sets
     end
@@ -23,7 +23,7 @@ module HQMF
     def self.select_value_sets(oid, value_sets)
       # Pick the value set for this DataCriteria. If it can't be found, it is an error from the value set source. We'll add the entry without codes for now.
       index = value_sets.index{|value_set| value_set["oid"] == oid}
-      value_sets = index.nil? ? { "code_sets" => [] } : value_sets[index]
+      value_sets = index.nil? ? { "concepts" => [] } : value_sets[index]
       value_sets
     end
 

data/lib/tpg/ext/data_criteria.rb

@@ -76,7 +76,7 @@ module HQMF
       entry.values ||= []
       values.each do |value|
         if value.type == "CD"
-          entry.values << CodedResultValue.new({codes: Coded.select_codes(value.code_list_id, value_sets), description: HQMF::Coded.select_value_sets(value.code_list_id, value_sets)["concept"]})
+          entry.values << CodedResultValue.new({codes: Coded.select_codes(value.code_list_id, value_sets), description: HQMF::Coded.select_value_sets(value.code_list_id, value_sets)["display_name"]})
         else
           entry.values << PhysicalQuantityResultValue.new(value.format)
         end
@@ -109,7 +109,7 @@ module HQMF
         # Format the field to be stored in a Record.
         if field.type == "CD"
           field_value = Coded.select_code(field.code_list_id, value_sets)
-          field_value["title"] = HQMF::Coded.select_value_sets(field.code_list_id, value_sets)["concept"] if field_value
+          field_value["title"] = HQMF::Coded.select_value_sets(field.code_list_id, value_sets)["display_name"] if field_value
         else
           field_value = field.format
         end

data/lib/tpg/generation/exporter.rb

@@ -5,9 +5,9 @@ module TPG
     # @param [Array] patients All of the patients that will be exported.
     # @param [String] format The desired format for the patients to be in.
     # @return A zip file containing all given patients in the requested format.
-    def self.zip(patients, format, concept_map=nil)
+    def self.zip(patients, format)
       file = Tempfile.new("patients-#{Time.now.to_i}")
-      
+      html_exporter = HealthDataStandards::Export::HTML.new
       Zip::ZipOutputStream.open(file.path) do |z|
         xslt = Nokogiri::XSLT(File.read("public/cda.xsl"))
         patients.each do |patient|
@@ -15,16 +15,16 @@ module TPG
 
           if format == "c32"
             z.put_next_entry("#{next_entry_path}.xml")
-            z << HealthDataStandards::Export::C32.export(patient)
+            z << HealthDataStandards::Export::C32.new.export(patient)
           elsif format == "ccr"
             z.put_next_entry("#{next_entry_path}.xml")
             z << HealthDataStandards::Export::CCR.export(patient)
           elsif format == "ccda"
             z.put_next_entry("#{next_entry_path}.xml")
-            z << HealthDataStandards::Export::CCDA.export(patient)
+            z << HealthDataStandards::Export::CCDA.new.export(patient)
           elsif format == "html"
             z.put_next_entry("#{next_entry_path}.html")
-            z << html_contents(patient, concept_map)
+            z << html_contents(patient, html_exporter)
           elsif format == "json"
             z.put_next_entry("#{next_entry_path}.json")
             z << JSON.pretty_generate(JSON.parse(patient.to_json))
@@ -43,13 +43,13 @@ module TPG
     # @return A zip file containing all of the QRDA Category 1 patients that were passed in.
     def self.zip_qrda_html_patients(measure_patients)
       file = Tempfile.new("patients-#{Time.now.to_i}")
-      
+      html_exporter = HealthDataStandards::Export::HTML.new
       Zip::ZipOutputStream.open(file.path) do |zip|
         xslt = Nokogiri::XSLT(File.read("public/cda.xsl"))
         measure_patients.each do |measure, patient|
           # Create a directory for this measure and insert the HTML for this patient.
           zip.put_next_entry(File.join(measure, "#{patient_filename(patient)}.html"))
-          zip << html_contents(patient)
+          zip << html_contents(patient, html_exporter)
         end
       end
       
@@ -70,7 +70,7 @@ module TPG
           measure_defs = measures.find {|m| m.id == nqf_id}
           # Create a directory for this measure and insert the HTML for this patient.
           zip.put_next_entry(File.join(measure_defs.hqmf_id, "#{patient_filename(patient)}.xml"))
-          zip << QrdaGenerator::Export::Cat1.export(patient, [measure_defs], Time.gm(2011, 1, 1), Time.gm(2011, 12, 31))
+          zip << HealthDataStandards::Export::Cat1.new.export(patient, [measure_defs], Time.gm(2011, 1, 1), Time.gm(2011, 12, 31))
         end
       end
       
@@ -82,8 +82,8 @@ module TPG
     #
     # @param [Record] patient The Record for which we're generating HTML content.
     # @return HTML content to be exported for a Record.
-    def self.html_contents(patient, concept_map=nil)
-      HealthDataStandards::Export::HTML.export(patient, concept_map)
+    def self.html_contents(patient, exporter = HealthDataStandards::Export::HTML.new)
+      exporter.export(patient)
     end
     
     # Join the first and last name with an underscore and replace any other punctuation that might interfere with file names.

data/lib/tpg/generation/generator.rb

@@ -1,11 +1,13 @@
 module HQMF
   class Generator
+
     # Generate patients from lists of DataCriteria. This is originally created for QRDA Category 1 validation testing,
     # i.e. a single patient will be generated per measure with an entry for every data criteria involved in the measure.
     # 
     # @param [Hash] measure_needs A hash of measure IDs mapped to a list of all their data criteria in JSON.
+    # @param [Hash] Value set hash to use for looking up codes for the data criteria passed in.  If null will resort to original behavior of 
     # @return [Hash] A hash of measure IDs mapped to a Record that includes all the given data criteria (values and times are arbitrary).
-    def self.generate_qrda_patients(measure_needs)      
+    def self.generate_qrda_patients(measure_needs, value_sets=nil)      
       return {} if measure_needs.nil?
       
       measure_patients = {}
@@ -13,7 +15,7 @@ module HQMF
         # Define a list of unique data criteria and matching value sets to create a patient for this measure.
         unique_data_criteria = select_unique_data_criteria(all_data_criteria)
         oids = select_unique_oids(all_data_criteria)
-        value_sets = create_oid_dictionary(oids)
+        value_sets = create_oid_dictionary(oids) if value_sets.nil?
         
         # Create a patient that includes an entry for every data criteria included in this measure.
         patient = Generator.create_base_patient
@@ -81,8 +83,18 @@ module HQMF
       
       unique_data_criteria = []
       all_data_criteria.each do |data_criteria|
-        index = unique_data_criteria.index {|dc| dc.code_list_id == data_criteria.code_list_id && dc.negation_code_list_id == data_criteria.negation_code_list_id && dc.field_values == data_criteria.field_values && dc.status == data_criteria.status && dc.definition == data_criteria.definition}
-        unique_data_criteria << data_criteria if index.nil?
+
+        fields1 = data_criteria.field_values || {}
+
+        index = unique_data_criteria.index {|dc| dc.code_list_id == data_criteria.code_list_id && dc.negation_code_list_id == data_criteria.negation_code_list_id && dc.status == data_criteria.status && dc.definition == data_criteria.definition}
+       
+        if index
+          crit = unique_data_criteria[index]
+          crit.field_values ||= {}
+          crit.field_values.merge! data_criteria.field_values || {} 
+        else
+         unique_data_criteria << data_criteria 
+        end
       end
 
       unique_data_criteria
@@ -95,10 +107,9 @@ module HQMF
     def self.create_oid_dictionary(oids)
       value_sets = []
       HealthDataStandards::SVS::ValueSet.any_in(oid: oids).each do |value_set|
-        code_sets = value_set.concepts.map { |concept| {"code_set" => concept.code_system_name, "codes" => [concept.code]} }
-        value_sets << {"code_sets" => code_sets, "oid" => value_set.oid, "concept" => value_set.display_name}
+        code_sets = value_set.concepts
+        value_sets << {"concepts" => code_sets, "oid" => value_set.oid}
       end
-
       value_sets
     end
 

metadata

@@ -1,15 +1,16 @@
 --- !ruby/object:Gem::Specification
 name: test-patient-generator
 version: !ruby/object:Gem::Version
-  version: 1.1.2
+  version: 1.2.0
   prerelease: 
 platform: ruby
 authors:
 - Adam Goldstein
+- Andre Quina
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-01-16 00:00:00.000000000 Z
+date: 2013-02-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: health-data-standards
@@ -18,7 +19,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 2.2.1
+        version: 3.0.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -26,7 +27,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 2.2.1
+        version: 3.0.1
 - !ruby/object:Gem::Dependency
   name: hquery-patient-api
   requirement: !ruby/object:Gem::Requirement
@@ -34,23 +35,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.0.0
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: 1.0.0
-- !ruby/object:Gem::Dependency
-  name: hqmf-parser
-  requirement: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: 1.1.0
+        version: 1.0.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -58,7 +43,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.1.0
+        version: 1.0.1
 - !ruby/object:Gem::Dependency
   name: hqmf2js
   requirement: !ruby/object:Gem::Requirement
@@ -66,7 +51,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.1.0
+        version: 1.2.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -74,23 +59,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.1.0
-- !ruby/object:Gem::Dependency
-  name: qrda_generator
-  requirement: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: 1.0.1
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: 1.0.1
+        version: 1.2.0
 description: A utility to generate patients for unit testing clinical quality measure
   logic. The instructions for generation are guided by HQMF documents and exported
   into various health standards, e.g. C32, CCR.