health-data-standards 3.0.6 → 3.1.0

data/templates/ccda/show.ccda.erb

@@ -4,7 +4,7 @@
   <typeId root="2.16.840.1.113883.1.3" extension="POCD_HD000040"/>
   <templateId root="2.16.840.1.113883.10.20.22.1.1" />
   <templateId root='2.16.840.1.113883.10.20.22.1.2'/> 
-  <id root="2.16.840.1.113883.3.72" extension="<%= patient.id %>" assigningAuthorityName="NIST Healthcare Project"/>
+  <id root="2.16.840.1.113883.19.5" extension="<%= patient.id %>" assigningAuthorityName="Cypress Project"/>
   <code code="34133-9" displayName="Summarization of episode note" codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC"/>
   <title>Cypress C32 Patient Test Record: <%= patient.first %> <%= patient.last %></title>
   <effectiveTime value="<%= Time.now.utc.to_formatted_s(:number) %>"/>

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: health-data-standards
 version: !ruby/object:Gem::Version
-  version: 3.0.6
+  version: 3.1.0
   prerelease: 
 platform: ruby
 authors:
@@ -13,7 +13,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-02-28 00:00:00.000000000 Z
+date: 2013-04-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rest-client
@@ -144,61 +144,29 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: spreadsheet
-  requirement: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - '='
-      - !ruby/object:Gem::Version
-        version: 0.6.8
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - '='
-      - !ruby/object:Gem::Version
-        version: 0.6.8
-- !ruby/object:Gem::Dependency
-  name: google-spreadsheet-ruby
-  requirement: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - '='
-      - !ruby/object:Gem::Version
-        version: 0.1.8
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - '='
-      - !ruby/object:Gem::Version
-        version: 0.1.8
-- !ruby/object:Gem::Dependency
-  name: roo
+  name: log4r
   requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - '='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: 1.10.1
+        version: 1.1.10
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - '='
+    - - ~>
       - !ruby/object:Gem::Version
-        version: 1.10.1
+        version: 1.1.10
 - !ruby/object:Gem::Dependency
-  name: log4r
+  name: memoist
   requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.1.10
+        version: 0.9.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -206,7 +174,7 @@ dependencies:
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
-        version: 1.1.10
+        version: 0.9.0
 description: A library for generating and consuming various healthcare related formats.
   This includes HITSP C32, ASTM CCR and PQRI.
 email: talk@projectpophealth.org
@@ -216,6 +184,7 @@ extra_rdoc_files: []
 files:
 - lib/health-data-standards/export/c32.rb
 - lib/health-data-standards/export/cat_1.rb
+- lib/health-data-standards/export/cat_3.rb
 - lib/health-data-standards/export/ccda.rb
 - lib/health-data-standards/export/ccr.rb
 - lib/health-data-standards/export/csv.rb
@@ -242,14 +211,19 @@ files:
 - lib/health-data-standards/import/cat1/diagnosis_active_importer.rb
 - lib/health-data-standards/import/cat1/diagnosis_inactive_importer.rb
 - lib/health-data-standards/import/cat1/diagnostic_study_order_importer.rb
+- lib/health-data-standards/import/cat1/ecog_status_importer.rb
 - lib/health-data-standards/import/cat1/encounter_order_importer.rb
 - lib/health-data-standards/import/cat1/entry_package.rb
 - lib/health-data-standards/import/cat1/gestational_age_importer.rb
 - lib/health-data-standards/import/cat1/lab_order_importer.rb
+- lib/health-data-standards/import/cat1/lab_result_importer.rb
+- lib/health-data-standards/import/cat1/medication_active_importer.rb
 - lib/health-data-standards/import/cat1/medication_dispensed_importer.rb
 - lib/health-data-standards/import/cat1/patient_importer.rb
 - lib/health-data-standards/import/cat1/procedure_intolerance_importer.rb
 - lib/health-data-standards/import/cat1/procedure_order_importer.rb
+- lib/health-data-standards/import/cat1/procedure_performed_importer.rb
+- lib/health-data-standards/import/cat1/symptom_active_importer.rb
 - lib/health-data-standards/import/cat1/tobacco_use_importer.rb
 - lib/health-data-standards/import/ccda/allergy_importer.rb
 - lib/health-data-standards/import/ccda/care_goal_importer.rb
@@ -302,10 +276,13 @@ files:
 - lib/health-data-standards/import/provider_import_utils.rb
 - lib/health-data-standards/models/address.rb
 - lib/health-data-standards/models/allergy.rb
+- lib/health-data-standards/models/cda_identifier.rb
 - lib/health-data-standards/models/coded_result_value.rb
 - lib/health-data-standards/models/condition.rb
+- lib/health-data-standards/models/cqm/aggregate_objects.rb
 - lib/health-data-standards/models/cqm/bundle.rb
 - lib/health-data-standards/models/cqm/measure.rb
+- lib/health-data-standards/models/cqm/query_cache.rb
 - lib/health-data-standards/models/encounter.rb
 - lib/health-data-standards/models/entry.rb
 - lib/health-data-standards/models/facility.rb
@@ -383,7 +360,6 @@ files:
 - lib/hqmf-parser/converter/pass2/comparison_converter.rb
 - lib/hqmf-parser/converter/pass2/operator_converter.rb
 - lib/hqmf-parser/parser.rb
-- lib/hqmf-parser/value_sets/value_set_parser.rb
 - lib/hqmf-parser.rb
 - lib/util/counter.rb
 - templates/_pedigree.hdata.erb
@@ -456,6 +432,11 @@ files:
 - templates/cat1/_reporting_parameters.cat1.erb
 - templates/cat1/_result_value.cat1.erb
 - templates/cat1/show.cat1.erb
+- templates/cat3/_continuous_variable_value.cat3.erb
+- templates/cat3/_measure_data.cat3.erb
+- templates/cat3/_performance_rate.cat3.erb
+- templates/cat3/_supplemental_data.cat3.erb
+- templates/cat3/show.cat3.erb
 - templates/ccda/_allergies.ccda.erb
 - templates/ccda/_allergies_no_current.ccda.erb
 - templates/ccda/_care_goals.ccda.erb
@@ -559,9 +540,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.24
+rubygems_version: 1.8.25
 signing_key: 
 specification_version: 3
 summary: A library for generating and consuming various healthcare related formats.
 test_files: []
-has_rdoc: 

data/lib/hqmf-parser/value_sets/value_set_parser.rb

@@ -1,241 +0,0 @@
-require 'zip/zipfilesystem'
-require 'spreadsheet'
-require 'google_spreadsheet'
-require 'roo'
-require 'iconv'
-
-module HQMF
-  module ValueSet
-    class Parser
-
-      attr_accessor :child_oids
-  
-      GROUP_CODE_SET = "GROUPING"
-  
-      ORGANIZATION_TITLE = "Value Set Developer"
-      OID_TITLE = "Value Set OID"
-      CONCEPT_TITLE = "Value Set Name"
-      CATEGORY_TITLE = "QDM Category"
-      CODE_SET_TITLE ="Code System"
-      VERSION_TITLE = "Code System Version"
-      CODE_TITLE = "Code"
-      DESCRIPTION_TITLE = "Descriptor"
-      
-      CODE_SYSTEM_NORMALIZER = {
-        'ICD-9'=>'ICD-9-CM',
-        'ICD-10'=>'ICD-10-CM',
-        'HL7 (2.16.840.1.113883.5.1)'=>'HL7'
-      }
-      IGNORED_CODE_SYSTEM_NAMES = ['Grouping', 'GROUPING' ,'HL7', "Administrative Sex"]
-  
-      def initialize()
-        @child_oids = []
-      end
-  
-      # import an excel matrix array into mongo
-      def parse(file, options={})
-        sheet_array = file_to_array(file, options)
-        by_oid_ungrouped = cells_to_hashs_by_oid(sheet_array)
-        value_sets = collapse_groups(by_oid_ungrouped)
-        translate_json(value_sets)
-      end
-  
-      def collapse_groups(by_oid_ungrouped)
-    
-        final = []
-    
-        # select the grouped code sets and fill in the children... also remove the children that are a
-        # member of a group.  We remove the children so that we can create parent groups for the orphans
-        (by_oid_ungrouped.select {|key,value| value["code_set"].upcase == GROUP_CODE_SET}).each do |key, value|
-          # remove the group so that it is not in the orphan list
-          by_oid_ungrouped.delete(value["oid"])
-          codes = []
-          value["codes"].each do |child_oid|
-#            codes << by_oid_ungrouped.delete(child_oid)
-            # do not delete the children of a group.  These may be referenced by other groups or directly by the measure
-            code = by_oid_ungrouped[child_oid]
-            @child_oids << child_oid
-            puts "\tcode could not be found: #{child_oid}" unless code
-            codes << code if code
-            # for hierarchies we need to probably have codes be a hash that we select from if we don't find the
-            # element in by_oid_ungrouped we may need to look for it in final
-          end
-          value["code_sets"] = codes
-          value.delete("codes")
-          value.delete("code_set")
-          final << value
-        end
-    
-        # fill out the orphans
-        by_oid_ungrouped.each do |key, orphan|
-          final << adopt_orphan(orphan)
-        end
-        
-        deleted = []
-        final.delete_if {|x| to_delete = x['code_sets'].nil? || x['code_sets'].empty?; deleted << x if to_delete; to_delete }
-        deleted.each do |value|
-          puts "\tDeleted value set with no code sets: #{value['oid']}"
-        end
-        final
-    
-      end
-  
-      def adopt_orphan(orphan)
-        parent = orphan.dup
-        parent["code_sets"] = [orphan]
-        parent.delete("codes")
-        parent.delete("code_set")
-        parent
-      end
-  
-      # take an excel matrix array and turn it into an array of db models
-      def cells_to_hashs_by_oid(array)
-        a = Array.new(array)                  # new variable for reentrant
-        headers = a.shift.map {|i| i.to_s }   # because of this shift
-        string_data = a.map {|row| row.map {|cell| cell.to_s } }
-        array_of_hashes = string_data.map {|row| Hash[*headers.zip(row).flatten] }
-
-        by_oid = {}
-        array_of_hashes.each do |row|
-          entry = convert_row(row)
-          
-          existing = by_oid[entry["oid"]]
-          if (existing)
-            existing["codes"].concat(entry["codes"])
-          else
-            by_oid[entry["oid"]] = entry
-          end
-        end
-    
-        by_oid
-      end
-  
-      def self.get_format(file_path)
-        if file_path =~ /xls$/
-          :xls
-        elsif file_path =~ /xlsx$/
-          :xlsx
-        end
-      end
-  
-      private
-  
-      def convert_row(row)
-        # Value Set Developer
-        # Value Set OID
-        # Value Set Name
-        # QDM Category
-        # Code System
-        # Code System Version
-        # Code
-        # Descriptor
-        value = {
-          "key" => normalize_names(row[CATEGORY_TITLE],row[CONCEPT_TITLE]),
-          "organization" => row[ORGANIZATION_TITLE],
-          "oid" => row[OID_TITLE].strip.gsub(/[^0-9\.]/i, ''),
-          "concept" => normalize_names(row[CONCEPT_TITLE]),
-          "category" => normalize_names(row[CATEGORY_TITLE]),
-          "code_set" => normalize_code_system(row[CODE_SET_TITLE]),
-          "version" => row[VERSION_TITLE],
-          "codes" => extract_code(row[CODE_TITLE], row[CODE_SET_TITLE]),
-          "description" => row[DESCRIPTION_TITLE]
-        }
-        value['codes'].map! {|code| code.strip.gsub(/[^0-9\.]/i, '')} if (value['code_set'].upcase == GROUP_CODE_SET)
-        value
-      end
-  
-      # Break all the supplied strings into separate words and return the resulting list as a
-      # new string with each word separated with '_'
-      def normalize_names(*components)
-        name = []
-        components.each do |component|
-          name.concat component.gsub(/\W/,' ').split.collect { |word| word.strip.downcase }
-        end
-        name.join '_'
-      end
-      
-      def normalize_code_system(code_system_name)
-        code_system_name = CODE_SYSTEM_NORMALIZER[code_system_name] if CODE_SYSTEM_NORMALIZER[code_system_name]
-        return code_system_name if IGNORED_CODE_SYSTEM_NAMES.include? code_system_name
-        oid = HealthDataStandards::Util::CodeSystemHelper.oid_for_code_system(code_system_name)
-        puts "\tbad code system name: #{code_system_name}" unless oid
-        code_system_name
-      end
-  
-      def extract_code(code, set)
-    
-        code.strip!
-        if set=='CPT' && code.include?('-')
-          eval(code.strip.gsub('-','..')).to_a.collect { |i| i.to_s }
-        else
-          [code]
-        end
-    
-      end
-  
-      def file_to_array(file_path, options)
-        defaults = {
-          :columns => 2,  # range of import
-          :sheet => 1     # only one sheet at a time can be worked on
-        }
-        options = defaults.merge(options)
-        
-        book = book_by_format(file_path, options[:format])
-        book.default_sheet=book.sheets[options[:sheet]]
-    
-        # catch double byte encoding problems in spreadsheet files
-        # Encoding::InvalidByteSequenceError: "\x9E\xDE" on UTF-16LE
-        begin
-          book.to_matrix.to_a
-        rescue Encoding::InvalidByteSequenceError => e
-          raise "Spreadsheet encoding problem: #{e}"
-        end
-      end
-      
-      def book_by_format(file_path, format)
-        format = HQMF::ValueSet::Parser.get_format(file_path) unless format
-        
-        if format == :xls
-          book = Excel.new(file_path, nil, :ignore)
-        elsif format == :xlsx
-          book = Excelx.new(file_path, nil, :ignore)
-        else
-          raise "File does not end in .xls or .xlsx"
-        end
-        book
-      end
-
-      def translate_json(value_sets)
-        value_set_models = []
-
-        value_sets.each do |value_set|
-          hds_value_set = HealthDataStandards::SVS::ValueSet.new() 
-          hds_value_set['oid'] = value_set['oid']
-          hds_value_set['display_name'] = value_set['key']
-          hds_value_set['version'] = value_set['version']
-          hds_value_set['concepts'] = []
-
-          value_set['code_sets'].each do |code_set|
-            code_set['codes'].map{ |code| 
-              concept = HealthDataStandards::SVS::Concept.new()
-              concept['code'] = code
-              concept['code_system'] = nil
-              concept['code_system_name'] = code_set['code_set']
-              concept['code_system_version'] = code_set['version']
-              concept['display_name'] = nil
-              hds_value_set['concepts'].concat([concept])
-            }
-          end
-          if hds_value_set['concepts'].include? nil
-            puts "Value Set has a bad code set (code set is null)"
-            hds_value_set['concepts'].compact!
-          end
-          value_set_models << hds_value_set
-        end
-        value_set_models
-      end
-  
-  
-    end
-  end
-end