cqm-reports 1.0.0.0

data/lib/qrda-import/data-element-importers/provider_care_experience_importer.rb

@@ -0,0 +1,19 @@
+module QRDA
+  module Cat1
+    class ProviderCareExperienceImporter < SectionImporter
+      def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.67']"))
+        super(entry_finder)
+        @id_xpath = './cda:id'
+        @code_xpath = "./cda:value"
+        @author_datetime_xpath = "./cda:author/cda:time"
+        @entry_class = QDM::ProviderCareExperience
+      end
+
+      def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
+        provider_care_experience = super
+        provider_care_experience
+      end
+
+    end
+  end
+end

data/lib/qrda-import/data-element-importers/provider_characteristic_importer.rb

@@ -0,0 +1,19 @@
+module QRDA
+  module Cat1
+    class ProviderCharacteristicImporter < SectionImporter
+      def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.114']"))
+        super(entry_finder)
+        @id_xpath = './cda:id'
+        @code_xpath = "./cda:value"
+        @author_datetime_xpath = "./cda:author/cda:time"
+        @entry_class = QDM::ProviderCharacteristic
+      end
+
+      def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
+        provider_characteristic = super
+        provider_characteristic
+      end
+
+    end
+  end
+end

data/lib/qrda-import/data-element-importers/substance_administered_importer.rb

@@ -0,0 +1,27 @@
+module QRDA
+  module Cat1
+    class SubstanceAdministeredImporter < SectionImporter
+      def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:substanceAdministration[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.42']"))
+        super(entry_finder)
+        @entry_does_not_have_reason = true
+        @id_xpath = './cda:id'
+        @code_xpath = "./cda:consumable/cda:manufacturedProduct/cda:manufacturedMaterial/cda:code"
+        @author_datetime_xpath = "./cda:author/cda:time"
+        @relevant_period_xpath = "./cda:effectiveTime"
+        @dosage_xpath = "./cda:doseQuantity"
+        @frequency_xpath = "./cda:effectiveTime[@operator='A']/cda:period"
+        @route_xpath = "./cda:routeCode"
+        @entry_class = QDM::SubstanceAdministered
+      end
+
+      def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
+        substance_administered = super
+        substance_administered.dosage = extract_scalar(entry_element, @dosage_xpath)
+        substance_administered.frequency = frequency_as_coded_value(entry_element, @frequency_xpath)
+        substance_administered.route = code_if_present(entry_element.at_xpath(@route_xpath))
+        substance_administered
+      end
+
+    end
+  end
+end

data/lib/qrda-import/data-element-importers/substance_order_importer.rb

@@ -0,0 +1,29 @@
+module QRDA
+  module Cat1
+    class SubstanceOrderImporter < SectionImporter
+      def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:substanceAdministration[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.47']"))
+        super(entry_finder)
+        @id_xpath = './cda:id'
+        @code_xpath = "./cda:consumable/cda:manufacturedProduct/cda:manufacturedMaterial/cda:code"
+        @author_datetime_xpath = "./cda:author/cda:time"
+        @dosage_xpath = "./cda:doseQuantity"
+        @supply_xpath = "./cda:entryRelationship/cda:supply[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.99']/cda:quantity"
+        @frequency_xpath = "./cda:effectiveTime[@operator='A']/cda:period"
+        @refills_xpath = "./cda:repeatNumber"
+        @route_xpath = "./cda:routeCode"
+        @entry_class = QDM::SubstanceOrder
+      end
+
+      def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
+        substance_order = super
+        substance_order.dosage = extract_scalar(entry_element, @dosage_xpath)
+        substance_order.supply = extract_scalar(entry_element, @supply_xpath)
+        substance_order.frequency = frequency_as_coded_value(entry_element, @frequency_xpath)
+        substance_order.refills = extract_scalar(entry_element, @refills_xpath)&.value
+        substance_order.route = code_if_present(entry_element.at_xpath(@route_xpath))
+        substance_order
+      end
+
+    end
+  end
+end

data/lib/qrda-import/data-element-importers/substance_recommended_importer.rb

@@ -0,0 +1,27 @@
+module QRDA
+  module Cat1
+    class SubstanceRecommendedImporter < SectionImporter
+      def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:substanceAdministration[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.75']"))
+        super(entry_finder)
+        @id_xpath = './cda:id'
+        @code_xpath = "./cda:consumable/cda:manufacturedProduct/cda:manufacturedMaterial/cda:code"
+        @author_datetime_xpath = "./cda:author/cda:time"
+        @dosage_xpath = "./cda:doseQuantity"
+        @frequency_xpath = "./cda:effectiveTime[@operator='A']/cda:period"
+        @refills_xpath = "./cda:repeatNumber"
+        @route_xpath = "./cda:routeCode"
+        @entry_class = QDM::SubstanceRecommended
+      end
+
+      def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
+        substance_recommended = super
+        substance_recommended.dosage = extract_scalar(entry_element, @dosage_xpath)
+        substance_recommended.frequency = frequency_as_coded_value(entry_element, @frequency_xpath)
+        substance_recommended.refills = extract_scalar(entry_element, @refills_xpath)&.value
+        substance_recommended.route = code_if_present(entry_element.at_xpath(@route_xpath))
+        substance_recommended
+      end
+
+    end
+  end
+end

data/lib/qrda-import/data-element-importers/symptom_importer.rb

@@ -0,0 +1,21 @@
+module QRDA
+  module Cat1
+    class SymptomImporter < SectionImporter
+      def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.138']"))
+        super(entry_finder)
+        @id_xpath = './cda:entryRelationship/cda:observation/cda:id'
+        @code_xpath = "./cda:entryRelationship/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.136']/cda:value"
+        @prevalence_period_xpath = "./cda:entryRelationship/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.136']/cda:effectiveTime"
+        @severity_xpath = "./cda:entryRelationship/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.136']/cda:entryRelationship/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.22.4.8']/cda:value"
+        @entry_class = QDM::Symptom
+      end
+
+      def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
+        symptom = super
+        symptom.severity = code_if_present(entry_element.at_xpath(@severity_xpath))
+        symptom
+      end
+
+    end
+  end
+end

data/lib/qrda-import/entry_finder.rb

@@ -0,0 +1,20 @@
+module QRDA
+  module Cat1
+    class EntryFinder
+      def initialize(entry_xpath)
+        @entry_xpath = entry_xpath
+      end
+
+      def entries(doc)
+        entry_elements = doc.xpath(@entry_xpath)
+        if block_given?
+          entry_elements.each do |entry_element|
+            yield entry_element
+          end
+        else
+          entry_elements
+        end
+      end
+    end
+  end
+end

data/lib/qrda-import/entry_package.rb

@@ -0,0 +1,16 @@
+module QRDA
+  module Cat1
+    class EntryPackage
+
+      attr_accessor :importer_type
+
+      def initialize(type)
+        self.importer_type = type
+      end  
+
+      def package_entries(doc, nrh)
+        importer_type.create_entries(doc, nrh)
+      end
+    end
+  end
+end

data/lib/qrda-import/narrative_reference_handler.rb

@@ -0,0 +1,33 @@
+module QRDA
+  module Cat1
+    class NarrativeReferenceHandler
+      def initialize
+        @id_map = {}
+      end
+
+      def build_id_map(doc)
+        path = "//*[@ID]"
+        ids = doc.xpath(path)
+        ids.each do |id|
+          tag = id['ID']
+          value = id.content
+          @id_map[tag] = value
+        end
+      end
+
+      # @param [String] tag      
+      # @return [String] text description of tag
+      def lookup_tag(tag)
+        value = @id_map[tag]
+        # Not sure why, but sometimes the reference is #<Reference> and the ID value is <Reference>, and 
+        # sometimes it is #<Reference>.  We look for both.
+        if !value and tag[0] == '#'  
+          tag = tag[1,tag.length]
+          value = @id_map[tag]
+        end
+
+        value
+      end
+    end
+  end
+end

data/lib/qrda-import/patient_importer.rb

@@ -0,0 +1,128 @@
+module QRDA
+  module Cat1
+    # This class is the central location for taking a QRDA Cat 1 XML document and converting it
+    # into the processed form we store in MongoDB. The class does this by running each measure
+    # independently on the XML document
+    #
+    # This class is a Singleton. It should be accessed by calling PatientImporter.instance
+    class PatientImporter
+      include Singleton
+      include DemographicsImporter
+
+      def initialize
+        # This differs from other HDS patient importers in that sections can have multiple importers
+        @data_element_importers = []
+        @data_element_importers << generate_importer(AdverseEventImporter)
+        @data_element_importers << generate_importer(AllergyIntoleranceImporter)
+        @data_element_importers << generate_importer(AssessmentOrderImporter)
+        @data_element_importers << generate_importer(AssessmentPerformedImporter)
+        @data_element_importers << generate_importer(AssessmentRecommendedImporter)
+        @data_element_importers << generate_importer(CommunicationPerformedImporter)
+        @data_element_importers << generate_importer(DeviceAppliedImporter)
+        @data_element_importers << generate_importer(DeviceOrderImporter)
+        @data_element_importers << generate_importer(DeviceRecommendedImporter)
+        @data_element_importers << generate_importer(DiagnosisImporter)
+        @data_element_importers << generate_importer(DiagnosticStudyOrderImporter)
+        @data_element_importers << generate_importer(DiagnosticStudyPerformedImporter)
+        @data_element_importers << generate_importer(DiagnosticStudyRecommendedImporter)
+        @data_element_importers << generate_importer(EncounterOrderImporter)
+        @data_element_importers << generate_importer(EncounterPerformedImporter)
+        @data_element_importers << generate_importer(EncounterRecommendedImporter)
+        @data_element_importers << generate_importer(FamilyHistoryImporter)
+        @data_element_importers << generate_importer(ImmunizationAdministeredImporter)
+        @data_element_importers << generate_importer(ImmunizationOrderImporter)
+        @data_element_importers << generate_importer(InterventionOrderImporter)
+        @data_element_importers << generate_importer(InterventionPerformedImporter)
+        @data_element_importers << generate_importer(InterventionRecommendedImporter)
+        @data_element_importers << generate_importer(LaboratoryTestOrderImporter)
+        @data_element_importers << generate_importer(LaboratoryTestPerformedImporter)
+        @data_element_importers << generate_importer(LaboratoryTestRecommendedImporter)
+        @data_element_importers << generate_importer(MedicationActiveImporter)
+        @data_element_importers << generate_importer(MedicationAdministeredImporter)
+        @data_element_importers << generate_importer(MedicationDischargeImporter)
+        @data_element_importers << generate_importer(MedicationDispensedImporter)
+        @data_element_importers << generate_importer(MedicationOrderImporter)
+        @data_element_importers << generate_importer(PatientCareExperienceImporter)
+        @data_element_importers << generate_importer(PatientCharacteristicClinicalTrialParticipantImporter)
+        @data_element_importers << generate_importer(PatientCharacteristicExpiredImporter)
+        @data_element_importers << generate_importer(PatientCharacteristicPayerImporter)
+        @data_element_importers << generate_importer(PhysicalExamOrderImporter)
+        @data_element_importers << generate_importer(PhysicalExamPerformedImporter)
+        @data_element_importers << generate_importer(PhysicalExamRecommendedImporter)
+        @data_element_importers << generate_importer(ProcedureOrderImporter)
+        @data_element_importers << generate_importer(ProcedurePerformedImporter)
+        @data_element_importers << generate_importer(ProcedureRecommendedImporter)
+        @data_element_importers << generate_importer(ProviderCareExperienceImporter)
+        @data_element_importers << generate_importer(ProviderCharacteristicImporter)
+        @data_element_importers << generate_importer(SubstanceAdministeredImporter)
+        @data_element_importers << generate_importer(SubstanceOrderImporter)
+        @data_element_importers << generate_importer(SubstanceRecommendedImporter)
+        @data_element_importers << generate_importer(SymptomImporter)
+      end 
+
+      def parse_cat1(doc)
+        patient = CQM::Patient.new
+        entry_id_map = {}
+        import_data_elements(patient, doc, entry_id_map)
+        normalize_references(patient, entry_id_map)
+        get_demographics(patient, doc)
+        patient
+      end
+
+      def import_data_elements(patient, doc, entry_id_map)
+        context = doc.xpath("/cda:ClinicalDocument/cda:component/cda:structuredBody/cda:component/cda:section[cda:templateId/@root = '2.16.840.1.113883.10.20.24.2.1']")
+        nrh = NarrativeReferenceHandler.new
+        nrh.build_id_map(doc)
+        @data_element_importers.each do |entry_package|
+          data_elements, id_map = entry_package.package_entries(context, nrh)
+          new_data_elements = []
+
+          id_map.each_value do |elem_ids|
+            
+            elem_id = elem_ids.first
+            data_element = data_elements.find { |de| de.id == elem_id }
+
+            elem_ids[1,elem_ids.length].each do |merge_id|
+              merge_element = data_elements.find { |de| de.id == merge_id }
+              data_element.merge!(merge_element)
+            end
+
+            new_data_elements << data_element
+          end
+
+          patient.qdmPatient.dataElements << new_data_elements
+          entry_id_map.merge!(id_map)
+        end
+      end
+
+      def get_patient_expired(record, doc)
+        entry_elements = doc.xpath("/cda:ClinicalDocument/cda:component/cda:structuredBody/cda:component/cda:section[cda:templateId/@root = '2.16.840.1.113883.10.20.24.2.1']/cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.54']")
+        return unless entry_elements.empty?
+
+        record.expired = true
+        record.deathdate = DateTime.parse(entry_elements.at_xpath("./cda:effectiveTime/cda:low")['value']).to_i
+      end
+
+      def normalize_references(patient, entry_id_map)
+        patient.qdmPatient.dataElements.each do |data_element|
+          next unless data_element.respond_to?(:relatedTo) && data_element.relatedTo
+
+          relations_to_add = []
+          data_element.relatedTo.each do |related_to|
+            relations_to_add << entry_id_map[related_to.value]
+          end
+          data_element.relatedTo.destroy
+          relations_to_add.each do |relation_to_add|
+            data_element.relatedTo << relation_to_add
+          end
+        end
+      end
+
+      private
+
+      def generate_importer(importer_class)
+        EntryPackage.new(importer_class.new)
+      end
+    end
+  end
+end

data/lib/util/code_system_helper.rb

@@ -0,0 +1,77 @@
+module HQMF
+  module Util
+    # General helpers for working with codes and code systems
+    class CodeSystemHelper
+      CODE_SYSTEMS = {
+        '2.16.840.1.113883.6.1' =>    'LOINC',
+        '2.16.840.1.113883.6.96' =>   'SNOMEDCT',
+        '2.16.840.1.113883.6.12' =>   'CPT',
+        #'2.16.840.1.113883.3.88.12.80.32' => 'CPT', # Encounter Type from C32, a subset of CPT
+        '2.16.840.1.113883.6.88' =>   'RXNORM',
+        '2.16.840.1.113883.6.103' =>  'ICD9CM',
+        '2.16.840.1.113883.6.104' =>  'ICD9CM',
+        '2.16.840.1.113883.6.4' =>   'ICD10PCS',
+        '2.16.840.1.113883.6.90' =>   'ICD10CM',
+        '2.16.840.1.113883.6.14' =>   'HCP',
+        '2.16.840.1.113883.6.285' =>   'HCPCS',
+        '2.16.840.1.113883.5.2' => "HL7 Marital Status",
+        '2.16.840.1.113883.12.292' => 'CVX',
+        '2.16.840.1.113883.5.83' => 'HITSP C80 Observation Status',
+        '2.16.840.1.113883.3.26.1.1' => 'NCI Thesaurus',
+        '2.16.840.1.113883.3.88.12.80.20' => 'FDA',
+        "2.16.840.1.113883.4.9" => "UNII",
+        "2.16.840.1.113883.6.69" => "NDC",
+        '2.16.840.1.113883.5.14' => 'HL7 ActStatus',
+        '2.16.840.1.113883.6.259' => 'HL7 Healthcare Service Location',
+        '2.16.840.1.113883.12.112' => 'DischargeDisposition',
+        '2.16.840.1.113883.5.4' => 'HL7 Act Code',
+        '2.16.840.1.113883.1.11.18877' => 'HL7 Relationship Code',
+        '2.16.840.1.113883.6.238' => 'CDCREC',
+        '2.16.840.1.113883.6.177' => 'NLM MeSH',
+        '2.16.840.1.113883.5.1076' => "Religious Affiliation",
+        '2.16.840.1.113883.1.11.19717' => "HL7 ActNoImmunicationReason",
+        '2.16.840.1.113883.3.88.12.80.33' => "NUBC",
+        '2.16.840.1.113883.1.11.78' => "HL7 Observation Interpretation",
+        '2.16.840.1.113883.3.221.5' => "Source of Payment Typology",
+        '2.16.840.1.113883.6.13' => 'CDT',
+        '2.16.840.1.113883.18.2' => 'AdministrativeSex',
+        '2.16.840.1.113883.5.1' => 'AdministrativeGender'
+      }
+
+      CODE_SYSTEM_ALIASES = {
+        'FDA SPL' => 'NCI Thesaurus',
+        'HSLOC' => 'HL7 Healthcare Service Location',
+        'SOP' => "Source of Payment Typology"
+      }
+
+      # Some old OID are still around in data, this hash maps retired OID values to
+      # the new value
+      OID_ALIASES = {
+        '2.16.840.1.113883.6.59' => '2.16.840.1.113883.12.292' # CVX
+      }
+
+      # Returns the name of a code system given an oid
+      # @param [String] oid of a code system
+      # @return [String] the name of the code system as described in the measure definition JSON
+      def self.code_system_for(oid)
+        oid = OID_ALIASES[oid] if OID_ALIASES[oid]
+        CODE_SYSTEMS[oid] || "Unknown"
+      end
+
+      # Returns the oid for a code system given a codesystem name
+      # @param [String] the name of the code system
+      # @return [String] the oid of the code system
+      def self.oid_for_code_system(code_system)
+        code_system = CODE_SYSTEM_ALIASES[code_system] if CODE_SYSTEM_ALIASES[code_system]
+        CODE_SYSTEMS.invert[code_system]
+      end
+
+      # Returns the whole map of OIDs to code systems
+      # @terurn [Hash] oids as keys, code system names as values
+      def self.code_systems
+        CODE_SYSTEMS
+      end
+    end
+  end
+end
+

data/lib/util/hqmf_template_helper.rb

@@ -0,0 +1,52 @@
+module HQMF
+  module Util
+    # General helpers for working with codes and code systems
+    class HQMFTemplateHelper
+
+      def self.definition_for_template_id(template_id, version="r1")
+        template_id_map(version)[template_id]
+      end
+
+      def self.template_id_map(version)
+        if @id_map.blank?
+          @id_map = {
+            'r1' => JSON.parse(File.read(File.expand_path('../hqmf_template_oid_map.json', __FILE__))),
+            'r2' => JSON.parse(File.read(File.expand_path('../hqmfr2_template_oid_map.json', __FILE__))),
+            'r2cql' => JSON.parse(File.read(File.expand_path('../hqmfr2cql_template_oid_map.json', __FILE__)))
+          }
+        end
+        @id_map[version]
+      end
+
+      def self.template_id_by_definition_and_status(definition, status, negation=false, version="r1")
+        case version
+        when "r1"
+          kv_pair = template_id_map(version).find {|k, v| v['definition'] == definition &&
+                                                 v['status'] == status &&
+                                                 v['negation'] == negation}
+        when "r2", "r2cql"
+          kv_pair = template_id_map(version).find {|k, v| v['definition'] == definition &&
+                                                 v['status'] == status}
+        end
+        if kv_pair
+          kv_pair.first
+        else
+          nil
+        end
+      end
+
+      # Returns a list of all hqmf_oids (regardless of version) for the combination of definition and status
+      def self.get_all_hqmf_oids(definition, status)
+        status ||= ""
+        version_negation_combinations = [{ version: 'r1', negation: false },
+                                         { version: 'r1', negation: true },
+                                         { version: 'r2', negation: false },
+                                         { version: 'r2cql', negation: false }]
+        hqmf_oids = version_negation_combinations.collect do |obj|
+          template_id_by_definition_and_status(definition, status, obj[:negation], obj[:version])
+        end
+        hqmf_oids
+      end
+    end
+  end
+end