cqm-parsers 0.2.2 → 3.0.0.0

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

@@ -1,17 +0,0 @@
-module QRDA
-  module Cat1
-    class MedicationActiveImporter < MedicationImporter
-      def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:substanceAdministration[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.41']"))
-        super(entry_finder)
-        @author_datetime_xpath = nil
-        @entry_class = QDM::MedicationActive
-      end
-
-      def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
-        medication_active = super
-        medication_active
-      end
-
-    end
-  end
-end

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

@@ -1,17 +0,0 @@
-module QRDA
-  module Cat1
-    class MedicationAdministeredImporter < MedicationImporter
-      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)
-        @route_xpath = "./cda:routeCode"
-        @entry_class = QDM::MedicationAdministered
-      end
-
-      def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
-        medication_administered = super
-        medication_administered
-      end
-
-    end
-  end
-end

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

@@ -1,19 +0,0 @@
-module QRDA
-  module Cat1
-    class MedicationDischargeImporter < MedicationImporter
-      def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.105']"))
-        super(entry_finder)
-        @code_xpath = "./cda:entryRelationship/cda:substanceAdministration[cda:templateId/@root = '2.16.840.1.113883.10.20.22.4.16']/cda:consumable/cda:manufacturedProduct/cda:manufacturedMaterial/cda:code"
-        @relevant_period_xpath = nil
-        @author_datetime_xpath = "./cda:entryRelationship/cda:substanceAdministration[cda:templateId/@root = '2.16.840.1.113883.10.20.22.4.16']/cda:author/cda:time"
-        @entry_class = QDM::MedicationDischarge
-      end
-
-      def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
-        medication_discharge = super
-        medication_discharge
-      end
-
-    end
-  end
-end

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

@@ -1,19 +0,0 @@
-module QRDA
-  module Cat1
-    class MedicationDispensedImporter < MedicationImporter
-      def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.139']"))
-        super(entry_finder)
-        @relevant_period_xpath = "./cda:entryRelationship/cda:supply[cda:templateId/@root = '2.16.840.1.113883.10.20.22.4.18']/cda:effectiveTime"
-        @author_datetime_xpath = "./cda:entryRelationship/cda:supply[cda:templateId/@root = '2.16.840.1.113883.10.20.22.4.18']/cda:author/cda:time"
-        @code_xpath = "./cda:entryRelationship/cda:supply[cda:templateId/@root = '2.16.840.1.113883.10.20.22.4.18']/cda:product/cda:manufacturedProduct/cda:manufacturedMaterial/cda:code"
-        @entry_class = QDM::MedicationDispensed
-      end
-
-      def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
-        medication_dispensed = super
-        medication_dispensed
-      end
-
-    end
-  end
-end

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

@@ -1,16 +0,0 @@
-module QRDA
-  module Cat1
-    class MedicationOrderImporter < MedicationImporter
-      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)
-        @entry_class = QDM::MedicationOrder
-      end
-
-      def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
-        medication_order = super
-        medication_order
-      end
-
-    end
-  end
-end

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

@@ -1,22 +0,0 @@
-module QRDA
-  module Cat1
-    class PatientCharacteristicExpired < SectionImporter
-      def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.54']"))
-        super(entry_finder)
-        @id_xpath = './cda:id'
-        @code_xpath = './cda:value'
-        @expired_datetime_xpath = './cda:effectiveTime/cda:low'
-        @cause = "./cda:entryRelationship/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.22.4.4']/cda:value"
-        @entry_class = QDM::PatientCharacteristicExpired
-      end
-
-      def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
-        patient_characteristic_expired = super
-        patient_characteristic_expired.expiredDatetime = extract_time(entry_element, @expired_datetime_xpath)
-        patient_characteristic_expired.cause = code_if_present(entry_element.at_xpath(@cause))
-        patient_characteristic_expired
-      end
-
-    end
-  end
-end

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

@@ -1,27 +0,0 @@
-module QRDA
-  module Cat1
-    class PhysicalExamPerformedImporter < SectionImporter
-      def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.59']"))
-        super(entry_finder)
-        @id_xpath = './cda:id'
-        @code_xpath = "./cda:code"
-        @relevant_period_xpath = "./cda:effectiveTime"
-        @author_datetime_xpath = "./cda:author/cda:time"
-        @method_xpath = './cda:methodCode'
-        @result_xpath = "./cda:value"
-        @anatomical_location_site_xpath = "./cda:targetSiteCode"
-        @components_xpath = "./cda:entryRelationship/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.149']"
-        @entry_class = QDM::PhysicalExamPerformed
-      end
-
-      def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
-        physical_exam_performed = super
-        physical_exam_performed.method = code_if_present(entry_element.at_xpath(@method_xpath))
-        physical_exam_performed.anatomicalLocationSite = code_if_present(entry_element.at_xpath(@anatomical_location_site_xpath))
-        physical_exam_performed.components = extract_components(entry_element)
-        physical_exam_performed
-      end
-
-    end
-  end
-end

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

@@ -1,27 +0,0 @@
-module QRDA
-  module Cat1
-    class ProcedureOrderImporter < SectionImporter
-      def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:procedure[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.63']"))
-        super(entry_finder)
-        @id_xpath = './cda:id'
-        @code_xpath = './cda:code'
-        @author_datetime_xpath = "./cda:author/cda:time"
-        @method_xpath = './cda:methodCode'
-        @anatomical_approach_site_xpath = "./cda:approachSiteCode"
-        @anatomical_location_site_xpath = "./cda:targetSiteCode"
-        @ordinality_xpath = "./cda:priorityCode"
-        @entry_class = QDM::ProcedureOrder
-      end
-
-      def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
-        procedure_order = super
-        procedure_order.method = code_if_present(entry_element.at_xpath(@method_xpath))
-        procedure_order.anatomicalApproachSite = code_if_present(entry_element.at_xpath(@anatomical_approach_site_xpath))
-        procedure_order.anatomicalLocationSite = code_if_present(entry_element.at_xpath(@anatomical_location_site_xpath))
-        procedure_order.ordinality = code_if_present(entry_element.at_xpath(@ordinality_xpath))
-        procedure_order
-      end
-
-    end
-  end
-end

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

@@ -1,35 +0,0 @@
-module QRDA
-  module Cat1
-    class ProcedurePerformedImporter < SectionImporter
-      def initialize(entry_finder = QRDA::Cat1::EntryFinder.new("./cda:entry/cda:procedure[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.64']"))
-        super(entry_finder)
-        @id_xpath = './cda:id'
-        @code_xpath = "./cda:code"
-        @relevant_period_xpath = "./cda:effectiveTime"
-        @author_datetime_xpath = "./cda:author/cda:time"
-        @method_xpath = './cda:methodCode'
-        @result_xpath = "./cda:entryRelationship[@typeCode='REFR']/cda:observation/cda:value"
-        @status_xpath = "./cda:entryRelationship/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.93']/cda:value"
-        @anatomical_approach_site_xpath = "./cda:approachSiteCode"
-        @anatomical_location_site_xpath = "./cda:targetSiteCode"
-        @ordinality_xpath = "./cda:priorityCode"
-        @incision_datetime_xpath = "./cda:entryRelationship/cda:procedure[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.89']/cda:effectiveTime"
-        @components_xpath = "./cda:entryRelationship/cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.149']"
-        @entry_class = QDM::ProcedurePerformed
-      end
-
-      def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
-        procedure_performed = super
-        procedure_performed.method = code_if_present(entry_element.at_xpath(@method_xpath))
-        procedure_performed.status = code_if_present(entry_element.at_xpath(@status_xpath))
-        procedure_performed.anatomicalApproachSite = code_if_present(entry_element.at_xpath(@anatomical_approach_site_xpath))
-        procedure_performed.anatomicalLocationSite = code_if_present(entry_element.at_xpath(@anatomical_location_site_xpath))
-        procedure_performed.ordinality = code_if_present(entry_element.at_xpath(@ordinality_xpath))
-        procedure_performed.incisionDatetime = extract_time(entry_element, @incision_datetime_xpath)
-        procedure_performed.components = extract_components(entry_element)
-        procedure_performed
-      end
-
-    end
-  end
-end

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

@@ -1,16 +0,0 @@
-module QRDA
-  module Cat1
-    class SubstanceAdministeredImporter < MedicationAdministeredImporter
-      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_class = QDM::SubstanceAdministered
-      end
-
-      def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
-        substance_administered = super
-        substance_administered
-      end
-
-    end
-  end
-end

data/lib/qrda-import/entry_finder.rb

@@ -1,20 +0,0 @@
-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

@@ -1,16 +0,0 @@
-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

@@ -1,33 +0,0 @@
-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

@@ -1,111 +0,0 @@
-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(EncounterPerformedImporter)
-        @data_element_importers << generate_importer(PhysicalExamPerformedImporter)
-        @data_element_importers << generate_importer(LaboratoryTestPerformedImporter)
-        @data_element_importers << generate_importer(DiagnosisImporter)
-        @data_element_importers << generate_importer(InterventionOrderImporter)
-        @data_element_importers << generate_importer(ProcedurePerformedImporter)
-        @data_element_importers << generate_importer(MedicationActiveImporter)
-        @data_element_importers << generate_importer(AllergyIntoleranceImporter)
-        @data_element_importers << generate_importer(MedicationOrderImporter)
-        @data_element_importers << generate_importer(DiagnosticStudyOrderImporter)
-
-        @data_element_importers << generate_importer(AdverseEventImporter)
-        @data_element_importers << generate_importer(AssessmentPerformedImporter)
-        @data_element_importers << generate_importer(CommunicationFromPatientToProviderImporter)
-        @data_element_importers << generate_importer(CommunicationFromProviderToPatientImporter)
-        @data_element_importers << generate_importer(CommunicationFromProviderToProviderImporter)
-        @data_element_importers << generate_importer(DeviceAppliedImporter)
-        @data_element_importers << generate_importer(DeviceOrderImporter)
-        @data_element_importers << generate_importer(DiagnosticStudyPerformedImporter)
-        @data_element_importers << generate_importer(EncounterOrderImporter)
-        @data_element_importers << generate_importer(ImmunizationAdministeredImporter)
-        @data_element_importers << generate_importer(InterventionPerformedImporter)
-        @data_element_importers << generate_importer(LaboratoryTestOrderImporter)
-        @data_element_importers << generate_importer(MedicationAdministeredImporter)
-        @data_element_importers << generate_importer(MedicationDischargeImporter)
-        @data_element_importers << generate_importer(MedicationDispensedImporter)
-        @data_element_importers << generate_importer(PatientCharacteristicExpired)
-        @data_element_importers << generate_importer(ProcedureOrderImporter)
-        @data_element_importers << generate_importer(SubstanceAdministeredImporter)
-
-      end 
-
-      def parse_cat1(doc)
-        patient = QDM::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.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 = HealthDataStandards::Util::HL7Helper.timestamp_to_integer(entry_elements.at_xpath("./cda:effectiveTime/cda:low")['value'])
-      end
-
-      def normalize_references(patient, entry_id_map)
-        patient.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