health-data-standards 3.0.6 → 3.1.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/README.md +3 -1
- data/Rakefile +2 -0
- data/lib/health-data-standards.rb +10 -0
- data/lib/health-data-standards/export/cat_3.rb +24 -0
- data/lib/health-data-standards/export/html.rb +2 -1
- data/lib/health-data-standards/import/bundle/importer.rb +178 -146
- data/lib/health-data-standards/import/cat1/diagnosis_active_importer.rb +0 -5
- data/lib/health-data-standards/import/cat1/diagnosis_inactive_importer.rb +1 -6
- data/lib/health-data-standards/import/cat1/diagnostic_study_order_importer.rb +0 -4
- data/lib/health-data-standards/import/cat1/ecog_status_importer.rb +12 -0
- data/lib/health-data-standards/import/cat1/encounter_order_importer.rb +0 -5
- data/lib/health-data-standards/import/cat1/lab_order_importer.rb +1 -5
- data/lib/health-data-standards/import/cat1/lab_result_importer.rb +18 -0
- data/lib/health-data-standards/import/cat1/medication_active_importer.rb +27 -0
- data/lib/health-data-standards/import/cat1/patient_importer.rb +54 -46
- data/lib/health-data-standards/import/cat1/procedure_performed_importer.rb +28 -0
- data/lib/health-data-standards/import/cat1/symptom_active_importer.rb +12 -0
- data/lib/health-data-standards/import/cda/condition_importer.rb +2 -0
- data/lib/health-data-standards/import/cda/encounter_importer.rb +6 -0
- data/lib/health-data-standards/import/cda/procedure_importer.rb +1 -0
- data/lib/health-data-standards/import/cda/section_importer.rb +27 -5
- data/lib/health-data-standards/models/cda_identifier.rb +17 -0
- data/lib/health-data-standards/models/cqm/aggregate_objects.rb +92 -0
- data/lib/health-data-standards/models/cqm/measure.rb +51 -30
- data/lib/health-data-standards/models/cqm/query_cache.rb +64 -0
- data/lib/health-data-standards/models/entry.rb +1 -1
- data/lib/health-data-standards/models/record.rb +28 -3
- data/lib/health-data-standards/models/svs/value_set.rb +20 -0
- data/lib/health-data-standards/tasks/bundle.rake +18 -8
- data/lib/health-data-standards/util/hqmf_template_helper.rb +6 -2
- data/lib/health-data-standards/util/hqmf_template_oid_map.json +4 -0
- data/lib/health-data-standards/util/vs_api.rb +9 -6
- data/lib/hqmf-model/data_criteria.json +10 -10
- data/lib/hqmf-parser.rb +0 -2
- data/lib/hqmf-parser/1.0/range.rb +21 -9
- data/templates/c32/show.c32.erb +1 -1
- data/templates/cat1/_2.16.840.1.113883.10.20.24.3.4.cat1.erb +1 -0
- data/templates/cat1/_2.16.840.1.113883.10.20.24.3.40.cat1.erb +2 -1
- data/templates/cat1/_2.16.840.1.113883.10.20.24.3.44.cat1.erb +1 -0
- data/templates/cat1/_2.16.840.1.113883.10.20.24.3.46.cat1.erb +1 -1
- data/templates/cat1/_2.16.840.1.113883.10.20.24.3.54.cat1.erb +16 -1
- data/templates/cat1/_2.16.840.1.113883.10.20.24.3.62.cat1.erb +1 -1
- data/templates/cat1/_2.16.840.1.113883.10.20.24.3.69.cat1.erb +7 -2
- data/templates/cat1/_2.16.840.1.113883.10.20.24.3.76.cat1.erb +2 -1
- data/templates/cat1/_medication_details.cat1.erb +4 -4
- data/templates/cat1/_record_target.cat1.erb +2 -2
- data/templates/cat1/_result_value.cat1.erb +1 -1
- data/templates/cat1/show.cat1.erb +2 -2
- data/templates/cat3/_continuous_variable_value.cat3.erb +20 -0
- data/templates/cat3/_measure_data.cat3.erb +126 -0
- data/templates/cat3/_performance_rate.cat3.erb +16 -0
- data/templates/cat3/_supplemental_data.cat3.erb +36 -0
- data/templates/cat3/show.cat3.erb +157 -0
- data/templates/ccda/show.ccda.erb +1 -1
- metadata +25 -45
- data/lib/hqmf-parser/value_sets/value_set_parser.rb +0 -241
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module HealthDataStandards
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module Import
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module Cat1
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class EcogStatusImporter < CDA::SectionImporter
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def initialize(entry_finder=CDA::EntryFinder.new("//cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.103']"))
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super(entry_finder)
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@code_xpath = './cda:value'
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end
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end
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end
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end
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end
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class EncounterOrderImporter < CDA::EncounterImporter
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def initialize(entry_finder=CDA::EntryFinder.new("//cda:encounter[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.22']"))
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super(entry_finder)
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@entry_class = Encounter
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end
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def create_entry(entry_element, nrh = CDA::NarrativeReferenceHandler.new)
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super
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end
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private
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@entry_class = LabResult
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end
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def create_entry(entry_element, nrh = CDA::NarrativeReferenceHandler.new)
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super
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end
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private
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def extract_dates(parent_element, entry, element_name="author")
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if parent_element.at_xpath("cda:#{element_name}/cda:time/@value")
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entry.
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entry.time = HL7Helper.timestamp_to_integer(parent_element.at_xpath("cda:#{element_name}/cda:time")['value'])
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end
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end
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end
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module HealthDataStandards
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module Import
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module Cat1
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class LabResultImporter < CDA::SectionImporter
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def initialize(entry_finder=CDA::EntryFinder.new("//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.40']"))
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super(entry_finder)
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@entry_class = LabResult
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end
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def create_entry(entry_element, nrh = CDA::NarrativeReferenceHandler.new)
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result = super
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result.end_time ||= result.start_time
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result
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end
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end
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end
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end
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end
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module HealthDataStandards
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module Import
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module Cat1
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class MedicationActiveImporter < CDA::MedicationImporter
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def initialize
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super(CDA::EntryFinder.new("//cda:substanceAdministration[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.41']"))
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end
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def create_entry(entry_element, nrh = CDA::NarrativeReferenceHandler.new)
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medication = super
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calculate_cumulative_medication_duration(medication)
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medication
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end
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private
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def calculate_cumulative_medication_duration(medication)
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if medication.start_time.present? && medication.end_time.present?
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duration_in_days = ((medication.end_time - medication.start_time) / (60*60*24)).floor + 1
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medication.cumulative_medication_duration = {'scalar' => duration_in_days, 'units' => 'days'}
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end
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end
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end
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end
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end
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end
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def initialize
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# This differs from other HDS patient importers in that sections can have multiple importers
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@section_importers = {}
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@section_importers[:care_goals] = [
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ecog_status_importer = CDA::SectionImporter.new(CDA::EntryFinder.new("//cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.103']"))
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ecog_status_importer.code_xpath = './cda:value'
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symptom_active_importer = CDA::SectionImporter.new(CDA::EntryFinder.new("//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.76']"))
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symptom_active_importer.code_xpath = './cda:value'
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@section_importers[:care_goals] = [generate_importer(CDA::SectionImporter, "//cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.1']", '2.16.840.1.113883.3.560.1.9')] #care goal
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@section_importers[:conditions] = [
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@section_importers[:conditions] = [generate_importer(GestationalAgeImporter, nil, '2.16.840.1.113883.3.560.1.1001'),
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generate_importer(EcogStatusImporter, nil, '2.16.840.1.113883.3.560.1.1001'),
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generate_importer(SymptomActiveImporter, nil, '2.16.840.1.113883.3.560.1.69', 'active'),
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generate_importer(DiagnosisActiveImporter, nil, '2.16.840.1.113883.3.560.1.2', 'active'),
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generate_importer(CDA::ConditionImporter, "//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.54']", '2.16.840.1.113883.3.560.1.404'), # patient characteristic age
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generate_importer(CDA::ConditionImporter, "//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.14']", '2.16.840.1.113883.3.560.1.24', 'resolved'), #diagnosis resolved
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generate_importer(DiagnosisInactiveImporter, nil, '2.16.840.1.113883.3.560.1.23', 'inactive')] #diagnosis inactive
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@section_importers[:medications] = [
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@section_importers[:medications] = [generate_importer(CDA::MedicationImporter, "//cda:act[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.105']/cda:entryRelationship/cda:substanceAdministration[cda:templateId/@root='2.16.840.1.113883.10.20.24.3.41']", '2.16.840.1.113883.3.560.1.199', 'discharge'), #discharge medication active
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generate_importer(MedicationActiveImporter, nil, '2.16.840.1.113883.3.560.1.13', 'active'), #medication active
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generate_importer(CDA::MedicationImporter, "//cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.42']/cda:entryRelationship/cda:substanceAdministration[cda:templateId/@root='2.16.840.1.113883.10.20.22.4.16']", '2.16.840.1.113883.3.560.1.14', 'administered'), #medication administered
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generate_importer(CDA::MedicationImporter, "//cda:substanceAdministration[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.47']", '2.16.840.1.113883.3.560.1.17', 'ordered'), #medication order TODO: ADD NEGATON REASON HANDLING SOMEHOW
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generate_importer(MedicationDispensedImporter, nil, '2.16.840.1.113883.3.560.1.8', 'dispensed')]
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@section_importers[:procedures] = [
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@section_importers[:procedures] = [generate_importer(CDA::ProcedureImporter, "//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.59']", '2.16.840.1.113883.3.560.1.57', 'performed'), #physical exam performed
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generate_importer(CDA::ProcedureImporter, "//cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.3']", '2.16.840.1.113883.3.560.1.131'), #comm from provider to patient
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generate_importer(CDA::ProcedureImporter, "//cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.31']", '2.16.840.1.113883.3.560.1.45', 'ordered'), #intervention ordered
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generate_importer(CDA::ProcedureImporter, "//cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.32']", '2.16.840.1.113883.3.560.1.46', 'performed'), #intervention performed
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generate_importer(CDA::ProcedureImporter, "//cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.34']", '2.16.840.1.113883.3.560.1.47'), #intervention result
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generate_importer(CDA::ProcedureImporter, "//cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.4']", '2.16.840.1.113883.3.560.1.129'), #comm from provider to provider
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generate_importer(CDA::ProcedureImporter, "//cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.2']", '2.16.840.1.113883.3.560.1.30'), #comm from patient to provider
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generate_importer(ProcedureOrderImporter, nil, '2.16.840.1.113883.3.560.1.62', 'ordered'),
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generate_importer(CDA::ProcedureImporter, "//cda:procedure[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.64']", '2.16.840.1.113883.3.560.1.6'),
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generate_importer(CDA::ProcedureImporter, "//cda:procedure[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.66']", '2.16.840.1.113883.3.560.1.63'),
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generate_importer(CDA::ProcedureImporter, "//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.69']", '2.16.840.1.113883.3.560.1.21'),
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generate_importer(CDA::ProcedureImporter, "//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.18']", '2.16.840.1.113883.3.560.1.103', 'performed'), #diagnostic study performed
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generate_importer(DiagnosticStudyOrderImporter, nil, '2.16.840.1.113883.3.560.1.40', 'ordered')]
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@section_importers[:allergies] = [
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@section_importers[:allergies] = [generate_importer(ProcedureIntoleranceImporter, nil, '2.16.840.1.113883.3.560.1.61'),
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generate_importer(CDA::AllergyImporter, "//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.46']", '2.16.840.1.113883.3.560.1.67'), #medication intolerance
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generate_importer(CDA::AllergyImporter, "//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.43']", '2.16.840.1.113883.3.560.1.7'), #medication adverse effect
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generate_importer(CDA::AllergyImporter, "//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.44']", '2.16.840.1.113883.3.560.1.1')] #medication allergy
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@section_importers[:medical_equipment] = [
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@section_importers[:medical_equipment] = [generate_importer(CDA::MedicalEquipmentImporter, "//cda:procedure[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.7']", '2.16.840.1.113883.3.560.1.110', 'applied')]
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@section_importers[:results] = [
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@section_importers[:results] = [generate_importer(LabOrderImporter, nil, '2.16.840.1.113883.3.560.1.50', 'ordered'), #lab ordered
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generate_importer(CDA::ResultImporter, "//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.38']", '2.16.840.1.113883.3.560.1.5', 'performed'), #lab performed
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generate_importer(CDA::ResultImporter, "//cda:act[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.34']", '2.16.840.1.113883.3.560.1.47'), #intervention result
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generate_importer(CDA::ResultImporter, "//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.57']", '2.16.840.1.113883.3.560.1.18'), #physical exam finding
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generate_importer(CDA::ResultImporter, "//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.28']", '2.16.840.1.113883.3.560.1.88'), #functional status result
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generate_importer(CDA::ResultImporter, "//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.20']", '2.16.840.1.113883.3.560.1.111'), #diagnostic study result not done
|
|
60
|
+
generate_importer(LabResultImporter, nil, '2.16.840.1.113883.3.560.1.12')] #lab result
|
|
65
61
|
|
|
66
|
-
@section_importers[:encounters] = [
|
|
67
|
-
|
|
62
|
+
@section_importers[:encounters] = [generate_importer(CDA::EncounterImporter, "//cda:encounter[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.23']", '2.16.840.1.113883.3.560.1.79', 'performed'), #encounter performed
|
|
63
|
+
generate_importer(EncounterOrderImporter, nil, '2.16.840.1.113883.3.560.1.83', 'ordered')]
|
|
68
64
|
|
|
69
|
-
@section_importers[:social_history] = [
|
|
65
|
+
@section_importers[:social_history] = [generate_importer(TobaccoUseImporter, nil, '2.16.840.1.113883.3.560.1.1001', 'completed')]
|
|
70
66
|
|
|
71
67
|
end
|
|
72
68
|
|
|
@@ -76,6 +72,7 @@ module HealthDataStandards
|
|
|
76
72
|
import_sections(record, doc)
|
|
77
73
|
get_clinical_trial_participant(record, doc)
|
|
78
74
|
get_patient_expired(record, doc)
|
|
75
|
+
record.dedup_record!
|
|
79
76
|
record
|
|
80
77
|
end
|
|
81
78
|
|
|
@@ -96,7 +93,18 @@ module HealthDataStandards
|
|
|
96
93
|
|
|
97
94
|
def get_patient_expired(record, doc)
|
|
98
95
|
entry_elements = doc.xpath("//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.54']")
|
|
99
|
-
record.expired = true unless entry_elements.
|
|
96
|
+
record.expired = true unless entry_elements.empty?
|
|
97
|
+
end
|
|
98
|
+
|
|
99
|
+
private
|
|
100
|
+
|
|
101
|
+
def generate_importer(importer_class, xpath, hqmf_oid, status=nil)
|
|
102
|
+
if importer_class.parent_name == "HealthDataStandards::Import::CDA"
|
|
103
|
+
importer = EntryPackage.new(importer_class.new(CDA::EntryFinder.new(xpath)), hqmf_oid, status)
|
|
104
|
+
else
|
|
105
|
+
importer = EntryPackage.new(importer_class.new, hqmf_oid, status)
|
|
106
|
+
end
|
|
107
|
+
importer
|
|
100
108
|
end
|
|
101
109
|
end
|
|
102
110
|
end
|
|
@@ -0,0 +1,28 @@
|
|
|
1
|
+
module HealthDataStandards
|
|
2
|
+
module Import
|
|
3
|
+
module Cat1
|
|
4
|
+
class ProcedurePerformedImporter < CDA::SectionImporter
|
|
5
|
+
def initialize(entry_finder=CDA::EntryFinder.new("//cda:procedure[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.64']"))
|
|
6
|
+
super(entry_finder)
|
|
7
|
+
@entry_class = Procedure
|
|
8
|
+
@ordinality_xpath = "./cda:priorityCode"
|
|
9
|
+
end
|
|
10
|
+
|
|
11
|
+
def create_entry(entry_element, nrh = CDA::NarrativeReferenceHandler.new)
|
|
12
|
+
procedure = super
|
|
13
|
+
extract_ordinality(entry_element, procedure)
|
|
14
|
+
procedure
|
|
15
|
+
end
|
|
16
|
+
|
|
17
|
+
private
|
|
18
|
+
|
|
19
|
+
def extract_ordinality(parent_element, procedure)
|
|
20
|
+
ordinality_element = parent_element.at_xpath(@ordinality_xpath)
|
|
21
|
+
if ordinality_element
|
|
22
|
+
procedure.ordinality = {CodeSystemHelper.code_system_for(ordinality_element['codeSystem']) => [ordinality_element['code']]}
|
|
23
|
+
end
|
|
24
|
+
end
|
|
25
|
+
end
|
|
26
|
+
end
|
|
27
|
+
end
|
|
28
|
+
end
|
|
@@ -0,0 +1,12 @@
|
|
|
1
|
+
module HealthDataStandards
|
|
2
|
+
module Import
|
|
3
|
+
module Cat1
|
|
4
|
+
class SymptomActiveImporter < CDA::SectionImporter
|
|
5
|
+
def initialize(entry_finder=CDA::EntryFinder.new("//cda:observation[cda:templateId/@root = '2.16.840.1.113883.10.20.24.3.76']"))
|
|
6
|
+
super(entry_finder)
|
|
7
|
+
@code_xpath = './cda:value'
|
|
8
|
+
end
|
|
9
|
+
end
|
|
10
|
+
end
|
|
11
|
+
end
|
|
12
|
+
end
|
|
@@ -6,12 +6,14 @@ module HealthDataStandards
|
|
|
6
6
|
def initialize(entry_finder=EntryFinder.new("//cda:section[cda:templateId/@root='2.16.840.1.113883.3.88.11.83.103']/cda:entry/cda:act/cda:entryRelationship/cda:observation"))
|
|
7
7
|
@entry_finder = entry_finder
|
|
8
8
|
@code_xpath = "./cda:value"
|
|
9
|
+
@id_xpath = "./cda:id"
|
|
9
10
|
@status_xpath = "./cda:entryRelationship/cda:observation[cda:templateId/@root='2.16.840.1.113883.10.20.1.50']/cda:value"
|
|
10
11
|
@ordinality_xpath = "./cda:priorityCode"
|
|
11
12
|
@description_xpath = "./cda:text/cda:reference[@value]"
|
|
12
13
|
@provider_xpath = "./cda:act[cda:templateId/@root='2.16.840.1.113883.10.20.1.27']/cda:performer"
|
|
13
14
|
@priority_xpath = "../cda:sequenceNumber"
|
|
14
15
|
@entry_class = Condition
|
|
16
|
+
@value_xpath = nil
|
|
15
17
|
end
|
|
16
18
|
|
|
17
19
|
def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
|
|
@@ -17,6 +17,7 @@ module HealthDataStandards
|
|
|
17
17
|
extract_reason(entry_element, encounter, nrh)
|
|
18
18
|
extract_negation(entry_element, encounter)
|
|
19
19
|
extract_admission(entry_element, encounter)
|
|
20
|
+
extract_discharge_disposition(entry_element, encounter)
|
|
20
21
|
encounter
|
|
21
22
|
end
|
|
22
23
|
|
|
@@ -54,6 +55,11 @@ module HealthDataStandards
|
|
|
54
55
|
def extract_admission(parent_element, encounter)
|
|
55
56
|
encounter.admit_type = extract_code(parent_element, "./cda:priorityCode")
|
|
56
57
|
end
|
|
58
|
+
|
|
59
|
+
def extract_discharge_disposition(parent_element, encounter)
|
|
60
|
+
encounter.discharge_time = encounter.end_time
|
|
61
|
+
encounter.discharge_disposition = extract_code(parent_element, "./sdtc:dischargeDispositionCode")
|
|
62
|
+
end
|
|
57
63
|
end
|
|
58
64
|
end
|
|
59
65
|
end
|
|
@@ -8,6 +8,7 @@ module HealthDataStandards
|
|
|
8
8
|
def initialize(entry_finder=EntryFinder.new("//cda:section[cda:templateId/@root!='2.16.840.1.113883.3.88.11.83.124']//cda:procedure"))
|
|
9
9
|
super(entry_finder)
|
|
10
10
|
@entry_class = Procedure
|
|
11
|
+
@value_xpath = nil
|
|
11
12
|
end
|
|
12
13
|
|
|
13
14
|
def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
|
|
@@ -10,11 +10,13 @@ module HealthDataStandards
|
|
|
10
10
|
def initialize(entry_finder)
|
|
11
11
|
@entry_finder = entry_finder
|
|
12
12
|
@code_xpath = "./cda:code"
|
|
13
|
+
@id_xpath = "./cda:id"
|
|
13
14
|
@status_xpath = nil
|
|
14
15
|
@priority_xpath = nil
|
|
15
16
|
@description_xpath = "./cda:code/cda:originalText/cda:reference[@value] | ./cda:text/cda:reference[@value]"
|
|
16
17
|
@check_for_usable = true
|
|
17
18
|
@entry_class = Entry
|
|
19
|
+
@value_xpath = 'cda:value'
|
|
18
20
|
end
|
|
19
21
|
|
|
20
22
|
# Traverses an HL7 CDA document passed in and creates an Array of Entry
|
|
@@ -39,9 +41,12 @@ module HealthDataStandards
|
|
|
39
41
|
|
|
40
42
|
def create_entry(entry_element, nrh = NarrativeReferenceHandler.new)
|
|
41
43
|
entry = @entry_class.new
|
|
44
|
+
extract_id(entry_element, entry)
|
|
42
45
|
extract_codes(entry_element, entry)
|
|
43
46
|
extract_dates(entry_element, entry)
|
|
44
|
-
|
|
47
|
+
if @value_xpath
|
|
48
|
+
extract_value(entry_element, entry)
|
|
49
|
+
end
|
|
45
50
|
entry.free_text = entry_element.at_xpath("./cda:text").try("text")
|
|
46
51
|
if @status_xpath
|
|
47
52
|
extract_status(entry_element, entry)
|
|
@@ -61,6 +66,16 @@ module HealthDataStandards
|
|
|
61
66
|
end
|
|
62
67
|
end
|
|
63
68
|
|
|
69
|
+
def extract_id(parent_element, entry)
|
|
70
|
+
id_element = parent_element.at_xpath(@id_xpath)
|
|
71
|
+
if id_element
|
|
72
|
+
identifier = CDAIdentifier.new
|
|
73
|
+
identifier.root = id_element['root']
|
|
74
|
+
identifier.extension = id_element['extension']
|
|
75
|
+
entry.cda_identifier = identifier
|
|
76
|
+
end
|
|
77
|
+
end
|
|
78
|
+
|
|
64
79
|
def extract_description(parent_element, entry, nrh)
|
|
65
80
|
code_elements = parent_element.xpath(@description_xpath)
|
|
66
81
|
code_elements.each do |code_element|
|
|
@@ -102,12 +117,19 @@ module HealthDataStandards
|
|
|
102
117
|
end
|
|
103
118
|
|
|
104
119
|
def extract_value(parent_element, entry)
|
|
105
|
-
value_element = parent_element.at_xpath(
|
|
120
|
+
value_element = parent_element.at_xpath(@value_xpath)
|
|
106
121
|
if value_element
|
|
107
122
|
value = value_element['value']
|
|
108
|
-
|
|
109
|
-
|
|
110
|
-
|
|
123
|
+
if value.present?
|
|
124
|
+
unit = value_element['unit']
|
|
125
|
+
entry.set_value(value.strip, unit)
|
|
126
|
+
elsif value_element['code'].present?
|
|
127
|
+
crv = CodedResultValue.new
|
|
128
|
+
add_code_if_present(value_element, crv)
|
|
129
|
+
entry.values << crv
|
|
130
|
+
else
|
|
131
|
+
value = value_element.text
|
|
132
|
+
unit = value_element['unit']
|
|
111
133
|
entry.set_value(value.strip, unit)
|
|
112
134
|
end
|
|
113
135
|
|
|
@@ -0,0 +1,17 @@
|
|
|
1
|
+
class CDAIdentifier
|
|
2
|
+
include Mongoid::Document
|
|
3
|
+
|
|
4
|
+
field :root, type: String
|
|
5
|
+
field :extension, type: String
|
|
6
|
+
embedded_in :entry
|
|
7
|
+
|
|
8
|
+
def ==(comparison_object)
|
|
9
|
+
if comparison_object.respond_to?(:root) && comparison_object.respond_to?(:extension)
|
|
10
|
+
self.root == comparison_object.root && self.extension == comparison_object.extension
|
|
11
|
+
end
|
|
12
|
+
end
|
|
13
|
+
|
|
14
|
+
def hash
|
|
15
|
+
"#{root}#{extension}".hash
|
|
16
|
+
end
|
|
17
|
+
end
|
|
@@ -0,0 +1,92 @@
|
|
|
1
|
+
module HealthDataStandards
|
|
2
|
+
module CQM
|
|
3
|
+
|
|
4
|
+
module PopulationSelectors
|
|
5
|
+
def numerator
|
|
6
|
+
populations.find {|pop| pop.type == 'NUMER'}
|
|
7
|
+
end
|
|
8
|
+
|
|
9
|
+
def denominator
|
|
10
|
+
populations.find {|pop| pop.type == 'DENOM'}
|
|
11
|
+
end
|
|
12
|
+
|
|
13
|
+
def denominator_exceptions
|
|
14
|
+
populations.find {|pop| pop.type == 'DENEXCEP'}
|
|
15
|
+
end
|
|
16
|
+
|
|
17
|
+
def denominator_exclusions
|
|
18
|
+
populations.find {|pop| pop.type == 'DENEX'}
|
|
19
|
+
end
|
|
20
|
+
|
|
21
|
+
def population_count(population_type, population_id)
|
|
22
|
+
population = populations.find {|pop| pop.type == population_type && pop.id == population_id}
|
|
23
|
+
if population
|
|
24
|
+
population.value
|
|
25
|
+
else
|
|
26
|
+
0
|
|
27
|
+
end
|
|
28
|
+
end
|
|
29
|
+
|
|
30
|
+
def population_id(population_type)
|
|
31
|
+
populations.find {|pop| pop.type == population_type}.id
|
|
32
|
+
end
|
|
33
|
+
|
|
34
|
+
def method_missing(method, *args, &block)
|
|
35
|
+
match_data = method.to_s.match(/^(.+)_count$/)
|
|
36
|
+
if match_data
|
|
37
|
+
population = self.send(match_data[1])
|
|
38
|
+
if population
|
|
39
|
+
population.value
|
|
40
|
+
else
|
|
41
|
+
0
|
|
42
|
+
end
|
|
43
|
+
else
|
|
44
|
+
super
|
|
45
|
+
end
|
|
46
|
+
end
|
|
47
|
+
|
|
48
|
+
# Returns true if there is more than one IPP or DENOM, etc.
|
|
49
|
+
def multiple_population_types?
|
|
50
|
+
population_groups = populations.group_by {|pop| pop.type}
|
|
51
|
+
population_groups.values.any? { |pops| pops.size > 1 }
|
|
52
|
+
end
|
|
53
|
+
end
|
|
54
|
+
|
|
55
|
+
class Population
|
|
56
|
+
attr_accessor :type, :value, :id
|
|
57
|
+
end
|
|
58
|
+
|
|
59
|
+
class Stratification
|
|
60
|
+
attr_accessor :id, :populations
|
|
61
|
+
include PopulationSelectors
|
|
62
|
+
|
|
63
|
+
def initialize
|
|
64
|
+
@populations = []
|
|
65
|
+
end
|
|
66
|
+
end
|
|
67
|
+
|
|
68
|
+
class AggregateCount
|
|
69
|
+
attr_accessor :measure_id, :stratifications, :top_level_populations, :supplemental_data
|
|
70
|
+
alias :populations :top_level_populations
|
|
71
|
+
include PopulationSelectors
|
|
72
|
+
|
|
73
|
+
def initialize
|
|
74
|
+
@stratifications = []
|
|
75
|
+
@top_level_populations = []
|
|
76
|
+
end
|
|
77
|
+
|
|
78
|
+
def is_cv?
|
|
79
|
+
top_level_populations.any? {|pop| pop.type == 'MSRPOPL'}
|
|
80
|
+
end
|
|
81
|
+
|
|
82
|
+
def performance_rate
|
|
83
|
+
numerator_count.to_f /
|
|
84
|
+
(denominator_count - denominator_exclusions_count - denominator_exceptions_count)
|
|
85
|
+
end
|
|
86
|
+
|
|
87
|
+
def supplemental_data_for(population_type, supplemental_data_type)
|
|
88
|
+
supplemental_data[population_type][supplemental_data_type]
|
|
89
|
+
end
|
|
90
|
+
end
|
|
91
|
+
end
|
|
92
|
+
end
|