health-data-standards 3.6.1 → 3.7.0
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- checksums.yaml +4 -4
- data/Gemfile +7 -2
- data/Rakefile +2 -1
- data/lib/health-data-standards.rb +22 -1
- data/lib/health-data-standards/export/cat_1.rb +25 -6
- data/lib/health-data-standards/export/cat_1_r2.rb +8 -2
- data/lib/health-data-standards/export/cat_3.rb +8 -7
- data/lib/health-data-standards/export/exceptions.rb +13 -0
- data/lib/health-data-standards/export/helper/cat1_view_helper.rb +17 -11
- data/lib/health-data-standards/export/helper/html_view_helper.rb +13 -7
- data/lib/health-data-standards/export/helper/scooped_view_helper.rb +68 -25
- data/lib/health-data-standards/export/html.rb +9 -4
- data/lib/health-data-standards/export/qrda/entry_template_resolver.rb +29 -11
- data/lib/health-data-standards/export/qrda/hqmf-qrda-oids.json +89 -5
- data/lib/health-data-standards/export/rendering_context.rb +2 -2
- data/lib/health-data-standards/export/template_helper.rb +7 -2
- data/lib/health-data-standards/export/view_helper.rb +107 -39
- data/lib/health-data-standards/import/bulk_record_importer.rb +8 -5
- data/lib/health-data-standards/import/bundle/importer.rb +21 -14
- data/lib/health-data-standards/import/c32/care_goal_importer.rb +1 -1
- data/lib/health-data-standards/import/c32/immunization_importer.rb +1 -1
- data/lib/health-data-standards/import/cat1/clinical_trial_participant_importer.rb +20 -0
- data/lib/health-data-standards/import/cat1/device_order_importer.rb +20 -0
- data/lib/health-data-standards/import/cat1/diagnosis_active_importer.rb +4 -9
- data/lib/health-data-standards/import/cat1/diagnosis_importer.rb +15 -0
- data/lib/health-data-standards/import/cat1/diagnosis_inactive_importer.rb +1 -1
- data/lib/health-data-standards/import/cat1/diagnostic_study_order_importer.rb +6 -0
- data/lib/health-data-standards/import/cat1/encounter_order_act_importer.rb +19 -0
- data/lib/health-data-standards/import/cat1/encounter_performed_act_importer.rb +19 -0
- data/lib/health-data-standards/import/cat1/encounter_performed_importer.rb +16 -0
- data/lib/health-data-standards/import/cat1/immunization_administered_importer.rb +14 -0
- data/lib/health-data-standards/import/cat1/medication_dispensed_act_importer.rb +18 -0
- data/lib/health-data-standards/import/cat1/patient_importer.rb +44 -17
- data/lib/health-data-standards/import/cat1/procedure_order_importer.rb +4 -4
- data/lib/health-data-standards/import/cat1/procedure_performed_importer.rb +1 -0
- data/lib/health-data-standards/import/cat1/transfer_from_act_importer.rb +18 -0
- data/lib/health-data-standards/import/cat1/transfer_from_importer.rb +24 -0
- data/lib/health-data-standards/import/cat1/transfer_to_act_importer.rb +18 -0
- data/lib/health-data-standards/import/cat1/transfer_to_importer.rb +23 -0
- data/lib/health-data-standards/import/cda/allergy_importer.rb +1 -1
- data/lib/health-data-standards/import/cda/communication_importer.rb +55 -0
- data/lib/health-data-standards/import/cda/condition_importer.rb +17 -1
- data/lib/health-data-standards/import/cda/encounter_importer.rb +23 -21
- data/lib/health-data-standards/import/cda/medical_equipment_importer.rb +1 -0
- data/lib/health-data-standards/import/cda/medication_importer.rb +14 -4
- data/lib/health-data-standards/import/cda/procedure_importer.rb +4 -4
- data/lib/health-data-standards/import/cda/result_importer.rb +1 -1
- data/lib/health-data-standards/import/cda/section_importer.rb +59 -18
- data/lib/health-data-standards/models/assessment.rb +3 -0
- data/lib/health-data-standards/models/care_experience.rb +2 -0
- data/lib/health-data-standards/models/care_goal.rb +4 -0
- data/lib/health-data-standards/models/communication.rb +3 -0
- data/lib/health-data-standards/models/condition.rb +12 -9
- data/lib/health-data-standards/models/cqm/bundle.rb +2 -1
- data/lib/health-data-standards/models/cqm/measure.rb +2 -1
- data/lib/health-data-standards/models/cqm/patient_cache.rb +7 -3
- data/lib/health-data-standards/models/cqm/query_cache.rb +2 -0
- data/lib/health-data-standards/models/encounter.rb +14 -1
- data/lib/health-data-standards/models/encounter_principal_diagnosis.rb +36 -0
- data/lib/health-data-standards/models/entry.rb +5 -1
- data/lib/health-data-standards/models/family_history.rb +4 -0
- data/lib/health-data-standards/models/immunization.rb +1 -0
- data/lib/health-data-standards/models/lab_result.rb +10 -1
- data/lib/health-data-standards/models/medical_equipment.rb +2 -1
- data/lib/health-data-standards/models/medication.rb +19 -2
- data/lib/health-data-standards/models/patient_preference.rb +5 -0
- data/lib/health-data-standards/models/procedure.rb +16 -3
- data/lib/health-data-standards/models/provider.rb +17 -1
- data/lib/health-data-standards/models/provider_preference.rb +5 -0
- data/lib/health-data-standards/models/record.rb +8 -9
- data/lib/health-data-standards/models/reference.rb +1 -1
- data/lib/health-data-standards/models/svs/value_set.rb +28 -10
- data/lib/health-data-standards/models/transfer.rb +6 -1
- data/lib/health-data-standards/tasks/bundle.rake +5 -3
- data/lib/health-data-standards/util/hqmf_template_helper.rb +20 -14
- data/lib/health-data-standards/util/hqmfr2_template_oid_map.json +382 -0
- data/lib/health-data-standards/util/nlm_helper.rb +14 -0
- data/lib/health-data-standards/util/vs_api.rb +72 -54
- data/lib/health-data-standards/validate/measure_validator.rb +8 -3
- data/lib/health-data-standards/validate/performance_rate_validator.rb +1 -1
- data/lib/health-data-standards/validate/qrda_qdm_template_validator.rb +253 -0
- data/lib/health-data-standards/validate/reported_result_extractor.rb +5 -1
- data/lib/health-data-standards/validate/schematron_validator.rb +6 -0
- data/lib/health-data-standards/validate/validators.rb +49 -1
- data/lib/hqmf-generator/document.xml.erb +6 -5
- data/lib/hqmf-generator/field.xml.erb +1 -0
- data/lib/hqmf-generator/hqmf-generator.rb +85 -41
- data/lib/hqmf-generator/subset.xml.erb +15 -0
- data/lib/hqmf-generator/temporal_relationship.xml.erb +8 -3
- data/lib/hqmf-generator/temporal_relationship_attribute.xml.erb +10 -0
- data/lib/hqmf-generator/value.xml.erb +2 -2
- data/lib/hqmf-model/data_criteria.json +88 -17
- data/lib/hqmf-model/data_criteria.rb +144 -72
- data/lib/hqmf-model/population_criteria.rb +20 -18
- data/lib/hqmf-model/precondition.rb +6 -3
- data/lib/hqmf-model/types.rb +1 -1
- data/lib/hqmf-parser.rb +9 -0
- data/lib/hqmf-parser/1.0/utilities.rb +1 -1
- data/lib/hqmf-parser/2.0/data_criteria.rb +293 -319
- data/lib/hqmf-parser/2.0/data_criteria_helpers/dc_base_extract.rb +80 -0
- data/lib/hqmf-parser/2.0/data_criteria_helpers/dc_definition_from_template_or_type_extract.rb +201 -0
- data/lib/hqmf-parser/2.0/data_criteria_helpers/dc_post_processing.rb +85 -0
- data/lib/hqmf-parser/2.0/data_criteria_helpers/dc_specific_occurrences_and_source_data_criteria_extract.rb +117 -0
- data/lib/hqmf-parser/2.0/document.rb +246 -222
- data/lib/hqmf-parser/2.0/document_helpers/doc_population_helper.rb +175 -0
- data/lib/hqmf-parser/2.0/document_helpers/doc_utilities.rb +131 -0
- data/lib/hqmf-parser/2.0/field_value_helper.rb +251 -0
- data/lib/hqmf-parser/2.0/population_criteria.rb +101 -32
- data/lib/hqmf-parser/2.0/precondition.rb +61 -35
- data/lib/hqmf-parser/2.0/source_data_criteria_helper.rb +112 -0
- data/lib/hqmf-parser/2.0/types.rb +253 -73
- data/lib/hqmf-parser/2.0/utilities.rb +27 -12
- data/lib/hqmf-parser/2.0/value_set_helper.rb +101 -0
- data/lib/hqmf-parser/converter/pass1/data_criteria_converter.rb +6 -1
- data/lib/hqmf-parser/converter/pass1/population_criteria_converter.rb +34 -30
- data/lib/hqmf-parser/parser.rb +5 -5
- data/resources/schematron/qrda/cat_1/{CDAR2_QRDA_I_R1_D3_2015MAY_Schematron.sch → HL7_CDAR2_QRDA_Category_I_2_12_16.sch} +4692 -4675
- data/resources/schematron/qrda/cat_1_r3_1/HL7 QRDA Category I STU 3.1.sch +3573 -0
- data/resources/schematron/qrda/cat_1_r3_1/HL7 QRDA Category III STU 1.1.sch +464 -0
- data/resources/schematron/qrda/cat_1_r3_1/QRDA Category I STU Release 3.1.sch +5394 -0
- data/resources/schematron/qrda/cat_1_r3_1/voc.xml +1229 -0
- data/resources/schematron/qrda/cat_1_r4/HL7 QRDA Category I STU 4.sch +3526 -0
- data/resources/schematron/qrda/cat_1_r4/voc.xml +1186 -0
- data/resources/schematron/qrda/cat_3_r1_1/HL7 QRDA Category III STU 1.1.sch +528 -0
- data/resources/schematron/qrda/cat_3_r1_1/voc.xml +8 -0
- data/resources/schematron/qrda/cat_3_r2/HL7 QRDA Category III STU 2.sch +677 -0
- data/resources/schematron/qrda/cat_3_r2/voc.xml +1186 -0
- data/resources/schematron/qrda/cat_3_r2_1/HL7 QRDA Category III STU 2.1.sch +678 -0
- data/resources/schematron/qrda/cat_3_r2_1/voc.xml +1186 -0
- data/templates/c32/_medical_equipment.c32.erb +1 -1
- data/templates/c32/_vital_signs.c32.erb +1 -1
- data/templates/cat1/{_2.16.840.1.113883.10.20.22.4.85.cat1.erb → r2/_2.16.840.1.113883.10.20.22.4.85.cat1.erb} +1 -1
- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.1.cat1.erb → r2/_2.16.840.1.113883.10.20.24.3.1.cat1.erb} +3 -3
- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.101.cat1.erb → r2/_2.16.840.1.113883.10.20.24.3.101.cat1.erb} +1 -1
- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.103.cat1.erb → r2/_2.16.840.1.113883.10.20.24.3.103.cat1.erb} +9 -5
- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.105.cat1.erb → r2/_2.16.840.1.113883.10.20.24.3.105.cat1.erb} +18 -10
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.11.cat1.erb +88 -0
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.12.cat1.erb +50 -0
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.13.cat1.erb +54 -0
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.135.cat1.erb +70 -0
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.136.cat1.erb +52 -0
- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.14.cat1.erb → r2/_2.16.840.1.113883.10.20.24.3.14.cat1.erb} +24 -6
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.140.cat1.erb +39 -0
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.17.cat1.erb +23 -0
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.18.cat1.erb +25 -0
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.2.cat1.erb +29 -0
- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.20.cat1.erb → r2/_2.16.840.1.113883.10.20.24.3.20.cat1.erb} +4 -4
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.22.cat1.erb +22 -0
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.23.cat1.erb +114 -0
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.26.cat1.erb +20 -0
- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.28.cat1.erb → r2/_2.16.840.1.113883.10.20.24.3.28.cat1.erb} +2 -2
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.3.cat1.erb +25 -0
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.31.cat1.erb +23 -0
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.32.cat1.erb +20 -0
- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.34.cat1.erb → r2/_2.16.840.1.113883.10.20.24.3.34.cat1.erb} +6 -6
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.37.cat1.erb +22 -0
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.38.cat1.erb +20 -0
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.4.cat1.erb +29 -0
- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.40.cat1.erb → r2/_2.16.840.1.113883.10.20.24.3.40.cat1.erb} +3 -3
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.41.cat1.erb +46 -0
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.42.cat1.erb +38 -0
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.43.cat1.erb +24 -0
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.44.cat1.erb +25 -0
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.45.cat1.erb +26 -0
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.46.cat1.erb +30 -0
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.47.cat1.erb +47 -0
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.51.cat1.erb +14 -0
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.54.cat1.erb +32 -0
- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.55.cat1.erb → r2/_2.16.840.1.113883.10.20.24.3.55.cat1.erb} +0 -0
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.57.cat1.erb +23 -0
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.59.cat1.erb +22 -0
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.62.cat1.erb +36 -0
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.63.cat1.erb +21 -0
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.64.cat1.erb +52 -0
- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.66.cat1.erb → r2/_2.16.840.1.113883.10.20.24.3.66.cat1.erb} +6 -6
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.69.cat1.erb +23 -0
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.7.cat1.erb +33 -0
- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.76.cat1.erb → r2/_2.16.840.1.113883.10.20.24.3.76.cat1.erb} +5 -3
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.81.cat1.erb +23 -0
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.82.cat1.erb +23 -0
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.24.3.9.cat1.erb +64 -0
- data/templates/cat1/r2/_2.16.840.1.113883.10.20.28.3.6.cat1.erb +17 -0
- data/templates/cat1/{_address.cat1.erb → r2/_address.cat1.erb} +0 -0
- data/templates/cat1/{_author.cat1.erb → r2/_author.cat1.erb} +0 -0
- data/templates/cat1/r2/_fulfills.cat1.erb +14 -0
- data/templates/cat1/{_id.cat1.erb → r2/_id.cat1.erb} +0 -0
- data/templates/cat1/{_measures.cat1.erb → r2/_measures.cat1.erb} +1 -1
- data/templates/cat1/{_medication_details.cat1.erb → r2/_medication_details.cat1.erb} +3 -2
- data/templates/cat1/r2/_medication_dispense.cat1.erb +22 -0
- data/templates/cat1/{_ordinality.cat1.erb → r2/_ordinality.cat1.erb} +0 -0
- data/templates/cat1/{_organization.cat1.erb → r2/_organization.cat1.erb} +0 -0
- data/templates/cat1/{_patient_data.cat1.erb → r2/_patient_data.cat1.erb} +4 -1
- data/templates/cat1/r2/_patient_data_r3_1.cat1.erb +17 -0
- data/templates/cat1/r2/_providers.cat1.erb +76 -0
- data/templates/cat1/r2/_reason.cat1.erb +45 -0
- data/templates/cat1/{_record_target.cat1.erb → r2/_record_target.cat1.erb} +3 -0
- data/templates/cat1/r2/_reporting_parameters.cat1.erb +31 -0
- data/templates/cat1/{_result_value.cat1.erb → r2/_result_value.cat1.erb} +1 -1
- data/templates/cat1/{_telecom.cat1.erb → r2/_telecom.cat1.erb} +0 -0
- data/templates/cat1/{show.cat1.erb → r2/show.cat1.erb} +52 -5
- data/templates/cat1/r3/_2.16.840.1.113883.10.20.24.3.1.cat1.erb +14 -0
- data/templates/cat1/r3/_2.16.840.1.113883.10.20.24.3.103.cat1.erb +17 -0
- data/templates/cat1/r3/_2.16.840.1.113883.10.20.24.3.105.cat1.erb +68 -0
- data/templates/cat1/r3/_2.16.840.1.113883.10.20.24.3.11.cat1.erb +58 -0
- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.12.cat1.erb → r3/_2.16.840.1.113883.10.20.24.3.12.cat1.erb} +4 -5
- data/templates/cat1/r3/_2.16.840.1.113883.10.20.24.3.13.cat1.erb +39 -0
- data/templates/cat1/r3/_2.16.840.1.113883.10.20.24.3.14.cat1.erb +39 -0
- data/templates/cat1/r3/_2.16.840.1.113883.10.20.24.3.17.cat1.erb +23 -0
- data/templates/cat1/r3/_2.16.840.1.113883.10.20.24.3.18.cat1.erb +25 -0
- data/templates/cat1/r3/_2.16.840.1.113883.10.20.24.3.2.cat1.erb +29 -0
- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.22.cat1.erb → r3/_2.16.840.1.113883.10.20.24.3.22.cat1.erb} +6 -5
- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.23.cat1.erb → r3/_2.16.840.1.113883.10.20.24.3.23.cat1.erb} +26 -30
- data/templates/cat1/r3/_2.16.840.1.113883.10.20.24.3.26.cat1.erb +20 -0
- data/templates/cat1/r3/_2.16.840.1.113883.10.20.24.3.3.cat1.erb +25 -0
- data/templates/cat1/r3/_2.16.840.1.113883.10.20.24.3.31.cat1.erb +23 -0
- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.32.cat1.erb → r3/_2.16.840.1.113883.10.20.24.3.32.cat1.erb} +4 -4
- data/templates/cat1/r3/_2.16.840.1.113883.10.20.24.3.37.cat1.erb +22 -0
- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.38.cat1.erb → r3/_2.16.840.1.113883.10.20.24.3.38.cat1.erb} +3 -3
- data/templates/cat1/r3/_2.16.840.1.113883.10.20.24.3.4.cat1.erb +29 -0
- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.41.cat1.erb → r3/_2.16.840.1.113883.10.20.24.3.41.cat1.erb} +8 -10
- data/templates/cat1/r3/_2.16.840.1.113883.10.20.24.3.42.cat1.erb +38 -0
- data/templates/cat1/r3/_2.16.840.1.113883.10.20.24.3.43.cat1.erb +24 -0
- data/templates/cat1/r3/_2.16.840.1.113883.10.20.24.3.44.cat1.erb +25 -0
- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.45.cat1.erb → r3/_2.16.840.1.113883.10.20.24.3.45.cat1.erb} +5 -5
- data/templates/cat1/r3/_2.16.840.1.113883.10.20.24.3.46.cat1.erb +30 -0
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- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.54.cat1.erb → r3/_2.16.840.1.113883.10.20.24.3.54.cat1.erb} +4 -4
- data/templates/cat1/r3/_2.16.840.1.113883.10.20.24.3.55.cat1.erb +18 -0
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- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.63.cat1.erb → r3/_2.16.840.1.113883.10.20.24.3.63.cat1.erb} +6 -8
- data/templates/cat1/r3/_2.16.840.1.113883.10.20.24.3.64.cat1.erb +51 -0
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- data/templates/cat1/r3/_address.cat1.erb +9 -0
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- data/templates/{cat3/_id.cat3.erb → cat1/r3/_id.cat1.erb} +0 -0
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- data/templates/cat1/r3_1/_2.16.840.1.113883.10.20.24.3.1.cat1.erb +14 -0
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- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.18.cat1.erb → r3_1/_2.16.840.1.113883.10.20.24.3.18.cat1.erb} +3 -3
- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.2.cat1.erb → r3_1/_2.16.840.1.113883.10.20.24.3.2.cat1.erb} +2 -2
- data/templates/cat1/r3_1/_2.16.840.1.113883.10.20.24.3.22.cat1.erb +30 -0
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- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.26.cat1.erb → r3_1/_2.16.840.1.113883.10.20.24.3.26.cat1.erb} +4 -2
- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.3.cat1.erb → r3_1/_2.16.840.1.113883.10.20.24.3.3.cat1.erb} +2 -2
- data/templates/cat1/r3_1/_2.16.840.1.113883.10.20.24.3.31.cat1.erb +24 -0
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- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.4.cat1.erb → r3_1/_2.16.840.1.113883.10.20.24.3.4.cat1.erb} +2 -2
- data/templates/cat1/r3_1/_2.16.840.1.113883.10.20.24.3.41.cat1.erb +45 -0
- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.42.cat1.erb → r3_1/_2.16.840.1.113883.10.20.24.3.42.cat1.erb} +4 -4
- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.43.cat1.erb → r3_1/_2.16.840.1.113883.10.20.24.3.43.cat1.erb} +3 -3
- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.44.cat1.erb → r3_1/_2.16.840.1.113883.10.20.24.3.44.cat1.erb} +3 -3
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- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.46.cat1.erb → r3_1/_2.16.840.1.113883.10.20.24.3.46.cat1.erb} +4 -4
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- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.57.cat1.erb → r3_1/_2.16.840.1.113883.10.20.24.3.57.cat1.erb} +3 -3
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- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.62.cat1.erb → r3_1/_2.16.840.1.113883.10.20.24.3.62.cat1.erb} +5 -5
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- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.64.cat1.erb → r3_1/_2.16.840.1.113883.10.20.24.3.64.cat1.erb} +7 -7
- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.69.cat1.erb → r3_1/_2.16.840.1.113883.10.20.24.3.69.cat1.erb} +2 -2
- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.7.cat1.erb → r3_1/_2.16.840.1.113883.10.20.24.3.7.cat1.erb} +12 -9
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- data/templates/cat1/{_2.16.840.1.113883.10.20.24.3.59.cat1.erb → r4/_2.16.840.1.113883.10.20.24.3.144.cat1.erb} +6 -6
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- data/templates/cat1/_2.16.840.1.113883.10.20.24.3.37.cat1.erb +0 -20
- data/templates/cat1/_2.16.840.1.113883.10.20.24.3.47.cat1.erb +0 -27
- data/templates/cat1/_2.16.840.1.113883.10.20.24.3.51.cat1.erb +0 -13
- data/templates/cat1/_reason.cat1.erb +0 -23
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module HQMF2
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# Contains extraction methods which are self-contained (rely only on the xml and an xpath, no other instance
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# variables)
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class DataCriteriaBaseExtractions
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include HQMF2::Utilities
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CONJUNCTION_CODE_TO_DERIVATION_OP = {
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'OR' => 'UNION',
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'AND' => 'XPRODUCT'
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}
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def initialize(entry)
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@entry = entry
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end
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# Extract the local variable name (held in the value of the localVariableName element)
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def extract_local_variable_name
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lvn = @entry.at_xpath('./cda:localVariableName')
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lvn['value'] if lvn
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end
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# Generate a list of child criterias
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def extract_child_criteria
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@entry.xpath("./*/cda:outboundRelationship[@typeCode='COMP']/cda:criteriaReference/cda:id",
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HQMF2::Document::NAMESPACES).collect do |ref|
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Reference.new(ref).id
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end.compact
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end
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# Extracts the derivation operator to be used by the data criteria, and fails out if it finds more than one (should
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# not be valid)
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def extract_derivation_operator
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codes = @entry.xpath("./*/cda:outboundRelationship[@typeCode='COMP']/cda:conjunctionCode/@code",
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HQMF2::Document::NAMESPACES)
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codes.inject(nil) do |d_op, code|
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if d_op && d_op != CONJUNCTION_CODE_TO_DERIVATION_OP[code.value]
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fail 'More than one derivation operator in data criteria'
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end
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CONJUNCTION_CODE_TO_DERIVATION_OP[code.value]
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end
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end
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def extract_temporal_references
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@entry.xpath('./*/cda:temporallyRelatedInformation', HQMF2::Document::NAMESPACES).collect do |temporal_reference|
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TemporalReference.new(temporal_reference)
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end
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end
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# Filters all the subset operators to only include the ones of type 'UNION' and 'XPRODUCT'
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def extract_subset_operators
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all_subset_operators.select do |operator|
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operator.type != 'UNION' && operator.type != 'XPRODUCT'
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end
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end
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# Extracts all subset operators contained in the entry xml
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def all_subset_operators
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@entry.xpath('./*/cda:excerpt', HQMF2::Document::NAMESPACES).collect do |subset_operator|
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SubsetOperator.new(subset_operator)
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end
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end
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def extract_template_ids
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@entry.xpath('./*/cda:templateId/cda:item', HQMF2::Document::NAMESPACES).collect do |template_def|
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HQMF2::Utilities.attr_val(template_def, '@root')
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end
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end
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# Extract the negation (and the negation_code_list_id if appropriate)
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def extract_negation
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negation = (attr_val('./*/@actionNegationInd') == 'true')
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negation_code_list_id = nil
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if negation
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res = @entry.at_xpath('./*/cda:outboundRelationship/*/cda:code[@code="410666004"]/../cda:value/@valueSet',
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HQMF2::Document::NAMESPACES)
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negation_code_list_id = res.value if res
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end
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[negation, negation_code_list_id]
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end
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end
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end
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module HQMF2
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# Extracts the type, and modifies the data criteria, based on the template id or definition
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module DataCriteriaTypeAndDefinitionExtraction
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VARIABLE_TEMPLATE = '0.1.2.3.4.5.6.7.8.9.1'
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SATISFIES_ANY_TEMPLATE = '2.16.840.1.113883.10.20.28.3.108'
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SATISFIES_ALL_TEMPLATE = '2.16.840.1.113883.10.20.28.3.109'
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def extract_definition_from_template_or_type
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# Try to determine what kind of data criteria we are dealing with
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# First we look for a template id and if we find one just use the definition
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# status and negation associated with that
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# If no template id or not one we recognize then try to determine type from
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# the definition element
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extract_definition_from_type unless extract_definition_from_template_id
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end
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# Given a template id, derive (if available) the definition for the template.
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# The definitions are stored in hqmf-model/data_criteria.json.
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def extract_definition_from_template_id
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found = false
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@template_ids.each do |template_id|
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defs = HQMF::DataCriteria.definition_for_template_id(template_id, 'r2')
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if defs
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@definition = defs['definition']
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@status = defs['status'].length > 0 ? defs['status'] : nil
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found ||= true
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else
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found ||= handle_known_template_id(template_id)
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end
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end
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found
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end
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# Given a template id, modify the variables inside this data criteria to reflect the template
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def handle_known_template_id(template_id)
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case template_id
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when VARIABLE_TEMPLATE
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@derivation_operator = HQMF::DataCriteria::INTERSECT if @derivation_operator == HQMF::DataCriteria::XPRODUCT
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@definition ||= 'derived'
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@variable = true
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@negation = false
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when SATISFIES_ANY_TEMPLATE
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@definition = HQMF::DataCriteria::SATISFIES_ANY
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@negation = false
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when SATISFIES_ALL_TEMPLATE
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@definition = HQMF::DataCriteria::SATISFIES_ALL
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@derivation_operator = HQMF::DataCriteria::INTERSECT
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@negation = false
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else
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return false
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end
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true
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end
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# Extract the definition (sometimes status, sometimes other elements) of the data criteria based on the type
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def extract_definition_from_type
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# If we have a specific occurrence of a variable, pull attributes from the reference.
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# IDEA set this up to be called from dc_specific_and_source_extract, the number of
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# fields changed by handle_specific_variable_ref may pose an issue.
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extract_information_for_specific_variable if @variable && @specific_occurrence
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if @entry.at_xpath('./cda:grouperCriteria')
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@definition ||= 'derived'
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return
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end
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# See if we can find a match for the entry definition value and status.
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entry_type = attr_val('./*/cda:definition/*/cda:id/@extension')
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handle_entry_type(entry_type)
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end
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# Extracts information from a reference for a specific
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def extract_information_for_specific_variable
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reference = @entry.at_xpath('./*/cda:outboundRelationship/cda:criteriaReference',
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HQMF2::Document::NAMESPACES)
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if reference
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ref_id = strip_tokens(
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"#{HQMF2::Utilities.attr_val(reference, 'cda:id/@extension')}_#{HQMF2::Utilities.attr_val(reference, 'cda:id/@root')}")
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end
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reference_criteria = @data_criteria_references[ref_id] if ref_id
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# if the reference is derived, pull from the original variable
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if reference_criteria && reference_criteria.definition == 'derived'
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reference_criteria = @data_criteria_references["GROUP_#{ref_id}"]
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end
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return unless reference_criteria
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handle_specific_variable_ref(reference_criteria)
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end
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# Apply additional information to a specific occurrence's elements from the criteria it references.
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def handle_specific_variable_ref(reference_criteria)
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# if there are no referenced children, then it's a variable representing
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# a single data criteria, so just reference it
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if reference_criteria.children_criteria.empty?
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@children_criteria = [reference_criteria.id]
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# otherwise pull all the data criteria info from the reference
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else
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@field_values = reference_criteria.field_values
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@temporal_references = reference_criteria.temporal_references
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@subset_operators = reference_criteria.subset_operators
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@derivation_operator = reference_criteria.derivation_operator
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@definition = reference_criteria.definition
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@description = reference_criteria.description
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@status = reference_criteria.status
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@children_criteria = reference_criteria.children_criteria
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end
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end
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# Generate the definition and/or status from the entry type in most cases.
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# If the entry type is nil, and the value is a specific occurrence, more parsing may be necessary.
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def handle_entry_type(entry_type)
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# settings is required to trigger exceptions, which set the definition
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HQMF::DataCriteria.get_settings_for_definition(entry_type, @status)
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@definition = entry_type
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rescue
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# if no exact match then try a string match just using entry definition value
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case entry_type
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when 'Medication', 'Medications'
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@definition = 'medication'
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@status = 'active' unless @status
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when 'RX'
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@definition = 'medication'
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@status = 'dispensed' unless @status
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when nil
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definition_for_nil_entry
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else
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@definition = extract_definition_from_entry_type(entry_type)
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end
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end
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# If there is no entry type, extract the entry type from what it references, and extract additional information for
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# specific occurrences. If there are no outbound references, print an error and mark it as variable.
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def definition_for_nil_entry
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reference = @entry.at_xpath('./*/cda:outboundRelationship/cda:criteriaReference', HQMF2::Document::NAMESPACES)
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ref_id = nil
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unless reference.nil?
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ref_id = "#{HQMF2::Utilities.attr_val(reference, 'cda:id/@extension')}_#{HQMF2::Utilities.attr_val(reference, 'cda:id/@root')}"
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end
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reference_criteria = @data_criteria_references[strip_tokens(ref_id)] unless ref_id.nil?
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if reference_criteria
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# we only want to copy the reference criteria definition, status, and code_list_id if this is this is not a grouping criteria (i.e., there are no children)
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if @children_criteria.blank?
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@definition = reference_criteria.definition
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@status = reference_criteria.status
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if @specific_occurrence
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@title = reference_criteria.title
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@description = reference_criteria.description
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@code_list_id = reference_criteria.code_list_id
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end
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else
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# if this is a grouping data criteria (has children) mark it as derived and only pull title and description from the reference criteria
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@definition = 'derived'
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if @specific_occurrence
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@title = reference_criteria.title
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@description = reference_criteria.description
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end
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end
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else
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puts "MISSING_DC_REF: #{ref_id}" unless @variable
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@definition = 'variable'
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end
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end
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# Given an entry type (which describes the criteria's purpose) return the appropriate defintino
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def extract_definition_from_entry_type(entry_type)
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case entry_type
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when 'Problem', 'Problems'
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'diagnosis'
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when 'Encounter', 'Encounters'
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'encounter'
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when 'LabResults', 'Results'
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'laboratory_test'
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when 'Procedure', 'Procedures'
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'procedure'
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when 'Demographics'
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definition_for_demographic
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when 'Derived'
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'derived'
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else
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fail "Unknown data criteria template identifier [#{entry_type}]"
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end
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end
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# Return the definition for a known subset of patient characteristics
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def definition_for_demographic
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demographic_type = attr_val('./cda:observationCriteria/cda:code/@code')
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demographic_translation = {
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'21112-8' => 'patient_characteristic_birthdate',
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'424144002' => 'patient_characteristic_age',
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'263495000' => 'patient_characteristic_gender',
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'102902016' => 'patient_characteristic_languages',
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'125680007' => 'patient_characteristic_marital_status',
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'103579009' => 'patient_characteristic_race'
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}
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if demographic_translation[demographic_type]
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demographic_translation[demographic_type]
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else
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fail "Unknown demographic identifier [#{demographic_type}]"
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end
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end
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end
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end
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@@ -0,0 +1,85 @@
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module HQMF2
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# Processing on data criteria after the initial extractions have taken place
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module DataCriteriaPostProcessing
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# Handles settings values after (most) values have been setup
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def post_processing
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extract_code_list_path_and_result_value
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# prefix ids that start with numerical values, and strip tokens from others
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@id = strip_tokens(@id)
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@children_criteria.map! { |cc| strip_tokens(cc) }
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# append "_source" to the criteria since all the source criteria are separated from the non-source with the "_source" identifier
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# "_source" is added to the SDC ids so that we are not duplicating ids between source and non source data criteria lists
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# the derived source data criteria maintain their original ids since they are duplicated in the data criteria and source data criteria lists from the simple xml
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@source_data_criteria = "#{@id}_source" unless (@definition == 'derived' || @definition == 'satisfies_all' || @definition == 'satisfies_any')
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@source_data_criteria = strip_tokens(@source_data_criteria) unless @source_data_criteria.nil?
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@specific_occurrence_const = strip_tokens(@specific_occurrence_const) unless @specific_occurrence_const.nil?
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change_xproduct_to_intersection
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handle_derived_specific_occurrences
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end
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# Extract the code_list_xpath and the criteria's value from either the location related to the specific occurrence,
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# or from any of the template ids (if multiple exist)
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def extract_code_list_path_and_result_value
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if @template_ids.empty? && @specific_occurrence
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template = @entry.document.at_xpath(
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"//cda:id[@root='#{@source_data_criteria_root}' and @extension='#{@source_data_criteria_extension}']/../cda:templateId/cda:item/@root")
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if template
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mapping = ValueSetHelper.get_mapping_for_template(template.to_s)
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handle_mapping_template(mapping)
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end
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end
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@template_ids.each do |t|
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mapping = ValueSetHelper.get_mapping_for_template(t)
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handle_mapping_template(mapping)
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break if mapping # quit if one template id with a mapping has set these values
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end
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end
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# Set the value and code_list_xpath using the template mapping held in the ValueSetHelper class
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def handle_mapping_template(mapping)
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if mapping
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if mapping[:valueset_path] && @entry.at_xpath(mapping[:valueset_path])
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@code_list_xpath = mapping[:valueset_path]
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end
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@value = DataCriteriaMethods.parse_value(@entry, mapping[:result_path]) if mapping[:result_path]
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end
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end
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# Changes XPRODUCT data criteria that has an associated tempalte(s) to an INTERSETION criteria.
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# UNION is used for all other cases.
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52
|
+
def change_xproduct_to_intersection
|
53
|
+
# Need to handle grouper criteria that do not have template ids -- these will be union of and intersection
|
54
|
+
# criteria
|
55
|
+
return unless @template_ids.empty?
|
56
|
+
# Change the XPRODUCT to an INTERSECT otherwise leave it as a UNION
|
57
|
+
@derivation_operator = HQMF::DataCriteria::INTERSECT if @derivation_operator == HQMF::DataCriteria::XPRODUCT
|
58
|
+
@description ||= (@derivation_operator == HQMF::DataCriteria::INTERSECT) ? 'Intersect' : 'Union'
|
59
|
+
end
|
60
|
+
|
61
|
+
# Apply some elements from the reference_criteria to the derived specific occurrence
|
62
|
+
def handle_derived_specific_occurrences
|
63
|
+
return unless @definition == 'derived'
|
64
|
+
|
65
|
+
# remove "_source" from source data critera. It gets added in in SpecificOccurrenceAndSource but
|
66
|
+
# when it gets added we have not yet determined the definition of the data criteria so we cannot
|
67
|
+
# skip adding it. Determining the definition before SpecificOccurrenceAndSource processes doesn't
|
68
|
+
# work because we need to know if it is a specific occurrence to be able to figure out the definition
|
69
|
+
@source_data_criteria = @source_data_criteria.gsub("_source",'') if @source_data_criteria
|
70
|
+
|
71
|
+
# Adds a child if none exists (specifically the source criteria)
|
72
|
+
@children_criteria << @source_data_criteria if @children_criteria.empty?
|
73
|
+
return if @children_criteria.length != 1 ||
|
74
|
+
(@source_data_criteria.present? && @children_criteria.first != @source_data_criteria)
|
75
|
+
# if child.first is nil, it will be caught in the second statement
|
76
|
+
reference_criteria = @data_criteria_references[@children_criteria.first]
|
77
|
+
return if reference_criteria.nil?
|
78
|
+
@is_derived_specific_occurrence_variable = true # easier to track than all testing all features of these cases
|
79
|
+
@subset_operators ||= reference_criteria.subset_operators
|
80
|
+
@derivation_operator ||= reference_criteria.derivation_operator
|
81
|
+
@description = reference_criteria.description
|
82
|
+
@variable = reference_criteria.variable
|
83
|
+
end
|
84
|
+
end
|
85
|
+
end
|
@@ -0,0 +1,117 @@
|
|
1
|
+
module HQMF2
|
2
|
+
# Handles various tasks that the Data Criteria needs performed to obtain and
|
3
|
+
# modify secific occurrences
|
4
|
+
class SpecificOccurrenceAndSource
|
5
|
+
include HQMF2::Utilities
|
6
|
+
|
7
|
+
def initialize(entry, id, local_variable_name, data_criteria_references, occurrences_map)
|
8
|
+
@entry = entry
|
9
|
+
@id = id
|
10
|
+
@local_variable_name = local_variable_name
|
11
|
+
@occurrences_map = occurrences_map
|
12
|
+
@is_variable = DataCriteriaMethods.extract_variable(@local_variable_name, @id)
|
13
|
+
@data_criteria_references = data_criteria_references
|
14
|
+
end
|
15
|
+
|
16
|
+
# Retrieve the specific occurrence and source data criteria information (or just source if there is no specific)
|
17
|
+
def extract_specific_occurrences_and_source_data_criteria
|
18
|
+
specific_def = @entry.at_xpath('./*/cda:outboundRelationship[@typeCode="OCCR"]', HQMF2::Document::NAMESPACES)
|
19
|
+
source_def = @entry.at_xpath('./*/cda:outboundRelationship[cda:subsetCode/@code="SOURCE"]',
|
20
|
+
HQMF2::Document::NAMESPACES)
|
21
|
+
if specific_def
|
22
|
+
source_data_criteria_extension = HQMF2::Utilities.attr_val(specific_def,
|
23
|
+
'./cda:criteriaReference/cda:id/@extension')
|
24
|
+
source_data_criteria_root = HQMF2::Utilities.attr_val(specific_def, './cda:criteriaReference/cda:id/@root')
|
25
|
+
|
26
|
+
occurrence_criteria = @data_criteria_references[strip_tokens("#{source_data_criteria_extension}_#{source_data_criteria_root}")]
|
27
|
+
|
28
|
+
return if occurrence_criteria.nil?
|
29
|
+
specific_occurrence_const = HQMF2::Utilities.attr_val(specific_def,
|
30
|
+
'./cda:localVariableName/@controlInformationRoot')
|
31
|
+
specific_occurrence = HQMF2::Utilities.attr_val(specific_def,
|
32
|
+
'./cda:localVariableName/@controlInformationExtension')
|
33
|
+
|
34
|
+
# FIXME: Remove debug statements after cleaning up occurrence handling
|
35
|
+
# build regex for extracting alpha-index of specific occurrences
|
36
|
+
occurrence_identifier = obtain_occurrence_identifier(strip_tokens(@id),
|
37
|
+
strip_tokens(@local_variable_name) || '',
|
38
|
+
strip_tokens(source_data_criteria_extension),
|
39
|
+
@is_variable)
|
40
|
+
|
41
|
+
handle_specific_and_source(occurrence_identifier, source_data_criteria_extension, source_data_criteria_root,
|
42
|
+
specific_occurrence_const, specific_occurrence)
|
43
|
+
|
44
|
+
elsif source_def
|
45
|
+
extension = HQMF2::Utilities.attr_val(source_def, './cda:criteriaReference/cda:id/@extension')
|
46
|
+
root = HQMF2::Utilities.attr_val(source_def, './cda:criteriaReference/cda:id/@root')
|
47
|
+
["#{extension}_#{root}_source", root, extension] # return the soruce data criteria itself, the rest will be blank
|
48
|
+
end
|
49
|
+
end
|
50
|
+
|
51
|
+
# Handle setting the specific and source instance variables with a given occurrence identifier
|
52
|
+
def handle_specific_and_source(occurrence_identifier, source_data_criteria_extension, source_data_criteria_root,
|
53
|
+
specific_occurrence_const, specific_occurrence)
|
54
|
+
source_data_criteria = "#{source_data_criteria_extension}_#{source_data_criteria_root}_source"
|
55
|
+
if !occurrence_identifier.blank?
|
56
|
+
# if it doesn't exist, add extracted occurrence to the map
|
57
|
+
# puts "\tSetting #{@source_data_criteria}-#{@source_data_criteria_root} to #{occurrence_identifier}"
|
58
|
+
@occurrences_map[strip_tokens(source_data_criteria)] ||= occurrence_identifier
|
59
|
+
specific_occurrence ||= occurrence_identifier
|
60
|
+
specific_occurrence_const = "#{source_data_criteria}".upcase
|
61
|
+
else
|
62
|
+
# create variable occurrences that do not already exist
|
63
|
+
if @is_variable
|
64
|
+
# puts "\tSetting #{@source_data_criteria}-#{@source_data_criteria_root} to #{occurrence_identifier}"
|
65
|
+
@occurrences_map[strip_tokens(source_data_criteria)] ||= occurrence_identifier
|
66
|
+
end
|
67
|
+
occurrence = @occurrences_map.try(:[], strip_tokens(source_data_criteria))
|
68
|
+
unless occurrence
|
69
|
+
fail "Could not find occurrence mapping for #{source_data_criteria}, #{source_data_criteria_root}"
|
70
|
+
end
|
71
|
+
# puts "\tUsing #{occurrence} for #{@id}"
|
72
|
+
specific_occurrence ||= occurrence
|
73
|
+
end
|
74
|
+
|
75
|
+
specific_occurrence = 'A' unless specific_occurrence
|
76
|
+
specific_occurrence_const = source_data_criteria.upcase unless specific_occurrence_const
|
77
|
+
[source_data_criteria, source_data_criteria_root, source_data_criteria_extension,
|
78
|
+
specific_occurrence, specific_occurrence_const]
|
79
|
+
end
|
80
|
+
|
81
|
+
# Using the id, source data criteria id, and local variable name (and whether or not it's a variable),
|
82
|
+
# extract the occurrence identifiter (if one exists).
|
83
|
+
def obtain_occurrence_identifier(stripped_id, stripped_lvn, stripped_sdc, is_variable)
|
84
|
+
if is_variable || (stripped_sdc.include? 'qdm_var')
|
85
|
+
occurrence_lvn_regex = 'occ[A-Z]of_qdm_var'
|
86
|
+
occurrence_id_regex = 'occ[A-Z]of_qdm_var'
|
87
|
+
occ_index = 3
|
88
|
+
return handle_occurrence_var(stripped_id, stripped_lvn, stripped_sdc, occurrence_id_regex, occurrence_lvn_regex, occ_index)
|
89
|
+
else
|
90
|
+
occurrence_lvn_regex = 'Occurrence[A-Z]of'
|
91
|
+
occurrence_id_regex = 'Occurrence[A-Z]_'
|
92
|
+
occ_index = 10
|
93
|
+
|
94
|
+
occurrence_identifier = handle_occurrence_var(
|
95
|
+
stripped_id, stripped_lvn, stripped_sdc,
|
96
|
+
"#{occurrence_id_regex}#{stripped_sdc}", "#{occurrence_lvn_regex}#{stripped_sdc}",
|
97
|
+
occ_index)
|
98
|
+
return occurrence_identifier if occurrence_identifier.present?
|
99
|
+
|
100
|
+
stripped_sdc[occ_index] if stripped_sdc.match(
|
101
|
+
/(^#{occurrence_id_regex}| ^#{occurrence_id_regex}qdm_var_| ^#{occurrence_lvn_regex})| ^#{occurrence_lvn_regex}qdm_var_/)
|
102
|
+
end
|
103
|
+
end
|
104
|
+
|
105
|
+
# If the occurrence is a variable, extract the occurrence identifier (if present)
|
106
|
+
def handle_occurrence_var(stripped_id, stripped_lvn, stripped_sdc, occurrence_id_compare, occurrence_lvn_compare, occ_index)
|
107
|
+
# TODO: Handle specific occurrences of variables that don't self-reference?
|
108
|
+
if stripped_id.match(/^#{occurrence_id_compare}/)
|
109
|
+
return stripped_id[occ_index]
|
110
|
+
elsif stripped_lvn.match(/^#{occurrence_lvn_compare}/)
|
111
|
+
return stripped_lvn[occ_index]
|
112
|
+
elsif stripped_sdc.match(/^#{occurrence_id_compare}/)
|
113
|
+
return stripped_sdc[occ_index]
|
114
|
+
end
|
115
|
+
end
|
116
|
+
end
|
117
|
+
end
|