cqm-reports 2.1.1 → 3.0.0.pre.alpha.1
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- checksums.yaml +5 -5
- data/Gemfile +1 -2
- data/README.md +0 -27
- data/lib/{cqm_report.rb → cqm-reports.rb} +4 -2
- data/lib/ext/code.rb +11 -0
- data/lib/ext/data_element.rb +24 -0
- data/lib/html-export/qdm-patient/qdm_patient.rb +3 -3
- data/lib/qrda-export/catI-r5/_header.mustache +2 -2
- data/lib/qrda-export/catI-r5/qrda1_r5.mustache +2 -6
- data/lib/qrda-export/catI-r5/qrda1_r5.rb +2 -28
- data/lib/qrda-export/catI-r5/qrda_header/_record_target.mustache +11 -24
- data/lib/qrda-export/catI-r5/qrda_templates/adverse_event.mustache +4 -4
- data/lib/qrda-export/catI-r5/qrda_templates/allergy_intolerance.mustache +6 -1
- data/lib/qrda-export/catI-r5/qrda_templates/communication_performed.mustache +2 -2
- data/lib/qrda-export/catI-r5/qrda_templates/diagnosis.mustache +6 -1
- data/lib/qrda-export/catI-r5/qrda_templates/encounter_performed.mustache +0 -4
- data/lib/qrda-export/catI-r5/qrda_templates/immunization_administered.mustache +2 -7
- data/lib/qrda-export/catI-r5/qrda_templates/medication_discharge.mustache +2 -0
- data/lib/qrda-export/catI-r5/qrda_templates/procedure_order.mustache +0 -4
- data/lib/qrda-export/catI-r5/qrda_templates/procedure_performed.mustache +0 -4
- data/lib/qrda-export/catI-r5/qrda_templates/procedure_recommended.mustache +0 -4
- data/lib/qrda-export/catI-r5/qrda_templates/substance_recommended.mustache +0 -1
- data/lib/qrda-export/catI-r5/qrda_templates/symptom.mustache +6 -1
- data/lib/qrda-export/catI-r5/qrda_templates/template_partials/_encounter_diagnosis.mustache +3 -1
- data/lib/qrda-export/catI-r5/qrda_templates/template_partials/_medication_supply_request.mustache +1 -1
- data/lib/qrda-export/catI-r5/qrda_templates/template_partials/_results.mustache +12 -0
- data/lib/qrda-export/helper/cat1_view_helper.rb +4 -6
- data/lib/qrda-export/helper/date_helper.rb +4 -0
- data/lib/qrda-import/base-importers/demographics_importer.rb +4 -4
- data/lib/qrda-import/base-importers/section_importer.rb +14 -58
- data/lib/qrda-import/data-element-importers/adverse_event_importer.rb +1 -1
- data/lib/qrda-import/data-element-importers/communication_performed_importer.rb +4 -4
- data/lib/qrda-import/data-element-importers/diagnostic_study_performed_importer.rb +1 -1
- data/lib/qrda-import/data-element-importers/encounter_performed_importer.rb +0 -12
- data/lib/qrda-import/data-element-importers/immunization_order_importer.rb +1 -1
- data/lib/qrda-import/data-element-importers/medication_dispensed_importer.rb +2 -2
- data/lib/qrda-import/data-element-importers/medication_order_importer.rb +1 -1
- data/lib/qrda-import/data-element-importers/procedure_order_importer.rb +0 -2
- data/lib/qrda-import/data-element-importers/procedure_performed_importer.rb +0 -2
- data/lib/qrda-import/data-element-importers/procedure_recommended_importer.rb +0 -2
- data/lib/qrda-import/entry_package.rb +16 -0
- data/lib/qrda-import/patient_importer.rb +62 -85
- metadata +15 -29
- data/lib/qrda-export/catI-r5/qrda_templates/provider_characteristic.mustache +0 -15
- data/lib/qrda-import/data-element-importers/provider_characteristic_importer.rb +0 -19
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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---
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-
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-
metadata.gz:
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-
data.tar.gz:
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+
SHA256:
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+
metadata.gz: 61e09a4750ca628e10f1e92fe0d37c28058ab629b59fcbc520ef167d369296a3
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+
data.tar.gz: 1035c18714e2ca53bdd527e91ebac55b96e5737cba137c105c8a1b2577418d3d
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: e1566656c60a1836df5e4846b6b07669ddddfb81c0aeee0bc0302790bc70abb0fea8711d6722e87f5ca02174ed535ffe7a04a7b4709c1800c5e03a37a07d7e7a
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7
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+
data.tar.gz: 3fb48e9b465962a7a7130a49879bb9b812bf59fb2ff94af064af571da1b3c92775861d262cd8dbbf66168e0020ad998de34389e4dcba9d1fed4b66e9753a99da
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data/Gemfile
CHANGED
@@ -4,8 +4,6 @@ gemspec :development_group => :test
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5
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gem 'mongoid', '~> 6.4.2'
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-
# gem 'cqm-models', git: 'https://github.com/projecttacoma/cqm-models.git', branch: 'master'
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-
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gem 'protected_attributes_continued'
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group :development, :test do
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@@ -28,5 +26,6 @@ group :test do
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gem 'minitest', '~> 5.3'
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gem 'minitest-reporters'
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gem 'awesome_print', :require => 'ap'
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+
gem 'cqm-validators'
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gem 'nokogiri-diff'
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end
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data/README.md
CHANGED
@@ -18,33 +18,6 @@ Starting with version **2.0.0** released on 6/20/2019, cqm-reports versioning ha
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For the versions available, see [tags on this repository](https://github.com/projecttacoma/cqm-validators/tags).
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=======
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Importing QRDA
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==========
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A QRDA document can be imported into a CQM::Patient (defined in [cqm-models](https://github.com/projecttacoma/cqm-models)) using the following commands.
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doc = Nokogiri::XML(file)
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patient, warnings = QRDA::Cat1::PatientImporter.instance.parse_cat1(doc)
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-
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-
Exporting QRDA Category I
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-
==========
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-
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Exporting a QRDA document from a CQM::Patient (defined in [cqm-models](https://github.com/projecttacoma/cqm-models)) using the following command.
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Qrda1R5.new(patient, measures, options).render
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* patient is a [CQM::Patient](https://github.com/projecttacoma/cqm-models/blob/master/app/models/cqm/patient.rb)
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* measures is an array of [CQM::Measure](https://github.com/projecttacoma/cqm-models/blob/master/app/models/cqm/measure.rb)
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* options is a hash that can be used to pass in:
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* provider
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* patient_addresses
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* patient_telecoms
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-
* start_time
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* end_time
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-
* submission_program
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-
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-
QRDA export requires the [mustache](https://github.com/mustache/mustache) gem
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-
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21
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## License
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Copyright 2019 The MITRE Corporation
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@@ -18,6 +18,7 @@ require_relative 'html-export/qdm-patient/qdm_patient.rb'
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require_relative 'qrda-export/catI-r5/qrda1_r5.rb'
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require_relative 'qrda-export/catIII-r2-1/qrda3_r21.rb'
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20
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+
require_relative 'qrda-import/entry_package.rb'
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require_relative 'qrda-import/cda_identifier.rb'
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require_relative 'qrda-import/narrative_reference_handler.rb'
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require_relative 'qrda-import/entry_finder.rb'
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@@ -66,9 +67,10 @@ require_relative 'qrda-import/data-element-importers/procedure_order_importer.rb
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require_relative 'qrda-import/data-element-importers/procedure_performed_importer.rb'
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require_relative 'qrda-import/data-element-importers/procedure_recommended_importer.rb'
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require_relative 'qrda-import/data-element-importers/provider_care_experience_importer.rb'
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-
require_relative 'qrda-import/data-element-importers/provider_characteristic_importer.rb'
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70
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require_relative 'qrda-import/data-element-importers/substance_administered_importer.rb'
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require_relative 'qrda-import/data-element-importers/substance_order_importer.rb'
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require_relative 'qrda-import/data-element-importers/substance_recommended_importer.rb'
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require_relative 'qrda-import/data-element-importers/symptom_importer.rb'
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-
require_relative 'qrda-import/patient_importer.rb'
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+
require_relative 'qrda-import/patient_importer.rb'
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+
require_relative 'ext/data_element.rb'
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76
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+
require_relative 'ext/code.rb'
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data/lib/ext/code.rb
ADDED
@@ -0,0 +1,24 @@
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1
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+
module QDM
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2
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class DataElement
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def merge!(other)
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# ensure they're the same category (e.g. 'encounter')
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return unless qdmCategory == other.qdmCategory
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# ensure they're the same status (e.g. 'performed'), and that they both have a status set (or that they both don't)
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return if respond_to?(:qdmStatus) && !other.respond_to?(:qdmStatus)
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return if !respond_to?(:qdmStatus) && other.respond_to?(:qdmStatus)
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return if respond_to?(:qdmStatus) && other.respond_to?(:qdmStatus) && qdmStatus != other.qdmStatus
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11
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+
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# iterate over non-code fields
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fields.each_key do |field|
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14
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next if field[0] == '_' || %w[dataElementCodes qdmCategory qdmVersion qdmStatus].include?(field)
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if send(field).nil?
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send(field + '=', other.send(field))
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end
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end
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self.dataElementCodes = dataElementCodes.concat(other.dataElementCodes).uniq
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end
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end
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end
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@@ -17,7 +17,7 @@ class QdmPatient < Mustache
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def data_elements
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de_hash = {}
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@qdmPatient.dataElements.each do |data_element|
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-
de_hash[data_element._type] ? de_hash[data_element._type]
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de_hash[data_element._type] ? de_hash[data_element._type][:element_list] << data_element : de_hash[data_element._type] = { title: data_element._type, element_list: [data_element] }
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end
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JSON.parse(de_hash.values.to_json)
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end
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@@ -27,11 +27,11 @@ class QdmPatient < Mustache
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end
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def code_code_system_string
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"#{self['code']} (#{HQMF::Util::CodeSystemHelper.code_system_for(self['
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"#{self['code']} (#{HQMF::Util::CodeSystemHelper.code_system_for(self['system'])})"
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31
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end
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def code_system_name
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34
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-
HQMF::Util::CodeSystemHelper.code_system_for(self['
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HQMF::Util::CodeSystemHelper.code_system_for(self['system'])
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35
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end
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def result_string
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@@ -6,9 +6,9 @@
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<!-- QRDA templateId -->
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<templateId root="2.16.840.1.113883.10.20.24.1.1" extension="2017-08-01"/>
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<!-- QDM-based QRDA templateId -->
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-
<templateId root="2.16.840.1.113883.10.20.24.1.2" extension="
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+
<templateId root="2.16.840.1.113883.10.20.24.1.2" extension="2017-08-01"/>
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<!-- CMS QRDA templateId -->
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-
<templateId root="2.16.840.1.113883.10.20.24.1.3" extension="
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+
<templateId root="2.16.840.1.113883.10.20.24.1.3" extension="2018-02-01"/>
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<!-- This is the globally unique identifier for this QRDA document -->
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<id root="{{random_id}}"/>
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<!-- QRDA document type code -->
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@@ -12,8 +12,8 @@
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<!-- This is the templateId for Patient Data section -->
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<templateId root="2.16.840.1.113883.10.20.17.2.4"/>
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<!-- This is the templateId for Patient Data QDM section -->
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-
<templateId extension="
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-
<templateId extension="
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+
<templateId extension="2017-08-01" root="2.16.840.1.113883.10.20.24.2.1"/>
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<templateId extension="2018-02-01" root="2.16.840.1.113883.10.20.24.2.1.1"/>
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<code code="55188-7" codeSystem="2.16.840.1.113883.6.1"/>
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<title>Patient Data</title>
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<text/>
|
@@ -178,10 +178,6 @@
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{{> qrda_templates/provider_care_experience}}
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{{/provider_care_experience}}
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180
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{{#provider_characteristic}}
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{{> qrda_templates/provider_characteristic}}
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{{/provider_characteristic}}
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-
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{{#substance_administered}}
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{{> qrda_templates/medication_administered}}
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{{/substance_administered}}
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@@ -13,33 +13,11 @@ class Qrda1R5 < Mustache
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@qdmPatient = patient.qdmPatient
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@measures = measures
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@provider = options[:provider]
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-
@patient_address_option = options[:patient_addresses]
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@patient_telecom_option = options[:patient_telecoms]
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@performance_period_start = options[:start_time]
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@performance_period_end = options[:end_time]
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@submission_program = options[:submission_program]
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end
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-
def patient_addresses
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@patient_address_option ||= [CQM::Address.new(
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use: 'HP',
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street: ['202 Burlington Rd.'],
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city: 'Bedford',
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state: 'MA',
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zip: '01730',
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country: 'US'
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)]
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JSON.parse(@patient_address_option.to_json)
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-
end
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-
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def patient_telecoms
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@patient_telecom_option ||= [CQM::Telecom.new(
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use: 'HP',
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value: '555-555-2003'
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-
)]
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JSON.parse(@patient_telecom_option.to_json)
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-
end
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-
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21
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def patient_characteristic_payer
|
44
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JSON.parse(@qdmPatient.get_data_elements('patient_characteristic', 'payer').to_json)
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end
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@@ -195,7 +173,7 @@ class Qrda1R5 < Mustache
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195
173
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def physical_exam_order
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174
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JSON.parse(@qdmPatient.get_data_elements('physical_exam', 'order').to_json)
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197
175
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end
|
198
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-
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176
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+
|
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177
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def physical_exam_performed
|
200
178
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JSON.parse(@qdmPatient.get_data_elements('physical_exam', 'performed').to_json)
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179
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end
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@@ -220,10 +198,6 @@ class Qrda1R5 < Mustache
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220
198
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JSON.parse(@qdmPatient.dataElements.where(hqmfOid: { '$in' => HQMF::Util::HQMFTemplateHelper.get_all_hqmf_oids('provider_care_experience', '') }).to_json)
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199
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end
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200
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-
def provider_characteristic
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JSON.parse(@qdmPatient.get_data_elements('provider_characteristic', nil).to_json)
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-
end
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226
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-
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201
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def substance_administered
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JSON.parse(@qdmPatient.get_data_elements('substance', 'administered').to_json)
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end
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@@ -235,7 +209,7 @@ class Qrda1R5 < Mustache
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def substance_recommended
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JSON.parse(@qdmPatient.get_data_elements('substance', 'recommended').to_json)
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end
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-
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+
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def symptom
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240
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JSON.parse(@qdmPatient.get_data_elements('symptom', nil).to_json)
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end
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@@ -1,20 +1,14 @@
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<recordTarget>
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<patientRole>
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<id extension="{{mrn}}" root="1.3.6.1.4.1.115" />
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-
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<
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-
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-
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<country>{{country}}</country>
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-
</addr>
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-
{{/patient_addresses}}
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-
{{#patient_telecoms}}
|
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-
<telecom use="{{use}}" value="tel:{{value}}"/>
|
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-
{{/patient_telecoms}}
|
4
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+
<addr use="HP">
|
5
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+
<streetAddressLine>202 Burlington Rd.</streetAddressLine>
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+
<city>Bedford</city>
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7
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+
<state>MA</state>
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8
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+
<postalCode>01730</postalCode>
|
9
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+
<country>US</country>
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+
</addr>
|
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+
<telecom use="WP" value="tel:+1-781-271-3000"/>
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12
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<patient>
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{{#patient}}
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14
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<name>
|
@@ -27,9 +21,6 @@
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27
21
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<administrativeGenderCode {{> _code}}/>
|
28
22
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{{/dataElementCodes}}
|
29
23
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{{/patient_characteristic_sex}}
|
30
|
-
{{^patient_characteristic_sex}}
|
31
|
-
<administrativeGenderCode nullFlavor="UNK"/>
|
32
|
-
{{/patient_characteristic_sex}}
|
33
24
|
{{#patient_characteristic_birthdate}}
|
34
25
|
{{{birth_date_time}}}
|
35
26
|
{{/patient_characteristic_birthdate}}
|
@@ -38,20 +29,16 @@
|
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38
29
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<raceCode {{> _code}}/>
|
39
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{{/dataElementCodes}}
|
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{{/patient_characteristic_race}}
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41
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-
{{^patient_characteristic_race}}
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-
<raceCode nullFlavor="UNK"/>
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43
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-
{{/patient_characteristic_race}}
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32
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{{#patient_characteristic_ethnicity}}
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{{#dataElementCodes}}
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34
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<ethnicGroupCode {{> _code}}/>
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35
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{{/dataElementCodes}}
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36
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{{/patient_characteristic_ethnicity}}
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49
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-
{{^patient_characteristic_ethnicity}}
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-
<ethnicGroupCode nullFlavor="UNK"/>
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{{/patient_characteristic_ethnicity}}
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<languageCommunication>
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38
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+
<templateId root="2.16.840.1.113883.3.88.11.83.2" assigningAuthorityName="HITSP/C83"/>
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39
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+
<templateId root="1.3.6.1.4.1.19376.1.5.3.1.2.1" assigningAuthorityName="IHE/PCC"/>
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53
40
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<languageCode code="eng"/>
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41
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</languageCommunication>
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42
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</patient>
|
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43
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</patientRole>
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-
</recordTarget>
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44
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+
</recordTarget>
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@@ -5,10 +5,10 @@
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5
5
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<id root="1.3.6.1.4.1.115" extension="{{object_id}}"/>
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6
6
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<code code="ASSERTION" codeSystem="2.16.840.1.113883.5.4"/>
|
7
7
|
<statusCode code="completed"/>
|
8
|
-
{{#
|
9
|
-
<!-- QDM Attribute: Relevant
|
10
|
-
{{{
|
11
|
-
{{/
|
8
|
+
{{#relevantDatetime}}
|
9
|
+
<!-- QDM Attribute: Relevant dateTime -->
|
10
|
+
{{{relevant_date_time}}}
|
11
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+
{{/relevantDatetime}}
|
12
12
|
<value xsi:type="CD" code="281647001" displayName="Adverse reaction" codeSystem="2.16.840.1.113883.6.96" codeSystemName="SNOMED CT"/>
|
13
13
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{{#authorDatetime}}
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14
14
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<!-- QDM Attribute: Author dateTime -->
|
@@ -6,8 +6,13 @@
|
|
6
6
|
<templateId root="2.16.840.1.113883.10.20.24.3.147" extension="2017-08-01"/>
|
7
7
|
<id root="1.3.6.1.4.1.115" extension="{{object_id}}"/>
|
8
8
|
<code code="ASSERTION" codeSystem="2.16.840.1.113883.5.4"/>
|
9
|
-
<statusCode code="completed" />
|
10
9
|
{{#prevalencePeriod}}
|
10
|
+
{{#completed_prevalence_period}}
|
11
|
+
<statusCode code="completed" />
|
12
|
+
{{/completed_prevalence_period}}
|
13
|
+
{{^completed_prevalence_period}}
|
14
|
+
<statusCode code="active" />
|
15
|
+
{{/completed_prevalence_period}}
|
11
16
|
<!-- QDM Attribute: Prevalence Period -->
|
12
17
|
{{{prevalence_period}}}
|
13
18
|
{{/prevalencePeriod}}
|
@@ -8,7 +8,7 @@
|
|
8
8
|
{{/category}}
|
9
9
|
{{^category}}
|
10
10
|
<!-- QDM Attribute: Category -->
|
11
|
-
<code nullFlavor="
|
11
|
+
<code nullFlavor="UNK"/>
|
12
12
|
{{/category}}
|
13
13
|
<statusCode code="completed"/>
|
14
14
|
{{#relevantPeriod}}
|
@@ -48,7 +48,7 @@
|
|
48
48
|
{{/negationRationale}}
|
49
49
|
<entryRelationship typeCode="REFR">
|
50
50
|
<observation classCode="OBS" moodCode="EVN">
|
51
|
-
<templateId root="2.16.840.1.113883.10.20.24.3.88" extension="
|
51
|
+
<templateId root="2.16.840.1.113883.10.20.24.3.88" extension="2014-12-01"/>
|
52
52
|
<id root="1.3.6.1.4.1.115" extension="{{object_id}}" />
|
53
53
|
<code code="77301-0" codeSystem="2.16.840.1.113883.6.1" displayName="reason" codeSystemName="LOINC"/>
|
54
54
|
<statusCode code="completed"/>
|
@@ -25,8 +25,13 @@
|
|
25
25
|
<code code="29308-4" codeSystem="2.16.840.1.113883.6.1">
|
26
26
|
<translation code="282291009" codeSystem="2.16.840.1.113883.6.96"/>
|
27
27
|
</code>
|
28
|
-
<statusCode code="completed" />
|
29
28
|
{{#prevalencePeriod}}
|
29
|
+
{{#completed_prevalence_period}}
|
30
|
+
<statusCode code="completed" />
|
31
|
+
{{/completed_prevalence_period}}
|
32
|
+
{{^completed_prevalence_period}}
|
33
|
+
<statusCode code="active" />
|
34
|
+
{{/completed_prevalence_period}}
|
30
35
|
<!-- QDM Attribute: Prevalence Period -->
|
31
36
|
{{{prevalence_period}}}
|
32
37
|
{{/prevalencePeriod}}
|
@@ -34,10 +34,6 @@
|
|
34
34
|
<!-- QDM Attribute: Admission Source -->
|
35
35
|
{{> qrda_templates/template_partials/_admission_source}}
|
36
36
|
{{/admissionSource}}
|
37
|
-
{{#principalDiagnosis}}
|
38
|
-
<!-- QDM Attribute: Principal Diagnosis -->
|
39
|
-
{{> qrda_templates/template_partials/_principal_diagnosis}}
|
40
|
-
{{/principalDiagnosis}}
|
41
37
|
{{#diagnoses}}
|
42
38
|
<!-- QDM Attribute: Diagnoses -->
|
43
39
|
{{> qrda_templates/template_partials/_encounter_diagnosis}}
|
@@ -1,12 +1,7 @@
|
|
1
1
|
<entry>
|
2
|
-
|
3
|
-
<substanceAdministration classCode="SBADM" moodCode="EVN" {{{negation_ind}}}>
|
4
|
-
{{/negated}}
|
5
|
-
{{^negated}}
|
6
|
-
<substanceAdministration classCode="SBADM" moodCode="EVN" negationInd="false">
|
7
|
-
{{/negated}}
|
2
|
+
<substanceAdministration classCode="SBADM" moodCode="EVN" {{{negation_ind}}}>
|
8
3
|
<!-- C-CDA R2 Immunization Activity -->
|
9
|
-
<templateId root="2.16.840.1.113883.10.20.22.4.52" extension="
|
4
|
+
<templateId root="2.16.840.1.113883.10.20.22.4.52" extension="2014-06-09"/>
|
10
5
|
<!-- Immunization Administered -->
|
11
6
|
<templateId root="2.16.840.1.113883.10.20.24.3.140" extension="2017-08-01"/>
|
12
7
|
<id root="1.3.6.1.4.1.115" extension="{{object_id}}"/>
|
@@ -9,6 +9,8 @@
|
|
9
9
|
<substanceAdministration moodCode="EVN" classCode="SBADM">
|
10
10
|
<!-- Medication Activity (consolidation) template -->
|
11
11
|
<templateId root="2.16.840.1.113883.10.20.22.4.16" extension="2014-06-09"/>
|
12
|
+
<!-- Medication, Active template -->
|
13
|
+
<templateId root="2.16.840.1.113883.10.20.24.3.41" extension="2016-02-01"/>
|
12
14
|
<id root="1.3.6.1.4.1.115" extension="{{object_id}}"/>
|
13
15
|
<text>{{description}}</text>
|
14
16
|
<statusCode code="active"/>
|
@@ -8,10 +8,6 @@
|
|
8
8
|
{{> _codes}}
|
9
9
|
<text>{{description}}</text>
|
10
10
|
<statusCode code="active"/>
|
11
|
-
{{#ordinality}}
|
12
|
-
<!-- QDM Attribute: Ordinality -->
|
13
|
-
{{> qrda_templates/template_partials/_ordinality}}
|
14
|
-
{{/ordinality}}
|
15
11
|
{{#anatomicalLocationSite}}
|
16
12
|
<!-- QDM Attribute: Anatomical Location Site -->
|
17
13
|
{{> qrda_templates/template_partials/_anatomical_location_site}}
|
@@ -12,10 +12,6 @@
|
|
12
12
|
<!-- QDM Attribute: Relevant Period -->
|
13
13
|
{{{relevant_period}}}
|
14
14
|
{{/relevantPeriod}}
|
15
|
-
{{#ordinality}}
|
16
|
-
<!-- QDM Attribute: Ordinality -->
|
17
|
-
{{> qrda_templates/template_partials/_ordinality}}
|
18
|
-
{{/ordinality}}
|
19
15
|
{{#method}}
|
20
16
|
<!-- QDM Attribute: Method -->
|
21
17
|
{{> qrda_templates/template_partials/_method}}
|
@@ -9,10 +9,6 @@
|
|
9
9
|
{{> _codes}}
|
10
10
|
<text>{{description}}</text>
|
11
11
|
<statusCode code="active"/>
|
12
|
-
{{#ordinality}}
|
13
|
-
<!-- QDM Attribute: Ordinality -->
|
14
|
-
{{> qrda_templates/template_partials/_ordinality}}
|
15
|
-
{{/ordinality}}
|
16
12
|
{{#anatomicalLocationSite}}
|
17
13
|
<!-- QDM Attribute: Anatomical Location Site -->
|
18
14
|
{{> qrda_templates/template_partials/_anatomical_location_site}}
|