cqm-parsers 0.1.0 → 0.1.1

data/lib/qrda-export/catI-r5/qrda_templates/template_partials/_admission_source.mustache

@@ -0,0 +1,6 @@
+<participant typeCode="LOC">
+  <participantRole classCode="SDLOC">
+    <templateId root="2.16.840.1.113883.10.20.24.3.151" extension="2017-08-01"/>
+    <code {{> _code}}/>
+  </participantRole>
+</participant>

data/lib/qrda-export/catI-r5/qrda_templates/template_partials/_anatomical_location_site.mustache

@@ -0,0 +1 @@
+<targetSiteCode {{> _code}}/>

data/lib/qrda-export/catI-r5/qrda_templates/template_partials/_author.mustache

@@ -0,0 +1,7 @@
+<author>
+  <templateId root="2.16.840.1.113883.10.20.24.3.155" extension="2017-08-01"/>
+  {{{author_time}}}
+  <assignedAuthor>
+      <id nullFlavor="NA"/>
+  </assignedAuthor>
+</author>

data/lib/qrda-export/catI-r5/qrda_templates/template_partials/_author_participation.mustache

@@ -0,0 +1,7 @@
+<author>
+  <templateId root="2.16.840.1.113883.10.20.22.4.119"/>
+  {{{author_time}}}
+  <assignedAuthor>
+      <id nullFlavor="NA"/>
+  </assignedAuthor>
+</author>

data/lib/qrda-export/catI-r5/qrda_templates/template_partials/_component.mustache

@@ -0,0 +1,11 @@
+<entryRelationship typeCode="REFR">
+     <observation classCode="OBS" moodCode="EVN">
+        <!-- Component -->
+        <templateId root="2.16.840.1.113883.10.20.24.3.149" extension="2017-08-01" />
+        <id root="{{random_id}}"/>
+        {{#code}}
+        <code {{> _code}}/>
+        {{/code}}
+        {{{result_value}}}
+    </observation>
+</entryRelationship>

data/lib/qrda-export/catI-r5/qrda_templates/template_partials/_encounter_diagnosis.mustache

@@ -0,0 +1,19 @@
+<entryRelationship typeCode="REFR">
+  <act classCode="ACT" moodCode="EVN">
+    <templateId extension="2015-08-01" root="2.16.840.1.113883.10.20.22.4.80"/>
+    <code code="29308-4" codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC" displayName="Diagnosis"/>
+    <entryRelationship typeCode="SUBJ">
+      <observation classCode="OBS" moodCode="EVN">
+        <!--  Problem observation template -->
+        <templateId extension="2015-08-01" root="2.16.840.1.113883.10.20.22.4.4"/>
+        <id root="{{random_id}}"/>
+        <code code="29308-4" codeSystem="2.16.840.1.113883.6.1">
+          <translation code="282291009" codeSystem="2.16.840.1.113883.6.96"/>
+        </code>
+        <statusCode code="completed"/>
+        {{{relevant_period}}}
+        <value {{> _code}} xsi:type="CD"/>
+      </observation>
+    </entryRelationship>
+  </act>
+</entryRelationship>

data/lib/qrda-export/catI-r5/qrda_templates/template_partials/_encounter_facility_location.mustache

@@ -0,0 +1,16 @@
+<participant typeCode="LOC">
+  <!-- Facility Location template -->
+  <templateId extension="2017-08-01" root="2.16.840.1.113883.10.20.24.3.100"/>
+  <time>
+    {{{facility_period}}}
+  </time>
+  <participantRole classCode="SDLOC">
+    {{#code}}
+    <code {{> _code}}/>
+    {{/code}}
+    <telecom nullFlavor="UNK"/>
+    <playingEntity classCode="PLC">
+      <name/>
+    </playingEntity>
+  </participantRole>
+</participant>

data/lib/qrda-export/catI-r5/qrda_templates/template_partials/_mediation_frequency.mustache

@@ -0,0 +1,3 @@
+<effectiveTime xsi:type="PIVL_TS" institutionSpecified="true" operator="A">
+  <period value="1" unit="d"/>
+</effectiveTime>

data/lib/qrda-export/catI-r5/qrda_templates/template_partials/_medication_details.mustache

@@ -0,0 +1,11 @@
+{{#route}}
+<routeCode {{> _code}}/>
+{{/route}}
+{{#negated}}
+	<doseQuantity nullFlavor="NA"/>
+{{/negated}}
+{{^negated}}
+{{#dosage}}
+	<doseQuantity value="{{value}}" unit="{{unit}}"/>
+{{/dosage}}
+{{/negated}}

data/lib/qrda-export/catI-r5/qrda_templates/template_partials/_ordinality.mustache

@@ -0,0 +1 @@
+<priorityCode {{> _code}}/>

data/lib/qrda-export/catI-r5/qrda_templates/template_partials/_principal_diagnosis.mustache

@@ -0,0 +1,8 @@
+<entryRelationship typeCode="REFR">
+  <observation classCode="OBS" moodCode="EVN">
+      <templateId root="2.16.840.1.113883.10.20.24.3.152" extension="2017-08-01"/>
+      <id root="{{random_id}}"/>
+      <code code="8319008" codeSystem="2.16.840.1.113883.6.96" displayName="Principal Diagnosis" codeSystemName="SNOMED"/>
+      <value {{> _code}} xsi:type="CD"/>
+  </observation>
+</entryRelationship>

data/lib/qrda-export/catI-r5/qrda_templates/template_partials/_reason.mustache

@@ -0,0 +1,12 @@
+<entryRelationship typeCode="RSON">
+  <observation classCode="OBS" moodCode="EVN">
+    <templateId root="2.16.840.1.113883.10.20.24.3.88" extension="2014-12-01"/>
+    <id root="1.3.6.1.4.1.115" extension="{{random_id}}" />
+    <code code="77301-0" codeSystem="2.16.840.1.113883.6.1" displayName="reason" codeSystemName="LOINC"/>
+    <statusCode code="completed"/>
+    {{#relevantPeriod}}
+    {{{relevant_period}}}
+    {{/relevantPeriod}}
+    <value {{> _code}} xsi:type="CD"/>
+  </observation>
+</entryRelationship>

data/lib/qrda-export/catI-r5/qrda_templates/template_partials/_related_to.mustache

@@ -0,0 +1,6 @@
+<sdtc:inFulfillmentOf1 typeCode="FLFS">
+  <sdtc:templateId root="2.16.840.1.113883.10.20.24.3.150" extension="2017-08-01"/>
+  <sdtc:actReference classCode="ACT" moodCode="EVN">
+    <sdtc:id root="1.3.6.1.4.1.115" extension="{{{as_id}}}"/>
+  </sdtc:actReference>
+</sdtc:inFulfillmentOf1>

data/lib/qrda-export/catI-r5/qrda_templates/template_partials/_results.mustache

@@ -0,0 +1,21 @@
+<entryRelationship typeCode="REFR">
+ <observation classCode="OBS" moodCode="EVN">
+    <!-- Conforms to C-CDA R2 Result Observation (V2) -->
+    <templateId root="2.16.840.1.113883.10.20.22.4.2" extension="2015-08-01"/>
+    <!-- Result (QRDA I R3) -->
+    <templateId root="2.16.840.1.113883.10.20.24.3.87" extension="2016-02-01"/>
+    <id root="1.3.6.1.4.1.115" extension="{{random_id}}"/>
+    {{> _codes}}
+    <statusCode code="completed"/>
+    {{#relevantPeriod}}
+    {{{relevant_period}}}
+    {{/relevantPeriod}}
+    {{^relevantPeriod}}
+      {{#authorDatetime}}
+      {{{author_effective_time}}}
+      {{/authorDatetime}}
+    {{/relevantPeriod}}
+    {{{result_value}}}
+ </observation>
+</entryRelationship>
+

data/lib/qrda-export/catI-r5/qrda_templates/template_partials/_severity.mustache

@@ -0,0 +1,8 @@
+<entryRelationship typeCode="REFR">
+  <observation classCode="OBS" moodCode="EVN">
+    <templateId root="2.16.840.1.113883.10.20.22.4.8" extension="2014-06-09" />
+    <code code="SEV" codeSystem="2.16.840.1.113883.5.4" />
+    <statusCode code="completed" />
+    <value xsi:type="CD" {{> _code}}/>
+  </observation>
+</entryRelationship>

data/lib/tasks/hqmf.rake

@@ -0,0 +1,170 @@
+require 'pathname'
+require 'fileutils'
+require 'json'
+require 'hqmf-parser'
+
+namespace :hqmf do
+
+  desc 'Parse all xml files to JSON and save them to ./tmp'
+  task :parse_all, [:path, :version] do |t, args|
+    
+    raise "You must specify the HQMF XML file path to convert" unless args.path
+
+    
+    FileUtils.mkdir_p File.join(".","tmp",'json','all')
+    path = File.expand_path(args.path)
+    version = args.version || HQMF::Parser::HQMF_VERSION_1
+
+    Dir.glob(File.join(path,'**','*.xml')) do |measure_def|
+      puts "####################################"
+      puts "### processing: #{measure_def}..."
+      puts "####################################"
+      if (version == HQMF::Parser::HQMF_VERSION_1)
+        doc = HQMF::Parser::V1Parser.new.parse(File.open(file).read, version)
+      else
+        doc = HQMF::Parser::V2Parser.new.parse(File.open(file).read, version)
+      end
+      filename = Pathname.new(measure_def).basename
+      
+      File.open(File.join(".","tmp",'json','all',"#{filename}.json"), 'w') {|f| f.write(doc.to_json.to_json(max_nesting: 100).gsub(/",/,"\",\n")) }
+      puts "\n"
+    end
+    
+  end
+
+  desc 'Parse specified xml file to JSON and save it to ./tmp'
+  task :parse, [:file,:version] do |t, args|
+    FileUtils.mkdir_p File.join(".","tmp",'json')
+    
+    raise "You must specify the HQMF XML file to convert" unless args.file
+    
+    version = args.version || HQMF::Parser::HQMF_VERSION_1
+    file = File.expand_path(args.file)
+    filename = Pathname.new(file).basename
+    
+    if (version == HQMF::Parser::HQMF_VERSION_1)
+      doc = HQMF::Parser::V1Parser.new.parse(File.open(file).read, version)
+    else
+      doc = HQMF::Parser::V2Parser.new.parse(File.open(file).read, version)
+    end
+    outfile = File.join(".","tmp",'json',"#{filename}.json")
+    File.open(outfile, 'w') {|f| f.write(JSON.pretty_generate(doc.to_json, max_nesting: 100)) }
+    
+    puts "wrote result to: #{outfile}"
+    
+  end
+  
+  desc 'Parse specified xml file to V1 JSON and save it to ./tmp'
+  task :parse_v1, [:file] do |t, args|
+    FileUtils.mkdir_p File.join(".","tmp",'json')
+    
+    raise "You must specify the HQMF XML file to convert" unless args.file
+    
+    file = File.expand_path(args.file)
+    filename = Pathname.new(file).basename
+    
+    doc = HQMF1::Document.new(File.open(file).read).to_json
+    outfile = File.join(".","tmp",'json',"#{filename}_v1.json")
+    File.open(outfile, 'w') {|f| f.write(JSON.pretty_generate(doc.to_json, max_nesting: 100)) }
+    puts "wrote result to: #{outfile}"
+    
+  end
+
+  desc 'Convert V1 JSON to V2 JSON and save it to ./tmp'
+  task :convert, [:file] do |t, args|
+    FileUtils.mkdir_p File.join(".","tmp",'json')
+    
+    raise "You must specify the V1 JSON file to convert" unless args.file
+    
+    file = File.expand_path(args.file)
+    filename = Pathname.new(file).basename
+
+    converted = HQMF::DocumentConverter.convert(JSON.parse(File.open(file).read,:symbolize_names => true))
+    
+    outfile = File.join(".","tmp",'json',"#{filename}_v2.json")
+
+    File.open(outfile, 'w') {|f| f.write(JSON.pretty_generate(converted.to_json, max_nesting: 100)) }
+    puts "wrote result to: #{outfile}"
+    
+  end
+  
+  desc 'Convert specified HQMF V1 xml file to HQMF V2 and save it to ./tmp'
+  task :upgrade, [:file] do |t, args|
+    FileUtils.mkdir_p File.join(".","tmp",'xml')
+    
+    raise "You must specify the HQMF XML file to convert" unless args.file
+    
+    version = HQMF::Parser::HQMF_VERSION_1
+    file = File.expand_path(args.file)
+    filename = Pathname.new(file).basename
+
+    doc = HQMF::Parser::V1Parser.new.parse(File.open(file).read, version)
+    
+    hqmf_xml = HQMF2::Generator::ModelProcessor.to_hqmf(doc)
+    xml = Nokogiri.XML(hqmf_xml) do |config|
+      config.default_xml.noblanks
+    end
+
+    outfile = File.join(".","tmp",'xml',"#{filename}")
+    File.open(outfile, 'w') {|f| f.write(xml.to_xml(:indent => 2)) }
+    
+    puts "wrote result to: #{outfile}"
+    
+  end
+
+  desc 'Convert specified HQMF V1 xml file to HQMF V2 and save it to ./tmp'
+  task :upgrade_all, [:dir] do |t, args|
+    outdir = File.join(".","tmp",'xml','upgrade')
+    FileUtils.mkdir_p outdir
+    
+    raise "You must specify the HQMF XML directory to convert" unless args.dir
+    
+
+    Dir.glob(File.join(args.dir,'**','*.xml')) do |file|
+      version = HQMF::Parser::HQMF_VERSION_1
+      file = File.expand_path(file)
+      filename = "#{Pathname.new(file).basename('.*')}_R2.xml"
+
+      doc = HQMF::Parser::V1Parser.new.parse(File.open(file).read, version)
+      
+      hqmf_xml = HQMF2::Generator::ModelProcessor.to_hqmf(doc)
+      xml = Nokogiri.XML(hqmf_xml) do |config|
+        config.default_xml.noblanks
+      end
+
+      outfile = File.join(outdir,"#{filename}")
+      File.open(outfile, 'w') {|f| f.write(xml.to_xml(:indent => 2)) }
+      
+      puts "wrote result to: #{outfile}"
+    end
+
+    
+  end
+  
+  desc 'Roundtrip specified HQMF V2 xml file through the model and back to HQMF V2 and save it to ./tmp'
+  task :roundtrip, [:file] do |t, args|
+    FileUtils.mkdir_p File.join(".","tmp",'xml')
+    
+    raise "You must specify the HQMF XML file to roundtrip" unless args.file
+    
+    version = HQMF::Parser::HQMF_VERSION_2
+    file = File.expand_path(args.file)
+    filename = Pathname.new(file).basename
+
+    doc = HQMF::Parser::V1Parser.new.parse(File.open(file).read, version)
+    
+    hqmf_xml = HQMF2::Generator::ModelProcessor.to_hqmf(doc)
+    xml = Nokogiri.XML(hqmf_xml) do |config|
+      config.default_xml.noblanks
+    end
+
+    outfile = File.join(".","tmp",'xml',"#{filename}")
+    File.open(outfile, 'w') {|f| f.write(xml.to_xml(:indent => 2)) }
+    
+    puts "wrote result to: #{outfile}"
+    
+  end
+  
+
+  
+end

data/lib/util/hqmf_template_oid_map.json

@@ -0,0 +1,674 @@
+{
+  "2.16.840.1.113883.3.560.1.1001":{
+      "definition":"patient_characteristic",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.3.560.1.25":{
+      "definition":"patient_characteristic_birthdate",
+      "status":"",
+      "negation":false},      
+  "2.16.840.1.113883.3.560.1.400":{
+      "definition":"patient_characteristic_birthdate",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.3.560.1.401":{
+      "definition":"patient_characteristic_clinical_trial_participant",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.3.560.1.402":{
+      "definition":"patient_characteristic_gender",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.3.560.1.403":{
+      "definition":"patient_characteristic_ethnicity",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.3.560.1.404":{
+      "definition":"patient_characteristic_expired",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.3.560.1.405":{
+      "definition":"patient_characteristic_payer",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.3.560.1.406":{
+      "definition":"patient_characteristic_race",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.3.560.1.4":{
+      "definition":"encounter",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.3.560.1.81":{
+      "definition":"encounter",
+      "status":"active",
+      "negation":false},
+  "2.16.840.1.113883.3.560.1.79":{
+      "definition":"encounter",
+      "status":"performed",
+      "negation":false},
+  "2.16.840.1.113883.3.560.1.82":{
+      "definition":"encounter",
+      "status":"performed",
+      "negation":false},
+  "2.16.840.1.113883.3.560.1.83":{
+      "definition":"encounter",
+      "status":"ordered",
+      "negation":false},
+  "2.16.840.1.113883.3.560.1.84":{
+      "definition":"encounter",
+      "status":"recommended",
+      "negation":false},
+  "2.16.840.1.113883.3.560.1.179":{
+      "definition":"encounter",
+      "status":"performed",
+      "negation":true},
+  "2.16.840.1.113883.3.560.1.182":{
+      "definition":"encounter",
+      "status":"performed",
+      "negation":true},
+  "2.16.840.1.113883.3.560.1.181":{
+      "definition":"encounter",
+      "status":"active",
+      "negation":true},
+  "2.16.840.1.113883.3.560.1.183":{
+      "definition":"encounter",
+      "status":"ordered",
+      "negation":true},
+  "2.16.840.1.113883.3.560.1.184":{
+      "definition":"encounter",
+      "status":"recommended",
+      "negation":true},
+  "2.16.840.1.113883.3.560.1.104":{
+      "definition":"encounter",
+      "status":"",
+      "negation":true},
+  "2.16.840.1.113883.3.560.1.6":{
+      "definition":"procedure",
+      "status":"performed",
+      "negation":false},
+  "2.16.840.1.113883.3.560.1.62":{
+      "definition":"procedure",
+      "status":"ordered",
+      "negation":false},
+  "2.16.840.1.113883.3.560.1.63":{
+      "definition":"procedure_result",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.3.560.1.60":{
+      "definition":"procedure_adverse_event",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.3.560.1.61":{
+      "definition":"procedure_intolerance",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.3.560.1.92":{
+      "definition":"procedure",
+      "status":"recommended",
+      "negation":false},
+  "2.16.840.1.113883.3.560.1.162":{
+      "definition":"procedure",
+      "status":"ordered",
+      "negation":true},
+  "2.16.840.1.113883.3.560.1.163":{
+      "definition":"procedure_result",
+      "status":"",
+      "negation":true},
+  "2.16.840.1.113883.3.560.1.160":{
+      "definition":"procedure_adverse_event",
+      "status":"",
+      "negation":true},
+  "2.16.840.1.113883.3.560.1.161":{
+      "definition":"procedure_intolerance",
+      "status":"",
+      "negation":true},
+  "2.16.840.1.113883.3.560.1.106":{
+      "definition":"procedure",
+      "status":"performed",
+      "negation":true},
+  "2.16.840.1.113883.3.560.1.192":{
+      "definition":"procedure",
+      "status":"recommended",
+      "negation":true},
+  "2.16.840.1.113883.3.560.1.2":{
+      "definition":"diagnosis",
+      "status":"active",
+      "negation":false},
+  "2.16.840.1.113883.3.560.1.24":{
+      "definition":"diagnosis",
+      "status":"resolved",
+      "negation":false},
+  "2.16.840.1.113883.3.560.1.32":{
+      "definition":"diagnosis",
+      "status":"family_history",
+      "negation":false},
+  "2.16.840.1.113883.3.560.1.23":{
+      "definition":"diagnosis",
+      "status":"inactive",
+      "negation":false},
+  "2.16.840.1.113883.3.560.1.33":{
+      "definition":"diagnosis_risk_of",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.3.560.1.124":{
+      "definition":"diagnosis",
+      "status":"resolved",
+      "negation":true},
+  "2.16.840.1.113883.3.560.1.132":{
+      "definition":"diagnosis",
+      "status":"family_history",
+      "negation":true},
+  "2.16.840.1.113883.3.560.1.123":{
+      "definition":"diagnosis",
+      "status":"inactive",
+      "negation":true},
+  "2.16.840.1.113883.3.560.1.102":{
+      "definition":"diagnosis",
+      "status":"active",
+      "negation":true},
+  "2.16.840.1.113883.3.560.1.133":{
+      "definition":"diagnosis_risk_of",
+      "status":"",
+      "negation":true},
+  "2.16.840.1.113883.3.560.1.3":{
+      "definition":"diagnostic_study",
+      "status":"performed",
+      "negation":false},
+  "2.16.840.1.113883.3.560.1.11":{
+      "definition":"diagnostic_study_result",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.3.560.1.38":{
+      "definition":"diagnostic_study_adverse_event",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.3.560.1.39":{
+      "definition":"diagnostic_study_intolerance",
+      "status":"",
+      "negation":false},
+  "2.16.840.1.113883.3.560.1.40":{
+      "definition":"diagnostic_study",
+      "status":"ordered",
+      "negation":false},
+  "2.16.840.1.113883.3.560.1.103":{
+      "definition":"diagnostic_study",
+      "status":"performed",
+      "negation":true},
+  "2.16.840.1.113883.3.560.1.138":{
+      "definition":"diagnostic_study_adverse_event",
+      "status":"",
+      "negation":true},
+  "2.16.840.1.113883.3.560.1.139":{
+      "definition":"diagnostic_study_intolerance",
+      "status":"",
+      "negation":true},
+  "2.16.840.1.113883.3.560.1.140":{
+      "definition":"diagnostic_study",
+      "status":"ordered",
+      "negation":true},
+  "2.16.840.1.113883.3.560.1.111":{
+      "definition":"diagnostic_study_result",
+      "status":"",
+      "negation":true},
+  "2.16.840.1.113883.3.560.1.8":{
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