cqm-converter 0.3.0

data/lib/cqm/converter/utils.rb

@@ -0,0 +1,202 @@
+# CQM Converter module for HDS models.
+module CQM::Converter
+  # CQM Converter class utilities.
+  class Utils
+    # Convert QDM codes structure to HDS codes structure.
+    def self.qdm_codes_to_hds_codes(qdm_codes)
+      codes = {}
+      qdm_codes.each do |qdm_code|
+        qdm_code = qdm_code.stringify_keys
+        code_system = qdm_code['codeSystem']
+        code_system = qdm_code['code_system'] if qdm_code['code_system']
+        codes[code_system] = [] unless codes.key? code_system
+        codes[code_system] << qdm_code['code'] if qdm_code['code']
+      end
+      codes
+    end
+
+    # Convert HDS codes structure to QDM codes structure.
+    def self.hds_codes_to_qdm_codes(hds_codes)
+      qdm_codes = []
+      hds_codes.each do |code_system, codes|
+        codes.each do |code|
+          qdm_codes << { codeSystem: code_system, code: code }
+        end
+      end
+      qdm_codes
+    end
+
+    # This helper method looks at the current state of cqm-models, and builds a hash of
+    # datatype models and their attributes.
+    def self.gather_qdm_model_attrs
+      qdm_model_attrs = {}
+      QDM.constants.each do |model|
+        if QDM.const_get(model).respond_to?('fields')
+          qdm_model_attrs[model.to_s] = QDM.const_get(model).fields.keys.map! { |a| a.camelize(:lower) }
+        end
+      end
+      # TODO: These fields are currently not supported. See:
+      # https://github.com/projecttacoma/cql_qdm_patientapi/search?q=does+not+currently+support
+      qdm_model_attrs['SubstanceAdministered'].delete('frequency')
+      qdm_model_attrs['SubstanceOrder'].delete('refills')
+      qdm_model_attrs['PatientCharacteristicExpired'].delete('cause')
+      qdm_model_attrs['MedicationDispensed'].delete('refills')
+      qdm_model_attrs['MedicationDispensed'].delete('frequency')
+      qdm_model_attrs['MedicationOrder'].delete('refills')
+      qdm_model_attrs['MedicationOrder'].delete('frequency')
+      qdm_model_attrs['MedicationActive'].delete('frequency')
+      qdm_model_attrs['MedicationAdministered'].delete('frequency')
+      qdm_model_attrs['MedicationDischarge'].delete('refills')
+      qdm_model_attrs['MedicationDischarge'].delete('frequency')
+      qdm_model_attrs
+    end
+
+    # Parse the cql_qdm_patientapi datatypes to infer how to construct corresponding
+    # HDS entries.
+    def self.gather_qdm_to_hds_mappings(qdm_model_attrs = nil)
+      qdm_model_attrs = gather_qdm_model_attrs if qdm_model_attrs.nil?
+      cql_qdm_patientapi_spec = Gem::Specification.find_by_name('cql_qdm_patientapi')
+      datatypes = Dir.glob(cql_qdm_patientapi_spec.gem_dir + '/app/assets/javascripts/datatypes/*.coffee')
+      # Read in all datatypes
+      datatypes_contents = ''
+      datatypes.each do |datatype|
+        datatypes_contents += File.read(datatype) + "\n"
+      end
+      datatypes_contents += 'class'
+      # Construct the mappings
+      qdm_to_hds_mappings = {}
+      qdm_model_attrs.each do |datatype, attributes|
+        datatype_pattern = /#{datatype} extends CQL_QDM.QDMDatatype.*?class/m
+        next unless (dc_class = datatype_pattern.match(datatypes_contents))
+        qdm_to_hds_mappings[datatype] = {}
+        attributes.each do |attribute|
+          attribute_pattern = /@_#{attribute}(Low|High| ).*?@entry.*?$/
+          dc_class.to_s.to_enum(:scan, attribute_pattern).map do
+            dc_attr = Regexp.last_match
+            # Handle possible mixed values.
+            if dc_attr.to_s.include? 'Low'
+              qdm_to_hds_mappings[datatype][attribute] = {} unless qdm_to_hds_mappings[datatype][attribute]
+              qdm_to_hds_mappings[datatype][attribute][:low] = dc_attr.to_s[/@entry.(.*?)(\)|$|\?)/m, 1]
+            elsif dc_attr.to_s.include? 'High'
+              qdm_to_hds_mappings[datatype][attribute] = {} unless qdm_to_hds_mappings[datatype][attribute]
+              qdm_to_hds_mappings[datatype][attribute][:high] = dc_attr.to_s[/@entry.(.*?)(\)|$|\?)/m, 1]
+            else
+              qdm_to_hds_mappings[datatype][attribute] = dc_attr.to_s[/@entry.(.*?)(\)|$|\?)/m, 1]
+            end
+          end
+        end
+      end
+      qdm_to_hds_mappings
+    end
+
+    # Builds JavaScript to assist the HDS Record to QDM Patient conversion.
+    def self.hds_to_qdm_js(js_dependencies, record, qdm_model_attrs)
+      record_json = JSON.parse(record.to_json)
+      # Bonnie changes start_date and end_date in the front end before calculation,
+      # and this is what is expected by the cql_qdm_patientapi, so make that change
+      # before generating the executable JavaScript.
+      record_json = record_json.deep_transform_keys { |key| key.to_s == 'start_date' ? 'start_time' : key }
+      record_json = record_json.deep_transform_keys { |key| key.to_s == 'end_date' ? 'end_time' : key }
+      <<-JS
+        window = {};
+        #{js_dependencies};
+        function PatientWrapper() {
+        }
+        PatientWrapper.prototype.get = function(attr) {
+          const contents = #{record_json.to_json};
+          return contents[attr];
+        }
+        cql = window.cql;
+        patient = new CQL_QDM.CQLPatient(new PatientWrapper());
+        raw_datatypes = patient.buildDatatypes();
+        qdm_model_attrs = #{qdm_model_attrs.to_json};
+        processed_datatypes = {};
+        // Loop over each QDM datatype.
+        Object.keys(raw_datatypes).forEach(function(key) {
+          processed_datatypes[key] = [];
+          // Collect the values of the QDM attributes.
+          raw_datatypes[key].forEach(function(datatype) {
+            results = {};
+            qdm_model_attrs[datatype.constructor.name].forEach(function(method) {
+              // Call the datatype attribute method to get its value.
+              if (datatype[method]) {
+                result = datatype[method]();
+                // Handle CQL execution engine type results.
+                if (result && result['toJSON']) {
+                  results[method] = result.toJSON();
+                } else {
+                  results[method] = result;
+                }
+              }
+            });
+            // Add codes to result.
+            results['dataElementCodes'] = datatype['getCode']();
+            // Add description to result.
+            results['description'] = datatype['entry']['description'];
+            // Add oid to result.
+            results['hqmfOid'] = datatype['entry']['oid'];
+            processed_datatypes[key].push(results);
+          });
+        });
+        return processed_datatypes;
+      JS
+    end
+
+    # Adjust improper date times from the cql_qdm_patientapi.
+    def self.date_time_adjuster(results)
+      if results.is_a?(Hash) && results.key?('year') && results.key?('minute')
+        DateTime.new(results['year'], results['month'], results['day'], results['hour'], results['minute'], results['second'], results['millisecond']).to_s
+      elsif results.is_a?(Hash)
+        results.each do |key, value|
+          results[key] = date_time_adjuster(value)
+        end
+      elsif results.is_a?(Array)
+        results.map! { |result| date_time_adjuster(result) }
+      else
+        results
+      end
+    end
+
+    # Remove any 'infinity' dates. The cql_qdm_patientapi adds an end time
+    # of 'infinity' if an event does not have an end time. Remove this when
+    # converting back to HDS from QDM.
+    def self.fix_infinity_dates(results)
+      if results.is_a?(Hash) && results.key?('end_time')
+        results.delete('end_time') if results['end_time'].to_s == '253402300799'
+      elsif results.is_a?(Hash)
+        results.each do |key, value|
+          results[key] = fix_infinity_dates(value)
+        end
+      elsif results.is_a?(Array)
+        results.map! { |result| fix_infinity_dates(result) }
+      else
+        results
+      end
+    end
+
+    # Helper method to handle mismatched HDS Class names for QDM things.
+    def self.qdm_to_hds_class_type(category)
+      if category.to_s.include? 'diagnostic'
+        'procedure'
+      elsif category.to_s.include? 'physical_exam'
+        'procedure'
+      elsif category.to_s.include? 'intervention'
+        'procedure'
+      elsif category.to_s.include? 'device'
+        'medical_equipment'
+      elsif category.to_s.include? 'laboratory'
+        'vital_sign'
+      elsif category.to_s.include? 'substance'
+        'medication'
+      elsif category.to_s.include? 'immunization'
+        'medication'
+      else
+        category
+      end
+    end
+
+    def self.code_system_helper(code_system)
+      HealthDataStandards::Util::CodeSystemHelper::CODE_SYSTEMS.key(code_system)
+    end
+  end
+end

data/lib/tasks/hds.rake

@@ -0,0 +1,16 @@
+namespace :cqm do
+  namespace :hds do
+    desc %(Convert an HDS Record, represented as a JSON file, into a QDM
+    Patient, represented as JSON.
+
+    You must specify an input HDS Record JSON file. The result will be
+    output to STDOUT.
+
+    $ rake cqm:hds:to_qdm RECORD=spec/fixtures/hds/records/ep/1.json)
+    task :to_qdm do
+      converter = CQM::Converter::HDSRecord.new
+      record = Record.new.from_json(File.read(ENV['RECORD']))
+      puts JSON.pretty_generate(JSON.parse(converter.to_qdm(record).to_json(except: '_id')))
+    end
+  end
+end

data/lib/tasks/qdm.rake

@@ -0,0 +1,16 @@
+namespace :cqm do
+  namespace :qdm do
+    desc %(Convert a QDM Patient, represented as a JSON file, into an HDS
+    Record, represented as JSON.
+
+    You must specify an input QDM Patient JSON file. The result will be
+    output to STDOUT.
+
+    $ rake cqm:qdm:to_hds RECORD=spec/fixtures/qdm/patients/ep/1.json)
+    task :to_hds do
+      converter = CQM::Converter::QDMPatient.new
+      patient = QDM::Patient.new.from_json(File.read(ENV['RECORD']))
+      puts JSON.pretty_generate(JSON.parse(converter.to_hds(patient).to_json(except: '_id', methods: :_type)))
+    end
+  end
+end

metadata

@@ -0,0 +1,230 @@
+--- !ruby/object:Gem::Specification
+name: cqm-converter
+version: !ruby/object:Gem::Version
+  version: 0.3.0
+platform: ruby
+authors:
+- aholmes@mitre.org
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2018-04-24 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: activesupport
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: byebug
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: coffee-script
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: cqm-models
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.7.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.7.2
+- !ruby/object:Gem::Dependency
+  name: execjs
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: health-data-standards
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 4.0.3
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 4.0.3
+- !ruby/object:Gem::Dependency
+  name: momentjs-rails
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rubocop
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: sprockets
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description: 
+email:
+- aholmes@mitre.org
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".github/PULL_REQUEST_TEMPLATE.md"
+- ".gitignore"
+- ".rspec"
+- ".rubocop.yml"
+- ".travis.yml"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- cqm-converter.gemspec
+- lib/cqm/converter.rb
+- lib/cqm/converter/hds_record.rb
+- lib/cqm/converter/qdm_patient.rb
+- lib/cqm/converter/utils.rb
+- lib/tasks/hds.rake
+- lib/tasks/qdm.rake
+homepage: https://github.com/projecttacoma/cqm-converter
+licenses:
+- Apache-2.0
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.5.2
+signing_key: 
+specification_version: 4
+summary: HDS <=> QDM Model Converter
+test_files: []