cqm-parsers 0.1.0
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- checksums.yaml +7 -0
- data/Gemfile +29 -0
- data/README.md +21 -0
- data/Rakefile +19 -0
- data/lib/ext/code.rb +10 -0
- data/lib/ext/data_element.rb +24 -0
- data/lib/hqmf-model/attribute.rb +63 -0
- data/lib/hqmf-model/data_criteria.rb +467 -0
- data/lib/hqmf-model/document.rb +253 -0
- data/lib/hqmf-model/population_criteria.rb +102 -0
- data/lib/hqmf-model/precondition.rb +94 -0
- data/lib/hqmf-model/types.rb +457 -0
- data/lib/hqmf-model/utilities.rb +52 -0
- data/lib/hqmf-parser.rb +116 -0
- data/lib/hqmf-parser/1.0/attribute.rb +121 -0
- data/lib/hqmf-parser/1.0/comparison.rb +34 -0
- data/lib/hqmf-parser/1.0/data_criteria.rb +92 -0
- data/lib/hqmf-parser/1.0/document.rb +195 -0
- data/lib/hqmf-parser/1.0/expression.rb +60 -0
- data/lib/hqmf-parser/1.0/observation.rb +61 -0
- data/lib/hqmf-parser/1.0/population_criteria.rb +75 -0
- data/lib/hqmf-parser/1.0/precondition.rb +90 -0
- data/lib/hqmf-parser/1.0/range.rb +76 -0
- data/lib/hqmf-parser/1.0/restriction.rb +162 -0
- data/lib/hqmf-parser/1.0/utilities.rb +55 -0
- data/lib/hqmf-parser/2.0/data_criteria.rb +372 -0
- 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 +304 -0
- data/lib/hqmf-parser/2.0/document_helpers/doc_population_helper.rb +173 -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 +134 -0
- data/lib/hqmf-parser/2.0/precondition.rb +73 -0
- data/lib/hqmf-parser/2.0/source_data_criteria_helper.rb +112 -0
- data/lib/hqmf-parser/2.0/types.rb +448 -0
- data/lib/hqmf-parser/2.0/utilities.rb +45 -0
- data/lib/hqmf-parser/2.0/value_set_helper.rb +104 -0
- data/lib/hqmf-parser/converter/pass1/data_criteria_converter.rb +257 -0
- data/lib/hqmf-parser/converter/pass1/document_converter.rb +133 -0
- data/lib/hqmf-parser/converter/pass1/population_criteria_converter.rb +185 -0
- data/lib/hqmf-parser/converter/pass1/precondition_converter.rb +173 -0
- data/lib/hqmf-parser/converter/pass1/precondition_extractor.rb +201 -0
- data/lib/hqmf-parser/converter/pass1/simple_data_criteria.rb +26 -0
- data/lib/hqmf-parser/converter/pass1/simple_operator.rb +89 -0
- data/lib/hqmf-parser/converter/pass1/simple_population_criteria.rb +10 -0
- data/lib/hqmf-parser/converter/pass1/simple_precondition.rb +51 -0
- data/lib/hqmf-parser/converter/pass1/simple_restriction.rb +64 -0
- data/lib/hqmf-parser/converter/pass2/comparison_converter.rb +112 -0
- data/lib/hqmf-parser/converter/pass2/operator_converter.rb +102 -0
- data/lib/hqmf-parser/cql/data_criteria.rb +57 -0
- data/lib/hqmf-parser/cql/data_criteria_helpers/dc_definition_from_template_or_type_extract.rb +79 -0
- data/lib/hqmf-parser/cql/data_criteria_helpers/dc_post_processing.rb +43 -0
- data/lib/hqmf-parser/cql/document.rb +78 -0
- data/lib/hqmf-parser/cql/document_helpers/doc_population_helper.rb +124 -0
- data/lib/hqmf-parser/cql/value_set_helper.rb +103 -0
- data/lib/hqmf-parser/parser.rb +100 -0
- data/lib/qrda-export/catI-r5/qrda1_r5.rb +125 -0
- data/lib/qrda-export/helper/cat_1_view_helper.rb +142 -0
- data/lib/qrda-export/helper/code_system_helper.rb +77 -0
- data/lib/qrda-export/helper/date_helper.rb +81 -0
- data/lib/qrda-import/base-importers/demographics_importer.rb +47 -0
- data/lib/qrda-import/base-importers/medication_importer.rb +22 -0
- data/lib/qrda-import/base-importers/section_importer.rb +196 -0
- data/lib/qrda-import/cda_identifier.rb +19 -0
- data/lib/qrda-import/data-element-importers/adverse_event_importer.rb +23 -0
- data/lib/qrda-import/data-element-importers/allergy_intolerance_importer.rb +21 -0
- data/lib/qrda-import/data-element-importers/assessment_performed_importer.rb +23 -0
- data/lib/qrda-import/data-element-importers/communication_from_patient_to_provider_importer.rb +18 -0
- data/lib/qrda-import/data-element-importers/communication_from_provider_to_patient_importer.rb +18 -0
- data/lib/qrda-import/data-element-importers/communication_from_provider_to_provider_importer.rb +20 -0
- data/lib/qrda-import/data-element-importers/device_applied_importer.rb +23 -0
- data/lib/qrda-import/data-element-importers/device_order_importer.rb +18 -0
- data/lib/qrda-import/data-element-importers/diagnosis_importer.rb +23 -0
- data/lib/qrda-import/data-element-importers/diagnostic_study_order_importer.rb +20 -0
- data/lib/qrda-import/data-element-importers/diagnostic_study_performed_importer.rb +30 -0
- data/lib/qrda-import/data-element-importers/encounter_order_importer.rb +20 -0
- data/lib/qrda-import/data-element-importers/encounter_performed_importer.rb +41 -0
- data/lib/qrda-import/data-element-importers/immunization_administered_importer.rb +18 -0
- data/lib/qrda-import/data-element-importers/intervention_order_importer.rb +18 -0
- data/lib/qrda-import/data-element-importers/intervention_performed_importer.rb +22 -0
- data/lib/qrda-import/data-element-importers/laboratory_test_order_importer.rb +20 -0
- data/lib/qrda-import/data-element-importers/laboratory_test_performed_importer.rb +28 -0
- data/lib/qrda-import/data-element-importers/medication_active_importer.rb +17 -0
- data/lib/qrda-import/data-element-importers/medication_administered_importer.rb +17 -0
- data/lib/qrda-import/data-element-importers/medication_discharge_importer.rb +19 -0
- data/lib/qrda-import/data-element-importers/medication_dispensed_importer.rb +19 -0
- data/lib/qrda-import/data-element-importers/medication_order_importer.rb +16 -0
- data/lib/qrda-import/data-element-importers/patient_characteristic_expired.rb +21 -0
- data/lib/qrda-import/data-element-importers/physical_exam_performed_importer.rb +26 -0
- data/lib/qrda-import/data-element-importers/procedure_order_importer.rb +26 -0
- data/lib/qrda-import/data-element-importers/procedure_performed_importer.rb +34 -0
- data/lib/qrda-import/data-element-importers/substance_administered_importer.rb +16 -0
- data/lib/qrda-import/entry_finder.rb +20 -0
- data/lib/qrda-import/entry_package.rb +16 -0
- data/lib/qrda-import/narrative_reference_handler.rb +33 -0
- data/lib/qrda-import/patient_importer.rb +105 -0
- data/lib/util/code_system_helper.rb +76 -0
- data/lib/util/counter.rb +20 -0
- data/lib/util/hqmf_template_helper.rb +39 -0
- metadata +340 -0
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module HQMF
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# Used to represent 'any value' in criteria that require a value be present but
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# don't specify any restrictions on that value
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class AnyValue
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include HQMF::Conversion::Utilities
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attr_reader :type
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def initialize(type='ANYNonNull')
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@type = type
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end
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def derived?
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false
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end
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def self.from_json(json)
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type = json["type"] || 'ANYNonNull'
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HQMF::AnyValue.new(type)
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end
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def to_json
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hash = build_hash(self, [:type])
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hash
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end
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end
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# Represents a bound within a HQMF pauseQuantity, has a value, a unit and an
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# inclusive/exclusive indicator
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class Value
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include HQMF::Conversion::Utilities
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attr_reader :unit,:expression
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attr_accessor :type, :value, :inclusive
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# Create a new HQMF::Value
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# @param [String] type
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# @param [String] unit
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# @param [String] value
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# @param [Boolean] inclusive
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# @param [Boolean] derived
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# @param [String] expression
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def initialize(type,unit,value,inclusive,derived,expression)
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@type = type || 'PQ'
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@unit = unit
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@value = value
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@inclusive = inclusive == nil ? true : inclusive
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@derived = derived || false
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@expression = expression
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end
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def self.from_json(json)
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type = json["type"] if json["type"]
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unit = json["unit"] if json["unit"]
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value = json["value"] if json["value"]
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inclusive = json["inclusive?"] unless json["inclusive?"].nil?
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derived = json["derived?"] unless json["derived?"].nil?
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expression = json["expression"] if json["expression"]
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HQMF::Value.new(type,unit,value,inclusive,derived,expression)
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end
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def inclusive?
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@inclusive
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end
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def derived?
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@derived
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end
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def to_json
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build_hash(self, [:type,:unit,:value,:inclusive?,:derived?,:expression])
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end
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def stringify
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"#{inclusive? ? '=' : ''}#{value}#{unit ? ' '+unit : ''}"
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end
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def ==(other)
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check_equality(self,other)
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end
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end
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# Represents a HQMF physical quantity which can have low and high bounds
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class Range
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include HQMF::Conversion::Utilities
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attr_accessor :type, :low, :high, :width
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# Create a new HQMF::Value
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# @param [String] type
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# @param [Value] low
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# @param [Value] high
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# @param [Value] width
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def initialize(type,low,high,width)
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@type = type || 'IVL_PQ'
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@low = low
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@high = high
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@width = width
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end
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def self.from_json(json)
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type = json["type"] if json["type"]
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low = HQMF::Value.from_json(json["low"]) if json["low"]
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high = HQMF::Value.from_json(json["high"]) if json["high"]
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width = HQMF::Value.from_json(json["width"]) if json["width"]
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HQMF::Range.new(type,low,high,width)
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end
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def to_json
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json = build_hash(self, [:type])
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json[:low] = self.low.to_json if self.low
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json[:high] = self.high.to_json if self.high
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json[:width] = self.width.to_json if self.width
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json
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end
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def stringify
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if (@high && @low)
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if (@high.value == @low.value and @high.inclusive? and low.inclusive?)
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"#{@low.stringify}"
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else
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">#{@low.stringify} and <#{@high.stringify}}"
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end
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elsif (@high)
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"<#{@high.stringify}"
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elsif (@low)
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">#{@low.stringify}"
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else
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raise "cannot convert range to string"
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end
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end
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def ==(other)
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check_equality(self,other)
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end
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end
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# Represents a HQMF effective time which is a specialization of a interval
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class EffectiveTime < Range
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def initialize(low,high,width)
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super('IVL_TS', low, high, width)
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end
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def type
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'IVL_TS'
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end
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end
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# Represents a HQMF CD value which has a code and codeSystem
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class Coded
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include HQMF::Conversion::Utilities
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attr_reader :type, :system, :code, :code_list_id, :title, :null_flavor, :original_text
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# Create a new HQMF::Coded
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# @param [String] type
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# @param [String] system
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# @param [String] code
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# @param [String] code_list_id
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def initialize(type,system,code,code_list_id=nil,title=nil,null_flavor=nil,original_text=nil)
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@type = type
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@system = system
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@code = code
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@code_list_id = code_list_id
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@title = title
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@null_flavor = null_flavor
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@original_text = original_text
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end
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def self.for_code_list(code_list_id,title=nil)
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HQMF::Coded.new('CD',nil,nil,code_list_id,title)
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end
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def self.for_single_code(system,code,title=nil)
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HQMF::Coded.new('CD',system,code,nil,title)
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end
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def self.for_null_flavor(null_flavor,original_text=nil)
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HQMF::Coded.new('CD',nil,nil,nil,nil,null_flavor,original_text)
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end
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def self.from_json(json)
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json = json.with_indifferent_access
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type = json["type"] if json["type"]
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system = json["system"] if json["system"]
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code = json["code"] if json["code"]
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code_list_id = json["code_list_id"] if json["code_list_id"]
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title = json["title"] if json["title"]
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null_flavor = json["null_flavor"] if json["null_flavor"]
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original_text = json["original_text"] if json["original_text"]
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HQMF::Coded.new(type,system,code,code_list_id,title, null_flavor, original_text)
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end
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def to_json
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build_hash(self, [:type,:system,:code,:code_list_id,:title,:null_flavor,:original_text])
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end
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def value
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code
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end
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def derived?
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false
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end
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def unit
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nil
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end
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def ==(other)
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check_equality(self,other)
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end
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end
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class TemporalReference
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include HQMF::Conversion::Utilities
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TYPES = ['DURING','OVERLAP','SBS','SAS','SBE','SAE','EBS','EAS','EBE','EAE','SDU','EDU','ECW','SCW','ECWS','SCWE','SBCW','SBCWE','SACW','SACWE','SBDU','EBCW','EBCWS','EACW','EACWS','EADU','CONCURRENT']
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INVERSION = {'SBS' => 'SAS','EAE' => 'EBE','SAS' => 'SBS','EBE' => 'EAE','SBE' => 'EAS','EAS' => 'SBE','SAE' => 'EBS','EBS' => 'SAE'}
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attr_reader :type, :reference, :range
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# @param [String] type
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# @param [Reference] reference
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# @param [Range] range
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def initialize(type, reference, range)
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@type = type
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@reference = reference
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if (range.is_a? HQMF::Value)
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@range = HQMF::Range.new('IVL_PQ', range, range, nil)
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else
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@range = range
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end
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end
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def self.from_json(json)
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type = json["type"] if json["type"]
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reference = HQMF::Reference.new(json["reference"]) if json["reference"]
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range = HQMF::Range.from_json(json["range"]) if json["range"]
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HQMF::TemporalReference.new(type,reference,range)
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end
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def to_json
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json = build_hash(self, [:type])
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json[:reference] = @reference.to_json if @reference
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json[:range] = @range.to_json if @range
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+
json
|
255
|
+
end
|
256
|
+
|
257
|
+
def ==(other)
|
258
|
+
check_equality(self,other)
|
259
|
+
end
|
260
|
+
|
261
|
+
end
|
262
|
+
|
263
|
+
class SubsetOperator
|
264
|
+
include HQMF::Conversion::Utilities
|
265
|
+
|
266
|
+
TYPES = ['COUNT', 'FIRST', 'SECOND', 'THIRD', 'FOURTH', 'FIFTH', 'RECENT', 'LAST', 'MIN', 'MAX', 'DATEDIFF', 'TIMEDIFF', 'DATETIMEDIFF', 'MEDIAN', 'MEAN', 'SUM']
|
267
|
+
|
268
|
+
attr_accessor :type, :value
|
269
|
+
# @param [String] type
|
270
|
+
# @param [Value] value
|
271
|
+
def initialize(type,value)
|
272
|
+
@type = type
|
273
|
+
if (value.is_a? HQMF::Value)
|
274
|
+
value.inclusive = true
|
275
|
+
@value = HQMF::Range.new('IVL_PQ',value,value,nil)
|
276
|
+
else
|
277
|
+
@value = value
|
278
|
+
end
|
279
|
+
end
|
280
|
+
|
281
|
+
def supports_grouper_criteria?
|
282
|
+
['FIRST', 'SECOND', 'THIRD', 'FOURTH', 'FIFTH', 'RECENT', 'LAST'].include? @type
|
283
|
+
end
|
284
|
+
|
285
|
+
def self.from_json(json)
|
286
|
+
type = json["type"] if json["type"]
|
287
|
+
value = HQMF::DataCriteria.convert_value(json["value"]) if json["value"]
|
288
|
+
HQMF::SubsetOperator.new(type,value)
|
289
|
+
end
|
290
|
+
|
291
|
+
|
292
|
+
def to_json
|
293
|
+
json = build_hash(self, [:type])
|
294
|
+
json[:value] = @value.to_json if @value
|
295
|
+
json
|
296
|
+
end
|
297
|
+
|
298
|
+
def ==(other)
|
299
|
+
check_equality(self,other)
|
300
|
+
end
|
301
|
+
|
302
|
+
end
|
303
|
+
|
304
|
+
# Represents a HQMF reference from a precondition to a data criteria
|
305
|
+
class TypedReference
|
306
|
+
include HQMF::Conversion::Utilities
|
307
|
+
attr_accessor :reference, :type, :mood
|
308
|
+
|
309
|
+
# Create a new HQMF::Reference
|
310
|
+
# @param [String] id
|
311
|
+
def initialize(reference,type,mood=nil)
|
312
|
+
@reference = reference
|
313
|
+
@type = type
|
314
|
+
@mood = mood
|
315
|
+
end
|
316
|
+
|
317
|
+
def self.from_json(json)
|
318
|
+
type = json["type"]
|
319
|
+
reference = json["reference"]
|
320
|
+
mood = json["mood"]
|
321
|
+
new(reference,type,mood)
|
322
|
+
end
|
323
|
+
|
324
|
+
def to_json
|
325
|
+
build_hash(self, [:type, :reference,:mood])
|
326
|
+
end
|
327
|
+
|
328
|
+
def ==(other)
|
329
|
+
check_equality(self,other)
|
330
|
+
end
|
331
|
+
|
332
|
+
end
|
333
|
+
|
334
|
+
# Represents a HQMF reference from a precondition to a data criteria
|
335
|
+
class Reference
|
336
|
+
include HQMF::Conversion::Utilities
|
337
|
+
attr_accessor :id
|
338
|
+
|
339
|
+
# Create a new HQMF::Reference
|
340
|
+
# @param [String] id
|
341
|
+
def initialize(id)
|
342
|
+
@id = id
|
343
|
+
end
|
344
|
+
|
345
|
+
def to_json
|
346
|
+
@id
|
347
|
+
end
|
348
|
+
|
349
|
+
def ==(other)
|
350
|
+
check_equality(self,other)
|
351
|
+
end
|
352
|
+
|
353
|
+
end
|
354
|
+
|
355
|
+
class Identifier
|
356
|
+
include HQMF::Conversion::Utilities
|
357
|
+
attr_accessor :type, :root, :extension
|
358
|
+
|
359
|
+
def initialize(type, root, extension=nil)
|
360
|
+
@type = type || 'II'
|
361
|
+
@root = root
|
362
|
+
@extension = extension
|
363
|
+
end
|
364
|
+
|
365
|
+
def self.from_json(json)
|
366
|
+
json = json.with_indifferent_access
|
367
|
+
HQMF::Identifier.new(json['type'], json['root'], json['extension'])
|
368
|
+
end
|
369
|
+
|
370
|
+
def to_json
|
371
|
+
build_hash(self, [:type, :root, :extension])
|
372
|
+
end
|
373
|
+
|
374
|
+
def ==(other)
|
375
|
+
check_equality(self,other)
|
376
|
+
end
|
377
|
+
end
|
378
|
+
|
379
|
+
# What does ED stand for?
|
380
|
+
# ED has a lot more elements / attributes to represent, but only caring about what I see used...
|
381
|
+
class ED
|
382
|
+
include HQMF::Conversion::Utilities
|
383
|
+
attr_accessor :type, :value, :media_type
|
384
|
+
|
385
|
+
def initialize(type, value, media_type)
|
386
|
+
@type = type || 'ED'
|
387
|
+
@value = value
|
388
|
+
@media_type = media_type
|
389
|
+
end
|
390
|
+
|
391
|
+
def self.from_json(json)
|
392
|
+
json = json.with_indifferent_access
|
393
|
+
HQMF::ED.new(json['type'], json['value'], json['media_type'])
|
394
|
+
end
|
395
|
+
|
396
|
+
def to_json
|
397
|
+
build_hash(self, [:type, :value, :media_type])
|
398
|
+
end
|
399
|
+
|
400
|
+
def ==(other)
|
401
|
+
check_equality(self,other)
|
402
|
+
end
|
403
|
+
end
|
404
|
+
|
405
|
+
class GenericValueContainer
|
406
|
+
include HQMF::Conversion::Utilities
|
407
|
+
attr_accessor :type, :value
|
408
|
+
|
409
|
+
def initialize(type, value)
|
410
|
+
@type = type
|
411
|
+
@value = value
|
412
|
+
end
|
413
|
+
|
414
|
+
def self.from_json(json)
|
415
|
+
json = json.with_indifferent_access
|
416
|
+
HQMF::GenericValueContainer.new(json['type'], json['value'])
|
417
|
+
end
|
418
|
+
|
419
|
+
def to_json
|
420
|
+
build_hash(self, [:type, :value])
|
421
|
+
end
|
422
|
+
|
423
|
+
def ==(other)
|
424
|
+
check_equality(self,other)
|
425
|
+
end
|
426
|
+
end
|
427
|
+
|
428
|
+
class Collection
|
429
|
+
include HQMF::Conversion::Utilities
|
430
|
+
attr_accessor :type, :values
|
431
|
+
|
432
|
+
def initialize(type, values)
|
433
|
+
@type = type || 'COL'
|
434
|
+
@values = values || []
|
435
|
+
end
|
436
|
+
|
437
|
+
def self.from_json(json)
|
438
|
+
json = json.with_indifferent_access
|
439
|
+
values = []
|
440
|
+
type = json['type']
|
441
|
+
json['values'].each { |value| values.push(HQMF::DataCriteria.convert_value(value))}
|
442
|
+
HQMF::Collection.new(type, values)
|
443
|
+
end
|
444
|
+
|
445
|
+
def to_json
|
446
|
+
json = build_hash(self, [:type])
|
447
|
+
json[:values] = []
|
448
|
+
@values.each {|value| json[:values] << value.to_json }
|
449
|
+
json
|
450
|
+
end
|
451
|
+
|
452
|
+
def ==(other)
|
453
|
+
check_equality(self,other)
|
454
|
+
end
|
455
|
+
end
|
456
|
+
|
457
|
+
end
|