fhir-mongoid-models 0.0.1

data/app/models/fhir/molecular_sequence_quality_roc.rb

@@ -0,0 +1,93 @@
+module FHIR
+  # fhir/molecular_sequence_quality_roc.rb
+  class MolecularSequenceQualityRoc < BackboneElement
+    include Mongoid::Document
+    embeds_many :score, class_name: 'FHIR::PrimitiveInteger'    
+    embeds_many :numTP, class_name: 'FHIR::PrimitiveInteger'    
+    embeds_many :numFP, class_name: 'FHIR::PrimitiveInteger'    
+    embeds_many :numFN, class_name: 'FHIR::PrimitiveInteger'    
+    embeds_many :precision, class_name: 'FHIR::PrimitiveDecimal'    
+    embeds_many :sensitivity, class_name: 'FHIR::PrimitiveDecimal'    
+    embeds_many :fMeasure, class_name: 'FHIR::PrimitiveDecimal'    
+    
+    def as_json(*args)
+      result = super      
+      unless self.score.nil?  || !self.score.any? 
+        result['score'] = self.score.compact().map{ |x| x.value }
+        serialized = Extension.serializePrimitiveExtensionArray(self.score)                              
+        result['_score'] = serialized unless serialized.nil? || !serialized.any?
+      end
+      unless self.numTP.nil?  || !self.numTP.any? 
+        result['numTP'] = self.numTP.compact().map{ |x| x.value }
+        serialized = Extension.serializePrimitiveExtensionArray(self.numTP)                              
+        result['_numTP'] = serialized unless serialized.nil? || !serialized.any?
+      end
+      unless self.numFP.nil?  || !self.numFP.any? 
+        result['numFP'] = self.numFP.compact().map{ |x| x.value }
+        serialized = Extension.serializePrimitiveExtensionArray(self.numFP)                              
+        result['_numFP'] = serialized unless serialized.nil? || !serialized.any?
+      end
+      unless self.numFN.nil?  || !self.numFN.any? 
+        result['numFN'] = self.numFN.compact().map{ |x| x.value }
+        serialized = Extension.serializePrimitiveExtensionArray(self.numFN)                              
+        result['_numFN'] = serialized unless serialized.nil? || !serialized.any?
+      end
+      unless self.precision.nil?  || !self.precision.any? 
+        result['precision'] = self.precision.compact().map{ |x| x.value }
+        serialized = Extension.serializePrimitiveExtensionArray(self.precision)                              
+        result['_precision'] = serialized unless serialized.nil? || !serialized.any?
+      end
+      unless self.sensitivity.nil?  || !self.sensitivity.any? 
+        result['sensitivity'] = self.sensitivity.compact().map{ |x| x.value }
+        serialized = Extension.serializePrimitiveExtensionArray(self.sensitivity)                              
+        result['_sensitivity'] = serialized unless serialized.nil? || !serialized.any?
+      end
+      unless self.fMeasure.nil?  || !self.fMeasure.any? 
+        result['fMeasure'] = self.fMeasure.compact().map{ |x| x.value }
+        serialized = Extension.serializePrimitiveExtensionArray(self.fMeasure)                              
+        result['_fMeasure'] = serialized unless serialized.nil? || !serialized.any?
+      end
+      result.delete('id')
+      unless self.fhirId.nil?
+        result['id'] = self.fhirId
+        result.delete('fhirId')
+      end  
+      result
+    end
+
+    def self.transform_json(json_hash, target = MolecularSequenceQualityRoc.new)
+    
+      result = self.superclass.transform_json(json_hash, target)
+      result['score'] = json_hash['score'].each_with_index.map do |var, i|
+        extension_hash = json_hash['_score'] && json_hash['_score'][i]
+        PrimitiveInteger.transform_json(var, extension_hash)
+      end unless json_hash['score'].nil?
+      result['numTP'] = json_hash['numTP'].each_with_index.map do |var, i|
+        extension_hash = json_hash['_numTP'] && json_hash['_numTP'][i]
+        PrimitiveInteger.transform_json(var, extension_hash)
+      end unless json_hash['numTP'].nil?
+      result['numFP'] = json_hash['numFP'].each_with_index.map do |var, i|
+        extension_hash = json_hash['_numFP'] && json_hash['_numFP'][i]
+        PrimitiveInteger.transform_json(var, extension_hash)
+      end unless json_hash['numFP'].nil?
+      result['numFN'] = json_hash['numFN'].each_with_index.map do |var, i|
+        extension_hash = json_hash['_numFN'] && json_hash['_numFN'][i]
+        PrimitiveInteger.transform_json(var, extension_hash)
+      end unless json_hash['numFN'].nil?
+      result['precision'] = json_hash['precision'].each_with_index.map do |var, i|
+        extension_hash = json_hash['_precision'] && json_hash['_precision'][i]
+        PrimitiveDecimal.transform_json(var, extension_hash)
+      end unless json_hash['precision'].nil?
+      result['sensitivity'] = json_hash['sensitivity'].each_with_index.map do |var, i|
+        extension_hash = json_hash['_sensitivity'] && json_hash['_sensitivity'][i]
+        PrimitiveDecimal.transform_json(var, extension_hash)
+      end unless json_hash['sensitivity'].nil?
+      result['fMeasure'] = json_hash['fMeasure'].each_with_index.map do |var, i|
+        extension_hash = json_hash['_fMeasure'] && json_hash['_fMeasure'][i]
+        PrimitiveDecimal.transform_json(var, extension_hash)
+      end unless json_hash['fMeasure'].nil?
+
+      result
+    end
+  end
+end

data/app/models/fhir/molecular_sequence_reference_seq.rb

@@ -0,0 +1,80 @@
+module FHIR
+  # fhir/molecular_sequence_reference_seq.rb
+  class MolecularSequenceReferenceSeq < BackboneElement
+    include Mongoid::Document
+    embeds_one :chromosome, class_name: 'FHIR::CodeableConcept'    
+    embeds_one :genomeBuild, class_name: 'FHIR::PrimitiveString'    
+    embeds_one :orientation, class_name: 'FHIR::OrientationType'    
+    embeds_one :referenceSeqId, class_name: 'FHIR::CodeableConcept'    
+    embeds_one :referenceSeqPointer, class_name: 'FHIR::Reference'    
+    embeds_one :referenceSeqString, class_name: 'FHIR::PrimitiveString'    
+    embeds_one :strand, class_name: 'FHIR::StrandType'    
+    embeds_one :windowStart, class_name: 'FHIR::PrimitiveInteger'    
+    embeds_one :windowEnd, class_name: 'FHIR::PrimitiveInteger'    
+    
+    def as_json(*args)
+      result = super      
+      unless self.chromosome.nil? 
+        result['chromosome'] = self.chromosome.as_json(*args)
+      end
+      unless self.genomeBuild.nil? 
+        result['genomeBuild'] = self.genomeBuild.value
+        serialized = Extension.serializePrimitiveExtension(self.genomeBuild)            
+        result['_genomeBuild'] = serialized unless serialized.nil?
+      end
+      unless self.orientation.nil? 
+        result['orientation'] = self.orientation.value
+        serialized = Extension.serializePrimitiveExtension(self.orientation)            
+        result['_orientation'] = serialized unless serialized.nil?
+      end
+      unless self.referenceSeqId.nil? 
+        result['referenceSeqId'] = self.referenceSeqId.as_json(*args)
+      end
+      unless self.referenceSeqPointer.nil? 
+        result['referenceSeqPointer'] = self.referenceSeqPointer.as_json(*args)
+      end
+      unless self.referenceSeqString.nil? 
+        result['referenceSeqString'] = self.referenceSeqString.value
+        serialized = Extension.serializePrimitiveExtension(self.referenceSeqString)            
+        result['_referenceSeqString'] = serialized unless serialized.nil?
+      end
+      unless self.strand.nil? 
+        result['strand'] = self.strand.value
+        serialized = Extension.serializePrimitiveExtension(self.strand)            
+        result['_strand'] = serialized unless serialized.nil?
+      end
+      unless self.windowStart.nil? 
+        result['windowStart'] = self.windowStart.value
+        serialized = Extension.serializePrimitiveExtension(self.windowStart)            
+        result['_windowStart'] = serialized unless serialized.nil?
+      end
+      unless self.windowEnd.nil? 
+        result['windowEnd'] = self.windowEnd.value
+        serialized = Extension.serializePrimitiveExtension(self.windowEnd)            
+        result['_windowEnd'] = serialized unless serialized.nil?
+      end
+      result.delete('id')
+      unless self.fhirId.nil?
+        result['id'] = self.fhirId
+        result.delete('fhirId')
+      end  
+      result
+    end
+
+    def self.transform_json(json_hash, target = MolecularSequenceReferenceSeq.new)
+    
+      result = self.superclass.transform_json(json_hash, target)
+      result['chromosome'] = CodeableConcept.transform_json(json_hash['chromosome']) unless json_hash['chromosome'].nil?
+      result['genomeBuild'] = PrimitiveString.transform_json(json_hash['genomeBuild'], json_hash['_genomeBuild']) unless json_hash['genomeBuild'].nil?
+      result['orientation'] = OrientationType.transform_json(json_hash['orientation'], json_hash['_orientation']) unless json_hash['orientation'].nil?
+      result['referenceSeqId'] = CodeableConcept.transform_json(json_hash['referenceSeqId']) unless json_hash['referenceSeqId'].nil?
+      result['referenceSeqPointer'] = Reference.transform_json(json_hash['referenceSeqPointer']) unless json_hash['referenceSeqPointer'].nil?
+      result['referenceSeqString'] = PrimitiveString.transform_json(json_hash['referenceSeqString'], json_hash['_referenceSeqString']) unless json_hash['referenceSeqString'].nil?
+      result['strand'] = StrandType.transform_json(json_hash['strand'], json_hash['_strand']) unless json_hash['strand'].nil?
+      result['windowStart'] = PrimitiveInteger.transform_json(json_hash['windowStart'], json_hash['_windowStart']) unless json_hash['windowStart'].nil?
+      result['windowEnd'] = PrimitiveInteger.transform_json(json_hash['windowEnd'], json_hash['_windowEnd']) unless json_hash['windowEnd'].nil?
+
+      result
+    end
+  end
+end

data/app/models/fhir/molecular_sequence_repository.rb

@@ -0,0 +1,65 @@
+module FHIR
+  # fhir/molecular_sequence_repository.rb
+  class MolecularSequenceRepository < BackboneElement
+    include Mongoid::Document
+    embeds_one :type, class_name: 'FHIR::RepositoryType'    
+    embeds_one :url, class_name: 'FHIR::PrimitiveUri'    
+    embeds_one :name, class_name: 'FHIR::PrimitiveString'    
+    embeds_one :datasetId, class_name: 'FHIR::PrimitiveString'    
+    embeds_one :variantsetId, class_name: 'FHIR::PrimitiveString'    
+    embeds_one :readsetId, class_name: 'FHIR::PrimitiveString'    
+    
+    def as_json(*args)
+      result = super      
+      unless self.type.nil? 
+        result['type'] = self.type.value
+        serialized = Extension.serializePrimitiveExtension(self.type)            
+        result['_type'] = serialized unless serialized.nil?
+      end
+      unless self.url.nil? 
+        result['url'] = self.url.value
+        serialized = Extension.serializePrimitiveExtension(self.url)            
+        result['_url'] = serialized unless serialized.nil?
+      end
+      unless self.name.nil? 
+        result['name'] = self.name.value
+        serialized = Extension.serializePrimitiveExtension(self.name)            
+        result['_name'] = serialized unless serialized.nil?
+      end
+      unless self.datasetId.nil? 
+        result['datasetId'] = self.datasetId.value
+        serialized = Extension.serializePrimitiveExtension(self.datasetId)            
+        result['_datasetId'] = serialized unless serialized.nil?
+      end
+      unless self.variantsetId.nil? 
+        result['variantsetId'] = self.variantsetId.value
+        serialized = Extension.serializePrimitiveExtension(self.variantsetId)            
+        result['_variantsetId'] = serialized unless serialized.nil?
+      end
+      unless self.readsetId.nil? 
+        result['readsetId'] = self.readsetId.value
+        serialized = Extension.serializePrimitiveExtension(self.readsetId)            
+        result['_readsetId'] = serialized unless serialized.nil?
+      end
+      result.delete('id')
+      unless self.fhirId.nil?
+        result['id'] = self.fhirId
+        result.delete('fhirId')
+      end  
+      result
+    end
+
+    def self.transform_json(json_hash, target = MolecularSequenceRepository.new)
+    
+      result = self.superclass.transform_json(json_hash, target)
+      result['type'] = RepositoryType.transform_json(json_hash['type'], json_hash['_type']) unless json_hash['type'].nil?
+      result['url'] = PrimitiveUri.transform_json(json_hash['url'], json_hash['_url']) unless json_hash['url'].nil?
+      result['name'] = PrimitiveString.transform_json(json_hash['name'], json_hash['_name']) unless json_hash['name'].nil?
+      result['datasetId'] = PrimitiveString.transform_json(json_hash['datasetId'], json_hash['_datasetId']) unless json_hash['datasetId'].nil?
+      result['variantsetId'] = PrimitiveString.transform_json(json_hash['variantsetId'], json_hash['_variantsetId']) unless json_hash['variantsetId'].nil?
+      result['readsetId'] = PrimitiveString.transform_json(json_hash['readsetId'], json_hash['_readsetId']) unless json_hash['readsetId'].nil?
+
+      result
+    end
+  end
+end

data/app/models/fhir/molecular_sequence_structure_variant.rb

@@ -0,0 +1,52 @@
+module FHIR
+  # fhir/molecular_sequence_structure_variant.rb
+  class MolecularSequenceStructureVariant < BackboneElement
+    include Mongoid::Document
+    embeds_one :variantType, class_name: 'FHIR::CodeableConcept'    
+    embeds_one :exact, class_name: 'FHIR::PrimitiveBoolean'    
+    embeds_one :length, class_name: 'FHIR::PrimitiveInteger'    
+    embeds_one :outer, class_name: 'FHIR::MolecularSequenceStructureVariantOuter'    
+    embeds_one :inner, class_name: 'FHIR::MolecularSequenceStructureVariantInner'    
+    
+    def as_json(*args)
+      result = super      
+      unless self.variantType.nil? 
+        result['variantType'] = self.variantType.as_json(*args)
+      end
+      unless self.exact.nil? 
+        result['exact'] = self.exact.value
+        serialized = Extension.serializePrimitiveExtension(self.exact)            
+        result['_exact'] = serialized unless serialized.nil?
+      end
+      unless self.length.nil? 
+        result['length'] = self.length.value
+        serialized = Extension.serializePrimitiveExtension(self.length)            
+        result['_length'] = serialized unless serialized.nil?
+      end
+      unless self.outer.nil? 
+        result['outer'] = self.outer.as_json(*args)
+      end
+      unless self.inner.nil? 
+        result['inner'] = self.inner.as_json(*args)
+      end
+      result.delete('id')
+      unless self.fhirId.nil?
+        result['id'] = self.fhirId
+        result.delete('fhirId')
+      end  
+      result
+    end
+
+    def self.transform_json(json_hash, target = MolecularSequenceStructureVariant.new)
+    
+      result = self.superclass.transform_json(json_hash, target)
+      result['variantType'] = CodeableConcept.transform_json(json_hash['variantType']) unless json_hash['variantType'].nil?
+      result['exact'] = PrimitiveBoolean.transform_json(json_hash['exact'], json_hash['_exact']) unless json_hash['exact'].nil?
+      result['length'] = PrimitiveInteger.transform_json(json_hash['length'], json_hash['_length']) unless json_hash['length'].nil?
+      result['outer'] = MolecularSequenceStructureVariantOuter.transform_json(json_hash['outer']) unless json_hash['outer'].nil?
+      result['inner'] = MolecularSequenceStructureVariantInner.transform_json(json_hash['inner']) unless json_hash['inner'].nil?
+
+      result
+    end
+  end
+end

data/app/models/fhir/molecular_sequence_structure_variant_inner.rb

@@ -0,0 +1,37 @@
+module FHIR
+  # fhir/molecular_sequence_structure_variant_inner.rb
+  class MolecularSequenceStructureVariantInner < BackboneElement
+    include Mongoid::Document
+    embeds_one :start, class_name: 'FHIR::PrimitiveInteger'    
+    embeds_one :end, class_name: 'FHIR::PrimitiveInteger'    
+    
+    def as_json(*args)
+      result = super      
+      unless self.start.nil? 
+        result['start'] = self.start.value
+        serialized = Extension.serializePrimitiveExtension(self.start)            
+        result['_start'] = serialized unless serialized.nil?
+      end
+      unless self.end.nil? 
+        result['end'] = self.end.value
+        serialized = Extension.serializePrimitiveExtension(self.end)            
+        result['_end'] = serialized unless serialized.nil?
+      end
+      result.delete('id')
+      unless self.fhirId.nil?
+        result['id'] = self.fhirId
+        result.delete('fhirId')
+      end  
+      result
+    end
+
+    def self.transform_json(json_hash, target = MolecularSequenceStructureVariantInner.new)
+    
+      result = self.superclass.transform_json(json_hash, target)
+      result['start'] = PrimitiveInteger.transform_json(json_hash['start'], json_hash['_start']) unless json_hash['start'].nil?
+      result['end'] = PrimitiveInteger.transform_json(json_hash['end'], json_hash['_end']) unless json_hash['end'].nil?
+
+      result
+    end
+  end
+end

data/app/models/fhir/molecular_sequence_structure_variant_outer.rb

@@ -0,0 +1,37 @@
+module FHIR
+  # fhir/molecular_sequence_structure_variant_outer.rb
+  class MolecularSequenceStructureVariantOuter < BackboneElement
+    include Mongoid::Document
+    embeds_one :start, class_name: 'FHIR::PrimitiveInteger'    
+    embeds_one :end, class_name: 'FHIR::PrimitiveInteger'    
+    
+    def as_json(*args)
+      result = super      
+      unless self.start.nil? 
+        result['start'] = self.start.value
+        serialized = Extension.serializePrimitiveExtension(self.start)            
+        result['_start'] = serialized unless serialized.nil?
+      end
+      unless self.end.nil? 
+        result['end'] = self.end.value
+        serialized = Extension.serializePrimitiveExtension(self.end)            
+        result['_end'] = serialized unless serialized.nil?
+      end
+      result.delete('id')
+      unless self.fhirId.nil?
+        result['id'] = self.fhirId
+        result.delete('fhirId')
+      end  
+      result
+    end
+
+    def self.transform_json(json_hash, target = MolecularSequenceStructureVariantOuter.new)
+    
+      result = self.superclass.transform_json(json_hash, target)
+      result['start'] = PrimitiveInteger.transform_json(json_hash['start'], json_hash['_start']) unless json_hash['start'].nil?
+      result['end'] = PrimitiveInteger.transform_json(json_hash['end'], json_hash['_end']) unless json_hash['end'].nil?
+
+      result
+    end
+  end
+end

data/app/models/fhir/molecular_sequence_variant.rb

@@ -0,0 +1,63 @@
+module FHIR
+  # fhir/molecular_sequence_variant.rb
+  class MolecularSequenceVariant < BackboneElement
+    include Mongoid::Document
+    embeds_one :start, class_name: 'FHIR::PrimitiveInteger'    
+    embeds_one :end, class_name: 'FHIR::PrimitiveInteger'    
+    embeds_one :observedAllele, class_name: 'FHIR::PrimitiveString'    
+    embeds_one :referenceAllele, class_name: 'FHIR::PrimitiveString'    
+    embeds_one :cigar, class_name: 'FHIR::PrimitiveString'    
+    embeds_one :variantPointer, class_name: 'FHIR::Reference'    
+    
+    def as_json(*args)
+      result = super      
+      unless self.start.nil? 
+        result['start'] = self.start.value
+        serialized = Extension.serializePrimitiveExtension(self.start)            
+        result['_start'] = serialized unless serialized.nil?
+      end
+      unless self.end.nil? 
+        result['end'] = self.end.value
+        serialized = Extension.serializePrimitiveExtension(self.end)            
+        result['_end'] = serialized unless serialized.nil?
+      end
+      unless self.observedAllele.nil? 
+        result['observedAllele'] = self.observedAllele.value
+        serialized = Extension.serializePrimitiveExtension(self.observedAllele)            
+        result['_observedAllele'] = serialized unless serialized.nil?
+      end
+      unless self.referenceAllele.nil? 
+        result['referenceAllele'] = self.referenceAllele.value
+        serialized = Extension.serializePrimitiveExtension(self.referenceAllele)            
+        result['_referenceAllele'] = serialized unless serialized.nil?
+      end
+      unless self.cigar.nil? 
+        result['cigar'] = self.cigar.value
+        serialized = Extension.serializePrimitiveExtension(self.cigar)            
+        result['_cigar'] = serialized unless serialized.nil?
+      end
+      unless self.variantPointer.nil? 
+        result['variantPointer'] = self.variantPointer.as_json(*args)
+      end
+      result.delete('id')
+      unless self.fhirId.nil?
+        result['id'] = self.fhirId
+        result.delete('fhirId')
+      end  
+      result
+    end
+
+    def self.transform_json(json_hash, target = MolecularSequenceVariant.new)
+    
+      result = self.superclass.transform_json(json_hash, target)
+      result['start'] = PrimitiveInteger.transform_json(json_hash['start'], json_hash['_start']) unless json_hash['start'].nil?
+      result['end'] = PrimitiveInteger.transform_json(json_hash['end'], json_hash['_end']) unless json_hash['end'].nil?
+      result['observedAllele'] = PrimitiveString.transform_json(json_hash['observedAllele'], json_hash['_observedAllele']) unless json_hash['observedAllele'].nil?
+      result['referenceAllele'] = PrimitiveString.transform_json(json_hash['referenceAllele'], json_hash['_referenceAllele']) unless json_hash['referenceAllele'].nil?
+      result['cigar'] = PrimitiveString.transform_json(json_hash['cigar'], json_hash['_cigar']) unless json_hash['cigar'].nil?
+      result['variantPointer'] = Reference.transform_json(json_hash['variantPointer']) unless json_hash['variantPointer'].nil?
+
+      result
+    end
+  end
+end

data/app/models/fhir/money.rb

@@ -0,0 +1,37 @@
+module FHIR
+  # fhir/money.rb
+  class Money < Element
+    include Mongoid::Document
+    embeds_one :value, class_name: 'FHIR::PrimitiveDecimal'    
+    embeds_one :currency, class_name: 'FHIR::CurrencyCode'    
+    
+    def as_json(*args)
+      result = super      
+      unless self.value.nil? 
+        result['value'] = self.value.value
+        serialized = Extension.serializePrimitiveExtension(self.value)            
+        result['_value'] = serialized unless serialized.nil?
+      end
+      unless self.currency.nil? 
+        result['currency'] = self.currency.value
+        serialized = Extension.serializePrimitiveExtension(self.currency)            
+        result['_currency'] = serialized unless serialized.nil?
+      end
+      result.delete('id')
+      unless self.fhirId.nil?
+        result['id'] = self.fhirId
+        result.delete('fhirId')
+      end  
+      result
+    end
+
+    def self.transform_json(json_hash, target = Money.new)
+    
+      result = self.superclass.transform_json(json_hash, target)
+      result['value'] = PrimitiveDecimal.transform_json(json_hash['value'], json_hash['_value']) unless json_hash['value'].nil?
+      result['currency'] = CurrencyCode.transform_json(json_hash['currency'], json_hash['_currency']) unless json_hash['currency'].nil?
+
+      result
+    end
+  end
+end