fhir_models 1.6.3 → 1.6.4

data/lib/{bootstrap → fhir_models/bootstrap}/hashable.rb

@@ -1,9 +1,10 @@
+require 'bigdecimal'
 module FHIR
   module Hashable
 
     def to_hash
       hash = Hash.new
-      self.class::METADATA.each do |key,value|
+      self.class::METADATA.each do |key, value|
         local_name = key
         local_name = value['local_name'] if value['local_name']
         hash[key] = self.instance_variable_get("@#{local_name}")
@@ -11,14 +12,14 @@ module FHIR
           hash[key] = hash[key].to_hash
         elsif hash[key].is_a? Array
           hash[key] = Array.new(hash[key]) # copy the array
-          hash[key].each_with_index do |item,index|
+          hash[key].each_with_index do |item, index|
             hash[key][index] = item.to_hash if item.respond_to?(:to_hash)
           end
         end
       end
-      hash.keep_if do |key,value|
-        !value.nil? && (  (value.is_a?(Hash) && !value.empty?) || 
-                          (value.is_a?(Array) && !value.empty?) || 
+      hash.keep_if do |_key, value|
+        !value.nil? && (  (value.is_a?(Hash) && !value.empty?) ||
+                          (value.is_a?(Array) && !value.empty?) ||
                           (!value.is_a?(Hash) && !value.is_a?(Array))
                        )
       end
@@ -28,19 +29,19 @@ module FHIR
 
     def from_hash(hash)
       # clear the existing variables
-      self.class::METADATA.each do |key,value|
+      self.class::METADATA.each do |key, value|
         local_name = key
         local_name = value['local_name'] if value['local_name']
-        self.instance_variable_set("@#{local_name}",nil)
+        self.instance_variable_set("@#{local_name}", nil)
       end
       # set the variables to the hash values
-      hash.each do |key,value|
+      hash.each do |key, value|
         key = key.to_s
         meta = self.class::METADATA[key]
         if !meta.nil?
           local_name = key
           local_name = meta['local_name'] if meta['local_name']
-          self.instance_variable_set("@#{local_name}",value) rescue nil
+          self.instance_variable_set("@#{local_name}", value) rescue nil
           # inflate the value if it isn't a primitive
           klass = Module.const_get("FHIR::#{meta['type']}") rescue nil
           if !klass.nil? && !value.nil?
@@ -48,13 +49,13 @@ module FHIR
             if value.is_a?(Array)
               value.map! do |child|
                 obj = child
-                unless [FHIR::RESOURCES, FHIR::TYPES].flatten.include? child.class.name.gsub('FHIR::','')
+                unless [FHIR::RESOURCES, FHIR::TYPES].flatten.include? child.class.name.gsub('FHIR::', '')
                   if child['resourceType']
                     klass = Module.const_get("FHIR::#{child['resourceType']}") rescue nil
                   end
                   begin
                     obj = klass.new(child)
-                  rescue Exception => e
+                  rescue => e
                     FHIR.logger.error("Unable to inflate embedded class #{klass}\n#{e.backtrace}")
                   end
                 end
@@ -67,27 +68,27 @@ module FHIR
               begin
                 obj = klass.new(value)
                 value = obj
-              rescue Exception => e
+              rescue => e
                 FHIR.logger.error("Unable to inflate embedded class #{klass}\n#{e.backtrace}")
               end
-              # if there is only one of these, but cardinality allows more, we need to wrap it in an array.              
+              # if there is only one of these, but cardinality allows more, we need to wrap it in an array.
               value = [ value ] if(value && (meta['max'] > 1))
             end
-            self.instance_variable_set("@#{local_name}",value)
+            self.instance_variable_set("@#{local_name}", value)
           elsif !FHIR::PRIMITIVES.include?(meta['type']) && meta['type']!='xhtml'
             FHIR.logger.error("Unhandled and unrecognized class/type: #{meta['type']}")
           else
             # primitive
             if value.is_a?(Array)
               # array of primitives
-              value.map!{|child| convert_primitive(child,meta)}
-              self.instance_variable_set("@#{local_name}",value)
+              value.map!{|child| convert_primitive(child, meta)}
+              self.instance_variable_set("@#{local_name}", value)
             else
               # single primitive
-              value = convert_primitive(value,meta)
-              # if there is only one of these, but cardinality allows more, we need to wrap it in an array.              
+              value = convert_primitive(value, meta)
+              # if there is only one of these, but cardinality allows more, we need to wrap it in an array.
               value = [ value ] if(value && (meta['max'] > 1))
-              self.instance_variable_set("@#{local_name}",value)
+              self.instance_variable_set("@#{local_name}", value)
             end
           end # !klass && !nil?
         end # !meta.nil?
@@ -95,7 +96,7 @@ module FHIR
       self
     end
 
-    def convert_primitive(value,meta)
+    def convert_primitive(value, meta)
       return value if !value.is_a?(String)
 
       rval = value

data/lib/{bootstrap → fhir_models/bootstrap}/json.rb

@@ -6,7 +6,6 @@ module FHIR
     #
 
     def to_json
-      hash = {}
       hash = self.to_hash
       JSON.pretty_unparse(hash)
     end
@@ -15,10 +14,10 @@ module FHIR
       hash = JSON.parse(json)
       resource = nil
       begin
-        resourceType = hash['resourceType']
-        klass = Module.const_get("FHIR::#{resourceType}")
+        resource_type = hash['resourceType']
+        klass = Module.const_get("FHIR::#{resource_type}")
         resource = klass.new(hash)
-      rescue Exception => e
+      rescue => e
         FHIR.logger.error("Failed to deserialize JSON:\n#{json}\n#{e.backtrace}")
         resource = nil
       end

data/lib/{bootstrap → fhir_models/bootstrap}/model.rb

@@ -1,3 +1,6 @@
+require 'nokogiri'
+require 'mime/types'
+require 'bcp47'
 module FHIR
   class Model
 
@@ -20,26 +23,26 @@ module FHIR
         return nil
       elsif (!@extension.nil? && !@extension.empty?)
         ext = @extension.select do |x|
-          name = x.url.gsub('-','_').split('/').last
+          name = x.url.tr('-', '_').split('/').last
           anchor = name.split('#').last
           (method.to_s==name || method.to_s==anchor)
         end
         if !ext.first.nil?
           if !ext.first.value.nil?
-            return ext.first.value 
+            return ext.first.value
           else
             return ext.first
           end
         end
       elsif (!@modifierExtension.nil? && !@modifierExtension.empty?)
         ext = @modifierExtension.select do |x|
-          name = x.url.gsub('-','_').split('/').last
+          name = x.url.tr('-', '_').split('/').last
           anchor = name.split('#').last
           (method.to_s==name || method.to_s==anchor)
         end
         if !ext.first.nil?
           if !ext.first.value.nil?
-            return ext.first.value 
+            return ext.first.value
           else
             return ext.first
           end
@@ -96,15 +99,15 @@ module FHIR
     end
 
     def validate(contained=nil)
-      validate_profile(self.class::METADATA,contained)
+      validate_profile(self.class::METADATA, contained)
     end
 
-    def validate_profile(metadata,contained=nil)
-      contained_here = [ self.instance_variable_get("@contained".to_sym) ].flatten
+    def validate_profile(metadata, contained=nil)
+      contained_here = [ self.instance_variable_get('@contained'.to_sym) ].flatten
       contained_here << contained
       contained_here = contained_here.flatten.compact
       errors = {}
-      metadata.each do |field,meta|
+      metadata.each do |field, meta|
         if meta.is_a?(Array)
           # this field has been 'sliced'
           meta.each do |slice|
@@ -118,19 +121,19 @@ module FHIR
                 subset = value
               end
             else
-              FHIR.logger.warn "Validation not supported on slices (except for Extensions)"
+              FHIR.logger.warn 'Validation not supported on slices (except for Extensions)'
             end
-            validate_field(field,subset,contained_here,slice,errors)
+            validate_field(field, subset, contained_here, slice, errors)
           end
         else
           local_name = meta['local_name'] || field
           value = [ self.instance_variable_get("@#{local_name}".to_sym) ].flatten.compact
-          validate_field(field,value,contained_here,meta,errors)
+          validate_field(field, value, contained_here, meta, errors)
         end
       end # metadata.each
       # check multiple types
       multiple_types = self.class::MULTIPLE_TYPES rescue {}
-      multiple_types.each do |prefix,suffixes|
+      multiple_types.each do |prefix, suffixes|
         count = 0
         present = []
         suffixes.each do |suffix|
@@ -139,7 +142,7 @@ module FHIR
           # check which multiple data types are actually present, not just errors
           # actually, this might be allowed depending on cardinality
           value = self.instance_variable_get("@#{typename}")
-          present << typename if !value.nil? || (value.is_a?(Array) && !value.empty?)          
+          present << typename if !value.nil? || (value.is_a?(Array) && !value.empty?)
         end
         errors[prefix] = ["#{prefix}[x]: more than one type present."] if(count > 1)
         # remove errors for suffixes that are not present
@@ -148,7 +151,7 @@ module FHIR
           errors.delete(typename) if !present.include?(typename)
         end
       end
-      errors.keep_if{|k,v|(v && !v.empty?)}
+      errors.keep_if{|_k, v|(v && !v.empty?)}
     end
 
     # ----- validate a field -----
@@ -157,7 +160,7 @@ module FHIR
     # contained_here: all contained resources to be considered
     # meta: the metadata definition for this field (or slice)
     # errors: the ongoing list of errors
-    def validate_field(field,value,contained_here,meta,errors)
+    def validate_field(field, value, contained_here, meta, errors)
       errors[field] = []
       # check cardinality
       count = value.length
@@ -167,7 +170,7 @@ module FHIR
       # check datatype
       datatype = meta['type']
       value.each do |v|
-        klassname = v.class.name.gsub('FHIR::','')
+        klassname = v.class.name.gsub('FHIR::', '')
         # if the data type is a generic Resource, validate it
         if datatype=='Resource'
           if FHIR::RESOURCES.include?(klassname)
@@ -196,7 +199,7 @@ module FHIR
                 # we need to look at the local contained resources
                 begin
                   r = contained_here.select{|x|x.id==v.reference[1..-1]}.first
-                rescue Exception => e
+                rescue
                   FHIR.logger.warn "Unable to resolve reference #{v.reference}"
                 end
                 if !r.nil?
@@ -226,7 +229,7 @@ module FHIR
             match = (v =~ Regexp.new(primitive_meta['regex']))
             errors[field] << "#{meta['path']}: #{v} does not match #{datatype} regex" if match.nil?
           else
-            errors[field] << "#{meta['path']}: #{v} is not a valid #{datatype}" if !is_primitive?(datatype,v)
+            errors[field] << "#{meta['path']}: #{v} is not a valid #{datatype}" if !is_primitive?(datatype, v)
           end
         end
         # check binding
@@ -240,13 +243,13 @@ module FHIR
             end
             has_valid_code = false
             if meta['valid_codes']
-              meta['valid_codes'].each do |key,codes|
+              meta['valid_codes'].each do |_key, codes|
                 has_valid_code = true if !(codes&the_codes).empty?
                 break if has_valid_code
               end
             else
               the_codes.each do |code|
-                has_valid_code = true if check_binding(meta['binding']['uri'],code)
+                has_valid_code = true if check_binding(meta['binding']['uri'], code)
                 break if has_valid_code
               end
             end
@@ -257,9 +260,9 @@ module FHIR
       errors.delete(field) if errors[field].empty?
     end
 
-    def is_primitive?(datatype,value)
+    def is_primitive?(datatype, value)
       # Remaining data types: handle special cases before checking type StructureDefinitions
-      return case datatype.downcase
+      case datatype.downcase
       when 'boolean'
         value==true || value==false || value.downcase=='true' || value.downcase=='false'
       when 'code'
@@ -277,7 +280,7 @@ module FHIR
       when 'instant'
         regex = /\A[0-9]{4}(-(0[1-9]|1[0-2])(-(0[0-9]|[1-2][0-9]|3[0-1])(T([01][0-9]|2[0-3]):[0-5][0-9]:[0-5][0-9](\.[0-9]+)?(Z|(\+|-)((0[0-9]|1[0-3]):[0-5][0-9]|14:00)))))\Z/
         value.is_a?(String) && !(regex =~ value).nil?
-      when 'integer','unsignedint'
+      when 'integer', 'unsignedint'
         (!Integer(value).nil? rescue false)
       when 'positiveint'
         (!Integer(value).nil? rescue false) && (Integer(value) >= 0)
@@ -285,10 +288,11 @@ module FHIR
         (!Float(value).nil? rescue false)
       else
         FHIR.logger.warn "Unable to check #{value} for datatype #{datatype}"
+        false
       end
     end
 
-    def check_binding(uri,value)
+    def check_binding(uri, value)
       valid = false
       if uri=='http://hl7.org/fhir/ValueSet/content-type' || uri=='http://www.rfc-editor.org/bcp/bcp13.txt'
         matches = MIME::Types[value]

data/lib/{bootstrap → fhir_models/bootstrap}/preprocess.rb

@@ -1,3 +1,4 @@
+require 'nokogiri'
 module FHIR
   module Boot
     class Preprocess
@@ -6,12 +7,12 @@ module FHIR
         # Read the file
         puts "Processing #{File.basename(filename)}..."
         start = File.size(filename)
-        json = File.open(filename,'r:UTF-8',&:read)
+        json = File.open(filename, 'r:UTF-8', &:read)
         hash = JSON.parse(json)
 
         # Remove entries that do not interest us: CompartmentDefinitions, OperationDefinitions, Conformance statements
         hash['entry'].select! do |entry|
-          ['StructureDefinition','ValueSet','CodeSystem','SearchParameter'].include? entry['resource']['resourceType']
+          ['StructureDefinition', 'ValueSet', 'CodeSystem', 'SearchParameter'].include? entry['resource']['resourceType']
         end
 
         # Remove unnecessary elements from the hash
@@ -26,7 +27,7 @@ module FHIR
         end
 
         # Output the post processed file
-        f = File.open(filename,'w:UTF-8')
+        f = File.open(filename, 'w:UTF-8')
         f.write(JSON.pretty_unparse(hash))
         f.close
         finish = File.size(filename)
@@ -35,32 +36,32 @@ module FHIR
 
       def self.pre_process_structuredefinition(hash)
         # Remove large HTML narratives and unused content
-        ['text','publisher','contact','description','requirements','mapping'].each{|key| hash.delete(key) }
-        
+        ['text', 'publisher', 'contact', 'description', 'requirements', 'mapping'].each{|key| hash.delete(key) }
+
         # Remove unused descriptions within the snapshot elements
         if(hash['snapshot'])
           hash['snapshot']['element'].each do |element|
-            ['short','definition','comments','requirements','alias','mapping'].each{|key| element.delete(key) }
+            ['short', 'definition', 'comments', 'requirements', 'alias', 'mapping'].each{|key| element.delete(key) }
           end
         end
         # Remove unused descriptions within the differential elements
         if(hash['differential'])
           hash['differential']['element'].each do |element|
-            ['short','definition','comments','requirements','alias','mapping'].each{|key| element.delete(key) }
+            ['short', 'definition', 'comments', 'requirements', 'alias', 'mapping'].each{|key| element.delete(key) }
           end
         end
       end
 
       def self.pre_process_valueset(hash)
         # Remove large HTML narratives and unused content
-        ['meta','text','publisher','contact','description','requirements'].each{|key| hash.delete(key) }
+        ['meta', 'text', 'publisher', 'contact', 'description', 'requirements'].each{|key| hash.delete(key) }
 
         if(hash['compose'] && hash['compose']['include'])
           hash['compose']['include'].each do |element|
             if(element['concept'])
               element['concept'].each do |concept|
                 concept.delete('designation')
-              end 
+              end
             end
           end
         end
@@ -70,7 +71,7 @@ module FHIR
             if(element['concept'])
               element['concept'].each do |concept|
                 concept.delete('designation')
-              end 
+              end
             end
           end
         end
@@ -78,7 +79,7 @@ module FHIR
 
       def self.pre_process_codesystem(hash)
         # Remove large HTML narratives and unused content
-        ['meta','text','publisher','contact','description','requirements'].each{|key| hash.delete(key) }
+        ['meta', 'text', 'publisher', 'contact', 'description', 'requirements'].each{|key| hash.delete(key) }
 
         if(hash['concept'])
           hash['concept'].each do |concept|
@@ -88,7 +89,7 @@ module FHIR
       end
 
       def self.pre_process_codesystem_concept(hash)
-        ['extension','definition','designation'].each{|key| hash.delete(key) }
+        ['extension', 'definition', 'designation'].each{|key| hash.delete(key) }
         if hash['concept']
           hash['concept'].each do |concept|
             pre_process_codesystem_concept(concept)
@@ -98,12 +99,12 @@ module FHIR
 
       def self.pre_process_searchparam(hash)
         # Remove large HTML narratives and unused content
-        ['id','url','name','date','publisher','contact','description','xpathUsage'].each{|key| hash.delete(key) }
+        ['id', 'url', 'name', 'date', 'publisher', 'contact', 'description', 'xpathUsage'].each{|key| hash.delete(key) }
       end
 
       def self.remove_fhir_comments(hash)
         hash.delete('fhir_comments')
-        hash.each do |key,value|
+        hash.each do |_key, value|
           if value.is_a?(Hash)
             remove_fhir_comments(value)
           elsif value.is_a?(Array)
@@ -112,7 +113,7 @@ module FHIR
             end
           end
         end
-        hash.keep_if do |key,value|
+        hash.keep_if do |_key, value|
           !value.is_a?(Hash) || !value.empty?
         end
       end
@@ -121,7 +122,7 @@ module FHIR
         # Read the file
         puts "Processing #{File.basename(filename)}..."
         start = File.size(filename)
-        raw = File.open(filename,'r:UTF-8',&:read)
+        raw = File.open(filename, 'r:UTF-8', &:read)
 
         # Remove annotations
         doc = Nokogiri::XML(raw)
@@ -129,7 +130,7 @@ module FHIR
         doc.search('//xs:annotation').each{ |e| e.remove }
 
         # Output the post processed file
-        f = File.open(filename,'w:UTF-8')
+        f = File.open(filename, 'w:UTF-8')
         f.write(doc.to_xml)
         f.close
         finish = File.size(filename)
@@ -138,4 +139,4 @@ module FHIR
 
     end
   end
-end
+end