fhir_client 1.6.3 → 1.6.7

data/lib/{client_exception.rb → fhir_client/client_exception.rb}

@@ -1,10 +1,8 @@
-class ClientException < Exception
-
+class ClientException < RuntimeError
   attr_accessor :reply
 
   def initialize(message, reply = nil)
     super(message)
     @reply = reply
   end
-
 end

data/lib/{ext → fhir_client/ext}/bundle.rb

@@ -1,24 +1,23 @@
 module FHIR
   class Bundle
-
     def self_link
-      link.select {|n| n.relation == 'self'}.first
+      link.select { |n| n.relation == 'self' }.first
     end
 
     def first_link
-      link.select {|n| n.relation == 'first'}.first
+      link.select { |n| n.relation == 'first' }.first
     end
 
     def last_link
-      link.select {|n| n.relation == 'last'}.first
+      link.select { |n| n.relation == 'last' }.first
     end
 
     def next_link
-      link.select {|n| n.relation == 'next'}.first
+      link.select { |n| n.relation == 'next' }.first
     end
 
     def previous_link
-      link.select {|n| n.relation == 'previous' || n.relation == 'prev'}.first
+      link.select { |n| n.relation == 'previous' || n.relation == 'prev' }.first
     end
 
     def get_by_id(id)
@@ -41,4 +40,3 @@ module FHIR
     end
   end
 end
-

data/lib/{ext → fhir_client/ext}/model.rb

@@ -84,7 +84,7 @@ module FHIR
     end
 
     def conditional_update(params)
-      handle_response client.conditional_update(self, self.id, params)
+      handle_response client.conditional_update(self, id, params)
     end
 
     def destroy
@@ -92,10 +92,18 @@ module FHIR
       nil
     end
 
+    def resolve(reference)
+      if reference.contained?
+        contained.detect { |c| c.id == reference.id }
+      else
+        reference.read
+      end
+    end
+
     private
 
     def self.handle_response(response)
-      raise ClientException.new "Server returned #{response.code}.", response if response.code.between?(400,599)
+      raise ClientException.new "Server returned #{response.code}.", response if response.code.between?(400, 599)
       response.resource
     end
 

data/lib/fhir_client/ext/reference.rb

@@ -0,0 +1,28 @@
+module FHIR
+  class Reference
+    def contained?
+      reference.to_s.start_with?('#')
+    end
+
+    def id
+      if contained?
+        reference.to_s[1..-1]
+      else
+        reference.to_s.split('/').last
+      end
+    end
+
+    def type
+      reference.to_s.split('/').first unless contained?
+    end
+
+    def resource_class
+      "FHIR::#{type}".constantize unless contained?
+    end
+
+    def read
+      return if contained? || type.blank? || id.blank?
+      resource_class.read(id, client)
+    end
+  end
+end

data/lib/{model → fhir_client/model}/client_reply.rb

@@ -1,7 +1,6 @@
 module FHIR
   class ClientReply
-
-    @@validation_rules = JSON.parse( File.open(File.join(File.expand_path('..',File.dirname(File.absolute_path(__FILE__))),'fhir_api_validation.json'),'r:UTF-8',&:read) )
+    @@validation_rules = JSON.parse(File.open(File.join(File.expand_path('..', File.dirname(File.absolute_path(__FILE__))), 'fhir_api_validation.json'), 'r:UTF-8', &:read))
     @@path_regexes = {
       '[type]' => "(#{FHIR::RESOURCES.join('|')})",
       '[id]' => FHIR::PRIMITIVES['id']['regex'],
@@ -20,9 +19,9 @@ module FHIR
        UT|GMT|EST|EDT|CST|CDT|MST|MDT|PST|PDT|[A-IK-Z])/ix
 
     @@header_regexes = {
-      'Content-Type' => Regexp.new("(#{FHIR::Formats::ResourceFormat::RESOURCE_XML.gsub('+','\\\+')}|#{FHIR::Formats::ResourceFormat::RESOURCE_JSON.gsub('+','\\\+')})(([ ;]+)(charset)([ =]+)(UTF-8|utf-8))?"),
-      'Accept' => Regexp.new("(#{FHIR::Formats::ResourceFormat::RESOURCE_XML.gsub('+','\\\+')}|#{FHIR::Formats::ResourceFormat::RESOURCE_JSON.gsub('+','\\\+')})"),
-      'Prefer' => Regexp.new("(return=minimal|return=representation)"),
+      'Content-Type' => Regexp.new("(#{FHIR::Formats::ResourceFormat::RESOURCE_XML.gsub('+', '\\\+')}|#{FHIR::Formats::ResourceFormat::RESOURCE_JSON.gsub('+', '\\\+')})(([ ;]+)(charset)([ =]+)(UTF-8|utf-8))?"),
+      'Accept' => Regexp.new("(#{FHIR::Formats::ResourceFormat::RESOURCE_XML.gsub('+', '\\\+')}|#{FHIR::Formats::ResourceFormat::RESOURCE_JSON.gsub('+', '\\\+')})"),
+      'Prefer' => Regexp.new('(return=minimal|return=representation)'),
       'ETag' => Regexp.new('(W\/)?"[\dA-Za-z]+"'),
       'If-Modified-Since' => @@rfs1123,
       'If-Match' => Regexp.new('(W\/)?"[\dA-Za-z]+"'),
@@ -39,13 +38,13 @@ module FHIR
     #   :headers => {},
     #   :payload => nil # body of request goes here in POST
     # }
-    attr_accessor :request  
+    attr_accessor :request
     # {
     #   :code => '200',
     #   :headers => {},
     #   :body => '{xml or json here}'
     # }
-    attr_accessor :response 
+    attr_accessor :response
     attr_accessor :resource # a FHIR resource
     attr_accessor :resource_class # class of the :resource
 
@@ -61,7 +60,7 @@ module FHIR
     def id
       return nil if @resource_class.nil?
       (self_link || @request[:url]) =~ %r{(?<=#{@resource_class.name.demodulize}\/)([^\/]+)}
-      $1
+      Regexp.last_match(1)
     end
 
     def version
@@ -71,7 +70,7 @@ module FHIR
         begin
           tokens = link.split('_history/')
           version = tokens.last.split('/').first
-        rescue Exception => e
+        rescue
           version = nil
         end
       end
@@ -100,49 +99,46 @@ module FHIR
     def validate
       errors = []
       @@validation_rules.each do |rule|
-        if rule['verb']==@request[:method].to_s.upcase
-          rule_match = false
-          rule['path'].each do |path|
-            rule_regex = path.gsub('/','(\/)').gsub('?','\?')
-            @@path_regexes.each do |token,regex|
-              rule_regex.gsub!(token,regex)
-            end
-            rule_match = true if(Regexp.new(rule_regex) =~ @request[:path])
-          end
-          if rule_match
-            # check the request headers
-            errors << validate_headers("#{rule['interaction'].upcase} REQUEST",@request[:headers],rule['request']['headers'])
-            # check the request body
-            errors << validate_body("#{rule['interaction'].upcase} REQUEST",@request[:payload],rule['request']['body'])
-            # check the response codes
-            if !rule['response']['status'].include?(@response[:code].to_i)
-              errors << "#{rule['interaction'].upcase} RESPONSE: Invalid response code: #{@response[:code]}" 
-            end
-            if @response[:code].to_i < 400
-              # check the response headers
-              errors << validate_headers("#{rule['interaction'].upcase} RESPONSE",@response[:headers],rule['response']['headers'])
-              # check the response body
-              errors << validate_body("#{rule['interaction'].upcase} RESPONSE",@response[:body],rule['response']['body'])
-            end
+        next unless rule['verb'] == @request[:method].to_s.upcase
+        rule_match = false
+        rule['path'].each do |path|
+          rule_regex = path.gsub('/', '(\/)').gsub('?', '\?')
+          @@path_regexes.each do |token, regex|
+            rule_regex.gsub!(token, regex)
           end
+          rule_match = true if Regexp.new(rule_regex) =~ @request[:path]
+        end
+        next unless rule_match
+        # check the request headers
+        errors << validate_headers("#{rule['interaction'].upcase} REQUEST", @request[:headers], rule['request']['headers'])
+        # check the request body
+        errors << validate_body("#{rule['interaction'].upcase} REQUEST", @request[:payload], rule['request']['body'])
+        # check the response codes
+        unless rule['response']['status'].include?(@response[:code].to_i)
+          errors << "#{rule['interaction'].upcase} RESPONSE: Invalid response code: #{@response[:code]}"
         end
+        next unless @response[:code].to_i < 400
+        # check the response headers
+        errors << validate_headers("#{rule['interaction'].upcase} RESPONSE", @response[:headers], rule['response']['headers'])
+        # check the response body
+        errors << validate_body("#{rule['interaction'].upcase} RESPONSE", @response[:body], rule['response']['body'])
       end
       errors.flatten
     end
 
-    def validate_headers(name,headers,header_rules)
+    def validate_headers(name, headers, header_rules)
       errors = []
-      header_rules.each do |header,present|
+      header_rules.each do |header, present|
         value = headers[header]
-        if present==true
+        if present == true
           if value
-            errors << "#{name}: Malformed value for header #{header}: #{value}" if !(@@header_regexes[header] =~ value)
+            errors << "#{name}: Malformed value for header #{header}: #{value}" unless @@header_regexes[header] =~ value
           else
             errors << "#{name}: Missing header: #{header}"
           end
-        elsif (present=='optional' && value)
-          errors << "#{name}: Malformed value for optional header #{header}: #{value}" if !(@@header_regexes[header] =~ value)
-#          binding.pry if !(@@header_regexes[header] =~ value)
+        elsif present == 'optional' && value
+          errors << "#{name}: Malformed value for optional header #{header}: #{value}" unless @@header_regexes[header] =~ value
+        #          binding.pry if !(@@header_regexes[header] =~ value)
         elsif !value.nil?
           errors << "#{name}: Should not have header: #{header}"
         end
@@ -150,24 +146,25 @@ module FHIR
       errors
     end
 
-    def validate_body(name,body,body_rules)
+    def validate_body(name, body, body_rules)
       errors = []
       if body && body_rules
         if body_rules['types']
           body_type_match = false
-          body_rules['types'].each do |type|
-            begin
-              content = FHIR.from_contents(body)
-              body_type_match = true if content.resourceType==type
-              body_type_match = true if type=='Resource' && FHIR::RESOURCES.include?(content.resourceType)
-            rescue
+          begin
+            content = FHIR.from_contents(body)
+            body_rules['types'].each do |type|
+              body_type_match = true if content.resourceType == type
+              body_type_match = true if type == 'Resource' && FHIR::RESOURCES.include?(content.resourceType)
             end
+          rescue
+            FHIR.logger.warn "ClientReply was unable to validate response body: #{body}"
           end
-          errors << "#{name}: Body does not match allowed types: #{body_rules['types'].join(', ')}" if !body_type_match              
+          errors << "#{name}: Body does not match allowed types: #{body_rules['types'].join(', ')}" unless body_type_match
         end
         if body_rules['regex']
           regex = Regexp.new(body_rules['regex'])
-          errors << "#{name}: Body does not match regular expression: #{body_rules['regex']}" if !(regex =~ body)
+          errors << "#{name}: Body does not match regular expression: #{body_rules['regex']}" unless regex =~ body
         end
       elsif body && !body_rules
         errors "#{name}: Body not allowed"
@@ -176,6 +173,5 @@ module FHIR
     end
 
     private :validate_headers, :validate_body
-
   end
-end
+end

data/lib/{model → fhir_client/model}/tag.rb

@@ -2,12 +2,12 @@ module FHIR
   class Tag
     # Each Tag is part of an HTTP header named "Category" with three parts: term, scheme, and label.
     # Each Tag can be in an individual "Category" header, or they can all be concatentated (with comma
-    # separation) inside a single "Category" header. 
+    # separation) inside a single "Category" header.
 
     # Term is a URI:
-    #   General tags: 
+    #   General tags:
     #     Bundle / FHIR Documents: "http://hl7.org/fhir/tag/document"
-    #     Bundle / FHIR Messages:  "http://hl7.org/fhir/tag/message" 
+    #     Bundle / FHIR Messages:  "http://hl7.org/fhir/tag/message"
     #   Profile tags: URL that references a profile resource.
     attr_accessor :term
 
@@ -22,7 +22,7 @@ module FHIR
 
     def to_header
       s = "#{term}; scheme=#{scheme}"
-      s += "; label=#{label}" if !label.nil?
+      s += "; label=#{label}" unless label.nil?
       s
     end
 
@@ -35,10 +35,10 @@ module FHIR
       tokens.each do |token|
         if !token.strip.index('scheme').nil?
           token.strip =~ %r{(?<=scheme)(\s*)=(\s*)([\".:_\-\/\w]+)}
-          h.scheme = $3
+          h.scheme = Regexp.last_match(3)
         elsif !token.strip.index('label').nil?
           token.strip =~ %r{(?<=label)(\s*)=(\s*)([\".:_\-\/\w\s]+)}
-          h.label = $3
+          h.label = Regexp.last_match(3)
         end
       end
       h
@@ -52,6 +52,5 @@ module FHIR
       tokens.each { |token| tags << FHIR::Tag.parse_tag(token) }
       tags
     end
-
   end
 end

data/lib/fhir_client/patch_format.rb

@@ -0,0 +1,8 @@
+module FHIR
+  module Formats
+    class PatchFormat
+      PATCH_XML = 'application/xml-patch+xml'.freeze
+      PATCH_JSON = 'application/json-patch+json'.freeze
+    end
+  end
+end

data/lib/{resource_address.rb → fhir_client/resource_address.rb}

@@ -1,139 +1,135 @@
-module FHIR
-  class ResourceAddress
-
-    DEFAULTS = {
-      id: nil,
-      resource: nil,
-      format: 'application/fhir+xml'
-    }
-
-    DEFAULT_CHARSET = 'UTF-8'
-
-    def fhir_headers(options, use_format_param=false)
-      options = DEFAULTS.merge(options)
-
-      format = options[:format] || FHIR::Formats::ResourceFormat::RESOURCE_XML
-      fhir_headers = {
-        'User-Agent' => 'Ruby FHIR Client',
-        'Content-Type' => format + ';charset=' + DEFAULT_CHARSET,
-        'Accept-Charset' => DEFAULT_CHARSET
-      }
-      # remove the content-type header if the format is 'xml' or 'json' because
-      # even those are valid _format parameter options, they are not valid MimeTypes.
-      fhir_headers.delete('Content-Type') if ['xml','json'].include?(format.downcase)
-
-      if(options[:category])
-        # options[:category] should be an Array of FHIR::Tag objects
-        tags = {
-          'Category' => options[:category].collect { |h| h.to_header }.join(',')
-        }
-        fhir_headers.merge!(tags)
-        options.delete(:category)
-      end
-
-      if use_format_param
-        fhir_headers.delete('Accept')
-        options.delete('Accept')
-        options.delete(:accept)
-      else
-        fhir_headers['Accept'] = format
-      end
-
-      fhir_headers.merge!(options) unless options.empty?
-      fhir_headers[:operation] = options[:operation][:name] if options[:operation] && options[:operation][:name]
-      fhir_headers
-    end
-
-    def resource_url(options, use_format_param=false)
-      options = DEFAULTS.merge(options)
-
-      params = {}
-      url = ""
-      # handle requests for resources by class or string; useful for testing nonexistent resource types
-      url += "/#{ options[:resource].try(:name).try(:demodulize) || options[:resource].split("::").last }" if options[:resource]
-      url += "/#{options[:id]}" if options[:id]
-      url += "/$validate" if options[:validate]
-
-      if(options[:operation])
-        opr = options[:operation]
-        p = opr[:parameters]
-        p = p.each{|k,v|p[k]=v[:value]} if p
-        params.merge!(p) if p && opr[:method]=='GET'
-
-        if (opr[:name] == :fetch_patient_record)
-          url += "/$everything"
-        elsif (opr[:name] == :value_set_expansion)
-          url += "/$expand"
-        elsif (opr  && opr[:name]== :value_set_based_validation)
-          url += "/$validate-code"
-        elsif (opr  && opr[:name]== :code_system_lookup)
-          url += "/$lookup"
-        elsif (opr  && opr[:name]== :concept_map_translate)
-          url += "/$translate"
-        elsif (opr  && opr[:name]== :closure_table_maintenance)
-          url += "/$closure"
-        end
-      end
-
-      if (options[:history])
-        history = options[:history]
-        url += "/_history/#{history[:id]}"
-        params[:_count] = history[:count] if history[:count]
-        params[:_since] = history[:since].iso8601 if history[:since]
-      end
-
-      if(options[:search])
-        search_options = options[:search]
-        url += '/_search' if search_options[:flag]
-        url += "/#{search_options[:compartment]}" if search_options[:compartment]
-
-        if search_options[:parameters]
-          search_options[:parameters].each do |key,value|
-            params[key.to_sym] = value
-          end
-        end
-      end
-
-      # options[:params] is simply appended at the end of a url and is used by testscripts
-      url += options[:params] if options[:params]
-
-      if(options[:summary])
-        params[:_summary] = options[:summary]
-      end
-
-      if use_format_param && options[:format]
-        params[:_format] = options[:format]
-      end
-
-      uri = Addressable::URI.parse(url)
-      # params passed in options takes precidence over params calculated in this method
-      # for use by testscript primarily
-      uri.query_values = params unless options[:params] && options[:params].include?("?")
-      uri.normalize.to_str
-    end
-
-    # Get the resource ID out of the URL (e.g. Bundle.entry.response.location)
-    def self.pull_out_id(resourceType,url)
-      id = nil
-      if !resourceType.nil? && !url.nil?
-        token = "#{resourceType}/"
-        if url.index(token)
-          start = url.index(token) + token.length
-          t = url[start..-1]
-          stop = (t.index("/") || 0)-1
-          stop = -1 if stop.nil?
-          id = t[0..stop]
-        else
-          id = nil
-        end
-      end
-      id
-    end
-
-    def self.append_forward_slash_to_path(path)
-      path += '/' unless path.last == '/'
-      path
-    end
-
-  end
-end
+module FHIR
+  class ResourceAddress
+    DEFAULTS = {
+      id: nil,
+      resource: nil,
+      format: 'application/fhir+xml'
+    }.freeze
+
+    DEFAULT_CHARSET = 'UTF-8'.freeze
+
+    def fhir_headers(options, use_format_param = false)
+      options = DEFAULTS.merge(options)
+
+      format = options[:format] || FHIR::Formats::ResourceFormat::RESOURCE_XML
+      fhir_headers = {
+        'User-Agent' => 'Ruby FHIR Client',
+        'Content-Type' => format + ';charset=' + DEFAULT_CHARSET,
+        'Accept-Charset' => DEFAULT_CHARSET
+      }
+      # remove the content-type header if the format is 'xml' or 'json' because
+      # even those are valid _format parameter options, they are not valid MimeTypes.
+      fhir_headers.delete('Content-Type') if %w(xml json).include?(format.downcase)
+
+      if options[:category]
+        # options[:category] should be an Array of FHIR::Tag objects
+        tags = {
+          'Category' => options[:category].collect(&:to_header).join(',')
+        }
+        fhir_headers.merge!(tags)
+        options.delete(:category)
+      end
+
+      if use_format_param
+        fhir_headers.delete('Accept')
+        options.delete('Accept')
+        options.delete(:accept)
+      else
+        fhir_headers['Accept'] = format
+      end
+
+      fhir_headers.merge!(options) unless options.empty?
+      fhir_headers[:operation] = options[:operation][:name] if options[:operation] && options[:operation][:name]
+      fhir_headers
+    end
+
+    def resource_url(options, use_format_param = false)
+      options = DEFAULTS.merge(options)
+
+      params = {}
+      url = ''
+      # handle requests for resources by class or string; useful for testing nonexistent resource types
+      url += "/#{options[:resource].try(:name).try(:demodulize) || options[:resource].split('::').last}" if options[:resource]
+      url += "/#{options[:id]}" if options[:id]
+      url += '/$validate' if options[:validate]
+
+      if options[:operation]
+        opr = options[:operation]
+        p = opr[:parameters]
+        p = p.each { |k, v| p[k] = v[:value] } if p
+        params.merge!(p) if p && opr[:method] == 'GET'
+
+        if opr[:name] == :fetch_patient_record
+          url += '/$everything'
+        elsif opr[:name] == :value_set_expansion
+          url += '/$expand'
+        elsif opr  && opr[:name] == :value_set_based_validation
+          url += '/$validate-code'
+        elsif opr  && opr[:name] == :code_system_lookup
+          url += '/$lookup'
+        elsif opr  && opr[:name] == :concept_map_translate
+          url += '/$translate'
+        elsif opr  && opr[:name] == :closure_table_maintenance
+          url += '/$closure'
+        end
+      end
+
+      if options[:history]
+        history = options[:history]
+        url += "/_history/#{history[:id]}"
+        params[:_count] = history[:count] if history[:count]
+        params[:_since] = history[:since].iso8601 if history[:since]
+      end
+
+      if options[:search]
+        search_options = options[:search]
+        url += '/_search' if search_options[:flag]
+        url += "/#{search_options[:compartment]}" if search_options[:compartment]
+
+        if search_options[:parameters]
+          search_options[:parameters].each do |key, value|
+            params[key.to_sym] = value
+          end
+        end
+      end
+
+      # options[:params] is simply appended at the end of a url and is used by testscripts
+      url += options[:params] if options[:params]
+
+      params[:_summary] = options[:summary] if options[:summary]
+
+      if use_format_param && options[:format]
+        params[:_format] = options[:format]
+      end
+
+      uri = Addressable::URI.parse(url)
+      # params passed in options takes precidence over params calculated in this method
+      # for use by testscript primarily
+      uri.query_values = params unless options[:params] && options[:params].include?('?')
+      uri.normalize.to_str
+    end
+
+    # Get the resource ID out of the URL (e.g. Bundle.entry.response.location)
+    def self.pull_out_id(resource_type, url)
+      id = nil
+      if !resource_type.nil? && !url.nil?
+        token = "#{resource_type}/"
+        if url.index(token)
+          start = url.index(token) + token.length
+          t = url[start..-1]
+          stop = (t.index('/') || 0) - 1
+          stop = -1 if stop.nil?
+          id = t[0..stop]
+        else
+          id = nil
+        end
+      end
+      id
+    end
+
+    def self.append_forward_slash_to_path(path)
+      path += '/' unless path.last == '/'
+      path
+    end
+  end
+end