Merge pull request #114 from fhir-crucible/r4

R4 Support

Author: arscan

.gitignore

@@ -36,3 +36,6 @@ Gemfile.lock
 # Logs
 *.log
 *.log.*
+
+# User-specific
+.idea

Gemfile

@@ -1,8 +1,5 @@
 source 'https://rubygems.org'
 
-# gem 'fhir_models', :path => '../fhir_models'
-# gem 'fhir_dstu2_models', :path => '../fhir_dstu2_models'
-
 gemspec
 
 group :test do

README.md

@@ -3,8 +3,8 @@
 Ruby FHIR client.
 
 Supports:
-* FHIR STU3 and DSTU2
-* XML and JSON
+* FHIR R4, STU3 and DSTU2
+* JSON and XML
 * All CRUD, including version read and history
 * Transactions and Batches
 * Search
@@ -58,8 +58,8 @@ patient.destroy
 
 ## Advanced Usage
 
-### STU3 and DSTU2
-The client defaults to `STU3` but can be switched to `DSTU2` or it can also attempt to autodetect the FHIR version based on the `metadata` endpoint.
+### Changing FHIR Versions
+The client defaults to `R4` but can be switched to `DSTU2` or `STU3`. It can also attempt to autodetect the FHIR version based on the `metadata` endpoint.
 
 ```ruby
 # autodetect the FHIR version
@@ -69,19 +69,42 @@ if version == :stu3
   puts 'FHIR Client using STU3'
 elsif version == :dstu2
   puts 'FHIR Client using DSTU2'
+elsif version == :r4
+  puts 'FHIR Client using R4'
 end
 
+# tell the client to use R4
+client.use_r4
+# now use the client with the DSTU2 models
+patient = FHIR::Patient.read('example')
+patient = client.read(FHIR::Patient, 'example').resource
+
 # tell the client to use STU3 (default)
 client.use_stu3
 # now use the client normally
-patient = FHIR::Patient.read('example')
-patient = client.read(FHIR::Patient, 'example').resource
+patient = FHIR::STU3::Patient.read('example')
+patient = client.read(FHIR::STU3::Patient, 'example').resource
 
 # tell the client to use DSTU2
 client.use_dstu2
 # now use the client with the DSTU2 models
 patient = FHIR::DSTU2::Patient.read('example')
 patient = client.read(FHIR::DSTU2::Patient, 'example').resource
+
+
+```
+
+### Changing FHIR Formats
+The client defaults to `json` representation of resources but can be switched to `xml` representations.
+
+```ruby
+client = FHIR::Client.new(url)
+
+# Tell the client to use xml
+client.default_xml
+
+# Tell the client to use json
+client.default_json
 ```
 
 ### Configuration
@@ -192,7 +215,7 @@ end
 
 # License
 
-Copyright 2014-2016 The MITRE Corporation
+Copyright 2014-2019 The MITRE Corporation
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

fhir_client.gemspec

@@ -22,8 +22,9 @@ Gem::Specification.new do |spec|
 
   spec.add_dependency 'activesupport', '>= 3'
   spec.add_dependency 'addressable', '>= 2.3'
-  spec.add_dependency 'fhir_models', '>= 3.0.3'
-  spec.add_dependency 'fhir_dstu2_models', '>= 1.0.4'
+  spec.add_dependency 'fhir_models', '>= 4.0.0'
+  spec.add_dependency 'fhir_stu3_models', '>= 3.0.0'
+  spec.add_dependency 'fhir_dstu2_models', '>= 1.0.9'
   spec.add_dependency 'nokogiri', '>= 1.8.2'
   spec.add_dependency 'oauth2', '~> 1.1'
   spec.add_dependency 'rack', '>= 1.5'

lib/fhir_client.rb

@@ -1,5 +1,6 @@
 require 'fhir_models'
 require 'fhir_dstu2_models'
+require 'fhir_stu3_models'
 require 'active_support/all'
 
 root = File.expand_path '.', File.dirname(File.absolute_path(__FILE__))
@@ -10,6 +11,7 @@
   require file
 end
 
+require_relative 'fhir_client/version_management'
 require_relative 'fhir_client/client'
 require_relative 'fhir_client/resource_address'
 require_relative 'fhir_client/resource_format'

lib/fhir_client/client.rb

@@ -11,6 +11,7 @@ class Client
     include FHIR::Sections::Search
     include FHIR::Sections::Operations
     include FHIR::Sections::Transactions
+    include FHIR::VersionManagement
 
     attr_accessor :reply
     attr_accessor :use_format_param
@@ -37,14 +38,14 @@ class Client
     # @param default_format Default Format Mime type
     # @return
     #
-    def initialize(base_service_url, default_format: FHIR::Formats::ResourceFormat::RESOURCE_XML, proxy: nil)
+    def initialize(base_service_url, default_format: FHIR::Formats::ResourceFormat::RESOURCE_JSON, proxy: nil)
       @base_service_url = base_service_url
       FHIR.logger.info "Initializing client with #{@base_service_url}"
       @use_format_param = false
       @use_accept_header = true
       @use_accept_charset = true
       @default_format = default_format
-      @fhir_version = :stu3
+      @fhir_version = :r4
       @use_return_preference = false
       @return_preference = FHIR::Formats::ReturnPreferences::REPRESENTATION
       @exception_class = ClientException
@@ -54,37 +55,26 @@ def initialize(base_service_url, default_format: FHIR::Formats::ResourceFormat::
     end
 
     def default_json
-      @default_format = if @fhir_version == :stu3
-                          FHIR::Formats::ResourceFormat::RESOURCE_JSON
-                        else
-                          FHIR::Formats::ResourceFormat::RESOURCE_JSON_DSTU2
-                        end
+      @default_format = versioned_format_class(:json)
     end
 
     def default_xml
-      @default_format = if @fhir_version == :stu3
-                          FHIR::Formats::ResourceFormat::RESOURCE_XML
-                        else
-                          FHIR::Formats::ResourceFormat::RESOURCE_XML_DSTU2
-                        end
+      @default_format = versioned_format_class(:xml)
     end
 
     def use_stu3
       @fhir_version = :stu3
-      @default_format = if @default_format.include?('xml')
-                          FHIR::Formats::ResourceFormat::RESOURCE_XML
-                        else
-                          FHIR::Formats::ResourceFormat::RESOURCE_JSON
-                        end
+      @default_format = versioned_format_class
     end
 
     def use_dstu2
       @fhir_version = :dstu2
-      @default_format = if @default_format.include?('xml')
-                          FHIR::Formats::ResourceFormat::RESOURCE_XML_DSTU2
-                        else
-                          FHIR::Formats::ResourceFormat::RESOURCE_JSON_DSTU2
-                        end
+      @default_format = versioned_format_class
+    end
+
+    def use_r4
+      @fhir_version = :r4
+      @default_format = versioned_format_class
     end
 
     #
@@ -101,23 +91,19 @@ def use_representation_preference
       @return_preference = FHIR::Formats::ReturnPreferences::REPRESENTATION
     end
 
-    def versioned_resource_class(klass)
-      if @fhir_version == :stu3
-        FHIR.const_get(klass)
-      else
-        FHIR::DSTU2.const_get(klass)
-      end
-    end
-
     def detect_version
       cap = capability_statement
       if cap.is_a?(FHIR::CapabilityStatement)
-        @fhir_version = :stu3
+        use_r4
+      elsif cap.is_a?(FHIR::STU3::CapabilityStatement)
+        use_stu3
       elsif cap.is_a?(FHIR::DSTU2::Conformance)
-        @fhir_version = :dstu2
+        use_dstu2
       else
-        @fhir_version = :stu3
+        use_r4
       end
+      # Should update the default_format when changing fhir_version
+      @default_format = versioned_format_class
       FHIR.logger.info("Detecting server FHIR version as #{@fhir_version} via metadata")
       @fhir_version
     end
@@ -279,22 +265,31 @@ def try_conformance_formats(default_format)
       formats.insert(0, default_format)
 
       @cached_capability_statement = nil
-      @default_format = nil
 
       formats.each do |frmt|
         reply = get 'metadata', fhir_headers({accept: "#{frmt}"})
         next unless reply.code == 200
+        use_r4
         begin
           @cached_capability_statement = parse_reply(FHIR::CapabilityStatement, frmt, reply)
         rescue
           @cached_capability_statement = nil
         end
-        unless @cached_capability_statement
+        if @cached_capability_statement.nil? || !@cached_capability_statement.fhirVersion.starts_with?('4')
+          use_stu3
           begin
-            @cached_capability_statement = parse_reply(FHIR::DSTU2::Conformance, frmt, reply)
+            @cached_capability_statement = parse_reply(FHIR::STU3::CapabilityStatement, frmt, reply)
           rescue
             @cached_capability_statement = nil
           end
+          unless @cached_capability_statement
+            use_dstu2
+            begin
+              @cached_capability_statement = parse_reply(FHIR::DSTU2::Conformance, frmt, reply)
+            rescue
+              @cached_capability_statement = nil
+            end
+          end
         end
         if @cached_capability_statement
           @default_format = frmt
@@ -328,12 +323,18 @@ def parse_reply(klass, format, response)
                 else
                   FHIR::DSTU2::Json.from_json(response.body)
                 end
-              else
+              elsif(@fhir_version == :r4 || klass&.ancestors&.include?(FHIR::Model))
                 if(format.include?('xml'))
                   FHIR::Xml.from_xml(response.body)
                 else
                   FHIR::Json.from_json(response.body)
                 end
+              else
+                if(format.include?('xml'))
+                  FHIR::STU3::Xml.from_xml(response.body)
+                else
+                  FHIR::STU3::Json.from_json(response.body)
+                end
               end
         res.client = self unless res.nil?
         FHIR.logger.warn "Expected #{klass} but got #{res.class}" if res.class != klass
@@ -353,11 +354,7 @@ def reissue_request(request)
         method(request['method']).call(request['url'], request['headers'])
       elsif [:post, :put].include?(request['method'])
         unless request['payload'].nil?
-          resource = if @fhir_version == :stu3
-                       FHIR.from_contents(request['payload'])
-                     else
-                       FHIR::DSTU2.from_contents(request['payload'])
-                     end
+          resource = versioned_resource_class.from_contents(request['payload'])
         end
         method(request['method']).call(request['url'], resource, request['headers'])
       end

lib/fhir_client/ext/bundle.rb

@@ -60,3 +60,11 @@ class Bundle
     end
   end
 end
+
+module FHIR
+  module STU3
+    class Bundle
+      include FHIR::BundleExtras
+    end
+  end
+end

lib/fhir_client/ext/model.rb

@@ -139,3 +139,11 @@ class Model
     end
   end
 end
+
+module FHIR
+  module STU3
+    class Model
+      include FHIR::ModelExtras
+    end
+  end
+end

lib/fhir_client/ext/reference.rb

@@ -39,7 +39,7 @@ def reference_id
       end
     end
 
-    def type
+    def resource_type
       return if contained?
       parts[:type]
     end
@@ -82,7 +82,7 @@ class Reference
     include FHIR::ReferenceExtras
 
     def resource_class
-      "FHIR::#{type}".constantize unless contained?
+      "FHIR::#{resource_type}".constantize unless contained?
     end
   end
 end
@@ -93,7 +93,19 @@ class Reference
       include FHIR::ReferenceExtras
 
       def resource_class
-        "FHIR::DSTU2::#{type}".constantize unless contained?
+        "FHIR::DSTU2::#{resource_type}".constantize unless contained?
+      end
+    end
+  end
+end
+
+module FHIR
+  module STU3
+    class Reference
+      include FHIR::ReferenceExtras
+
+      def resource_class
+        "FHIR::STU3::#{resource_type}".constantize unless contained?
       end
     end
   end

lib/fhir_client/model/client_reply.rb

@@ -1,5 +1,8 @@
 module FHIR
   class ClientReply
+
+    include FHIR::VersionManagement
+
     @@path_regexes = {
       '[type]' => "(#{FHIR::RESOURCES.join('|')})",
       '[id]' => FHIR::PRIMITIVES['id']['regex'],
@@ -157,11 +160,7 @@ def validate_body(name, body, body_rules)
         if body_rules['types']
           body_type_match = false
           begin
-            content = if @fhir_version == :stu3
-                        FHIR.from_contents(body)
-                      else
-                        FHIR::DSTU2.from_contents(body)
-                      end
+            content = versioned_resource_class().from_contents(body)
             body_rules['types'].each do |type|
               body_type_match = true if content.resourceType == type
               body_type_match = true if type == 'Resource' && validate_resource(content.resourceType)
@@ -182,12 +181,7 @@ def validate_body(name, body, body_rules)
     end
 
     def validate_resource(resource_type)
-      if @fhir_version == :stu3
-        return true if FHIR::RESOURCES.include?(resource_type)
-      else
-        return true if FHIR::DSTU2::RESOURCES.include?(resource_type)
-      end
-      false
+      versioned_resource_class(:RESOURCES).include?(resource_type)? true : false
     end
 
     private :validate_headers, :validate_body, :validate_resource