fhir_client 3.1.2 → 4.0.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/.gitignore

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

data/.rubocop.yml

@@ -1,5 +1,7 @@
+inherit_from: .rubocop_todo.yml
+
 AllCops:
-  TargetRubyVersion: 2.3
+  TargetRubyVersion: 2.4
   Exclude:
     - '*.gemspec'
     - 'Gemfile*'
@@ -24,4 +26,4 @@ Performance/Casecmp:
   Enabled: false
 
 Naming:
-  Enabled: false
+  Enabled: false

data/.rubocop_todo.yml

@@ -0,0 +1,19 @@
+# This configuration was generated by
+# `rubocop --auto-gen-config`
+# on 2019-03-22 01:56:17 -0400 using RuboCop version 0.52.1.
+# The point is for the user to remove these configuration records
+# one by one as the offenses are removed from the code base.
+# Note that changes in the inspected code, or installation of new
+# versions of RuboCop, may require this file to be generated again.
+
+# Offense count: 4
+# Cop supports --auto-correct.
+Performance/RegexpMatch:
+  Exclude:
+    - 'lib/fhir_client/model/client_reply.rb'
+
+# Offense count: 197
+# Configuration parameters: AllowHeredoc, AllowURI, URISchemes, IgnoreCopDirectives, IgnoredPatterns.
+# URISchemes: http, https
+Metrics/LineLength:
+  Max: 210

data/.travis.yml

@@ -1,6 +1,5 @@
 language: ruby
 rvm:
-  - 2.3
   - 2.4
   - 2.5
   - 2.6

data/Gemfile

@@ -1,12 +1,9 @@
 source 'https://rubygems.org'
 
-# gem 'fhir_models', :path => '../fhir_models'
-# gem 'fhir_dstu2_models', :path => '../fhir_dstu2_models'
-
 gemspec
 
 group :test do
   gem 'codeclimate-test-reporter', require: nil
-  gem 'rubocop', '~> 0.56.0', require: false
+  gem 'rubocop', '~> 0.52.1', require: false
   gem 'awesome_print', require: 'ap'
 end

data/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.

data/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'

data/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 @@ Dir.glob(File.join(root, 'fhir_client', 'ext', '**', '*.rb')).each do |file|
   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'

data/lib/fhir_client/client.rb

@@ -11,6 +11,7 @@ module FHIR
     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 @@ module FHIR
     # @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 @@ module FHIR
     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 @@ module FHIR
       @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 @@ module FHIR
       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 @@ module FHIR
                 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 @@ module FHIR
         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

data/lib/fhir_client/ext/bundle.rb

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

data/lib/fhir_client/ext/model.rb

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

data/lib/fhir_client/ext/reference.rb

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

data/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 @@ module FHIR
         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 @@ module FHIR
     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

data/lib/fhir_client/sections/crud.rb

@@ -209,17 +209,11 @@ module FHIR
           type = reply.response[:headers].detect{|x, _y| x.downcase=='content-type'}.try(:last)
           if !type.nil?
             reply.resource = if type.include?('xml') && !reply.body.empty?
-                               if @fhir_version == :stu3
-                                 FHIR::Xml.from_xml(reply.body)
-                               else
-                                 FHIR::DSTU2::Xml.from_xml(reply.body)
-                               end
+                               klass = self.versioned_resource_class(:Xml)
+                               klass.from_xml(reply.body)
                              elsif type.include?('json') && !reply.body.empty?
-                               if @fhir_version == :stu3
-                                 FHIR::Json.from_json(reply.body)
-                               else
-                                 FHIR::DSTU2::Json.from_json(reply.body)
-                               end
+                               klass = self.versioned_resource_class(:Json)
+                               klass.from_json(reply.body)
                              else
                                resource # just send back the submitted resource
                              end

data/lib/fhir_client/sections/history.rb

@@ -28,11 +28,7 @@ module FHIR
         reply = get resource_url(options), fhir_headers
 
         # The history reply should be a bundle
-        bundle_klass = if @fhir_version == :stu3
-                         FHIR::Bundle
-                       else
-                         FHIR::DSTU2::Bundle
-                       end
+        bundle_klass = self.versioned_resource_class(:Bundle)
 
         reply.resource = parse_reply(bundle_klass, options[:format], reply)
         reply.resource_class = options[:resource]

data/lib/fhir_client/sections/operations.rb

@@ -73,10 +73,10 @@ module FHIR
 
       # Concept Look Up [base]/CodeSystem/$lookup
       def code_system_lookup(params = {}, format = @default_format)
-        klass = if @fhir_version == :stu3
-                  FHIR::CodeSystem
-                else
+        klass = if @fhir_version == :dstu2
                   FHIR::DSTU2::ValueSet
+                else
+                  self.versioned_resource_class(:CodeSystem)
                 end
         options = { resource: klass, operation: { name: :code_system_lookup } }
         options.deep_merge!(params)

data/lib/fhir_client/version.rb

@@ -1,5 +1,5 @@
 module FHIR
   class Client
-    VERSION = '3.1.2'
+    VERSION = '4.0.0'
   end
 end

data/lib/fhir_client/version_management.rb

@@ -0,0 +1,44 @@
+module FHIR
+  module VersionManagement
+
+    def versioned_resource_class(klass = nil)
+      mod = case @fhir_version
+            when :stu3
+              FHIR::STU3
+            when :dstu2
+              FHIR::DSTU2
+            else
+              FHIR
+            end
+      return mod if klass.nil?
+      mod.const_get(klass)
+    end
+
+    def versioned_format_class(format = nil)
+      if @fhir_version == :dstu2
+        case format
+        when nil
+          @default_format.include?('xml') ?
+              FHIR::Formats::ResourceFormat::RESOURCE_XML_DSTU2 :
+              FHIR::Formats::ResourceFormat::RESOURCE_JSON_DSTU2
+        when :xml
+          FHIR::Formats::ResourceFormat::RESOURCE_XML_DSTU2
+        else
+          FHIR::Formats::ResourceFormat::RESOURCE_JSON_DSTU2
+        end
+      else
+        case format
+        when nil
+          @default_format.include?('xml') ?
+              FHIR::Formats::ResourceFormat::RESOURCE_XML :
+              FHIR::Formats::ResourceFormat::RESOURCE_JSON
+        when :xml
+          FHIR::Formats::ResourceFormat::RESOURCE_XML
+        else
+          FHIR::Formats::ResourceFormat::RESOURCE_JSON
+        end
+      end
+    end
+
+  end
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: fhir_client
 version: !ruby/object:Gem::Version
-  version: 3.1.2
+  version: 4.0.0
 platform: ruby
 authors:
 - Andre Quina
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2019-03-21 00:00:00.000000000 Z
+date: 2019-04-24 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activesupport
@@ -46,28 +46,42 @@ dependencies:
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 3.0.3
+        version: 4.0.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 3.0.3
+        version: 4.0.0
+- !ruby/object:Gem::Dependency
+  name: fhir_stu3_models
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.0.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.0.0
 - !ruby/object:Gem::Dependency
   name: fhir_dstu2_models
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.0.4
+        version: 1.0.9
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.0.4
+        version: 1.0.9
 - !ruby/object:Gem::Dependency
   name: nokogiri
   requirement: !ruby/object:Gem::Requirement
@@ -235,6 +249,7 @@ files:
 - ".eslintrc"
 - ".gitignore"
 - ".rubocop.yml"
+- ".rubocop_todo.yml"
 - ".simplecov"
 - ".travis.yml"
 - Gemfile
@@ -266,6 +281,7 @@ files:
 - lib/fhir_client/sections/transactions.rb
 - lib/fhir_client/tasks/tasks.rake
 - lib/fhir_client/version.rb
+- lib/fhir_client/version_management.rb
 homepage: https://github.com/fhir-crucible/fhir_client
 licenses: []
 metadata: {}