fhir_client 4.0.4 → 5.0.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: c0f74ff0812b021eac3244300451f4970bf4eb12b81fc647a7abd8f6d270c310
-  data.tar.gz: 10f8902a26af03ed539b80631621210d9bbdae5664ef37abcc41a59054d4b55d
+  metadata.gz: 89d03abbe3eca9297ffb9babe42c7c60c7ca2049dc7281f601a6394e963ff64f
+  data.tar.gz: a2a57d32d9d21a35a8bd7ce8f974615b1b7e8dce9686e146841709e9b6a9aff2
 SHA512:
-  metadata.gz: 824e2cf15a2387215ddf7d21ce1b03be870700f9eec697850360579d4405351d94b7710e3146baad5150c3b9ccf4ffe79d0a0f990c42e80663213b459bd3281b
-  data.tar.gz: c57df2cd3af870ec55470ee8536947b2601c2328ac7e1c41071ae8bda12d107e3cac96edf94ee6f8f8c2bf9e10c947e7373336dedccee036615c782518461f6c
+  metadata.gz: 752717f497d72a424f21b9c7c3e4f48de356fdf9a16678f0808009d8284dd32a4c362dfa89e993acf594245d0b6e4fdef5f3d19ba17ea86226eaf9eab3565d1d
+  data.tar.gz: dcea71cd74854f955b4acfb453ae4263b30c31b29575319f213c48b704ff5a5578409170909bf2a495d59c71601063726abd99b332220dc18fd2091b305b3e3e

data/.github/workflows/ruby.yml

@@ -0,0 +1,26 @@
+name: Ruby
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        ruby-version: ['2.6', '2.7']
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Ruby
+      uses: ruby/setup-ruby@v1
+      with:
+        ruby-version: ${{ matrix.ruby-version }}
+        bundler-cache: true # runs 'bundle install' and caches installed gems automatically
+    - name: Run tests
+      run: bundle exec rake
+    - name: Rubocop
+      run: bundle exec rubocop

data/README.md

@@ -151,9 +151,14 @@ client.destroy(FHIR::Patient, patient_id)
 
 ### Searching
 ```ruby
+# via GET
 reply = client.search(FHIR::Patient, search: {parameters: {name: 'P'}})
+
+# via POST
+reply = client.search(FHIR::Patient, search: {body: {name: 'P'}})
+
 bundle = reply.resource
-patient = bundle.entry.first.resource
+patient = bundle&.entry&.first&.resource
 ```
 
 ### Fetching a Bundle
@@ -215,7 +220,7 @@ end
 
 # License
 
-Copyright 2014-2019 The MITRE Corporation
+Copyright 2014-2022 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/Rakefile

@@ -19,8 +19,4 @@ task :rubocop do
   RuboCop::RakeTask.new
 end
 
-task test: [:rubocop] do
-  system('open coverage/index.html')
-end
-
 task default: [:test]

data/fhir_client.gemspec

@@ -6,8 +6,9 @@ require 'fhir_client/version'
 Gem::Specification.new do |spec|
   spec.name          = 'fhir_client'
   spec.version       = FHIR::Client::VERSION
-  spec.authors       = ['Andre Quina', 'Jason Walonoski', 'Janoo Fernandes']
+  spec.authors       = ['Andre Quina', 'Jason Walonoski', 'Robert Scanlon', 'Reece Adamson']
   spec.email         = ['jwalonoski@mitre.org']
+  spec.licenses      = ['Apache-2.0']
 
   spec.summary       = %q{A Gem for handling FHIR client requests in ruby}
   spec.description   = %q{A Gem for handling FHIR client requests in ruby}
@@ -22,9 +23,9 @@ Gem::Specification.new do |spec|
 
   spec.add_dependency 'activesupport', '>= 3'
   spec.add_dependency 'addressable', '>= 2.3'
-  spec.add_dependency 'fhir_models', '>= 4.0.2'
-  spec.add_dependency 'fhir_stu3_models', '>= 3.0.1'
-  spec.add_dependency 'fhir_dstu2_models', '>= 1.0.10'
+  spec.add_dependency 'fhir_models', '>= 4.2.0'
+  spec.add_dependency 'fhir_stu3_models', '>= 3.1.0'
+  spec.add_dependency 'fhir_dstu2_models', '>= 1.1.0'
   spec.add_dependency 'nokogiri', '>= 1.10.4'
   spec.add_dependency 'oauth2', '~> 1.1'
   spec.add_dependency 'rack', '>= 1.5'
@@ -32,7 +33,7 @@ Gem::Specification.new do |spec|
   spec.add_dependency 'tilt', '>= 1.1'
 
   spec.add_development_dependency 'bundler', '~> 2.0'
-  spec.add_development_dependency 'rake', '~> 10.0'
+  spec.add_development_dependency 'rake', '>= 12.3.3'
   spec.add_development_dependency 'pry'
   spec.add_development_dependency 'webmock'
   spec.add_development_dependency 'test-unit'

data/lib/fhir_client.rb

@@ -3,6 +3,11 @@ require 'fhir_dstu2_models'
 require 'fhir_stu3_models'
 require 'active_support/all'
 
+# Default to INFO level logging for all FHIR namespaced logging. Since there is
+# no single gem that 'owns' the FHIR namespace, we use the client as the spot
+# to set the default. Otherwise the default is set to DEBUG, which is too high.
+FHIR.logger.level = Logger::INFO
+
 root = File.expand_path '.', File.dirname(File.absolute_path(__FILE__))
 Dir.glob(File.join(root, 'fhir_client', 'sections', '**', '*.rb')).each do |file|
   require file

data/lib/fhir_client/client.rb

@@ -315,35 +315,46 @@ module FHIR
     def parse_reply(klass, format, response)
       FHIR.logger.debug "Parsing response with {klass: #{klass}, format: #{format}, code: #{response.code}}."
       return nil unless [200, 201].include? response.code
-      res = nil
-      begin
-        res = if(@fhir_version == :dstu2 || klass&.ancestors&.include?(FHIR::DSTU2::Model))
-                if(format.include?('xml'))
-                  FHIR::DSTU2::Xml.from_xml(response.body)
-                else
-                  FHIR::DSTU2::Json.from_json(response.body)
-                end
-              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?
-      rescue => e
-        FHIR.logger.error "Failed to parse #{format} as resource #{klass}: #{e.message}"
-        res = nil
-      end
+      res =
+        begin
+          if(@fhir_version == :dstu2 || klass&.ancestors&.include?(FHIR::DSTU2::Model))
+            if(format.include?('xml'))
+              FHIR::DSTU2::Xml.from_xml(response.body)
+            else
+              FHIR::DSTU2::Json.from_json(response.body)
+            end
+          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
+        rescue => e
+          FHIR.logger.error "Failed to parse #{format} as resource #{klass}: #{e.message}"
+          nil
+        end
+      set_client_on_resource(res) unless res.nil?
       res
     end
 
+    def set_client_on_resource(resource)
+      return if resource.nil?
+
+      resource.client = self
+      resource.each_element do |element, _, _|
+        if element.is_a?(Reference) || element.is_a?(STU3::Reference) || element.is_a?(DSTU2::Reference) || element.respond_to?(:resourceType)
+          element.client = self
+        end
+      end
+    end
+
     def strip_base(path)
       path.gsub(@base_service_url, '')
     end
@@ -374,6 +385,7 @@ module FHIR
     end
 
     # Extract the request payload in the specified format, defaults to XML
+    # Note that the payload is usually a resource, but could be a form post for searches depending on content type
     def request_payload(resource, headers)
       if headers
         format_specified = headers['Content-Type']
@@ -383,6 +395,10 @@ module FHIR
           resource.to_xml
         elsif format_specified.downcase.include?('json')
           resource.to_json
+        elsif format_specified.downcase == 'application/x-www-form-urlencoded'
+          # Special case where this is a search body and not a resource.
+          # Leave as hash because underlying libraries automatically URL encode it.
+          resource
         else
           resource.to_xml
         end

data/lib/fhir_client/ext/model.rb

@@ -2,17 +2,14 @@ module FHIR
   module ModelExtras
 
     def self.included base
-      base.send :include, InstanceMethods
+      base.include InstanceMethods
       base.extend ClassMethods
+      base.attr_writer :client
     end
 
     module InstanceMethods
       def client
-        FHIR::Model.client
-      end
-
-      def client=(client)
-        FHIR::Model.client = client
+        @client || FHIR::Model.client
       end
 
       def vread(version_id)
@@ -146,4 +143,4 @@ module FHIR
       include FHIR::ModelExtras
     end
   end
-end
+end

data/lib/fhir_client/sections/crud.rb

@@ -226,7 +226,7 @@ module FHIR
           resource.id = FHIR::ResourceAddress.pull_out_id(resource.class.name.demodulize, reply.self_link)
           reply.resource = resource # just send back the submitted resource
         end
-        reply.resource.client = self
+        set_client_on_resource(reply.resource)
         reply.resource_class = resource.class
         reply
       end

data/lib/fhir_client/sections/operations.rb

@@ -132,8 +132,11 @@ module FHIR
         add_resource_parameter(params, 'resource', resource)
         add_parameter(params, 'onlyCertainMatches', 'Boolean', options[:onlyCertainMatches]) unless options[:onlyCertainMatches].nil?
         add_parameter(params, 'count', 'Integer', options[:matchCount]) if options[:matchCount].is_a?(Integer)
-        post resource_url(options), params, fhir_headers({content_type: "#{format || @default_format}",
-                                                          accept: "#{format || @default_format}"})
+        post(
+          resource_url(options),
+          params,
+          fhir_headers({content_type: "#{format || @default_format}", accept: "#{format || @default_format}"})
+        ).tap { |reply| set_client_on_resource(reply.resource) }
       end
 
       #
@@ -154,7 +157,8 @@ module FHIR
         params = versioned_resource_class('Parameters').new
         add_resource_parameter(params, 'resource', resource)
         add_parameter(params, 'profile', 'Uri', options[:profile_uri]) unless options[:profile_uri].nil?
-        post resource_url(options), params, fhir_headers(headers)
+        post(resource_url(options), params, fhir_headers(headers))
+          .tap { |reply| set_client_on_resource(reply.resource) }
       end
 
       def validate_existing(resource, id, options = {}, format = @default_format)
@@ -165,7 +169,8 @@ module FHIR
         params = versioned_resource_class('Parameters').new
         add_resource_parameter(params, 'resource', resource)
         add_parameter(params, 'profile', 'Uri', options[:profile_uri]) unless options[:profile_uri].nil?
-        post resource_url(options), params, fhir_headers(headers)
+        post(resource_url(options), params, fhir_headers(headers))
+          .tap { |reply| set_client_on_resource(reply.resource) }
       end
 
       private

data/lib/fhir_client/sections/search.rb

@@ -12,40 +12,28 @@ module FHIR
         options[:resource] = klass
         options[:format] = format
 
-        reply = if options[:search] && options[:search][:flag]
-                  post resource_url(options), nil, fhir_headers({content_type: 'application/x-www-form-urlencoded'})
-                else
+        reply = if options.dig(:search, :flag) != true && options.dig(:search, :body).nil?
                   get resource_url(options), fhir_headers
+                else
+                  options[:search][:flag] = true
+                  post resource_url(options), options.dig(:search, :body), fhir_headers({content_type: 'application/x-www-form-urlencoded'})
                 end
-        # reply = get resource_url(options), fhir_headers(options)
+
         reply.resource = parse_reply(klass, format, reply)
         reply.resource_class = klass
         reply
       end
 
+      # It does not appear that this is part of the specification (any more?)
+      # Investigate removing in next major version.
       def search_existing(klass, id, options = {}, format = @default_format)
-        options.merge!(resource: klass, id: id, format: format)
-        # if options[:search][:flag]
-        reply = if options[:search] && options[:search][:flag]
-                  post resource_url(options), nil, fhir_headers({content_type: 'application/x-www-form-urlencoded'})
-                else
-                  get resource_url(options), fhir_headers
-                end
-        reply.resource = parse_reply(klass, format, reply)
-        reply.resource_class = klass
-        reply
+        options[:id] = id
+        search(klass, options, format)
       end
 
       def search_all(options = {}, format = @default_format)
         options[:format] = format
-        reply = if options[:search] && options[:search][:flag]
-                  post resource_url(options), nil, fhir_headers({content_type: 'application/x-www-form-urlencoded'})
-                else
-                  get resource_url(options), fhir_headers
-                end
-        reply.resource = parse_reply(nil, format, reply)
-        reply.resource_class = nil
-        reply
+        search(nil, options, format)
       end
     end
   end

data/lib/fhir_client/sections/transactions.rb

@@ -74,6 +74,7 @@ module FHIR
         rescue
           reply.resource = nil
         end
+        set_client_on_resource(reply.resource)
         reply.resource_class = reply.resource.class
         reply
       end

data/lib/fhir_client/version.rb

@@ -1,5 +1,5 @@
 module FHIR
   class Client
-    VERSION = '4.0.4'
+    VERSION = '5.0.1'.freeze
   end
 end

metadata

@@ -1,16 +1,17 @@
 --- !ruby/object:Gem::Specification
 name: fhir_client
 version: !ruby/object:Gem::Version
-  version: 4.0.4
+  version: 5.0.1
 platform: ruby
 authors:
 - Andre Quina
 - Jason Walonoski
-- Janoo Fernandes
-autorequire: 
+- Robert Scanlon
+- Reece Adamson
+autorequire:
 bindir: exe
 cert_chain: []
-date: 2020-02-26 00:00:00.000000000 Z
+date: 2021-08-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activesupport
@@ -46,42 +47,42 @@ dependencies:
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 4.0.2
+        version: 4.2.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 4.0.2
+        version: 4.2.0
 - !ruby/object:Gem::Dependency
   name: fhir_stu3_models
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 3.0.1
+        version: 3.1.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 3.0.1
+        version: 3.1.0
 - !ruby/object:Gem::Dependency
   name: fhir_dstu2_models
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.0.10
+        version: 1.1.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.0.10
+        version: 1.1.0
 - !ruby/object:Gem::Dependency
   name: nokogiri
   requirement: !ruby/object:Gem::Requirement
@@ -170,16 +171,16 @@ dependencies:
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '10.0'
+        version: 12.3.3
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '10.0'
+        version: 12.3.3
 - !ruby/object:Gem::Dependency
   name: pry
   requirement: !ruby/object:Gem::Requirement
@@ -247,11 +248,11 @@ files:
 - ".csslintrc"
 - ".eslintignore"
 - ".eslintrc"
+- ".github/workflows/ruby.yml"
 - ".gitignore"
 - ".rubocop.yml"
 - ".rubocop_todo.yml"
 - ".simplecov"
-- ".travis.yml"
 - Gemfile
 - LICENSE
 - README.md
@@ -283,9 +284,10 @@ files:
 - lib/fhir_client/version.rb
 - lib/fhir_client/version_management.rb
 homepage: https://github.com/fhir-crucible/fhir_client
-licenses: []
+licenses:
+- Apache-2.0
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -300,9 +302,9 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
+rubyforge_project:
 rubygems_version: 2.7.6.2
-signing_key: 
+signing_key:
 specification_version: 4
 summary: A Gem for handling FHIR client requests in ruby
 test_files: []

data/.travis.yml

@@ -1,21 +0,0 @@
-language: ruby
-rvm:
-  - 2.4
-  - 2.5
-  - 2.6
-before_install:
-  - gem update --system
-  - gem install bundler
-before_script:
-  - curl -L https://codeclimate.com/downloads/test-reporter/test-reporter-latest-linux-amd64 > ./cc-test-reporter
-  - chmod +x ./cc-test-reporter
-  - ./cc-test-reporter before-build
-script:
-  - bundle exec rake test
-after_script:
-  - ./cc-test-reporter after-build -t simplecov --exit-code $TRAVIS_TEST_RESULT
-notifications:
-  email:
-    recipients:
-      - fhir-testing-list@lists.mitre.org
-    on_failure: change