fhir_client 4.0.0 → 4.0.5

checksums.yaml

@@ -1,7 +1,7 @@
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data/.travis.yml

@@ -1,19 +1,20 @@
 language: ruby
 rvm:
-  - 2.4
-  - 2.5
   - 2.6
+  - 2.7
 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
-  - bundle exec codeclimate-test-reporter
+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
-addons:
-    code_climate:
-        repo_token: ac1640edaefa720557e56bfaba4e09808559d7d61812f96d58ea4aa5f4669738

data/Gemfile

@@ -3,7 +3,6 @@ source 'https://rubygems.org'
 gemspec
 
 group :test do
-  gem 'codeclimate-test-reporter', require: nil
   gem 'rubocop', '~> 0.52.1', require: false
   gem 'awesome_print', require: 'ap'
 end

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/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}
@@ -22,17 +23,17 @@ Gem::Specification.new do |spec|
 
   spec.add_dependency 'activesupport', '>= 3'
   spec.add_dependency 'addressable', '>= 2.3'
-  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 '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 'nokogiri', '>= 1.10.4'
   spec.add_dependency 'oauth2', '~> 1.1'
   spec.add_dependency 'rack', '>= 1.5'
   spec.add_dependency 'rest-client', '~> 2.0'
   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

@@ -337,7 +337,6 @@ module FHIR
                 end
               end
         res.client = self unless res.nil?
-        FHIR.logger.warn "Expected #{klass} but got #{res.class}" if res.class != klass
       rescue => e
         FHIR.logger.error "Failed to parse #{format} as resource #{klass}: #{e.message}"
         res = nil
@@ -375,6 +374,7 @@ 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']
@@ -384,6 +384,10 @@ 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
@@ -433,7 +437,7 @@ module FHIR
         begin
           response = @client.get(url, headers: headers)
         rescue => e
-          unless e.response
+          if !e.respond_to?(:response) || e.response.nil?
             # Re-raise the client error if there's no response. Otherwise, logging
             # and other things break below!
             FHIR.logger.error "GET - Request: #{url} failed! No response from server: #{e}"
@@ -480,7 +484,7 @@ module FHIR
           @reply = FHIR::ClientReply.new(req, res, self)
           return @reply
         rescue => e
-          unless e.response
+          if !e.respond_to?(:response) || e.response.nil?
             # Re-raise the client error if there's no response. Otherwise, logging
             # and other things break below!
             FHIR.logger.error "GET - Request: #{url} failed! No response from server: #{e}"
@@ -515,7 +519,7 @@ module FHIR
         begin
           response = @client.post(url, headers: headers, body: payload)
         rescue => e
-          unless e.response
+          if !e.respond_to?(:response) || e.response.nil?
             # Re-raise the client error if there's no response. Otherwise, logging
             # and other things break below!
             FHIR.logger.error "POST - Request: #{url} failed! No response from server: #{e}"
@@ -562,7 +566,7 @@ module FHIR
         begin
           response = @client.put(url, headers: headers, body: payload)
         rescue => e
-          unless e.response
+          if !e.respond_to?(:response) || e.response.nil?
             # Re-raise the client error if there's no response. Otherwise, logging
             # and other things break below!
             FHIR.logger.error "PUT - Request: #{url} failed! No response from server: #{e}"
@@ -609,7 +613,7 @@ module FHIR
         begin
           response = @client.patch(url, headers: headers, body: payload)
         rescue => e
-          unless e.response
+          if !e.respond_to?(:response) || e.response.nil?
             # Re-raise the client error if there's no response. Otherwise, logging
             # and other things break below!
             FHIR.logger.error "PATCH - Request: #{url} failed! No response from server: #{e}"
@@ -645,7 +649,7 @@ module FHIR
             @reply = FHIR::ClientReply.new(request.args, res, self)
           end
         rescue => e
-          unless e.response
+          if !e.respond_to?(:response) || e.response.nil?
             # Re-raise the client error if there's no response. Otherwise, logging
             # and other things break below!
             FHIR.logger.error "PATCH - Request: #{url} failed! No response from server: #{e}"
@@ -677,7 +681,7 @@ module FHIR
         begin
           response = @client.delete(url, headers: headers)
         rescue => e
-          unless e.response
+          if !e.respond_to?(:response) || e.response.nil?
             # Re-raise the client error if there's no response. Otherwise, logging
             # and other things break below!
             FHIR.logger.error "DELETE - Request: #{url} failed! No response from server: #{e}"

data/lib/fhir_client/resource_address.rb

@@ -80,7 +80,7 @@ module FHIR
       fhir_headers.merge!(headers) unless headers.empty?
       fhir_headers.merge!(additional_headers)
       if /\Aapplication\/(fhir\+xml|xml\+fhir|fhir\+json|json\+fhir)\z/.match? fhir_headers['Content-Type']
-        fhir_headers['Content-Type'] << ";charset=#{DEFAULT_CHARSET}"
+        fhir_headers['Content-Type'] = "#{fhir_headers['Content-Type']};charset=#{DEFAULT_CHARSET}"
       end
       fhir_headers
     end

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).nil? && 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/tasks/tasks.rake

@@ -38,22 +38,26 @@ namespace :fhir do
   end
 
   desc 'count all resources for a given server'
-  task :count, [:url, :display_zero] do |_t, args|
+  task :count, [:url, :display_zero, :include_all] do |_t, args|
     client = FHIR::Client.new(args.url)
     client.try_conformance_formats(FHIR::Formats::ResourceFormat::RESOURCE_JSON)
     display_zero = (args.display_zero == 'true')
+    include_all = (args.include_all == 'true')
     counts = {}
     fhir_resources.each do |klass|
       reply = client.read_feed(klass)
-      if !reply.resource.nil? && (reply.resource.total > 0 || display_zero)
-        counts[klass.name.demodulize.to_s] = reply.resource.total
+      total = reply.resource.nil? ? 0 : reply.resource.total
+      total = reply.resource.each.reduce(0) { |s| s + 1 } if total.nil? && include_all
+      total = 'n/a' if total.nil?
+      if total.to_s != "0" || display_zero
+        counts[klass.name.demodulize.to_s] = total.to_s
       end
     end
-    printf "  %-30s %5s\n", 'Resource', 'Count'
-    printf "  %-30s %5s\n", '--------', '-----'
+    format = "  %-35s %7s\n"
+    printf format, 'Resource', 'Count'
+    printf format, '--------', '-----'
     counts.each do |key, value|
-      # puts "#{key}  #{value}"
-      printf "  %-30s %5s\n", key, value
+      printf format, key, value
     end
   end
 

data/lib/fhir_client/version.rb

@@ -1,5 +1,5 @@
 module FHIR
   class Client
-    VERSION = '4.0.0'
+    VERSION = '4.0.5'.freeze
   end
 end

metadata

@@ -1,16 +1,17 @@
 --- !ruby/object:Gem::Specification
 name: fhir_client
 version: !ruby/object:Gem::Version
-  version: 4.0.0
+  version: 4.0.5
 platform: ruby
 authors:
 - Andre Quina
 - Jason Walonoski
-- Janoo Fernandes
+- Robert Scanlon
+- Reece Adamson
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2019-04-24 00:00:00.000000000 Z
+date: 2021-03-31 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activesupport
@@ -46,56 +47,56 @@ dependencies:
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 4.0.0
+        version: 4.0.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 4.0.0
+        version: 4.0.2
 - !ruby/object:Gem::Dependency
   name: fhir_stu3_models
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 3.0.0
+        version: 3.0.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 3.0.0
+        version: 3.0.1
 - !ruby/object:Gem::Dependency
   name: fhir_dstu2_models
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.0.9
+        version: 1.0.10
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.0.9
+        version: 1.0.10
 - !ruby/object:Gem::Dependency
   name: nokogiri
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.8.2
+        version: 1.10.4
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.8.2
+        version: 1.10.4
 - !ruby/object:Gem::Dependency
   name: oauth2
   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
@@ -283,7 +284,8 @@ 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: 
 rdoc_options: []
@@ -300,8 +302,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.7.7
+rubygems_version: 3.1.4
 signing_key: 
 specification_version: 4
 summary: A Gem for handling FHIR client requests in ruby