fhir_client 4.0.4 → 5.0.1

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@@ -0,0 +1,26 @@
1
+ name: Ruby
2
+
3
+ on:
4
+ push:
5
+ branches: [ master ]
6
+ pull_request:
7
+ branches: [ master ]
8
+
9
+ jobs:
10
+ test:
11
+ runs-on: ubuntu-latest
12
+ strategy:
13
+ matrix:
14
+ ruby-version: ['2.6', '2.7']
15
+
16
+ steps:
17
+ - uses: actions/checkout@v2
18
+ - name: Set up Ruby
19
+ uses: ruby/setup-ruby@v1
20
+ with:
21
+ ruby-version: ${{ matrix.ruby-version }}
22
+ bundler-cache: true # runs 'bundle install' and caches installed gems automatically
23
+ - name: Run tests
24
+ run: bundle exec rake
25
+ - name: Rubocop
26
+ run: bundle exec rubocop
data/README.md CHANGED
@@ -151,9 +151,14 @@ client.destroy(FHIR::Patient, patient_id)
151
151
 
152
152
  ### Searching
153
153
  ```ruby
154
+ # via GET
154
155
  reply = client.search(FHIR::Patient, search: {parameters: {name: 'P'}})
156
+
157
+ # via POST
158
+ reply = client.search(FHIR::Patient, search: {body: {name: 'P'}})
159
+
155
160
  bundle = reply.resource
156
- patient = bundle.entry.first.resource
161
+ patient = bundle&.entry&.first&.resource
157
162
  ```
158
163
 
159
164
  ### Fetching a Bundle
@@ -215,7 +220,7 @@ end
215
220
 
216
221
  # License
217
222
 
218
- Copyright 2014-2019 The MITRE Corporation
223
+ Copyright 2014-2022 The MITRE Corporation
219
224
 
220
225
  Licensed under the Apache License, Version 2.0 (the "License");
221
226
  you may not use this file except in compliance with the License.
data/Rakefile CHANGED
@@ -19,8 +19,4 @@ task :rubocop do
19
19
  RuboCop::RakeTask.new
20
20
  end
21
21
 
22
- task test: [:rubocop] do
23
- system('open coverage/index.html')
24
- end
25
-
26
22
  task default: [:test]
data/fhir_client.gemspec CHANGED
@@ -6,8 +6,9 @@ require 'fhir_client/version'
6
6
  Gem::Specification.new do |spec|
7
7
  spec.name = 'fhir_client'
8
8
  spec.version = FHIR::Client::VERSION
9
- spec.authors = ['Andre Quina', 'Jason Walonoski', 'Janoo Fernandes']
9
+ spec.authors = ['Andre Quina', 'Jason Walonoski', 'Robert Scanlon', 'Reece Adamson']
10
10
  spec.email = ['jwalonoski@mitre.org']
11
+ spec.licenses = ['Apache-2.0']
11
12
 
12
13
  spec.summary = %q{A Gem for handling FHIR client requests in ruby}
13
14
  spec.description = %q{A Gem for handling FHIR client requests in ruby}
@@ -22,9 +23,9 @@ Gem::Specification.new do |spec|
22
23
 
23
24
  spec.add_dependency 'activesupport', '>= 3'
24
25
  spec.add_dependency 'addressable', '>= 2.3'
25
- spec.add_dependency 'fhir_models', '>= 4.0.2'
26
- spec.add_dependency 'fhir_stu3_models', '>= 3.0.1'
27
- spec.add_dependency 'fhir_dstu2_models', '>= 1.0.10'
26
+ spec.add_dependency 'fhir_models', '>= 4.2.0'
27
+ spec.add_dependency 'fhir_stu3_models', '>= 3.1.0'
28
+ spec.add_dependency 'fhir_dstu2_models', '>= 1.1.0'
28
29
  spec.add_dependency 'nokogiri', '>= 1.10.4'
29
30
  spec.add_dependency 'oauth2', '~> 1.1'
30
31
  spec.add_dependency 'rack', '>= 1.5'
@@ -32,7 +33,7 @@ Gem::Specification.new do |spec|
32
33
  spec.add_dependency 'tilt', '>= 1.1'
33
34
 
34
35
  spec.add_development_dependency 'bundler', '~> 2.0'
35
- spec.add_development_dependency 'rake', '~> 10.0'
36
+ spec.add_development_dependency 'rake', '>= 12.3.3'
36
37
  spec.add_development_dependency 'pry'
37
38
  spec.add_development_dependency 'webmock'
38
39
  spec.add_development_dependency 'test-unit'
data/lib/fhir_client.rb CHANGED
@@ -3,6 +3,11 @@ require 'fhir_dstu2_models'
3
3
  require 'fhir_stu3_models'
4
4
  require 'active_support/all'
5
5
 
6
+ # Default to INFO level logging for all FHIR namespaced logging. Since there is
7
+ # no single gem that 'owns' the FHIR namespace, we use the client as the spot
8
+ # to set the default. Otherwise the default is set to DEBUG, which is too high.
9
+ FHIR.logger.level = Logger::INFO
10
+
6
11
  root = File.expand_path '.', File.dirname(File.absolute_path(__FILE__))
7
12
  Dir.glob(File.join(root, 'fhir_client', 'sections', '**', '*.rb')).each do |file|
8
13
  require file
@@ -315,35 +315,46 @@ module FHIR
315
315
  def parse_reply(klass, format, response)
316
316
  FHIR.logger.debug "Parsing response with {klass: #{klass}, format: #{format}, code: #{response.code}}."
317
317
  return nil unless [200, 201].include? response.code
318
- res = nil
319
- begin
320
- res = if(@fhir_version == :dstu2 || klass&.ancestors&.include?(FHIR::DSTU2::Model))
321
- if(format.include?('xml'))
322
- FHIR::DSTU2::Xml.from_xml(response.body)
323
- else
324
- FHIR::DSTU2::Json.from_json(response.body)
325
- end
326
- elsif(@fhir_version == :r4 || klass&.ancestors&.include?(FHIR::Model))
327
- if(format.include?('xml'))
328
- FHIR::Xml.from_xml(response.body)
329
- else
330
- FHIR::Json.from_json(response.body)
331
- end
332
- else
333
- if(format.include?('xml'))
334
- FHIR::STU3::Xml.from_xml(response.body)
335
- else
336
- FHIR::STU3::Json.from_json(response.body)
337
- end
338
- end
339
- res.client = self unless res.nil?
340
- rescue => e
341
- FHIR.logger.error "Failed to parse #{format} as resource #{klass}: #{e.message}"
342
- res = nil
343
- end
318
+ res =
319
+ begin
320
+ if(@fhir_version == :dstu2 || klass&.ancestors&.include?(FHIR::DSTU2::Model))
321
+ if(format.include?('xml'))
322
+ FHIR::DSTU2::Xml.from_xml(response.body)
323
+ else
324
+ FHIR::DSTU2::Json.from_json(response.body)
325
+ end
326
+ elsif(@fhir_version == :r4 || klass&.ancestors&.include?(FHIR::Model))
327
+ if(format.include?('xml'))
328
+ FHIR::Xml.from_xml(response.body)
329
+ else
330
+ FHIR::Json.from_json(response.body)
331
+ end
332
+ else
333
+ if(format.include?('xml'))
334
+ FHIR::STU3::Xml.from_xml(response.body)
335
+ else
336
+ FHIR::STU3::Json.from_json(response.body)
337
+ end
338
+ end
339
+ rescue => e
340
+ FHIR.logger.error "Failed to parse #{format} as resource #{klass}: #{e.message}"
341
+ nil
342
+ end
343
+ set_client_on_resource(res) unless res.nil?
344
344
  res
345
345
  end
346
346
 
347
+ def set_client_on_resource(resource)
348
+ return if resource.nil?
349
+
350
+ resource.client = self
351
+ resource.each_element do |element, _, _|
352
+ if element.is_a?(Reference) || element.is_a?(STU3::Reference) || element.is_a?(DSTU2::Reference) || element.respond_to?(:resourceType)
353
+ element.client = self
354
+ end
355
+ end
356
+ end
357
+
347
358
  def strip_base(path)
348
359
  path.gsub(@base_service_url, '')
349
360
  end
@@ -374,6 +385,7 @@ module FHIR
374
385
  end
375
386
 
376
387
  # Extract the request payload in the specified format, defaults to XML
388
+ # Note that the payload is usually a resource, but could be a form post for searches depending on content type
377
389
  def request_payload(resource, headers)
378
390
  if headers
379
391
  format_specified = headers['Content-Type']
@@ -383,6 +395,10 @@ module FHIR
383
395
  resource.to_xml
384
396
  elsif format_specified.downcase.include?('json')
385
397
  resource.to_json
398
+ elsif format_specified.downcase == 'application/x-www-form-urlencoded'
399
+ # Special case where this is a search body and not a resource.
400
+ # Leave as hash because underlying libraries automatically URL encode it.
401
+ resource
386
402
  else
387
403
  resource.to_xml
388
404
  end
@@ -2,17 +2,14 @@ module FHIR
2
2
  module ModelExtras
3
3
 
4
4
  def self.included base
5
- base.send :include, InstanceMethods
5
+ base.include InstanceMethods
6
6
  base.extend ClassMethods
7
+ base.attr_writer :client
7
8
  end
8
9
 
9
10
  module InstanceMethods
10
11
  def client
11
- FHIR::Model.client
12
- end
13
-
14
- def client=(client)
15
- FHIR::Model.client = client
12
+ @client || FHIR::Model.client
16
13
  end
17
14
 
18
15
  def vread(version_id)
@@ -146,4 +143,4 @@ module FHIR
146
143
  include FHIR::ModelExtras
147
144
  end
148
145
  end
149
- end
146
+ end
@@ -226,7 +226,7 @@ module FHIR
226
226
  resource.id = FHIR::ResourceAddress.pull_out_id(resource.class.name.demodulize, reply.self_link)
227
227
  reply.resource = resource # just send back the submitted resource
228
228
  end
229
- reply.resource.client = self
229
+ set_client_on_resource(reply.resource)
230
230
  reply.resource_class = resource.class
231
231
  reply
232
232
  end
@@ -132,8 +132,11 @@ module FHIR
132
132
  add_resource_parameter(params, 'resource', resource)
133
133
  add_parameter(params, 'onlyCertainMatches', 'Boolean', options[:onlyCertainMatches]) unless options[:onlyCertainMatches].nil?
134
134
  add_parameter(params, 'count', 'Integer', options[:matchCount]) if options[:matchCount].is_a?(Integer)
135
- post resource_url(options), params, fhir_headers({content_type: "#{format || @default_format}",
136
- accept: "#{format || @default_format}"})
135
+ post(
136
+ resource_url(options),
137
+ params,
138
+ fhir_headers({content_type: "#{format || @default_format}", accept: "#{format || @default_format}"})
139
+ ).tap { |reply| set_client_on_resource(reply.resource) }
137
140
  end
138
141
 
139
142
  #
@@ -154,7 +157,8 @@ module FHIR
154
157
  params = versioned_resource_class('Parameters').new
155
158
  add_resource_parameter(params, 'resource', resource)
156
159
  add_parameter(params, 'profile', 'Uri', options[:profile_uri]) unless options[:profile_uri].nil?
157
- post resource_url(options), params, fhir_headers(headers)
160
+ post(resource_url(options), params, fhir_headers(headers))
161
+ .tap { |reply| set_client_on_resource(reply.resource) }
158
162
  end
159
163
 
160
164
  def validate_existing(resource, id, options = {}, format = @default_format)
@@ -165,7 +169,8 @@ module FHIR
165
169
  params = versioned_resource_class('Parameters').new
166
170
  add_resource_parameter(params, 'resource', resource)
167
171
  add_parameter(params, 'profile', 'Uri', options[:profile_uri]) unless options[:profile_uri].nil?
168
- post resource_url(options), params, fhir_headers(headers)
172
+ post(resource_url(options), params, fhir_headers(headers))
173
+ .tap { |reply| set_client_on_resource(reply.resource) }
169
174
  end
170
175
 
171
176
  private
@@ -12,40 +12,28 @@ module FHIR
12
12
  options[:resource] = klass
13
13
  options[:format] = format
14
14
 
15
- reply = if options[:search] && options[:search][:flag]
16
- post resource_url(options), nil, fhir_headers({content_type: 'application/x-www-form-urlencoded'})
17
- else
15
+ reply = if options.dig(:search, :flag) != true && options.dig(:search, :body).nil?
18
16
  get resource_url(options), fhir_headers
17
+ else
18
+ options[:search][:flag] = true
19
+ post resource_url(options), options.dig(:search, :body), fhir_headers({content_type: 'application/x-www-form-urlencoded'})
19
20
  end
20
- # reply = get resource_url(options), fhir_headers(options)
21
+
21
22
  reply.resource = parse_reply(klass, format, reply)
22
23
  reply.resource_class = klass
23
24
  reply
24
25
  end
25
26
 
27
+ # It does not appear that this is part of the specification (any more?)
28
+ # Investigate removing in next major version.
26
29
  def search_existing(klass, id, options = {}, format = @default_format)
27
- options.merge!(resource: klass, id: id, format: format)
28
- # if options[:search][:flag]
29
- reply = if options[:search] && options[:search][:flag]
30
- post resource_url(options), nil, fhir_headers({content_type: 'application/x-www-form-urlencoded'})
31
- else
32
- get resource_url(options), fhir_headers
33
- end
34
- reply.resource = parse_reply(klass, format, reply)
35
- reply.resource_class = klass
36
- reply
30
+ options[:id] = id
31
+ search(klass, options, format)
37
32
  end
38
33
 
39
34
  def search_all(options = {}, format = @default_format)
40
35
  options[:format] = format
41
- reply = if options[:search] && options[:search][:flag]
42
- post resource_url(options), nil, fhir_headers({content_type: 'application/x-www-form-urlencoded'})
43
- else
44
- get resource_url(options), fhir_headers
45
- end
46
- reply.resource = parse_reply(nil, format, reply)
47
- reply.resource_class = nil
48
- reply
36
+ search(nil, options, format)
49
37
  end
50
38
  end
51
39
  end
@@ -74,6 +74,7 @@ module FHIR
74
74
  rescue
75
75
  reply.resource = nil
76
76
  end
77
+ set_client_on_resource(reply.resource)
77
78
  reply.resource_class = reply.resource.class
78
79
  reply
79
80
  end
@@ -1,5 +1,5 @@
1
1
  module FHIR
2
2
  class Client
3
- VERSION = '4.0.4'
3
+ VERSION = '5.0.1'.freeze
4
4
  end
5
5
  end
metadata CHANGED
@@ -1,16 +1,17 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: fhir_client
3
3
  version: !ruby/object:Gem::Version
4
- version: 4.0.4
4
+ version: 5.0.1
5
5
  platform: ruby
6
6
  authors:
7
7
  - Andre Quina
8
8
  - Jason Walonoski
9
- - Janoo Fernandes
10
- autorequire:
9
+ - Robert Scanlon
10
+ - Reece Adamson
11
+ autorequire:
11
12
  bindir: exe
12
13
  cert_chain: []
13
- date: 2020-02-26 00:00:00.000000000 Z
14
+ date: 2021-08-13 00:00:00.000000000 Z
14
15
  dependencies:
15
16
  - !ruby/object:Gem::Dependency
16
17
  name: activesupport
@@ -46,42 +47,42 @@ dependencies:
46
47
  requirements:
47
48
  - - ">="
48
49
  - !ruby/object:Gem::Version
49
- version: 4.0.2
50
+ version: 4.2.0
50
51
  type: :runtime
51
52
  prerelease: false
52
53
  version_requirements: !ruby/object:Gem::Requirement
53
54
  requirements:
54
55
  - - ">="
55
56
  - !ruby/object:Gem::Version
56
- version: 4.0.2
57
+ version: 4.2.0
57
58
  - !ruby/object:Gem::Dependency
58
59
  name: fhir_stu3_models
59
60
  requirement: !ruby/object:Gem::Requirement
60
61
  requirements:
61
62
  - - ">="
62
63
  - !ruby/object:Gem::Version
63
- version: 3.0.1
64
+ version: 3.1.0
64
65
  type: :runtime
65
66
  prerelease: false
66
67
  version_requirements: !ruby/object:Gem::Requirement
67
68
  requirements:
68
69
  - - ">="
69
70
  - !ruby/object:Gem::Version
70
- version: 3.0.1
71
+ version: 3.1.0
71
72
  - !ruby/object:Gem::Dependency
72
73
  name: fhir_dstu2_models
73
74
  requirement: !ruby/object:Gem::Requirement
74
75
  requirements:
75
76
  - - ">="
76
77
  - !ruby/object:Gem::Version
77
- version: 1.0.10
78
+ version: 1.1.0
78
79
  type: :runtime
79
80
  prerelease: false
80
81
  version_requirements: !ruby/object:Gem::Requirement
81
82
  requirements:
82
83
  - - ">="
83
84
  - !ruby/object:Gem::Version
84
- version: 1.0.10
85
+ version: 1.1.0
85
86
  - !ruby/object:Gem::Dependency
86
87
  name: nokogiri
87
88
  requirement: !ruby/object:Gem::Requirement
@@ -170,16 +171,16 @@ dependencies:
170
171
  name: rake
171
172
  requirement: !ruby/object:Gem::Requirement
172
173
  requirements:
173
- - - "~>"
174
+ - - ">="
174
175
  - !ruby/object:Gem::Version
175
- version: '10.0'
176
+ version: 12.3.3
176
177
  type: :development
177
178
  prerelease: false
178
179
  version_requirements: !ruby/object:Gem::Requirement
179
180
  requirements:
180
- - - "~>"
181
+ - - ">="
181
182
  - !ruby/object:Gem::Version
182
- version: '10.0'
183
+ version: 12.3.3
183
184
  - !ruby/object:Gem::Dependency
184
185
  name: pry
185
186
  requirement: !ruby/object:Gem::Requirement
@@ -247,11 +248,11 @@ files:
247
248
  - ".csslintrc"
248
249
  - ".eslintignore"
249
250
  - ".eslintrc"
251
+ - ".github/workflows/ruby.yml"
250
252
  - ".gitignore"
251
253
  - ".rubocop.yml"
252
254
  - ".rubocop_todo.yml"
253
255
  - ".simplecov"
254
- - ".travis.yml"
255
256
  - Gemfile
256
257
  - LICENSE
257
258
  - README.md
@@ -283,9 +284,10 @@ files:
283
284
  - lib/fhir_client/version.rb
284
285
  - lib/fhir_client/version_management.rb
285
286
  homepage: https://github.com/fhir-crucible/fhir_client
286
- licenses: []
287
+ licenses:
288
+ - Apache-2.0
287
289
  metadata: {}
288
- post_install_message:
290
+ post_install_message:
289
291
  rdoc_options: []
290
292
  require_paths:
291
293
  - lib
@@ -300,9 +302,9 @@ required_rubygems_version: !ruby/object:Gem::Requirement
300
302
  - !ruby/object:Gem::Version
301
303
  version: '0'
302
304
  requirements: []
303
- rubyforge_project:
305
+ rubyforge_project:
304
306
  rubygems_version: 2.7.6.2
305
- signing_key:
307
+ signing_key:
306
308
  specification_version: 4
307
309
  summary: A Gem for handling FHIR client requests in ruby
308
310
  test_files: []
data/.travis.yml DELETED
@@ -1,21 +0,0 @@
1
- language: ruby
2
- rvm:
3
- - 2.4
4
- - 2.5
5
- - 2.6
6
- before_install:
7
- - gem update --system
8
- - gem install bundler
9
- before_script:
10
- - curl -L https://codeclimate.com/downloads/test-reporter/test-reporter-latest-linux-amd64 > ./cc-test-reporter
11
- - chmod +x ./cc-test-reporter
12
- - ./cc-test-reporter before-build
13
- script:
14
- - bundle exec rake test
15
- after_script:
16
- - ./cc-test-reporter after-build -t simplecov --exit-code $TRAVIS_TEST_RESULT
17
- notifications:
18
- email:
19
- recipients:
20
- - fhir-testing-list@lists.mitre.org
21
- on_failure: change