fhir_client 3.1.2 → 4.0.0

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data/.gitignore CHANGED
@@ -36,3 +36,6 @@ Gemfile.lock
36
36
  # Logs
37
37
  *.log
38
38
  *.log.*
39
+
40
+ # User-specific
41
+ .idea
data/.rubocop.yml CHANGED
@@ -1,5 +1,7 @@
1
+ inherit_from: .rubocop_todo.yml
2
+
1
3
  AllCops:
2
- TargetRubyVersion: 2.3
4
+ TargetRubyVersion: 2.4
3
5
  Exclude:
4
6
  - '*.gemspec'
5
7
  - 'Gemfile*'
@@ -24,4 +26,4 @@ Performance/Casecmp:
24
26
  Enabled: false
25
27
 
26
28
  Naming:
27
- Enabled: false
29
+ Enabled: false
data/.rubocop_todo.yml ADDED
@@ -0,0 +1,19 @@
1
+ # This configuration was generated by
2
+ # `rubocop --auto-gen-config`
3
+ # on 2019-03-22 01:56:17 -0400 using RuboCop version 0.52.1.
4
+ # The point is for the user to remove these configuration records
5
+ # one by one as the offenses are removed from the code base.
6
+ # Note that changes in the inspected code, or installation of new
7
+ # versions of RuboCop, may require this file to be generated again.
8
+
9
+ # Offense count: 4
10
+ # Cop supports --auto-correct.
11
+ Performance/RegexpMatch:
12
+ Exclude:
13
+ - 'lib/fhir_client/model/client_reply.rb'
14
+
15
+ # Offense count: 197
16
+ # Configuration parameters: AllowHeredoc, AllowURI, URISchemes, IgnoreCopDirectives, IgnoredPatterns.
17
+ # URISchemes: http, https
18
+ Metrics/LineLength:
19
+ Max: 210
data/.travis.yml CHANGED
@@ -1,6 +1,5 @@
1
1
  language: ruby
2
2
  rvm:
3
- - 2.3
4
3
  - 2.4
5
4
  - 2.5
6
5
  - 2.6
data/Gemfile CHANGED
@@ -1,12 +1,9 @@
1
1
  source 'https://rubygems.org'
2
2
 
3
- # gem 'fhir_models', :path => '../fhir_models'
4
- # gem 'fhir_dstu2_models', :path => '../fhir_dstu2_models'
5
-
6
3
  gemspec
7
4
 
8
5
  group :test do
9
6
  gem 'codeclimate-test-reporter', require: nil
10
- gem 'rubocop', '~> 0.56.0', require: false
7
+ gem 'rubocop', '~> 0.52.1', require: false
11
8
  gem 'awesome_print', require: 'ap'
12
9
  end
data/README.md CHANGED
@@ -3,8 +3,8 @@
3
3
  Ruby FHIR client.
4
4
 
5
5
  Supports:
6
- * FHIR STU3 and DSTU2
7
- * XML and JSON
6
+ * FHIR R4, STU3 and DSTU2
7
+ * JSON and XML
8
8
  * All CRUD, including version read and history
9
9
  * Transactions and Batches
10
10
  * Search
@@ -58,8 +58,8 @@ patient.destroy
58
58
 
59
59
  ## Advanced Usage
60
60
 
61
- ### STU3 and DSTU2
62
- 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.
61
+ ### Changing FHIR Versions
62
+ 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.
63
63
 
64
64
  ```ruby
65
65
  # autodetect the FHIR version
@@ -69,19 +69,42 @@ if version == :stu3
69
69
  puts 'FHIR Client using STU3'
70
70
  elsif version == :dstu2
71
71
  puts 'FHIR Client using DSTU2'
72
+ elsif version == :r4
73
+ puts 'FHIR Client using R4'
72
74
  end
73
75
 
76
+ # tell the client to use R4
77
+ client.use_r4
78
+ # now use the client with the DSTU2 models
79
+ patient = FHIR::Patient.read('example')
80
+ patient = client.read(FHIR::Patient, 'example').resource
81
+
74
82
  # tell the client to use STU3 (default)
75
83
  client.use_stu3
76
84
  # now use the client normally
77
- patient = FHIR::Patient.read('example')
78
- patient = client.read(FHIR::Patient, 'example').resource
85
+ patient = FHIR::STU3::Patient.read('example')
86
+ patient = client.read(FHIR::STU3::Patient, 'example').resource
79
87
 
80
88
  # tell the client to use DSTU2
81
89
  client.use_dstu2
82
90
  # now use the client with the DSTU2 models
83
91
  patient = FHIR::DSTU2::Patient.read('example')
84
92
  patient = client.read(FHIR::DSTU2::Patient, 'example').resource
93
+
94
+
95
+ ```
96
+
97
+ ### Changing FHIR Formats
98
+ The client defaults to `json` representation of resources but can be switched to `xml` representations.
99
+
100
+ ```ruby
101
+ client = FHIR::Client.new(url)
102
+
103
+ # Tell the client to use xml
104
+ client.default_xml
105
+
106
+ # Tell the client to use json
107
+ client.default_json
85
108
  ```
86
109
 
87
110
  ### Configuration
@@ -192,7 +215,7 @@ end
192
215
 
193
216
  # License
194
217
 
195
- Copyright 2014-2016 The MITRE Corporation
218
+ Copyright 2014-2019 The MITRE Corporation
196
219
 
197
220
  Licensed under the Apache License, Version 2.0 (the "License");
198
221
  you may not use this file except in compliance with the License.
data/fhir_client.gemspec CHANGED
@@ -22,8 +22,9 @@ Gem::Specification.new do |spec|
22
22
 
23
23
  spec.add_dependency 'activesupport', '>= 3'
24
24
  spec.add_dependency 'addressable', '>= 2.3'
25
- spec.add_dependency 'fhir_models', '>= 3.0.3'
26
- spec.add_dependency 'fhir_dstu2_models', '>= 1.0.4'
25
+ spec.add_dependency 'fhir_models', '>= 4.0.0'
26
+ spec.add_dependency 'fhir_stu3_models', '>= 3.0.0'
27
+ spec.add_dependency 'fhir_dstu2_models', '>= 1.0.9'
27
28
  spec.add_dependency 'nokogiri', '>= 1.8.2'
28
29
  spec.add_dependency 'oauth2', '~> 1.1'
29
30
  spec.add_dependency 'rack', '>= 1.5'
data/lib/fhir_client.rb CHANGED
@@ -1,5 +1,6 @@
1
1
  require 'fhir_models'
2
2
  require 'fhir_dstu2_models'
3
+ require 'fhir_stu3_models'
3
4
  require 'active_support/all'
4
5
 
5
6
  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|
10
11
  require file
11
12
  end
12
13
 
14
+ require_relative 'fhir_client/version_management'
13
15
  require_relative 'fhir_client/client'
14
16
  require_relative 'fhir_client/resource_address'
15
17
  require_relative 'fhir_client/resource_format'
@@ -11,6 +11,7 @@ module FHIR
11
11
  include FHIR::Sections::Search
12
12
  include FHIR::Sections::Operations
13
13
  include FHIR::Sections::Transactions
14
+ include FHIR::VersionManagement
14
15
 
15
16
  attr_accessor :reply
16
17
  attr_accessor :use_format_param
@@ -37,14 +38,14 @@ module FHIR
37
38
  # @param default_format Default Format Mime type
38
39
  # @return
39
40
  #
40
- def initialize(base_service_url, default_format: FHIR::Formats::ResourceFormat::RESOURCE_XML, proxy: nil)
41
+ def initialize(base_service_url, default_format: FHIR::Formats::ResourceFormat::RESOURCE_JSON, proxy: nil)
41
42
  @base_service_url = base_service_url
42
43
  FHIR.logger.info "Initializing client with #{@base_service_url}"
43
44
  @use_format_param = false
44
45
  @use_accept_header = true
45
46
  @use_accept_charset = true
46
47
  @default_format = default_format
47
- @fhir_version = :stu3
48
+ @fhir_version = :r4
48
49
  @use_return_preference = false
49
50
  @return_preference = FHIR::Formats::ReturnPreferences::REPRESENTATION
50
51
  @exception_class = ClientException
@@ -54,37 +55,26 @@ module FHIR
54
55
  end
55
56
 
56
57
  def default_json
57
- @default_format = if @fhir_version == :stu3
58
- FHIR::Formats::ResourceFormat::RESOURCE_JSON
59
- else
60
- FHIR::Formats::ResourceFormat::RESOURCE_JSON_DSTU2
61
- end
58
+ @default_format = versioned_format_class(:json)
62
59
  end
63
60
 
64
61
  def default_xml
65
- @default_format = if @fhir_version == :stu3
66
- FHIR::Formats::ResourceFormat::RESOURCE_XML
67
- else
68
- FHIR::Formats::ResourceFormat::RESOURCE_XML_DSTU2
69
- end
62
+ @default_format = versioned_format_class(:xml)
70
63
  end
71
64
 
72
65
  def use_stu3
73
66
  @fhir_version = :stu3
74
- @default_format = if @default_format.include?('xml')
75
- FHIR::Formats::ResourceFormat::RESOURCE_XML
76
- else
77
- FHIR::Formats::ResourceFormat::RESOURCE_JSON
78
- end
67
+ @default_format = versioned_format_class
79
68
  end
80
69
 
81
70
  def use_dstu2
82
71
  @fhir_version = :dstu2
83
- @default_format = if @default_format.include?('xml')
84
- FHIR::Formats::ResourceFormat::RESOURCE_XML_DSTU2
85
- else
86
- FHIR::Formats::ResourceFormat::RESOURCE_JSON_DSTU2
87
- end
72
+ @default_format = versioned_format_class
73
+ end
74
+
75
+ def use_r4
76
+ @fhir_version = :r4
77
+ @default_format = versioned_format_class
88
78
  end
89
79
 
90
80
  #
@@ -101,23 +91,19 @@ module FHIR
101
91
  @return_preference = FHIR::Formats::ReturnPreferences::REPRESENTATION
102
92
  end
103
93
 
104
- def versioned_resource_class(klass)
105
- if @fhir_version == :stu3
106
- FHIR.const_get(klass)
107
- else
108
- FHIR::DSTU2.const_get(klass)
109
- end
110
- end
111
-
112
94
  def detect_version
113
95
  cap = capability_statement
114
96
  if cap.is_a?(FHIR::CapabilityStatement)
115
- @fhir_version = :stu3
97
+ use_r4
98
+ elsif cap.is_a?(FHIR::STU3::CapabilityStatement)
99
+ use_stu3
116
100
  elsif cap.is_a?(FHIR::DSTU2::Conformance)
117
- @fhir_version = :dstu2
101
+ use_dstu2
118
102
  else
119
- @fhir_version = :stu3
103
+ use_r4
120
104
  end
105
+ # Should update the default_format when changing fhir_version
106
+ @default_format = versioned_format_class
121
107
  FHIR.logger.info("Detecting server FHIR version as #{@fhir_version} via metadata")
122
108
  @fhir_version
123
109
  end
@@ -279,22 +265,31 @@ module FHIR
279
265
  formats.insert(0, default_format)
280
266
 
281
267
  @cached_capability_statement = nil
282
- @default_format = nil
283
268
 
284
269
  formats.each do |frmt|
285
270
  reply = get 'metadata', fhir_headers({accept: "#{frmt}"})
286
271
  next unless reply.code == 200
272
+ use_r4
287
273
  begin
288
274
  @cached_capability_statement = parse_reply(FHIR::CapabilityStatement, frmt, reply)
289
275
  rescue
290
276
  @cached_capability_statement = nil
291
277
  end
292
- unless @cached_capability_statement
278
+ if @cached_capability_statement.nil? || !@cached_capability_statement.fhirVersion.starts_with?('4')
279
+ use_stu3
293
280
  begin
294
- @cached_capability_statement = parse_reply(FHIR::DSTU2::Conformance, frmt, reply)
281
+ @cached_capability_statement = parse_reply(FHIR::STU3::CapabilityStatement, frmt, reply)
295
282
  rescue
296
283
  @cached_capability_statement = nil
297
284
  end
285
+ unless @cached_capability_statement
286
+ use_dstu2
287
+ begin
288
+ @cached_capability_statement = parse_reply(FHIR::DSTU2::Conformance, frmt, reply)
289
+ rescue
290
+ @cached_capability_statement = nil
291
+ end
292
+ end
298
293
  end
299
294
  if @cached_capability_statement
300
295
  @default_format = frmt
@@ -328,12 +323,18 @@ module FHIR
328
323
  else
329
324
  FHIR::DSTU2::Json.from_json(response.body)
330
325
  end
331
- else
326
+ elsif(@fhir_version == :r4 || klass&.ancestors&.include?(FHIR::Model))
332
327
  if(format.include?('xml'))
333
328
  FHIR::Xml.from_xml(response.body)
334
329
  else
335
330
  FHIR::Json.from_json(response.body)
336
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
337
338
  end
338
339
  res.client = self unless res.nil?
339
340
  FHIR.logger.warn "Expected #{klass} but got #{res.class}" if res.class != klass
@@ -353,11 +354,7 @@ module FHIR
353
354
  method(request['method']).call(request['url'], request['headers'])
354
355
  elsif [:post, :put].include?(request['method'])
355
356
  unless request['payload'].nil?
356
- resource = if @fhir_version == :stu3
357
- FHIR.from_contents(request['payload'])
358
- else
359
- FHIR::DSTU2.from_contents(request['payload'])
360
- end
357
+ resource = versioned_resource_class.from_contents(request['payload'])
361
358
  end
362
359
  method(request['method']).call(request['url'], resource, request['headers'])
363
360
  end
@@ -60,3 +60,11 @@ module FHIR
60
60
  end
61
61
  end
62
62
  end
63
+
64
+ module FHIR
65
+ module STU3
66
+ class Bundle
67
+ include FHIR::BundleExtras
68
+ end
69
+ end
70
+ end
@@ -139,3 +139,11 @@ module FHIR
139
139
  end
140
140
  end
141
141
  end
142
+
143
+ module FHIR
144
+ module STU3
145
+ class Model
146
+ include FHIR::ModelExtras
147
+ end
148
+ end
149
+ end
@@ -39,7 +39,7 @@ module FHIR
39
39
  end
40
40
  end
41
41
 
42
- def type
42
+ def resource_type
43
43
  return if contained?
44
44
  parts[:type]
45
45
  end
@@ -82,7 +82,7 @@ module FHIR
82
82
  include FHIR::ReferenceExtras
83
83
 
84
84
  def resource_class
85
- "FHIR::#{type}".constantize unless contained?
85
+ "FHIR::#{resource_type}".constantize unless contained?
86
86
  end
87
87
  end
88
88
  end
@@ -93,7 +93,19 @@ module FHIR
93
93
  include FHIR::ReferenceExtras
94
94
 
95
95
  def resource_class
96
- "FHIR::DSTU2::#{type}".constantize unless contained?
96
+ "FHIR::DSTU2::#{resource_type}".constantize unless contained?
97
+ end
98
+ end
99
+ end
100
+ end
101
+
102
+ module FHIR
103
+ module STU3
104
+ class Reference
105
+ include FHIR::ReferenceExtras
106
+
107
+ def resource_class
108
+ "FHIR::STU3::#{resource_type}".constantize unless contained?
97
109
  end
98
110
  end
99
111
  end
@@ -1,5 +1,8 @@
1
1
  module FHIR
2
2
  class ClientReply
3
+
4
+ include FHIR::VersionManagement
5
+
3
6
  @@path_regexes = {
4
7
  '[type]' => "(#{FHIR::RESOURCES.join('|')})",
5
8
  '[id]' => FHIR::PRIMITIVES['id']['regex'],
@@ -157,11 +160,7 @@ module FHIR
157
160
  if body_rules['types']
158
161
  body_type_match = false
159
162
  begin
160
- content = if @fhir_version == :stu3
161
- FHIR.from_contents(body)
162
- else
163
- FHIR::DSTU2.from_contents(body)
164
- end
163
+ content = versioned_resource_class().from_contents(body)
165
164
  body_rules['types'].each do |type|
166
165
  body_type_match = true if content.resourceType == type
167
166
  body_type_match = true if type == 'Resource' && validate_resource(content.resourceType)
@@ -182,12 +181,7 @@ module FHIR
182
181
  end
183
182
 
184
183
  def validate_resource(resource_type)
185
- if @fhir_version == :stu3
186
- return true if FHIR::RESOURCES.include?(resource_type)
187
- else
188
- return true if FHIR::DSTU2::RESOURCES.include?(resource_type)
189
- end
190
- false
184
+ versioned_resource_class(:RESOURCES).include?(resource_type)? true : false
191
185
  end
192
186
 
193
187
  private :validate_headers, :validate_body, :validate_resource
@@ -209,17 +209,11 @@ module FHIR
209
209
  type = reply.response[:headers].detect{|x, _y| x.downcase=='content-type'}.try(:last)
210
210
  if !type.nil?
211
211
  reply.resource = if type.include?('xml') && !reply.body.empty?
212
- if @fhir_version == :stu3
213
- FHIR::Xml.from_xml(reply.body)
214
- else
215
- FHIR::DSTU2::Xml.from_xml(reply.body)
216
- end
212
+ klass = self.versioned_resource_class(:Xml)
213
+ klass.from_xml(reply.body)
217
214
  elsif type.include?('json') && !reply.body.empty?
218
- if @fhir_version == :stu3
219
- FHIR::Json.from_json(reply.body)
220
- else
221
- FHIR::DSTU2::Json.from_json(reply.body)
222
- end
215
+ klass = self.versioned_resource_class(:Json)
216
+ klass.from_json(reply.body)
223
217
  else
224
218
  resource # just send back the submitted resource
225
219
  end
@@ -28,11 +28,7 @@ module FHIR
28
28
  reply = get resource_url(options), fhir_headers
29
29
 
30
30
  # The history reply should be a bundle
31
- bundle_klass = if @fhir_version == :stu3
32
- FHIR::Bundle
33
- else
34
- FHIR::DSTU2::Bundle
35
- end
31
+ bundle_klass = self.versioned_resource_class(:Bundle)
36
32
 
37
33
  reply.resource = parse_reply(bundle_klass, options[:format], reply)
38
34
  reply.resource_class = options[:resource]
@@ -73,10 +73,10 @@ module FHIR
73
73
 
74
74
  # Concept Look Up [base]/CodeSystem/$lookup
75
75
  def code_system_lookup(params = {}, format = @default_format)
76
- klass = if @fhir_version == :stu3
77
- FHIR::CodeSystem
78
- else
76
+ klass = if @fhir_version == :dstu2
79
77
  FHIR::DSTU2::ValueSet
78
+ else
79
+ self.versioned_resource_class(:CodeSystem)
80
80
  end
81
81
  options = { resource: klass, operation: { name: :code_system_lookup } }
82
82
  options.deep_merge!(params)
@@ -1,5 +1,5 @@
1
1
  module FHIR
2
2
  class Client
3
- VERSION = '3.1.2'
3
+ VERSION = '4.0.0'
4
4
  end
5
5
  end
@@ -0,0 +1,44 @@
1
+ module FHIR
2
+ module VersionManagement
3
+
4
+ def versioned_resource_class(klass = nil)
5
+ mod = case @fhir_version
6
+ when :stu3
7
+ FHIR::STU3
8
+ when :dstu2
9
+ FHIR::DSTU2
10
+ else
11
+ FHIR
12
+ end
13
+ return mod if klass.nil?
14
+ mod.const_get(klass)
15
+ end
16
+
17
+ def versioned_format_class(format = nil)
18
+ if @fhir_version == :dstu2
19
+ case format
20
+ when nil
21
+ @default_format.include?('xml') ?
22
+ FHIR::Formats::ResourceFormat::RESOURCE_XML_DSTU2 :
23
+ FHIR::Formats::ResourceFormat::RESOURCE_JSON_DSTU2
24
+ when :xml
25
+ FHIR::Formats::ResourceFormat::RESOURCE_XML_DSTU2
26
+ else
27
+ FHIR::Formats::ResourceFormat::RESOURCE_JSON_DSTU2
28
+ end
29
+ else
30
+ case format
31
+ when nil
32
+ @default_format.include?('xml') ?
33
+ FHIR::Formats::ResourceFormat::RESOURCE_XML :
34
+ FHIR::Formats::ResourceFormat::RESOURCE_JSON
35
+ when :xml
36
+ FHIR::Formats::ResourceFormat::RESOURCE_XML
37
+ else
38
+ FHIR::Formats::ResourceFormat::RESOURCE_JSON
39
+ end
40
+ end
41
+ end
42
+
43
+ end
44
+ end
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: fhir_client
3
3
  version: !ruby/object:Gem::Version
4
- version: 3.1.2
4
+ version: 4.0.0
5
5
  platform: ruby
6
6
  authors:
7
7
  - Andre Quina
@@ -10,7 +10,7 @@ authors:
10
10
  autorequire:
11
11
  bindir: exe
12
12
  cert_chain: []
13
- date: 2019-03-21 00:00:00.000000000 Z
13
+ date: 2019-04-24 00:00:00.000000000 Z
14
14
  dependencies:
15
15
  - !ruby/object:Gem::Dependency
16
16
  name: activesupport
@@ -46,28 +46,42 @@ dependencies:
46
46
  requirements:
47
47
  - - ">="
48
48
  - !ruby/object:Gem::Version
49
- version: 3.0.3
49
+ version: 4.0.0
50
50
  type: :runtime
51
51
  prerelease: false
52
52
  version_requirements: !ruby/object:Gem::Requirement
53
53
  requirements:
54
54
  - - ">="
55
55
  - !ruby/object:Gem::Version
56
- version: 3.0.3
56
+ version: 4.0.0
57
+ - !ruby/object:Gem::Dependency
58
+ name: fhir_stu3_models
59
+ requirement: !ruby/object:Gem::Requirement
60
+ requirements:
61
+ - - ">="
62
+ - !ruby/object:Gem::Version
63
+ version: 3.0.0
64
+ type: :runtime
65
+ prerelease: false
66
+ version_requirements: !ruby/object:Gem::Requirement
67
+ requirements:
68
+ - - ">="
69
+ - !ruby/object:Gem::Version
70
+ version: 3.0.0
57
71
  - !ruby/object:Gem::Dependency
58
72
  name: fhir_dstu2_models
59
73
  requirement: !ruby/object:Gem::Requirement
60
74
  requirements:
61
75
  - - ">="
62
76
  - !ruby/object:Gem::Version
63
- version: 1.0.4
77
+ version: 1.0.9
64
78
  type: :runtime
65
79
  prerelease: false
66
80
  version_requirements: !ruby/object:Gem::Requirement
67
81
  requirements:
68
82
  - - ">="
69
83
  - !ruby/object:Gem::Version
70
- version: 1.0.4
84
+ version: 1.0.9
71
85
  - !ruby/object:Gem::Dependency
72
86
  name: nokogiri
73
87
  requirement: !ruby/object:Gem::Requirement
@@ -235,6 +249,7 @@ files:
235
249
  - ".eslintrc"
236
250
  - ".gitignore"
237
251
  - ".rubocop.yml"
252
+ - ".rubocop_todo.yml"
238
253
  - ".simplecov"
239
254
  - ".travis.yml"
240
255
  - Gemfile
@@ -266,6 +281,7 @@ files:
266
281
  - lib/fhir_client/sections/transactions.rb
267
282
  - lib/fhir_client/tasks/tasks.rake
268
283
  - lib/fhir_client/version.rb
284
+ - lib/fhir_client/version_management.rb
269
285
  homepage: https://github.com/fhir-crucible/fhir_client
270
286
  licenses: []
271
287
  metadata: {}