Merge pull request #49 from fhir-crucible/port

Porting recent fhir_dstu2_model changes

.rubocop.yml

@@ -6,6 +6,7 @@ AllCops:
  - 'spec/**/*'
  - 'lib/fhir_models/fhir/**/*'
  - 'lib/fhir_models/fluentpath/evaluate.rb'
+ - 'lib/**/*.rake'
  - 'tmp/**/*'
  - '*.gemspec'
  - 'bin/*'

.rubocop_todo.yml

@@ -27,7 +27,7 @@ Metrics/BlockLength:
 # Offense count: 1
 # Configuration parameters: CountBlocks.
 Metrics/BlockNesting:
- Max: 4
+ Max: 8
 
 # Offense count: 5
 # Configuration parameters: CountComments.
@@ -41,7 +41,7 @@ Metrics/CyclomaticComplexity:
 # Offense count: 40
 # Configuration parameters: CountComments.
 Metrics/MethodLength:
- Max: 109
+ Max: 150
 
 # Offense count: 1
 # Configuration parameters: CountComments.

.travis.yml

@@ -2,10 +2,10 @@ language: ruby
 env:
  - TESTMEMORY=0 GCDELAY=2.0
 rvm:
- - 2.2
  - 2.3
  - 2.4
  - 2.5
+ - 2.6
 script:
  - bundle exec rake
  - bundle exec codeclimate-test-reporter

fhir_models.gemspec

@@ -23,7 +23,7 @@ Gem::Specification.new do |spec|
  spec.add_dependency 'nokogiri', '>= 1.8.2'
  spec.add_dependency 'date_time_precision', '>= 0.8'
  spec.add_dependency 'bcp47', '>= 0.3'
- spec.add_dependency 'mime-types', '>= 1.16', '< 3'
+ spec.add_dependency 'mime-types', '>= 3.0'
 
  spec.add_development_dependency 'bundler'
  spec.add_development_dependency 'rake'

lib/fhir_models/bootstrap/hashable.rb

@@ -51,7 +51,7 @@ def from_hash(hash)
  if !klass.nil? && !value.nil?
  # handle array of objects
  if value.is_a?(Array)
- value.map! do |child|
+ value = value.map do |child|
  obj = child
  unless [FHIR::RESOURCES, FHIR::TYPES].flatten.include? child.class.name.gsub('FHIR::', '')
  obj = make_child(child, klass)
@@ -68,7 +68,7 @@ def from_hash(hash)
  FHIR.logger.error("Unhandled and unrecognized class/type: #{meta['type']}")
  elsif value.is_a?(Array)
  # array of primitives
- value.map! { |child| convert_primitive(child, meta) }
+ value = value.map { |child| convert_primitive(child, meta) }
  instance_variable_set("@#{local_name}", value)
  else
  # single primitive
@@ -111,7 +111,7 @@ def convert_primitive(value, meta)
  elsif FHIR::PRIMITIVES.include?(meta['type'])
  primitive_meta = FHIR::PRIMITIVES[meta['type']]
  if primitive_meta['type'] == 'number'
- rval = BigDecimal.new(value.to_s)
+ rval = BigDecimal(value.to_s)
  rval = rval.frac.zero? ? rval.to_i : rval.to_f
  end # primitive is number
  end # boolean else

lib/fhir_models/bootstrap/model.rb

@@ -200,8 +200,8 @@ def validate_field(field, value, contained_here, meta, errors)
  else
  errors[field] << "#{meta['path']}: expected Reference, found #{klassname}"
  end
- # if the data type is a particular resource or complex type
- elsif FHIR::RESOURCES.include?(datatype) || FHIR::TYPES.include?(datatype)
+ # if the data type is a particular resource or complex type or BackBone element within this resource
+ elsif FHIR::RESOURCES.include?(datatype) || FHIR::TYPES.include?(datatype) || v.class.name.start_with?(self.class.name)
  if datatype == klassname
  validation = v.validate(contained_here)
  errors[field] << validation unless validation.empty?

lib/fhir_models/examples/json/capabilitystatement-example.json

@@ -216,7 +216,7 @@
  "mode": "consumer",
  "documentation": "Basic rules for all documents in the EHR system",
  "profile": {
- "reference": "http://fhir.hl7.org/base/Profilebc054d23-75e1-4dc6-aca5-838b6b1ac81d/_history/b5fdd9fc-b021-4ea1-911a-721a60663796"
+ "reference": "http://fhir.hl7.org/StructureDefinition/Profilebc054d23-75e1-4dc6-aca5-838b6b1ac81d/_history/b5fdd9fc-b021-4ea1-911a-721a60663796"
  }
  }
  ]

lib/fhir_models/examples/json/claim-example-oral-contained-identifier.json

@@ -109,7 +109,7 @@
  "sequence": 1,
  "focal": true,
  "coverage": {
- "reference": "http://www.jurisdiction.com/nationalplan/123AB345"
+ "reference": "http://www.jurisdiction.com/Coverage/123AB345"
  }
  }
  ],

lib/fhir_models/examples/json/dataelement-example.json

@@ -186,7 +186,7 @@
  "mapping": [
  {
  "identity": "fhir",
- "language": "application/xquery",
+ "language": "application/xml",
  "map": "return f:/Patient/f:gender"
  }
  ]

lib/fhir_models/examples/json/endpoint-examples-general-template.json

@@ -199,7 +199,7 @@
  }
  ],
  "payloadMimeType": [
- "PDF"
+ "application/pdf"
  ],
  "address": "https://sqlonfhir-dstu2.azurewebsites.net/fhir"
  }
@@ -232,7 +232,7 @@
  }
  ],
  "payloadMimeType": [
- "HL7v2"
+ "application/fhir+json"
  ],
  "address": "127.0.0.1"
  }
@@ -265,7 +265,7 @@
  }
  ],
  "payloadMimeType": [
- "XDA/XDS"
+ "application/xml"
  ],
  "address": "https://open.epic.com/Interface/XDS.b"
  }
@@ -298,7 +298,7 @@
  }
  ],
  "payloadMimeType": [
- "DICOM WADO-RS"
+ "application/dicom"
  ],
  "address": "https://pacs.hospital.org/dicomweb"
  }
@@ -331,7 +331,7 @@
  }
  ],
  "payloadMimeType": [
- "DICOM QIDO-RS"
+ "application/dicom"
  ],
  "address": "https://pacs.hospital.org/dicomweb"
  }
@@ -364,7 +364,7 @@
  }
  ],
  "payloadMimeType": [
- "DICOM STOW-RS"
+ "application/dicom"
  ],
  "address": "https://pacs.hospital.org/dicomweb"
  }
@@ -397,7 +397,7 @@
  }
  ],
  "payloadMimeType": [
- "DICOM STOW-RS"
+ "application/dicom"
  ],
  "address": "https://pacs.hospital.org/dicomweb"
  }
@@ -430,7 +430,7 @@
  }
  ],
  "payloadMimeType": [
- "DICOM WADO-URI"
+ "application/dicom"
  ],
  "address": "https://pacs.hospital.org/wadoUri"
  }
@@ -463,7 +463,7 @@
  }
  ],
  "payloadMimeType": [
- "IHE IID"
+ "application/dicom"
  ],
  "address": "https://pacs.hospital.org/IHEInvokeImageDisplay"
  }

lib/fhir_models/examples/json/provenance-example-sig.json

@@ -35,7 +35,7 @@
  ]
  }
  ],
- "whoUri": "mailto://[email protected]"
+ "whoUri": "mailto:[email protected]"
  }
  ],
  "signature": [

lib/fhir_models/examples/xml/capabilitystatement-example.xml

@@ -211,7 +211,7 @@
  <!-- this is the important element: a reference to a published document profile 
  note that this is a version specific reference. -->
  <profile>
- <reference value="http://fhir.hl7.org/base/Profilebc054d23-75e1-4dc6-aca5-838b6b1ac81d/_history/b5fdd9fc-b021-4ea1-911a-721a60663796"/>
+ <reference value="http://fhir.hl7.org/StructureDefinition/Profilebc054d23-75e1-4dc6-aca5-838b6b1ac81d/_history/b5fdd9fc-b021-4ea1-911a-721a60663796"/>
  </profile>
  </document>
 </CapabilityStatement>

lib/fhir_models/examples/xml/claim-example-oral-contained-identifier.xml

@@ -99,7 +99,7 @@
  <sequence value="1"/>
  <focal value="true"/>
  <coverage>
- <reference value="http://www.jurisdiction.com/nationalplan/123AB345"/>
+ <reference value="http://www.jurisdiction.com/Coverage/123AB345"/>
  </coverage>
  </insurance>
 

lib/fhir_models/examples/xml/dataelement-example.xml

@@ -254,7 +254,7 @@
  </binding>
  <mapping>
  <identity value="fhir"/>
- <language value="application/xquery"/>
+ <language value="application/xml"/>
  <map value="return f:/Patient/f:gender"/>
  </mapping>
  </element>

lib/fhir_models/examples/xml/endpoint-examples-general-template.xml

@@ -209,7 +209,7 @@
  <code value="CDA-EventSummary"/>
  </coding>
  </payloadType>
- <payloadMimeType value="PDF"/>
+ <payloadMimeType value="application/pdf"/>
  <address value="https://sqlonfhir-dstu2.azurewebsites.net/fhir"/>
  </Endpoint>
  </resource>
@@ -244,7 +244,7 @@
  <code value="REF-I12"/>
  </coding>
  </payloadType>
- <payloadMimeType value="HL7v2"/>
+ <payloadMimeType value="application/fhir+json"/>
  <address value="127.0.0.1"/>
  </Endpoint>
  </resource>
@@ -279,7 +279,7 @@
  <code value="CDA-EventSummary"/>
  </coding>
  </payloadType>
- <payloadMimeType value="XDA/XDS"/>
+ <payloadMimeType value="application/xml"/>
  <address value="https://open.epic.com/Interface/XDS.b"/>
  </Endpoint>
  </resource>
@@ -314,7 +314,7 @@
  <code value="varies (application/dicom, application/dicom+xml, image/jpeg, and many more)"/>
  </coding>
  </payloadType>
- <payloadMimeType value="DICOM WADO-RS"/>
+ <payloadMimeType value="application/dicom"/>
  <address value="https://pacs.hospital.org/dicomweb"/>
  </Endpoint>
  </resource>
@@ -349,7 +349,7 @@
  <code value="varies (application/dicom, application/dicom+xml, image/jpeg, and many more)"/>
  </coding>
  </payloadType>
- <payloadMimeType value="DICOM QIDO-RS"/>
+ <payloadMimeType value="application/dicom"/>
  <address value="https://pacs.hospital.org/dicomweb"/>
  </Endpoint>
  </resource>
@@ -384,7 +384,7 @@
  <code value="varies (application/dicom, application/dicom+xml, image/jpeg, and many more)"/>
  </coding>
  </payloadType>
- <payloadMimeType value="DICOM STOW-RS"/>
+ <payloadMimeType value="application/dicom"/>
  <address value="https://pacs.hospital.org/dicomweb"/>
  </Endpoint>
  </resource>
@@ -419,7 +419,7 @@
  <code value="varies (application/dicom, application/dicom+xml, image/jpeg, and many more)"/>
  </coding>
  </payloadType>
- <payloadMimeType value="DICOM STOW-RS"/>
+ <payloadMimeType value="application/dicom"/>
  <address value="https://pacs.hospital.org/dicomweb"/>
  </Endpoint>
  </resource>
@@ -454,7 +454,7 @@
  <code value="varies (application/dicom, application/dicom+xml, image/jpeg, and many more)"/>
  </coding>
  </payloadType>
- <payloadMimeType value="DICOM WADO-URI"/>
+ <payloadMimeType value="application/dicom"/>
  <address value="https://pacs.hospital.org/wadoUri"/>
  </Endpoint>
  </resource>
@@ -489,7 +489,7 @@
  <code value="varies (application/dicom, application/dicom+xml, image/jpeg, and many more)"/>
  </coding>
  </payloadType>
- <payloadMimeType value="IHE IID"/>
+ <payloadMimeType value="application/dicom"/>
  <address value="https://pacs.hospital.org/IHEInvokeImageDisplay"/>
  </Endpoint>
  </resource>

lib/fhir_models/examples/xml/provenance-example-sig.xml

@@ -36,7 +36,7 @@
  <!-- very often, the user won't have a known system - these aren't available 
  for security system log ons. But where you can define it, you should.
  Most of the time the userId is fully qualfied such as an email address -->
- <whoUri value="mailto://[email protected]"/>
+ <whoUri value="mailto:[email protected]"/>
  </agent>
  <signature>
  <!-- verification signature -->