fhir_models 3.0.3 → 3.0.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
-SHA1:
-  metadata.gz: c3fdfeb04eb8924b4a590995cdbe08778b332a33
-  data.tar.gz: b35c0d5269b9395a79f811030f0dce515c1d827f
+SHA256:
+  metadata.gz: a066b68471cc4a3c0a992618366b6079428e3d8fa6446d079cc7dd05d77edbf6
+  data.tar.gz: 61b0ae3ef6638cd5faed92bd479a63923bf2bda53ec8cddb522bc766044bbe47
 SHA512:
-  metadata.gz: 18d279a2b1b6835f17a2f4e7aef462acf480885a505e0baf0abc06bdce6a2f8fc75d998bf1e3c644c569daa64d445bc5b90d93311e3a643f9c34bc92f8c55697
-  data.tar.gz: 04480769af209854c5d75d1d7a2c4e5ff1ef2790f66033f087ace3f1e292cc347ce4c6451bd205ddaa8fcf201609837d7b9e751e9e13f099f0e7dbdbb78a9656
+  metadata.gz: a0bd4ab336564cfceb8bd562199e439d496504d0b0b69096f3921530e01eda72f5dcdca51f40485eec4a98c644e9b9359900613285c1643ea808132a30f7f539
+  data.tar.gz: 780033deebc6af7ec05eb092b9279f5512f97b660fbe91320b9aa73060e0a4e09062c74f37e081189d75a7db2db0d52eb4e9d1616c6c4f66bd352c2602d3e182

data/.rubocop.yml

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

data/.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.

data/.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

data/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'

data/lib/fhir_models/bootstrap/hashable.rb

@@ -51,7 +51,7 @@ module FHIR
         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 @@ module FHIR
           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 @@ module FHIR
       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

data/lib/fhir_models/bootstrap/model.rb

@@ -200,8 +200,8 @@ module FHIR
           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?

data/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"
       }
     }
   ]

data/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"
       }
     }
   ],

data/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"
         }
       ]

data/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"
       }

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

@@ -35,7 +35,7 @@
           ]
         }
       ],
-      "whoUri": "mailto://hhd@ssa.gov"
+      "whoUri": "mailto:hhd@ssa.gov"
     }
   ],
   "signature": [

data/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>

data/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>
   

data/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>

data/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>

data/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://hhd@ssa.gov"/>
+    <whoUri value="mailto:hhd@ssa.gov"/>
   </agent>
    <signature>
   <!--  verification signature  -->

data/lib/fhir_models/fhir_ext/structure_definition.rb

@@ -15,6 +15,20 @@ module FHIR
     #                            Profile Validation
     # -------------------------------------------------------------------------
 
+    class << self; attr_accessor :vs_validators end
+    @vs_validators = {}
+    def self.validates_vs(valueset_uri, &validator_fn)
+      @vs_validators[valueset_uri] = validator_fn
+    end
+
+    def self.clear_validates_vs(valueset_uri)
+      @vs_validators.delete valueset_uri
+    end
+
+    def self.clear_all_validates_vs
+      @vs_validators = {}
+    end
+
     def validates_resource?(resource)
       validate_resource(resource).empty?
     end
@@ -147,6 +161,7 @@ module FHIR
       if !element.type.empty? && element.path != id
         # element.type not being empty implies data_type_found != nil, for valid profiles
         codeable_concept_pattern = element.pattern && element.pattern.is_a?(FHIR::CodeableConcept)
+        codeable_concept_binding = element.binding
         matching_pattern = false
         nodes.each do |value|
           matching_type = 0
@@ -169,7 +184,7 @@ module FHIR
             temp_messages += @errors
             @errors = temp
           end
-          if verified_extension || verified_data_type
+          if data_type_found && (verified_extension || verified_data_type)
             matching_type += 1
             if data_type_found == 'code' # then check the binding
               unless element.binding.nil?
@@ -183,11 +198,45 @@ module FHIR
                   matching_pattern = true if vcoding.system == pcoding.system && vcoding.code == pcoding.code
                 end
               end
+            elsif data_type_found == 'CodeableConcept' && codeable_concept_binding
+              binding_issues =
+                if element.binding.strength == 'extensible'
+                  @warnings
+                elsif element.binding.strength == 'required'
+                  @errors
+                else # e.g., example-strength or unspecified
+                  [] # Drop issues errors on the floor, in throwaway array
+                end
+
+              valueset_uri = element.binding && element.binding.valueSetReference && element.binding.valueSetReference.reference
+              vcc = FHIR::CodeableConcept.new(value)
+              if valueset_uri && self.class.vs_validators[valueset_uri]
+                check_fn = self.class.vs_validators[valueset_uri]
+                has_valid_code = vcc.coding && vcc.coding.any? { |c| check_fn.call(c) }
+                unless has_valid_code
+                  binding_issues << "#{describe_element(element)} has no codings from #{valueset_uri}. Codings evaluated: #{vcc.to_json}"
+                end
+              end
+
+              unless has_valid_code
+                vcc.coding.each do |c|
+                  check_fn = self.class.vs_validators[c.system]
+                  if check_fn && !check_fn.call(c)
+                    binding_issues << "#{describe_element(element)} has no codings from it's specified system: #{c.system}.  "\
+                                      "Codings evaluated: #{vcc.to_json}"
+                  end
+                end
+              end
+
             elsif data_type_found == 'String' && !element.maxLength.nil? && (value.size > element.maxLength)
               @errors << "#{describe_element(element)} exceed maximum length of #{element.maxLength}: #{value}"
             end
-          else
+          elsif data_type_found
             temp_messages << "#{describe_element(element)} is not a valid #{data_type_found}: '#{value}'"
+          else
+            # we don't know the data type... so we say "OK"
+            matching_type += 1
+            @warnings >> "Unable to guess data type for #{describe_element(element)}"
           end
 
           if matching_type <= 0

data/lib/fhir_models/tasks/tasks.rake

@@ -38,6 +38,54 @@ namespace :fhir do
     end
   end
 
+  desc 'shrink implementation guide'
+  task :shrinkig, [:file_path] do |_t, args|
+    file_path = args[:file_path]
+    files = Dir.glob(File.join(file_path, '*.json'))
+    files.each do |filename|
+      # Load each file
+      start = File.size(filename)
+      json = File.open(filename, 'r:UTF-8', &:read)
+      hash = JSON.parse(json)
+
+      # process each file
+      FHIR::Boot::Preprocess.pre_process_structuredefinition(hash) if 'StructureDefinition' == hash['resourceType']
+      FHIR::Boot::Preprocess.pre_process_valueset(hash) if 'ValueSet' == hash['resourceType']
+      FHIR::Boot::Preprocess.pre_process_codesystem(hash) if 'CodeSystem' == hash['resourceType']
+      FHIR::Boot::Preprocess.pre_process_searchparam(hash) if 'SearchParameter' == hash['resourceType']
+      FHIR::Boot::Preprocess.remove_fhir_comments(hash)
+
+      # if BlueButton, fix URLs
+      if 'StructureDefinition' == hash['resourceType']
+        # hash['url'].gsub!('http://hl7.org/fhir/StructureDefinition/','https://bluebutton.cms.gov/assets/ig/StructureDefinition-')
+        fix_blue_button_urls(hash)
+      end
+
+      # Output the post processed file
+      f = File.open(filename, 'w:UTF-8')
+      f.write(JSON.pretty_unparse(hash))
+      f.close
+      finish = File.size(filename)
+      puts "  Removed #{(start - finish) / 1024} KB" if start != finish
+    end
+  end
+
+  def self.fix_blue_button_urls(hash)
+    hash.each do |key, value|
+      if value.is_a?(String)
+        if value.start_with?('http://hl7.org/fhir/StructureDefinition/bluebutton')
+          hash[key] = value.gsub('http://hl7.org/fhir/StructureDefinition/bluebutton', 'https://bluebutton.cms.gov/assets/ig/StructureDefinition-bluebutton')
+        end
+      elsif value.is_a?(Hash)
+        fix_blue_button_urls(value)
+      elsif value.is_a?(Array)
+        value.each do |v|
+          fix_blue_button_urls(v) if v.is_a?(Hash)
+        end
+      end
+    end
+  end
+
   desc 'copy artifacts from FHIR build'
   task :update, [:fhir_build_path] do |_t, args|
     fhir_build_path = args[:fhir_build_path]

data/lib/fhir_models/version.rb

@@ -1,5 +1,5 @@
 module FHIR
   module Models
-    VERSION = '3.0.3'.freeze
+    VERSION = '3.0.4'.freeze
   end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: fhir_models
 version: !ruby/object:Gem::Version
-  version: 3.0.3
+  version: 3.0.4
 platform: ruby
 authors:
 - Jason Walonoski
@@ -11,7 +11,7 @@ authors:
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2018-05-01 00:00:00.000000000 Z
+date: 2019-02-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri
@@ -61,20 +61,14 @@ dependencies:
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: '1.16'
-    - - "<"
-      - !ruby/object:Gem::Version
-        version: '3'
+        version: '3.0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: '1.16'
-    - - "<"
-      - !ruby/object:Gem::Version
-        version: '3'
+        version: '3.0'
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
@@ -1634,7 +1628,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.6.12
+rubygems_version: 2.7.7
 signing_key: 
 specification_version: 4
 summary: A Gem for handling FHIR models in ruby