fhir_models 4.0.2 → 4.1.0

checksums.yaml

@@ -1,7 +1,7 @@
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+  metadata.gz: 71b25db2dba6739f0186495302fc247b4479675488525afb5b3569408446cdd5
+  data.tar.gz: 3760305ed63a524fd5d1fa6903904ad4c28cfc12ae90ed15cacc01f16478b4ef
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+  data.tar.gz: a370fb9b55024b8eda8e48d5414e8fb349ceb5242b893c798d8f5ae05d502d861868940e069ca54980f57c97d73e3d324b03d65de4ec012f1855bf59f3fbcd5f

data/.gitattributes

@@ -0,0 +1,3 @@
+lib/fhir_models/definitions/** linguist-generated=true
+lib/fhir_models/examples/** linguist-generated=true
+

data/.rubocop.yml

@@ -5,7 +5,7 @@ AllCops:
     - 'test/**/*'
     - 'spec/**/*'
     - 'lib/fhir_models/fhir/**/*'
-    - 'lib/fhir_models/fluentpath/evaluate.rb'
+    - 'lib/fhir_models/fhirpath/evaluate.rb'
     - 'lib/**/*.rake'
     - 'tmp/**/*'
     - '*.gemspec'

data/.rubocop_todo.yml

@@ -20,7 +20,7 @@ Layout/EmptyLineAfterGuardClause:
     - 'lib/fhir_models/fhir_ext/element_definition.rb'
     - 'lib/fhir_models/fhir_ext/structure_definition.rb'
     - 'lib/fhir_models/fhir_ext/structure_definition_compare.rb'
-    - 'lib/fhir_models/fluentpath/parse.rb'
+    - 'lib/fhir_models/fhirpath/parse.rb'
 
 # Offense count: 1
 # Cop supports --auto-correct.
@@ -108,7 +108,7 @@ Style/AccessModifierDeclarations:
 Style/ClassVars:
   Exclude:
     - 'lib/fhir_models/bootstrap/definitions.rb'
-    - 'lib/fhir_models/fluentpath/parse.rb'
+    - 'lib/fhir_models/fhirpath/parse.rb'
 
 # Offense count: 6
 Style/CommentedKeyword:
@@ -133,8 +133,8 @@ Style/Documentation:
     - 'lib/fhir_models/fhir.rb'
     - 'lib/fhir_models/fhir_ext/structure_definition.rb'
     - 'lib/fhir_models/fhir_ext/structure_definition_finding.rb'
-    - 'lib/fhir_models/fluentpath/expression.rb'
-    - 'lib/fhir_models/fluentpath/parse.rb'
+    - 'lib/fhir_models/fhirpath/expression.rb'
+    - 'lib/fhir_models/fhirpath/parse.rb'
 
 # Offense count: 28
 # Cop supports --auto-correct.
@@ -195,8 +195,8 @@ Style/RescueStandardError:
     - 'lib/fhir_models/fhir.rb'
     - 'lib/fhir_models/fhir_ext/structure_definition.rb'
     - 'lib/fhir_models/fhir_ext/structure_definition_finding.rb'
-    - 'lib/fhir_models/fluentpath/expression.rb'
-    - 'lib/fhir_models/fluentpath/parse.rb'
+    - 'lib/fhir_models/fhirpath/expression.rb'
+    - 'lib/fhir_models/fhirpath/parse.rb'
 
 # Offense count: 4
 # Cop supports --auto-correct.
@@ -215,4 +215,4 @@ Style/SafeNavigation:
 Style/YodaCondition:
   Exclude:
     - 'lib/fhir_models/bootstrap/preprocess.rb'
-    - 'lib/fhir_models/fluentpath/parse.rb'
+    - 'lib/fhir_models/fhirpath/parse.rb'

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    fhir_models (4.0.2)
+    fhir_models (4.1.0)
       bcp47 (>= 0.3)
       date_time_precision (>= 0.8)
       mime-types (>= 3.0)
@@ -14,7 +14,7 @@ GEM
     bcp47 (0.3.3)
       i18n
     coderay (1.1.2)
-    concurrent-ruby (1.1.5)
+    concurrent-ruby (1.1.6)
     coolline (0.5.0)
       unicode_utils (~> 1.4)
     date_time_precision (0.8.1)
@@ -39,7 +39,7 @@ GEM
     guard-test (2.0.8)
       guard-compat (~> 1.2)
       test-unit (~> 3.0)
-    i18n (1.6.0)
+    i18n (1.8.2)
       concurrent-ruby (~> 1.0)
     jaro_winkler (1.5.3)
     json (2.2.0)
@@ -49,12 +49,12 @@ GEM
       ruby_dep (~> 1.2)
     lumberjack (1.0.13)
     method_source (0.9.2)
-    mime-types (3.2.2)
+    mime-types (3.3.1)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2019.0331)
+    mime-types-data (3.2019.1009)
     mini_portile2 (2.4.0)
     nenv (0.3.0)
-    nokogiri (1.10.4)
+    nokogiri (1.10.8)
       mini_portile2 (~> 2.4.0)
     nokogiri-diff (0.2.0)
       nokogiri (~> 1.5)

data/lib/fhir_models.rb

@@ -24,8 +24,8 @@ Dir.glob(File.join(root, 'lib', 'fhir_models', 'fhir', '**', '*.rb')).each do |f
   require file
 end
 
-# Require the fluentpath code
-Dir.glob(File.join(root, 'lib', 'fhir_models', 'fluentpath', '*.rb')).each do |file|
+# Require the FHIRPath code
+Dir.glob(File.join(root, 'lib', 'fhir_models', 'fhirpath', '*.rb')).each do |file|
   require file
 end
 

data/lib/fhir_models/bootstrap/definitions.rb

@@ -200,24 +200,28 @@ module FHIR
       valueset = expansions.find { |x| x['url'] == uri } || valuesets.find { |x| x['url'] == uri && x['resourceType'] == 'ValueSet' }
       unless valueset.nil?
         @@cache[uri] = {}
-        if !valueset['expansion'].nil? && !valueset['expansion']['contains'].nil?
+        # if the expansion is completed already, use it...
+        # except for http://hl7.org/fhir/ValueSet/c80-doc-typecodes, because that expansion is missing codes
+        if !valueset['expansion'].nil? && !valueset['expansion']['contains'].nil? && uri != 'http://hl7.org/fhir/ValueSet/c80-doc-typecodes'
           keys = valueset['expansion']['contains'].map { |x| x['system'] }.uniq
           keys.each { |x| @@cache[uri][x] = [] }
           valueset['expansion']['contains'].each { |x| @@cache[uri][x['system']] << x['code'] }
-        end
-        if !valueset['compose'].nil? && !valueset['compose']['include'].nil?
-          # for each system, if codes are included add those, otherwise lookup the codesystem in the list
-          included_systems = []
+        elsif !valueset['compose'].nil? && !valueset['compose']['include'].nil?
+          # the expansion is not available, so we have to include values
+          # and possibly partially expand the Valueset by including extra CodeSystems
+          # So, for each system, if codes are included add them...
           valueset['compose']['include'].each do |code_group|
             system_url = code_group['system']
             @@cache[uri][system_url] ||= []
-            code_group['concept'].each { |y| @@cache[uri][system_url] << y['code'] } if code_group['concept']
-            included_systems << system_url
-          end
-          included_systems.each { |x| @@cache[uri][x] ||= [] }
-          systems = valuesets.select { |x| x['resourceType'] == 'CodeSystem' && included_systems.include?(x['url']) }
-          systems.each do |included_system|
-            included_system['concept'].each { |y| @@cache[uri][included_system['url']] << y['code'] } if included_system['concept']
+            if !code_group['concept'].nil?
+              code_group['concept'].each { |y| @@cache[uri][system_url] << y['code'] } if code_group['concept']
+            elsif code_group.size == 1
+              # i.e. the only key is 'system', so you import the entire thing
+              systems = valuesets.select { |x| x['resourceType'] == 'CodeSystem' && x['url'] == system_url }
+              systems.each do |included_system|
+                included_system['concept'].each { |y| @@cache[uri][system_url] << y['code'] } if included_system['concept']
+              end
+            end
           end
         end
         @@cache[uri].each { |_system, codes| codes.uniq! }

data/lib/fhir_models/bootstrap/generator.rb

@@ -1,6 +1,8 @@
 module FHIR
   module Boot
     class Generator
+      KNOWN_MISSING_EXPANSIONS = %w[bcp47 bcp13.txt mimetypes LL379-9].freeze
+
       attr_accessor :lib
       attr_accessor :defn
       # templates keeps track of all the templates in context within a given StructureDefinition
@@ -40,8 +42,7 @@ module FHIR
           type = p['snapshot']['element'].select { |e| e['path'].end_with?('.value') }.first['type'].first
 
           # try to find the JSON data type
-          ext = type['_code']['extension'].find { |e| e['url'] == 'http://hl7.org/fhir/StructureDefinition/structuredefinition-json-type' }
-          field.type = ext ? ext['valueString'] : 'string'
+          field.type = type['code'].gsub('http://hl7.org/fhirpath/System.', '').downcase
 
           # try to find a regex
           if type['extension']
@@ -174,8 +175,14 @@ module FHIR
             end
 
             # generate a field for each valid datatype... this is for things like Resource.attribute[x]
-            element['type'].map { |t| t['code'] }.uniq.each do |data_type|
-              data_type = 'string' unless data_type
+            element['type'].each do |type|
+              extension = type['extension']
+              data_type = type['code'] || 'string'
+              if element['path'].end_with?('.id')
+                data_type = element['base']['path'] == 'Resource.id' ? 'id' : 'string'
+              elsif data_type == 'http://hl7.org/fhirpath/System.String' && extension
+                data_type = extension.first['valueUrl']
+              end
               capitalized = cap_first(data_type)
               fieldname = field_base_name.gsub('[x]', capitalized)
               field = FHIR::Field.new(fieldname)
@@ -196,10 +203,11 @@ module FHIR
                 field.binding.delete('extension')
                 # set the actual code list
                 binding_uri = field.binding['uri']
-                binding_uri = binding_uri[0..-7] if binding_uri&.end_with?('|4.0.0')
+                # Strip off the |4.0.0 or |4.0.1 or |2014-03-26 or similar from the ends of URLs
+                binding_uri&.gsub!(/\|[A-Za-z0-9\.\-]*/, '')
                 codes = @defn.get_codes(binding_uri)
                 field.valid_codes = codes unless codes.nil?
-                if field.valid_codes.empty? && field.binding['uri'] && !binding_uri.end_with?('bcp47') && !binding_uri.end_with?('bcp13.txt')
+                if field.valid_codes.empty? && binding_uri && !binding_uri.end_with?(*KNOWN_MISSING_EXPANSIONS)
                   FHIR.logger.warn "  MISSING EXPANSION -- #{field.path} #{field.min}..#{field.max}: #{binding_uri} (#{field.binding['strength']})"
                   @missing_expansions = true
                   @missing_required_expansion = (field.binding['strength'] == 'required') unless @missing_required_expansion

data/lib/fhir_models/bootstrap/hashable.rb

@@ -121,8 +121,7 @@ module FHIR
       if meta['type'] == 'boolean'
         rval = value.strip == 'true'
       elsif FHIR::PRIMITIVES.include?(meta['type'])
-        primitive_meta = FHIR::PRIMITIVES[meta['type']]
-        if primitive_meta['type'] == 'number'
+        if %w[decimal integer positiveInt unsignedInt].include?(meta['type'])
           rval = BigDecimal(value.to_s)
           rval = rval.frac.zero? ? rval.to_i : rval.to_f
         end # primitive is number

data/lib/fhir_models/bootstrap/model.rb

@@ -279,7 +279,8 @@ module FHIR
 
     def check_binding_uri(uri, value)
       valid = false
-      uri = uri[0..-7] if uri.end_with?('|4.0.0')
+      # Strip off the |4.0.0 or |4.0.1 or |2014-03-26 or similar from the ends of URLs
+      uri&.gsub!(/\|[A-Za-z0-9\.\-]*/, '')
       valueset = FHIR::Definitions.get_codes(uri)
 
       if uri == 'http://hl7.org/fhir/ValueSet/mimetypes' || uri == 'http://www.rfc-editor.org/bcp/bcp13.txt'

data/lib/fhir_models/bootstrap/preprocess.rb

@@ -152,6 +152,15 @@ module FHIR
         f = File.open(filename, 'w:UTF-8')
         f.write(doc.to_xml)
         f.close
+
+        # Remove the weird parantheses on xml example filenames
+        # we do this so they match the names of the json examples
+        if filename.include?('(') && filename.include?(')')
+          rename = filename.gsub(/\([A-Za-z0-9\-\.]*\)/, '')
+          File.rename(filename, rename)
+          filename = rename
+        end
+
         finish = File.size(filename)
         puts "  Removed #{(start - finish) / 1024} KB" if start != finish
       end

data/lib/fhir_models/definitions/schema/account.xsd

@@ -27,7 +27,7 @@
   POSSIBILITY OF SUCH DAMAGE.
   
 
-  Generated on Thu, Dec 27, 2018 22:37+1100 for FHIR v4.0.0 
+  Generated on Fri, Nov 1, 2019 09:29+1100 for FHIR v4.0.1 
 
   Note: the schemas & schematrons do not contain all of the rules about what makes resources
   valid. Implementers will still need to be familiar with the content of the specification and with

data/lib/fhir_models/definitions/schema/activitydefinition.xsd

@@ -27,7 +27,7 @@
   POSSIBILITY OF SUCH DAMAGE.
   
 
-  Generated on Thu, Dec 27, 2018 22:37+1100 for FHIR v4.0.0 
+  Generated on Fri, Nov 1, 2019 09:29+1100 for FHIR v4.0.1 
 
   Note: the schemas & schematrons do not contain all of the rules about what makes resources
   valid. Implementers will still need to be familiar with the content of the specification and with

data/lib/fhir_models/definitions/schema/adverseevent.xsd

@@ -27,7 +27,7 @@
   POSSIBILITY OF SUCH DAMAGE.
   
 
-  Generated on Thu, Dec 27, 2018 22:37+1100 for FHIR v4.0.0 
+  Generated on Fri, Nov 1, 2019 09:29+1100 for FHIR v4.0.1 
 
   Note: the schemas & schematrons do not contain all of the rules about what makes resources
   valid. Implementers will still need to be familiar with the content of the specification and with

data/lib/fhir_models/definitions/schema/allergyintolerance.xsd

@@ -27,7 +27,7 @@
   POSSIBILITY OF SUCH DAMAGE.
   
 
-  Generated on Thu, Dec 27, 2018 22:37+1100 for FHIR v4.0.0 
+  Generated on Fri, Nov 1, 2019 09:29+1100 for FHIR v4.0.1 
 
   Note: the schemas & schematrons do not contain all of the rules about what makes resources
   valid. Implementers will still need to be familiar with the content of the specification and with

data/lib/fhir_models/definitions/schema/appointment.xsd

@@ -27,7 +27,7 @@
   POSSIBILITY OF SUCH DAMAGE.
   
 
-  Generated on Thu, Dec 27, 2018 22:37+1100 for FHIR v4.0.0 
+  Generated on Fri, Nov 1, 2019 09:29+1100 for FHIR v4.0.1 
 
   Note: the schemas & schematrons do not contain all of the rules about what makes resources
   valid. Implementers will still need to be familiar with the content of the specification and with

data/lib/fhir_models/definitions/schema/appointmentresponse.xsd

@@ -27,7 +27,7 @@
   POSSIBILITY OF SUCH DAMAGE.
   
 
-  Generated on Thu, Dec 27, 2018 22:37+1100 for FHIR v4.0.0 
+  Generated on Fri, Nov 1, 2019 09:29+1100 for FHIR v4.0.1 
 
   Note: the schemas & schematrons do not contain all of the rules about what makes resources
   valid. Implementers will still need to be familiar with the content of the specification and with

data/lib/fhir_models/definitions/schema/auditevent.xsd

@@ -27,7 +27,7 @@
   POSSIBILITY OF SUCH DAMAGE.
   
 
-  Generated on Thu, Dec 27, 2018 22:37+1100 for FHIR v4.0.0 
+  Generated on Fri, Nov 1, 2019 09:29+1100 for FHIR v4.0.1 
 
   Note: the schemas & schematrons do not contain all of the rules about what makes resources
   valid. Implementers will still need to be familiar with the content of the specification and with

data/lib/fhir_models/definitions/schema/basic.xsd

@@ -27,7 +27,7 @@
   POSSIBILITY OF SUCH DAMAGE.
   
 
-  Generated on Thu, Dec 27, 2018 22:37+1100 for FHIR v4.0.0 
+  Generated on Fri, Nov 1, 2019 09:29+1100 for FHIR v4.0.1 
 
   Note: the schemas & schematrons do not contain all of the rules about what makes resources
   valid. Implementers will still need to be familiar with the content of the specification and with

data/lib/fhir_models/definitions/schema/binary.xsd

@@ -27,7 +27,7 @@
   POSSIBILITY OF SUCH DAMAGE.
   
 
-  Generated on Thu, Dec 27, 2018 22:37+1100 for FHIR v4.0.0 
+  Generated on Fri, Nov 1, 2019 09:29+1100 for FHIR v4.0.1 
 
   Note: the schemas & schematrons do not contain all of the rules about what makes resources
   valid. Implementers will still need to be familiar with the content of the specification and with

data/lib/fhir_models/definitions/schema/biologicallyderivedproduct.xsd

@@ -27,7 +27,7 @@
   POSSIBILITY OF SUCH DAMAGE.
   
 
-  Generated on Thu, Dec 27, 2018 22:37+1100 for FHIR v4.0.0 
+  Generated on Fri, Nov 1, 2019 09:29+1100 for FHIR v4.0.1 
 
   Note: the schemas & schematrons do not contain all of the rules about what makes resources
   valid. Implementers will still need to be familiar with the content of the specification and with

data/lib/fhir_models/definitions/schema/bodystructure.xsd

@@ -27,7 +27,7 @@
   POSSIBILITY OF SUCH DAMAGE.
   
 
-  Generated on Thu, Dec 27, 2018 22:37+1100 for FHIR v4.0.0 
+  Generated on Fri, Nov 1, 2019 09:29+1100 for FHIR v4.0.1 
 
   Note: the schemas & schematrons do not contain all of the rules about what makes resources
   valid. Implementers will still need to be familiar with the content of the specification and with

data/lib/fhir_models/definitions/schema/bundle.xsd

@@ -27,7 +27,7 @@
   POSSIBILITY OF SUCH DAMAGE.
   
 
-  Generated on Thu, Dec 27, 2018 22:37+1100 for FHIR v4.0.0 
+  Generated on Fri, Nov 1, 2019 09:29+1100 for FHIR v4.0.1 
 
   Note: the schemas & schematrons do not contain all of the rules about what makes resources
   valid. Implementers will still need to be familiar with the content of the specification and with

data/lib/fhir_models/definitions/schema/capabilitystatement.xsd

@@ -27,7 +27,7 @@
   POSSIBILITY OF SUCH DAMAGE.
   
 
-  Generated on Thu, Dec 27, 2018 22:37+1100 for FHIR v4.0.0 
+  Generated on Fri, Nov 1, 2019 09:29+1100 for FHIR v4.0.1 
 
   Note: the schemas & schematrons do not contain all of the rules about what makes resources
   valid. Implementers will still need to be familiar with the content of the specification and with

data/lib/fhir_models/definitions/schema/careplan.xsd

@@ -27,7 +27,7 @@
   POSSIBILITY OF SUCH DAMAGE.
   
 
-  Generated on Thu, Dec 27, 2018 22:37+1100 for FHIR v4.0.0 
+  Generated on Fri, Nov 1, 2019 09:29+1100 for FHIR v4.0.1 
 
   Note: the schemas & schematrons do not contain all of the rules about what makes resources
   valid. Implementers will still need to be familiar with the content of the specification and with

data/lib/fhir_models/definitions/schema/careteam.xsd

@@ -27,7 +27,7 @@
   POSSIBILITY OF SUCH DAMAGE.
   
 
-  Generated on Thu, Dec 27, 2018 22:37+1100 for FHIR v4.0.0 
+  Generated on Fri, Nov 1, 2019 09:29+1100 for FHIR v4.0.1 
 
   Note: the schemas & schematrons do not contain all of the rules about what makes resources
   valid. Implementers will still need to be familiar with the content of the specification and with

data/lib/fhir_models/definitions/schema/catalogentry.xsd

@@ -27,7 +27,7 @@
   POSSIBILITY OF SUCH DAMAGE.
   
 
-  Generated on Thu, Dec 27, 2018 22:37+1100 for FHIR v4.0.0 
+  Generated on Fri, Nov 1, 2019 09:29+1100 for FHIR v4.0.1 
 
   Note: the schemas & schematrons do not contain all of the rules about what makes resources
   valid. Implementers will still need to be familiar with the content of the specification and with

data/lib/fhir_models/definitions/schema/chargeitem.xsd

@@ -27,7 +27,7 @@
   POSSIBILITY OF SUCH DAMAGE.
   
 
-  Generated on Thu, Dec 27, 2018 22:37+1100 for FHIR v4.0.0 
+  Generated on Fri, Nov 1, 2019 09:29+1100 for FHIR v4.0.1 
 
   Note: the schemas & schematrons do not contain all of the rules about what makes resources
   valid. Implementers will still need to be familiar with the content of the specification and with

data/lib/fhir_models/definitions/schema/chargeitemdefinition.xsd

@@ -27,7 +27,7 @@
   POSSIBILITY OF SUCH DAMAGE.
   
 
-  Generated on Thu, Dec 27, 2018 22:37+1100 for FHIR v4.0.0 
+  Generated on Fri, Nov 1, 2019 09:29+1100 for FHIR v4.0.1 
 
   Note: the schemas & schematrons do not contain all of the rules about what makes resources
   valid. Implementers will still need to be familiar with the content of the specification and with

data/lib/fhir_models/definitions/schema/claim.xsd

@@ -27,7 +27,7 @@
   POSSIBILITY OF SUCH DAMAGE.
   
 
-  Generated on Thu, Dec 27, 2018 22:37+1100 for FHIR v4.0.0 
+  Generated on Fri, Nov 1, 2019 09:29+1100 for FHIR v4.0.1 
 
   Note: the schemas & schematrons do not contain all of the rules about what makes resources
   valid. Implementers will still need to be familiar with the content of the specification and with

data/lib/fhir_models/definitions/schema/claimresponse.xsd

@@ -27,7 +27,7 @@
   POSSIBILITY OF SUCH DAMAGE.
   
 
-  Generated on Thu, Dec 27, 2018 22:37+1100 for FHIR v4.0.0 
+  Generated on Fri, Nov 1, 2019 09:29+1100 for FHIR v4.0.1 
 
   Note: the schemas & schematrons do not contain all of the rules about what makes resources
   valid. Implementers will still need to be familiar with the content of the specification and with