us_core_test_kit 0.11.5 → 1.0.0

data/lib/us_core_test_kit/generator/validation_test_generator.rb

@@ -96,7 +96,7 @@ module USCoreTestKit
 
       def generate
         FileUtils.mkdir_p(output_file_directory)
-        File.open(output_file_name, 'w') { |f| f.write(output) }
+        File.write(output_file_name, output)
 
         test_metadata = {
           id: test_id,
@@ -112,26 +112,26 @@ module USCoreTestKit
 
       def description
         <<~DESCRIPTION
-        #{description_intro}
-        It verifies the presence of mandatory elements and that elements with
-        required bindings contain appropriate values. CodeableConcept element
-        bindings will fail if none of their codings have a code/system belonging
-        to the bound ValueSet. Quantity, Coding, and code element bindings will
-        fail if their code/system are not found in the valueset.
+          #{description_intro}
+          It verifies the presence of mandatory elements and that elements with
+          required bindings contain appropriate values. CodeableConcept element
+          bindings will fail if none of their codings have a code/system belonging
+          to the bound ValueSet. Quantity, Coding, and code element bindings will
+          fail if their code/system are not found in the valueset.
         DESCRIPTION
       end
 
       def description_intro
         if resource_type == 'Medication'
           <<~MEDICATION_INTRO
-          This test verifies resources returned from previous tests conform to
-          the [#{profile_name}](#{profile_url}).
+            This test verifies resources returned from previous tests conform to
+            the [#{profile_name}](#{profile_url}).
           MEDICATION_INTRO
         else
           <<~GENERIC_INTRO
-          This test verifies resources returned from the first search conform to
-          the [#{profile_name}](#{profile_url}).
-          Systems must demonstrate at least one valid example in order to pass this test.
+            This test verifies resources returned from the first search conform to
+            the [#{profile_name}](#{profile_url}).
+            Systems must demonstrate at least one valid example in order to pass this test.
           GENERIC_INTRO
         end
       end

data/lib/us_core_test_kit/generator/value_extractor.rb

@@ -44,7 +44,27 @@ module USCoreTestKit
       end
 
       def value_set(the_element)
-        ig_resources.value_set_by_url(value_set_binding(the_element)&.valueSet)
+        binding = value_set_binding(the_element)
+        target_valueset = binding&.valueSet
+
+        additional_binding_ext = binding&.extension&.find do |ext|
+          ext.url == 'http://hl7.org/fhir/tools/StructureDefinition/additional-binding' &&
+          ext.extension.any? { |sub_ext| sub_ext.url == 'purpose' && sub_ext.valueCode == 'minimum' }
+        end
+
+        min_valueset_ext = binding&.extension&.find do |ext|
+          ext.url == 'http://hl7.org/fhir/StructureDefinition/elementdefinition-minValueSet'
+        end
+
+        if additional_binding_ext.present?
+          min_valueset = additional_binding_ext.extension.find { |ext| ext.url == 'valueSet' }
+
+          target_valueset = min_valueset.valueCanonical if min_valueset.present?
+        elsif min_valueset_ext.present?
+          target_valueset = min_valueset_ext.valueCanonical
+        end
+
+        ig_resources.value_set_by_url(target_valueset)
       end
 
       def bound_systems(the_element)

data/lib/us_core_test_kit/generator/verifies_requirements.rb

@@ -0,0 +1,99 @@
+module USCoreTestKit
+  class Generator
+    class VerifiesRequirements
+
+      attr_accessor :requirement_lists
+      
+      V610 = 'USCoreV610'
+      V700 = 'USCoreV700'
+      V800 = 'USCoreV800'
+
+      MIN_VERSION = V610
+
+      MODULE_NAMESPACE_MAP = {
+        V610 => 'hl7.fhir.us.core_6.1.0',
+        V700 => 'hl7.fhir.us.core_7.0.0',
+        V800 => 'hl7.fhir.us.core_8.0.0'
+      }.freeze
+
+      def initialize
+        @requirement_lists = {
+          V610 => {
+            :base => [],
+            :map => {},
+            :remove => []
+          },
+          V700 => {
+            :base => [],
+            :map => {},
+            :remove => []
+          },
+          V800 => {
+            :base => [],
+            :map => {},
+            :remove => []
+          }
+        }
+      end
+
+      def get_ids(module_name, class_name)
+        if module_name < MIN_VERSION
+          return
+        end
+
+        all_ids = []
+
+        if module_name >= V610
+          all_ids += @requirement_lists[V610][:base]
+          all_ids += @requirement_lists[V610][:map][class_name] if @requirement_lists[V610][:map][class_name]
+          all_ids -= @requirement_lists[V610][:remove]
+        end
+
+        if module_name >= V700
+          all_ids += @requirement_lists[V700][:base]
+          all_ids += @requirement_lists[V700][:map][class_name] if @requirement_lists[V700][:map][class_name]
+          all_ids -= @requirement_lists[V700][:remove]
+        end
+
+        if module_name >= V800
+          all_ids += @requirement_lists[V800][:base]
+          all_ids += @requirement_lists[V800][:map][class_name] if @requirement_lists[V800][:map][class_name]
+          all_ids -= @requirement_lists[V800][:remove]
+        end
+
+        all_ids
+      end
+
+      def create_verifies_requirements(module_name, class_name, indent_spaces = 6)
+        if module_name < MIN_VERSION
+          return
+        end
+
+        ids = get_ids(module_name, class_name)
+        create_verifies_requirements_from_ids(module_name, ids, indent_spaces) if ids.any?
+      end
+
+      def create_verifies_requirements_from_ids(module_name, ids, indent_spaces = 6)
+        if module_name < MIN_VERSION
+          return
+        end
+
+        namespace = MODULE_NAMESPACE_MAP[module_name]
+        verifies_requirements = ' ' * indent_spaces + "verifies_requirements "
+        indent_spaces = verifies_requirements.length
+        verifies_requirements += ids.map.with_index do |id, i|
+          "'#{namespace}@#{id}'" + (i < ids.size - 1 ? ',' : '')
+        end.join("\n" + ' ' * indent_spaces)
+
+        verifies_requirements
+      end
+
+      def has_requirements?(module_name, class_name)
+        return false if module_name < V610
+
+        ids = get_ids(module_name, class_name)
+        ids && ids.any?
+      end
+    end
+  end
+end

data/lib/us_core_test_kit/generator.rb

@@ -16,6 +16,8 @@ require_relative 'generator/search_test_generator'
 require_relative 'generator/suite_generator'
 require_relative 'generator/validation_test_generator'
 require_relative 'generator/practitioner_address_test_generator'
+require_relative 'generator/interpreter_required_extension_test_generator'
+require_relative 'generator/verifies_requirements'
 
 module USCoreTestKit
   class Generator
@@ -46,6 +48,7 @@ module USCoreTestKit
       generate_must_support_tests
       generate_reference_resolution_tests
       generate_practitioner_address_tests
+      generate_interpreter_required_extension_test_generator
 
       generate_granular_scope_tests
 
@@ -67,9 +70,7 @@ module USCoreTestKit
     end
 
     def write_metadata
-      File.open(File.join(base_output_dir, 'metadata.yml'), 'w') do |file|
-        file.write(YAML.dump(ig_metadata.to_hash))
-      end
+      File.write(File.join(base_output_dir, 'metadata.yml'), YAML.dump(ig_metadata.to_hash))
     end
 
     def base_output_dir
@@ -126,6 +127,10 @@ module USCoreTestKit
       PractitionerAddressTestGenerator.generate(ig_metadata, base_output_dir)
     end
 
+    def generate_interpreter_required_extension_test_generator
+      InterpreterRequiredExtensionTestGenerator.generate(ig_metadata, base_output_dir)
+    end
+
     def generate_suites
       SuiteGenerator.generate(ig_metadata, base_output_dir)
     end

data/lib/us_core_test_kit/igs/us_core_800/CodeSystem-observation-category.json

@@ -0,0 +1,83 @@
+{
+  "resourceType" : "CodeSystem",
+  "id" : "observation-category",
+  "meta" : {
+    "lastUpdated" : "2020-04-09T21:10:28.568+00:00",
+    "profile" : ["http://hl7.org/fhir/StructureDefinition/shareablecodesystem"]
+  },
+  "text" : {
+    "status" : "generated",
+    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p>This code system <code>http://terminology.hl7.org/CodeSystem/observation-category</code> defines the following codes:</p><table class=\"codes\"><tr><td style=\"white-space:nowrap\"><b>Code</b></td><td><b>Display</b></td><td><b>Definition</b></td></tr><tr><td style=\"white-space:nowrap\">social-history<a name=\"observation-category-social-history\"> </a></td><td>Social History</td><td>Social History Observations define the patient's occupational, personal (e.g., lifestyle), social, familial, and environmental history and health risk factors that may impact the patient's health.</td></tr><tr><td style=\"white-space:nowrap\">vital-signs<a name=\"observation-category-vital-signs\"> </a></td><td>Vital Signs</td><td>Clinical observations measure the body's basic functions such as blood pressure, heart rate, respiratory rate, height, weight, body mass index, head circumference, pulse oximetry, temperature, and body surface area.</td></tr><tr><td style=\"white-space:nowrap\">imaging<a name=\"observation-category-imaging\"> </a></td><td>Imaging</td><td>Observations generated by imaging. The scope includes observations regarding plain x-ray, ultrasound, CT, MRI, angiography, echocardiography, and nuclear medicine.</td></tr><tr><td style=\"white-space:nowrap\">laboratory<a name=\"observation-category-laboratory\"> </a></td><td>Laboratory</td><td>The results of observations generated by laboratories.  Laboratory results are typically generated by laboratories providing analytic services in areas such as chemistry, hematology, serology, histology, cytology, anatomic pathology (including digital pathology), microbiology, and/or virology. These observations are based on analysis of specimens obtained from the patient and submitted to the laboratory.</td></tr><tr><td style=\"white-space:nowrap\">procedure<a name=\"observation-category-procedure\"> </a></td><td>Procedure</td><td>Observations generated by other procedures.  This category includes observations resulting from interventional and non-interventional procedures excluding laboratory and imaging (e.g., cardiology catheterization, endoscopy, electrodiagnostics, etc.).  Procedure results are typically generated by a clinician to provide more granular information about component observations made during a procedure.  An example would be when a gastroenterologist reports the size of a polyp observed during a colonoscopy.</td></tr><tr><td style=\"white-space:nowrap\">survey<a name=\"observation-category-survey\"> </a></td><td>Survey</td><td>Assessment tool/survey instrument observations (e.g., Apgar Scores, Montreal Cognitive Assessment (MoCA)).</td></tr><tr><td style=\"white-space:nowrap\">exam<a name=\"observation-category-exam\"> </a></td><td>Exam</td><td>Observations generated by physical exam findings including direct observations made by a clinician and use of simple instruments and the result of simple maneuvers performed directly on the patient's body.</td></tr><tr><td style=\"white-space:nowrap\">therapy<a name=\"observation-category-therapy\"> </a></td><td>Therapy</td><td>Observations generated by non-interventional treatment protocols (e.g. occupational, physical, radiation, nutritional and medication therapy)</td></tr><tr><td style=\"white-space:nowrap\">activity<a name=\"observation-category-activity\"> </a></td><td>Activity</td><td>Observations that measure or record any bodily activity that enhances or maintains physical fitness and overall health and wellness.  Not under direct supervision of practitioner such as a physical therapist. (e.g., laps swum, steps, sleep data)</td></tr></table></div>"
+  },
+  "extension" : [{
+    "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
+    "valueCode" : "oo"
+  }],
+  "url" : "http://terminology.hl7.org/CodeSystem/observation-category",
+  "identifier" : [{
+    "system" : "urn:ietf:rfc:3986",
+    "value" : "urn:oid:2.16.840.1.113883.4.642.1.1125"
+  }],
+  "version" : "0.1.0",
+  "name" : "ObservationCategoryCodes",
+  "title" : "Observation Category Codes",
+  "status" : "draft",
+  "experimental" : false,
+  "date" : "2023-02-25T11:07:30-07:00",
+  "publisher" : "FHIR Project team",
+  "contact" : [{
+    "telecom" : [{
+      "system" : "url",
+      "value" : "http://hl7.org/fhir"
+    }]
+  }],
+  "description" : "Observation Category codes.",
+  "caseSensitive" : true,
+  "valueSet" : "http://terminology.hl7.org/ValueSet/observation-category",
+  "content" : "complete",
+  "concept" : [{
+    "code" : "social-history",
+    "display" : "Social History",
+    "definition" : "Social History Observations define the patient's occupational, personal (e.g., lifestyle), social, familial, and environmental history and health risk factors that may impact the patient's health."
+  },
+  {
+    "code" : "vital-signs",
+    "display" : "Vital Signs",
+    "definition" : "Clinical observations measure the body's basic functions such as blood pressure, heart rate, respiratory rate, height, weight, body mass index, head circumference, pulse oximetry, temperature, and body surface area."
+  },
+  {
+    "code" : "imaging",
+    "display" : "Imaging",
+    "definition" : "Observations generated by imaging. The scope includes observations regarding plain x-ray, ultrasound, CT, MRI, angiography, echocardiography, and nuclear medicine."
+  },
+  {
+    "code" : "laboratory",
+    "display" : "Laboratory",
+    "definition" : "The results of observations generated by laboratories.  Laboratory results are typically generated by laboratories providing analytic services in areas such as chemistry, hematology, serology, histology, cytology, anatomic pathology (including digital pathology), microbiology, and/or virology. These observations are based on analysis of specimens obtained from the patient and submitted to the laboratory."
+  },
+  {
+    "code" : "procedure",
+    "display" : "Procedure",
+    "definition" : "Observations generated by other procedures.  This category includes observations resulting from interventional and non-interventional procedures excluding laboratory and imaging (e.g., cardiology catheterization, endoscopy, electrodiagnostics, etc.).  Procedure results are typically generated by a clinician to provide more granular information about component observations made during a procedure.  An example would be when a gastroenterologist reports the size of a polyp observed during a colonoscopy."
+  },
+  {
+    "code" : "survey",
+    "display" : "Survey",
+    "definition" : "Assessment tool/survey instrument observations (e.g., Apgar Scores, Montreal Cognitive Assessment (MoCA))."
+  },
+  {
+    "code" : "exam",
+    "display" : "Exam",
+    "definition" : "Observations generated by physical exam findings including direct observations made by a clinician and use of simple instruments and the result of simple maneuvers performed directly on the patient's body."
+  },
+  {
+    "code" : "therapy",
+    "display" : "Therapy",
+    "definition" : "Observations generated by non-interventional treatment protocols (e.g. occupational, physical, radiation, nutritional and medication therapy)"
+  },
+  {
+    "code" : "activity",
+    "display" : "Activity",
+    "definition" : "Observations that measure or record any bodily activity that enhances or maintains physical fitness and overall health and wellness.  Not under direct supervision of practitioner such as a physical therapist. (e.g., laps swum, steps, sleep data)"
+  }]
+}

data/lib/us_core_test_kit/igs/us_core_800/Resource-lastUpdated.json

@@ -0,0 +1,43 @@
+{
+  "resourceType" : "SearchParameter",
+  "id" : "Resource-lastUpdated",
+  "extension" : [{
+    "url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status",
+    "valueCode" : "trial-use"
+  }],
+  "url" : "http://hl7.org/fhir/SearchParameter/Resource-lastUpdated",
+  "version" : "4.0.1",
+  "name" : "_lastUpdated",
+  "status" : "draft",
+  "experimental" : false,
+  "date" : "2019-11-01T09:29:23+11:00",
+  "publisher" : "Health Level Seven International (FHIR Infrastructure)",
+  "contact" : [{
+    "telecom" : [{
+      "system" : "url",
+      "value" : "http://hl7.org/fhir"
+    }]
+  },
+  {
+    "telecom" : [{
+      "system" : "url",
+      "value" : "http://www.hl7.org/Special/committees/fiwg/index.cfm"
+    }]
+  }],
+  "description" : "When the resource version last changed",
+  "code" : "_lastUpdated",
+  "base" : ["Resource"],
+  "type" : "date",
+  "expression" : "Resource.meta.lastUpdated",
+  "xpath" : "f:Resource/f:meta/f:lastUpdated",
+  "xpathUsage" : "normal",
+  "comparator" : ["eq",
+  "ne",
+  "gt",
+  "ge",
+  "lt",
+  "le",
+  "sa",
+  "eb",
+  "ap"]
+}

data/lib/us_core_test_kit/igs/us_core_800/StructureDefinition-condition-assertedDate.json

@@ -0,0 +1,280 @@
+{
+  "resourceType": "StructureDefinition",
+  "id": "condition-assertedDate",
+  "extension": [
+    {
+      "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
+      "valueCode": "pc"
+    },
+    {
+      "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm",
+      "valueInteger": 1
+    }
+  ],
+  "url": "http://hl7.org/fhir/StructureDefinition/condition-assertedDate",
+  "version": "4.0.1",
+  "name": "assertedDate",
+  "title": "assertedDate",
+  "status": "draft",
+  "date": "2015-02-21",
+  "publisher": "Health Level Seven, Inc. - FHIR WG",
+  "contact": [
+    {
+      "telecom": [
+        {
+          "system": "url",
+          "value": "HL7"
+        }
+      ]
+    }
+  ],
+  "description": "The date on which the existence of the Condition was first asserted or acknowledged.",
+  "fhirVersion": "4.0.1",
+  "mapping": [
+    {
+      "identity": "rim",
+      "uri": "http://hl7.org/v3",
+      "name": "RIM Mapping"
+    }
+  ],
+  "kind": "complex-type",
+  "abstract": false,
+  "context": [
+    {
+      "type": "element",
+      "expression": "Condition"
+    }
+  ],
+  "type": "Extension",
+  "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Extension",
+  "derivation": "constraint",
+  "snapshot": {
+    "element": [
+      {
+        "id": "Extension",
+        "path": "Extension",
+        "short": "Date the condition was first asserted",
+        "definition": "The date on which the existence of the Condition was first asserted or acknowledged.",
+        "comment": "The assertedDate is in the context of the recording practitioner and might not be the same as the recordedDate.",
+        "min": 0,
+        "max": "1",
+        "base": {
+          "path": "Extension",
+          "min": 0,
+          "max": "*"
+        },
+        "condition": [
+          "ele-1"
+        ],
+        "constraint": [
+          {
+            "key": "ele-1",
+            "severity": "error",
+            "human": "All FHIR elements must have a @value or children",
+            "expression": "hasValue() or (children().count() > id.count())",
+            "xpath": "@value|f:*|h:div",
+            "source": "http://hl7.org/fhir/StructureDefinition/Element"
+          },
+          {
+            "key": "ext-1",
+            "severity": "error",
+            "human": "Must have either extensions or value[x], not both",
+            "expression": "extension.exists() != value.exists()",
+            "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])",
+            "source": "http://hl7.org/fhir/StructureDefinition/Extension"
+          }
+        ],
+        "isModifier": false
+      },
+      {
+        "id": "Extension.id",
+        "path": "Extension.id",
+        "representation": [
+          "xmlAttr"
+        ],
+        "short": "Unique id for inter-element referencing",
+        "definition": "Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
+        "min": 0,
+        "max": "1",
+        "base": {
+          "path": "Element.id",
+          "min": 0,
+          "max": "1"
+        },
+        "type": [
+          {
+            "extension": [
+              {
+                "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
+                "valueUrl": "string"
+              }
+            ],
+            "code": "http://hl7.org/fhirpath/System.String"
+          }
+        ],
+        "isModifier": false,
+        "isSummary": false,
+        "mapping": [
+          {
+            "identity": "rim",
+            "map": "n/a"
+          }
+        ]
+      },
+      {
+        "id": "Extension.extension",
+        "path": "Extension.extension",
+        "slicing": {
+          "discriminator": [
+            {
+              "type": "value",
+              "path": "url"
+            }
+          ],
+          "description": "Extensions are always sliced by (at least) url",
+          "rules": "open"
+        },
+        "short": "Extension",
+        "definition": "An Extension",
+        "min": 0,
+        "max": "0",
+        "base": {
+          "path": "Element.extension",
+          "min": 0,
+          "max": "*"
+        },
+        "type": [
+          {
+            "code": "Extension"
+          }
+        ],
+        "constraint": [
+          {
+            "key": "ele-1",
+            "severity": "error",
+            "human": "All FHIR elements must have a @value or children",
+            "expression": "hasValue() or (children().count() > id.count())",
+            "xpath": "@value|f:*|h:div",
+            "source": "http://hl7.org/fhir/StructureDefinition/Element"
+          },
+          {
+            "key": "ext-1",
+            "severity": "error",
+            "human": "Must have either extensions or value[x], not both",
+            "expression": "extension.exists() != value.exists()",
+            "xpath": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), \"value\")])",
+            "source": "http://hl7.org/fhir/StructureDefinition/Extension"
+          }
+        ],
+        "isModifier": false,
+        "isSummary": false
+      },
+      {
+        "id": "Extension.url",
+        "path": "Extension.url",
+        "representation": [
+          "xmlAttr"
+        ],
+        "short": "identifies the meaning of the extension",
+        "definition": "Source of the definition for the extension code - a logical name or a URL.",
+        "comment": "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension.",
+        "min": 1,
+        "max": "1",
+        "base": {
+          "path": "Extension.url",
+          "min": 1,
+          "max": "1"
+        },
+        "type": [
+          {
+            "extension": [
+              {
+                "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type",
+                "valueUrl": "uri"
+              }
+            ],
+            "code": "http://hl7.org/fhirpath/System.String"
+          }
+        ],
+        "fixedUri": "http://hl7.org/fhir/StructureDefinition/condition-assertedDate",
+        "isModifier": false,
+        "isSummary": false,
+        "mapping": [
+          {
+            "identity": "rim",
+            "map": "N/A"
+          }
+        ]
+      },
+      {
+        "id": "Extension.value[x]",
+        "path": "Extension.value[x]",
+        "short": "Value of extension",
+        "definition": "Value of extension - must be one of a constrained set of the data types (see [Extensibility](http://hl7.org/fhir/extensibility.html) for a list).",
+        "min": 1,
+        "max": "1",
+        "base": {
+          "path": "Extension.value[x]",
+          "min": 0,
+          "max": "1"
+        },
+        "type": [
+          {
+            "code": "dateTime"
+          }
+        ],
+        "constraint": [
+          {
+            "key": "ele-1",
+            "severity": "error",
+            "human": "All FHIR elements must have a @value or children",
+            "expression": "hasValue() or (children().count() > id.count())",
+            "xpath": "@value|f:*|h:div",
+            "source": "http://hl7.org/fhir/StructureDefinition/Element"
+          }
+        ],
+        "isModifier": false,
+        "isSummary": false,
+        "mapping": [
+          {
+            "identity": "rim",
+            "map": "N/A"
+          }
+        ]
+      }
+    ]
+  },
+  "differential": {
+    "element": [
+      {
+        "id": "Extension",
+        "path": "Extension",
+        "short": "Date the condition was first asserted",
+        "definition": "The date on which the existence of the Condition was first asserted or acknowledged.",
+        "comment": "The assertedDate is in the context of the recording practitioner and might not be the same as the recordedDate.",
+        "min": 0,
+        "max": "1"
+      },
+      {
+        "id": "Extension.extension",
+        "path": "Extension.extension",
+        "max": "0"
+      },
+      {
+        "id": "Extension.url",
+        "path": "Extension.url",
+        "fixedUri": "http://hl7.org/fhir/StructureDefinition/condition-assertedDate"
+      },
+      {
+        "id": "Extension.value[x]",
+        "path": "Extension.value[x]",
+        "min": 1,
+        "type": [
+          {
+            "code": "dateTime"
+          }
+        ]
+      }
+    ]
+  }
+}