uds_plus_test_kit 0.9.1 → 1.0.1

data/lib/uds_plus_test_kit/input_resource_tests/resource_group.rb

@@ -15,6 +15,20 @@ require_relative '../validate_procedure_test'
 require_relative '../validate_sexual_orientation_test'
 require_relative './read_manifest_ind_test'
 require_relative '../manifest_tests/validate_manifest_test'
+require_relative './read_special_observation_test'
+require_relative '../validate_special_observation_test'
+require_relative './read_related_person_test'
+require_relative '../validate_related_person_test'
+require_relative './read_immunization_test'
+require_relative '../validate_immunization_test'
+require_relative './read_lab_test'
+require_relative '../validate_lab_test'
+require_relative './read_med_request_test'
+require_relative '../validate_med_request_test'
+require_relative './read_med_statement_test'
+require_relative '../validate_med_statement_test'
+require_relative './read_service_request_test'
+require_relative '../validate_service_request_test'
 
 module UDSPlusTestKit
     class UDSPlusResourceTestGroup < Inferno::TestGroup
@@ -39,13 +53,27 @@ module UDSPlusTestKit
         test from: :uds_plus_validate_diagnosis_test
         test from: :uds_plus_read_encounter_test
         test from: :uds_plus_validate_encounter_test
-        test from: :uds_plus_read_income_test
-        test from: :uds_plus_validate_income_test
         test from: :uds_plus_read_patient_test
         test from: :uds_plus_validate_patient_test
         test from: :uds_plus_read_procedure_test
         test from: :uds_plus_validate_procedure_test
+        test from: :uds_plus_read_related_person_test
+        test from: :uds_plus_validate_related_person_test
+        test from: :uds_plus_read_immunization_test
+        test from: :uds_plus_validate_immunization_test
+        test from: :uds_plus_read_income_test
+        test from: :uds_plus_validate_income_test
         test from: :uds_plus_read_sexual_orientation_test
         test from: :uds_plus_validate_sexual_orientation_test
+        test from: :uds_plus_read_lab_test
+        test from: :uds_plus_validate_lab_test
+        test from: :uds_plus_read_special_observation_test
+        test from: :uds_plus_read_medication_request_test
+        test from: :uds_plus_validate_medication_request_test
+        test from: :uds_plus_read_medication_statement_test
+        test from: :uds_plus_validate_medication_statement_test
+        test from: :uds_plus_read_service_request_test
+        test from: :uds_plus_validate_service_request_test
+        test from: :uds_plus_validate_special_observation_test
     end
 end

data/lib/uds_plus_test_kit/manifest_tests/invalid_type_test.rb

@@ -17,7 +17,10 @@ module UDSPlusTestKit
         def valid_data_types
             [
                 'Coverage', 'Condition', 'Encounter', 
-                'Observation', 'Patient', 'Procedure'
+                'Observation', 'Patient', 'Procedure',
+                'RelatedPerson', 'Immunization',
+                'ServiceRequest', 'MedicationRequest', 
+                'MedicationStatement'
             ]
         end
 

data/lib/uds_plus_test_kit/manifest_tests/uds_plus_test_group.rb

@@ -10,10 +10,17 @@ require_relative './validate_manifest_test'
 require_relative '../validate_patient_test'
 require_relative '../validate_procedure_test'
 require_relative '../validate_sexual_orientation_test'
+require_relative '../validate_special_observation_test'
+require_relative '../validate_related_person_test'
+require_relative '../validate_immunization_test'
+require_relative '../validate_lab_test'
+require_relative '../validate_med_request_test'
+require_relative '../validate_med_statement_test'
+require_relative '../validate_service_request_test'
 
 module UDSPlusTestKit
     class UDSPlusTestGroup < Inferno::TestGroup
-        title 'Data Submitter Tests'
+        title 'Import Manifest Tests'
         id :uds_plus_test_group 
         description %(
             The tests below validate the import manifest produced by a UDS+ Data Submitter. 
@@ -30,10 +37,17 @@ module UDSPlusTestKit
         test from: :uds_plus_validate_coverage_test
         test from: :uds_plus_validate_diagnosis_test
         test from: :uds_plus_validate_encounter_test
-        test from: :uds_plus_validate_income_test
         test from: :uds_plus_validate_patient_test
         test from: :uds_plus_validate_procedure_test
+        test from: :uds_plus_validate_related_person_test
+        test from: :uds_plus_validate_immunization_test
+        test from: :uds_plus_validate_income_test
         test from: :uds_plus_validate_sexual_orientation_test
+        test from: :uds_plus_validate_lab_test
+        test from: :uds_plus_validate_special_observation_test
+        test from: :uds_plus_validate_medication_request_test
+        test from: :uds_plus_validate_medication_statement_test
+        test from: :uds_plus_validate_service_request_test
         test from: :uds_plus_invalid_type_test
     end
 end

data/lib/uds_plus_test_kit/post_tests/post_group.rb

@@ -0,0 +1,59 @@
+
+require_relative '../version'
+
+require_relative './post_manifest_test'
+require_relative './read_post_test'
+
+require_relative '../manifest_tests/invalid_type_test'
+require_relative '../manifest_tests/read_data_test'
+require_relative '../manifest_tests/validate_manifest_test'
+
+require_relative '../validate_coverage_test'
+require_relative '../validate_diagnosis_test'
+require_relative '../validate_encounter_test'
+require_relative '../validate_income_test'
+require_relative '../validate_patient_test'
+require_relative '../validate_procedure_test'
+require_relative '../validate_sexual_orientation_test'
+require_relative '../validate_special_observation_test'
+require_relative '../validate_related_person_test'
+require_relative '../validate_immunization_test'
+require_relative '../validate_lab_test'
+require_relative '../validate_med_request_test'
+require_relative '../validate_med_statement_test'
+require_relative '../validate_service_request_test'
+
+module UDSPlusTestKit
+    class UDSPlusPostGroup < Inferno::TestGroup
+        title 'End-to-End Import Manifest Tests'
+        id :uds_plus_manifest_post_group 
+        description %(
+            The tests below validate the import manifest produced by a UDS+ Data Submitter. 
+            This receiver will take a provided Import Manifest via POST request to a given 
+            location and validate its contents. This includes validating the structure 
+            of the manifest, as well as the structure of the data the manifest points to.
+        )
+
+        run_as_group
+
+        test from: :uds_plus_post_manifest_test
+        test from: :uds_plus_read_post_test
+        test from: :uds_plus_validate_manifest_test
+        test from: :uds_plus_read_data_test
+        test from: :uds_plus_validate_coverage_test
+        test from: :uds_plus_validate_diagnosis_test
+        test from: :uds_plus_validate_encounter_test
+        test from: :uds_plus_validate_patient_test
+        test from: :uds_plus_validate_procedure_test
+        test from: :uds_plus_validate_related_person_test
+        test from: :uds_plus_validate_immunization_test
+        test from: :uds_plus_validate_income_test
+        test from: :uds_plus_validate_sexual_orientation_test
+        test from: :uds_plus_validate_lab_test
+        test from: :uds_plus_validate_special_observation_test
+        test from: :uds_plus_validate_medication_request_test
+        test from: :uds_plus_validate_medication_statement_test
+        test from: :uds_plus_validate_service_request_test
+        test from: :uds_plus_invalid_type_test
+    end
+end

data/lib/uds_plus_test_kit/post_tests/post_manifest_test.rb

@@ -0,0 +1,41 @@
+require 'json'
+
+
+module UDSPlusTestKit
+    class PostManifestTest < Inferno::Test
+        id :uds_plus_post_manifest_test
+        title 'Receive UDS+ Import Manifest via POST request'
+        description %(
+            Test waits for an import manifest to be posted at the 
+            provided location. Test passes if it recieves a post
+            request within 3 mins of test start.
+        )
+
+        receives_request :import_manifest
+
+        def id_gen
+            output = ''
+            ranNum = Random.new
+            for _ in 1..10
+                output += ranNum.rand(10).to_s
+            end
+            output
+        end
+
+        run do
+            session_id = id_gen
+            wait(
+                identifier: session_id,
+                timeout: 300,
+                message: %(
+                    Post your Import Manifest JSON to the following URL:
+                    #{Inferno::Application['base_url']}/custom/uds_plus/postHere?id=#{session_id}
+
+                    If the test times out or is cancelled for any reason, rerunning the test group will restart the timeout.
+
+                    Your request body MUST be your Import Manifest in raw json format. Testing will resume automatically after a valid POST is received.
+                )
+            )
+        end
+    end
+end

data/lib/uds_plus_test_kit/post_tests/read_post_test.rb

@@ -0,0 +1,32 @@
+require 'json'
+
+
+module UDSPlusTestKit
+    class ReadPostTest < Inferno::Test
+        id :uds_plus_read_post_test
+        title 'Read Input from POST Request'
+        description %(
+            Test takes the file POSTed in the previous test,
+            and validates whether a FHIR resource can be generated from the input data.
+        )
+        
+        uses_request :import_manifest
+
+        def manifest_scratch
+            scratch[:manifest_resources] ||= {}
+        end
+
+        def manifest_resources
+            manifest_scratch[:all] ||= []
+        end
+
+        run do
+            found_resource = FHIR::Json.from_json(request.request_body)
+            assert found_resource.is_a?(FHIR::Model), "Could not generate a valid resource from the input provided"    
+            
+            if found_resource.is_a?(FHIR::Model)
+                manifest_resources << found_resource
+            end
+        end
+    end
+end

data/lib/uds_plus_test_kit/uds_plus_test_suite.rb

@@ -2,6 +2,7 @@ require 'inferno/dsl/oauth_credentials'
 require_relative './version'
 require_relative './manifest_tests/uds_plus_test_group'
 require_relative './input_resource_tests/resource_group'
+require_relative './post_tests/post_group'
 
 module UDSPlusTestKit
     class UDSPlusTestSuite < Inferno::TestSuite
@@ -29,6 +30,44 @@ module UDSPlusTestKit
 
         id :uds_plus
 
+        # Example urls generated here
+        patient_ex = File.read(File.join(__dir__, 'examples/patient.ndjson'))
+        patient_ex_route_handler = proc { [200, { 'Content-Type' => 'application/ndjson' }, [patient_ex]] }
+        route(:get, "/examples/patient", patient_ex_route_handler)
+
+        condition_ex = File.read(File.join(__dir__, 'examples/condition.ndjson'))
+        condition_ex_route_handler = proc { [200, { 'Content-Type' => 'application/ndjson' }, [condition_ex]] }
+        route(:get, "/examples/condition", condition_ex_route_handler)
+
+        encounter_ex = File.read(File.join(__dir__, 'examples/encounter.ndjson'))
+        encounter_ex_route_handler = proc { [200, { 'Content-Type' => 'application/ndjson' }, [encounter_ex]] }
+        route(:get, "/examples/encounter", encounter_ex_route_handler)
+
+        manifest_ex = File.read(File.join(__dir__, 'examples/manifest.json'))
+        manifest_ex_route_handler = proc { [200, { 'Content-Type' => 'application/json' }, [manifest_ex]] }
+        route(:get, "/examples/manifest", manifest_ex_route_handler)
+        
+        bad_condition_ex = File.read(File.join(__dir__, 'examples/invalid_condition.ndjson'))
+        bad_condition_ex_route_handler = proc { [200, { 'Content-Type' => 'application/ndjson' }, [bad_condition_ex]] }
+        route(:get, "/examples/invalid_condition", bad_condition_ex_route_handler)
+
+        bad_patient_ex = File.read(File.join(__dir__, 'examples/invalid_patient.ndjson'))
+        bad_patient_ex_route_handler = proc { [200, { 'Content-Type' => 'application/ndjson' }, [bad_patient_ex]] }
+        route(:get, "/examples/invalid_patient", bad_patient_ex_route_handler)
+
+        bad_encounter_ex = File.read(File.join(__dir__, 'examples/invalid_encounter.ndjson'))
+        bad_encounter_ex_route_handler = proc { [200, { 'Content-Type' => 'application/ndjson' }, [bad_encounter_ex]] }
+        route(:get, "/examples/invalid_encounter", bad_encounter_ex_route_handler)
+
+        observation_ex = File.read(File.join(__dir__, 'examples/observation.ndjson'))
+        observation_ex_route_handler = proc { [200, { 'Content-Type' => 'application/ndjson' }, [observation_ex]] }
+        route(:get, "/examples/observation", observation_ex_route_handler)
+
+        # Receive Manifest via POST set-up
+        resume_test_route :post, '/postHere' do |request|
+            request.query_parameters["id"]
+        end
+
         links [
             {
               label: 'Report Issue',
@@ -45,6 +84,7 @@ module UDSPlusTestKit
           ]
 
         group from: :uds_plus_test_group
+        group from: :uds_plus_manifest_post_group 
         group from: :uds_plus_resource_test_group
     end
 end

data/lib/uds_plus_test_kit/validate_immunization_test.rb

@@ -0,0 +1,33 @@
+require 'json'
+require_relative './version'
+
+module UDSPlusTestKit
+    class ValidateImmunizationTest < Inferno::Test
+        id :uds_plus_validate_immunization_test
+        title 'Validate UDS+ Immunization Data'
+        description %(
+            Test takes the Immunization resources identified 
+            by the import manifest, and validates whether they conform 
+            to their UDS+ Structure Definitions.
+        )
+
+        def data_scratch
+            scratch[:data_resources] ||= {}
+        end
+
+        def data_to_test
+            data_scratch['Immunization'] ||= []
+        end
+
+        run do
+            omit_if data_to_test.empty?, "No data of this type was identified."
+
+            profile_definition = 'http://hl7.org/fhir/us/uds-plus/StructureDefinition/uds-plus-immunization'
+            profile_with_version = "#{profile_definition}|#{UDS_PLUS_VERSION}"
+
+            data_to_test.each do |resource|
+                assert_valid_resource(resource: resource, profile_url: profile_with_version)
+            end
+        end
+    end
+end

data/lib/uds_plus_test_kit/validate_income_test.rb

@@ -22,21 +22,20 @@ module UDSPlusTestKit
         run do
             omit_if data_to_test.empty?, "No data of this type was identified."
 
-            profile_definition = 'http://hl7.org/fhir/us/uds-plus/StructureDefinition/uds-plus-income-observation'
+            profile_definition = 'http://hl7.org/fhir/us/uds-plus/StructureDefinition/de-identified-uds-plus-income-observation'
             profile_with_version = "#{profile_definition}|#{UDS_PLUS_VERSION}"
 
             no_resource_of_this_type = true
             identifier_fail_message = %(Resource.meta.profile should contain the HTTP location of the 
                                         resource's Structure Definition. Resource.meta.profile either does 
                                         not exist in this resource, or its contents do not point to a valid
-                                        location for type Observation (Income/Sexual Orientation). **NOTE:**
-                                        If this error occurs, it will trigger a fail for both the Income and
-                                        Sexual Orientation tests, regardless of whether both tests were meant
-                                        to run.)
+                                        location for type Observation. **NOTE:**
+                                        If this error occurs, it can trigger a fail for all observation-type tests, 
+                                        regardless of whether both tests were meant to run.)
 
             data_to_test.each do |resource|
-                # All these assertions are to differentaite Observation data between Income Data and Sexual Orientation data.
-                # A resource is skipped if it is a sexual orientation resource and fails if it cannot be identified as an income resource.
+                # All these assertions are to differentaite Observation data between orientation types.
+                # A resource is skipped if it cannot be identified as an income resource.
                 type_identifier = resource.to_hash
                 assert type_identifier['meta'].present?, identifier_fail_message
 
@@ -51,10 +50,8 @@ module UDSPlusTestKit
 
                 type_identifier = type_identifier.first
                 assert type_identifier.is_a?(String), identifier_fail_message
-                if type_identifier.include?("sexual-orientation")
+                if !type_identifier.include?("income")
                     next
-                else 
-                    assert type_identifier.include?("income"), identifier_fail_message
                 end
                     
                 no_resource_of_this_type = false

data/lib/uds_plus_test_kit/validate_lab_test.rb

@@ -0,0 +1,65 @@
+require 'json'
+require_relative './version'
+
+module UDSPlusTestKit
+    class ValidateLabTest < Inferno::Test
+        id :uds_plus_validate_lab_test
+        title 'Validate UDS+ Lab Observation Data'
+        description %(
+            Test takes the Lab Observation resources identified 
+            by the import manifest, and validates whether they conform 
+            to their UDS+ Structure Definitions.
+        )
+
+        def data_scratch
+            scratch[:data_resources] ||= {}
+        end
+
+        def data_to_test
+            data_scratch['Observation'] ||= []
+        end
+
+        run do
+            omit_if data_to_test.empty?, "No data of this type was identified."
+
+            profile_definition = 'http://hl7.org/fhir/us/uds-plus/StructureDefinition/uds-plus-lab-observation'
+            profile_with_version = "#{profile_definition}|#{UDS_PLUS_VERSION}"
+
+            no_resource_of_this_type = true
+            identifier_fail_message = %(Resource.meta.profile should contain the HTTP location of the 
+                                        resource's Structure Definition. Resource.meta.profile either does 
+                                        not exist in this resource, or its contents do not point to a valid
+                                        location for type Observation. **NOTE:**
+                                        If this error occurs, it can trigger a fail for all observation-type tests, 
+                                        regardless of whether both tests were meant to run.)
+
+            data_to_test.each do |resource|
+                # All these assertions are to differentaite Observation data between Income Data and Sexual Orientation data.
+                # A resource is skipped if it is a sexual orientation resource and fails if it cannot be identified as an income resource.
+                type_identifier = resource.to_hash
+                assert type_identifier['meta'].present?, identifier_fail_message
+
+                type_identifier = type_identifier['meta']
+                assert type_identifier.is_a?(Hash), identifier_fail_message
+                assert type_identifier['profile'].present?, identifier_fail_message
+
+                type_identifier = type_identifier['profile']
+                assert type_identifier.is_a?(Array), identifier_fail_message
+                assert !type_identifier.empty?, identifier_fail_message
+
+
+                type_identifier = type_identifier.first
+                assert type_identifier.is_a?(String), identifier_fail_message
+                if !type_identifier.include?("-lab-")
+                    next
+                end
+                    
+                no_resource_of_this_type = false
+
+                assert_valid_resource(resource: resource, profile_url: profile_with_version)
+            end
+
+            omit_if no_resource_of_this_type, "No data of this type was identified."
+        end
+    end
+end

data/lib/uds_plus_test_kit/validate_med_request_test.rb

@@ -0,0 +1,33 @@
+require 'json'
+require_relative './version'
+
+module UDSPlusTestKit
+    class ValidateMedicationRequestTest < Inferno::Test
+        id :uds_plus_validate_medication_request_test
+        title 'Validate UDS+ Medication Request Data'
+        description %(
+            Test takes the Medication Request resources identified 
+            by the import manifest, and validates whether they conform 
+            to their UDS+ Structure Definitions.
+        )
+
+        def data_scratch
+            scratch[:data_resources] ||= {}
+        end
+
+        def data_to_test
+            data_scratch['MedicationRequest'] ||= []
+        end
+
+        run do
+            omit_if data_to_test.empty?, "No data of this type was identified."
+
+            profile_definition = 'http://hl7.org/fhir/us/uds-plus/StructureDefinition/uds-plus-medicationrequest'
+            profile_with_version = "#{profile_definition}|#{UDS_PLUS_VERSION}"
+
+            data_to_test.each do |resource|
+                assert_valid_resource(resource: resource, profile_url: profile_with_version)
+            end
+        end
+    end
+end

data/lib/uds_plus_test_kit/validate_med_statement_test.rb

@@ -0,0 +1,33 @@
+require 'json'
+require_relative './version'
+
+module UDSPlusTestKit
+    class ValidateMedicationStatementTest < Inferno::Test
+        id :uds_plus_validate_medication_statement_test
+        title 'Validate UDS+ Medication Statement Data'
+        description %(
+            Test takes the Medication Statement resources identified 
+            by the import manifest, and validates whether they conform 
+            to their UDS+ Structure Definitions.
+        )
+
+        def data_scratch
+            scratch[:data_resources] ||= {}
+        end
+
+        def data_to_test
+            data_scratch['MedicationStatement'] ||= []
+        end
+
+        run do
+            omit_if data_to_test.empty?, "No data of this type was identified."
+
+            profile_definition = 'http://hl7.org/fhir/us/uds-plus/StructureDefinition/uds-plus-medicationstatement'
+            profile_with_version = "#{profile_definition}|#{UDS_PLUS_VERSION}"
+
+            data_to_test.each do |resource|
+                assert_valid_resource(resource: resource, profile_url: profile_with_version)
+            end
+        end
+    end
+end

data/lib/uds_plus_test_kit/validate_related_person_test.rb

@@ -0,0 +1,33 @@
+require 'json'
+require_relative './version'
+
+module UDSPlusTestKit
+    class ValidateRelatedPersonTest < Inferno::Test
+        id :uds_plus_validate_related_person_test
+        title 'Validate UDS+ Related Person Data'
+        description %(
+            Test takes the Related Person resources identified 
+            by the import manifest, and validates whether they conform 
+            to their UDS+ Structure Definitions.
+        )
+
+        def data_scratch
+            scratch[:data_resources] ||= {}
+        end
+
+        def data_to_test
+            data_scratch['RelatedPerson'] ||= []
+        end
+
+        run do
+            omit_if data_to_test.empty?, "No data of this type was identified."
+
+            profile_definition = 'http://hl7.org/fhir/us/uds-plus/StructureDefinition/de-identified-uds-plus-relatedperson'
+            profile_with_version = "#{profile_definition}|#{UDS_PLUS_VERSION}"
+
+            data_to_test.each do |resource|
+                assert_valid_resource(resource: resource, profile_url: profile_with_version)
+            end
+        end
+    end
+end

data/lib/uds_plus_test_kit/validate_service_request_test.rb

@@ -0,0 +1,33 @@
+require 'json'
+require_relative './version'
+
+module UDSPlusTestKit
+    class ValidateServiceRequestTest < Inferno::Test
+        id :uds_plus_validate_service_request_test
+        title 'Validate UDS+ Service Request Data'
+        description %(
+            Test takes the Service Request resources identified 
+            by the import manifest, and validates whether they conform 
+            to their UDS+ Structure Definitions.
+        )
+
+        def data_scratch
+            scratch[:data_resources] ||= {}
+        end
+
+        def data_to_test
+            data_scratch['ServiceRequest'] ||= []
+        end
+
+        run do
+            omit_if data_to_test.empty?, "No data of this type was identified."
+
+            profile_definition = 'http://hl7.org/fhir/us/uds-plus/StructureDefinition/uds-plus-servicerequest'
+            profile_with_version = "#{profile_definition}|#{UDS_PLUS_VERSION}"
+
+            data_to_test.each do |resource|
+                assert_valid_resource(resource: resource, profile_url: profile_with_version)
+            end
+        end
+    end
+end

data/lib/uds_plus_test_kit/validate_sexual_orientation_test.rb

@@ -29,14 +29,13 @@ module UDSPlusTestKit
             identifier_fail_message = %(Resource.meta.profile should contain the HTTP location of the 
                                         resource's Structure Definition. Resource.meta.profile either does 
                                         not exist in this resource, or its contents do not point to a valid
-                                        location for type Observation (Income/Sexual Orientation). **NOTE:**
-                                        If this error occurs, it will trigger a fail for both the Income and
-                                        Sexual Orientation tests, regardless of whether both tests were meant
-                                        to run.)
+                                        location for type Observation. **NOTE:**
+                                        If this error occurs, it can trigger a fail for all observation-type tests, 
+                                        regardless of whether both tests were meant to run.)
 
             data_to_test.each do |resource|
-                # All these assertions are to differentaite Observation data between Income Data and Sexual Orientation data.
-                # A resource is skipped if it is an income resource and fails if it cannot be identified as a sexual orientation resource.
+                # All these assertions are to differentaite Observation data between orientation types.
+                # A resource is skipped if it cannot be identified as a sexual orientation resource.
                 type_identifier = resource.to_hash
                 assert type_identifier['meta'].present?, identifier_fail_message
 
@@ -51,10 +50,8 @@ module UDSPlusTestKit
 
                 type_identifier = type_identifier.first
                 assert type_identifier.is_a?(String), identifier_fail_message
-                if type_identifier.include?("income")
+                if !type_identifier.include?("sexual-orientation")
                     next
-                else 
-                    assert type_identifier.include?("sexual-orientation"), identifier_fail_message
                 end
                     
                 no_resource_of_this_type = false