Merge pull request #65 from NHSDigital/GEL1001

Addition of Specimen inputs/outputs to Tasks
NHSDigital · Apr 9, 2024 · f338f55 · f338f55
2 parents d1fae0d + ba7e6a1
commit f338f55
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diff --git a/CapabilityStatement/CapabilityStatement-genomics-application.json b/CapabilityStatement/CapabilityStatement-genomics-application.json
@@ -65,7 +65,7 @@
 			"resource":  [
 				{
 					"type": "AuditEvent",
-					"profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-AuditEvent",
+					"profile": "http://hl7.org/fhir/StructureDefinition/AuditEvent",
 					"documentation": "For searching recorded AuditEvents",
 					"interaction": [
 						{
@@ -104,7 +104,7 @@
 				},
 				{
 					"type": "Bundle",
-					"profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Bundle", 
+					"profile": "http://hl7.org/fhir/StructureDefinition/Bundle", 
 					"documentation": "For posting FHIR transaction bundles (http://hl7.org/fhir/R4B/http.html#transaction) to the server.",
 					"interaction": [
 						{
@@ -280,7 +280,7 @@
 				},
 				{
 					"type": "MessageDefinition",
-					"profile": "https://fhir.nhs.uk/StructureDefinition/NHSDigital-MessageDefinition-Genomics",
+					"profile": "http://hl7.org/fhir/StructureDefinition/MessageDefinition",
 					"documentation": "For searching supported MessageDefinitions",
 					"interaction": [
 						{
@@ -416,7 +416,7 @@
 				},
 				{
 					"type": "MessageHeader",
-					"profile": "https://fhir.nhs.uk/StructureDefinition/NHSDigital-MessageHeader-Genomics",
+					"profile": "http://hl7.org/fhir/StructureDefinition/MessageHeader",
 					"documentation": "Endpoints for interacting with MessageHeader resources",
 					"interaction": [
 						{
@@ -523,7 +523,7 @@
 				},
 				{
 					"type": "CapabilityStatement",
-					"profile": "https://fhir.nhs.uk/StructureDefinition/NHSDigital-CapabilityStatement",
+					"profile": "http://hl7.org/fhir/StructureDefinition/CapabilityStatement",
 					"documentation": "For searching provided CapabilityStatements",
 					"interaction": [
 						{
@@ -566,7 +566,7 @@
 				},
 				{
 					"type": "Task",
-					"profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Task",
+					"profile": "http://hl7.org/fhir/StructureDefinition/Task",
 					"documentation": "Endpoints for interacting with Task resources",
 					"interaction": [
 						{
@@ -1253,7 +1253,7 @@
 				},
 				{
 					"type": "Consent",
-					"profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Consent",
+					"profile": "http://hl7.org/fhir/StructureDefinition/Consent",
 					"documentation": "Endpoints for interacting with Consent resources",
 					"interaction": [
 						{
@@ -1540,7 +1540,7 @@
 				},
 				{
 					"type": "Questionnaire",
-					"profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Questionnaire",
+					"profile": "http://hl7.org/fhir/StructureDefinition/Questionnaire",
 					"documentation": "For searching supported Questionnaires",
 					"interaction": [
 						{
@@ -1587,7 +1587,7 @@
 				},
 				{
 					"type": "QuestionnaireResponse",
-					"profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-QuestionnaireResponse",
+					"profile": "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse",
 					"documentation": "Endpoints for interacting with QuestionnaireResponse resources",
 					"interaction": [
 						{
@@ -1654,11 +1654,11 @@
 				},
 				{
 					"type": "OperationDefinition",
-					"profile": "https://fhir.nhs.uk/StructureDefinition/NHSDigital-OperationDefinition"
+					"profile": "https://hl7.org/fhir/StructureDefinition/OperationDefinition"
 				},
 				{
 					"type": "OperationOutcome",
-					"profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-OperationOutcome",
+					"profile": "http://hl7.org/fhir/StructureDefinition/OperationOutcome",
 					"documentation": "For searching historical OperationOutcomes",
 					"interaction": [
 						{
@@ -1726,7 +1726,7 @@
 				},
 				{
 					"type": "Provenance",
-					"profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Provenance",
+					"profile": "http://hl7.org/fhir/StructureDefinition/Provenance",
 					"documentation": "For searching stored Provenance resources",
 					"interaction": [
 						{

diff --git a/CapabilityStatement/CapabilityStatement-genomics-requirements.json b/CapabilityStatement/CapabilityStatement-genomics-requirements.json
@@ -33,11 +33,11 @@
 			"resource": [
 				{
 					"type": "AuditEvent",
-					"profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-AuditEvent"
+					"profile": "http://hl7.org/fhir/StructureDefinition/AuditEvent"
 				},
 				{
 					"type": "Bundle",
-					"profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Bundle"
+					"profile": "http://hl7.org/fhir/StructureDefinition/Bundle"
 				},
 				{
 					"type": "CodeSystem",
@@ -53,7 +53,7 @@
 				},
 				{
 					"type": "MessageDefinition",
-					"profile": "https://fhir.nhs.uk/StructureDefinition/NHSDigital-MessageDefinition-Genomics"
+					"profile": "http://hl7.org/fhir/StructureDefinition/MessageDefinition"
 				},
 				{
 					"type": "NamingSystem",
@@ -73,19 +73,19 @@
 				},
 				{
 					"type": "MessageHeader",
-					"profile": "https://fhir.nhs.uk/StructureDefinition/NHSDigital-MessageHeader-Genomics"
+					"profile": "http://hl7.org/fhir/StructureDefinition/MessageHeader"
 				},
 				{
 					"type": "Subscription",
 					"profile": "http://hl7.org/fhir/StructureDefinition/Subscription"
 				},
 				{
 					"type": "CapabilityStatement",
-					"profile": "https://fhir.nhs.uk/StructureDefinition/NHSDigital-CapabilityStatement"
+					"profile": "http://hl7.org/fhir/StructureDefinition/CapabilityStatement"
 				},
 				{
 					"type": "Task",
-					"profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Task"
+					"profile": "http://hl7.org/fhir/StructureDefinition/Task"
 				},
 				{
 					"type": "ServiceRequest",
@@ -121,7 +121,7 @@
 				},
 				{
 					"type": "Consent",
-					"profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Consent"
+					"profile": "http://hl7.org/fhir/StructureDefinition/Consent"
 				},
 				{
 					"type": "Condition",
@@ -141,27 +141,27 @@
 				},
 				{
 					"type": "Questionnaire",
-					"profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Questionnaire"
+					"profile": "http://hl7.org/fhir/StructureDefinition/Questionnaire"
 				},
 				{
 					"type": "QuestionnaireResponse",
-					"profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-QuestionnaireResponse"
+					"profile": "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse"
 				},
 				{
 					"type": "OperationDefinition",
-					"profile": "https://fhir.nhs.uk/StructureDefinition/NHSDigital-OperationDefinition"
+					"profile": "http://hl7.org/fhir/StructureDefinition/OperationDefinition"
 				},
 				{
 					"type": "OperationOutcome",
-					"profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-OperationOutcome"
+					"profile": "http://hl7.org/fhir/StructureDefinition/OperationOutcome"
 				},
 				{
 					"type": "BodyStructure",
 					"profile": "http://hl7.org/fhir/StructureDefinition/BodyStructure"
 				},
 				{
 					"type": "Provenance",
-					"profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Provenance"
+					"profile": "http://hl7.org/fhir/StructureDefinition/Provenance"
 				}
 			]
 		}

diff --git a/MessageDefinition/MessageDefinition-genomictestrequest.json b/MessageDefinition/MessageDefinition-genomictestrequest.json
@@ -45,7 +45,7 @@
         },
         {
             "code": "QuestionnaireResponse",
-            "profile": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-QuestionnaireResponse",
+            "profile": "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse",
             "min": 0,
             "max": "1"
         },

diff --git a/StructureDefinition/NHSDigital-Consent-Genomics.StructureDefinition.json b/StructureDefinition/NHSDigital-Consent-Genomics.StructureDefinition.json
@@ -7,7 +7,7 @@
   "kind": "resource",
   "abstract": false,
   "type": "Consent",
-  "baseDefinition": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Consent",
+  "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Consent",
   "derivation": "constraint",
   "differential": {
     "element": [
@@ -89,9 +89,9 @@
           {
             "code": "Reference",
             "targetProfile": [
-              "https://fhir.hl7.org.uk/StructureDefinition/UKCore-DocumentReference",
+              "http://hl7.org/fhir/StructureDefinition/DocumentReference",
               "http://hl7.org/fhir/StructureDefinition/Contract",
-              "https://fhir.hl7.org.uk/StructureDefinition/UKCore-QuestionnaireResponse",
+              "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse",
               "https://fhir.nhs.uk/StructureDefinition/NHSDigital-Consent-Genomics"
             ],
             "aggregation": [
@@ -132,9 +132,9 @@
           {
             "code": "Reference",
             "targetProfile": [
-              "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Device",
+              "http://hl7.org/fhir/StructureDefinition/Device",
               "http://hl7.org/fhir/StructureDefinition/Group",
-              "https://fhir.hl7.org.uk/StructureDefinition/UKCore-CareTeam",
+              "http://hl7.org/fhir/StructureDefinition/CareTeam",
               "https://fhir.hl7.org.uk/StructureDefinition/UKCore-RelatedPerson",
               "https://fhir.nhs.uk/StructureDefinition/NHSDigital-Organization-Genomics",
               "https://fhir.nhs.uk/StructureDefinition/NHSDigital-Patient-Genomics",

diff --git a/StructureDefinition/NHSDigital-FamilyMemberHistory-Genomics.StructureDefinition.json b/StructureDefinition/NHSDigital-FamilyMemberHistory-Genomics.StructureDefinition.json
@@ -49,7 +49,7 @@
             "code": "Reference",
             "targetProfile": [
               "https://fhir.hl7.org.uk/StructureDefinition/UKCore-AllergyIntolerance",
-              "https://fhir.hl7.org.uk/StructureDefinition/UKCore-QuestionnaireResponse",
+              "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse",
               "https://fhir.hl7.org.uk/StructureDefinition/UKCore-DocumentReference",
               "https://fhir.nhs.uk/StructureDefinition/NHSDigital-Condition-Genomics",
               "https://fhir.nhs.uk/StructureDefinition/NHSDigital-Observation-Genomics",

diff --git a/StructureDefinition/NHSDigital-MessageHeader-Genomics.StructureDefinition.json b/StructureDefinition/NHSDigital-MessageHeader-Genomics.StructureDefinition.json
@@ -7,7 +7,7 @@
   "kind": "resource",
   "abstract": false,
   "type": "MessageHeader",
-  "baseDefinition": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-MessageHeader",
+  "baseDefinition": "http://hl7.org/fhir/StructureDefinition/MessageHeader",
   "derivation": "constraint",
   "differential": {
     "element": [

diff --git a/StructureDefinition/NHSDigital-Observation-Genomics.StructureDefinition.json b/StructureDefinition/NHSDigital-Observation-Genomics.StructureDefinition.json
@@ -35,7 +35,7 @@
             "code": "Reference",
             "targetProfile": [
               "http://hl7.org/fhir/StructureDefinition/Group",
-              "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Device",
+              "http://hl7.org/fhir/StructureDefinition/Device",
               "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Location",
               "https://fhir.nhs.uk/StructureDefinition/NHSDigital-Patient-Genomics"
             ],
@@ -92,7 +92,7 @@
           {
             "code": "Reference",
             "targetProfile": [
-              "https://fhir.hl7.org.uk/StructureDefinition/UKCore-CareTeam",
+              "http://hl7.org/fhir/StructureDefinition/CareTeam",
               "https://fhir.hl7.org.uk/StructureDefinition/UKCore-RelatedPerson",
               "https://fhir.nhs.uk/StructureDefinition/NHSDigital-Organization-Genomics",
               "https://fhir.nhs.uk/StructureDefinition/NHSDigital-Patient-Genomics",

diff --git a/StructureDefinition/NHSDigital-ServiceRequest-Genomics.StructureDefinition.json b/StructureDefinition/NHSDigital-ServiceRequest-Genomics.StructureDefinition.json
@@ -123,7 +123,7 @@
           {
             "code": "Reference",
             "targetProfile": [
-              "https://fhir.hl7.org.uk/StructureDefinition/UKCore-CarePlan",
+              "http://hl7.org/fhir/StructureDefinition/CarePlan",
               "https://fhir.hl7.org.uk/StructureDefinition/UKCore-MedicationRequest",
               "https://fhir.nhs.uk/StructureDefinition/NHSDigital-ServiceRequest-Genomics"
             ],
@@ -187,7 +187,7 @@
             "code": "Reference",
             "targetProfile": [
               "http://hl7.org/fhir/StructureDefinition/Group",
-              "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Device",
+              "http://hl7.org/fhir/StructureDefinition/Device",
               "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Location",
               "https://fhir.nhs.uk/StructureDefinition/NHSDigital-Patient-Genomics"
             ],
@@ -229,7 +229,7 @@
           {
             "code": "Reference",
             "targetProfile": [
-              "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Device",
+              "http://hl7.org/fhir/StructureDefinition/Device",
               "https://fhir.hl7.org.uk/StructureDefinition/UKCore-RelatedPerson",
               "https://fhir.nhs.uk/StructureDefinition/NHSDigital-Organization-Genomics",
               "https://fhir.nhs.uk/StructureDefinition/NHSDigital-Patient-Genomics",
@@ -250,8 +250,8 @@
           {
             "code": "Reference",
             "targetProfile": [
-              "https://fhir.hl7.org.uk/StructureDefinition/UKCore-CareTeam",
-              "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Device",
+              "http://hl7.org/fhir/StructureDefinition/CareTeam",
+              "http://hl7.org/fhir/StructureDefinition/Device",
               "https://fhir.hl7.org.uk/StructureDefinition/UKCore-HealthcareService",
               "https://fhir.hl7.org.uk/StructureDefinition/UKCore-RelatedPerson",
               "https://fhir.nhs.uk/StructureDefinition/NHSDigital-Organization-Genomics",
@@ -289,7 +289,7 @@
             "code": "Reference",
             "targetProfile": [
               "https://fhir.hl7.org.uk/StructureDefinition/UKCore-DiagnosticReport",
-              "https://fhir.hl7.org.uk/StructureDefinition/UKCore-DocumentReference",
+              "http://hl7.org/fhir/StructureDefinition/DocumentReference",
               "https://fhir.nhs.uk/StructureDefinition/NHSDigital-Condition-Genomics",
               "https://fhir.nhs.uk/StructureDefinition/NHSDigital-Observation-Genomics"
             ],

diff --git a/StructureDefinition/NHSDigital-Specimen-Genomics.StructureDefinition.json b/StructureDefinition/NHSDigital-Specimen-Genomics.StructureDefinition.json
@@ -89,7 +89,7 @@
             "code": "Reference",
             "targetProfile": [
               "http://hl7.org/fhir/StructureDefinition/Group",
-              "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Device",
+              "http://hl7.org/fhir/StructureDefinition/Device",
               "http://hl7.org/fhir/StructureDefinition/Substance",
               "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Location",
               "https://fhir.nhs.uk/StructureDefinition/NHSDigital-Patient-Genomics"

diff --git a/StructureDefinition/NHSDigital-Task-Genomics.StructureDefinition.json b/StructureDefinition/NHSDigital-Task-Genomics.StructureDefinition.json
@@ -7,7 +7,7 @@
   "kind": "resource",
   "abstract": false,
   "type": "Task",
-  "baseDefinition": "https://fhir.hl7.org.uk/StructureDefinition/UKCore-Task",
+  "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Task",
   "derivation": "constraint",
   "differential": {
     "element": [

diff --git a/Task/Task-NonWGSRareDiseaseTestOrderAccepted-SufficientSample-Example.json b/Task/Task-NonWGSRareDiseaseTestOrderAccepted-SufficientSample-Example.json
@@ -48,5 +48,21 @@
         {
             "text": "Optional Free Text field to record any additional details"
         }
+    ],
+    "output": [
+        {
+            "type": {
+                "coding":  [
+                    {
+                        "system": "http://snomed.info/sct",
+                        "code": "123038009",
+                        "display": "Specimen"
+                    }
+                ]
+            },
+            "valueReference": {
+                "reference": "Specimen/Specimen-CancerSolidTumor-Example"
+            }
+        }
     ]
 }
diff --git a/Task/Task-NonWGSRareDiseaseTestOrderForwareded-CancerSolidTumor-Example.json b/Task/Task-NonWGSRareDiseaseTestOrderForwareded-CancerSolidTumor-Example.json
@@ -39,5 +39,21 @@
         {
             "text": "Free to capture additional comments"
         }
+    ],
+    "input":  [
+        {
+            "type": {
+                "coding":  [
+                    {
+                        "system": "http://snomed.info/sct",
+                        "code": "123038009",
+                        "display": "Specimen"
+                    }
+                ]
+            },
+            "valueReference": {
+                "reference": "Specimen/Specimen-CancerSolidTumor-Example"
+            }
+        }
     ]
 }