Add brith sex, pronouns and gender identity

aehrc · Aug 30, 2023 · fc1689a · fc1689a
1 parent ab018d3
commit fc1689a
Show file tree

Hide file tree

Showing 13 changed files with 719 additions and 31 deletions.
diff --git a/_updatePublisher.sh b/_updatePublisher.sh
@@ -117,13 +117,16 @@ if [[ $skipPrompts == true ]] || [[ $response =~ ^[yY].*$ ]]; then
 
   curl -L $gencont_sh_url -o /tmp/_gencontinuous.new
   cp /tmp/_gencontinuous.new _gencontinuous.sh
+  chmod +x _gencontinuous.sh
   rm /tmp/_gencontinuous.new
 
   curl -L $gen_sh_url -o /tmp/_genonce.new
   cp /tmp/_genonce.new _genonce.sh
+  chmod +x _genonce.sh
   rm  /tmp/_genonce.new
 
   curl -L $update_sh_url -o /tmp/_updatePublisher.new
   cp /tmp/_updatePublisher.new _updatePublisher.sh
+  chmod +x _updatePublisher.sh
   rm /tmp/_updatePublisher.new
 fi
diff --git a/fsh-generated/includes/fsh-link-references.md b/fsh-generated/includes/fsh-link-references.md
@@ -34,13 +34,16 @@
 [SubstanceUse]: Questionnaire-SubstanceUse.html
 [AboriginalTorresStraitIslander]: ValueSet-AboriginalTorresStraitIslander.html
 [AustralianStatesAndTerritories]: ValueSet-australian-states-territories-2.html
+[BiologicalSex]: ValueSet-biological-sex-1.html
 [ConditionClinicalStatusCodes]: ValueSet-condition-clinical.html
 [ContainedResourceReference]: StructureDefinition-ContainedResourceReference.html
+[GenderIdentityResponse]: ValueSet-gender-identity-response-1.html
 [MedicalHistory]: ValueSet-MedicalHistory.html
 [MedicalHistoryShortListAdolescents]: ValueSet-MedicalHistoryShortListAdolescents.html
 [MedicalHistoryShortListAdultsAndOlderPeople]: ValueSet-MedicalHistoryShortListAdultsAndOlderPeople.html
 [MedicalHistoryShortListInfants]: ValueSet-MedicalHistoryShortListInfants.html
 [MedicalHistoryShortListPrimarySchool]: ValueSet-MedicalHistoryShortListPrimarySchool.html
+[PersonalPronouns]: ValueSet-pronouns.html
 [PhysicalActivityAndScreenTime]: Questionnaire-PhysicalActivityAndScreenTime.html
 [PrimaryCarerParentGrandparent]: ValueSet-PrimaryCarerParentGrandparent.html
 [QuestionnaireItemControlExtended]: CodeSystem-QuestionnaireItemControlExtended.html

diff --git a/fsh-generated/resources/ImplementationGuide-csiro.fhir.au.smartforms.json b/fsh-generated/resources/ImplementationGuide-csiro.fhir.au.smartforms.json
@@ -329,6 +329,14 @@
         "description": "The Australian States and Territories value set includes values that represent the Australian states and territories.",
         "exampleBoolean": false
       },
+      {
+        "reference": {
+          "reference": "ValueSet/biological-sex-1"
+        },
+        "name": "Biological Sex",
+        "description": "The Biological Sex value set includes values that represent the biological sex of an individual.",
+        "exampleBoolean": false
+      },
       {
         "reference": {
           "reference": "ValueSet/condition-clinical"
@@ -345,6 +353,14 @@
         "description": "This extension is intended to be used as a work around to a known bug whereby contained resources that are not referenced with the type, 'Reference' are removed before a resource is created in a HAPI FHIR server. This is problematic when referencing with the type, 'canonical'. The extension can be used to reference contained resources so they are retained when added to a HAPI FHIR server.",
         "exampleBoolean": false
       },
+      {
+        "reference": {
+          "reference": "ValueSet/gender-identity-response-1"
+        },
+        "name": "Gender Identity Response",
+        "description": "The Gender Identity Response value set includes values that may be used to represent a response for an individual’s gender. A person's gender is a social and cultural identity, expression and experience.",
+        "exampleBoolean": false
+      },
       {
         "reference": {
           "reference": "ValueSet/MedicalHistory"
@@ -385,6 +401,14 @@
         "description": "The Medical History Short List for Primary School Children value set includes values to represent conditions for use in a pick list for the MBS 715 Health Check for Primary School Children.",
         "exampleBoolean": false
       },
+      {
+        "reference": {
+          "reference": "ValueSet/pronouns"
+        },
+        "name": "Personal Pronouns",
+        "description": "Codes that indicate the pronouns to be used when communicating with or about an individual.",
+        "exampleBoolean": false
+      },
       {
         "reference": {
           "reference": "Questionnaire/PhysicalActivityAndScreenTime"

diff --git a/fsh-generated/resources/Questionnaire-AboutTheHealthCheck.json b/fsh-generated/resources/Questionnaire-AboutTheHealthCheck.json
@@ -152,12 +152,28 @@
               "url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-initialExpression",
               "valueExpression": {
                 "language": "text/fhirpath",
-                "expression": "%QuestionnaireResponseLatestComplete.entry.resource.authored"
+                "expression": "%QuestionnaireResponseLatest.entry.resource.where(status=in-progress).exists()"
               }
             }
           ],
           "linkId": "5960c096-d5f7-4745-bd74-44ff2775bde9",
-          "text": "Date of last health check",
+          "text": "Health check already in progress?",
+          "type": "boolean",
+          "repeats": false,
+          "readOnly": true
+        },
+        {
+          "extension": [
+            {
+              "url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-initialExpression",
+              "valueExpression": {
+                "language": "text/fhirpath",
+                "expression": "%QuestionnaireResponseLatestCompleted.entry.resource.authored"
+              }
+            }
+          ],
+          "linkId": "5960c096-d5f7-4745-bd74-44ff2775bde9",
+          "text": "Date of last completed health check",
           "type": "dateTime",
           "repeats": false
         },
@@ -167,7 +183,7 @@
               "url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-initialExpression",
               "valueExpression": {
                 "language": "text/fhirpath",
-                "expression": "today()"
+                "expression": "now()"
               }
             }
           ],

diff --git a/fsh-generated/resources/Questionnaire-AssemblyInstructions.json b/fsh-generated/resources/Questionnaire-AssemblyInstructions.json
@@ -47,7 +47,7 @@
           "valueExpression": {
             "name": "female",
             "language": "text/fhirpath",
-            "expression": "iif(item.where(linkId='5b224753-9365-44e3-823b-9c17e7394005').item.where(linkId='418e4a02-de77-48a0-a92a-fe8fcc52b1aa').answer.value.code='female', 1, 0)"
+            "expression": "iif(item.where(linkId='5b224753-9365-44e3-823b-9c17e7394005').item.where(linkId='56ef44bb-3d1d-4972-aad1-834b69185d61').answer.value.code='248152002', 1, 0)"
           }
         },
         {
@@ -1865,11 +1865,19 @@
     {
       "url": "http://hl7.org/fhir/StructureDefinition/variable",
       "valueExpression": {
-        "name": "QuestionnaireResponseLatestComplete",
+        "name": "QuestionnaireResponseLatestCompleted",
         "language": "application/x-fhir-query",
         "expression": "QuestionnaireResponse?status=completed&_count=1&_sort=-authored&patient={{%patient.id}}"
       }
     },
+    {
+      "url": "http://hl7.org/fhir/StructureDefinition/variable",
+      "valueExpression": {
+        "name": "QuestionnaireResponseLatest",
+        "language": "application/x-fhir-query",
+        "expression": "QuestionnaireResponse?_count=1&_sort=-authored&patient={{%patient.id}}"
+      }
+    },
     {
       "url": "http://hl7.org/fhir/StructureDefinition/variable",
       "valueExpression": {
@@ -1878,6 +1886,14 @@
         "expression": "Condition?patient={{%patient.id}}"
       }
     },
+    {
+      "url": "http://hl7.org/fhir/StructureDefinition/variable",
+      "valueExpression": {
+        "name": "ObsSex",
+        "language": "application/x-fhir-query",
+        "expression": "Observation?code=1515311000168102&status=final&_count=1&_sort=-date&patient={{%patient.id}}"
+      }
+    },
     {
       "url": "http://hl7.org/fhir/StructureDefinition/variable",
       "valueExpression": {

diff --git a/fsh-generated/resources/Questionnaire-PatientDetails.json b/fsh-generated/resources/Questionnaire-PatientDetails.json
@@ -114,29 +114,53 @@
               "url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-initialExpression",
               "valueExpression": {
                 "language": "text/fhirpath",
-                "expression": "%patient.birthDate"
+                "expression": "%patient.extension.where(url='http://hl7.org/fhir/StructureDefinition/individual-pronouns').extension.where(url='value').value.coding"
+              }
+            },
+            {
+              "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl",
+              "valueCodeableConcept": {
+                "coding": [
+                  {
+                    "code": "drop-down",
+                    "system": "http://hl7.org/fhir/questionnaire-item-control"
+                  }
+                ]
               }
             }
           ],
-          "linkId": "90ad8f16-16e4-4438-a7aa-b3189f510da2",
-          "text": "Date of birth",
-          "type": "date",
-          "repeats": false
+          "linkId": "540b1034-7c9a-4aba-a9ef-afb77d445a58",
+          "text": "Preferred pronouns",
+          "type": "choice",
+          "repeats": false,
+          "answerValueSet": "http://terminology.hl7.org/ValueSet/pronouns"
         },
         {
           "extension": [
             {
               "url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-initialExpression",
               "valueExpression": {
                 "language": "text/fhirpath",
-                "expression": "iif(today().toString().select(substring(5,2) & substring(8,2)).toInteger() > %patient.birthDate.toString().select(substring(5,2) & substring(8,2)).toInteger(), today().toString().substring(0,4).toInteger() - %patient.birthDate.toString().substring(0,4).toInteger(), today().toString().substring(0,4).toInteger() - %patient.birthDate.toString().substring(0,4).toInteger() - 1)"
+                "expression": "%patient.extension.where(url='http://hl7.org/fhir/StructureDefinition/patient-genderIdentity').value.coding"
+              }
+            },
+            {
+              "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl",
+              "valueCodeableConcept": {
+                "coding": [
+                  {
+                    "code": "drop-down",
+                    "system": "http://hl7.org/fhir/questionnaire-item-control"
+                  }
+                ]
               }
             }
           ],
-          "linkId": "e2a16e4d-2765-4b61-b286-82cfc6356b30",
-          "text": "Age",
-          "type": "integer",
-          "repeats": false
+          "linkId": "f669a4fe-4818-429a-8847-d20da88d2bb3",
+          "text": "Gender identity",
+          "type": "choice",
+          "repeats": false,
+          "answerValueSet": "https://healthterminologies.gov.au/fhir/ValueSet/gender-identity-response-1"
         },
         {
           "extension": [
@@ -157,14 +181,75 @@
                   }
                 ]
               }
+            },
+            {
+              "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-hidden",
+              "valueBoolean": true
             }
           ],
           "linkId": "418e4a02-de77-48a0-a92a-fe8fcc52b1aa",
-          "text": "Gender",
+          "text": "Administrative gender",
           "type": "choice",
           "repeats": false,
           "answerValueSet": "http://hl7.org/fhir/ValueSet/administrative-gender"
         },
+        {
+          "extension": [
+            {
+              "url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-initialExpression",
+              "valueExpression": {
+                "language": "text/fhirpath",
+                "expression": "%ObsSex.entry.resource.value.coding"
+              }
+            },
+            {
+              "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl",
+              "valueCodeableConcept": {
+                "coding": [
+                  {
+                    "code": "drop-down",
+                    "system": "http://hl7.org/fhir/questionnaire-item-control"
+                  }
+                ]
+              }
+            }
+          ],
+          "linkId": "56ef44bb-3d1d-4972-aad1-834b69185d61",
+          "text": "Sex assigned at birth",
+          "type": "choice",
+          "repeats": false,
+          "answerValueSet": "https://healthterminologies.gov.au/fhir/ValueSet/biological-sex-1"
+        },
+        {
+          "extension": [
+            {
+              "url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-initialExpression",
+              "valueExpression": {
+                "language": "text/fhirpath",
+                "expression": "%patient.birthDate"
+              }
+            }
+          ],
+          "linkId": "90ad8f16-16e4-4438-a7aa-b3189f510da2",
+          "text": "Date of birth",
+          "type": "date",
+          "repeats": false
+        },
+        {
+          "extension": [
+            {
+              "url": "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-initialExpression",
+              "valueExpression": {
+                "language": "text/fhirpath",
+                "expression": "iif(today().toString().select(substring(5,2) & substring(8,2)).toInteger() > %patient.birthDate.toString().select(substring(5,2) & substring(8,2)).toInteger(), today().toString().substring(0,4).toInteger() - %patient.birthDate.toString().substring(0,4).toInteger(), today().toString().substring(0,4).toInteger() - %patient.birthDate.toString().substring(0,4).toInteger() - 1)"
+              }
+            }
+          ],
+          "linkId": "e2a16e4d-2765-4b61-b286-82cfc6356b30",
+          "text": "Age",
+          "type": "integer",
+          "repeats": false
+        },
         {
           "extension": [
             {

diff --git a/fsh-generated/resources/ValueSet-biological-sex-1.json b/fsh-generated/resources/ValueSet-biological-sex-1.json
@@ -0,0 +1,87 @@
+{
+  "resourceType": "ValueSet",
+  "status": "active",
+  "name": "BiologicalSex",
+  "id": "biological-sex-1",
+  "title": "Biological Sex",
+  "description": "The Biological Sex value set includes values that represent the biological sex of an individual.",
+  "url": "https://healthterminologies.gov.au/fhir/ValueSet/biological-sex-1",
+  "meta": {
+    "profile": [
+      "http://hl7.org/fhir/StructureDefinition/shareablevalueset",
+      "https://healthterminologies.gov.au/fhir/StructureDefinition/composed-value-set-4"
+    ]
+  },
+  "identifier": [
+    {
+      "system": "urn:ietf:rfc:3986",
+      "value": "urn:oid:1.2.36.1.2001.1004.201.10198"
+    }
+  ],
+  "version": "1.0.0",
+  "experimental": false,
+  "date": "2020-12-31",
+  "publisher": "Australian Digital Health Agency",
+  "contact": [
+    {
+      "telecom": [
+        {
+          "system": "email",
+          "value": "[email protected]"
+        }
+      ]
+    }
+  ],
+  "copyright": "Copyright © 2020 Australian Digital Health Agency - All rights reserved. Except for the material identified below, this content is licensed under a Creative Commons Attribution 4.0 International License. See https://creativecommons.org/licenses/by/4.0/. \n\nThis resource includes SNOMED Clinical Terms™ (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO). All rights reserved. SNOMED CT®, was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO. \n\nThe rights to use and implement or implementation of SNOMED CT content are limited to the extent it is necessary to allow for the end use of this material.  No further rights are granted in respect of the International Release and no further use of any SNOMED CT content by any other party is permitted. \n\nAll copies of this resource must include this copyright statement and all information contained in this statement.",
+  "expansion": {
+    "identifier": "urn:uuid:e9cff1c2-8743-48cb-9bde-8f4af914544b",
+    "timestamp": "2023-08-30T10:41:59+10:00",
+    "total": 4,
+    "parameter": [
+      {
+        "name": "version",
+        "valueUri": "http://snomed.info/sct|http://snomed.info/sct/32506021000036107/version/20230831"
+      },
+      {
+        "name": "used-codesystem",
+        "valueUri": "http://snomed.info/sct|http://snomed.info/sct/32506021000036107/version/20230831"
+      }
+    ],
+    "contains": [
+      {
+        "system": "http://snomed.info/sct",
+        "code": "248152002",
+        "display": "Female"
+      },
+      {
+        "system": "http://snomed.info/sct",
+        "code": "32570681000036106",
+        "display": "Indeterminate sex"
+      },
+      {
+        "system": "http://snomed.info/sct",
+        "code": "32570691000036108",
+        "display": "Intersex"
+      },
+      {
+        "system": "http://snomed.info/sct",
+        "code": "248153007",
+        "display": "Male"
+      }
+    ]
+  },
+  "compose": {
+    "include": [
+      {
+        "system": "http://snomed.info/sct",
+        "filter": [
+          {
+            "property": "constraint",
+            "op": "=",
+            "value": "^ 32570631000036107|Sex reference set|"
+          }
+        ]
+      }
+    ]
+  }
+}