Update aidbox types and converter

Refs: beda-software/fhir-emr#323
beda-software · Nov 11, 2024 · b853c59 · b853c59
1 parent 0d51238
commit b853c59
Show file tree

Hide file tree

Showing 31 changed files with 246 additions and 28 deletions.
diff --git a/...rf/src/converter/__tests__/resources/questionnaire_response_fce/allergies_inprogress.json b/...rf/src/converter/__tests__/resources/questionnaire_response_fce/allergies_inprogress.json
@@ -72,6 +72,10 @@
     "id": "683e382b-fed4-433e-9b6d-a847a7953bc0",
     "resourceType": "Patient"
   },
+  "subject": {
+    "id": "683e382b-fed4-433e-9b6d-a847a7953bc0",
+    "resourceType": "Patient"
+  },
   "status": "in-progress",
   "id": "f0a0b4cf-ff0e-47e2-814d-3327a138653e",
   "authored": "2023-04-06T02:48:17.734Z"

diff --git a/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fce/cardiology.json b/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fce/cardiology.json
@@ -90,6 +90,10 @@
     "id": "683e382b-fed4-433e-9b6d-a847a7953bc0",
     "resourceType": "Patient"
   },
+  "subject": {
+    "id": "683e382b-fed4-433e-9b6d-a847a7953bc0",
+    "resourceType": "Patient"
+  },
   "status": "completed",
   "id": "16917bdf-309f-4cd7-9a8a-56a928dbedea",
   "authored": "2023-04-06T02:43:39Z"

diff --git a/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fce/few_answers.json b/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fce/few_answers.json
@@ -37,6 +37,10 @@
     "id": "test-patient",
     "resourceType": "Patient"
   },
+  "subject": {
+    "id": "test-patient",
+    "resourceType": "Patient"
+  },
   "status": "completed",
   "authored": "2023-04-14T09:36:35Z",
   "questionnaire": "allergies",

diff --git a/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fce/gad_7.json b/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fce/gad_7.json
@@ -159,6 +159,10 @@
     "id": "683e382b-fed4-433e-9b6d-a847a7953bc0",
     "resourceType": "Patient"
   },
+  "subject": {
+    "id": "683e382b-fed4-433e-9b6d-a847a7953bc0",
+    "resourceType": "Patient"
+  },
   "status": "completed",
   "id": "a00b8309-f74f-462c-a7e4-64852d5bf707",
   "authored": "2023-04-06T01:29:05Z"

diff --git a/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fce/immunization.json b/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fce/immunization.json
@@ -80,6 +80,10 @@
     "id": "683e382b-fed4-433e-9b6d-a847a7953bc0",
     "resourceType": "Patient"
   },
+  "subject": {
+    "id": "683e382b-fed4-433e-9b6d-a847a7953bc0",
+    "resourceType": "Patient"
+  },
   "status": "completed",
   "id": "5d59e534-a7ce-4254-8a41-31b3895ea525",
   "authored": "2023-04-06T02:39:02Z"

diff --git a/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fce/medication.json b/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fce/medication.json
@@ -110,6 +110,10 @@
     "id": "683e382b-fed4-433e-9b6d-a847a7953bc0",
     "resourceType": "Patient"
   },
+  "subject": {
+    "id": "683e382b-fed4-433e-9b6d-a847a7953bc0",
+    "resourceType": "Patient"
+  },
   "status": "completed",
   "id": "3d077aed-ccd4-43d4-843e-0e2224e7571e",
   "authored": "2023-04-06T01:59:41Z"

diff --git a/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fce/phq_2_phq_9.json b/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fce/phq_2_phq_9.json
@@ -189,5 +189,9 @@
     "id": "683e382b-fed4-433e-9b6d-a847a7953bc0",
     "resourceType": "Patient"
   },
+  "subject": {
+    "id": "683e382b-fed4-433e-9b6d-a847a7953bc0",
+    "resourceType": "Patient"
+  },
   "status": "completed"
 }
diff --git a/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fce/physicalexam.json b/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fce/physicalexam.json
@@ -181,6 +181,10 @@
     "id": "683e382b-fed4-433e-9b6d-a847a7953bc0",
     "resourceType": "Patient"
   },
+  "subject": {
+    "id": "683e382b-fed4-433e-9b6d-a847a7953bc0",
+    "resourceType": "Patient"
+  },
   "status": "completed",
   "id": "288fd914-b836-47dd-863a-e7d86a923f28",
   "authored": "2023-04-06T02:05:51Z"

diff --git a/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fce/review_of_systems.json b/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fce/review_of_systems.json
@@ -125,5 +125,9 @@
     "id": "683e382b-fed4-433e-9b6d-a847a7953bc0",
     "resourceType": "Patient"
   },
+  "subject": {
+    "id": "683e382b-fed4-433e-9b6d-a847a7953bc0",
+    "resourceType": "Patient"
+  },
   "status": "completed"
 }
diff --git a/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fce/vitals.json b/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fce/vitals.json
@@ -162,6 +162,10 @@
     "id": "683e382b-fed4-433e-9b6d-a847a7953bc0",
     "resourceType": "Patient"
   },
+  "subject": {
+    "id": "683e382b-fed4-433e-9b6d-a847a7953bc0",
+    "resourceType": "Patient"
+  },
   "status": "completed",
   "id": "a583cc11-99c6-4719-acab-cb3fb72f5078",
   "authored": "2023-04-06T02:20:25Z"

diff --git a/...f/src/converter/__tests__/resources/questionnaire_response_fhir/allergies_inprogress.json b/...f/src/converter/__tests__/resources/questionnaire_response_fhir/allergies_inprogress.json
@@ -67,6 +67,9 @@
     "source": {
         "reference": "Patient/683e382b-fed4-433e-9b6d-a847a7953bc0"
     },
+    "subject": {
+        "reference": "Patient/683e382b-fed4-433e-9b6d-a847a7953bc0"
+    },
     "status": "in-progress",
     "id": "f0a0b4cf-ff0e-47e2-814d-3327a138653e",
     "authored": "2023-04-06T02:48:17.734Z"

diff --git a/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fhir/cardiology.json b/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fhir/cardiology.json
@@ -81,6 +81,9 @@
   "source": {
     "reference": "Patient/683e382b-fed4-433e-9b6d-a847a7953bc0"
   },
+  "subject": {
+    "reference": "Patient/683e382b-fed4-433e-9b6d-a847a7953bc0"
+  },
   "status": "completed",
   "id": "16917bdf-309f-4cd7-9a8a-56a928dbedea",
   "authored": "2023-04-06T02:43:39Z"

diff --git a/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fhir/few_answers.json b/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fhir/few_answers.json
@@ -30,6 +30,9 @@
   "source": {
     "reference": "Patient/test-patient"
   },
+  "subject": {
+    "reference": "Patient/test-patient"
+  },
   "status": "completed",
   "authored": "2023-04-14T09:36:35Z",
   "questionnaire": "allergies",

diff --git a/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fhir/gad_7.json b/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fhir/gad_7.json
@@ -140,6 +140,9 @@
   "source": {
     "reference": "Patient/683e382b-fed4-433e-9b6d-a847a7953bc0"
   },
+  "subject": {
+    "reference": "Patient/683e382b-fed4-433e-9b6d-a847a7953bc0"
+  },
   "status": "completed",
   "id": "a00b8309-f74f-462c-a7e4-64852d5bf707",
   "authored": "2023-04-06T01:29:05Z"

diff --git a/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fhir/immunization.json b/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fhir/immunization.json
@@ -71,6 +71,9 @@
   "source": {
     "reference": "Patient/683e382b-fed4-433e-9b6d-a847a7953bc0"
   },
+  "subject": {
+    "reference": "Patient/683e382b-fed4-433e-9b6d-a847a7953bc0"
+  },
   "status": "completed",
   "id": "5d59e534-a7ce-4254-8a41-31b3895ea525",
   "authored": "2023-04-06T02:39:02Z"

diff --git a/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fhir/medication.json b/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fhir/medication.json
@@ -95,6 +95,9 @@
   "source": {
     "reference": "Patient/683e382b-fed4-433e-9b6d-a847a7953bc0"
   },
+  "subject": {
+    "reference": "Patient/683e382b-fed4-433e-9b6d-a847a7953bc0"
+  },
   "status": "completed",
   "id": "3d077aed-ccd4-43d4-843e-0e2224e7571e",
   "authored": "2023-04-06T01:59:41Z"

diff --git a/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fhir/phq_2_phq_9.json b/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fhir/phq_2_phq_9.json
@@ -166,5 +166,8 @@
   "source": {
     "reference": "Patient/683e382b-fed4-433e-9b6d-a847a7953bc0"
   },
+  "subject": {
+    "reference": "Patient/683e382b-fed4-433e-9b6d-a847a7953bc0"
+  },
   "status": "completed"
 }
diff --git a/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fhir/physicalexam.json b/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fhir/physicalexam.json
@@ -152,6 +152,9 @@
   "source": {
     "reference": "Patient/683e382b-fed4-433e-9b6d-a847a7953bc0"
   },
+  "subject": {
+    "reference": "Patient/683e382b-fed4-433e-9b6d-a847a7953bc0"
+  },
   "status": "completed",
   "id": "288fd914-b836-47dd-863a-e7d86a923f28",
   "authored": "2023-04-06T02:05:51Z"

diff --git a/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fhir/review_of_systems.json b/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fhir/review_of_systems.json
@@ -114,5 +114,8 @@
   "source": {
     "reference": "Patient/683e382b-fed4-433e-9b6d-a847a7953bc0"
   },
+  "subject": {
+    "reference": "Patient/683e382b-fed4-433e-9b6d-a847a7953bc0"
+  },
   "status": "completed"
 }
diff --git a/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fhir/vitals.json b/sdc-qrf/src/converter/__tests__/resources/questionnaire_response_fhir/vitals.json
@@ -139,6 +139,9 @@
   "source": {
     "reference": "Patient/683e382b-fed4-433e-9b6d-a847a7953bc0"
   },
+  "subject": {
+    "reference": "Patient/683e382b-fed4-433e-9b6d-a847a7953bc0"
+  },
   "status": "completed",
   "id": "a583cc11-99c6-4719-acab-cb3fb72f5078",
   "authored": "2023-04-06T02:20:25Z"

diff --git a/sdc-qrf/src/converter/extensions.ts b/sdc-qrf/src/converter/extensions.ts
@@ -7,7 +7,26 @@ export enum ExtensionIdentifier {
     ItemControl = 'http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl',
     SliderStepValue = 'http://hl7.org/fhir/StructureDefinition/questionnaire-sliderStepValue',
     Unit = 'http://hl7.org/fhir/StructureDefinition/questionnaire-unit',
+    UnitOption = 'http://hl7.org/fhir/StructureDefinition/questionnaire-unitOption',
     ReferenceResource = 'http://hl7.org/fhir/StructureDefinition/questionnaire-referenceResource',
+    EntryFormat = 'http://hl7.org/fhir/StructureDefinition/entryFormat',
+    ColumnSize = 'http://aidbox.io/questionnaire-itemColumnSize',
+    ItemMedia = 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-itemMedia',
+    Regex = 'http://hl7.org/fhir/StructureDefinition/regex',
+    ObservationExtract = 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-observationExtract',
+    ObservationLinkPeriod = 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-observationLinkPeriod',
+    MinValue = 'http://hl7.org/fhir/StructureDefinition/minValue',
+    MaxValue = 'http://hl7.org/fhir/StructureDefinition/maxValue',
+    MinQuantity = 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-minQuantity',
+    MaxQuantity = 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-maxQuantity',
+    ShowOrdinalValue = 'http://aidbox.io/questionnaire-showOrdinalValue',
+    PreferredTerminologyServer = 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-preferredTerminologyServer',
+    OpenLabel = 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-openLabel',
+    BackgroundImage = 'http://aidbox.io/questionnaire-backgroundImage',
+    Language = 'http://hl7.org/fhir/StructureDefinition/language',
+    ChoiceOrientation = 'http://hl7.org/fhir/StructureDefinition/questionnaire-choiceOrientation',
+    InlineChoiceDirection = 'https://beda.software/fhir-emr-questionnaire/inline-choice-direction',
+    ChoiceColumns = 'http://aidbox.io/fhir/StructureDefinition/questionnaire-choiceColumns',
 
     ItemPopulationContext = 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-itemPopulationContext',
     InitialExpression = 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-initialExpression',
@@ -22,6 +41,7 @@ export enum ExtensionIdentifier {
     HelpText = 'https://beda.software/fhir-emr-questionnaire/help-text',
     StopLabel = 'https://beda.software/fhir-emr-questionnaire/slider-stop-label',
     Macro = 'https://beda.software/fhir-emr-questionnaire/macro',
+    RowsNumber = 'https://beda.software/fhir-emr-questionnaire/rows-number',
 }
 
 export type ExtensionTransformer = {
@@ -52,9 +72,18 @@ export const extensionTransformers: ExtensionTransformer = {
     [ExtensionIdentifier.SliderStepValue]: {
         path: { extension: 'valueInteger', questionnaire: 'sliderStepValue' },
     },
+    [ExtensionIdentifier.EntryFormat]: {
+        path: { extension: 'valueString', questionnaire: 'entryFormat' },
+    },
     [ExtensionIdentifier.Unit]: {
         path: { extension: 'valueCoding', questionnaire: 'unit' },
     },
+    [ExtensionIdentifier.UnitOption]: {
+        path: { extension: 'valueCoding', questionnaire: 'unitOption' },
+    },
+    [ExtensionIdentifier.RowsNumber]: {
+        path: { extension: 'valueInteger', questionnaire: 'rowsNumber' },
+    },
     [ExtensionIdentifier.ReferenceResource]: {
         transform: {
             fromExtension: (extension) => {
@@ -74,6 +103,69 @@ export const extensionTransformers: ExtensionTransformer = {
             },
         },
     },
+    [ExtensionIdentifier.ColumnSize]: {
+        path: { extension: 'valueInteger', questionnaire: 'columnSize' },
+    },
+    [ExtensionIdentifier.ItemMedia]: {
+        path: { extension: 'valueAttachment', questionnaire: 'itemMedia' },
+    },
+    [ExtensionIdentifier.Regex]: {
+        path: { extension: 'valueString', questionnaire: 'regex' },
+    },
+    [ExtensionIdentifier.ObservationExtract]: {
+        path: { extension: 'valueBoolean', questionnaire: 'observationExtract' },
+    },
+    [ExtensionIdentifier.ObservationLinkPeriod]: {
+        path: { extension: 'valueDuration', questionnaire: 'observationLinkPeriod' },
+    },
+    [ExtensionIdentifier.MinValue]: {
+        transform: {
+            fromExtension: (extension) => ({ minValue: extension }),
+            toExtension: (item) => item.minValue,
+        },
+    },
+    [ExtensionIdentifier.MaxValue]: {
+        transform: {
+            fromExtension: (extension) => ({ maxValue: extension }),
+            toExtension: (item) => item.maxValue,
+        },
+    },
+    [ExtensionIdentifier.MinQuantity]: {
+        transform: {
+            fromExtension: (extension) => ({ minQuantity: extension }),
+            toExtension: (item) => item.minQuantity,
+        },
+    },
+    [ExtensionIdentifier.MaxQuantity]: {
+        transform: {
+            fromExtension: (extension) => ({ maxQuantity: extension }),
+            toExtension: (item) => item.maxQuantity,
+        },
+    },
+    [ExtensionIdentifier.ShowOrdinalValue]: {
+        path: { extension: 'valueBoolean', questionnaire: 'showOrdinalValue' },
+    },
+    [ExtensionIdentifier.PreferredTerminologyServer]: {
+        path: { extension: 'valueUri', questionnaire: 'preferredTerminologyServer' },
+    },
+    [ExtensionIdentifier.OpenLabel]: {
+        path: { extension: 'valueString', questionnaire: 'openLabel' },
+    },
+    [ExtensionIdentifier.BackgroundImage]: {
+        path: { extension: 'valueAttachment', questionnaire: 'backgroundImage' },
+    },
+    [ExtensionIdentifier.Language]: {
+        path: { extension: 'valueCoding', questionnaire: 'language' },
+    },
+    [ExtensionIdentifier.ChoiceOrientation]: {
+        path: { extension: 'valueCode', questionnaire: 'choiceOrientation' },
+    },
+    [ExtensionIdentifier.InlineChoiceDirection]: {
+        path: { extension: 'valueString', questionnaire: 'choiceOrientation' },
+    },
+    [ExtensionIdentifier.ChoiceColumns]: {
+        path: { extension: 'valueInteger', questionnaire: 'choiceColumns' },
+    },
 
     [ExtensionIdentifier.ItemPopulationContext]: {
         path: { extension: 'valueExpression', questionnaire: 'itemPopulationContext' },

diff --git a/sdc-qrf/src/converter/fceToFhir/questionnaire/processItems.ts b/sdc-qrf/src/converter/fceToFhir/questionnaire/processItems.ts
@@ -5,6 +5,7 @@ import {
     QuestionnaireItemAnswerOption as FHIRQuestionnaireItemAnswerOption,
     QuestionnaireItemInitial as FHIRQuestionnaireItemInitial,
 } from 'fhir/r4b';
+import _ from 'lodash';
 
 import {
     QuestionnaireItem as FCEQuestionnaireItem,
@@ -14,11 +15,7 @@ import {
     QuestionnaireItemInitial as FCEQuestionnaireItemInitial,
 } from 'shared/src/contrib/aidbox';
 
-import {
-    convertFromFHIRExtension,
-    convertToFHIRExtension,
-    toFHIRReference,
-} from '../../../converter';
+import { convertFromFHIRExtension, convertToFHIRExtension, toFHIRReference } from '../..';
 
 export function processItems(items: FCEQuestionnaireItem[]): FHIRQuestionnaireItem[] {
     return items.map((item) => {
@@ -29,6 +26,7 @@ export function processItems(items: FCEQuestionnaireItem[]): FHIRQuestionnaireIt
                 .filter((ext): ext is Partial<FCEQuestionnaireItem> => ext !== undefined)
                 .flatMap(Object.keys);
             for (const field of fieldsToOmit) {
+                //@ts-ignore
                 delete item[field];
             }
             item.extension = extensions.sort();
@@ -78,6 +76,7 @@ const convertEnableWhen = (
     answerType: string,
     result: FHIRQuestionnaireItemEnableWhen,
 ) => {
+    //@ts-ignore
     if (answer[answerType] !== undefined) {
         switch (answerType) {
             case 'boolean':
@@ -124,22 +123,26 @@ function processAnswerOption(
 
         const fhirOption: FHIRQuestionnaireItemAnswerOption = { ...commonOptions };
 
-        if (value?.Coding) {
+        if (!value) {
+            return fhirOption;
+        }
+
+        if (value.Coding) {
             fhirOption.valueCoding = value.Coding;
         }
-        if (value?.string) {
+        if (value.string) {
             fhirOption.valueString = value.string;
         }
-        if (value?.Reference) {
+        if (value.Reference) {
             fhirOption.valueReference = toFHIRReference(value.Reference);
         }
-        if (value?.date) {
+        if (value.date) {
             fhirOption.valueDate = value.date;
         }
-        if (value?.integer) {
+        if (_.isNumber(value.integer)) {
             fhirOption.valueInteger = value.integer;
         }
-        if (value?.time) {
+        if (value.time) {
             fhirOption.valueTime = value.time;
         }