sdc-qrf 0.2.0 → 0.3.2

package/src/converter/__tests__/resources/questionnaire_response_fhir/practitioner.json

@@ -0,0 +1,54 @@
+{
+  "authored": "2023-04-05T06:09:09Z",
+  "id": "cedd0c3e-be1a-4c1b-92af-351ed76fe41e",
+  "item": [
+    {
+      "answer": [
+        {
+          "valueString": "Patel"
+        }
+      ],
+      "linkId": "last-name"
+    },
+    {
+      "answer": [
+        {
+          "valueString": "Sanjay"
+        }
+      ],
+      "linkId": "first-name"
+    },
+    {
+      "answer": [
+        {
+          "valueString": "Kumar"
+        }
+      ],
+      "linkId": "middle-name"
+    },
+    {
+      "answer": [
+        {
+          "valueCoding": {
+            "code": "394579002",
+            "display": "Cardiology",
+            "system": "http://snomed.info/sct"
+          }
+        }
+      ],
+      "linkId": "specialty"
+    }
+  ],
+  "meta": {
+    "extension": [
+      {
+        "url": "ex:createdAt",
+        "valueInstant": "2023-04-05T06:09:10.640955Z"
+      }
+    ],
+    "lastUpdated": "2023-04-05T06:09:10.640955Z",
+    "versionId": "20415"
+  },
+  "resourceType": "QuestionnaireResponse",
+  "status": "completed"
+}

package/src/converter/__tests__/resources/questionnaire_response_fhir/reference_answer_with_assoc.json

@@ -0,0 +1,86 @@
+{
+    "authored": "2023-04-05T06:27:57Z",
+    "id": "cf6d9d4b-bfcd-463f-9d26-b6769c2a3fc3",
+    "item": [
+        {
+            "answer": [
+                {
+                    "valueString": "683e382b-fed4-433e-9b6d-a847a7953bc0"
+                }
+            ],
+            "linkId": "patientId"
+        },
+        {
+            "answer": [
+                {
+                    "valueString": "Emily Nguyen"
+                }
+            ],
+            "linkId": "patientName"
+        },
+        {
+            "answer": [
+                {
+                    "valueReference": {
+                        "display": "Sanjay Patel - Cardiology",
+                        "reference": "PractitionerRole/429e6a55-8a64-4ede-ad12-1206522253eb"
+                    }
+                }
+            ],
+            "linkId": "practitioner-role"
+        },
+        {
+            "answer": [
+                {
+                    "valueCoding": {
+                        "code": "consultation",
+                        "display": "The first appointment",
+                        "system": "http://fhir.org/guides/argonaut-scheduling/CodeSystem/visit-type"
+                    }
+                }
+            ],
+            "linkId": "service"
+        },
+        {
+            "answer": [
+                {
+                    "valueDate": "2023-04-26"
+                }
+            ],
+            "linkId": "date"
+        },
+        {
+            "item": [
+                {
+                    "answer": [
+                        {
+                            "valueTime": "15:00:00"
+                        }
+                    ],
+                    "linkId": "start-time"
+                },
+                {
+                    "answer": [
+                        {
+                            "valueTime": "16:00:00"
+                        }
+                    ],
+                    "linkId": "end-time"
+                }
+            ],
+            "linkId": "Time period"
+        }
+    ],
+    "meta": {
+        "extension": [
+            {
+                "url": "ex:createdAt",
+                "valueInstant": "2023-04-05T06:27:58.499391Z"
+            }
+        ],
+        "lastUpdated": "2023-04-05T06:27:58.499391Z",
+        "versionId": "20420"
+    },
+    "resourceType": "QuestionnaireResponse",
+    "status": "completed"
+}

package/src/converter/__tests__/resources/questionnaire_response_fhir/review_of_systems.json

@@ -0,0 +1,118 @@
+{
+  "authored": "2023-04-06T02:11:08Z",
+  "encounter": {
+    "reference": "Encounter/e133b999-9e91-4ebd-967e-450bad770682"
+  },
+  "id": "d575fe05-9db2-4df8-b131-48bb5d27509d",
+  "item": [
+    {
+      "answer": [
+        {
+          "valueBoolean": true
+        }
+      ],
+      "linkId": "provider-viewed-confirmation"
+    },
+    {
+      "item": [
+        {
+          "answer": [],
+          "linkId": "general"
+        },
+        {
+          "answer": [
+            {
+              "valueBoolean": true
+            }
+          ],
+          "linkId": "heent"
+        },
+        {
+          "answer": [
+            {
+              "valueString": "heent"
+            }
+          ],
+          "linkId": "heent-comment"
+        },
+        {
+          "answer": [],
+          "linkId": "cardiovascular"
+        },
+        {
+          "answer": [],
+          "linkId": "respiratory"
+        },
+        {
+          "answer": [
+            {
+              "valueBoolean": true
+            }
+          ],
+          "linkId": "gastrointestinal"
+        },
+        {
+          "answer": [
+            {
+              "valueString": "gastrointestinal"
+            }
+          ],
+          "linkId": "gastrointestinal-comment"
+        },
+        {
+          "answer": [],
+          "linkId": "genitourinary"
+        },
+        {
+          "answer": [],
+          "linkId": "musculoskeletal"
+        },
+        {
+          "answer": [],
+          "linkId": "neurologic"
+        },
+        {
+          "answer": [
+            {
+              "valueBoolean": true
+            }
+          ],
+          "linkId": "psychiatric"
+        },
+        {
+          "answer": [
+            {
+              "valueString": "psychiatric"
+            }
+          ],
+          "linkId": "psychiatric-comment"
+        },
+        {
+          "answer": [],
+          "linkId": "skin"
+        },
+        {
+          "answer": [],
+          "linkId": "other"
+        }
+      ],
+      "linkId": "abnormal-systems-group"
+    }
+  ],
+  "meta": {
+    "extension": [
+      {
+        "url": "ex:createdAt",
+        "valueInstant": "2023-04-06T02:10:37.718483Z"
+      }
+    ],
+    "lastUpdated": "2023-04-06T02:11:09.776717Z",
+    "versionId": "20480"
+  },
+  "questionnaire": "review-of-systems",
+  "resourceType": "QuestionnaireResponse",
+  "source": {
+    "reference": "Patient/683e382b-fed4-433e-9b6d-a847a7953bc0"
+  },
+  "status": "completed"
+}

package/src/converter/__tests__/resources/questionnaire_response_fhir/vitals.json

@@ -0,0 +1,145 @@
+{
+  "questionnaire": "vitals",
+  "meta": {
+    "lastUpdated": "2023-04-06T02:20:25.903562Z",
+    "versionId": "20492",
+    "extension": [
+      {
+        "url": "ex:createdAt",
+        "valueInstant": "2023-04-06T02:19:51.712237Z"
+      }
+    ]
+  },
+  "encounter": {
+    "reference": "Encounter/e133b999-9e91-4ebd-967e-450bad770682"
+  },
+  "item": [
+    {
+      "answer": [
+        {
+          "valueString": "683e382b-fed4-433e-9b6d-a847a7953bc0"
+        }
+      ],
+      "linkId": "patientId"
+    },
+    {
+      "answer": [
+        {
+          "valueString": "Emily Nguyen"
+        }
+      ],
+      "linkId": "patientName"
+    },
+    {
+      "answer": [
+        {
+          "valueInteger": 180
+        }
+      ],
+      "linkId": "height"
+    },
+    {
+      "answer": [
+        {
+          "valueInteger": 80
+        }
+      ],
+      "linkId": "weight"
+    },
+    {
+      "answer": [
+        {
+          "valueInteger": 36
+        }
+      ],
+      "linkId": "temperature"
+    },
+    {
+      "answer": [
+        {
+          "valueInteger": 56
+        }
+      ],
+      "linkId": "oxygen-saturation"
+    },
+    {
+      "answer": [
+        {
+          "valueInteger": 100
+        }
+      ],
+      "linkId": "pulse-rate"
+    },
+    {
+      "answer": [
+        {
+          "valueInteger": 50
+        }
+      ],
+      "linkId": "respiratory-rate"
+    },
+    {
+      "item": [
+        {
+          "item": [
+            {
+              "answer": [
+                {
+                  "valueInteger": 45
+                }
+              ],
+              "linkId": "blood-pressure-systolic"
+            },
+            {
+              "answer": [
+                {
+                  "valueInteger": 67
+                }
+              ],
+              "linkId": "blood-pressure-diastolic"
+            }
+          ],
+          "linkId": "blood-pressure-systolic-diastolic"
+        },
+        {
+          "answer": [
+            {
+              "valueCoding": {
+                "code": "sitting",
+                "display": "Sitting"
+              }
+            }
+          ],
+          "linkId": "blood-pressure-positions"
+        },
+        {
+          "answer": [
+            {
+              "valueCoding": {
+                "code": "biceps-left",
+                "display": "Biceps left"
+              }
+            }
+          ],
+          "linkId": "blood-pressure-arm"
+        }
+      ],
+      "linkId": "blood-pressure"
+    },
+    {
+      "answer": [
+        {
+          "valueInteger": 24.69
+        }
+      ],
+      "linkId": "bmi"
+    }
+  ],
+  "resourceType": "QuestionnaireResponse",
+  "source": {
+    "reference": "Patient/683e382b-fed4-433e-9b6d-a847a7953bc0"
+  },
+  "status": "completed",
+  "id": "a583cc11-99c6-4719-acab-cb3fb72f5078",
+  "authored": "2023-04-06T02:20:25Z"
+}

package/src/converter/extensions.ts

@@ -0,0 +1,153 @@
+import { Extension as FHIRExtension } from 'fhir/r4b';
+
+import { QuestionnaireItem as FCEQuestionnaireItem } from 'shared/src/contrib/aidbox';
+
+export enum ExtensionIdentifier {
+    Hidden = 'http://hl7.org/fhir/StructureDefinition/questionnaire-hidden',
+    ItemControl = 'http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl',
+    SliderStepValue = 'http://hl7.org/fhir/StructureDefinition/questionnaire-sliderStepValue',
+    Unit = 'http://hl7.org/fhir/StructureDefinition/questionnaire-unit',
+    ReferenceResource = 'http://hl7.org/fhir/StructureDefinition/questionnaire-referenceResource',
+    CqfExpression = 'http://hl7.org/fhir/StructureDefinition/cqf-expression',
+
+    ItemPopulationContext = 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-itemPopulationContext',
+    InitialExpression = 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-initialExpression',
+    ChoiceColumn = 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-choiceColumn',
+    CalculatedExpression = 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-calculatedExpression',
+    EnableWhenExpression = 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-enableWhenExpression',
+    AnswerExpression = 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-answerExpression',
+
+    AdjustLastToRight = 'https://beda.software/fhir-emr-questionnaire/adjust-last-to-right',
+    SliderStart = 'https://beda.software/fhir-emr-questionnaire/slider-start',
+    SliderStop = 'https://beda.software/fhir-emr-questionnaire/slider-stop',
+    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',
+}
+
+export type ExtensionTransformer = {
+    [key in ExtensionIdentifier]:
+        | {
+              transform: {
+                  fromExtension: (
+                      extension: FHIRExtension,
+                  ) => Partial<FCEQuestionnaireItem> | undefined;
+                  toExtension: (item: FCEQuestionnaireItem) => FHIRExtension | undefined;
+              };
+          }
+        | {
+              path: {
+                  extension: keyof FHIRExtension;
+                  questionnaire: keyof FCEQuestionnaireItem;
+              };
+          };
+};
+
+export const extensionTransformers: ExtensionTransformer = {
+    [ExtensionIdentifier.Hidden]: {
+        path: { extension: 'valueBoolean', questionnaire: 'hidden' },
+    },
+    [ExtensionIdentifier.ItemControl]: {
+        path: { extension: 'valueCodeableConcept', questionnaire: 'itemControl' },
+    },
+    [ExtensionIdentifier.SliderStepValue]: {
+        path: { extension: 'valueInteger', questionnaire: 'sliderStepValue' },
+    },
+    [ExtensionIdentifier.Unit]: {
+        path: { extension: 'valueCoding', questionnaire: 'unit' },
+    },
+    [ExtensionIdentifier.ReferenceResource]: {
+        transform: {
+            fromExtension: (extension) => {
+                if (extension.valueCode) {
+                    return { referenceResource: [extension.valueCode] };
+                } else {
+                    return {};
+                }
+            },
+            toExtension: (item) => {
+                if (item.referenceResource?.length) {
+                    return {
+                        url: ExtensionIdentifier.ReferenceResource,
+                        valueCode: item.referenceResource[0],
+                    };
+                }
+            },
+        },
+    },
+    [ExtensionIdentifier.CqfExpression]: {
+        path: { extension: 'valueExpression', questionnaire: 'cqfExpression' },
+    },
+
+    [ExtensionIdentifier.ItemPopulationContext]: {
+        path: { extension: 'valueExpression', questionnaire: 'itemPopulationContext' },
+    },
+    [ExtensionIdentifier.InitialExpression]: {
+        path: { extension: 'valueExpression', questionnaire: 'initialExpression' },
+    },
+    [ExtensionIdentifier.CalculatedExpression]: {
+        path: { extension: 'valueExpression', questionnaire: 'calculatedExpression' },
+    },
+    [ExtensionIdentifier.EnableWhenExpression]: {
+        path: { extension: 'valueExpression', questionnaire: 'enableWhenExpression' },
+    },
+    [ExtensionIdentifier.AnswerExpression]: {
+        path: { extension: 'valueExpression', questionnaire: 'answerExpression' },
+    },
+    [ExtensionIdentifier.ChoiceColumn]: {
+        transform: {
+            fromExtension: (extension) => {
+                const choiceColumnExtension = extension.extension;
+                if (choiceColumnExtension) {
+                    return {
+                        choiceColumn: [
+                            {
+                                forDisplay:
+                                    choiceColumnExtension.find((obj) => obj.url === 'forDisplay')
+                                        ?.valueBoolean ?? false,
+                                path: choiceColumnExtension.find((obj) => obj.url === 'path')
+                                    ?.valueString,
+                            },
+                        ],
+                    };
+                }
+            },
+            toExtension: (item) => {
+                if (item.choiceColumn) {
+                    return {
+                        url: ExtensionIdentifier.ChoiceColumn,
+                        extension: [
+                            {
+                                url: 'forDisplay',
+                                valueBoolean: item.choiceColumn[0]?.forDisplay,
+                            },
+                            {
+                                url: 'path',
+                                valueString: item.choiceColumn[0]?.path,
+                            },
+                        ],
+                    };
+                }
+            },
+        },
+    },
+
+    [ExtensionIdentifier.AdjustLastToRight]: {
+        path: { extension: 'valueBoolean', questionnaire: 'adjustLastToRight' },
+    },
+    [ExtensionIdentifier.SliderStart]: {
+        path: { extension: 'valueInteger', questionnaire: 'start' },
+    },
+    [ExtensionIdentifier.SliderStop]: {
+        path: { extension: 'valueInteger', questionnaire: 'stop' },
+    },
+    [ExtensionIdentifier.HelpText]: {
+        path: { extension: 'valueString', questionnaire: 'helpText' },
+    },
+    [ExtensionIdentifier.StopLabel]: {
+        path: { extension: 'valueString', questionnaire: 'stopLabel' },
+    },
+    [ExtensionIdentifier.Macro]: {
+        path: { extension: 'valueString', questionnaire: 'macro' },
+    },
+};

package/src/converter/fceToFhir/index.ts

@@ -0,0 +1,27 @@
+import {
+    Questionnaire as FHIRQuestionnaire,
+    QuestionnaireResponse as FHIRQuestionnaireResponse,
+} from 'fhir/r4b';
+
+import {
+    Questionnaire as FCEQuestionnaire,
+    QuestionnaireResponse as FCEQuestionnaireResponse,
+} from 'shared/src/contrib/aidbox';
+
+import { convertQuestionnaire } from './questionnaire';
+import { convertQuestionnaireResponse } from './questionnaireResponse';
+
+export function fromFirstClassExtension(
+    fceQuestionnaireResponse: FCEQuestionnaireResponse,
+): FHIRQuestionnaireResponse;
+export function fromFirstClassExtension(fceQuestionnaire: FCEQuestionnaire): FHIRQuestionnaire;
+export function fromFirstClassExtension(
+    fceResource: FCEQuestionnaire | FCEQuestionnaireResponse,
+): FHIRQuestionnaireResponse | FHIRQuestionnaire {
+    switch (fceResource.resourceType) {
+        case 'Questionnaire':
+            return convertQuestionnaire(fceResource);
+        case 'QuestionnaireResponse':
+            return convertQuestionnaireResponse(fceResource);
+    }
+}

package/src/converter/fceToFhir/questionnaire/index.ts

@@ -0,0 +1,15 @@
+import { Questionnaire as FHIRQuestionnaire } from 'fhir/r4b';
+import cloneDeep from 'lodash/cloneDeep';
+
+import { Questionnaire as FCEQuestionnaire } from 'shared/src/contrib/aidbox';
+
+import { processExtensions } from './processExtensions';
+import { processItems } from './processItems';
+import { processMeta } from './processMeta';
+
+export function convertQuestionnaire(questionnaire: FCEQuestionnaire): FHIRQuestionnaire {
+    questionnaire = cloneDeep(questionnaire);
+    questionnaire.meta = questionnaire.meta ? processMeta(questionnaire.meta) : questionnaire.meta;
+    questionnaire.item = processItems(questionnaire.item ?? []);
+    return processExtensions(questionnaire) as FHIRQuestionnaire;
+}

package/src/converter/fceToFhir/questionnaire/processExtensions.ts

@@ -0,0 +1,75 @@
+import { Extension as FHIRExtension, Questionnaire as FHIRQuestionnaire } from 'fhir/r4b';
+
+import { Questionnaire as FCEQuestionnaire } from 'shared/src/contrib/aidbox';
+
+export function processExtensions(questionnaire: FCEQuestionnaire): FHIRQuestionnaire {
+    const { launchContext, mapping, sourceQueries, targetStructureMap, ...fhirQuestionnaire } =
+        questionnaire;
+
+    let extensions: FHIRExtension[] = [];
+
+    if (launchContext) {
+        for (const launchContextItem of launchContext) {
+            const name = launchContextItem.name;
+            const typeList = launchContextItem.type;
+            const description = launchContextItem.description;
+            const launchContextExtension: FHIRExtension[] = [
+                {
+                    url: 'name',
+                    valueCoding: name,
+                },
+            ];
+
+            for (const typeCode of typeList ?? []) {
+                launchContextExtension.push({ url: 'type', valueCode: typeCode });
+            }
+
+            if (description !== undefined) {
+                launchContextExtension.push({
+                    url: 'description',
+                    valueString: description,
+                });
+            }
+
+            extensions.push({
+                url: 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-launchContext',
+                extension: launchContextExtension,
+            });
+        }
+    }
+
+    if (mapping) {
+        extensions = extensions.concat(
+            mapping.map((m) => ({
+                url: 'http://beda.software/fhir-extensions/questionnaire-mapper',
+                valueReference: {
+                    reference: `Mapping/${m.id}`,
+                },
+            })),
+        );
+    }
+
+    if (sourceQueries) {
+        extensions = extensions.concat(
+            sourceQueries.map((item) => ({
+                url: 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-sourceQueries',
+                valueReference: { reference: `#${item.localRef}` },
+            })),
+        );
+    }
+
+    if (targetStructureMap) {
+        extensions = extensions.concat(
+            targetStructureMap.map((targetStructureMapRef) => ({
+                url: 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-targetStructureMap',
+                valueCanonical: targetStructureMapRef,
+            })),
+        );
+    }
+
+    if (extensions.length) {
+        fhirQuestionnaire.extension = (fhirQuestionnaire.extension ?? []).concat(extensions);
+    }
+
+    return fhirQuestionnaire as FHIRQuestionnaire;
+}