sdc-qrf 0.1.3 → 0.3.1

package/src/converter/__tests__/fce.test.ts

@@ -0,0 +1,224 @@
+import {
+    QuestionnaireResponse as FHIRQuestionnaireResponse,
+    Questionnaire as FHIRQuestionnaire,
+} from 'fhir/r4b';
+import cloneDeep from 'lodash/cloneDeep';
+
+import {
+    QuestionnaireResponse as FCEQuestionnaireResponse,
+    Questionnaire as FCEQuestionnaire,
+} from 'shared/src/contrib/aidbox';
+
+// fce questionnaire
+import fce_allergies from './resources/questionnaire_fce/allergies.json';
+import fce_beverages from './resources/questionnaire_fce/beverages.json';
+import fce_choice_answer_option from './resources/questionnaire_fce/choice_answer_option.json';
+import fce_consent from './resources/questionnaire_fce/consent.json';
+import fce_enable_when from './resources/questionnaire_fce/enable_when.json';
+import fce_encounter_create from './resources/questionnaire_fce/encounter_create.json';
+import fce_gad_7 from './resources/questionnaire_fce/gad_7.json';
+import fce_immunization from './resources/questionnaire_fce/immunization.json';
+import fce_medication from './resources/questionnaire_fce/medication.json';
+import fce_multiple_type_launch_context from './resources/questionnaire_fce/multiple_type_launch_context.json';
+import fce_patient_create from './resources/questionnaire_fce/patient_create.json';
+import fce_patient_edit from './resources/questionnaire_fce/patient_edit.json';
+import fce_phq_2_phq_9 from './resources/questionnaire_fce/phq_2_phq_9.json';
+import fce_physicalexam from './resources/questionnaire_fce/physicalexam.json';
+import fce_practitioner_create from './resources/questionnaire_fce/practitioner_create.json';
+import fce_practitioner_create_structure_map from './resources/questionnaire_fce/practitioner_create_structure_map.json';
+import fce_practitioner_edit from './resources/questionnaire_fce/practitioner_edit.json';
+import fce_practitioner_role_create from './resources/questionnaire_fce/practitioner_role_create.json';
+import fce_public_appointment from './resources/questionnaire_fce/public_appointment.json';
+import fce_review_of_systems from './resources/questionnaire_fce/review_of_systems.json';
+import fce_source_queries from './resources/questionnaire_fce/source_queries.json';
+import fce_vitals from './resources/questionnaire_fce/vitals.json';
+// fhir questionnaire
+import fhir_allergies from './resources/questionnaire_fhir/allergies.json';
+import fhir_beverages from './resources/questionnaire_fhir/beverages.json';
+import fhir_choice_answer_option from './resources/questionnaire_fhir/choice_answer_option.json';
+import fhir_consent from './resources/questionnaire_fhir/consent.json';
+import fhir_enable_when from './resources/questionnaire_fhir/enable_when.json';
+import fhir_encounter_create from './resources/questionnaire_fhir/encounter_create.json';
+import fhir_gad_7 from './resources/questionnaire_fhir/gad_7.json';
+import fhir_immunization from './resources/questionnaire_fhir/immunization.json';
+import fhir_medication from './resources/questionnaire_fhir/medication.json';
+import fhir_multiple_type_launch_context from './resources/questionnaire_fhir/multiple_type_launch_context.json';
+import fhir_patient_create from './resources/questionnaire_fhir/patient_create.json';
+import fhir_patient_edit from './resources/questionnaire_fhir/patient_edit.json';
+import fhir_phq_2_phq_9 from './resources/questionnaire_fhir/phq_2_phq_9.json';
+import fhir_physicalexam from './resources/questionnaire_fhir/physicalexam.json';
+import fhir_practitioner_create from './resources/questionnaire_fhir/practitioner_create.json';
+import fhir_practitioner_create_structure_map from './resources/questionnaire_fhir/practitioner_create_structure_map.json';
+import fhir_practitioner_edit from './resources/questionnaire_fhir/practitioner_edit.json';
+import fhir_practitioner_role_create from './resources/questionnaire_fhir/practitioner_role_create.json';
+import fhir_public_appointment from './resources/questionnaire_fhir/public_appointment.json';
+import fhir_review_of_systems from './resources/questionnaire_fhir/review_of_systems.json';
+import fhir_source_queries from './resources/questionnaire_fhir/source_queries.json';
+import fhir_vitals from './resources/questionnaire_fhir/vitals.json';
+// fce questionnaire response
+import fce_allergies_inprogress_qr from './resources/questionnaire_response_fce/allergies_inprogress.json';
+import fce_cardiology_qr from './resources/questionnaire_response_fce/cardiology.json';
+import fce_few_answers_qr from './resources/questionnaire_response_fce/few_answers.json';
+import fce_gad_7_qr from './resources/questionnaire_response_fce/gad_7.json';
+import fce_immunization_qr from './resources/questionnaire_response_fce/immunization.json';
+import fce_medication_qr from './resources/questionnaire_response_fce/medication.json';
+import fce_new_appointment_qr from './resources/questionnaire_response_fce/new_appointment.json';
+import fce_patient_qr from './resources/questionnaire_response_fce/patient.json';
+import fce_phq_2_phq_9_qr from './resources/questionnaire_response_fce/phq_2_phq_9.json';
+import fce_physicalexam_qr from './resources/questionnaire_response_fce/physicalexam.json';
+import fce_practitioner_qr from './resources/questionnaire_response_fce/practitioner.json';
+import fce_reference_answer_with_assoc from './resources/questionnaire_response_fce/reference_answer_with_assoc.json';
+import fce_review_of_systems_qr from './resources/questionnaire_response_fce/review_of_systems.json';
+import fce_vitals_qr from './resources/questionnaire_response_fce/vitals.json';
+// fhir questionnaire response
+import fhir_allergies_inprogress_qr from './resources/questionnaire_response_fhir/allergies_inprogress.json';
+import fhir_cardiology_qr from './resources/questionnaire_response_fhir/cardiology.json';
+import fhir_few_answers_qr from './resources/questionnaire_response_fhir/few_answers.json';
+import fhir_gad_7_qr from './resources/questionnaire_response_fhir/gad_7.json';
+import fhir_immunization_qr from './resources/questionnaire_response_fhir/immunization.json';
+import fhir_medication_qr from './resources/questionnaire_response_fhir/medication.json';
+import fhir_new_appointment_qr from './resources/questionnaire_response_fhir/new_appointment.json';
+import fhir_patient_qr from './resources/questionnaire_response_fhir/patient.json';
+import fhir_phq_2_phq_9_qr from './resources/questionnaire_response_fhir/phq_2_phq_9.json';
+import fhir_physicalexam_qr from './resources/questionnaire_response_fhir/physicalexam.json';
+import fhir_practitioner_qr from './resources/questionnaire_response_fhir/practitioner.json';
+import fhir_reference_answer_with_assoc from './resources/questionnaire_response_fhir/reference_answer_with_assoc.json';
+import fhir_review_of_systems_qr from './resources/questionnaire_response_fhir/review_of_systems.json';
+import fhir_vitals_qr from './resources/questionnaire_response_fhir/vitals.json';
+import { toFirstClassExtension, fromFirstClassExtension } from '../../converter';
+
+function sortExtensionsRecursive(object: any) {
+    if (typeof object !== 'object' || object === null) {
+        return object;
+    }
+    for (const [key, property] of Object.entries(object)) {
+        if (Array.isArray(property)) {
+            if (key === 'extension') {
+                property.sort((a, b) => (a.url === b.url ? 0 : a.url < b.url ? -1 : 1));
+            }
+            for (const nestedProperty of property) {
+                sortExtensionsRecursive(nestedProperty);
+            }
+        } else {
+            sortExtensionsRecursive(property);
+        }
+    }
+    return object;
+}
+
+export function sortExtensionsList(object: any) {
+    return sortExtensionsRecursive(cloneDeep(object));
+}
+
+describe('Questionanire and QuestionnaireResponses transformation', () => {
+    test.each([
+        [fhir_allergies, fce_allergies],
+        [fhir_beverages, fce_beverages],
+        [fhir_choice_answer_option, fce_choice_answer_option],
+        [fhir_encounter_create, fce_encounter_create],
+        [fhir_gad_7, fce_gad_7],
+        [fhir_immunization, fce_immunization],
+        [fhir_medication, fce_medication],
+        [fhir_multiple_type_launch_context, fce_multiple_type_launch_context],
+        [fhir_patient_create, fce_patient_create],
+        [fhir_patient_edit, fce_patient_edit],
+        [fhir_phq_2_phq_9, fce_phq_2_phq_9],
+        [fhir_physicalexam, fce_physicalexam],
+        [fhir_practitioner_create, fce_practitioner_create],
+        [fhir_practitioner_edit, fce_practitioner_edit],
+        [fhir_practitioner_role_create, fce_practitioner_role_create],
+        [fhir_public_appointment, fce_public_appointment],
+        [fhir_review_of_systems, fce_review_of_systems],
+        [fhir_source_queries, fce_source_queries],
+        [fhir_vitals, fce_vitals],
+        [fhir_practitioner_create_structure_map, fce_practitioner_create_structure_map],
+        [fhir_consent, fce_consent],
+        [fhir_enable_when, fce_enable_when],
+    ])(
+        'Each FHIR Questionnaire should convert to FCE',
+        async (fhir_questionnaire, fce_questionnaire) => {
+            expect(toFirstClassExtension(fhir_questionnaire as FHIRQuestionnaire)).toStrictEqual(
+                fce_questionnaire,
+            );
+        },
+    );
+
+    test.each([
+        [fce_allergies, fhir_allergies],
+        [fce_beverages, fhir_beverages],
+        [fce_choice_answer_option, fhir_choice_answer_option],
+        [fce_encounter_create, fhir_encounter_create],
+        [fce_gad_7, fhir_gad_7],
+        [fce_immunization, fhir_immunization],
+        [fce_medication, fhir_medication],
+        [fce_multiple_type_launch_context, fhir_multiple_type_launch_context],
+        [fce_patient_create, fhir_patient_create],
+        [fce_patient_edit, fhir_patient_edit],
+        [fce_phq_2_phq_9, fhir_phq_2_phq_9],
+        [fce_physicalexam, fhir_physicalexam],
+        [fce_practitioner_create, fhir_practitioner_create],
+        [fce_practitioner_edit, fhir_practitioner_edit],
+        [fce_practitioner_role_create, fhir_practitioner_role_create],
+        [fce_public_appointment, fhir_public_appointment],
+        [fce_review_of_systems, fhir_review_of_systems],
+        [fce_source_queries, fhir_source_queries],
+        [fce_vitals, fhir_vitals],
+        [fce_practitioner_create_structure_map, fhir_practitioner_create_structure_map],
+        [fce_consent, fhir_consent],
+        [fce_enable_when, fhir_enable_when],
+    ])(
+        'Each FCE Questionnaire should convert to FHIR',
+        async (fce_questionnaire, fhir_questionnaire) => {
+            expect(
+                sortExtensionsList(fromFirstClassExtension(fce_questionnaire as FCEQuestionnaire)),
+            ).toStrictEqual(sortExtensionsList(fhir_questionnaire));
+        },
+    );
+
+    test.each([
+        [fhir_allergies_inprogress_qr, fce_allergies_inprogress_qr],
+        [fhir_cardiology_qr, fce_cardiology_qr],
+        [fhir_few_answers_qr, fce_few_answers_qr],
+        [fhir_gad_7_qr, fce_gad_7_qr],
+        [fhir_immunization_qr, fce_immunization_qr],
+        [fhir_medication_qr, fce_medication_qr],
+        [fhir_new_appointment_qr, fce_new_appointment_qr],
+        [fhir_patient_qr, fce_patient_qr],
+        [fhir_phq_2_phq_9_qr, fce_phq_2_phq_9_qr],
+        [fhir_physicalexam_qr, fce_physicalexam_qr],
+        [fhir_practitioner_qr, fce_practitioner_qr],
+        [fhir_review_of_systems_qr, fce_review_of_systems_qr],
+        [fhir_vitals_qr, fce_vitals_qr],
+    ])(
+        'Each FHIR QuestionnaireResponse should convert to FCE',
+        async (fhirQuestionnaireResponse, expectedFCE) => {
+            expect(
+                toFirstClassExtension(fhirQuestionnaireResponse as FHIRQuestionnaireResponse),
+            ).toStrictEqual(expectedFCE);
+        },
+    );
+
+    test.each([
+        [fce_allergies_inprogress_qr, fhir_allergies_inprogress_qr],
+        [fce_cardiology_qr, fhir_cardiology_qr],
+        [fce_few_answers_qr, fhir_few_answers_qr],
+        [fce_gad_7_qr, fhir_gad_7_qr],
+        [fce_immunization_qr, fhir_immunization_qr],
+        [fce_medication_qr, fhir_medication_qr],
+        [fce_new_appointment_qr, fhir_new_appointment_qr],
+        [fce_patient_qr, fhir_patient_qr],
+        [fce_phq_2_phq_9_qr, fhir_phq_2_phq_9_qr],
+        [fce_physicalexam_qr, fhir_physicalexam_qr],
+        [fce_practitioner_qr, fhir_practitioner_qr],
+        [fce_review_of_systems_qr, fhir_review_of_systems_qr],
+        [fce_vitals_qr, fhir_vitals_qr],
+        [fce_reference_answer_with_assoc, fhir_reference_answer_with_assoc],
+    ])(
+        'Each FCE QuestionnaireResponse should convert to FHIR',
+        async (fceQuestionnaireResponse, expectedFHIR) => {
+            expect(
+                fromFirstClassExtension(fceQuestionnaireResponse as FCEQuestionnaireResponse),
+            ).toStrictEqual(expectedFHIR);
+        },
+    );
+});

package/src/converter/__tests__/resources/questionnaire_fce/allergies.json

@@ -0,0 +1,405 @@
+{
+    "subjectType": ["Encounter", "Patient"],
+    "meta": {
+        "profile": ["https://beda.software/beda-emr-questionnaire"],
+        "lastUpdated": "2023-04-10T03:43:34.792167Z",
+        "createdAt": "2023-04-05T05:22:35.752466Z",
+        "versionId": "694"
+    },
+    "launchContext": [
+        {
+            "name": {
+                "code": "LaunchPatient",
+                "system": "http://hl7.org/fhir/uv/sdc/CodeSystem/launchContext"
+            },
+            "type": ["Patient"]
+        },
+        {
+            "name": {
+                "code": "Author",
+                "system": "http://hl7.org/fhir/uv/sdc/CodeSystem/launchContext"
+            },
+            "type": ["Resource"]
+        }
+    ],
+    "name": "Allergies",
+    "item": [
+        {
+            "text": "DateTime",
+            "type": "dateTime",
+            "hidden": true,
+            "linkId": "dateTime",
+            "initialExpression": {
+                "language": "text/fhirpath",
+                "expression": "now()"
+            }
+        },
+        {
+            "text": "PatientId",
+            "type": "string",
+            "hidden": true,
+            "linkId": "patientId",
+            "initialExpression": {
+                "language": "text/fhirpath",
+                "expression": "%Patient.id"
+            }
+        },
+        {
+            "text": "PatientName",
+            "type": "string",
+            "hidden": true,
+            "linkId": "patientName",
+            "initialExpression": {
+                "language": "text/fhirpath",
+                "expression": "%Patient.name.given[0] + ' ' + %Patient.name.family"
+            }
+        },
+        {
+            "text": "Type",
+            "type": "choice",
+            "linkId": "type",
+            "required": true,
+            "itemControl": {
+                "coding": [
+                    {
+                        "code": "inline-choice"
+                    }
+                ]
+            },
+            "answerOption": [
+                {
+                    "value": {
+                        "Coding": {
+                            "code": "418634005",
+                            "system": "http://hl7.org/fhir/allergy-intolerance-category",
+                            "display": "Drug"
+                        }
+                    }
+                },
+                {
+                    "value": {
+                        "Coding": {
+                            "code": "414285001",
+                            "system": "http://hl7.org/fhir/allergy-intolerance-category",
+                            "display": "Food"
+                        }
+                    }
+                },
+                {
+                    "value": {
+                        "Coding": {
+                            "code": "426232007",
+                            "system": "http://hl7.org/fhir/allergy-intolerance-category",
+                            "display": "Environmental"
+                        }
+                    }
+                }
+            ]
+        },
+        {
+            "text": "Reaction",
+            "type": "choice",
+            "linkId": "reaction",
+            "repeats": true,
+            "itemControl": {
+                "coding": [
+                    {
+                        "code": "inline-choice"
+                    }
+                ]
+            },
+            "answerOption": [
+                {
+                    "value": {
+                        "Coding": {
+                            "code": "39579001",
+                            "system": "http://snomed.ct",
+                            "display": "Anaphylaxis"
+                        }
+                    }
+                },
+                {
+                    "value": {
+                        "Coding": {
+                            "code": "25064002",
+                            "system": "http://snomed.ct",
+                            "display": "Headache"
+                        }
+                    }
+                },
+                {
+                    "value": {
+                        "Coding": {
+                            "code": "247472004",
+                            "system": "http://snomed.ct",
+                            "display": "Hives (Wheal)"
+                        }
+                    }
+                },
+                {
+                    "value": {
+                        "Coding": {
+                            "code": "422587007",
+                            "system": "http://snomed.ct",
+                            "display": "Nausea"
+                        }
+                    }
+                },
+                {
+                    "value": {
+                        "Coding": {
+                            "code": "422400008",
+                            "system": "http://snomed.ct",
+                            "display": "Vomiting"
+                        }
+                    }
+                }
+            ]
+        },
+        {
+            "text": "Substance",
+            "type": "choice",
+            "linkId": "substance-drug",
+            "enableWhen": [
+                {
+                    "answer": {
+                        "Coding": {
+                            "code": "418634005",
+                            "system": "http://snomed.ct"
+                        }
+                    },
+                    "operator": "=",
+                    "question": "type"
+                }
+            ],
+            "itemControl": {
+                "coding": [
+                    {
+                        "code": "inline-choice"
+                    }
+                ]
+            },
+            "answerOption": [
+                {
+                    "value": {
+                        "Coding": {
+                            "code": "LA26702-3",
+                            "system": "http://loinc.org",
+                            "display": "Aspirin"
+                        }
+                    }
+                },
+                {
+                    "value": {
+                        "Coding": {
+                            "code": "LA30119-4",
+                            "system": "http://loinc.org",
+                            "display": "Iodine"
+                        }
+                    }
+                },
+                {
+                    "value": {
+                        "Coding": {
+                            "code": "LA14348-9",
+                            "system": "http://loinc.org",
+                            "display": "Naproxen, ketoprofen or other non-steroidal"
+                        }
+                    }
+                },
+                {
+                    "value": {
+                        "Coding": {
+                            "code": "LA28487-9",
+                            "system": "http://loinc.org",
+                            "display": "Penicillin"
+                        }
+                    }
+                },
+                {
+                    "value": {
+                        "Coding": {
+                            "code": "LA30118-6",
+                            "system": "http://loinc.org",
+                            "display": "Sulfa drugs"
+                        }
+                    }
+                }
+            ]
+        },
+        {
+            "text": "Substance",
+            "type": "choice",
+            "linkId": "substance-food",
+            "enableWhen": [
+                {
+                    "answer": {
+                        "Coding": {
+                            "code": "414285001",
+                            "system": "http://snomed.ct"
+                        }
+                    },
+                    "operator": "=",
+                    "question": "type"
+                }
+            ],
+            "itemControl": {
+                "coding": [
+                    {
+                        "code": "inline-choice"
+                    }
+                ]
+            },
+            "answerOption": [
+                {
+                    "value": {
+                        "Coding": {
+                            "code": "102259006",
+                            "system": "http://snomed.ct",
+                            "display": "Citrus fruit"
+                        }
+                    }
+                },
+                {
+                    "value": {
+                        "Coding": {
+                            "code": "102260001",
+                            "system": "http://snomed.ct",
+                            "display": "Peanut butter"
+                        }
+                    }
+                },
+                {
+                    "value": {
+                        "Coding": {
+                            "code": "102261002",
+                            "system": "http://snomed.ct",
+                            "display": "Strawberry"
+                        }
+                    }
+                },
+                {
+                    "value": {
+                        "Coding": {
+                            "code": "102262009",
+                            "system": "http://snomed.ct",
+                            "display": "Chocolate"
+                        }
+                    }
+                },
+                {
+                    "value": {
+                        "Coding": {
+                            "code": "102263004",
+                            "system": "http://snomed.ct",
+                            "display": "Eggs"
+                        }
+                    }
+                },
+                {
+                    "value": {
+                        "Coding": {
+                            "code": "102264005",
+                            "system": "http://snomed.ct",
+                            "display": "Cheese"
+                        }
+                    }
+                }
+            ]
+        },
+        {
+            "text": "Substance",
+            "type": "choice",
+            "linkId": "substance-environmental",
+            "enableWhen": [
+                {
+                    "answer": {
+                        "Coding": {
+                            "code": "426232007",
+                            "system": "http://snomed.ct"
+                        }
+                    },
+                    "operator": "=",
+                    "question": "type"
+                }
+            ],
+            "itemControl": {
+                "coding": [
+                    {
+                        "code": "inline-choice"
+                    }
+                ]
+            },
+            "answerOption": [
+                {
+                    "value": {
+                        "Coding": {
+                            "code": "111088007",
+                            "system": "http://snomed.ct",
+                            "display": "Latex"
+                        }
+                    }
+                },
+                {
+                    "value": {
+                        "Coding": {
+                            "code": "256259004",
+                            "system": "http://snomed.ct",
+                            "display": "Pollen"
+                        }
+                    }
+                },
+                {
+                    "value": {
+                        "Coding": {
+                            "code": "256277009",
+                            "system": "http://snomed.ct",
+                            "display": "Grass pollen"
+                        }
+                    }
+                },
+                {
+                    "value": {
+                        "Coding": {
+                            "code": "256417003",
+                            "system": "http://snomed.ct",
+                            "display": "Horse dander"
+                        }
+                    }
+                }
+            ]
+        },
+        {
+            "text": "Notes",
+            "type": "string",
+            "linkId": "notes"
+        },
+        {
+            "text": "Active",
+            "type": "string",
+            "hidden": true,
+            "linkId": "status",
+            "initial": [
+                {
+                    "value": {
+                        "Coding": {
+                            "code": "active",
+                            "system": "http://terminology.hl7.org/ValueSet/allergyintolerance-clinical",
+                            "display": "Active"
+                        }
+                    }
+                }
+            ]
+        }
+    ],
+    "mapping": [
+        {
+            "id": "allergy-extract",
+            "resourceType": "Mapping"
+        }
+    ],
+    "resourceType": "Questionnaire",
+    "status": "active",
+    "id": "allergies",
+    "url": "https://aidbox.emr.beda.software/ui/console#/entities/Questionnaire/allergies"
+}