feat(#147): adding value types (#149)

mediator/src/controllers/cht.ts

@@ -79,10 +79,8 @@ export async function createEncounter(chtReport: any) {
   }
 
   for (const entry of chtReport.observations) {
-    if (entry.valueCode || entry.valueString || entry.valueDateTime) {
-      const observation = buildFhirObservationFromCht(chtReport.patient_uuid, fhirEncounter, entry);
-      createFhirResource(observation);
-    }
+    const observation = buildFhirObservationFromCht(chtReport.patient_uuid, fhirEncounter, entry);
+    createFhirResource(observation);
   }
 
   return { status: 200, data: {} };

mediator/src/mappers/cht.ts

@@ -103,6 +103,39 @@ export function buildFhirEncounterFromCht(chtReport: any): fhir4.Encounter {
   return encounter
 }
 
+/*
+ * Copy the value from the form mapping to observation
+ * value are expected to already have been validated
+ * for types which are native to JSON (Integer, String, Boolean) just copy them exactly
+ * copy Time and DateTime as strings (they have been validated already)
+ * valueQuantity will be an object, but also just copy it directly
+ */
+function copyObservationValue(observation: any, entry: any) {
+  const copyValueTypes = [
+    'valueString',
+    'valueDateTime',
+    'valueTime',
+    'valueBoolean',
+    'valueInteger',
+    'valueQuantity'
+  ];
+  copyValueTypes.forEach((name) => {
+    if (entry.hasOwnProperty(name)) {
+      observation[name] = entry[name];
+    }
+  });
+
+  // valueCode needs a little bit of conversion; we are not requiring cht forms to
+  // map to codeableConcept, just to give the string
+  if ('valueCode' in entry){
+    observation.valueCodeableConcept = {
+      coding: [{
+        code: entry['valueCode']
+      }]
+    };
+  } 
+}
+
 export function buildFhirObservationFromCht(patient_id: string, encounter: fhir4.Encounter, entry: any): fhir4.Observation {
   const patientRef: fhir4.Reference = {
 	  reference: `Patient/${patient_id}`,
@@ -130,17 +163,7 @@ export function buildFhirObservationFromCht(patient_id: string, encounter: fhir4
     issued: now
   };
 
-  if ('valueCode' in entry){
-    observation.valueCodeableConcept = {
-      coding: [{
-        code: entry['valueCode']
-      }]
-    };
-  } else if ('valueDateTime' in entry){
-    observation.valueDateTime = entry['valueDateTime'];
-  } else if ('valueString' in entry){
-    observation.valueString = entry['valueString'];
-  }
+  copyObservationValue(observation, entry);
 
   return observation;
 }

mediator/src/middlewares/schemas/cht.ts

@@ -0,0 +1,41 @@
+import joi from 'joi';
+
+export const ChtPatientSchema = joi.object({
+  doc: joi.object({
+    _id: joi.string().uuid().required(),
+    name: joi.string().required(),
+    phone: joi.string().required(),
+    date_of_birth: joi.string().required(),
+    sex: joi.string().required(),
+    patient_id: joi.string().required()
+  }).required()
+});
+
+export const ChtPatientIdsSchema = joi.object({
+  doc: joi.object({
+    patient_id: joi.string().required(),
+    external_id: joi.string().required()
+  })
+});
+
+export const ValueTypeSchema = joi.object({
+  code: joi.string().required(),
+  valueString: joi.string(),
+  valueCode: joi.string(),
+  valueBoolean: joi.boolean(),
+  valueInteger: joi.number().integer(),
+  valueDateTime: joi.string().isoDate(),
+  valueTime: joi.string().regex(/^([01]\d|2[0-3]):([0-5]\d)(:[0-5]\d(\.\d{1,3})?)?$/),  // matches HH:mm[:ss[.SSS]]
+  valueQuantity: joi.object({
+    value: joi.number().required(),
+    unit: joi.string().required(),
+    system: joi.string().uri().optional(),
+    code: joi.string().optional()
+  })
+}).or('valueString', 'valueCode', 'valueBoolean', 'valueInteger', 'valueDateTime', 'valueTime', 'valueQuantity');
+
+export const ChtEncounterFormSchema = joi.object({
+  patient_uuid: joi.string().required(),
+  reported_date: joi.number().required(), //timestamp
+  observations: joi.array().items(ValueTypeSchema).optional()
+});

mediator/src/middlewares/schemas/tests/cht-request-factories.ts

@@ -50,10 +50,6 @@ export const ChtPregnancyForm = Factory.define('chtPregnancyDoc')
       "code": "17a57368-5f59-42c8-aaab-f2774d21501e",
       "valueCode": "ea6a020e-05cd-4fea-b618-abd7494ac571"
     },
-    {
-      "code": "17a57368-5f59-42c8-aaab-f2774d21501e",
-      "valueCode": false
-    },
     {
       "code": "17a57368-5f59-42c8-aaab-f2774d21501e",
       "valueCode": "0d9e45d6-9288-494e-841c-80f3f9b8e126"
@@ -75,7 +71,19 @@ export const ChtPregnancyForm = Factory.define('chtPregnancyDoc')
       "valueDateTime": "2024-08-26"
     },
     {
-      "code": "13179cce-a424-43d7-9ad1-dce7861946e8",
-      "valueString": ""
+      "code": "73179cce-a424-43d7-9ad1-dce7861946e8",
+      "valueString": "String"
+    },
+    {
+      "code": "53179cce-a424-43d7-9ad1-dce7861946e8",
+      "valueQuantity": { "value": 160, "unit": "kg" }
+    },
+    {
+      "code": "37a57368-5f59-42c8-aaab-f2774d21501e",
+      "valueBoolean": false
+    },
+    {
+      "code": "47a57368-5f54-42c8-aaab-f2774d21501e",
+      "valueInteger": 12
     }
   ]);

mediator/src/routes/cht.ts

@@ -1,5 +1,7 @@
 import { Router } from 'express';
 import { requestHandler } from '../utils/request';
+import { validateBodyAgainst } from '../middlewares';
+import { ChtPatientSchema, ChtPatientIdsSchema, ChtEncounterFormSchema } from '../middlewares/schemas/cht';
 import { createPatient, updatePatientIds, createEncounter } from '../controllers/cht'
 
 const router = Router();
@@ -8,16 +10,19 @@ const resourceType = 'Patient';
 
 router.post(
   '/patient',
+  validateBodyAgainst(ChtPatientSchema),
   requestHandler((req) => createPatient(req.body))
 );
 
 router.post(
   '/patient_ids',
+  validateBodyAgainst(ChtPatientIdsSchema),
   requestHandler((req) => updatePatientIds(req.body))
 );
 
 router.post(
   '/encounter',
+  validateBodyAgainst(ChtEncounterFormSchema),
   requestHandler((req) => createEncounter(req.body))
 );
 

mediator/src/routes/tests/cht.spec.ts

@@ -0,0 +1,53 @@
+import request from 'supertest';
+import app from '../../..';
+import { ChtPatientFactory, ChtPatientIdsFactory, ChtPregnancyForm } from '../../middlewares/schemas/tests/cht-request-factories';
+
+describe('POST /cht/patient', () => {
+  it('doesn\'t accept incoming request with invalid patient resource', async () => {
+    const data = ChtPatientFactory.build();
+    delete data.doc._id;
+
+    const res = await request(app).post('/cht/patient').send(data);
+
+    expect(res.status).toBe(400);
+    expect(res.body.valid).toBe(false);
+    expect(res.body.message).toMatchInlineSnapshot(
+      `""doc._id" is required"`
+    );
+  });
+});
+
+describe('POST /cht/patient_ids', () => {
+  it('doesn\'t accept incoming request with invalid patient resource', async () => {
+    const data = ChtPatientIdsFactory.build();
+    delete data.doc.patient_id;
+
+    const res = await request(app).post('/cht/patient_ids').send(data);
+
+    expect(res.status).toBe(400);
+    expect(res.body.valid).toBe(false);
+    expect(res.body.message).toMatchInlineSnapshot(
+      `""doc.patient_id" is required"`
+    );
+  });
+});
+
+describe('POST /cht/encounter', () => {
+  it('doesn\'t accept incoming request with invalid form', async () => {
+    const data = ChtPregnancyForm.build();
+
+    // push an invalid observation
+    data.observations.push({
+      "code": "17a57368-5f59-42c8-aaab-f2774d21501e",
+      "valueDateTime": "This is not a valid date"
+    })
+
+    const res = await request(app).post('/cht/encounter').send(data);
+
+    expect(res.status).toBe(400);
+    expect(res.body.valid).toBe(false);
+    expect(res.body.message).toMatchInlineSnapshot(
+      `""observations[13].valueDateTime" must be in iso format"`
+    );
+  });
+});