Fhir api tests

docker-compose.dev.yml

@@ -14,6 +14,8 @@ services:
       hapi.fhir.client_id_strategy: ANY
       hapi.fhir.cors.allowed_origin: "*"
       hapi.fhir.fhir_version: R4
+      hapi.fhir.allow_cascading_deletes: true
+      hapi.fhir.reuse_cached_search_results_millis: -1
   fhir-db:
     image: postgres:latest
     volumes:

src/fhir/api.test.ts

@@ -7,8 +7,92 @@ import { geneCoding } from "../code_systems/hgnc";
 const fhir = new Fhir();
 
 const reportedGenes = [geneCoding("HGNC:4389", "GNA01")];
+const FHIR_URL = process.env.REACT_APP_FHIR_URL || "";
+
+const getPatients = async () => {
+  const url = `${FHIR_URL}/Patient`;
+  const response = await fetch(url);
+  if (!response.ok) {
+    console.error(response.statusText);
+    console.error(response.body);
+    throw new Error(response.statusText);
+  }
+  return await response.json();
+};
+
+const check = async (response: any) => {
+  // would like to figure out which type response should be
+  const r = await response.json();
+  console.error(r.body);
+};
+
+const deletePatients = async (patientId?: string) => {
+  /**
+   * This method can take a string to delete a particular patient's records
+   * or it can accept a bundle with a number of entries from which
+   * it will extract the ID(s) and delete the patient(s)
+   */
+  const baseURL = `${FHIR_URL}/Patient`;
+  const patientData = await getPatients();
+  if (!("entry" in patientData)) {
+    return;
+  }
+
+  const deletePatientEntry = async (entry: any) => {
+    let id;
+    if (typeof entry === "string") {
+      console.info("entry is string", patientId);
+      return (id = patientId);
+    }
+    id = entry[0].resource.id;
+    console.info("deleting records related to " + id);
+    const response = await fetch(`${baseURL}/${id}?_cascade=delete`, {
+      method: "DELETE",
+    });
+    if (!response.ok) {
+      console.error(response.statusText);
+      console.error(response.body);
+    }
+    check(response);
+    await new Promise((r) => setTimeout(r, 1500));
+  };
+
+  const patientEntry = patientData.entry;
+  deletePatientEntry(patientEntry);
+};
 
 describe("FHIR resources", () => {
+  beforeEach(async () => {
+    fetchMock.dontMock();
+    await deletePatients();
+  });
+
+  test("database is clear on setup", async () => {
+    /**
+     * Before doing tests on the database, we want to clear all its data
+     */
+
+    const postDelete = await getPatients();
+    expect("entry" in postDelete).toBeFalsy();
+  });
+
+  test("bundle creates patient", async () => {
+    const bundle = createBundle(initialValues, reportedGenes);
+
+    const createPatient = await fetch(`${FHIR_URL}/`, {
+      method: "POST",
+      body: JSON.stringify(bundle),
+      headers: {
+        "Content-Type": "application/json",
+      },
+    });
+
+    check(createPatient);
+    const patientData = await getPatients();
+    expect("entry" in patientData).toBeTruthy();
+    expect(patientData.entry[0].resource.identifier[0].value).toEqual(initialValues.patient.mrn);
+  });
+
   /**
    * Given that form data has been correctly populated
    * When a FHIR bundle is created
@@ -19,7 +103,7 @@ describe("FHIR resources", () => {
 
     const output = fhir.validate(bundle);
     console.info("Validation output");
-    console.info(JSON.stringify(output.messages, null, 2));
+    // console.info(JSON.stringify(output.messages, null, 2));
     expect(output.valid).toBeTruthy();
   });
 
@@ -46,7 +130,7 @@ describe("FHIR resources", () => {
     // fhir validation
     const output = fhir.validate(bundle);
     console.info("Validation output");
-    console.info(JSON.stringify(output.messages, null, 2));
+    // console.info(JSON.stringify(output.messages, null, 2));
     expect(output.valid).toBeTruthy();
   });
 });