Add immunization query backend (#292)

Co-authored-by: m-goggins <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Nick Clyde <[email protected]>
Co-authored-by: Marcelle <[email protected]>

query-connector/flyway/conf/flyway.conf

@@ -2,4 +2,4 @@ flyway.url=jdbc:postgresql://db:5432/tefca_db
 flyway.locations=filesystem:/flyway/sql
 flyway.user=postgres
 flyway.password=pw
-flyway.baselineOnMigrate=false
+flyway.baselineOnMigrate=false

query-connector/flyway/sql/V04_01__add_fhir_server_disable_cert_validation.sql

@@ -0,0 +1,12 @@
+ALTER TABLE fhir_servers
+ADD COLUMN disable_cert_validation BOOLEAN DEFAULT FALSE;
+
+-- Update rows with eHealthExchange in the server name to have disable_cert_validation set to true
+UPDATE fhir_servers
+SET disable_cert_validation = TRUE
+WHERE name LIKE '%eHealthExchange%';
+
+-- Update rows with eHealthExchange in the server name to strip the trailing slash from the hostname
+UPDATE fhir_servers
+SET hostname = regexp_replace(hostname, '/$', '')
+WHERE name LIKE '%eHealthExchange%';

query-connector/src/app/CustomQuery.ts

@@ -30,6 +30,7 @@ export class CustomQuery {
   socialHistoryQuery: string = "";
   encounterQuery: string = "";
   encounterClassTypeQuery: string = "";
+  immunizationQuery: string = "";
 
   // Some queries need to be batched in waves because their encounter references
   // might depend on demographic information
@@ -94,6 +95,8 @@ export class CustomQuery {
       classTypeFilter !== ""
         ? `/Encounter?subject=${patientId}&class=${classTypeFilter}`
         : "";
+
+    this.immunizationQuery = `/Immunization?patient=${patientId}`;
   }
 
   /**
@@ -109,6 +112,7 @@ export class CustomQuery {
       this.socialHistoryQuery,
       this.encounterQuery,
       this.encounterClassTypeQuery,
+      this.immunizationQuery,
     ];
     const filteredRequests = queryRequests.filter((q) => q !== "");
     return filteredRequests;
@@ -136,6 +140,8 @@ export class CustomQuery {
         return this.encounterQuery;
       case "encounterClass":
         return this.encounterClassTypeQuery;
+      case "immunization":
+        return this.immunizationQuery;
       default:
         return "";
     }

query-connector/src/app/constants.ts

@@ -7,6 +7,7 @@ import {
   Medication,
   MedicationAdministration,
   MedicationRequest,
+  Immunization,
 } from "fhir/r4";
 
 export const USE_CASE_DETAILS = {
@@ -30,6 +31,10 @@ export const USE_CASE_DETAILS = {
     queryName: "Cancer case investigation",
     condition: "Cancer (Leukemia)",
   },
+  immunization: {
+    queryName: "Immunization",
+    condition: "Immunization",
+  },
 } as const;
 
 export type USE_CASES = keyof typeof USE_CASE_DETAILS;
@@ -285,7 +290,8 @@ export type FhirResource =
   | Encounter
   | Medication
   | MedicationAdministration
-  | MedicationRequest;
+  | MedicationRequest
+  | Immunization;
 
 /**
  * A type guard function that checks if the given resource is a valid FHIR resource.
@@ -327,6 +333,7 @@ export type FhirServerConfig = {
   last_connection_attempt: Date;
   last_connection_successful: boolean;
   headers: Record<string, string>;
+  disable_cert_validation: boolean;
 };
 
 export const INVALID_USE_CASE = `Invalid use_case. Please provide a valid use_case. Valid use_cases include ${Object.keys(

query-connector/src/app/database-service.ts

@@ -765,13 +765,15 @@ export async function getFhirServerConfig(fhirServerName: string) {
  * Inserts a new FHIR server configuration into the database.
  * @param name - The name of the FHIR server
  * @param hostname - The URL/hostname of the FHIR server
+ * @param disableCertValidation - Whether to disable certificate validation
  * @param lastConnectionSuccessful - Optional boolean indicating if the last connection was successful
  * @param bearerToken - Optional bearer token for authentication
  * @returns An object indicating success or failure with optional error message
  */
 export async function insertFhirServer(
   name: string,
   hostname: string,
+  disableCertValidation: boolean,
   lastConnectionSuccessful?: boolean,
   bearerToken?: string,
 ) {
@@ -781,9 +783,10 @@ export async function insertFhirServer(
       hostname, 
       last_connection_attempt,
       last_connection_successful,
-      headers
+      headers,
+      disable_cert_validation
     )
-    VALUES ($1, $2, $3, $4, $5);
+    VALUES ($1, $2, $3, $4, $5, $6);
   `;
 
   try {
@@ -800,6 +803,7 @@ export async function insertFhirServer(
       new Date(),
       lastConnectionSuccessful,
       headers,
+      disableCertValidation,
     ]);
 
     // Clear the cache so the next getFhirServerConfigs call will fetch fresh data
@@ -826,6 +830,7 @@ export async function insertFhirServer(
  * @param id - The ID of the FHIR server to update
  * @param name - The new name of the FHIR server
  * @param hostname - The new URL/hostname of the FHIR server
+ * @param disableCertValidation - Whether to disable certificate validation
  * @param lastConnectionSuccessful - Optional boolean indicating if the last connection was successful
  * @param bearerToken - Optional bearer token for authentication
  * @returns An object indicating success or failure with optional error message
@@ -834,6 +839,7 @@ export async function updateFhirServer(
   id: string,
   name: string,
   hostname: string,
+  disableCertValidation: boolean,
   lastConnectionSuccessful?: boolean,
   bearerToken?: string,
 ) {
@@ -844,7 +850,8 @@ export async function updateFhirServer(
       hostname = $3,
       last_connection_attempt = CURRENT_TIMESTAMP,
       last_connection_successful = $4,
-      headers = $5
+      headers = $5,
+      disable_cert_validation = $6
     WHERE id = $1
     RETURNING *;
   `;
@@ -891,6 +898,7 @@ export async function updateFhirServer(
       hostname,
       lastConnectionSuccessful,
       headers,
+      disableCertValidation,
     ]);
 
     // Clear the cache so the next getFhirServerConfigs call will fetch fresh data

query-connector/src/app/fhir-servers.ts

@@ -2,8 +2,6 @@ import fetch, { RequestInit, HeaderInit, Response } from "node-fetch";
 import { FhirServerConfig } from "./constants";
 import https from "https";
 
-type DevFhirServerConfig = FhirServerConfig & { trustSelfSigned?: boolean };
-
 /**
  * A client for querying a FHIR server
  * @param server The FHIR server to query
@@ -15,7 +13,7 @@ class FHIRClient {
 
   constructor(server: string, configurations: FhirServerConfig[]) {
     // Get the configuration for the server if it exists
-    let config: DevFhirServerConfig | undefined = configurations.find(
+    let config: FhirServerConfig | undefined = configurations.find(
       (config) => config.name === server,
     );
 
@@ -30,7 +28,7 @@ class FHIRClient {
       headers: config.headers as HeaderInit,
     };
     // Trust eHealth Exchange's self-signed certificate
-    if (config.trustSelfSigned) {
+    if (config.disable_cert_validation) {
       init.agent = new https.Agent({
         rejectUnauthorized: false,
       });

query-connector/src/app/fhir-servers/page.tsx

@@ -15,6 +15,7 @@ import styles from "./fhirServers.module.scss";
 import classNames from "classnames";
 import SiteAlert from "../query/designSystem/SiteAlert";
 import Table from "../query/designSystem/table/Table";
+import Checkbox from "../query/designSystem/checkbox/Checkbox";
 
 // Dynamic import with proper typing for Modal
 import type { ModalProps } from "../query/designSystem/modal/Modal";
@@ -37,6 +38,7 @@ const FhirServers: React.FC = () => {
   const [serverUrl, setServerUrl] = useState("");
   const [authMethod, setAuthMethod] = useState<"none" | "basic">("none");
   const [bearerToken, setBearerToken] = useState("");
+  const [disableCertValidation, setDisableCertValidation] = useState(false);
   const [connectionStatus, setConnectionStatus] = useState<
     "idle" | "success" | "error"
   >("idle");
@@ -78,6 +80,7 @@ const FhirServers: React.FC = () => {
       setServerName(server.name);
       setServerUrl(server.hostname);
       setConnectionStatus("idle");
+      setDisableCertValidation(server.disable_cert_validation);
 
       // Set auth method and bearer token if they exist
       if (server.headers?.Authorization?.startsWith("Bearer ")) {
@@ -146,6 +149,7 @@ const FhirServers: React.FC = () => {
       const result = await insertFhirServer(
         serverName,
         serverUrl,
+        disableCertValidation,
         connectionResult.success,
         authMethod === "basic" ? bearerToken : undefined,
       );
@@ -164,6 +168,7 @@ const FhirServers: React.FC = () => {
         selectedServer.id,
         serverName,
         serverUrl,
+        disableCertValidation,
         connectionResult.success,
         authMethod === "basic" ? bearerToken : undefined,
       );
@@ -404,6 +409,12 @@ const FhirServers: React.FC = () => {
               />
             </>
           )}
+          <Checkbox
+            id="disable-cert-validation"
+            label="Disable certificate validation"
+            checked={disableCertValidation}
+            onChange={(e) => setDisableCertValidation(e.target.checked)}
+          />
         </Modal>
       </div>
     </>

query-connector/src/app/format-service.tsx

@@ -5,6 +5,8 @@ import {
   Address,
   ContactPoint,
   Identifier,
+  Immunization,
+  Coding,
 } from "fhir/r4";
 import { DibbsValueSet } from "./constants";
 import { QueryStruct } from "./query-service";
@@ -304,3 +306,17 @@ export const formatValueSetsAsQuerySpec = async (
 
   return spec;
 };
+
+/**
+ * Formats the route of a FHIR Immunization object.
+ * @param immunization - The Immunization object to format.
+ * @returns The formatted route .
+ */
+export const formatImmunizationRoute = (immunization: Immunization): string => {
+  const initial = immunization.route?.coding?.[0].display ?? "";
+  const readable = immunization.route?.coding?.filter(
+    (code: Coding) =>
+      code.system === "http://terminology.hl7.org/CodeSystem/v2-0162",
+  );
+  return readable?.[0].display ?? initial;
+};

query-connector/src/app/query-service.ts

@@ -202,6 +202,8 @@ async function generalizedQuery(
   // Special cases for newborn screening, which just use one query
   if (useCase === "newborn-screening") {
     response = await fhirClient.get(builtQuery.getQuery("observation"));
+  } else if (useCase === "immunization") {
+    response = await fhirClient.get(builtQuery.getQuery("immunization"));
   } else {
     const queryRequests: string[] = builtQuery.getAllQueries();
     response = await fhirClient.getBatch(queryRequests);

query-connector/src/app/query/components/ResultsView.tsx

@@ -15,6 +15,7 @@ import Backlink from "./backLink/Backlink";
 import { USE_CASES, USE_CASE_DETAILS } from "@/app/constants";
 import { RETURN_LABEL } from "@/app/query/components/stepIndicator/StepIndicator";
 import TitleBox from "./stepIndicator/TitleBox";
+import ImmunizationTable from "./resultsView/tableComponents/ImmunizationTable";
 
 type ResultsViewProps = {
   useCaseQueryResponse: UseCaseQueryResponse;
@@ -113,6 +114,9 @@ function mapQueryResponseToAccordionDataStructure(
   const medicationRequests = useCaseQueryResponse.MedicationRequest
     ? useCaseQueryResponse.MedicationRequest
     : null;
+  const immunizations = useCaseQueryResponse.Immunization
+    ? useCaseQueryResponse.Immunization
+    : null;
 
   const accordionItems: ResultsViewAccordionItem[] = [
     {
@@ -146,6 +150,12 @@ function mapQueryResponseToAccordionDataStructure(
         <MedicationRequestTable medicationRequests={medicationRequests} />
       ) : null,
     },
+    {
+      title: "Immunizations",
+      content: immunizations ? (
+        <ImmunizationTable immunizations={immunizations} />
+      ) : null,
+    },
   ];
   return accordionItems;
 }

query-connector/src/app/query/components/resultsView/tableComponents/ImmunizationTable.tsx

@@ -0,0 +1,53 @@
+import React from "react";
+import Table from "@/app/query/designSystem/table/Table";
+import { Immunization } from "fhir/r4";
+import {
+  formatDate,
+  formatImmunizationRoute,
+} from "../../../../format-service";
+import styles from "./resultsTables.module.scss";
+
+/**
+ * The props for the ImmunizationTable component.
+ */
+export interface ImmunizationTableProps {
+  immunizations: Immunization[];
+}
+
+/**
+ * Displays a table of data from array of Immunization resources.
+ * @param props - Immunization table props.
+ * @param props.immunizations - The array of Immunization resources.
+ * @returns - The ImmunizationTable component.
+ */
+const ImmunizationTable: React.FC<ImmunizationTableProps> = ({
+  immunizations,
+}) => {
+  return (
+    <Table bordered={false} className="margin-top-0-important">
+      <thead>
+        <tr className={styles.immunizationRow}>
+          <th>Date</th>
+          <th>Vaccine name</th>
+          <th>Dose</th>
+          <th>Route</th>
+        </tr>
+      </thead>
+      <tbody>
+        {immunizations.map((immunization) => (
+          <tr className={styles.immunizationRow} key={immunization.id}>
+            <td>{formatDate(immunization.occurrenceDateTime)}</td>
+            <td>{immunization.vaccineCode.coding?.[0].display}</td>
+            <td>
+              {immunization.doseQuantity?.value}{" "}
+              {immunization.doseQuantity?.code}
+            </td>
+            <td>{formatImmunizationRoute(immunization)}</td>
+          </tr>
+        ))}
+      </tbody>
+    </Table>
+  );
+};
+
+export default ImmunizationTable;

query-connector/src/app/query/components/resultsView/tableComponents/resultsTables.module.scss

@@ -6,6 +6,7 @@ $medicationColumnSpacing: 1fr 3fr 1fr;
 $encountersColumnSpacing: 2fr 1fr 1fr 1fr;
 $diagnosticsColumnSpacing: 1fr 3fr;
 $demographicsColumnSpacing: 1fr 3fr;
+$immunizationColumnSpacing: 1fr 3fr 1fr 1fr;
 
 .demographicsRow {
   grid-template-columns: $demographicsColumnSpacing;
@@ -36,3 +37,8 @@ $demographicsColumnSpacing: 1fr 3fr;
   grid-template-columns: $diagnosticsColumnSpacing;
   gap: $columnGap;
 }
+
+.immunizationRow {
+  grid-template-columns: $immunizationColumnSpacing;
+  gap: $columnGap;
+}

query-connector/src/styles/custom-styles.scss

@@ -574,4 +574,8 @@ ul.usa-sidenav
       flex: 1 1 0%;
     }
   }
+
+  .usa-checkbox {
+    background-color: transparent;
+  }
 }