Configure database variables in dataflow

plugins/fhir_functions/fhir-init/deno.json

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+{
+  "workspace": [],
+  "nodeModulesDir": "auto",
+  "compilerOptions": {
+    "lib": [
+      "deno.window"
+    ],
+    "strict": false,
+    "experimentalDecorators": true,
+    "emitDecoratorMetadata": true
+  },
+  "imports": {
+    "axios": "npm:axios@1.7.7",
+    "./src/seed": "./src/seed.ts",
+    "./src/env": "./src/env.ts",
+    "./src/api/DbCredentialsAPI": "./src/api/DbCredentialsAPI.ts",
+    "./src/utils/credentialProcessor": "./src/utils/credentialProcessor.ts",
+    "./src/utils/type": "./src/utils/type.ts",
+    "./src/utils/request-util": "./src/utils/request-util.ts"
+  }
+}

plugins/fhir_functions/fhir-init/index.ts

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+import { seed } from "./src/seed"
+
+try {
+    await seed();
+} catch (error) {
+    console.error("FHIR init failed:", error);
+    throw error;
+}

plugins/fhir_functions/fhir-init/src/api/DbCredentialsAPI.ts

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+import { env, services } from "../env.ts";
+import { get, post } from "../utils/request-util";
+import type { IDbCreateDto, IDbDto } from "../utils/type";
+import http from "node:http";
+
+export class DbCredentialsAPI {
+  protected readonly logger = console;
+  private readonly baseURL: string;
+  private agent: any;
+  private accessToken: string;
+  private readonly oauthUrl: string;
+
+  constructor() {
+    this.accessToken = "";
+    this.oauthUrl = env.ALP_GATEWAY_OAUTH__URL;
+    this.agent = new http.Agent({ keepAlive: true });
+    if (services.trex) {
+      this.baseURL = services.trex;
+    } else {
+      this.logger.error("No url is set for DbCredentialsApi");
+      throw new Error("No url is set for DbCredentialsApi");
+    }
+  }
+
+  async getClientCredentialsToken() {
+    try {
+      const params = {
+        grant_type: "client_credentials",
+        client_id: env.IDP__ALP_DATA__CLIENT_ID,
+        client_secret: env.IDP__ALP_DATA__CLIENT_SECRET,
+      };
+
+      const options = {
+        headers: {
+          "Content-Type": "application/x-www-form-urlencoded",
+        },
+      };
+      const data = Object.keys(params)
+        .map(
+          (key) =>
+            `${encodeURIComponent(key)}=${encodeURIComponent(params[key])}`
+        )
+        .join("&");
+      const result = await post(this.oauthUrl, data, options);
+      this.accessToken = `Bearer ${result.data.access_token}`;
+      return this.accessToken;
+    } catch (error: any) {
+      console.error(`Error obtaining client credentials token: ${error.response?.data || error.message}`);
+      throw error;
+    }
+  }
+
+  private async getRequestConfig() {
+    return {
+      headers: {
+        Authorization: this.accessToken,
+      },
+    };
+  }
+
+  async getDbList(): Promise<IDbDto[]> {
+    try {
+      this.logger.info("Get database list");
+      const options = await this.getRequestConfig();
+      const url = `${this.baseURL}/trex/db/`;
+      const result = await get(url, options);
+      return result.data;
+    } catch (error) {
+      console.error(`Error while getting database list: ${error}`);
+      throw error;
+    }
+  }
+
+  async createDb(dto: IDbCreateDto) {
+    try {
+      this.logger.info("Create database");
+      const options = await this.getRequestConfig();
+      const url = `${this.baseURL}/trex/db/`;
+      const result = await post(url, dto, options);
+      return result.data;
+    } catch (error) {
+      console.error(`Error while creating database: ${error}`);
+      throw error;
+    }
+  }
+}

plugins/fhir_functions/fhir-init/src/env.ts

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+const _env = Deno.env.toObject();
+
+const certEscapeNewLine = (str: string) => {
+  return str.replace(/-----BEGIN PUBLIC KEY-----(.*?)-----END PUBLIC KEY-----/gs, (match) => {
+    return match.replace(/\n/g, "\\n");
+  });
+}
+export const env = {
+  NODE_ENV: _env.NODE_ENV,
+  FHIR_DATABASE_CODE: _env.FHIR_DATABASE_CODE,
+  SERVICE_ROUTES: _env.SERVICE_ROUTES || "{}",
+  TREX_SQL_HOST: _env.TREX__SQL__HOST,
+  TREX_SQL_PORT: _env.TREX__SQL__PORT,
+  TREX_SQL_USER: _env.TREX__SQL__USER,
+  TREX_SQL_PASSWORD: _env.TREX__SQL__PASSWORD,
+  FHIR_DB_NAME: _env.FHIR__DB_NAME,
+  ALP_GATEWAY_OAUTH__URL: _env.ALP_GATEWAY_OAUTH__URL,
+  IDP__ALP_DATA__CLIENT_ID: _env.IDP__ALP_DATA_CLIENT_ID,
+  IDP__ALP_DATA__CLIENT_SECRET: _env.IDP__ALP_DATA__CLIENT_SECRET,
+  DB_CREDENTIALS_PUBLIC_KEYS: certEscapeNewLine(_env.DB_CREDENTIALS__PUBLIC_KEYS || "").replace('}\\n', '}'),
+}
+export const services = JSON.parse(env.SERVICE_ROUTES);

plugins/fhir_functions/fhir-init/src/seed.ts

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+import { DbCredentialsAPI } from "./api/DbCredentialsAPI";
+import { env } from "./env";
+import { DbCredentialProcessor } from "./utils/credentialProcessor";
+import { AUTHENTICATION_MODES, IDbCreateDto, IDbCredential } from "./utils/type"
+
+export async function seed(): Promise<void> {
+  try {
+    let logger = console;
+    logger.info("Adding FHIR database (trex pgwire)");
+
+    const dbCredentialsAPI = new DbCredentialsAPI();
+    await dbCredentialsAPI.getClientCredentialsToken()
+
+    const dbList = await dbCredentialsAPI.getDbList();
+    const exist = dbList.find((db) => db.code === env.FHIR_DATABASE_CODE);
+    if (exist && exist.dialect === "trex") {
+      logger.info(`Database exist: ${JSON.stringify(exist)}`);
+      return;
+    }
+    if (exist) {
+      // Stale entry from the pre-trex FHIR setup (dialect "postgres");
+      // POST upserts via ON CONFLICT, replacing it with the trex pgwire entry.
+      logger.info(`Database ${env.FHIR_DATABASE_CODE} exists with dialect "${exist.dialect}" — updating to trex`);
+    }
+    const dbCredentialProcessor = new DbCredentialProcessor();
+    let credentials: IDbCredential;
+    let encryptedPasswords: IDbCredential[] = [];
+    credentials = {
+      username: env.TREX_SQL_USER,
+      password: env.TREX_SQL_PASSWORD,
+      serviceScope: "Internal",
+      salt: "",
+      userScope: "Admin"
+    }
+    encryptedPasswords.push(await dbCredentialProcessor.encryptDbCredential(credentials))
+
+    credentials = {
+      username: env.TREX_SQL_USER,
+      password: env.TREX_SQL_PASSWORD,
+      serviceScope: "Internal",
+      salt: "",
+      userScope: "Read",
+    }
+    encryptedPasswords.push(await dbCredentialProcessor.encryptDbCredential(credentials))
+
+    const db: IDbCreateDto = {
+      name: env.FHIR_DB_NAME,
+      code: env.FHIR_DATABASE_CODE,
+      vocabSchemas: [],
+      credentials: encryptedPasswords,
+      host: env.TREX_SQL_HOST,
+      port: Number(env.TREX_SQL_PORT),
+      dialect: "trex",
+      authenticationMode: AUTHENTICATION_MODES.PASSWORD,
+      extra: {
+        Internal: {
+          "queryTimeout": 60000,
+          "statementTimeout": 60000,
+        }
+      }
+    };
+    const result = await dbCredentialsAPI.createDb(db);
+    logger.info(`Database added: ${JSON.stringify(result)}`);
+    return result;
+  } catch (error: any) {
+    console.error("Error seeding database:", error.response?.data || error.message);
+    throw error;
+  }
+}