fix: get mongodb url and database name from MONGODB_URI variable

Author: martin-trajanovski

.env.example

@@ -34,6 +34,4 @@ SITE=<SITE>
 SMTP_HOST=<SMTP_HOST>
 SMTP_MESSAGE_FROM=<SMTP_MESSAGE_FROM>
 SMTP_PORT=<SMTP_PORT>
-SMTP_SECURE=<SMTP_SECURE>
-DB_MIGRATE_MONGODB_URL="mongodb://<HOST>:<PORT>"
-DB_MIGRATE_DATABASE_NAME="<DATABASE_NAME>"
+SMTP_SECURE=<SMTP_SECURE>

README.md

@@ -108,7 +108,7 @@ Valid environment variables for the .env file. See [.env.example](/.env.example)
 
 Where the [current SciCat Backend](https://github.com/SciCatProject/backend) accepts id fields in the database named `pid`, `doi`, or similar, this implementation requires there to be an id field of the form `_id` on every document. It is therefore necessary to run a database migration script towards MongoDB instance from a place where you have access to it and can install `migrate-mongo` package.
 
-All database [migration scripts](https://github.com/SciCatProject/scicat-backend-next/tree/master/migrations) located in the [migrations](/migrations/) folder. Copy these together with [`migrate-mongo-config.js`](https://github.com/SciCatProject/scicat-backend-next/blob/master/migrate-mongo-config.js) file to a location were you can access your MongoDB instance and have `migrate-mongo` package installed either globally(which is preferred) or locally if global installation is not possible. Then modify the config file to contain your MongoDB instance details like database name and url. Once modified, start the migration by running
+All database [migration scripts](https://github.com/SciCatProject/scicat-backend-next/tree/master/migrations) located in the [migrations](/migrations/) folder. To start the migration use:
 
 ```sh
 npm run migrate:db:up

migrate-mongo-config.js

@@ -1,19 +1,27 @@
 // In this file you can configure migrate-mongo
+const MONGODB_URI = require("dotenv").config().parsed.MONGODB_URI;
+
+if (!MONGODB_URI) {
+  throw new Error("Environment variable MONGODB_URI not set");
+}
+
+const lastSlashIndex = MONGODB_URI.lastIndexOf("/");
+// NOTE: Get the database url and name from the MONGODB_URI and use them instead of defining new variables.
+const DATABASE_URL = MONGODB_URI.substring(0, lastSlashIndex);
+const DATABASE_NAME = MONGODB_URI.substring(lastSlashIndex + 1);
 
 const config = {
   mongodb: {
-    // TODO Change (or review) the url to your MongoDB:
-    url: process.env.DB_MIGRATE_MONGODB_URL,
+    url: DATABASE_URL,
 
-    // TODO Change this to your database name:
-    databaseName: process.env.DB_MIGRATE_DATABASE_NAME,
+    databaseName: DATABASE_NAME,
 
     options: {
       useNewUrlParser: true, // removes a deprecation warning when connecting
       useUnifiedTopology: true, // removes a deprecating warning when connecting
       //   connectTimeoutMS: 3600000, // increase connection timeout to 1 hour
       //   socketTimeoutMS: 3600000, // increase socket timeout to 1 hour
-    }
+    },
   },
 
   // The migrations dir, can be an relative or absolute path. Only edit this when really necessary.
@@ -22,15 +30,15 @@ const config = {
   // The mongodb collection where the applied changes are stored. Only edit this when really necessary.
   changelogCollectionName: "changelog",
 
-  // The file extension to create migrations and search for in migration dir 
+  // The file extension to create migrations and search for in migration dir
   migrationFileExtension: ".js",
 
   // Enable the algorithm to create a checksum of the file contents and use that in the comparison to determine
   // if the file should be run.  Requires that scripts are coded to be run multiple times.
   useFileHash: false,
 
   // Don't change this, unless you know what you're doing
-  moduleSystem: 'commonjs',
+  moduleSystem: "commonjs",
 };
 
 module.exports = config;

package.json

@@ -10,8 +10,8 @@
     "prebuild": "rimraf dist",
     "build": "nest build",
     "format": "prettier --write \"src/**/*.ts\" \"test/**/*.ts\"",
-    "migrate:db:up": "node ./scripts/setVariables.js && node ./node_modules/migrate-mongo/bin/migrate-mongo.js up",
-    "migrate:db:down": "node ./scripts/setVariables.js && node ./node_modules/migrate-mongo/bin/migrate-mongo.js down",
+    "migrate:db:up": "node ./node_modules/migrate-mongo/bin/migrate-mongo.js up",
+    "migrate:db:down": "node ./node_modules/migrate-mongo/bin/migrate-mongo.js down",
     "start": "nest start",
     "start:dev": "nest start --watch",
     "start:debug": "nest start --debug --watch",