Use env vars for mongo creds

Author: josemduarte

eppic-dbtools/src/main/java/eppic/db/loaders/FindIfNewUniProt.java

@@ -93,7 +93,7 @@ public static void main(String[] args) throws IOException, ExecutionException, I
             dbName = propsReader.getDbName();
         }
 
-        MongoDatabase mongoDb = MongoUtils.getMongoDatabase(dbName, connUri);
+        MongoDatabase mongoDb = MongoUtils.getMongoDatabase(dbName, connUri, MongoUtils.MONGO_USER_ENV_VAR, MongoUtils.MONGO_PASSWORD_ENV_VAR);
 
         String dbVersion = null;
 

eppic-dbtools/src/main/java/eppic/db/loaders/FindPdbIdsToLoad.java

@@ -150,7 +150,7 @@ public static void main(String[] args) throws IOException, ExecutionException, I
             dbName = propsReader.getDbName();
         }
 
-        MongoDatabase mongoDb = MongoUtils.getMongoDatabase(dbName, connUri);
+        MongoDatabase mongoDb = MongoUtils.getMongoDatabase(dbName, connUri, MongoUtils.MONGO_USER_ENV_VAR, MongoUtils.MONGO_PASSWORD_ENV_VAR);
 
         if (full) {
             // remove content and create collections and index

eppic-dbtools/src/main/java/eppic/db/loaders/RemoveUserJobs.java

@@ -79,7 +79,7 @@ public static void main(String[] args) throws IOException, DaoException {
 		String dbName = propsReader.getDbNameUserJobs();
 
 		logger.info("Will use db name {}", dbName);
-		MongoDatabase mongoDb = MongoUtils.getMongoDatabase(dbName, connUri);
+		MongoDatabase mongoDb = MongoUtils.getMongoDatabase(dbName, connUri, MongoUtils.MONGO_USERJOBS_USER_ENV_VAR, MongoUtils.MONGO_USERJOBS_PASSWORD_ENV_VAR);
 
 		dao = new PDBInfoDAOMongo(mongoDb);
 		interfResDao = new InterfaceResidueFeaturesDAOMongo(mongoDb);

eppic-dbtools/src/main/java/eppic/db/loaders/UploadSearchSeqCacheToDb.java

@@ -102,7 +102,7 @@ public static void main(String[] args) throws IOException, InterruptedException
         DbPropertiesReader propsReader = new DbPropertiesReader(configFile);
         String connUri = propsReader.getMongoUri();
 
-        MongoDatabase mongoDb = MongoUtils.getMongoDatabase(propsReader.getDbName(), connUri);
+        MongoDatabase mongoDb = MongoUtils.getMongoDatabase(propsReader.getDbName(), connUri, MongoUtils.MONGO_USER_ENV_VAR, MongoUtils.MONGO_PASSWORD_ENV_VAR);
 
         HitHspDAO hitHspDAO = new HitHspDAOMongo(mongoDb);
 

eppic-dbtools/src/main/java/eppic/db/loaders/UploadToDb.java

@@ -157,7 +157,7 @@ public static void main(String[] args) throws ExecutionException, InterruptedExc
 			dbName = propsReader.getDbNameUserJobs();
 
 		logger.info("Will use db name {}", dbName);
-		MongoDatabase mongoDb = MongoUtils.getMongoDatabase(dbName, connUri);
+		MongoDatabase mongoDb = MongoUtils.getMongoDatabase(dbName, connUri, MongoUtils.MONGO_USER_ENV_VAR, MongoUtils.MONGO_PASSWORD_ENV_VAR);
 
 		dao = new PDBInfoDAOMongo(mongoDb);
 		interfResDao = new InterfaceResidueFeaturesDAOMongo(mongoDb);

eppic-dbtools/src/main/java/eppic/db/loaders/UploadUniprotInfoToDb.java

@@ -111,7 +111,7 @@ public static void main(String[] args) throws IOException, InterruptedException
         DbPropertiesReader propsReader = new DbPropertiesReader(configFile);
         String connUri = propsReader.getMongoUri();
 
-        MongoDatabase mongoDb = MongoUtils.getMongoDatabase(propsReader.getDbName(), connUri);
+        MongoDatabase mongoDb = MongoUtils.getMongoDatabase(propsReader.getDbName(), connUri, MongoUtils.MONGO_USER_ENV_VAR, MongoUtils.MONGO_PASSWORD_ENV_VAR);
 
         if (full) {
             logger.info("FULL mode: dropping collection and recreating index");

eppic-dbtools/src/main/java/eppic/db/mongoutils/MongoSettings.java

@@ -9,7 +9,7 @@ public class MongoSettings {
 
     public MongoSettings(String dbName, String connUri) {
         this.dbName = dbName;
-        mongoDatabase = MongoUtils.getMongoDatabase(dbName, connUri);
+        mongoDatabase = MongoUtils.getMongoDatabase(dbName, connUri, MongoUtils.MONGO_USER_ENV_VAR, MongoUtils.MONGO_PASSWORD_ENV_VAR);
     }
 
     public MongoDatabase getMongoDatabase() {

eppic-dbtools/src/main/java/eppic/db/mongoutils/MongoUtils.java

@@ -16,10 +16,13 @@
 import javax.persistence.Index;
 import javax.persistence.Table;
 
+import java.net.URLEncoder;
+import java.nio.charset.StandardCharsets;
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
+import java.util.regex.Pattern;
 import java.util.stream.Collectors;
 
 import static com.mongodb.client.model.Indexes.ascending;
@@ -29,6 +32,12 @@ public class MongoUtils {
 
     private static final Logger logger = LoggerFactory.getLogger(MongoUtils.class);
 
+    public static final String MONGO_USER_ENV_VAR = "MONGO_USER";
+    public static final String MONGO_PASSWORD_ENV_VAR = "MONGO_PWD";
+    public static final String MONGO_USERJOBS_USER_ENV_VAR = "MONGO_USERJOBS_USER";
+    public static final String MONGO_USERJOBS_PASSWORD_ENV_VAR = "MONGO_USERJOBS_PWD";
+
+
     /**
      * Writes a single {@link Object} to a {@param collectionName} collection in the given {@param mongoDatabase}.
      *
@@ -81,7 +90,25 @@ public static Document convertValueToDocument(Object o) {
      * @param connUriStr the Mongo connection URI
      * @return {@link com.mongodb.client.MongoDatabase} database
      */
-    public static MongoDatabase getMongoDatabase(String dbName, String connUriStr) {
+    public static MongoDatabase getMongoDatabase(String dbName, String connUriStr, String mongoUserEnv, String mongoPasswordEnv) {
+
+        int numPlaceHolders = (int) Pattern.compile("%s").matcher(connUriStr).results().count();
+        if (numPlaceHolders != 2) {
+            logger.error("Mongo connection URI string [ {} ] does not contain exactly 2 placeholders. " +
+                    "Please check dw.db.connection.uri property", connUriStr);
+            throw new IllegalArgumentException("Mongo connection URI string does not contain exactly 2 placeholders");
+        }
+
+        String mongoUser = System.getenv(mongoUserEnv);
+        String mongoPassword = System.getenv(mongoPasswordEnv);
+        if (mongoUser == null || mongoUser.isBlank() || mongoPassword == null || mongoPassword.isBlank()) {
+            logger.error("Mongo user or password is not defined. Please set environment variable {} and {}", mongoUserEnv, mongoPasswordEnv);
+            throw new IllegalArgumentException(String.format("Mongo user or password is not defined. Please set environment variable %s and %s", mongoUserEnv, mongoPasswordEnv));
+        }
+        // whatever goes into the Mongo URI must be url encoded so that the URI is valid. Otherwise chars with a special URL semantic (which can typically appear in passwords) would break the URI
+        mongoUser = URLEncoder.encode(mongoUser, StandardCharsets.UTF_8);
+        mongoPassword = URLEncoder.encode(mongoPassword, StandardCharsets.UTF_8);
+        connUriStr = String.format(connUriStr, mongoUser, mongoPassword);
 
         MongoClient mongoClient;
         try {

eppic-rest/src/main/java/eppic/rest/service/JobService.java

@@ -71,8 +71,8 @@ public JobService(EppicRestProperties eppicRestProperties) {
 
     private void initDaos() {
 
-        MongoDatabase mongoDb = MongoUtils.getMongoDatabase(eppicRestProperties.getDbName(), eppicRestProperties.getMongoUri());
-        MongoDatabase mongoDbUserJobs = MongoUtils.getMongoDatabase(eppicRestProperties.getDbNameUserjobs(), eppicRestProperties.getMongoUriUserjobs());
+        MongoDatabase mongoDb = MongoUtils.getMongoDatabase(eppicRestProperties.getDbName(), eppicRestProperties.getMongoUri(), MongoUtils.MONGO_USER_ENV_VAR, MongoUtils.MONGO_PASSWORD_ENV_VAR);
+        MongoDatabase mongoDbUserJobs = MongoUtils.getMongoDatabase(eppicRestProperties.getDbNameUserjobs(), eppicRestProperties.getMongoUriUserjobs(), MongoUtils.MONGO_USERJOBS_USER_ENV_VAR, MongoUtils.MONGO_USERJOBS_PASSWORD_ENV_VAR);
 
         pdbInfoDAO = new PDBInfoDAOMongo(mongoDb);
         featuresDAO = new InterfaceResidueFeaturesDAOMongo(mongoDb);

eppic-rest/src/main/java/eppic/rest/service/SubmitService.java

@@ -94,7 +94,7 @@ private void init() {
 
         logger.info("Initialised email data: {}", emailData);
 
-        mongoDbUserJobs = MongoUtils.getMongoDatabase(eppicRestProperties.getDbNameUserjobs(), eppicRestProperties.getMongoUriUserjobs());
+        mongoDbUserJobs = MongoUtils.getMongoDatabase(eppicRestProperties.getDbNameUserjobs(), eppicRestProperties.getMongoUriUserjobs(), MongoUtils.MONGO_USERJOBS_USER_ENV_VAR, MongoUtils.MONGO_USERJOBS_PASSWORD_ENV_VAR);
     }
 
     /**