separated code that depends only on the core driver

JaneliaSciComp · Aug 7, 2024 · b0bafa9 · b0bafa9
1 parent 9028e26
commit b0bafa9
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Showing 5 changed files with 68 additions and 47 deletions.
diff --git a/colormipsearch-persist/src/main/java/org/janelia/colormipsearch/dao/DaosProvider.java b/colormipsearch-persist/src/main/java/org/janelia/colormipsearch/dao/DaosProvider.java
@@ -11,7 +11,7 @@
 import org.janelia.colormipsearch.dao.mongo.PPPmURLsMongoDao;
 import org.janelia.colormipsearch.dao.mongo.PublishedLMImageMongoDao;
 import org.janelia.colormipsearch.dao.mongo.PublishedURLsMongoDao;
-import org.janelia.colormipsearch.dao.mongo.support.MongoDBHelper;
+import org.janelia.colormipsearch.dao.mongo.support.MongoClientProvider;
 import org.janelia.colormipsearch.model.AbstractNeuronEntity;
 import org.janelia.colormipsearch.model.AbstractSessionEntity;
 import org.janelia.colormipsearch.model.CDMatchEntity;
@@ -34,7 +34,8 @@ public static synchronized DaosProvider getInstance(Config config) {
     private final IdGenerator idGenerator;
 
     private DaosProvider(Config config) {
-        MongoClient mongoClient = MongoDBHelper.createMongoClient(config.getStringPropertyValue("MongoDB.ConnectionURL"),
+        MongoClient mongoClient = MongoClientProvider.createMongoClient(
+                config.getStringPropertyValue("MongoDB.ConnectionURL"),
                 config.getStringPropertyValue("MongoDB.Server"),
                 config.getStringPropertyValue("MongoDB.AuthDatabase"),
                 config.getStringPropertyValue("MongoDB.Username"),
@@ -48,7 +49,7 @@ private DaosProvider(Config config) {
                 config.getIntegerPropertyValue("MongoDB.MaxConnectionIdleSecs", 0),
                 config.getIntegerPropertyValue("MongoDB.MaxConnectionLifeSecs", 0)
         );
-        this.mongoDatabase = MongoDBHelper.createMongoDatabase(mongoClient, config.getStringPropertyValue("MongoDB.Database"));
+        this.mongoDatabase = MongoClientProvider.createMongoDatabase(mongoClient, config.getStringPropertyValue("MongoDB.Database"));
         this.idGenerator = new TimebasedIdGenerator(config.getIntegerPropertyValue("TimebasedId.Context", 0));
     }
 

diff --git a/...rsist/src/main/java/org/janelia/colormipsearch/dao/mongo/support/MongoClientProvider.java b/...rsist/src/main/java/org/janelia/colormipsearch/dao/mongo/support/MongoClientProvider.java
@@ -0,0 +1,40 @@
+package org.janelia.colormipsearch.dao.mongo.support;
+
+import com.mongodb.MongoClientSettings;
+import com.mongodb.client.MongoClient;
+import com.mongodb.client.MongoClients;
+import com.mongodb.client.MongoDatabase;
+
+public class MongoClientProvider {
+
+    public static MongoClient createMongoClient(
+            String mongoConnectionURL,
+            String mongoServer,
+            String mongoAuthDatabase,
+            String mongoUsername,
+            String mongoPassword,
+            String mongoReplicaSet,
+            boolean useSSL,
+            int connectionsPerHost,
+            int connectTimeoutInMillis,
+            int maxConnecting,
+            int maxWaitTimeInSecs,
+            int maxConnectionIdleTimeInSecs,
+            int maxConnLifeTimeInSecs) {
+        return createMongoClient(
+                MongoSettingsProvider.prepareMongoSettings(
+                    mongoConnectionURL, mongoServer, mongoAuthDatabase, mongoUsername, mongoPassword, mongoReplicaSet, useSSL,
+                    connectionsPerHost, connectTimeoutInMillis, maxConnecting, maxWaitTimeInSecs, maxConnectionIdleTimeInSecs, maxConnLifeTimeInSecs
+                )
+        );
+    }
+
+    public static MongoClient createMongoClient(MongoClientSettings clientSettings) {
+        return MongoClients.create(clientSettings);
+    }
+
+    public static MongoDatabase createMongoDatabase(MongoClient mongoClient, String mongoDatabaseName) {
+        return mongoClient.getDatabase(mongoDatabaseName);
+    }
+
+}
diff --git a/...arch/dao/mongo/support/MongoDBHelper.java → .../mongo/support/MongoSettingsProvider.java b/...arch/dao/mongo/support/MongoDBHelper.java → .../mongo/support/MongoSettingsProvider.java
@@ -15,9 +15,6 @@
 import com.mongodb.ReadPreference;
 import com.mongodb.ServerAddress;
 import com.mongodb.WriteConcern;
-import com.mongodb.client.MongoClient;
-import com.mongodb.client.MongoClients;
-import com.mongodb.client.MongoDatabase;
 
 import org.apache.commons.lang3.StringUtils;
 import org.bson.codecs.configuration.CodecRegistries;
@@ -26,11 +23,11 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-public class MongoDBHelper {
+public class MongoSettingsProvider {
 
-    private static final Logger LOG = LoggerFactory.getLogger(MongoDBHelper.class);
+    private static final Logger LOG = LoggerFactory.getLogger(MongoSettingsProvider.class);
 
-    public static MongoClient createMongoClient(
+    public static MongoClientSettings prepareMongoSettings(
             String mongoConnectionURL,
             String mongoServer,
             String mongoAuthDatabase,
@@ -44,7 +41,7 @@ public static MongoClient createMongoClient(
             int maxWaitTimeInSecs,
             int maxConnectionIdleTimeInSecs,
             int maxConnLifeTimeInSecs) {
-        CodecRegistry codecRegistry = RegistryHelper.createCodecRegistry();
+        CodecRegistry codecRegistry = createCodecRegistry();
         MongoClientSettings.Builder mongoClientSettingsBuilder = MongoClientSettings.builder()
                 .codecRegistry(CodecRegistries.fromRegistries(
                         MongoClientSettings.getDefaultCodecRegistry(),
@@ -101,14 +98,28 @@ public static MongoClient createMongoClient(
             char[] passwordChars = StringUtils.isBlank(mongoPassword) ? null : mongoPassword.toCharArray();
             mongoClientSettingsBuilder.credential(MongoCredential.createCredential(mongoUsername, mongoAuthDatabase, passwordChars));
         }
-        return MongoClients.create(mongoClientSettingsBuilder.build());
+
+        return mongoClientSettingsBuilder.build();
     }
 
-    public static MongoDatabase createMongoDatabase(MongoClient mongoClient, String mongoDatabaseName) {
-        return mongoClient.getDatabase(mongoDatabaseName);
+    private static CodecRegistry createCodecRegistry() {
+        ObjectMapper objectMapper = createMongoObjectMapper();
+
+        return CodecRegistries.fromRegistries(
+                CodecRegistries.fromCodecs(
+                        new BigIntegerCodec(),
+                        new FileDataCodec(objectMapper)
+                ),
+                CodecRegistries.fromProviders(
+                        new EnumCodecProvider()
+                ),
+                CodecRegistries.fromProviders(
+                        new JacksonCodecProvider(objectMapper)
+                )
+        );
     }
 
-    static ObjectMapper createMongoObjectMapper() {
+    private static ObjectMapper createMongoObjectMapper() {
         SimpleFilterProvider filterProvider = new SimpleFilterProvider();
         filterProvider.addFilter(MongoIgnoredFieldFilter.FILTER_NAME, new MongoIgnoredFieldFilter());
         return new ObjectMapper()

diff --git a/...ch-persist/src/main/java/org/janelia/colormipsearch/dao/mongo/support/RegistryHelper.java b/...ch-persist/src/main/java/org/janelia/colormipsearch/dao/mongo/support/RegistryHelper.java
diff --git a/pom.xml b/pom.xml
@@ -330,13 +330,13 @@
             <dependency>
                 <groupId>org.mongodb</groupId>
                 <artifactId>mongodb-driver-sync</artifactId>
-                <version>5.0.1</version>
+                <version>5.1.2</version>
             </dependency>
 
             <dependency>
                 <groupId>org.mongodb</groupId>
                 <artifactId>bson</artifactId>
-                <version>5.0.1</version>
+                <version>5.1.2</version>
             </dependency>
 
             <!-- Testing -->