Merge pull request #126 from jgi-kbase/dev-add_retryWrites

Add retryWrites

RELEASE_NOTES.md

@@ -1,5 +1,11 @@
 # Assembly Homology Service release notes
 
+## 0.1.5
+
+* The MongoDB clients have been updated to the most recent version.
+* Added the ``mongo-retrywrites`` configuration setting in ``deploy.cfg``, defaulting to
+  ``false``.
+
 ## 0.1.4
 
 * Switched the build system from Ant to Gradle. As such, all build artifacts, including the

deploy.cfg.example

@@ -10,6 +10,10 @@ mongo-db=
 mongo-user=
 mongo-pwd=
 
+# Whether to enable ('true') the MongoDB retryWrites parameter or not (anything other than 'true').
+# See https://www.mongodb.com/docs/manual/core/retryable-writes/
+mongo-retrywrites=false
+
 # A directory to use for temporary files:
 temp-dir=./assemblyhomology_temp
 

deployment/conf/.templates/deployment.cfg.templ

@@ -3,6 +3,7 @@ mongo-host={{ default .Env.mongo_host "ci-mongo" }}
 mongo-db={{ default .Env.mongo_db "assemblyhomology" }}
 mongo-user={{ default .Env.mongo_user "" }}
 mongo-pwd={{ default .Env.mongo_pwd "" }}
+mongo-retrywrites={{ default .Env.mongo_retrywrites "false" }}
 temp-dir={{ default .Env.temp_dir "./tmp_ah" }}
 minhash-timeout={{ default .Env.minhash_timeout "60" }}
 

src/main/java/us/kbase/assemblyhomology/build/AssemblyHomologyBuilder.java

@@ -80,8 +80,10 @@ public AssemblyHomologyBuilder(
 
 	private MongoClient buildMongo(final AssemblyHomologyConfig c) throws StorageInitException {
 		//TODO ZLATER MONGO handle shards & replica sets
-		final MongoClientSettings.Builder mongoBuilder = MongoClientSettings.builder().applyToClusterSettings(
-				builder -> builder.hosts(Arrays.asList(new ServerAddress(c.getMongoHost()))));
+		final MongoClientSettings.Builder mongoBuilder = MongoClientSettings.builder()
+				.retryWrites(c.getMongoRetryWrites())
+				.applyToClusterSettings(builder -> builder.hosts(
+						Arrays.asList(new ServerAddress(c.getMongoHost()))));
 		try {
 			if (c.getMongoUser().isPresent()) {
 				final MongoCredential creds = MongoCredential.createCredential(

src/main/java/us/kbase/assemblyhomology/config/AssemblyHomologyConfig.java

@@ -59,6 +59,7 @@ public class AssemblyHomologyConfig {
 	private static final String KEY_MONGO_DB = "mongo-db";
 	private static final String KEY_MONGO_USER = "mongo-user";
 	private static final String KEY_MONGO_PWD = "mongo-pwd";
+	private static final String KEY_MONGO_RETRY_WRITES = "mongo-retrywrites";
 	private static final String KEY_TEMP_DIR = "temp-dir";
 	private static final String KEY_MINHASH_TIMEOUT = "minhash-timeout";
 	private static final String KEY_IGNORE_IP_HEADERS = "dont-trust-x-ip-headers";
@@ -78,6 +79,7 @@ public class AssemblyHomologyConfig {
 	private final String mongoDB;
 	private final Optional<String> mongoUser;
 	private final Optional<char[]> mongoPwd;
+	private final boolean mongoRetryWrites;
 	private final Path tempDir;
 	private final int minhashTimeoutSec;
 	private final SLF4JAutoLogger logger;
@@ -137,6 +139,7 @@ private AssemblyHomologyConfig(
 		tempDir = Paths.get(getString(KEY_TEMP_DIR, cfg, true));
 		mongoHost = getString(KEY_MONGO_HOST, cfg, true);
 		mongoDB = getString(KEY_MONGO_DB, cfg, true);
+		mongoRetryWrites = TRUE.equals(getString(KEY_MONGO_RETRY_WRITES, cfg));
 		mongoUser = Optional.fromNullable(getString(KEY_MONGO_USER, cfg));
 		Optional<String> mongop = Optional.fromNullable(getString(KEY_MONGO_PWD, cfg));
 		if (mongoUser.isPresent() ^ mongop.isPresent()) {
@@ -328,13 +331,20 @@ public String getMongoHost() {
 		return mongoHost;
 	}
 
-	/** Ge the MongoDB database to use.
+	/** Get the MongoDB database to use.
 	 * @return the database.
 	 */
 	public String getMongoDatabase() {
 		return mongoDB;
 	}
 
+	/** Get whether the MongoDB retryWrites parameter should be set.
+	 * @return True to set the retryWrites parameter when connecting to MongoDB, false otherwise.
+	 */
+	public boolean getMongoRetryWrites() {
+		return mongoRetryWrites;
+	}
+
 	/** Get the MongoDB user name, if any. If provided a password will also be provided.
 	 * @return the user name
 	 */

src/main/java/us/kbase/assemblyhomology/service/api/Root.java

@@ -26,7 +26,7 @@ public class Root {
 	//TODO ZLATER ROOT add configurable contact email or link
 	//TODO ZLATER swagger
 
-	private static final String VERSION = "0.1.4";
+	private static final String VERSION = "0.1.5";
 	private static final String SERVER_NAME = "Assembly Homology service";
 
 	/** Return the root information.

src/test/java/us/kbase/test/assemblyhomology/config/AssemblyHomologyConfigTest.java

@@ -85,6 +85,7 @@ public void sysPropAssemHomolNoUserNoIgnoreIPNoTimeout() throws Throwable {
 		assertThat("incorrect mongo db", cfg.getMongoDatabase(), is("database"));
 		assertThat("incorrect mongo user", cfg.getMongoUser(), is(Optional.absent()));
 		assertThat("incorrect mongo pwd", cfg.getMongoPwd(), is(Optional.absent()));
+		assertThat("incorrect retry writes", cfg.getMongoRetryWrites(), is(false));
 		assertThat("incorrect minhash timeout", cfg.getMinhashTimeoutSec(), is(30));
 		assertThat("incorrect temp dir", cfg.getPathToTemporaryFileDirectory(),
 				is(Paths.get("/foo/bar/baz")));
@@ -106,6 +107,7 @@ public void sysPropKBNoUserNoIgnoreIPNoTimout() throws Throwable {
 					 "mongo-db=database\n" +
 					 "mongo-user=\n" +
 					 "mongo-pwd=\n" +
+					 "mongo-retrywrites=\n" +
 					 "minhash-timeout=\n" +
 					 "dont-trust-x-ip-headers=true1\n" +
 					 "temp-dir=/foo/bar/baz\n" +
@@ -121,6 +123,7 @@ public void sysPropKBNoUserNoIgnoreIPNoTimout() throws Throwable {
 		assertThat("incorrect mongo db", cfg.getMongoDatabase(), is("database"));
 		assertThat("incorrect mongo user", cfg.getMongoUser(), is(Optional.absent()));
 		assertThat("incorrect mongo pwd", cfg.getMongoPwd(), is(Optional.absent()));
+		assertThat("incorrect retry writes", cfg.getMongoRetryWrites(), is(false));
 		assertThat("incorrect minhash timeout", cfg.getMinhashTimeoutSec(), is(30));
 		assertThat("incorrect temp dir", cfg.getPathToTemporaryFileDirectory(),
 				is(Paths.get("/foo/bar/baz")));
@@ -143,6 +146,7 @@ public void envVarAssemHomolWithUserWithIgnoreIPWithTimeoutWithFilters() throws
 					 "mongo-db=database\n" +
 					 "mongo-user=userfoo\n" +
 					 "mongo-pwd=somepwd\n" +
+					 "mongo-retrywrites=	false	\n" +
 					 "minhash-timeout=600\n" +
 					 "dont-trust-x-ip-headers=true\n" +
 					 "temp-dir=/foo/bar/baz\n" +
@@ -164,6 +168,7 @@ public void envVarAssemHomolWithUserWithIgnoreIPWithTimeoutWithFilters() throws
 		assertThat("incorrect mongo user", cfg.getMongoUser(), is(Optional.of("userfoo")));
 		assertThat("incorrect mongo pwd", cfg.getMongoPwd().get(),
 				equalTo("somepwd".toCharArray()));
+		assertThat("incorrect retry writes", cfg.getMongoRetryWrites(), is(false));
 		assertThat("incorrect minhash timeout", cfg.getMinhashTimeoutSec(), is(600));
 		assertThat("incorrect temp dir", cfg.getPathToTemporaryFileDirectory(),
 				is(Paths.get("/foo/bar/baz")));
@@ -187,6 +192,7 @@ public void envVarKBWithUserWithIgnoreIPWithTimeout() throws Throwable {
 					 "mongo-db=database\n" +
 					 "mongo-user=userfoo\n" +
 					 "mongo-pwd=somepwd\n" +
+					 "mongo-retrywrites=true\n" +
 					 "minhash-timeout=15\n" +
 					 "dont-trust-x-ip-headers=true\n" +
 					 "temp-dir=/foo/bar/baz")
@@ -201,6 +207,7 @@ public void envVarKBWithUserWithIgnoreIPWithTimeout() throws Throwable {
 		assertThat("incorrect mongo user", cfg.getMongoUser(), is(Optional.of("userfoo")));
 		assertThat("incorrect mongo pwd", cfg.getMongoPwd().get(),
 				equalTo("somepwd".toCharArray()));
+		assertThat("incorrect retry writes", cfg.getMongoRetryWrites(), is(true));
 		assertThat("incorrect minhash timeout", cfg.getMinhashTimeoutSec(), is(15));
 		assertThat("incorrect temp dir", cfg.getPathToTemporaryFileDirectory(),
 				is(Paths.get("/foo/bar/baz")));
@@ -224,6 +231,7 @@ public void pathNoUserNoIgnoreIPStdLogger() throws Throwable {
 		assertThat("incorrect mongo db", cfg.getMongoDatabase(), is("database"));
 		assertThat("incorrect mongo user", cfg.getMongoUser(), is(Optional.absent()));
 		assertThat("incorrect mongo pwd", cfg.getMongoPwd(), is(Optional.absent()));
+		assertThat("incorrect retry writes", cfg.getMongoRetryWrites(), is(false));
 		assertThat("incorrect minhash timeout", cfg.getMinhashTimeoutSec(), is(30));
 		assertThat("incorrect temp dir", cfg.getPathToTemporaryFileDirectory(),
 				is(Paths.get("/foo/bar/baz")));
@@ -241,6 +249,7 @@ public void pathWithUserWithIgnoreIPNullLoggerWithFilters() throws Throwable {
 				 "mongo-db=database\n" +
 				 "mongo-user=userfoo\n" +
 				 "mongo-pwd=somepwd\n" +
+				 "mongo-retrywrites=true	\n" +
 				 "dont-trust-x-ip-headers=true\n" +
 				 "temp-dir=/foo/bar/baz\n" + 
 				 "filters=foo,  \t   ,   bar  \n" +
@@ -256,6 +265,7 @@ public void pathWithUserWithIgnoreIPNullLoggerWithFilters() throws Throwable {
 		assertThat("incorrect mongo user", cfg.getMongoUser(), is(Optional.of("userfoo")));
 		assertThat("incorrect mongo pwd", cfg.getMongoPwd().get(),
 				equalTo("somepwd".toCharArray()));
+		assertThat("incorrect retry writes", cfg.getMongoRetryWrites(), is(true));
 		assertThat("incorrect minhash timeout", cfg.getMinhashTimeoutSec(), is(30));
 		assertThat("incorrect temp dir", cfg.getPathToTemporaryFileDirectory(),
 				is(Paths.get("/foo/bar/baz")));

src/test/java/us/kbase/test/assemblyhomology/service/api/RootTest.java

@@ -17,7 +17,7 @@
 
 public class RootTest {
 
-	public static final String SERVER_VER = "0.1.4";
+	public static final String SERVER_VER = "0.1.5";
 	private static final String GIT_ERR = 
 			"Missing git commit file gitcommit, should be in us.kbase.assemblyhomology";