Merge pull request #101 from kbase/dev-add_retryWrites

add retryWrites

RELEASE_NOTES.txt

@@ -3,10 +3,12 @@ NARRATIVE METHOD STORE OVERVIEW
 The Narrative Method Store provides an API to dynamically access the available
 narrative method/app/type specifications and documentation.
 
-VERSION: 0.3.12 (Released TBD)
+VERSION: 0.3.12 (Released 10/28/2024)
 ------------------------------------
 
 UPDATED FEATURES:
+- The MongoDB clients have been updated to the most recent version.
+- Added the ``mongo-retrywrites`` configuration setting in ``deploy.cfg``, defaulting to ``false``.
 - Added the `exact_match_on` field to the dynamic dropdown options.
 - Changed the build system from Make / Ant to Gradle.
 

deploy.cfg

@@ -58,6 +58,10 @@ method-spec-admin-users = kbaseadmin,kbaseadmin2
 endpoint-host=https://ci.kbase.us
 endpoint-base=/services
 
+# Whether to enable ('true') the MongoDB retryWrites parameter or not (anything other than 'true').
+# See https://www.mongodb.com/docs/manual/core/retryable-writes/
+method-spec-mongo-retrywrites=false
+
 # Default tag used when tag is not specified in Narrative requests.
 # It should be changed into 'release' in production deployment.
 method-spec-default-tag = dev

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

@@ -35,6 +35,7 @@ method-spec-mongo-host = {{ default .Env.method_spec_mongo_host "localhost:27017
 method-spec-mongo-dbname = {{ default .Env.method_spec_mongo_dbname "method_store_repo_db" }}
 method-spec-mongo-user = {{ default .Env.method_spec_mongo_user "" }}
 method-spec-mongo-password = {{ default .Env.method_spec_mongo_password "" }}
+method-spec-mongo-retrywrites={{ default .Env.method_spec_mongo_retrywrites "false" }}
 method-spec-admin-users = {{ default .Env.method_spec_admin_users "kbaseadmin,kbaseadmin2" }}
 endpoint-host={{ default .Env.endpoint_host "https://ci.kbase.us" }}
 endpoint-base={{ default .Env.endpoint_base "/services" }}

src/main/java/us/kbase/narrativemethodstore/NarrativeMethodStoreServer.java

@@ -54,6 +54,7 @@ public class NarrativeMethodStoreServer extends JsonServerServlet {
     public static final String       CFG_PROP_MONGO_USER = "method-spec-mongo-user";
     public static final String   CFG_PROP_MONGO_PASSWORD = "method-spec-mongo-password";
     public static final String   CFG_PROP_MONGO_READONLY = "method-spec-mongo-readonly";
+    public static final String   CFG_PROP_MONGO_RETRY_WRITES = "method-spec-mongo-retrywrites";
     public static final String      CFG_PROP_ADMIN_USERS = "method-spec-admin-users";
     public static final String    CFG_PROP_ENDPOINT_BASE = "endpoint-base";
     public static final String    CFG_PROP_ENDPOINT_HOST = "endpoint-host";
@@ -190,6 +191,10 @@ public static synchronized LocalGitDB getLocalGitDB() throws Exception {
             String dbPwd = nullIfWhitespace(config().get(CFG_PROP_MONGO_PASSWORD));
             System.out.println(NarrativeMethodStoreServer.class.getName() + ": " + CFG_PROP_MONGO_USER +" = " + (dbUser == null ? "<not-set>" : dbUser));
             System.out.println(NarrativeMethodStoreServer.class.getName() + ": " + CFG_PROP_MONGO_PASSWORD +" = " + (dbPwd == null ? "<not-set>" : "[*****]"));
+
+            final boolean retryWrites = config().get(CFG_PROP_MONGO_RETRY_WRITES).equals("true");
+            System.out.println(NarrativeMethodStoreServer.class.getName() + ": " + CFG_PROP_MONGO_RETRY_WRITES +" = " + retryWrites);
+
             String mongoReadOnlyText = config().get(CFG_PROP_MONGO_READONLY);
             boolean mongoRO = mongoReadOnlyText != null && (mongoReadOnlyText.equals("1") || mongoReadOnlyText.equals("true") ||
                     mongoReadOnlyText.equals("y") || mongoReadOnlyText.equals("yes"));
@@ -213,7 +218,7 @@ public static synchronized LocalGitDB getLocalGitDB() throws Exception {
             System.out.println(NarrativeMethodStoreServer.class.getName() + ": " + CFG_PROP_AUTH_INSECURE +" = " +
                     (authAllowInsecure == null ? "<not-set> ('false' will be used)" : authAllowInsecure));
             localGitDB = new LocalGitDB(new URL(getGitRepo()), getGitBranch(), new File(getGitLocalDir()), getGitRefreshRate(), getCacheSize(),
-                    new MongoDynamicRepoDB(getMongoHost(), getMongoDbname(), dbUser, dbPwd, adminUsers, mongoRO),
+                    new MongoDynamicRepoDB(getMongoHost(), getMongoDbname(), dbUser, dbPwd, adminUsers, mongoRO, retryWrites),
                     new File(getTempDir()),
                     new ServiceUrlTemplateEvaluater(endpointHost, endpointBase), RepoTag.valueOf(defaultTag));
         }

src/main/java/us/kbase/narrativemethodstore/db/mongo/MongoDynamicRepoDB.java

@@ -77,11 +77,12 @@ public MongoDynamicRepoDB(
             final String dbUser,
             final String dbPwd,
             final List<String> globalAdminUserIds,
-            final boolean isReadOnly)
+            final boolean isReadOnly,
+            final boolean retryWrites)
             throws NarrativeMethodStoreException {
         this.isReadOnly = isReadOnly;
         try {
-            db = getDB(host, database, dbUser, dbPwd);
+            db = getDB(host, database, dbUser, dbPwd, retryWrites);
             if (!isReadOnly)
                 ensureIndeces();
             globalAdmins = new HashSet<String>(globalAdminUserIds);
@@ -90,9 +91,11 @@ public MongoDynamicRepoDB(
         }
     }
 
-    private MongoDatabase getDB(final String host, final String db, final String user, final String pwd) {
-        final MongoClientSettings.Builder mongoBuilder = MongoClientSettings.builder().applyToClusterSettings(
-                builder -> builder.hosts(Arrays.asList(new ServerAddress(host))));
+    private MongoDatabase getDB(final String host, final String db, final String user,
+                                final String pwd, final boolean retryWrites) {
+        final MongoClientSettings.Builder mongoBuilder = MongoClientSettings.builder()
+                .retryWrites(retryWrites)
+                .applyToClusterSettings(builder -> builder.hosts(Arrays.asList(new ServerAddress(host))));
         final MongoClient cli;
         if (user != null) {
             final MongoCredential creds = MongoCredential.createCredential(user, db, pwd.toCharArray());

src/test/java/us/kbase/test/narrativemethodstore/FullServerTest.java

@@ -1472,6 +1472,7 @@ public void debug(String arg0) {}
 		ws.add("method-spec-temp-dir", dbHelper.getWorkDir());
 		ws.add("method-spec-mongo-host", "localhost:" + dbHelper.getMongoPort());
 		ws.add("method-spec-mongo-dbname", dbName);
+		ws.add("method-spec-mongo-retrywrites", "false");
 		ws.add("method-spec-admin-users", admin1 + "," + admin2);
         ws.add("endpoint-host", "https://ci.kbase.us");
         ws.add("endpoint-base", "/services");

src/test/java/us/kbase/test/narrativemethodstore/db/mongo/MongoDynamicRepoDB2Test.java

@@ -304,6 +304,7 @@ private MongoDynamicRepoDB getDB(final List<String> admins)
                 null,
                 null,
                 admins,
+                false,
                 false);
     }
 

src/test/java/us/kbase/test/narrativemethodstore/db/mongo/MongoDynamicRepoDBTest.java

@@ -79,7 +79,7 @@ private void testRepo(boolean localFiles) throws Exception {
 
         String host = "localhost:" + dbHelper.getMongoPort();
         MongoDynamicRepoDB db = new MongoDynamicRepoDB(host, dbName, null, null, 
-                Arrays.asList(globalAdmin), false);
+                Arrays.asList(globalAdmin), false, false);
         Assert.assertEquals(0, db.listRepoModuleNames().size());
         RepoProvider pvd = localFiles ? new FileRepoProvider(new File(localPath)) :
             new GitHubRepoProvider(new URL(gitUrl), null, dbHelper.getWorkDir());
@@ -209,7 +209,7 @@ public void testPy() throws Exception {
         String globalAdmin = "admin";
         String host = "localhost:" + dbHelper.getMongoPort();
         MongoDynamicRepoDB db = new MongoDynamicRepoDB(host, dbName, null, null, 
-                Arrays.asList(globalAdmin), false);
+                Arrays.asList(globalAdmin), false, false);
         Assert.assertEquals(0, db.listRepoModuleNames().size());
         RepoProvider pvd = new FileRepoProvider(repoDir);
         db.registerRepo(userId, pvd);