Add mybatis runtime feature (#565)

* add mybatis runtime feature

* remove run_migration task from ci

* update configs module

* remove unused variables

* remove data migration scripts

* update server core version

* update configs module

.github/workflows/ci.yml

@@ -60,10 +60,7 @@ jobs:
 
     - name: Show running services
       run: sudo netstat -tuplen # listing all the port for debug purpose.
-
-    - name: Configure migrations
-      run: chmod +x configs/assets/migrations/run_mybatis_migrations.sh && sudo ./configs/assets/migrations/run_mybatis_migrations.sh
-
+
     - name: Create multimedia dir
       run: sudo mkdir -p /opt/multimedia/patient_images && id
 

pom.xml

@@ -5,7 +5,7 @@
 
 	<artifactId>opensrp-server-core</artifactId>
 	<packaging>jar</packaging>
-	<version>2.13.5-SNAPSHOT</version>
+	<version>2.14.0-SNAPSHOT</version>
 	<name>opensrp-server-core</name>
 	<description>OpenSRP Server Core module</description>
 	<url>https://github.com/OpenSRP/opensrp-server-core</url>
@@ -327,6 +327,12 @@
 			<artifactId>log4j-core</artifactId>
 			<version>${log4j.version}</version>
 		  </dependency>
+		<!-- https://mvnrepository.com/artifact/org.mybatis/mybatis-migrations -->
+		<dependency>
+			<groupId>org.mybatis</groupId>
+			<artifactId>mybatis-migrations</artifactId>
+			<version>3.3.10</version>
+		</dependency>
 
 		<!-- Test dependencies -->
 		<dependency>
@@ -398,6 +404,14 @@
 				<directory>src/main/java/org/opensrp/repository/postgres/mapper/custom/xml</directory>
 				<targetPath>org/opensrp/repository/postgres/mapper/custom/xml</targetPath>
 			</resource>
+			<resource>
+				<directory>configs/assets/migrations/environments</directory>
+				<targetPath>mybatis/environments</targetPath>
+			</resource>
+			<resource>
+				<directory>configs/assets/migrations/scripts</directory>
+				<targetPath>mybatis/scripts</targetPath>
+			</resource>
 		</resources>
 		<plugins>
 			<plugin>

src/main/java/org/opensrp/migrations/MybatisMigration.java

@@ -0,0 +1,72 @@
+package org.opensrp.migrations;
+
+import com.google.gson.FieldNamingPolicy;
+import com.google.gson.Gson;
+import com.google.gson.GsonBuilder;
+import org.apache.ibatis.migration.DataSourceConnectionProvider;
+import org.apache.ibatis.migration.FileMigrationLoader;
+import org.apache.ibatis.migration.operations.UpOperation;
+import org.apache.ibatis.migration.options.DatabaseOperationOption;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.json.JSONObject;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.core.io.ClassPathResource;
+import org.springframework.core.io.Resource;
+import org.springframework.core.io.support.PropertiesLoaderUtils;
+import org.springframework.stereotype.Component;
+
+import javax.annotation.PostConstruct;
+import javax.sql.DataSource;
+import java.io.IOException;
+import java.nio.charset.StandardCharsets;
+import java.util.Properties;
+
+@Component
+public class MybatisMigration {
+
+	private static Logger logger = LogManager.getLogger(MybatisMigration.class.getName());
+
+	@Autowired
+	private DataSource dataSource;
+
+	private static final String CONFIG_FILE = "mybatis/environments/deployment.properties";
+
+	private static final String SCRIPTS_FOLDER = "mybatis/scripts";
+
+	@PostConstruct
+	public void initializeMybatisMigration() {
+		logger.info("Running migrations.");
+		Resource resource = new ClassPathResource(CONFIG_FILE);
+		try {
+			Properties props = PropertiesLoaderUtils.loadProperties(resource);
+			Gson gson = new GsonBuilder()
+					.setFieldNamingPolicy(FieldNamingPolicy.LOWER_CASE_WITH_UNDERSCORES)
+					.create();
+
+			JSONObject dbOperationOptionObject = new JSONObject(gson.toJson(new DatabaseOperationOption()));
+			for(String key : dbOperationOptionObject.keySet()){
+				if(props.containsKey(key)){
+					dbOperationOptionObject.put(key, props.getProperty(key));
+				}
+			}
+
+			DatabaseOperationOption databaseOperationOption = gson.fromJson(dbOperationOptionObject.toString(), DatabaseOperationOption.class);
+
+			runMigrationOperation(props, databaseOperationOption);
+
+			logger.info("Migration done.");
+		}
+		catch (IOException e) {
+			logger.error(e);
+		}
+	}
+
+	protected void runMigrationOperation(Properties props, DatabaseOperationOption databaseOperationOption) throws IOException {
+		new UpOperation().operate(
+				new DataSourceConnectionProvider(dataSource),
+				new FileMigrationLoader(new ClassPathResource(SCRIPTS_FOLDER).getFile(), StandardCharsets.UTF_8.toString(),
+						props), databaseOperationOption, System.out);
+	}
+
+}

src/test/java/org/opensrp/migrations/MybatisMigrationTest.java

@@ -0,0 +1,47 @@
+package org.opensrp.migrations;
+
+import org.apache.ibatis.migration.options.DatabaseOperationOption;
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.mockito.ArgumentCaptor;
+import org.mockito.Mockito;
+import org.mockito.junit.MockitoJUnitRunner;
+
+import java.io.IOException;
+import java.util.Properties;
+
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+
+@RunWith(MockitoJUnitRunner.class)
+public class MybatisMigrationTest {
+
+	private MybatisMigration mybatisMigration;
+
+	@Before
+	public void setUp() {
+		mybatisMigration = Mockito.spy(new MybatisMigration());
+	}
+
+	@Test
+	public void testInitializeMybatisMigrationShouldInvokeRunMigrationOperation() throws IOException {
+		Mockito.doNothing().when(mybatisMigration).runMigrationOperation(Mockito.any(Properties.class), Mockito.any(
+				DatabaseOperationOption.class));
+
+		mybatisMigration.initializeMybatisMigration();
+
+		ArgumentCaptor<Properties> propertiesArgumentCaptor = ArgumentCaptor.forClass(Properties.class);
+		ArgumentCaptor<DatabaseOperationOption> databaseOperationOptionArgumentCaptor = ArgumentCaptor.forClass(
+				DatabaseOperationOption.class);
+
+		Mockito.verify(mybatisMigration).runMigrationOperation(propertiesArgumentCaptor.capture(),
+				databaseOperationOptionArgumentCaptor.capture());
+
+		assertNotNull(databaseOperationOptionArgumentCaptor.getValue());
+		assertNotNull(propertiesArgumentCaptor.getValue());
+
+		// Has to be set to false
+		assertFalse(databaseOperationOptionArgumentCaptor.getValue().isAutoCommit());
+	}
+}

src/test/resources/test-applicationContext-opensrp.xml

@@ -24,7 +24,9 @@
 	<context:component-scan base-package="org.opensrp.config"/>
 	<context:component-scan base-package="org.opensrp.queue"/>
 	<context:component-scan base-package="org.opensrp.validator"/>
+	<context:component-scan base-package="org.opensrp.migrations"/>
 	<context:component-scan base-package="org.opensrp.service">
+
 		<!--These classes are excluded to enable the context load. This is because
 			EventsListener has EventsRouter as a dependency, problem is that IHandlerMapper
 			in EventsRouter is an interface that has its implementation in opensrp-register