Add schema initialization

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/partition/PartitionLookupSvcImpl.java

@@ -88,7 +88,6 @@ public class PartitionLookupSvcImpl implements IPartitionLookupSvc {
 				myPartitionDao.save(partitionEntity);
 			}
 		});
-
 	}
 
 	@Override

hapi-fhir-jpaserver-batch/pom.xml

@@ -18,7 +18,7 @@
 	<dependencies>
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
-			<artifactId>hapi-fhir-server-empi</artifactId>
+			<artifactId>hapi-fhir-jpaserver-migrate</artifactId>
 			<version>${project.version}</version>
 		</dependency>
 		<dependency>

hapi-fhir-jpaserver-batch/src/main/java/ca/uhn/fhir/jpa/batch/config/BatchConfig.java

@@ -1,24 +0,0 @@
-package ca.uhn.fhir.jpa.batch.config;
-
-import ca.uhn.fhir.jpa.batch.svc.DummyService;
-import org.springframework.batch.core.configuration.annotation.BatchConfigurer;
-import org.springframework.batch.core.configuration.annotation.EnableBatchProcessing;
-import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.Configuration;
-
-@Configuration
-@EnableBatchProcessing
-public class BatchConfig {
-
-	@Bean
-	public DummyService dummyService() {
-		return new DummyService();
-	}
-
-	@Bean
-	public BatchConfigurer jpaBatchConfigurer() {
-		return new JpaBatchConfigurer();
-	}
-
-
-}

hapi-fhir-jpaserver-batch/src/main/java/ca/uhn/fhir/jpa/batch/config/JpaBatchConfigurer.java

@@ -2,17 +2,22 @@ package ca.uhn.fhir.jpa.batch.config;
 
 import org.springframework.batch.core.configuration.annotation.DefaultBatchConfigurer;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.stereotype.Component;
 import org.springframework.transaction.PlatformTransactionManager;
-
+/*//
 @Component
 public class JpaBatchConfigurer extends DefaultBatchConfigurer {
 
 	@Autowired
-	private PlatformTransactionManager myPlatformTransactionManager;
+	@Qualifier
+	private JpaTransactionManager myPlatformTransactionManager;
 
 	@Override
 	public PlatformTransactionManager getTransactionManager() {
 		return myPlatformTransactionManager;
 	}
+
 }
+*/

hapi-fhir-jpaserver-batch/src/test/java/ca/uhn/fhir/jpa/batch/BaseBatchR4Test.java

@@ -2,8 +2,9 @@ package ca.uhn.fhir.jpa.batch;
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
-import ca.uhn.fhir.jpa.batch.config.BatchConfig;
+import ca.uhn.fhir.jpa.batch.config.BaseTestBatchConfig;
 import ca.uhn.fhir.jpa.batch.svc.DummyService;
+import ca.uhn.fhir.jpa.config.TestJpaR4Config;
 import ca.uhn.fhir.jpa.dao.index.IdHelperService;
 import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
 import org.hl7.fhir.r4.model.Patient;
@@ -11,17 +12,26 @@ import org.hl7.fhir.r4.model.Person;
 import org.hl7.fhir.r4.model.Practitioner;
 import org.junit.runner.RunWith;
 import org.slf4j.Logger;
+import org.springframework.batch.core.Job;
+import org.springframework.batch.core.launch.JobLauncher;
+import org.springframework.batch.test.JobLauncherTestUtils;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.SpringRunner;
+import org.springframework.transaction.PlatformTransactionManager;
+
+import javax.annotation.PostConstruct;
 
 import static org.slf4j.LoggerFactory.getLogger;
 
 @RunWith(SpringRunner.class)
-@ContextConfiguration(classes = {BatchConfig.class})
+@ContextConfiguration(classes = {BaseTestBatchConfig.class, TestJpaR4Config.class})
 abstract public class BaseBatchR4Test extends BaseJpaR4Test {
  	private static final Logger ourLog = getLogger(BaseBatchR4Test.class);
 
+ 	@Autowired
+	protected PlatformTransactionManager myPlatformTransactionManager;
+
 	@Autowired
 	protected FhirContext myFhirContext;
 	@Autowired
@@ -34,4 +44,9 @@ abstract public class BaseBatchR4Test extends BaseJpaR4Test {
 	protected IdHelperService myIdHelperService;
 	@Autowired
 	protected DummyService myDummyService;
+	@Autowired
+	protected JobLauncher myJobLauncher;
+	@Autowired
+	protected Job myJob;
+
 }

hapi-fhir-jpaserver-batch/src/test/java/ca/uhn/fhir/jpa/batch/config/BaseTestBatchConfig.java

@@ -1,8 +1,57 @@
 package ca.uhn.fhir.jpa.batch.config;
 
+import ca.uhn.fhir.jpa.batch.svc.DummyService;
+import ca.uhn.fhir.jpa.config.TestJpaConfig;
+import org.springframework.batch.core.Job;
+import org.springframework.batch.core.Step;
+import org.springframework.batch.core.configuration.annotation.DefaultBatchConfigurer;
+import org.springframework.batch.core.configuration.annotation.EnableBatchProcessing;
+import org.springframework.batch.core.configuration.annotation.JobBuilderFactory;
+import org.springframework.batch.core.configuration.annotation.StepBuilderFactory;
+import org.springframework.batch.repeat.RepeatStatus;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
+import org.springframework.orm.jpa.JpaTransactionManager;
+import org.springframework.transaction.PlatformTransactionManager;
 
 @Configuration
-public class BaseTestBatchConfig {
+@EnableBatchProcessing
+public class BaseTestBatchConfig extends DefaultBatchConfigurer {
 
+	@Autowired
+	private JpaTransactionManager myPlatformTransactionManager;
+
+
+	@Autowired
+	private JobBuilderFactory myJobBuilderFactory;
+
+	@Autowired
+	private StepBuilderFactory myStepBuilderFactory;
+
+
+	@Override
+	public PlatformTransactionManager getTransactionManager() {
+		return myPlatformTransactionManager;
+	}
+
+	@Bean
+	public DummyService myDummyService() {
+		return new DummyService();
+	}
+
+	@Bean
+	public Job testJob() {
+		return myJobBuilderFactory.get("testJob")
+			.start(testStep())
+			.build();
+	}
+
+	@Bean
+	public Step testStep() {
+		return myStepBuilderFactory.get("testStep").tasklet((theStepContribution, theChunkContext) -> {
+			System.out.println("woo!");
+			return RepeatStatus.FINISHED;
+		}).build();
+	}
 }

hapi-fhir-jpaserver-batch/src/test/java/ca/uhn/fhir/jpa/batch/svc/BatchSvcTest.java

@@ -2,11 +2,17 @@ package ca.uhn.fhir.jpa.batch.svc;
 
 import ca.uhn.fhir.jpa.batch.BaseBatchR4Test;
 import org.junit.Test;
+import org.springframework.batch.core.JobParameters;
+import org.springframework.batch.core.JobParametersInvalidException;
+import org.springframework.batch.core.repository.JobExecutionAlreadyRunningException;
+import org.springframework.batch.core.repository.JobInstanceAlreadyCompleteException;
+import org.springframework.batch.core.repository.JobRestartException;
 
 public class BatchSvcTest extends BaseBatchR4Test {
 
 	@Test
-	public void testApplicationContextLoads(){
+	public void testApplicationContextLoads() throws JobParametersInvalidException, JobExecutionAlreadyRunningException, JobRestartException, JobInstanceAlreadyCompleteException {
 		myDummyService.test();
+		myJobLauncher.run(myJob, new JobParameters());
 	}
 }

hapi-fhir-jpaserver-batch/src/test/resources/logback-test.xml

@@ -1,7 +1,7 @@
 <configuration>
 	<appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
 		<filter class="ch.qos.logback.classic.filter.ThresholdFilter">
-			<level>TRACE</level>
+			<level>INFO</level>
 		</filter>
 		<encoder>
 			<pattern>%d{yyyy-MM-dd HH:mm:ss.SSS} [%thread] %-5level %logger{36} [%file:%line] %msg%n</pattern>
@@ -48,7 +48,7 @@
 		<appender-ref ref="STDOUT" />
 	</logger>
 	<appender name="BATCH_TROUBLESHOOTING" class="ch.qos.logback.core.rolling.RollingFileAppender">
-		<filter class="ch.qos.logback.classic.filter.ThresholdFilter"><level>DEBUG</level></filter>
+		<filter class="ch.qos.logback.classic.filter.ThresholdFilter"><level>INFO</level></filter>
 		<file>${smile.basedir}/log/batch-troubleshooting.log</file>
 		<rollingPolicy class="ch.qos.logback.core.rolling.FixedWindowRollingPolicy">
 			<fileNamePattern>${smile.basedir}/log/batch-troubleshooting.log.%i.gz</fileNamePattern>

hapi-fhir-jpaserver-migrate/pom.xml

@@ -42,6 +42,12 @@
 			<artifactId>hapi-fhir-jpaserver-base</artifactId>
 			<version>${project.version}</version>
 		</dependency>
+		<!-- Need this for the schema files from spring batch -->
+		<dependency>
+			<groupId>org.springframework.batch</groupId>
+			<artifactId>spring-batch-core</artifactId>
+			<version>4.2.2.RELEASE</version>
+		</dependency>
 
 		<!-- Test Database -->
 		<dependency>

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/providers/SpringBatchSchemaMigrationProvider.java

@@ -0,0 +1,35 @@
+package ca.uhn.fhir.jpa.migrate.providers;
+
+import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
+import ca.uhn.fhir.jpa.migrate.tasks.SchemaInitializationProvider;
+import com.google.common.collect.Maps;
+
+import javax.annotation.Nonnull;
+import java.util.Map;
+
+public class SpringBatchSchemaMigrationProvider extends SchemaInitializationProvider {
+
+	private static final Map<DriverTypeEnum, String> ourBatchDriverMap;
+
+	static {
+		ourBatchDriverMap = Maps.newHashMap();
+		ourBatchDriverMap.put(DriverTypeEnum.H2_EMBEDDED, "schema-h2.sql");
+		ourBatchDriverMap.put(DriverTypeEnum.DERBY_EMBEDDED, "schema-derby.sql");
+		ourBatchDriverMap.put(DriverTypeEnum.MARIADB_10_1, "schema-mysql.sql");//not sure if correct
+		ourBatchDriverMap.put(DriverTypeEnum.MYSQL_5_7, "schema-mysql.sql");//not sure if correct
+		ourBatchDriverMap.put(DriverTypeEnum.POSTGRES_9_4, "schema-postgresql.sql");
+		ourBatchDriverMap.put(DriverTypeEnum.ORACLE_12C, "schema-oracle10g.sql");//not sure if correct
+		ourBatchDriverMap.put(DriverTypeEnum.MSSQL_2012, "schema-mysql.sql");//not sure if correct
+	}
+
+	public SpringBatchSchemaMigrationProvider() {
+		super("Spring Batch", "/org/springframework/batch/core", "BATCH_JOB_INSTANCE");
+
+	}
+
+	@Nonnull
+	@Override
+	protected String getInitScript(DriverTypeEnum theDriverType) {
+		return ourBatchDriverMap.get(theDriverType);
+	}
+}

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java

@@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.migrate.tasks;
  */
 
 import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
+import ca.uhn.fhir.jpa.migrate.providers.SpringBatchSchemaMigrationProvider;
 import ca.uhn.fhir.jpa.migrate.taskdef.AddColumnTask;
 import ca.uhn.fhir.jpa.migrate.taskdef.ArbitrarySqlTask;
 import ca.uhn.fhir.jpa.migrate.taskdef.BaseTableColumnTypeTask;
@@ -103,6 +104,8 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
 
 
 		empiLink.addIndex("20200517.5", "IDX_EMPI_PERSON_TGT").unique(true).withColumns("PERSON_PID", "TARGET_PID");
+
+		version.initializeSchema("20200526.1", "Spring Batch", new SpringBatchSchemaMigrationProvider());
 	}
 
 	protected void init500() { // 20200218 - 20200519

hapi-fhir-jpaserver-migrate/src/test/java/ca/uhn/fhir/jpa/migrate/taskdef/InitializeSchemaTaskTest.java

@@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.migrate.taskdef;
 
 import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
 import ca.uhn.fhir.jpa.migrate.JdbcUtils;
+import ca.uhn.fhir.jpa.migrate.providers.SpringBatchSchemaMigrationProvider;
 import ca.uhn.fhir.jpa.migrate.tasks.api.ISchemaInitializationProvider;
 import org.apache.commons.lang3.builder.HashCodeBuilder;
 import org.junit.Test;
@@ -12,6 +13,7 @@ import java.util.List;
 import java.util.function.Supplier;
 
 import static org.hamcrest.Matchers.containsInAnyOrder;
+import static org.hamcrest.Matchers.hasItems;
 import static org.junit.Assert.assertThat;
 
 public class InitializeSchemaTaskTest extends BaseTest {
@@ -34,6 +36,21 @@ public class InitializeSchemaTaskTest extends BaseTest {
 		getMigrator().migrate();
 	}
 
+	@Test
+	public void testInitializeBatch() throws SQLException {
+		InitializeSchemaTask task = new InitializeSchemaTask("1", "2", new SpringBatchSchemaMigrationProvider());
+		getMigrator().addTask(task);
+		getMigrator().migrate();
+		assertThat(JdbcUtils.getTableNames(getConnectionProperties()), hasItems(
+			"BATCH_JOB_INSTANCE",
+			"BATCH_JOB_EXECUTION",
+			"BATCH_JOB_EXECUTION_PARAMS",
+			"BATCH_JOB_EXECUTION_CONTEXT",
+			"BATCH_STEP_EXECUTION",
+			"BATCH_STEP_EXECUTION_CONTEXT"
+			));
+	}
+
 	private class TestProvider implements ISchemaInitializationProvider {
 		@Override
 		public List<String> getSqlStatements(DriverTypeEnum theDriverType) {

hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/config/TestJpaConfig.java

@@ -24,10 +24,13 @@ import ca.uhn.fhir.jpa.api.config.DaoConfig;
 import ca.uhn.fhir.jpa.model.config.PartitionSettings;
 import ca.uhn.fhir.jpa.model.entity.ModelConfig;
 import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Primary;
 import org.springframework.orm.jpa.JpaTransactionManager;
 
 import javax.persistence.EntityManagerFactory;
-// TODO RC1 can use in jpa tests?
+
+@Configuration
 public class TestJpaConfig {
 	@Bean
 	public DaoConfig daoConfig() {
@@ -41,6 +44,7 @@ public class TestJpaConfig {
 	}
 
 	@Bean
+	@Primary
 	public JpaTransactionManager transactionManager(EntityManagerFactory entityManagerFactory) {
 		JpaTransactionManager retVal = new JpaTransactionManager();
 		retVal.setEntityManagerFactory(entityManagerFactory);

hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/BaseJpaR4Test.java

@@ -22,8 +22,6 @@ package ca.uhn.fhir.jpa.test;
 
 import ca.uhn.fhir.jpa.config.TestJpaR4Config;
 import org.springframework.test.context.ContextConfiguration;
-
-@ContextConfiguration(classes = {TestJpaR4Config.class})
 public abstract class BaseJpaR4Test extends BaseJpaTest {
 
 }