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Add migrator to uhnfhirtest (#5508) 

* Add migrator to uhnfhirtest

* Fix spotless

* Test fix
This commit is contained in:
James Agnew 2023-11-29 09:16:41 -05:00 committed by GitHub
parent 6e683405a1
commit 469873aff7
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GPG Key ID: 4AEE18F83AFDEB23
10 changed files with 98 additions and 30 deletions
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10
hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/HapiFlywayMigrateDatabaseCommandTest.java
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@ -5,11 +5,14 @@ import ca.uhn.fhir.jpa.migrate.JdbcUtils;
import ca.uhn.fhir.jpa.migrate.SchemaMigrator;
import ca.uhn.fhir.jpa.migrate.dao.HapiMigrationDao;
import ca.uhn.fhir.jpa.migrate.entity.HapiMigrationEntity;
import ca.uhn.fhir.jpa.util.RandomTextUtils;
import ca.uhn.fhir.system.HapiSystemProperties;
import com.google.common.base.Charsets;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.junit.jupiter.api.MethodOrderer;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.TestMethodOrder;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.jdbc.core.JdbcTemplate;
@ -35,10 +38,11 @@ import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue;
@TestMethodOrder(MethodOrderer.MethodName.class)
public class HapiFlywayMigrateDatabaseCommandTest {
private static final Logger ourLog = LoggerFactory.getLogger(HapiFlywayMigrateDatabaseCommandTest.class);
public static final String DB_DIRECTORY = "target/h2_test";
private final String myDbDirectory = "target/h2_test/" + RandomTextUtils.newSecureRandomAlphaNumericString(5);
static {
HapiSystemProperties.enableTestMode();
@ -252,12 +256,12 @@ public class HapiFlywayMigrateDatabaseCommandTest {
@Nonnull
private File getLocation(String theDatabaseName) throws IOException {
File directory = new File(DB_DIRECTORY);
File directory = new File(myDbDirectory);
if (directory.exists()) {
FileUtils.deleteDirectory(directory);
}
return new File(DB_DIRECTORY + "/" + theDatabaseName);
return new File(myDbDirectory + "/" + theDatabaseName);
}
private void seedDatabase340(DriverTypeEnum.ConnectionProperties theConnectionProperties) {

49
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
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@ -977,27 +977,34 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
// Ugh. Only oracle supports using IDX_TAG_DEF_TP_CD_SYS to enforce this constraint. The others will
// create another index.
// For Sql Server, should change the index to be unique with include columns. Do this in 6.1
tagTable.dropIndex("20220429.8", "IDX_TAGDEF_TYPESYSCODE");
Map<DriverTypeEnum, String> addTagDefConstraint = new HashMap<>();
addTagDefConstraint.put(
DriverTypeEnum.H2_EMBEDDED,
"ALTER TABLE HFJ_TAG_DEF ADD CONSTRAINT IDX_TAGDEF_TYPESYSCODE UNIQUE (TAG_TYPE, TAG_CODE, TAG_SYSTEM)");
addTagDefConstraint.put(
DriverTypeEnum.MARIADB_10_1,
"ALTER TABLE HFJ_TAG_DEF ADD CONSTRAINT IDX_TAGDEF_TYPESYSCODE UNIQUE (TAG_TYPE, TAG_CODE, TAG_SYSTEM)");
addTagDefConstraint.put(
DriverTypeEnum.MSSQL_2012,
"ALTER TABLE HFJ_TAG_DEF ADD CONSTRAINT IDX_TAGDEF_TYPESYSCODE UNIQUE (TAG_TYPE, TAG_CODE, TAG_SYSTEM)");
addTagDefConstraint.put(
DriverTypeEnum.MYSQL_5_7,
"ALTER TABLE HFJ_TAG_DEF ADD CONSTRAINT IDX_TAGDEF_TYPESYSCODE UNIQUE (TAG_TYPE, TAG_CODE, TAG_SYSTEM)");
addTagDefConstraint.put(
DriverTypeEnum.ORACLE_12C,
"ALTER TABLE HFJ_TAG_DEF ADD CONSTRAINT IDX_TAGDEF_TYPESYSCODE UNIQUE (TAG_TYPE, TAG_CODE, TAG_SYSTEM)");
addTagDefConstraint.put(
DriverTypeEnum.POSTGRES_9_4,
"ALTER TABLE HFJ_TAG_DEF ADD CONSTRAINT IDX_TAGDEF_TYPESYSCODE UNIQUE (TAG_TYPE, TAG_CODE, TAG_SYSTEM)");
version.executeRawSql("20220429.9", addTagDefConstraint);
// tagTable.dropIndex("20220429.8", "IDX_TAGDEF_TYPESYSCODE");
// Map<DriverTypeEnum, String> addTagDefConstraint = new HashMap<>();
// addTagDefConstraint.put(
// DriverTypeEnum.H2_EMBEDDED,
// "ALTER TABLE HFJ_TAG_DEF ADD CONSTRAINT IDX_TAGDEF_TYPESYSCODE UNIQUE (TAG_TYPE, TAG_CODE,
// TAG_SYSTEM)");
// addTagDefConstraint.put(
// DriverTypeEnum.MARIADB_10_1,
// "ALTER TABLE HFJ_TAG_DEF ADD CONSTRAINT IDX_TAGDEF_TYPESYSCODE UNIQUE (TAG_TYPE, TAG_CODE,
// TAG_SYSTEM)");
// addTagDefConstraint.put(
// DriverTypeEnum.MSSQL_2012,
// "ALTER TABLE HFJ_TAG_DEF ADD CONSTRAINT IDX_TAGDEF_TYPESYSCODE UNIQUE (TAG_TYPE, TAG_CODE,
// TAG_SYSTEM)");
// addTagDefConstraint.put(
// DriverTypeEnum.MYSQL_5_7,
// "ALTER TABLE HFJ_TAG_DEF ADD CONSTRAINT IDX_TAGDEF_TYPESYSCODE UNIQUE (TAG_TYPE, TAG_CODE,
// TAG_SYSTEM)");
// addTagDefConstraint.put(
// DriverTypeEnum.ORACLE_12C,
// "ALTER TABLE HFJ_TAG_DEF ADD CONSTRAINT IDX_TAGDEF_TYPESYSCODE UNIQUE (TAG_TYPE, TAG_CODE,
// TAG_SYSTEM)");
// addTagDefConstraint.put(
// DriverTypeEnum.POSTGRES_9_4,
// "ALTER TABLE HFJ_TAG_DEF ADD CONSTRAINT IDX_TAGDEF_TYPESYSCODE UNIQUE (TAG_TYPE, TAG_CODE,
// TAG_SYSTEM)");
// version.executeRawSql("20220429.9", addTagDefConstraint);
version.addNop("20220429.9");
}
// Fix for https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/328

6
hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/CommonConfig.java
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@ -23,6 +23,7 @@ import ca.uhn.fhir.storage.interceptor.balp.IBalpAuditEventSink;
import ca.uhn.fhirtest.ScheduledSubscriptionDeleter;
import ca.uhn.fhirtest.interceptor.AnalyticsInterceptor;
import ca.uhn.fhirtest.joke.HolyFooCowInterceptor;
import ca.uhn.fhirtest.migrate.FhirTestAutoMigrator;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
@ -131,6 +132,11 @@ public class CommonConfig {
return new FhirTestBalpAuditContextServices();
}
@Bean
public FhirTestAutoMigrator migrator() {
return new FhirTestAutoMigrator();
}
public static boolean isLocalTestMode() {
return "true".equalsIgnoreCase(System.getProperty("testmode.local"));
}

2
hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestAuditConfig.java
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@ -120,7 +120,7 @@ public class TestAuditConfig {
}
extraProperties.put("hibernate.format_sql", "false");
extraProperties.put("hibernate.show_sql", "false");
extraProperties.put("hibernate.hbm2ddl.auto", "update");
extraProperties.put("hibernate.hbm2ddl.auto", "none");
extraProperties.put("hibernate.jdbc.batch_size", "20");
extraProperties.put("hibernate.cache.use_query_cache", "false");
extraProperties.put("hibernate.cache.use_second_level_cache", "false");

2
hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu2Config.java
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@ -138,7 +138,7 @@ public class TestDstu2Config {
}
extraProperties.put("hibernate.format_sql", "false");
extraProperties.put("hibernate.show_sql", "false");
extraProperties.put("hibernate.hbm2ddl.auto", "update");
extraProperties.put("hibernate.hbm2ddl.auto", "none");
extraProperties.put("hibernate.jdbc.batch_size", "20");
extraProperties.put("hibernate.cache.use_query_cache", "false");
extraProperties.put("hibernate.cache.use_second_level_cache", "false");

2
hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestDstu3Config.java
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@ -138,7 +138,7 @@ public class TestDstu3Config {
}
extraProperties.put("hibernate.format_sql", "false");
extraProperties.put("hibernate.show_sql", "false");
extraProperties.put("hibernate.hbm2ddl.auto", "update");
extraProperties.put("hibernate.hbm2ddl.auto", "none");
extraProperties.put("hibernate.jdbc.batch_size", "20");
extraProperties.put("hibernate.cache.use_query_cache", "false");
extraProperties.put("hibernate.cache.use_second_level_cache", "false");

2
hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestR4BConfig.java
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@ -136,7 +136,7 @@ public class TestR4BConfig {
}
extraProperties.put("hibernate.format_sql", "false");
extraProperties.put("hibernate.show_sql", "false");
extraProperties.put("hibernate.hbm2ddl.auto", "update");
extraProperties.put("hibernate.hbm2ddl.auto", "none");
extraProperties.put("hibernate.jdbc.batch_size", "20");
extraProperties.put("hibernate.cache.use_query_cache", "false");
extraProperties.put("hibernate.cache.use_second_level_cache", "false");

2
hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestR4Config.java
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@ -139,7 +139,7 @@ public class TestR4Config {
}
extraProperties.put("hibernate.format_sql", "false");
extraProperties.put("hibernate.show_sql", "false");
extraProperties.put("hibernate.hbm2ddl.auto", "update");
extraProperties.put("hibernate.hbm2ddl.auto", "none");
extraProperties.put("hibernate.jdbc.batch_size", "20");
extraProperties.put("hibernate.cache.use_query_cache", "false");
extraProperties.put("hibernate.cache.use_second_level_cache", "false");

2
hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/config/TestR5Config.java
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@ -148,7 +148,7 @@ public class TestR5Config {
}
extraProperties.put("hibernate.format_sql", "false");
extraProperties.put("hibernate.show_sql", "false");
extraProperties.put("hibernate.hbm2ddl.auto", "update");
extraProperties.put("hibernate.hbm2ddl.auto", "none");
extraProperties.put("hibernate.jdbc.batch_size", "20");
extraProperties.put("hibernate.cache.use_query_cache", "false");
extraProperties.put("hibernate.cache.use_second_level_cache", "false");

51
hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/migrate/FhirTestAutoMigrator.java Normal file
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@ -0,0 +1,51 @@
package ca.uhn.fhirtest.migrate;
import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
import ca.uhn.fhir.jpa.migrate.HapiMigrationStorageSvc;
import ca.uhn.fhir.jpa.migrate.MigrationTaskList;
import ca.uhn.fhir.jpa.migrate.SchemaMigrator;
import ca.uhn.fhir.jpa.migrate.dao.HapiMigrationDao;
import ca.uhn.fhir.jpa.migrate.tasks.HapiFhirJpaMigrationTasks;
import ca.uhn.fhir.util.VersionEnum;
import ca.uhn.fhirtest.config.CommonConfig;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.Properties;
import java.util.Set;
import javax.annotation.PostConstruct;
import javax.sql.DataSource;
public class FhirTestAutoMigrator {
private static final Logger ourLog = LoggerFactory.getLogger(FhirTestAutoMigrator.class);
public static final String MIGRATION_TABLENAME = "MIGRATIONS";
@Autowired
private DataSource myDataSource;
@PostConstruct
public void run() {
DriverTypeEnum driver;
if (CommonConfig.isLocalTestMode()) {
driver = DriverTypeEnum.H2_EMBEDDED;
} else {
driver = DriverTypeEnum.POSTGRES_9_4;
}
HapiMigrationDao hapiMigrationDao = new HapiMigrationDao(myDataSource, driver, MIGRATION_TABLENAME);
HapiMigrationStorageSvc hapiMigrationStorageSvc = new HapiMigrationStorageSvc(hapiMigrationDao);
MigrationTaskList tasks = new HapiFhirJpaMigrationTasks(Set.of()).getAllTasks(VersionEnum.values());
SchemaMigrator schemaMigrator = new SchemaMigrator(
"HAPI FHIR", MIGRATION_TABLENAME, myDataSource, new Properties(), tasks, hapiMigrationStorageSvc);
schemaMigrator.setDriverType(driver);
ourLog.info("About to run migration...");
schemaMigrator.createMigrationTableIfRequired();
schemaMigrator.migrate();
ourLog.info("Migration complete");
}
}