flyway initial implementation (with FIXMEs)

This commit is contained in:
Ken Stevens 2019-10-06 17:55:10 -04:00
parent 3c4c6f7925
commit 790f655a95
11 changed files with 359 additions and 11 deletions

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@ -248,6 +248,10 @@
<artifactId>jansi</artifactId>
</dependency>
<dependency>
<groupId>org.flywaydb</groupId>
<artifactId>flyway-core</artifactId>
</dependency>
</dependencies>
<build>

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@ -0,0 +1,112 @@
package ca.uhn.fhir.cli;
/*-
* #%L
* HAPI FHIR - Command Line Client - API
* %%
* Copyright (C) 2014 - 2019 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
import ca.uhn.fhir.jpa.migrate.FlywayMigrator;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
import java.util.Set;
import java.util.stream.Collectors;
public abstract class FlywayMigrateDatabaseCommand<T extends Enum> extends BaseCommand {
private static final String FLYWAY_MIGRATE_DATABASE = "flyway-migrate-database";
private Set<String> myFlags;
protected Set<String> getFlags() {
return myFlags;
}
@Override
public String getCommandDescription() {
return "This command migrates a HAPI FHIR JPA database from one version of HAPI FHIR to a newer version";
}
protected abstract List<T> provideAllowedVersions();
protected abstract Class<T> provideVersionEnumType();
@Override
public String getCommandName() {
return FLYWAY_MIGRATE_DATABASE;
}
@Override
public List<String> provideUsageNotes() {
String versions = "The following versions are supported: " +
provideAllowedVersions().stream().map(Enum::name).collect(Collectors.joining(", "));
return Collections.singletonList(versions);
}
@Override
public Options getOptions() {
Options retVal = new Options();
addOptionalOption(retVal, "r", "dry-run", false, "Log the SQL statements that would be executed but to not actually make any changes");
addRequiredOption(retVal, "u", "url", "URL", "The JDBC database URL");
addRequiredOption(retVal, "n", "username", "Username", "The JDBC database username");
addRequiredOption(retVal, "p", "password", "Password", "The JDBC database password");
addRequiredOption(retVal, "d", "driver", "Driver", "The database driver to use (Options are " + driverOptions() + ")");
addOptionalOption(retVal, null, "no-column-shrink", false, "If this flag is set, the system will not attempt to reduce the length of columns. This is useful in environments with a lot of existing data, where shrinking a column can take a very long time.");
return retVal;
}
private String driverOptions() {
return Arrays.stream(DriverTypeEnum.values()).map(Enum::name).collect(Collectors.joining(", "));
}
@Override
public void run(CommandLine theCommandLine) throws ParseException {
String url = theCommandLine.getOptionValue("u");
String username = theCommandLine.getOptionValue("n");
String password = theCommandLine.getOptionValue("p");
DriverTypeEnum driverType;
String driverTypeString = theCommandLine.getOptionValue("d");
try {
driverType = DriverTypeEnum.valueOf(driverTypeString);
} catch (Exception e) {
throw new ParseException("Invalid driver type \"" + driverTypeString + "\". Valid values are: " + driverOptions());
}
boolean dryRun = theCommandLine.hasOption("r");
boolean noColumnShrink = theCommandLine.hasOption("no-column-shrink");
FlywayMigrator migrator = new FlywayMigrator();
migrator.setConnectionUrl(url);
migrator.setDriverType(driverType);
migrator.setUsername(username);
migrator.setPassword(password);
migrator.setDryRun(dryRun);
migrator.setNoColumnShrink(noColumnShrink);
migrator.migrate();
}
}

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@ -75,6 +75,11 @@
<artifactId>annotations</artifactId>
</dependency>
<dependency>
<groupId>org.flywaydb</groupId>
<artifactId>flyway-core</artifactId>
</dependency>
</dependencies>
<build>

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@ -99,7 +99,7 @@ public enum DriverTypeEnum {
return new ConnectionProperties(dataSource, txTemplate, this);
}
public static class ConnectionProperties {
public static class ConnectionProperties implements AutoCloseable {
private final DriverTypeEnum myDriverType;
private final DataSource myDataSource;
@ -139,6 +139,7 @@ public enum DriverTypeEnum {
return myTxTemplate;
}
@Override
public void close() {
if (myDataSource instanceof DisposableBean) {
try {

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@ -0,0 +1,74 @@
package ca.uhn.fhir.jpa.migrate;
import ca.uhn.fhir.jpa.migrate.taskdef.BaseTask;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import org.flywaydb.core.api.MigrationVersion;
import org.flywaydb.core.api.migration.Context;
import org.flywaydb.core.api.migration.JavaMigration;
import java.sql.SQLException;
import static org.apache.commons.lang3.StringUtils.isBlank;
public class FlywayMigration implements JavaMigration {
private final BaseTask myTask;
private final FlywayMigrator myFlywayMigrator;
private DriverTypeEnum.ConnectionProperties myConnectionProperties;
public FlywayMigration(BaseTask theTask, FlywayMigrator theFlywayMigrator) {
myTask = theTask;
myFlywayMigrator = theFlywayMigrator;
}
@Override
public MigrationVersion getVersion() {
return MigrationVersion.fromVersion(myTask.getVersion());
}
@Override
public String getDescription() {
String retval = myTask.getDescription();
if (retval == null) {
retval = myTask.getClass().getSimpleName() + " " + getVersion();
}
return retval;
}
@Override
public Integer getChecksum() {
// FIXME KHS
return 0;
}
@Override
public boolean isUndo() {
return false;
}
@Override
public boolean canExecuteInTransaction() {
return false;
}
@Override
public void migrate(Context theContext) throws Exception {
myTask.setDriverType(myFlywayMigrator.getDriverType());
myTask.setDryRun(myFlywayMigrator.isDryRun());
myTask.setNoColumnShrink(myFlywayMigrator.isNoColumnShrink());
myTask.setConnectionProperties(myConnectionProperties);
try {
myTask.execute();
} catch (SQLException e) {
String description = myTask.getDescription();
if (isBlank(description)) {
description = myTask.getClass().getSimpleName();
}
String prefix = "Failure executing task \"" + description + "\", aborting! Cause: ";
throw new InternalErrorException(prefix + e.toString(), e);
}
}
public void setConnectionProperties(DriverTypeEnum.ConnectionProperties theConnectionProperties) {
myConnectionProperties = theConnectionProperties;
}
}

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@ -0,0 +1,127 @@
package ca.uhn.fhir.jpa.migrate;
/*-
* #%L
* HAPI FHIR JPA Server - Migration
* %%
* Copyright (C) 2014 - 2019 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.jpa.migrate.taskdef.BaseTask;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import com.google.common.annotations.VisibleForTesting;
import org.flywaydb.core.Flyway;
import org.flywaydb.core.api.MigrationVersion;
import org.flywaydb.core.api.migration.Context;
import org.flywaydb.core.api.migration.JavaMigration;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.List;
import java.util.Objects;
import static org.apache.commons.lang3.StringUtils.isBlank;
public class FlywayMigrator {
private static final Logger ourLog = LoggerFactory.getLogger(FlywayMigrator.class);
// FIXME KHS
private static int ourVersion = 0;
private DriverTypeEnum myDriverType;
private String myConnectionUrl;
private String myUsername;
private String myPassword;
private List<FlywayMigration> myTasks = new ArrayList<>();
private boolean myDryRun;
private boolean myNoColumnShrink;
public void setDriverType(DriverTypeEnum theDriverType) {
myDriverType = theDriverType;
}
public void setConnectionUrl(String theConnectionUrl) {
myConnectionUrl = theConnectionUrl;
}
public void setUsername(String theUsername) {
myUsername = theUsername;
}
public void setPassword(String thePassword) {
myPassword = thePassword;
}
public void addTask(BaseTask<?> theTask) {
if (theTask.getVersion() == null) {
theTask.setVersion("2." + (++ourVersion));
}
myTasks.add(new FlywayMigration(theTask, this));
}
public void setDryRun(boolean theDryRun) {
myDryRun = theDryRun;
}
public void migrate() {
try (DriverTypeEnum.ConnectionProperties connectionProperties = myDriverType.newConnectionProperties(myConnectionUrl, myUsername, myPassword)) {
Flyway flyway = Flyway.configure()
.dataSource(myConnectionUrl, myUsername, myPassword)
.baselineOnMigrate(true)
.javaMigrations(myTasks.toArray(new JavaMigration[0]))
.load();
for (FlywayMigration task : myTasks) {
task.setConnectionProperties(connectionProperties);
}
flyway.migrate();
}
}
public void addTasks(List<BaseTask<?>> theTasks) {
theTasks.forEach(this::addTask);
}
public void setNoColumnShrink(boolean theNoColumnShrink) {
myNoColumnShrink = theNoColumnShrink;
}
public DriverTypeEnum getDriverType() {
return myDriverType;
}
public String getConnectionUrl() {
return myConnectionUrl;
}
public String getUsername() {
return myUsername;
}
public String getPassword() {
return myPassword;
}
public boolean isDryRun() {
return myDryRun;
}
public boolean isNoColumnShrink() {
return myNoColumnShrink;
}
}

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@ -434,6 +434,9 @@ public class JdbcUtils {
if ("SYSTEM TABLE".equalsIgnoreCase(tableType)) {
continue;
}
if ("FLYWAY_SCHEMA_HISTORY".equalsIgnoreCase(tableName)) {
continue;
}
columnNames.add(tableName);
}

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@ -43,6 +43,8 @@ public abstract class BaseTask<T extends BaseTask> {
private boolean myDryRun;
private List<ExecutedStatement> myExecutedStatements = new ArrayList<>();
private boolean myNoColumnShrink;
// FIXME KHS final
private String version;
public boolean isNoColumnShrink() {
return myNoColumnShrink;
@ -130,6 +132,15 @@ public abstract class BaseTask<T extends BaseTask> {
public abstract void execute() throws SQLException;
public String getVersion() {
return version;
}
public BaseTask<T> setVersion(String theVersion) {
version = theVersion;
return this;
}
public static class ExecutedStatement {
private final String mySql;
private final List<Object> myArguments;

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@ -1,6 +1,7 @@
package ca.uhn.fhir.jpa.migrate.taskdef;
import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
import ca.uhn.fhir.jpa.migrate.FlywayMigrator;
import ca.uhn.fhir.jpa.migrate.Migrator;
import org.intellij.lang.annotations.Language;
import org.junit.After;
@ -14,7 +15,7 @@ public class BaseTest {
private static int ourDatabaseUrl = 0;
private String myUrl;
private Migrator myMigrator;
private FlywayMigrator myMigrator;
private DriverTypeEnum.ConnectionProperties myConnectionProperties;
public String getUrl() {
@ -25,6 +26,10 @@ public class BaseTest {
return myConnectionProperties;
}
@After
public void resetMigrationVersion() {
executeSql("DELETE from \"flyway_schema_history\" where \"installed_rank\" > 0");
}
protected void executeSql(@Language("SQL") String theSql, Object... theArgs) {
myConnectionProperties.getTxTemplate().execute(t -> {
@ -39,7 +44,7 @@ public class BaseTest {
});
}
public Migrator getMigrator() {
public FlywayMigrator getMigrator() {
return myMigrator;
}
@ -56,7 +61,7 @@ public class BaseTest {
myConnectionProperties = DriverTypeEnum.H2_EMBEDDED.newConnectionProperties(myUrl, "SA", "SA");
myMigrator = new Migrator();
myMigrator = new FlywayMigrator();
myMigrator.setConnectionUrl(myUrl);
myMigrator.setDriverType(DriverTypeEnum.H2_EMBEDDED);
myMigrator.setUsername("SA");

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@ -2,6 +2,7 @@ package ca.uhn.fhir.jpa.migrate.taskdef;
import ca.uhn.fhir.jpa.migrate.JdbcUtils;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import org.flywaydb.core.api.FlywayException;
import org.junit.Test;
import java.sql.SQLException;
@ -63,8 +64,8 @@ public class RenameColumnTaskTest extends BaseTest {
try {
getMigrator().migrate();
fail();
} catch (InternalErrorException e) {
assertEquals("Failure executing task \"Drop an index\", aborting! Cause: java.sql.SQLException: Can not rename SOMETABLE.myTextCol to TEXTCOL because both columns exist and data exists in TEXTCOL", e.getMessage());
} catch (FlywayException e) {
assertEquals("Failure executing task \"Drop an index\", aborting! Cause: java.sql.SQLException: Can not rename SOMETABLE.myTextCol to TEXTCOL because both columns exist and data exists in TEXTCOL", e.getCause().getCause().getMessage());
}
}
@ -98,8 +99,8 @@ public class RenameColumnTaskTest extends BaseTest {
try {
getMigrator().migrate();
fail();
} catch (InternalErrorException e) {
assertEquals("Failure executing task \"RenameColumnTask\", aborting! Cause: java.sql.SQLException: Can not rename SOMETABLE.myTextCol to TEXTCOL because neither column exists!", e.getMessage());
} catch (FlywayException e) {
assertEquals("Failure executing task \"RenameColumnTask\", aborting! Cause: java.sql.SQLException: Can not rename SOMETABLE.myTextCol to TEXTCOL because neither column exists!", e.getCause().getCause().getMessage());
}
@ -132,8 +133,8 @@ public class RenameColumnTaskTest extends BaseTest {
try {
getMigrator().migrate();
fail();
} catch (InternalErrorException e) {
assertEquals("Failure executing task \"RenameColumnTask\", aborting! Cause: java.sql.SQLException: Can not rename SOMETABLE.PID to PID2 because both columns exist!", e.getMessage());
} catch (FlywayException e) {
assertEquals("Failure executing task \"RenameColumnTask\", aborting! Cause: java.sql.SQLException: Can not rename SOMETABLE.PID to PID2 because both columns exist!", e.getCause().getCause().getMessage());
}

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@ -1415,6 +1415,11 @@
<artifactId>xpp3_xpath</artifactId>
<version>1.1.4c</version>
</dependency>
<dependency>
<groupId>org.flywaydb</groupId>
<artifactId>flyway-core</artifactId>
<version>6.0.4</version>
</dependency>
</dependencies>
</dependencyManagement>