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[#255] Fixing 'liquibase' domain issues against Core 2.5.5+. (#256)
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@mseaton
mseaton authored Nov 9, 2023
1 parent 4be0bf7 commit 65e4661
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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -197,6 +197,7 @@ See the [documentation on Initializer's logging properties](readme/rtprops.md#lo
#### Version 2.7.0
* Added support for 'queues' domain.
* Added support for 'addresshierarchy' domain.
* Fix for Liquibase Loader to ensure compatibility with OpenMRS versions 2.5.5+

#### Version 2.6.0
* Added support for 'cohorttypes' and 'cohortattributetypes' domains.
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106 changes: 106 additions & 0 deletions api-2.5/pom.xml
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<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<parent>
<artifactId>initializer</artifactId>
<groupId>org.openmrs.module</groupId>
<version>2.7.0-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>

<artifactId>initializer-api-2.5</artifactId>
<packaging>jar</packaging>
<name>Initializer API 2.5</name>
<description>API 2.5 project for Initializer</description>

<properties>
<openmrsPlatformVersion>${openmrsVersion2.5}</openmrsPlatformVersion>
<datafilterVersion>2.2.0</datafilterVersion>
</properties>

<dependencies>

<dependency>
<groupId>org.openmrs.test</groupId>
<artifactId>openmrs-test</artifactId>
<type>pom</type>
<version>${openmrsPlatformVersion}</version>
<scope>test</scope>
<exclusions>
<exclusion>
<groupId>org.powermock</groupId>
<artifactId>powermock-api-mockito2</artifactId>
</exclusion>
</exclusions>
</dependency>

<dependency>
<groupId>${project.parent.groupId}</groupId>
<artifactId>${project.parent.artifactId}-api</artifactId>
<version>${project.parent.version}</version>
<scope>provided</scope>
</dependency>

<dependency>
<groupId>${project.parent.groupId}</groupId>
<artifactId>${project.parent.artifactId}-api</artifactId>
<version>${project.parent.version}</version>
<scope>test</scope>
<type>test-jar</type>
</dependency>

<dependency>
<groupId>${project.parent.groupId}</groupId>
<artifactId>${project.parent.artifactId}-api-2.4</artifactId>
<version>${project.parent.version}</version>
<scope>provided</scope>
</dependency>

<dependency>
<groupId>${project.parent.groupId}</groupId>
<artifactId>${project.parent.artifactId}-api-2.3</artifactId>
<version>${project.parent.version}</version>
<scope>provided</scope>
</dependency>

<dependency>
<groupId>${project.parent.groupId}</groupId>
<artifactId>${project.parent.artifactId}-api-2.3</artifactId>
<version>${project.parent.version}</version>
<scope>test</scope>
<type>test-jar</type>
</dependency>

<dependency>
<groupId>${project.parent.groupId}</groupId>
<artifactId>${project.parent.artifactId}-api-2.2</artifactId>
<version>${project.parent.version}</version>
<scope>provided</scope>
</dependency>

<dependency>
<groupId>${project.parent.groupId}</groupId>
<artifactId>${project.parent.artifactId}-api-2.2</artifactId>
<version>${project.parent.version}</version>
<scope>test</scope>
<type>test-jar</type>
</dependency>

<dependency>
<groupId>org.openmrs.module</groupId>
<artifactId>fhir2-api-2.5</artifactId>
<version>${fhir2Version}</version>
<scope>provided</scope>
</dependency>

<dependency>
<groupId>org.openmrs.module</groupId>
<artifactId>datafilter-api</artifactId>
<version>${datafilterVersion}</version>
<scope>provided</scope>
</dependency>

</dependencies>

</project>
96 changes: 96 additions & 0 deletions api-2.5/src/main/java/org/openmrs/module/initializer/api/loaders/LiquibaseLoader2_5.java
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package org.openmrs.module.initializer.api.loaders;

import org.openmrs.annotation.OpenmrsProfile;
import org.openmrs.api.context.Context;
import org.openmrs.liquibase.ChangeSetExecutorCallback;
import org.openmrs.module.initializer.Domain;
import org.openmrs.module.initializer.api.ConfigDirUtil;
import org.openmrs.util.DatabaseUpdater;
import org.openmrs.util.OpenmrsUtil;

import java.io.File;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.List;

@OpenmrsProfile(openmrsPlatformVersion = "2.5.5")
public class LiquibaseLoader2_5 extends BaseFileLoader {

public static final String LIQUIBASE_FILE_NAME = "liquibase";

@Override
protected Domain getDomain() {
return Domain.LIQUIBASE;
}

@Override
protected String getFileExtension() {
return "xml";
}

@Override
protected void load(File file) throws Exception {
if (file.getName().equalsIgnoreCase(LIQUIBASE_FILE_NAME + "." + getFileExtension())) {
// Because liquibase uses the path provided as an identifier of the changeset, we need to relativize it
// This ensures that liquibase changesets are not re-executed if the absolute path on the server changes
String absolutePath = file.getAbsolutePath();
String relativePath = getPathRelativeToApplicationDataDirectory(file);
updateExistingLiquibaseChangeLogPathsIfNeeded(absolutePath, relativePath);
try {
DatabaseUpdater.executeChangelog(relativePath, (ChangeSetExecutorCallback) null);
}
catch (Exception e) {
log.error("An error occurred executing liquibase file: " + file, e);
throw e;
}
}
}

/**
* If a particular changeset file is being executed, and this is referenced by the given oldPath,
* then update that changeset to reference the given newPath
*/
protected void updateExistingLiquibaseChangeLogPathsIfNeeded(String oldPath, String newPath) {
log.debug("Checking if liquibase filenames need to be updated for " + oldPath);
int numRows = sqlCount("select count(*) from liquibasechangelog where filename = '" + oldPath + "'");
if (numRows > 0) {
log.warn("Liquibase filename update is needed for " + oldPath + ". Updating to " + newPath);
sqlUpdate("update liquibasechangelog set filename = '" + newPath + "' where filename = '" + oldPath + "'");
} else {
log.debug("Liquibase filename update is not required");
}
}

/**
* @param file the file to relativize
* @return the path of the given file, relativized to the OpenMRS application data directory
*/
protected String getPathRelativeToApplicationDataDirectory(File file) {
Path appDataDirPath = Paths.get(OpenmrsUtil.getApplicationDataDirectory());
Path liquibaseFilePath = file.toPath();
return appDataDirPath.relativize(liquibaseFilePath).toString();
}

/**
* @param sql the sql to execute
* @return the results of that execution, where the first column of the first row is returned as an
* integer count
*/
private int sqlCount(String sql) {
List<List<Object>> results = Context.getAdministrationService().executeSQL(sql, true);
Object singleResult = results.get(0).get(0);
return Integer.parseInt(singleResult.toString());
}

/**
* @param sql the sql to execute as a database update operation
*/
private void sqlUpdate(String sql) {
Context.getAdministrationService().executeSQL(sql, false);
}

@Override
public ConfigDirUtil getDirUtil() {
return new ConfigDirUtil(iniz.getConfigDirPath(), iniz.getChecksumsDirPath(), getDomainName(), true);
}
}
110 changes: 110 additions & 0 deletions ...est/java/org/openmrs/module/initializer/api/loaders/LiquibaseLoader25IntegrationTest.java
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/**
* This Source Code Form is subject to the terms of the Mozilla Public License,
* v. 2.0. If a copy of the MPL was not distributed with this file, You can
* obtain one at http://mozilla.org/MPL/2.0/. OpenMRS is also distributed under
* the terms of the Healthcare Disclaimer located at http://openmrs.org/license.
*
* Copyright (C) OpenMRS Inc. OpenMRS is a registered trademark and the OpenMRS
* graphic logo is a trademark of OpenMRS Inc.
*/
package org.openmrs.module.initializer.api.loaders;

import org.apache.commons.io.IOUtils;
import org.junit.After;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
import org.openmrs.api.AdministrationService;
import org.openmrs.module.initializer.DomainBaseModuleContextSensitiveTest;
import org.openmrs.util.OpenmrsClassLoader;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;

import java.nio.charset.StandardCharsets;
import java.util.List;

public class LiquibaseLoader25IntegrationTest extends DomainBaseModuleContextSensitiveTest {

@Autowired
private LiquibaseLoader2_5 loader;

@Autowired
@Qualifier("adminService")
private AdministrationService adminService;

@Before
public void setup() throws Exception {
System.setProperty("useInMemoryDatabase", "true");
ClassLoader cl = OpenmrsClassLoader.getInstance();
String schemaSql = IOUtils.resourceToString("liquibase-schema.sql", StandardCharsets.UTF_8, cl);
adminService.executeSQL(schemaSql, false);
}

@After
public void teardown() {
adminService.executeSQL("drop table LIQUIBASECHANGELOG", false);
adminService.executeSQL("drop table LIQUIBASECHANGELOGLOCK", false);
}

@Test
public void load_shouldExecuteNewChangeSet() {
String relativePath = "configuration/liquibase/liquibase.xml";
String absolutePath = getAppDataDirPath() + relativePath;
Assert.assertEquals(0, numChangeLogEntries(absolutePath));
Assert.assertEquals(0, numChangeLogEntries(relativePath));
Assert.assertNull(adminService.getGlobalProperty("test_changes_1"));
Assert.assertNull(adminService.getGlobalProperty("test_changes_2"));
loader.load();
Assert.assertEquals(0, numChangeLogEntries(absolutePath));
Assert.assertEquals(2, numChangeLogEntries(relativePath));
Assert.assertEquals("true", adminService.getGlobalProperty("test_changes_1"));
Assert.assertEquals("true", adminService.getGlobalProperty("test_changes_2"));
}

@Test
public void load_shouldUpdateAbsolutePathToRelativePathIfNeeded() {
String relativePath = "configuration/liquibase/liquibase.xml";
String absolutePath = getAppDataDirPath() + relativePath;
insertExistingChangeLogEntry(absolutePath);
Assert.assertEquals(1, numChangeLogEntries(absolutePath));
Assert.assertEquals(0, numChangeLogEntries(relativePath));
loader.updateExistingLiquibaseChangeLogPathsIfNeeded(absolutePath, relativePath);
Assert.assertEquals(0, numChangeLogEntries(absolutePath));
Assert.assertEquals(1, numChangeLogEntries(relativePath));
}

private int numChangeLogEntries(String filename) {
List<List<Object>> ret = adminService
.executeSQL("select count(*) from liquibasechangelog where filename = '" + filename + "'", true);
return Integer.parseInt(ret.get(0).get(0).toString());
}

private void insertExistingChangeLogEntry(String filename) {
StringBuilder sb = new StringBuilder();
sb.append("INSERT INTO LIQUIBASECHANGELOG (");
sb.append(" ID, ");
sb.append(" AUTHOR, ");
sb.append(" FILENAME, ");
sb.append(" DATEEXECUTED, ");
sb.append(" ORDEREXECUTED, ");
sb.append(" EXECTYPE, ");
sb.append(" MD5SUM, ");
sb.append(" DESCRIPTION, ");
sb.append(" COMMENTS, ");
sb.append(" LIQUIBASE ");
sb.append(") ");
sb.append("values (");
sb.append(" 'previousSqlFileChangeset', ");
sb.append(" 'iniz', ");
sb.append(" '").append(filename).append("', ");
sb.append(" '2023-11-01 00:00:00', ");
sb.append(" 1, ");
sb.append(" 'EXECUTED', ");
sb.append(" '8:4019e34234869ff55c81acf9d779f2a7', ");
sb.append(" 'sqlFile', ");
sb.append(" '', ");
sb.append(" '4.4.1'");
sb.append(")");
adminService.executeSQL(sb.toString(), false);
}
}
27 changes: 27 additions & 0 deletions api-2.5/src/test/resources/liquibase-schema.sql
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CREATE TABLE LIQUIBASECHANGELOG
(
ID varchar(255) NOT NULL,
AUTHOR varchar(255) NOT NULL,
FILENAME varchar(255) NOT NULL,
DATEEXECUTED datetime NOT NULL,
ORDEREXECUTED int(11) NOT NULL,
EXECTYPE varchar(10) NOT NULL,
MD5SUM varchar(35),
DESCRIPTION varchar(255),
COMMENTS varchar(255),
TAG varchar(255),
LIQUIBASE varchar(20),
CONTEXTS varchar(255),
LABELS varchar(255),
DEPLOYMENT_ID varchar(10),
PRIMARY KEY (ID, AUTHOR, FILENAME)
);

CREATE TABLE LIQUIBASECHANGELOGLOCK
(
ID int(11) NOT NULL,
LOCKED tinyint(1) NOT NULL,
LOCKGRANTED datetime,
LOCKEDBY varchar(255),
PRIMARY KEY (ID)
);
34 changes: 34 additions & 0 deletions api-2.5/src/test/resources/log4j2.xml
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<?xml version="1.0" encoding="UTF-8" ?>
<!--
This Source Code Form is subject to the terms of the Mozilla Public License,
v. 2.0. If a copy of the MPL was not distributed with this file, You can
obtain one at http://mozilla.org/MPL/2.0/. OpenMRS is also distributed under
the terms of the Healthcare Disclaimer located at http://openmrs.org/license.
Copyright (C) OpenMRS Inc. OpenMRS is a registered trademark and the OpenMRS
graphic logo is a trademark of OpenMRS Inc.
-->

<Configuration xmlns="http://logging.apache.org/log4j/2.0/config">
<Properties>
<!-- The default pattern is stored as a property so that it's only defined once.
It's also quite challenging to escape using Log4j2's variable substitution. -->
<Property name="defaultPattern">%p - %C{1}.%M(%L) |%d{ISO8601}| %m%n</Property>
</Properties>
<Appenders>
<!-- the console appender is not required but usually a good idea -->
<Console name="CONSOLE" target="SYSTEM_OUT">
<PatternLayout pattern="${openmrs:logLayout:-${defaultPattern}}" />
</Console>
</Appenders>
<Loggers>
<Logger name="org.openmrs.module.initializer" level="INFO" />
<Logger name="org.springframework" additivity="false" level="WARN" />
<Logger name="org.hibernate" additivity="false" level="ERROR" />
<Root level="WARN">
<AppenderRef ref="CONSOLE" />
</Root>
</Loggers>
</Configuration>
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