[#255] Fixing 'liquibase' domain issues against Core 2.5.5+.

api-2.5/pom.xml

@@ -0,0 +1,106 @@
+<?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>

api-2.5/src/main/java/org/openmrs/module/initializer/api/loaders/LiquibaseLoader2_5.java

@@ -0,0 +1,96 @@
+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")
+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);
+	}
+}

api-2.5/src/test/java/org/openmrs/module/initializer/api/loaders/LiquibaseLoader25IntegrationTest.java

@@ -0,0 +1,110 @@
+/**
+ * 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);
+	}
+}

api-2.5/src/test/resources/liquibase-schema.sql

@@ -0,0 +1,27 @@
+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)
+);

api-2.5/src/test/resources/log4j2.xml

@@ -0,0 +1,34 @@
+<?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>

api-2.5/src/test/resources/testAppDataDir/configuration/liquibase/liquibase.xml

@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<databaseChangeLog
+		xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
+		xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+		xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-2.0.xsd">
+
+	<changeSet id="previousSqlFileChangeset" author="iniz" runAlways="true" runOnChange="true">
+		<sqlFile endDelimiter="#" path="sql/test_changes_1.sql" relativeToChangelogFile="true" stripComments="true" />
+	</changeSet>
+
+	<changeSet id="newSqlFileChangeset" author="iniz" runAlways="true" runOnChange="true">
+		<sqlFile endDelimiter="#" path="sql/test_changes_2.sql" relativeToChangelogFile="true" stripComments="true" />
+	</changeSet>
+
+</databaseChangeLog>

api-2.5/src/test/resources/testAppDataDir/configuration/liquibase/sql/test_changes_1.sql

@@ -0,0 +1 @@
+insert into global_property (uuid, property, property_value) values (uuid(), 'test_changes_1', 'true');