TRUNK-6208: Upgrade 2.7 Platform to Liquibase 4.27.0

api/src/main/java/org/openmrs/api/db/hibernate/HibernateEncounterDAO.java

@@ -19,21 +19,18 @@
 import javax.persistence.criteria.Predicate;
 import javax.persistence.criteria.Root;
 import java.util.ArrayList;
-import java.util.Collection;
 import java.util.Collections;
 import java.util.Date;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.stream.Collectors;
 
-import liquibase.pro.packaged.Q;
 import org.apache.commons.lang3.StringUtils;
 import org.hibernate.FlushMode;
 import org.hibernate.SQLQuery;
 import org.hibernate.Session;
 import org.hibernate.SessionFactory;
-import org.hibernate.criterion.Order;
 import org.openmrs.Cohort;
 import org.openmrs.Encounter;
 import org.openmrs.EncounterProvider;

api/src/main/java/org/openmrs/liquibase/ChangeLogDetective.java

@@ -17,6 +17,7 @@
 import liquibase.LabelExpression;
 import liquibase.Liquibase;
 import liquibase.changelog.ChangeSet;
+import liquibase.command.core.StatusCommandStep;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -86,8 +87,11 @@ public String getInitialLiquibaseSnapshotVersion(String context, LiquibaseProvid
 			try {
 				for (String filename : changeSets) {
 					liquibase = liquibaseProvider.getLiquibase(filename);
-					List<ChangeSet> rawUnrunChangeSets = liquibase.listUnrunChangeSets(new Contexts(context),
-					    new LabelExpression());
+
+					List<ChangeSet> rawUnrunChangeSets = new StatusCommandStep()
+						.listUnrunChangeSets(new Contexts(context), 
+							new LabelExpression(), liquibase.getDatabaseChangeLog(), liquibase.getDatabase());
+
 					liquibase.close();
 
 					List<ChangeSet> refinedUnrunChangeSets = excludeVintageChangeSets(filename, rawUnrunChangeSets);
@@ -142,8 +146,11 @@ public List<String> getUnrunLiquibaseUpdateFileNames(String snapshotVersion, Str
 		try {
 			for (String filename : updateFileNames) {
 				liquibase = liquibaseProvider.getLiquibase(filename);
-				List<ChangeSet> unrunChangeSets = liquibase.listUnrunChangeSets(new Contexts(context),
-				    new LabelExpression());
+
+				List<ChangeSet> unrunChangeSets = new StatusCommandStep()
+					.listUnrunChangeSets(new Contexts(context),
+						new LabelExpression(), liquibase.getDatabaseChangeLog(), liquibase.getDatabase());
+
 				liquibase.close();
 
 				log.info("file '{}' contains {} un-run change sets", filename, unrunChangeSets.size());

api/src/main/java/org/openmrs/liquibase/OpenmrsClassLoaderResourceAccessor.java

@@ -11,16 +11,21 @@
 
 import liquibase.resource.ClassLoaderResourceAccessor;
 import liquibase.resource.InputStreamList;
+import liquibase.resource.Resource;
 import org.openmrs.util.OpenmrsClassLoader;
 
 import java.io.IOException;
-import java.io.InputStream;
 import java.net.URI;
+import java.util.List;
 
 /**
  * A customization of Liquibase's {@link ClassLoaderResourceAccessor} which defaults to the OpenMRS ClassLoader and has
  * special handling for our liquibase.xml files, which occur multiple times on the classpath.
+ * @deprecated As of 2.7.0, replaced by the usage of {@link #search(String, boolean)} or {@link #getAll(String)},
+ * as this provides a better handling of paths that map to multiple resources using Liquibase's DUPLICATE_FILE_MODE.
+ * Refer to {@link liquibase.GlobalConfiguration#DUPLICATE_FILE_MODE} for the configuration and usage details.
  */
+@Deprecated
 public class OpenmrsClassLoaderResourceAccessor extends ClassLoaderResourceAccessor {
 
 	public OpenmrsClassLoaderResourceAccessor() {
@@ -33,15 +38,23 @@ public OpenmrsClassLoaderResourceAccessor(ClassLoader classLoader) {
 
 	@Override
 	public InputStreamList openStreams(String relativeTo, String streamPath) throws IOException {
-		InputStreamList result = super.openStreams(relativeTo, streamPath);
-		if (result != null && !result.isEmpty() && result.size() > 1) {
+		List<Resource> resources = super.getAll(streamPath);
+		InputStreamList result = new InputStreamList();
+		if (resources == null || resources.isEmpty()) {
+			return result;
+		}
+
+		for (Resource resource : resources) {
+			result.add(resource.getUri(), resource.openInputStream());
+		}
+		if (!result.isEmpty() && result.size() > 1) {
 			try (InputStreamList oldResult = result) {
 				URI uri = oldResult.getURIs().get(0);
 				result = new InputStreamList(uri, uri.toURL().openStream());
 			}
-			
+
 		}
-		
+
 		return result;
 	}
 }

api/src/main/java/org/openmrs/util/DatabaseUpdater.java

@@ -10,6 +10,7 @@
 package org.openmrs.util;
 
 import liquibase.Contexts;
+import liquibase.GlobalConfiguration;
 import liquibase.LabelExpression;
 import liquibase.Liquibase;
 import liquibase.RuntimeEnvironment;
@@ -23,6 +24,7 @@
 import liquibase.changelog.filter.DbmsChangeSetFilter;
 import liquibase.changelog.filter.ShouldRunChangeSetFilter;
 import liquibase.changelog.visitor.UpdateVisitor;
+import liquibase.command.core.StatusCommandStep;
 import liquibase.database.Database;
 import liquibase.database.DatabaseFactory;
 import liquibase.database.jvm.JdbcConnection;
@@ -215,7 +217,10 @@ public static List<String> executeChangelog(String changeLogFile, Contexts conte
 		log.debug("Setting up liquibase object to run changelog: {}", changeLogFile);
 		Liquibase liquibase = getLiquibase(changeLogFile, cl);
 
-		int numChangeSetsToRun = liquibase.listUnrunChangeSets(contexts, new LabelExpression()).size();
+		int numChangeSetsToRun = new StatusCommandStep()
+			.listUnrunChangeSets(contexts,
+				new LabelExpression(), liquibase.getDatabaseChangeLog(), liquibase.getDatabase()).size();
+
 		Database database = null;
 		LockService lockHandler = null;
 
@@ -233,7 +238,7 @@ public static List<String> executeChangelog(String changeLogFile, Contexts conte
 
 			// ensure that the change log history service is initialised
 			//
-			ChangeLogHistoryServiceFactory.getInstance().getChangeLogService(database).init();
+			Scope.getCurrentScope().getSingleton(ChangeLogHistoryServiceFactory.class).getChangeLogService(database).init();
 
 			logIterator.run(new OpenmrsUpdateVisitor(database, callback, numChangeSetsToRun),
 			    new RuntimeEnvironment(database, contexts, new LabelExpression()));
@@ -426,8 +431,13 @@ private static Liquibase getLiquibase(String changeLogFile, ClassLoader cl) thro
 				changeLogFile = EMPTY_CHANGE_LOG_FILE;
 			}
 
+			configureLiquibaseDuplicateFileMode();
+
 			// ensure that the change log history service is initialised
-			ChangeLogHistoryServiceFactory.getInstance().getChangeLogService(database).init();
+			Scope.getCurrentScope()
+				.getSingleton(ChangeLogHistoryServiceFactory.class)
+				.getChangeLogService(database)
+				.init();
 			return new Liquibase(changeLogFile, getCompositeResourceAccessor(cl), database);
 		}
 		catch (Exception e) {
@@ -673,8 +683,10 @@ public static List<OpenMRSChangeSet> getUnrunDatabaseChanges(String... changeLog
 				Liquibase liquibase = getLiquibase(changelogFile, null);
 				database = liquibase.getDatabase();
 
-				List<ChangeSet> changeSets = liquibase.listUnrunChangeSets(new Contexts(CONTEXT), new LabelExpression());
-
+				List<ChangeSet> changeSets = new StatusCommandStep()
+					.listUnrunChangeSets(new Contexts(CONTEXT),
+						new LabelExpression(), liquibase.getDatabaseChangeLog(), liquibase.getDatabase());
+
 				for (ChangeSet changeSet : changeSets) {
 					OpenMRSChangeSet omrschangeset = new OpenMRSChangeSet(changeSet, database);
 					results.add(omrschangeset);
@@ -884,4 +896,15 @@ private static CompositeResourceAccessor getCompositeResourceAccessor(ClassLoade
 		ResourceAccessor fsFO = new FileSystemResourceAccessor(OpenmrsUtil.getApplicationDataDirectoryAsFile());
 		return new CompositeResourceAccessor(openmrsFO, fsFO);
 	}
+
+	private static void configureLiquibaseDuplicateFileMode() {
+		final String dupFlagModeKey = GlobalConfiguration.DUPLICATE_FILE_MODE.getKey();
+		final String dupFlagMode = Context.getRuntimeProperties().getProperty(dupFlagModeKey);
+
+		if (dupFlagMode != null) {
+			System.setProperty(dupFlagModeKey, dupFlagMode);
+		} else if (System.getProperty(dupFlagModeKey) == null) {
+			System.setProperty(dupFlagModeKey, OpenmrsConstants.LIQUIBASE_DUPLICATE_FILE_MODE_DEFAULT);
+		}
+	}
 }

api/src/main/java/org/openmrs/util/OpenmrsConstants.java

@@ -20,6 +20,7 @@
 import java.util.Map;
 import java.util.Properties;
 
+import liquibase.GlobalConfiguration;
 import org.apache.commons.io.IOUtils;
 import org.openmrs.GlobalProperty;
 import org.openmrs.api.context.Context;
@@ -1314,6 +1315,9 @@ public static enum PERSON_TYPE {
 	/** Value for the long person name format */
 	public static final String PERSON_NAME_FORMAT_LONG = "long";
 
+	// Liquibase Constants
+	public static String LIQUIBASE_DUPLICATE_FILE_MODE_DEFAULT = GlobalConfiguration.DuplicateFileMode.WARN.name();
+
 	private OpenmrsConstants() {
 	}
 

api/src/main/resources/org/openmrs/liquibase/snapshots/core-data/liquibase-core-data-2.6.x.xml

@@ -11,7 +11,7 @@
     graphic logo is a trademark of OpenMRS Inc.
 
 -->
-<databaseChangeLog xmlns="http://www.liquibase.org/xml/ns/dbchangelog" xmlns:ext="http://www.liquibase.org/xml/ns/dbchangelog-ext" xmlns:pro="http://www.liquibase.org/xml/ns/pro" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog-ext http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-ext.xsd http://www.liquibase.org/xml/ns/pro http://www.liquibase.org/xml/ns/pro/liquibase-pro-4.6.xsd http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-4.6.xsd">  
+<databaseChangeLog logicalFilePath="liquibase-core-data.xml" xmlns="http://www.liquibase.org/xml/ns/dbchangelog" xmlns:ext="http://www.liquibase.org/xml/ns/dbchangelog-ext" xmlns:pro="http://www.liquibase.org/xml/ns/pro" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog-ext http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-ext.xsd http://www.liquibase.org/xml/ns/pro http://www.liquibase.org/xml/ns/pro/liquibase-pro-4.6.xsd http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-4.6.xsd">  
   <changeSet author="manoj (generated)" id="1698595908058-17"> 
     <insert tableName="person"> 
       <column name="person_id" valueNumeric="1"/>  

api/src/main/resources/org/openmrs/liquibase/snapshots/schema-only/liquibase-schema-only-2.6.x.xml

@@ -11,7 +11,7 @@
     graphic logo is a trademark of OpenMRS Inc.
 
 -->
-<databaseChangeLog xmlns="http://www.liquibase.org/xml/ns/dbchangelog" xmlns:ext="http://www.liquibase.org/xml/ns/dbchangelog-ext" xmlns:pro="http://www.liquibase.org/xml/ns/pro" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog-ext http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-ext.xsd http://www.liquibase.org/xml/ns/pro http://www.liquibase.org/xml/ns/pro/liquibase-pro-4.6.xsd http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-4.6.xsd">  
+<databaseChangeLog logicalFilePath="liquibase-schema-only.xml" xmlns="http://www.liquibase.org/xml/ns/dbchangelog" xmlns:ext="http://www.liquibase.org/xml/ns/dbchangelog-ext" xmlns:pro="http://www.liquibase.org/xml/ns/pro" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.liquibase.org/xml/ns/dbchangelog-ext http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-ext.xsd http://www.liquibase.org/xml/ns/pro http://www.liquibase.org/xml/ns/pro/liquibase-pro-4.6.xsd http://www.liquibase.org/xml/ns/dbchangelog http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-4.6.xsd">  
   <changeSet author="manoj (generated)" id="1698595905189-1"> 
     <createTable tableName="allergy"> 
       <column autoIncrement="true" name="allergy_id" type="INT"> 

api/src/main/resources/org/openmrs/liquibase/updates/liquibase-update-to-latest-2.0.x.xml

@@ -1790,6 +1790,7 @@
 		<validCheckSum>1b6141be59a8a243b9e56d0aad952af</validCheckSum> <!-- checksum from before idExceptions added -->
 		<validCheckSum>89cc7a14b0582f157ea2dbb9de092fd</validCheckSum> <!-- current checksum with idExceptions param added -->
 		<validCheckSum><comment>Changes to new concept_reference tables</comment>3:4edd135921eb263d4811cf1c22ef4846</validCheckSum>
+		<validCheckSum><comment>Account for trailing whitespace</comment>9:5d41399f930d6de5c0030986b78f35e5</validCheckSum>
 		<preConditions onFail="MARK_RAN">
 			<not>
 				<or>
@@ -3521,6 +3522,7 @@
 		<validCheckSum><comment>After changing to boolean</comment>3:b57c0f651ed477457fd16e503eaf51a4</validCheckSum>
 		<validCheckSum>3:002108aacdf55731f4fd472d5308c5c8</validCheckSum>
         <validCheckSum>3:6a72bbb390155596e52da4e8d065d1a2</validCheckSum>
+        <validCheckSum><comment>Account for trailing whitespace</comment>9:f41906e41efde3f7473abaa52fa161dc</validCheckSum>
         <validCheckSum><comment>Fixing TRUNK-4040</comment>3:74026cd4543ebbf561999a81c276224d</validCheckSum>
 		<preConditions onFail="MARK_RAN">
 			<not>

api/src/main/resources/org/openmrs/liquibase/updates/liquibase-update-to-latest-2.6.x.xml

@@ -11,6 +11,7 @@
 
 -->
 <databaseChangeLog
+	logicalFilePath="liquibase-update-to-latest.xml"
 	xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
 	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
 	xmlns:ext="http://www.liquibase.org/xml/ns/dbchangelog-ext"

api/src/main/resources/org/openmrs/liquibase/updates/liquibase-update-to-latest-2.7.x.xml

@@ -11,6 +11,7 @@
 
 -->
 <databaseChangeLog
+	logicalFilePath="liquibase-update-to-latest.xml"
 	xmlns="http://www.liquibase.org/xml/ns/dbchangelog"
 	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
 	xmlns:ext="http://www.liquibase.org/xml/ns/dbchangelog-ext"
@@ -99,5 +100,14 @@
         	CREATE FUNCTION UUID() RETURNS UUID LANGUAGE SQL AS $$ SELECT uuid_generate_v1() $$;
         </sql>
     </changeSet>
+
+	<changeSet id="TRUNK-6208-2024-05-18-1004" author="k4pran" dbms="h2">
+		<!-- 
+		Changing the column type to int(10) due to Liquibase change where integer precision
+		greater than 10 is now interpreted as BIGINT in H2 databases. 
+		See: https://github.com/liquibase/liquibase/pull/4008/files 
+		-->
+		<modifyDataType tableName="program_attribute_type" columnName="retired_by" newDataType="int(10)"/>
+	</changeSet>
 
 </databaseChangeLog>

api/src/test/java/org/openmrs/util/DatabaseUpdaterDatabaseIT.java

@@ -30,7 +30,7 @@ public class DatabaseUpdaterDatabaseIT extends H2DatabaseIT {
 	 * This constant needs to be updated when adding new Liquibase update files to openmrs-core.
 	 */
 
-	private static final int CHANGE_SET_COUNT_FOR_GREATER_THAN_2_1_X = 897;
+	private static final int CHANGE_SET_COUNT_FOR_GREATER_THAN_2_1_X = 898;
 
 	private static final int CHANGE_SET_COUNT_FOR_2_1_X = 870;