TRUNK-6208: Upgrade 2.7 Platform to Liquibase 4.27.0 (openmrs#4637)

* TRUNK-6208: Upgrade 2.7 Platform to Liquibase 4.27.0 * TRUNK-6208 remove h2 changeset * TRUNK-6208 update changeset count after remove h2 changeset * TRUNK-6208 change type from int(11) to int --------- Co-authored-by: dkayiwa <[email protected]>
Wandji69 · Jun 27, 2024 · 834c0bd · 834c0bd
1 parent 55ac37f
commit 834c0bd
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Showing 15 changed files with 126 additions and 30 deletions.
diff --git a/api/src/main/java/org/openmrs/api/db/hibernate/HibernateEncounterDAO.java b/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;

diff --git a/api/src/main/java/org/openmrs/liquibase/ChangeLogDetective.java b/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;
 
@@ -85,9 +86,16 @@ public String getInitialLiquibaseSnapshotVersion(String context, LiquibaseProvid
 			Liquibase liquibase = null;
 			try {
 				for (String filename : changeSets) {
+					String scopeId = LiquibaseScopeHandling.enterLiquibaseUILoggingService();
+
 					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());
+
+
+					LiquibaseScopeHandling.exitLiquibaseScope(scopeId);
 					liquibase.close();
 
 					List<ChangeSet> refinedUnrunChangeSets = excludeVintageChangeSets(filename, rawUnrunChangeSets);
@@ -141,9 +149,14 @@ public List<String> getUnrunLiquibaseUpdateFileNames(String snapshotVersion, Str
 		Liquibase liquibase = null;
 		try {
 			for (String filename : updateFileNames) {
+				String scopeId = LiquibaseScopeHandling.enterLiquibaseUILoggingService();
 				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());
+
+				LiquibaseScopeHandling.exitLiquibaseScope(scopeId);
 				liquibase.close();
 
 				log.info("file '{}' contains {} un-run change sets", filename, unrunChangeSets.size());

diff --git a/api/src/main/java/org/openmrs/liquibase/LiquibaseScopeHandling.java b/api/src/main/java/org/openmrs/liquibase/LiquibaseScopeHandling.java
@@ -0,0 +1,33 @@
+/**
+ * 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.liquibase;
+
+import java.util.Collections;
+import java.util.Map;
+import java.util.logging.Level;
+
+import liquibase.Scope;
+import liquibase.ui.LoggerUIService;
+
+public class LiquibaseScopeHandling {
+
+	public static String enterLiquibaseUILoggingService() throws Exception {
+		// Temp workaround to silence liquibase writing to stdout - https://github.com/liquibase/liquibase/issues/2396,
+		// https://github.com/liquibase/liquibase/issues/3651
+		LoggerUIService loggerUIService = new LoggerUIService();
+		loggerUIService.setStandardLogLevel(Level.FINE);
+		Map<String, Object> m = Collections.singletonMap(Scope.Attr.ui.name(), loggerUIService);
+		return Scope.enter(m);
+	}
+
+	public static void exitLiquibaseScope(String scopeId) throws Exception {
+		Scope.exit(scopeId);
+	}
+}
diff --git a/api/src/main/java/org/openmrs/liquibase/OpenmrsClassLoaderResourceAccessor.java b/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;
 	}
 }
diff --git a/api/src/main/java/org/openmrs/util/DatabaseUpdater.java b/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;
@@ -33,13 +35,15 @@
 import liquibase.resource.CompositeResourceAccessor;
 import liquibase.resource.FileSystemResourceAccessor;
 import liquibase.resource.ResourceAccessor;
+import liquibase.ui.LoggerUIService;
 import org.apache.commons.io.IOUtils;
 import org.openmrs.annotation.Authorized;
 import org.openmrs.api.context.Context;
 import org.openmrs.liquibase.ChangeLogDetective;
 import org.openmrs.liquibase.ChangeLogVersionFinder;
 import org.openmrs.liquibase.ChangeSetExecutorCallback;
 import org.openmrs.liquibase.LiquibaseProvider;
+import org.openmrs.liquibase.LiquibaseScopeHandling;
 import org.openmrs.liquibase.OpenmrsClassLoaderResourceAccessor;
 import org.openmrs.module.ModuleClassLoader;
 import org.slf4j.Logger;
@@ -68,6 +72,7 @@
 import java.util.Map;
 import java.util.Properties;
 import java.util.Set;
+import java.util.logging.Level;
 
 /**
  * This class uses Liquibase to update the database. <br>
@@ -214,8 +219,13 @@ 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();
+
+		String scopeId = LiquibaseScopeHandling.enterLiquibaseUILoggingService();
+		int numChangeSetsToRun = new StatusCommandStep()
+			.listUnrunChangeSets(contexts,
+				new LabelExpression(), liquibase.getDatabaseChangeLog(), liquibase.getDatabase()).size();
+		LiquibaseScopeHandling.exitLiquibaseScope(scopeId);
+
 		Database database = null;
 		LockService lockHandler = null;
 
@@ -233,7 +243,7 @@ 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 +436,13 @@ 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) {
@@ -604,13 +619,15 @@ public static List<OpenMRSChangeSet> getDatabaseChanges() throws Exception {
 		Liquibase liquibase = null;
 		try {
 			for (String filename : changeLogFileNames) {
+				String scopeId = LiquibaseScopeHandling.enterLiquibaseUILoggingService();
 				liquibase = getLiquibase(filename);
 				List<ChangeSet> changeSets = liquibase.getDatabaseChangeLog().getChangeSets();
 
 				for (ChangeSet changeSet : changeSets) {
 					OpenMRSChangeSet openMRSChangeSet = new OpenMRSChangeSet(changeSet, liquibase.getDatabase());
 					result.add(openMRSChangeSet);
 				}
+				LiquibaseScopeHandling.exitLiquibaseScope(scopeId);
 				liquibase.close();
 			}
 		}
@@ -669,18 +686,22 @@ public static List<OpenMRSChangeSet> getUnrunDatabaseChanges(String... changeLog
 
 			List<OpenMRSChangeSet> results = new ArrayList<>();
 
+			String scopeId = LiquibaseScopeHandling.enterLiquibaseUILoggingService();
 			for (String changelogFile : changeLogFilenames) {
 				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);
 				}
 			}
 
+			LiquibaseScopeHandling.exitLiquibaseScope(scopeId);
 			return results;
 
 		}
@@ -884,4 +905,15 @@ 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);
+		}
+	}
 }
diff --git a/api/src/main/java/org/openmrs/util/OpenmrsConstants.java b/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 final String LIQUIBASE_DUPLICATE_FILE_MODE_DEFAULT = GlobalConfiguration.DuplicateFileMode.WARN.name();
+
 	private OpenmrsConstants() {
 	}
 

diff --git a/api/src/main/resources/org/openmrs/liquibase/updates/liquibase-update-to-latest-2.0.x.xml b/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>

diff --git a/api/src/main/resources/org/openmrs/liquibase/updates/liquibase-update-to-latest-2.2.x.xml b/api/src/main/resources/org/openmrs/liquibase/updates/liquibase-update-to-latest-2.2.x.xml
@@ -63,7 +63,7 @@
                 <column name="retired" type="boolean" defaultValueBoolean="false">
                     <constraints nullable="false" />
                 </column>
-                <column name="retired_by" type="int(11)" />
+                <column name="retired_by" type="int" />
                 <column name="date_retired" type="datetime" />
                 <column name="retire_reason" type="varchar(255)" defaultValue="null" />
                 <column name="uuid" type="char(38)">