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Upgrade to Spring Boot 4, Spring Framework 7, and Tomcat 11 #7331

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95232a3
Upgrade to Spring Boot 4, Spring Framework 7, and Tomcat 11
labkey-jeckels Jan 15, 2026
0ab14df
Simplify cleaning
labkey-jeckels Jan 15, 2026
f519901
Simplify cleaning
labkey-jeckels Jan 15, 2026
421ff89
Stop checking Tomcat version since we embed it
labkey-jeckels Jan 15, 2026
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2 changes: 0 additions & 2 deletions api/src/org/labkey/api/ApiModule.java
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Original file line number Diff line number Diff line change
Expand Up @@ -106,7 +106,6 @@
import org.labkey.api.module.ModuleLoader;
import org.labkey.api.module.ModuleLoader.StartupPropertyStartupListener;
import org.labkey.api.module.ModuleXml;
import org.labkey.api.module.TomcatVersion;
import org.labkey.api.query.AbstractQueryUpdateService;
import org.labkey.api.query.AliasManager;
import org.labkey.api.query.DetailsURL;
Expand Down Expand Up @@ -522,7 +521,6 @@ public void registerServlets(ServletContext servletCtx)
Table.TestCase.class,
TableSelectorTestCase.class,
TempTableInClauseGenerator.TestCase.class,
TomcatVersion.TestCase.class,
URLHelper.TestCase.class,
UserManager.TestCase.class,
ViewCategoryManager.TestCase.class,
Expand Down
147 changes: 47 additions & 100 deletions api/src/org/labkey/api/data/TempTableTracker.java
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Original file line number Diff line number Diff line change
Expand Up @@ -16,53 +16,77 @@

package org.labkey.api.data;

import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.labkey.api.cache.CacheManager;
import org.labkey.api.data.dialect.SqlDialect;
import org.labkey.api.util.FileUtil;
import org.labkey.api.util.ShutdownListener;
import org.labkey.api.util.logging.LogHelper;

import java.io.File;
import java.io.IOException;
import java.io.RandomAccessFile;
import java.lang.ref.Reference;
import java.lang.ref.ReferenceQueue;
import java.lang.ref.WeakReference;
import java.lang.ref.Cleaner;
import java.util.Map;
import java.util.TreeMap;
import java.util.TreeSet;
import java.util.concurrent.atomic.AtomicBoolean;

/**
* User: Matthew
* Date: May 4, 2006
* Time: 7:27:50 PM
*/
public class TempTableTracker extends WeakReference<Object>
public class TempTableTracker
{
private static final Logger _log = LogManager.getLogger(TempTableTracker.class);
private static final Logger _log = LogHelper.getLogger(TempTableTracker.class, "Manages temp tables and their deletion");
private static final String LOGFILE = "CPAS_sqlTempTables.log";
private static final Map<String, TempTableTracker> createdTableNames = new TreeMap<>();
private static final ReferenceQueue<Object> cleanupQueue = new ReferenceQueue<>();
private static final Cleaner cleaner = Cleaner.create();

private static RandomAccessFile tempTableLog = null;

private final DbSchema schema;
private final String schemaName;
private final String tableName;
private final String qualifiedName;
private final Cleaner.Cleanable cleanable;
private final CleanupState state;

private boolean deleted = false;
private static class CleanupState implements Runnable
{
private final DbSchema schema;
private final String tableName;
private final String qualifiedName;
private final String schemaName;
private boolean deleted = false;

private CleanupState(DbSchema schema, String tableName, String qualifiedName, String schemaName)
{
this.schema = schema;
this.tableName = tableName;
this.qualifiedName = qualifiedName;
this.schemaName = schemaName;
}

@Override
public void run()
{
if (!deleted)
{
_log.debug("Deleting table " + schema.getName() + "." + tableName);
schema.dropTableIfExists(tableName);

deleted = true;
untrack(qualifiedName, schemaName, tableName);
}
}
}

private TempTableTracker(DbSchema schema, String tableName, Object ref)
{
super(ref, cleanupQueue);
this.schema = schema;
this.schemaName = schema.getName();
this.tableName = tableName;
this.qualifiedName = this.schemaName + "." + this.tableName;
this.state = new CleanupState(schema, tableName, qualifiedName, schemaName);
cleanable = cleaner.register(ref, state);
}


Expand All @@ -71,21 +95,19 @@ private TempTableTracker(String schemaName, String tableName, Object ref)
this(DbSchema.get(schemaName), tableName, ref); // TODO: Treat as provisioned?
}

private static final Object initlock = new Object();
private static final Object LOCK = new Object();
private static boolean initialized = false;

// make sure temp table tracker is initialized
public static void init()
{
synchronized(initlock)
synchronized(LOCK)
{
if (!initialized)
{
initialized = true;
synchronizeLog(true);
purgeTempSchema();
tempTableThread.setDaemon(true);
tempTableThread.start();
}
}
}
Expand Down Expand Up @@ -120,56 +142,22 @@ private static TempTableTracker track(TempTableTracker ttt)
}
}


private DbSchema getSchema()
{
return schema;
}


public synchronized void delete()
{
if (deleted)
return;

sqlDelete();

deleted = true;
untrack();
}


private boolean sqlDelete()
{
DbSchema schema = getSchema();
_log.debug("Deleting table " + schema.getName() + "." + tableName);
schema.dropTableIfExists(tableName);
return true;
cleanable.clean();
}


@Override
protected void finalize() throws Throwable
{
if (!deleted)
_log.error("finalizing undeleted TempTableTracker: " + qualifiedName);
super.finalize();
}


private void untrack()
private static void untrack(String qualifiedName, String schemaName, String tableName)
{
_log.debug("untrack(" + qualifiedName + ")");

synchronized(createdTableNames)
{
var ttt = createdTableNames.remove(qualifiedName);
createdTableNames.remove(qualifiedName);
appendToLog("-" + schemaName + "\t" + tableName + "\n");

if (createdTableNames.isEmpty() || System.currentTimeMillis() > lastSync + CacheManager.DAY)
synchronizeLog(false);

ttt.clear();
}
}

Expand Down Expand Up @@ -267,7 +255,7 @@ else if (s.charAt(0) == '-')
tempTableLog.setLength(0);
for (TempTableTracker ttt : createdTableNames.values())
{
if (!ttt.deleted)
if (!ttt.state.deleted)
appendToLog("+" + ttt.schemaName + "\t" + ttt.tableName + "\n");
}
}
Expand All @@ -285,47 +273,12 @@ else if (s.charAt(0) == '-')

static final TempTableThread tempTableThread = new TempTableThread();

static class TempTableThread extends Thread implements ShutdownListener
public static class TempTableThread implements ShutdownListener
{
AtomicBoolean _shutdown = new AtomicBoolean(false);

TempTableThread()
{
super("Temp table cleanup");
setDaemon(true);
}

@Override
public void run()
{
while (true)
{
try
{
Reference<?> r = _shutdown.get() ? cleanupQueue.poll() : cleanupQueue.remove();
if (_shutdown.get() && r == null)
return;
//noinspection RedundantCast
TempTableTracker t = (TempTableTracker)(Object)r;
t.delete();
}
catch (InterruptedException x)
{
_log.debug("interrupted");
}
catch (Throwable x)
{
_log.error("unexpected error", x);
}
}
}


@Override
public void shutdownPre()
public String getName()
{
_shutdown.set(true);
interrupt();
return "Temp table cleanup";
}

@Override
Expand All @@ -335,16 +288,10 @@ public void shutdownStarted()
{
for (TempTableTracker ttt : createdTableNames.values())
{
ttt.sqlDelete();
ttt.deleted = true;
ttt.state.run();
}
}

try
{
join(5000);
}
catch (InterruptedException ignored) {}
synchronizeLog(false);
}
}
Expand Down
20 changes: 0 additions & 20 deletions api/src/org/labkey/api/module/ModuleLoader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -173,7 +173,6 @@ public class ModuleLoader implements MemTrackerListener, ShutdownListener

private static Throwable _startupFailure = null;
private static boolean _newInstall = false;
private static TomcatVersion _tomcatVersion = null;
private static JavaVersion _javaVersion = null;

private static final String BANNER = """
Expand Down Expand Up @@ -535,8 +534,6 @@ private void doInit(Execution execution) throws ServletException

AppProps.getInstance().setContextPath(_servletContext.getContextPath());

setTomcatVersion();

File root = FileUtil.getAbsoluteCaseSensitiveFile(new File(_servletContext.getRealPath(""))).getParentFile();
FileLike labkeyRoot = new FileSystemLike.Builder(root).readwrite().noMemCheck().root();
_webappDir = labkeyRoot.resolveChild("labkeyWebapp");
Expand Down Expand Up @@ -1399,23 +1396,6 @@ public JavaVersion getJavaVersion()
return _javaVersion;
}

/**
* Sets the running Tomcat version, if servlet container is recognized and supported. Otherwise, ConfigurationException is thrown and server fails to start.
* <p>
* Warnings for deprecated Tomcat versions are handled in CoreWarningProvider.
*
* @throws ConfigurationException if Tomcat version is not recognized or supported
*/
private void setTomcatVersion()
{
_tomcatVersion = TomcatVersion.get();
}

public TomcatVersion getTomcatVersion()
{
return _tomcatVersion;
}

/**
* Initialize and update the Core module first. We want to change the core tables before we display pages, request
* login, check permissions, or initialize any of the other modules.
Expand Down
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