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Delete search index in an indexing task #7376

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d410742
Delete search index in an indexing task
labkey-jeckels Feb 1, 2026
7bec58e
More cleanup
labkey-jeckels Feb 1, 2026
074be5b
Update search/src/org/labkey/search/model/LuceneSearchServiceImpl.java
labkey-jeckels Feb 2, 2026
35a12ad
Merge branch 'develop' into fb_676_deleteIndexAsTask
labkey-danield Feb 4, 2026
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2 changes: 1 addition & 1 deletion api/src/org/labkey/api/cache/BlockingCache.java
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Original file line number Diff line number Diff line change
Expand Up @@ -99,7 +99,7 @@ public V get(@NotNull K key, @Nullable Object argument, CacheLoader<K, V> loader
if (null == loader)
loader = _loader;

try (var ignored = DebugInfoDumper.pushThreadDumpContext(this.getClass().getSimpleName() + ".get(" + key + ")"))
try (var _ = DebugInfoDumper.pushThreadDumpContext(this.getClass().getSimpleName() + ".get(" + key + ")"))
{
synchronized (loader == null ? _cache : loader.getSyncObject(_cache))
{
Expand Down
60 changes: 37 additions & 23 deletions api/src/org/labkey/api/util/DebugInfoDumper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -162,7 +162,7 @@ record ThreadExtraContext(String context, StackTraceElement[] stack, long startT
* This is primarily intended to help understand deadlocks. Developers are encouraged to
* add information related to attaining locks or starting transactions.
*/
public static _PopAutoCloseable pushThreadDumpContext(String context)
public static QuietCloser pushThreadDumpContext(String context)
{
final var arr = _threadDumpExtraContext.computeIfAbsent(Thread.currentThread(), (_) -> Collections.synchronizedList(new ArrayList<>()));
int size = arr.size();
Expand All @@ -178,7 +178,7 @@ public static void resetThreadDumpContext()
}


public static class _PopAutoCloseable implements AutoCloseable
public static class _PopAutoCloseable implements QuietCloser
{
final int _size;

Expand All @@ -193,7 +193,7 @@ public void close()
var arr = _threadDumpExtraContext.get(Thread.currentThread());
assert null != arr;
while (arr.size() > _size)
arr.remove(arr.size() - 1);
arr.removeLast();
}
}

Expand Down Expand Up @@ -407,7 +407,7 @@ public static synchronized void dumpThreads(LoggerWriter logWriter)
logWriter.debug("*********************************************");
}

// GitHib Issue 713: Automatically include PG locks and active queries in thread dumps
// GitHub Issue 713: Automatically include PG locks and active queries in thread dumps
UserSchema schema = QueryService.get().getUserSchema(User.getAdminServiceUser(), ContainerManager.getRoot(), BasePostgreSqlDialect.POSTGRES_SCHEMA_NAME);
// Schema won't exist on SQLServer
if (schema != null)
Expand Down Expand Up @@ -489,26 +489,9 @@ private static void dumpOneThread(Thread thread, LoggerWriter logWriter, Map<Thr
// subtract 1 because dumpThreads includes Thread.run() in the stack trace
logWriter.debug(String.format("%3d\t\t%s", stack.length-i-1, stack[i].toString()));
}
var extraInfo = _threadDumpExtraContext.get(thread);
if (null != extraInfo && !extraInfo.isEmpty())
for (String line : getFormattedExtraContext(thread))
{
logWriter.debug("extra stack context (may not match stacktrace if thread is not blocked)");
var messages = extraInfo.toArray(new ThreadExtraContext[0]);
for (var i = messages.length-1 ; i>= 0 ; i--)
{
logWriter.debug("\t" + messages[i].context.replace('\n',' ') + "\tage: " + (System.currentTimeMillis() - messages[i].startTime) + "ms");
var messageStack = messages[i].stack();
if (null != messageStack)
{
for (int j=0, count=0 ; j<messageStack.length && count < 4; j++)
{
if (skipMethods.contains(messageStack[j].getMethodName()))
continue;
logWriter.debug(String.format("%3d\t\t%s", messageStack.length - j, messageStack[j].toString()));
count++;
}
}
}
logWriter.debug(line);
}

if (ConnectionWrapper.getProbableLeakCount() > 0)
Expand All @@ -517,6 +500,37 @@ private static void dumpOneThread(Thread thread, LoggerWriter logWriter, Map<Thr
}
}

/**
* Returns formatted extra stack context lines for the given thread, suitable for display in thread dumps.
* Returns an empty list if the thread has no extra context.
*/
public static List<String> getFormattedExtraContext(Thread thread)
{
var extraInfo = _threadDumpExtraContext.get(thread);
if (extraInfo == null || extraInfo.isEmpty())
return List.of();

List<String> result = new ArrayList<>();
result.add("extra stack context (may not match stacktrace if thread is not blocked)");
var messages = extraInfo.toArray(new ThreadExtraContext[0]);
for (int i = messages.length - 1; i >= 0; i--)
{
result.add("\t" + messages[i].context.replace('\n', ' ') + "\tage: " + (System.currentTimeMillis() - messages[i].startTime) + "ms");
var messageStack = messages[i].stack();
if (messageStack != null)
{
for (int j = 0, count = 0; j < messageStack.length && count < 4; j++)
{
if (skipMethods.contains(messageStack[j].getMethodName()))
continue;
result.add(String.format("%3d\t\t%s", messageStack.length - j, messageStack[j].toString()));
count++;
}
}
}
return result;
}

/**
* Writes the current set of thread stacks once to the supplied logger.
*/
Expand Down
7 changes: 7 additions & 0 deletions core/src/org/labkey/core/admin/threads.jsp
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,8 @@
<%@ page import="java.util.Date" %>
<%@ page import="java.util.Set" %>
<%@ page import="org.labkey.api.data.TransactionFilter" %>
<%@ page import="org.labkey.api.util.DebugInfoDumper" %>
<%@ page import="java.util.List" %>
<%@ page extends="org.labkey.api.jsp.JspBase" %>
<%
HttpView<AdminController.ThreadsBean> me = HttpView.currentView();
Expand Down Expand Up @@ -70,6 +72,11 @@ for (Thread t : bean.threads)
{
%><%= h(" at " + e + "\n") %><%
}
List<String> extraContext = DebugInfoDumper.getFormattedExtraContext(t);
for (String line : extraContext)
{
%><%= h(line + "\n") %><%
}
}
catch (Exception x)
{
Expand Down
32 changes: 24 additions & 8 deletions search/src/org/labkey/search/model/AbstractSearchService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,7 @@
import org.labkey.api.security.User;
import org.labkey.api.services.ServiceRegistry;
import org.labkey.api.util.ContextListener;
import org.labkey.api.util.DebugInfoDumper;
import org.labkey.api.util.ExceptionUtil;
import org.labkey.api.util.Formats;
import org.labkey.api.util.GUID;
Expand All @@ -51,6 +52,7 @@
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.util.Pair;
import org.labkey.api.util.Path;
import org.labkey.api.util.QuietCloser;
import org.labkey.api.util.ShutdownListener;
import org.labkey.api.util.StringUtilsLabKey;
import org.labkey.api.util.SystemMaintenance;
Expand Down Expand Up @@ -227,7 +229,7 @@ void complete(boolean success)
}
};
addItem(i);
final Item r = new Item(this, (q) -> queueItem(i), pri, null);
final Item r = new Item(this, (_) -> queueItem(i), pri, null);
queueItem(r);
}

Expand Down Expand Up @@ -412,7 +414,13 @@ public int compareTo(@NotNull AbstractSearchService.Item o)
}


final Item _commitItem = new Item(null, (q) -> {}, PRIORITY.commit, null);
private static String getSearchThreadDumpContext(Item i)
{
String taskDescription = i._task != null ? i._task.getDescription() : "unknown";
return "Search item: " + i._id + " (task: " + taskDescription + ")";
}

final Item _commitItem = new Item(null, (_) -> {}, PRIORITY.commit, null);


@Override
Expand Down Expand Up @@ -469,7 +477,7 @@ public void setLastIndexedForPath(Path path, long time, long indexed)
@Override
public final void deleteContainer(final String id)
{
Consumer<TaskIndexingQueue> r = (q) -> {
Consumer<TaskIndexingQueue> r = (_) -> {
deleteIndexedContainer(id);
synchronized (_commitLock)
{
Expand Down Expand Up @@ -512,7 +520,7 @@ public void clearLastIndexed()
public void reindexContainerFiles(Container c)
{
//Create new runnable instead of using existing methods so they can be run within the same job.
Consumer<TaskIndexingQueue> r = (q) -> {
Consumer<TaskIndexingQueue> r = (_) -> {
//Remove old items
clearIndexedFileSystemFiles(c);

Expand Down Expand Up @@ -721,7 +729,7 @@ public void indexError(Resource r, Throwable t)
});
// The indexer uses multiple threads for different types of work. Queue a Runnable first, and when it executes,
// queue an Item to ensure all queues are cleared
task.addRunnable(null, priority, (q) -> {
task.addRunnable(null, priority, (_) -> {
logQueueStatus("drainQueue's Runnable.run()");
task.addNoop(priority);
});
Expand Down Expand Up @@ -865,7 +873,7 @@ public Map<String, Map<String, Object>> getCustomSearchJsonMap(User user, @NotNu
if (resourceResolverKeyIdentifier == null)
continue;
resolverIdentifiers
.computeIfAbsent(resourceResolverKeyIdentifier.first, (k) -> new HashMap<>())
.computeIfAbsent(resourceResolverKeyIdentifier.first, (_) -> new HashMap<>())
.put(resourceResolverKeyIdentifier.second, resourceIdentifier);
}

Expand Down Expand Up @@ -1078,6 +1086,7 @@ public void shutdownStarted()
{
Item i = null;
boolean success = true;
QuietCloser threadDumpContext = null;

try
{
Expand All @@ -1086,9 +1095,10 @@ public void shutdownStarted()
if (null != i)
{
final Item item = i;
threadDumpContext = DebugInfoDumper.pushThreadDumpContext(getSearchThreadDumpContext(item));
while (!_shuttingDown && _itemQueue.size() > 1000)
{
try {Thread.sleep(100);}catch(InterruptedException ignored){}
try {Thread.sleep(100);}catch(InterruptedException _){}
}

Container c;
Expand Down Expand Up @@ -1149,6 +1159,8 @@ public Container getContainer()
}
finally
{
if (threadDumpContext != null)
threadDumpContext.close();
if (null != i)
{
try
Expand Down Expand Up @@ -1248,6 +1260,7 @@ private void _indexLoop()
{
Item i = null;
boolean success = false;
QuietCloser threadDumpContext = null;
try
{
i = getItemToIndex();
Expand All @@ -1267,6 +1280,7 @@ private void _indexLoop()
return;
}

threadDumpContext = DebugInfoDumper.pushThreadDumpContext(getSearchThreadDumpContext(i));
WebdavResource r = i.getResource();
if (null == r || !r.exists())
{
Expand Down Expand Up @@ -1331,6 +1345,8 @@ private void _indexLoop()
{
try
{
if (threadDumpContext != null)
threadDumpContext.close();
if (null != i)
i.complete(success);
}
Expand Down Expand Up @@ -1525,7 +1541,7 @@ public Map<String, Object> getIndexerStats()
history.addAll(_history);
}

IndexerRateAccumulator historyAccumulator = new IndexerRateAccumulator(history.get(history.size() - 1).getStart());
IndexerRateAccumulator historyAccumulator = new IndexerRateAccumulator(history.getLast().getStart());
SimpleDateFormat f = new SimpleDateFormat("h:mm a");
StringBuilder hourly = new StringBuilder();
hourly.append("<table>");
Expand Down
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