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@LongRunningScript, search logging, warning providers improvements #7482

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db5c32e
@LongRunningScript, search logging, warning providers improvements
labkey-adam Mar 9, 2026
a2944e4
Switch MailHelper warning provider to provide static warnings
labkey-adam Mar 9, 2026
9ccf24e
AttachmentContainerListener now detects for orphaned attachments
labkey-adam Mar 9, 2026
c6a28fa
Check for orphans before deleting containers
labkey-adam Mar 10, 2026
0b204a1
Log all orphaned attachments
labkey-adam Mar 10, 2026
29afe37
Merge remote-tracking branch 'origin/develop' into fb_long_running_sc…
labkey-adam Mar 10, 2026
a9c2369
Correct comment
labkey-adam Mar 10, 2026
1e8f795
Remove container param
labkey-adam Mar 10, 2026
18e6df4
Code review feedback
labkey-adam Mar 14, 2026
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2 changes: 2 additions & 0 deletions api/src/org/labkey/api/attachments/AttachmentService.java
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Expand Up @@ -140,6 +140,8 @@ static AttachmentService get()

HttpView<?> getFindAttachmentParentsView();

void detectOrphans();

class DuplicateFilenameException extends IOException implements SkipMothershipLogging
{
private final List<String> _errors = new ArrayList<>();
Expand Down
42 changes: 23 additions & 19 deletions api/src/org/labkey/api/data/ContainerManager.java
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Expand Up @@ -38,6 +38,7 @@
import org.labkey.api.admin.FolderWriterImpl;
import org.labkey.api.admin.StaticLoggerGetter;
import org.labkey.api.attachments.AttachmentParent;
import org.labkey.api.attachments.AttachmentService;
import org.labkey.api.audit.AuditLogService;
import org.labkey.api.audit.AuditTypeEvent;
import org.labkey.api.audit.provider.ContainerAuditProvider;
Expand Down Expand Up @@ -422,6 +423,7 @@ public static Container createContainerFromTemplate(Container parent, String nam

// import objects into the target folder
XmlObject folderXml = vf.getXmlBean("folder.xml");

if (folderXml instanceof FolderDocument folderDoc)
{
FolderImportContext importCtx = new FolderImportContext(user, c, folderDoc, null, new StaticLoggerGetter(LogManager.getLogger(FolderImporterImpl.class)), vf);
Expand Down Expand Up @@ -1539,7 +1541,7 @@ else if (hasAncestryRead)
}

if (!addFolder)
LOG.debug("isNavAccessOpen restriction: \"" + f.getPath() + "\"");
LOG.debug("isNavAccessOpen restriction: \"{}\"", f.getPath());
}

if (addFolder)
Expand Down Expand Up @@ -1915,7 +1917,7 @@ private static boolean delete(final Container c, User user, @Nullable String com
throw new IllegalStateException("Container not flagged as being deleted: " + c.getPath());
}

LOG.debug("Starting container delete for " + c.getContainerNoun(true) + " " + c.getPath());
LOG.debug("Starting container delete for {} {}", c.getContainerNoun(true), c.getPath());

// Tell the search indexer to drop work for the container that's about to be deleted
SearchService.get().purgeForContainer(c);
Expand All @@ -1942,6 +1944,8 @@ private static boolean delete(final Container c, User user, @Nullable String com
setContainerTabDeleted(c.getParent(), c.getName(), c.getParent().getFolderType().getName());
}

AttachmentService.get().detectOrphans();

fireDeleteContainer(c, user);

SqlExecutor sqlExecutor = new SqlExecutor(CORE.getSchema());
Expand Down Expand Up @@ -1981,11 +1985,11 @@ private static boolean delete(final Container c, User user, @Nullable String com
boolean success = CORE.getSchema().getScope().executeWithRetry(tryDeleteContainer);
if (success)
{
LOG.debug("Completed container delete for " + c.getContainerNoun(true) + " " + c.getPath());
LOG.debug("Completed container delete for {} {}", c.getContainerNoun(true), c.getPath());
}
else
{
LOG.warn("Failed to delete container: " + c.getPath());
LOG.warn("Failed to delete container: {}", c.getPath());
}
return success;
}
Expand Down Expand Up @@ -2025,13 +2029,13 @@ public static void deleteAll(Container root, User user, @Nullable String comment
if (!hasTreePermission(root, user, DeletePermission.class))
throw new UnauthorizedException("You don't have delete permissions to all folders");

LOG.debug("Starting container (and children) delete for " + root.getContainerNoun(true) + " " + root.getPath());
LOG.debug("Starting container (and children) delete for {} {}", root.getContainerNoun(true), root.getPath());
Set<Container> depthFirst = getAllChildrenDepthFirst(root);
depthFirst.add(root);

delete(depthFirst, user, comment);

LOG.debug("Completed container (and children) delete for " + root.getContainerNoun(true) + " " + root.getPath());
LOG.debug("Completed container (and children) delete for {} {}", root.getContainerNoun(true), root.getPath());
}

public static void deleteAll(Container root, User user) throws UnauthorizedException
Expand Down Expand Up @@ -2426,7 +2430,7 @@ protected static void fireCreateContainer(Container c, User user, @Nullable Stri
}
catch (Throwable t)
{
LOG.error("fireCreateContainer for " + cl.getClass().getName(), t);
LOG.error("fireCreateContainer for {}", cl.getClass().getName(), t);
}
}
}
Expand All @@ -2437,14 +2441,14 @@ protected static void fireDeleteContainer(Container c, User user)

for (ContainerListener l : list)
{
LOG.debug("Deleting " + c.getPath() + ": fireDeleteContainer for " + l.getClass().getName());
LOG.debug("Deleting {}: fireDeleteContainer for {}", c.getPath(), l.getClass().getName());
try
{
l.containerDeleted(c, user);
}
catch (RuntimeException e)
{
LOG.error("fireDeleteContainer for " + l.getClass().getName(), e);
LOG.error("fireDeleteContainer for {}", l.getClass().getName(), e);

// Issue 17560: Fail fast (first Throwable aborts iteration)
throw e;
Expand Down Expand Up @@ -2490,7 +2494,7 @@ public static void firePropertyChangeEvent(ContainerPropertyChangeEvent evt)
}
catch (Throwable t)
{
LOG.error("firePropertyChangeEvent for " + l.getClass().getName(), t);
LOG.error("firePropertyChangeEvent for {}", l.getClass().getName(), t);
}
}
}
Expand Down Expand Up @@ -2523,8 +2527,8 @@ public static Container createDefaultSupportContainer()
// create a "support" container. Admins can do anything,
// Users can read/write, Guests can read.
return bootstrapContainer(DEFAULT_SUPPORT_PROJECT_PATH,
RoleManager.getRole(AuthorRole.class),
RoleManager.getRole(ReaderRole.class)
RoleManager.getRole(AuthorRole.class),
RoleManager.getRole(ReaderRole.class)
);
}

Expand Down Expand Up @@ -2693,7 +2697,7 @@ public static Container bootstrapContainer(String path, @NotNull Role userRole,

if (c == null)
{
LOG.debug("Creating new container for path '" + path + "'");
LOG.debug("Creating new container for path '{}'", path);
newContainer = true;
c = ensureContainer(path, user);
}
Expand All @@ -2710,7 +2714,7 @@ public static Container bootstrapContainer(String path, @NotNull Role userRole,

if (newContainer || 0 == policyCount.intValue())
{
LOG.debug("Setting permissions for '" + path + "'");
LOG.debug("Setting permissions for '{}'", path);
MutableSecurityPolicy policy = new MutableSecurityPolicy(c);
policy.addRoleAssignment(SecurityManager.getGroup(Group.groupUsers), userRole);
if (guestRole != null)
Expand Down Expand Up @@ -2881,25 +2885,25 @@ public void testFolderType()

private void testOneFolderType(FolderType folderType)
{
LOG.info("testOneFolderType(" + folderType.getName() + "): creating container");
LOG.info("testOneFolderType({}): creating container", folderType.getName());
Container newFolder = createContainer(_testRoot, "folderTypeTest", TestContext.get().getUser());
FolderType ft = newFolder.getFolderType();
assertEquals(FolderType.NONE, ft);

Container newFolderFromCache = getForId(newFolder.getId());
assertNotNull(newFolderFromCache);
assertEquals(FolderType.NONE, newFolderFromCache.getFolderType());
LOG.info("testOneFolderType(" + folderType.getName() + "): setting folder type");
LOG.info("testOneFolderType({}): setting folder type", folderType.getName());
newFolder.setFolderType(folderType, TestContext.get().getUser());

newFolderFromCache = getForId(newFolder.getId());
assertNotNull(newFolderFromCache);
assertEquals(newFolderFromCache.getFolderType().getName(), folderType.getName());
assertEquals(newFolderFromCache.getFolderType().getDescription(), folderType.getDescription());

LOG.info("testOneFolderType(" + folderType.getName() + "): deleteAll");
LOG.info("testOneFolderType({}): deleteAll", folderType.getName());
deleteAll(newFolder, TestContext.get().getUser()); // There might be subfolders because of container tabs
LOG.info("testOneFolderType(" + folderType.getName() + "): deleteAll complete");
LOG.info("testOneFolderType({}): deleteAll complete", folderType.getName());
Container deletedContainer = getForId(newFolder.getId());

if (deletedContainer != null)
Expand Down Expand Up @@ -2946,7 +2950,7 @@ private static void logNode(MultiValuedMap<String, String> mm, String name, int

for (String childName : nodes)
{
LOG.debug(StringUtils.repeat(" ", offset) + childName);
LOG.debug("{}{}", StringUtils.repeat(" ", offset), childName);
logNode(mm, childName, offset + 1);
}
}
Expand Down
100 changes: 49 additions & 51 deletions api/src/org/labkey/api/data/SqlScriptManager.java
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Expand Up @@ -41,6 +41,8 @@
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.regex.Matcher;
import java.util.regex.Pattern;


/**
Expand Down Expand Up @@ -172,7 +174,27 @@ public Set<SqlScript> getPreviouslyRunScripts()
return runScripts;
}

@NotNull
public Collection<String> getPreviouslyRunSqlScriptNames()
{
TableInfo tinfo = getTableInfoSqlScripts();

// Skip if the table hasn't been created yet (bootstrap case)
if (getTableInfoSqlScripts().getTableType() == DatabaseTableType.NOT_IN_DB)
return Collections.emptySet();

SimpleFilter filter = new SimpleFilter();
ColumnInfo fileNameColumn = tinfo.getColumn("FileName");
filter.addCondition(tinfo.getColumn("ModuleName"), _provider.getProviderName());
filter.addCondition(tinfo.getColumn("FileName"), _schema.getResourcePrefix() + "-", CompareType.STARTS_WITH);

return new TableSelector(tinfo, Collections.singleton(fileNameColumn), filter, null).getCollection(String.class);
}

private static final String SKIP_SCRIPT_ANNOTATION = "@SkipScriptIfSchemaExists";
// Use to annotate a script that may take a long time to execute. A message will be logged, including a reason and
// strongly discouraging server shutdown or restart during upgrade.
private static final Pattern LONG_RUNNING_SCRIPT_ANNOTATION_PATTERN = Pattern.compile("@LongRunningScript\\('(?<reason>.+)'\\)");

public void runScript(@Nullable User user, SqlScript script, ModuleContext moduleContext, @Nullable Connection conn) throws SqlScriptException
{
Expand Down Expand Up @@ -204,74 +226,50 @@ public void runScript(@Nullable User user, SqlScript script, ModuleContext modul
}
else
{
Matcher matcher = LONG_RUNNING_SCRIPT_ANNOTATION_PATTERN.matcher(contents);
if (matcher.find())
{
// Reason is expected to be a gerund phrase that summarizes the time-consuming action(s) that the
// script is taking. It should start with a lowercase letter and should not end with punctuation.
// Examples:
// - updating all ObjectId columns to BIGINT
// - restructuring the way workflow jobs are stored
String reason = matcher.group("reason");
LOG.info(
"""
This script could take a long time to execute because it is {}.
Do NOT shut down or restart the server until this script and the rest of the upgrade is complete.
Any interruption will likely corrupt the schemas, requiring a database restore and a restart of the upgrade process.
""",
reason
);
}
dialect.runSql(description, schema, contents, moduleContext, conn);
LOG.info("Finished running script: {}", description);
}
}
catch(Throwable t)
catch (Throwable t)
{
throw new SqlScriptException(t, description);
}

if (script.isValidName())
{
// Should never be true, unless getNewScripts() isn't doing its job. TODO: Remove update() branch below.
assert !hasBeenRun(script);
if (hasBeenRun(script))
update(user, script);
else
insert(user, script);
}
insert(user, script);
}

@NotNull
public Collection<String> getPreviouslyRunSqlScriptNames()
private void insert(@Nullable User user, SqlScript script)
{
TableInfo tinfo = getTableInfoSqlScripts();

// Skip if the table hasn't been created yet (bootstrap case)
if (getTableInfoSqlScripts().getTableType() == DatabaseTableType.NOT_IN_DB)
return Collections.emptySet();

SimpleFilter filter = new SimpleFilter();
ColumnInfo fileNameColumn = tinfo.getColumn("FileName");
filter.addCondition(tinfo.getColumn("ModuleName"), _provider.getProviderName());
filter.addCondition(tinfo.getColumn("FileName"), _schema.getResourcePrefix() + "-", CompareType.STARTS_WITH);

return new TableSelector(tinfo, Collections.singleton(fileNameColumn), filter, null).getCollection(String.class);
}

public boolean hasBeenRun(SqlScript script)
{
TableInfo tinfo = getTableInfoSqlScripts();

// Make sure DbSchema thinks SqlScript table is in the database. If not, we're bootstrapping and it's either just before or just after the first
// script is run. In either case, invalidate to force reloading schema from database meta data.
// Make sure DbSchema thinks SqlScripts table is in the database. If not, we're bootstrapping, and it's just
// after the first script has run. Invalidate to force reloading the schema from database metadata.
if (tinfo.getTableType() == DatabaseTableType.NOT_IN_DB)
{
CacheManager.clearAllKnownCaches();
return false;
tinfo = getTableInfoSqlScripts(); // Reload to update table type
}

PkFilter filter = new PkFilter(tinfo, new String[]{_provider.getProviderName(), script.getDescription()});

return new TableSelector(getTableInfoSqlScripts(), filter, null).exists();
}


public void insert(@Nullable User user, SqlScript script)
{
SqlScriptBean ss = new SqlScriptBean(script.getProvider().getProviderName(), script.getDescription());

Table.insert(user, getTableInfoSqlScripts(), ss);
}


public void update(@Nullable User user, SqlScript script)
{
Object[] pk = new Object[]{script.getProvider().getProviderName(), script.getDescription()};

Table.update(user, getTableInfoSqlScripts(), new HashMap<>(), pk); // Update user and modified date
Table.insert(user, tinfo, new SqlScriptBean(script.getProvider().getProviderName(), script.getDescription()));
}

// Allow null version for oddball cases like gel_reports, which claims to have schemas but no schema version. That
Expand Down Expand Up @@ -301,15 +299,15 @@ public void updateSchemaVersion(Double version)
}


public @NotNull SchemaBean ensureSchemaBean()
protected @NotNull SchemaBean ensureSchemaBean()
{
SchemaBean bean = getSchemaBean();

return null != bean ? bean : new SchemaBean(_schema.getDisplayName(), _provider.getProviderName(), 0);
}


protected @Nullable SchemaBean getSchemaBean()
private @Nullable SchemaBean getSchemaBean()
{
TableInfo tinfo = getTableInfoSchemas();

Expand Down
1 change: 0 additions & 1 deletion api/src/org/labkey/api/reports/model/ReportPropsManager.java
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Expand Up @@ -47,7 +47,6 @@

import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;

Expand Down
5 changes: 2 additions & 3 deletions api/src/org/labkey/api/search/NoopSearchService.java
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Expand Up @@ -29,7 +29,6 @@
import org.labkey.api.webdav.WebdavResource;

import java.io.Reader;
import java.time.Duration;
import java.util.Collection;
import java.util.Collections;
import java.util.Date;
Expand Down Expand Up @@ -292,7 +291,7 @@ public void deleteIndex(String reason)
}

@Override
public void clearLastIndexed()
public void clearLastIndexed(String reason)
{
}

Expand Down Expand Up @@ -379,7 +378,7 @@ public boolean isRunning()
}

@Override
public void updateIndex()
public void updateIndex(String reason)
{
}

Expand Down
5 changes: 2 additions & 3 deletions api/src/org/labkey/api/search/SearchService.java
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Expand Up @@ -54,7 +54,6 @@
import java.io.IOException;
import java.io.InputStream;
import java.io.Reader;
import java.net.URISyntaxException;
import java.sql.SQLException;
import java.sql.Timestamp;
import java.util.ArrayList;
Expand Down Expand Up @@ -438,7 +437,7 @@ public String normalizeHref(Path contextPath, Container c)
void resetIndex();
void startCrawler();
void pauseCrawler();
void updateIndex();
void updateIndex(String reason);
void refreshNow();

@Nullable Throwable getConfigurationError();
Expand Down Expand Up @@ -472,7 +471,7 @@ public String normalizeHref(Path contextPath, Container c)
void deleteContainer(String id);

void deleteIndex(String reason); // close the index if it's been initialized, then delete the index directory and reset lastIndexed values
void clearLastIndexed(); // reset lastIndexed values and initiate aggressive crawl. must be callable before (and after) start() has been called.
void clearLastIndexed(String reason); // reset lastIndexed values and initiate aggressive crawl. must be callable before (and after) start() has been called.
void maintenance();

//
Expand Down
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