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Issue 695: Upgrade script version of fixing container for sample files that have moved #7365

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labkey-susanh merged 2 commits into from
Jan 29, 2026
Merged

Issue 695: Upgrade script version of fixing container for sample files that have moved #7365

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Issue 695: Upgrade script version of fixing container for sample file…
labkey-susanh Jan 28, 2026
7004998
Remove info logging
labkey-susanh Jan 28, 2026
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1 change: 1 addition & 0 deletions experiment/resources/schemas/dbscripts/postgresql/exp-26.001-26.002.sql
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@@ -0,0 +1 @@
SELECT core.executeJavaUpgradeCode('fixContainerForMovedSampleFiles');
1 change: 1 addition & 0 deletions experiment/resources/schemas/dbscripts/sqlserver/exp-26.001-26.002.sql
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@@ -0,0 +1 @@
EXEC core.executeJavaUpgradeCode 'fixContainerForMovedSampleFiles';
2 changes: 1 addition & 1 deletion experiment/src/org/labkey/experiment/ExperimentModule.java
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Expand Up @@ -205,7 +205,7 @@ public String getName()
@Override
public Double getSchemaVersion()
{
return 26.001;
return 26.002;
}

@Nullable
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25 changes: 25 additions & 0 deletions experiment/src/org/labkey/experiment/ExperimentUpgradeCode.java
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Expand Up @@ -52,6 +52,7 @@
import org.labkey.api.exp.property.Domain;
import org.labkey.api.exp.property.DomainUtil;
import org.labkey.api.exp.property.PropertyService;
import org.labkey.api.files.FileContentService;
import org.labkey.api.module.ModuleContext;
import org.labkey.api.module.ModuleLoader;
import org.labkey.api.ontology.Unit;
Expand Down Expand Up @@ -484,4 +485,28 @@ else if (kind.getStorageSchemaName() == null)

return new ProvisionedSampleTypeContext(domain, provisionedTable);
}

/**
* Called from exp-26.001-26.002.sql
*/
@SuppressWarnings("unused")
public static void fixContainerForMovedSampleFiles(ModuleContext context)
{
if (context.isNewInstall())
return;

try (DbScope.Transaction tx = ExperimentService.get().ensureTransaction())
{
FileContentService service = FileContentService.get();
if (service == null)
{
LOG.error("No FileContentService found. Aborting.");
return;
}
LimitedUser admin = new LimitedUser(context.getUpgradeUser(), SiteAdminRole.class);
int numDuplicates = service.fixContainerForExpDataFiles(admin);
LOG.info("Fixed {} duplicate data files.", numDuplicates);
}
}

}
19 changes: 0 additions & 19 deletions experiment/src/org/labkey/experiment/controllers/exp/ExperimentController.java
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Expand Up @@ -7460,25 +7460,6 @@ public Object execute(Object o, BindException errors) throws Exception
}
}

@Marshal(Marshaller.Jackson)
@RequiresPermission(AdminPermission.class)
public static class RepairExpDataFilesAction extends MutatingApiAction<Object>
{
@Override
public Object execute(Object form, BindException errors)
{
FileContentService service = FileContentService.get();
if (service == null)
{
errors.reject(ERROR_GENERIC, "No FileContentService found");
return new SimpleResponse<>(false, "No FileContentService found");
}

int numDuplicates = service.fixContainerForExpDataFiles(getUser());
return success(Map.of("hadRepairs", numDuplicates > 0));
}
}

@RequiresPermission(UpdatePermission.class)
public static class UpdateMaterialQueryRowAction extends UserSchemaAction
{
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6 changes: 2 additions & 4 deletions filecontent/src/org/labkey/filecontent/FileContentServiceImpl.java
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Expand Up @@ -154,7 +154,8 @@ WHERE datafileurl IN (SELECT DataFileURL
FROM exp.data
WHERE DataFileURL IS NOT NULL
GROUP BY DataFileUrl) c
WHERE c.count > 1))""");
WHERE c.count > 1))
AND datafileurl LIKE '%/sampletype/%'""");
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@cnathe cnathe Jan 28, 2026

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unrelated to this line, but the logging for this upgrade script seems excessive. I am getting the "Ensuring file data in container /Assay Security Test" INFO log for every container in my server, twice! Seems like we could take that log info statement out?

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@labkey-susanh labkey-susanh Jan 28, 2026

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Yes, you are right. I noticed that too and thought it of questionable utility.

int count = new SqlExecutor(ExperimentService.get().getSchema().getScope()).execute(sql);
_log.info("Deleted {} duplicate entries from exp.data", count);
_log.info("Repopulating file data in exp.data.");
Expand All @@ -169,10 +170,7 @@ private void ensureFileDataInAllContainers(User user)

ExpDataTable expDataTable = ExperimentService.get().createDataTable("data", new ExpSchema(user, c), null);
if (expDataTable != null)
{
_log.info("Ensuring file data in container {}", c.getPath());
ensureFileDataUnsynchronized(expDataTable);
}
}
);
}
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