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Guard material writes in ExpGeneratorHelper with UpdatePermission #8043

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7574aef
Guard material writes in ExpGeneratorHelper with UpdatePermission
ankurjuneja Sep 13, 2026
35de233
claude code review changes
ankurjuneja Sep 14, 2026
ea8474a
Merge branch 'develop' into fb_provenanceLineagePermCheck_1452
ankurjuneja Sep 16, 2026
da3265a
code review comments
ankurjuneja Sep 16, 2026
1f0dafe
Merge branch 'develop' into fb_provenanceLineagePermCheck_1452
ankurjuneja Sep 18, 2026
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42 changes: 38 additions & 4 deletions experiment/src/org/labkey/experiment/pipeline/ExpGeneratorHelper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@
*/
package org.labkey.experiment.pipeline;

import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.jetbrains.annotations.NotNull;
import org.jetbrains.annotations.Nullable;
Expand All @@ -38,6 +39,7 @@
import org.labkey.api.exp.api.ExpRun;
import org.labkey.api.exp.api.ExperimentService;
import org.labkey.api.exp.api.ProvenanceService;
import org.labkey.api.exp.api.SampleTypeService;
import org.labkey.api.pipeline.PipelineJob;
import org.labkey.api.pipeline.PipelineJobException;
import org.labkey.api.pipeline.PipelineJobService;
Expand All @@ -50,7 +52,11 @@
import org.labkey.api.query.FieldKey;
import org.labkey.api.query.ValidationException;
import org.labkey.api.security.User;
import org.labkey.api.security.permissions.Permission;
import org.labkey.api.security.permissions.ReadPermission;
import org.labkey.api.util.FileUtil;
import org.labkey.api.view.NotFoundException;
import org.labkey.api.view.UnauthorizedException;
import org.labkey.experiment.api.ExpDataImpl;
import org.labkey.experiment.api.ExpMaterialImpl;
import org.labkey.experiment.api.ExpRunImpl;
Expand All @@ -72,6 +78,8 @@
*/
public class ExpGeneratorHelper
{
private static final Logger LOG = LogManager.getLogger(ExpGeneratorHelper.class);

static private ExpData addData(Container container, User user, Map<URI, ExpData> datas, URI originalURI, XarSource source) throws ExperimentException
{
ExpData data = datas.get(originalURI);
Expand Down Expand Up @@ -278,6 +286,30 @@ static public ExpRunImpl insertRun(Container container, User user,
return run;
}

private static ExpMaterial resolveReadableMaterial(User user, String lsid)
{
ExpMaterial material = ExperimentService.get().getExpMaterial(lsid);
if (material == null || !material.getContainer().hasPermission(user, ReadPermission.class))
throw new NotFoundException("Could not find material with LSID '" + lsid + "'");
return material;
}

// Unresolved and unauthorized both return NotFoundException, so a foreign LSID is never confirmed.
private static void assertCanEditLineage(User user, String lsid, ExpMaterial material)
{
Class<? extends Permission> permission = SampleTypeService.SampleOperations.EditLineage.getPermissionClass();
if (material == null || (permission != null && !material.getContainer().hasPermission(user, permission)))
{
if (material != null)
LOG.warn("User {} cannot edit lineage of material {} in {}", user, lsid, material.getContainer().getPath());
throw new NotFoundException("Could not find material with LSID '" + lsid + "'");
}

if (!material.isOperationPermitted(SampleTypeService.SampleOperations.EditLineage))
throw new UnauthorizedException(SampleTypeService.get().getOperationNotPermittedMessage(
List.of(material), SampleTypeService.SampleOperations.EditLineage));
}

static private ExpRunImpl _insertRun(Container container,
User user,
String runName,
Expand Down Expand Up @@ -373,18 +405,19 @@ else if (action.isEnd())
stepApp.setProperty(user, pd, prop.getValue());
}

// material inputs
// material inputs - adds an edge
for (String lsid : action.getMaterialInputs())
{
ExpMaterial material = ExperimentService.get().getExpMaterial(lsid);
ExpMaterial material = resolveReadableMaterial(user, lsid);
material.setRun(run);
stepApp.addMaterialInput(user, material, null, null);
}

// material outputs
// material outputs - these rewrite the material's lineage, so require edit rights
for (String lsid : action.getMaterialOutputs())
{
ExpMaterialImpl material = (ExpMaterialImpl) ExperimentService.get().getExpMaterial(lsid);
assertCanEditLineage(user, lsid, material);
material.setSourceApplication(stepApp);
// set up the output to the run
if (action.isEnd())
Expand Down Expand Up @@ -537,9 +570,10 @@ static private void promoteInputs(Set<RecordedAction> actions, ExpRun run, Map<U
}
}

// Promotes a step input to a run input
static private void addMaterialInput(ExpRun run, ExpProtocolApplication app, String lsid, User user)
{
ExpMaterial material = ExperimentService.get().getExpMaterial(lsid);
ExpMaterial material = resolveReadableMaterial(user, lsid);
material.setRun(run);
app.addMaterialInput(user, material, null, null);
}
Expand Down
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