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Merged
labkey-adam merged 4 commits into from
Sep 25, 2026
Merged

Pass containers into ExperimentService methods #1074

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452f778
Pass containers into ExperimentService methods
labkey-adam Sep 22, 2026
df58b31
Pass more containers
labkey-adam Sep 22, 2026
1c93678
Push container
labkey-adam Sep 23, 2026
83fc10f
Update .gitattributes
labkey-adam Sep 24, 2026
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2 changes: 0 additions & 2 deletions .gitattributes
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Expand Up @@ -554,8 +554,6 @@ ms2/resources/queries/protein/GOMolecularFunction.query.xml -text
ms2/resources/queries/protein/GOMolecularFunction.sql -text
ms2/resources/schemas/dbscripts/postgresql/ms2-create.sql -text
ms2/resources/schemas/dbscripts/postgresql/ms2-drop.sql -text
ms2/resources/schemas/dbscripts/sqlserver/ms2-create.sql -text
ms2/resources/schemas/dbscripts/sqlserver/ms2-drop.sql -text
ms2/resources/schemas/ms2.xml -text
ms2/resources/views/runsOverview.html -text
ms2/resources/views/runsOverview.view.xml -text
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2 changes: 1 addition & 1 deletion elisa/src/org/labkey/elisa/ElisaController.java
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Expand Up @@ -111,7 +111,7 @@ public static class GetCurveFitXYPairs extends ReadOnlyApiAction<GetCurveFitXYPa
public void validateForm(GetCurveFitXYPairsForm form, Errors errors)
{
// GitHub Kanban #1236: getExpRun() resolves by global rowId; ensure the run belongs to the current container
_run = ExperimentService.get().getExpRun(form.getRunId(), getContainer());
_run = ExperimentService.get().getExpRun(getContainer(), form.getRunId());
if (_run == null)
throw new NotFoundException("Run " + form.getRunId() + " does not exist.");
if (form.getNumberOfPoints() < 2)
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16 changes: 8 additions & 8 deletions elispotassay/src/org/labkey/elispot/ElispotController.java
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Expand Up @@ -123,8 +123,8 @@ public class RunDetailsAction extends SimpleViewAction<DetailsForm>
@Override
public ModelAndView getView(DetailsForm form, BindException errors)
{
_run = ExperimentService.get().getExpRun(form.getRowId());
if (_run == null || !_run.getContainer().equals(getContainer()))
_run = ExperimentService.get().getExpRun(getContainer(), form.getRowId());
if (_run == null)
{
throw new NotFoundException("Run " + form.getRowId() + " does not exist.");
}
Expand Down Expand Up @@ -291,7 +291,7 @@ public class RunDetailRedirectAction extends SimpleRedirectAction<DetailsForm>
public ActionURL getRedirectURL(DetailsForm form)
{
// GitHub Kanban #1236: getExpRun() resolves by rowId; ensure the run belongs to the current container
ExpRun run = ExperimentService.get().getExpRun(form.getRowId(), getContainer());
ExpRun run = ExperimentService.get().getExpRun(getContainer(), form.getRowId());
if (run == null)
{
throw new NotFoundException("Run " + form.getRowId() + " does not exist.");
Expand All @@ -313,8 +313,8 @@ public ApiResponse execute(DetailsForm form, BindException errors)
{
ApiSimpleResponse response = new ApiSimpleResponse();

ExpRun run = ExperimentService.get().getExpRun(form.getRowId());
if (run == null || !run.getContainer().equals(getContainer()))
ExpRun run = ExperimentService.get().getExpRun(getContainer(), form.getRowId());
if (run == null)
{
throw new NotFoundException("Run " + form.getRowId() + " does not exist.");
}
Expand Down Expand Up @@ -558,7 +558,7 @@ public boolean handlePost(Object o, BindException errors) throws Exception
for (String selection : selections)
{
int rowId = NumberUtils.toInt(selection, -1);
ExpRun run = rowId != -1 ? ExperimentService.get().getExpRun(rowId, getContainer()) : null;
ExpRun run = rowId != -1 ? ExperimentService.get().getExpRun(getContainer(), rowId) : null;
if (run == null)
throw new NotFoundException("Run " + selection + " does not exist.");
}
Expand Down Expand Up @@ -614,8 +614,8 @@ public void testRunDetailRedirectContainerScoping() throws Exception
// Control: the same run resolves through the container-scoped lookup from its own container but not from
// folder A, demonstrating the mechanism the fix relies on (the run exists identically in both calls).
ExperimentService exp = ExperimentService.get();
assertNotNull("Run should resolve within its own container", exp.getExpRun(runInB.getRowId(), _folderB));
assertNull("Run must not resolve from a foreign container", exp.getExpRun(runInB.getRowId(), _folderA));
assertNotNull("Run should resolve within its own container", exp.getExpRun(_folderB, runInB.getRowId()));
assertNull("Run must not resolve from a foreign container", exp.getExpRun(_folderA, runInB.getRowId()));
}

private ExpRun createRun(Container c) throws Exception
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7 changes: 6 additions & 1 deletion elispotassay/src/org/labkey/elispot/pipeline/BackgroundSubtractionJob.java
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Expand Up @@ -102,7 +102,12 @@ public void run()

if (rowId != -1)
{
ExpRun run = ExperimentService.get().getExpRun(rowId);
ExpRun run = ExperimentService.get().getExpRun(getContainer(), rowId);
if (run == null)
{
info("Skipping run " + runId + ": not found in this folder.");
continue;
}

try (DbScope.Transaction transaction = ExperimentService.get().getSchema().getScope().ensureTransaction())
{
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2 changes: 1 addition & 1 deletion flow/src/org/labkey/flow/data/FlowProtocol.java
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Expand Up @@ -199,7 +199,7 @@ static public FlowProtocol getForContainer(Container container, String name)
return null;
}

// For serialzation
// For serialization
protected FlowProtocol() {}

public FlowProtocol(ExpProtocol protocol)
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20 changes: 0 additions & 20 deletions flow/src/org/labkey/flow/data/FlowWell.java
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Expand Up @@ -65,26 +65,6 @@ static public FlowWell fromWellId(long id)
return null;
}

static public List<? extends FlowWell> fromWellIds(long... ids)
{
List<FlowWell> wells = new ArrayList<>(ids.length);
List<FlowDataObject> flowobjs = fromRowIds(ids);
for (FlowDataObject flowobj : flowobjs)
if (flowobj instanceof FlowWell)
wells.add((FlowWell)flowobj);
return wells;
}

static public List<FlowWell> fromWellIds(Collection<Long> ids)
{
List<FlowWell> wells = new ArrayList<>(ids.size());
List<FlowDataObject> flowobjs = fromRowIds(ids);
for (FlowDataObject flowobj : flowobjs)
if (flowobj instanceof FlowWell)
wells.add((FlowWell)flowobj);
return wells;
}

static public FlowWell fromURL(ActionURL url, Container actionContainer, User user)
{
return fromURL(url, null, actionContainer, user);
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9 changes: 2 additions & 7 deletions luminex/src/org/labkey/luminex/LuminexController.java
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Expand Up @@ -633,17 +633,12 @@ public void validateForm(LuminexSaveExclusionsForm form, Errors errors)
}

// verify that the runId is valid and matches an existing run
if (form.getRunId() == null || ExperimentService.get().getExpRun(form.getRunId()) == null)
ExpRun run = form.getRunId() != null ? ExperimentService.get().getExpRun(getContainer(), form.getRunId()) : null;
if (run == null)
{
errors.reject(ERROR_MSG, "No run found for id " + form.getRunId());
}

ExpRun run = ExperimentService.get().getExpRun(form.getRunId());
if (!getContainer().equals(run.getContainer()))
{
errors.reject(ERROR_MSG, "The run for id " + form.getRunId() + " does not exist in the current container");
}

form.validate(errors);
}

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14 changes: 7 additions & 7 deletions nab/src/org/labkey/nab/NabAssayController.java
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Expand Up @@ -233,7 +233,7 @@ public ModelAndView getView(RenderAssayForm form, BindException errors) throws E
throw new NotFoundException("No run specified");
}
// GitHub Kanban #1892: getExpRun() resolves by global rowId; ensure the run belongs to the current container
ExpRun run = ExperimentService.get().getExpRun(form.getRowId(), getContainer());
ExpRun run = ExperimentService.get().getExpRun(getContainer(), form.getRowId());
if (run == null)
{
throw new NotFoundException("Run " + form.getRowId() + " does not exist.");
Expand Down Expand Up @@ -483,7 +483,7 @@ public void validateCommand(DeleteRunForm form, Errors errors)
throw new NotFoundException("No run specified");
}
// GitHub Kanban #1892: getExpRun() resolves by global rowId; ensure the run belongs to the current container
_run = ExperimentService.get().getExpRun(form.getRowId(), getContainer());
_run = ExperimentService.get().getExpRun(getContainer(), form.getRowId());
if (_run == null)
throw new NotFoundException("Run " + form.getRowId() + " does not exist.");

Expand Down Expand Up @@ -841,7 +841,7 @@ public ModelAndView getView(NabQCForm form, BindException errors)
form.setEdit(false);

// GitHub Kanban #1892: Resolve the run scoped to the current container
ExpRun run = ExperimentService.get().getExpRun(form.getRowId(), getContainer());
ExpRun run = ExperimentService.get().getExpRun(getContainer(), form.getRowId());
if (run == null)
{
throw new NotFoundException("Run " + form.getRowId() + " does not exist.");
Expand Down Expand Up @@ -884,7 +884,7 @@ public ApiResponse execute(NabQCForm form, BindException errors) throws Exceptio
{
ApiSimpleResponse response = new ApiSimpleResponse();
// GitHub Kanban #1892: Resolve the run scoped to the current container
ExpRun run = ExperimentService.get().getExpRun(form.getRowId(), getContainer());
ExpRun run = ExperimentService.get().getExpRun(getContainer(), form.getRowId());
if (run == null)
{
throw new NotFoundException("Run " + form.getRowId() + " does not exist.");
Expand Down Expand Up @@ -1083,7 +1083,7 @@ public class SaveQCControlInfoAction extends MutatingApiAction<QCControlInfo>
public void validateForm(QCControlInfo form, Errors errors)
{
// GitHub Kanban #1892: Resolve the run scoped to the current container
_run = ExperimentService.get().getExpRun(form.getRunId(), getContainer());
_run = ExperimentService.get().getExpRun(getContainer(), form.getRunId());
if (_run == null)
{
errors.reject(ERROR_MSG, "NAb Run " + form.getRunId() + " does not exist.");
Expand All @@ -1096,7 +1096,7 @@ public ApiResponse execute(QCControlInfo form, BindException errors) throws Exce
ApiSimpleResponse response = new ApiSimpleResponse();
DbSchema schema = DilutionManager.getSchema();
DbScope scope = schema.getScope();
ExpRun run = ExperimentService.get().getExpRun(form.getRunId());
ExpRun run = _run;

if (run != null)
{
Expand Down Expand Up @@ -1312,7 +1312,7 @@ public ApiResponse execute(RenderAssayBean form, BindException errors)
{
ApiSimpleResponse response = new ApiSimpleResponse();
// GitHub Kanban #1892: Resolve the run scoped to the current container
ExpRun run = ExperimentService.get().getExpRun(form.getRowId(), getContainer());
ExpRun run = ExperimentService.get().getExpRun(getContainer(), form.getRowId());
if (run != null)
{
List<WellExclusion> exclusions = new ArrayList<>();
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2 changes: 1 addition & 1 deletion viability/src/org/labkey/viability/ViabilityAssayUploadWizardAction.java
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Expand Up @@ -369,7 +369,7 @@ public boolean executeStep(ViabilityAssayRunUploadForm form, BindException error
ExpExperiment experiment = null;
if (form.getReRunId() != null)
{
ExpRun reRun = ExperimentService.get().getExpRun(form.getReRunId());
ExpRun reRun = ExperimentService.get().getExpRun(getContainer(), form.getReRunId());
if (reRun != null)
{
experiment = findExperiment(reRun);
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