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Scope laboratory assay run template lookups to the appropriate container #290

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Scope laboratory assay run template lookups to the appropriate container #290

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7bd95a9
Scope laboratory assay template lookups to the request container
labkey-martyp Jun 23, 2026
8ac6b0e
Scope assay template lookups to the workbook parent as well
labkey-martyp Jun 23, 2026
4a0ec2a
Extract assay template container-scoping into a shared helper
labkey-martyp Jun 23, 2026
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26 changes: 23 additions & 3 deletions laboratory/api-src/org/labkey/api/laboratory/assay/DefaultAssayParser.java
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,7 @@
import org.json.JSONArray;
import org.json.JSONObject;
import org.labkey.api.collections.CaseInsensitiveHashMap;
import org.labkey.api.data.CompareType;
import org.labkey.api.data.Container;
import org.labkey.api.data.ConvertHelper;
import org.labkey.api.data.DbSchema;
Expand Down Expand Up @@ -462,13 +463,30 @@ protected void validateRows(List<Map<String, Object>> rows, ImportContext contex
errors.confirmNoErrors();
}

/**
* Returns the set of container ids in which an assay run template for a request in the given container may
* legitimately live: the container itself, plus its parent when the request runs in a workbook (mirroring the
* run-template picker, which sources templates from Laboratory.Utils.getQueryContainerPath). Used to scope
* assay_run_templates lookups to the request's folder tree without reaching an unrelated container.
*/
public static List<String> getTemplateContainerIds(Container c)
{
List<String> ids = new ArrayList<>();
ids.add(c.getId());
if (c.isWorkbook())
ids.add(c.getParent().getId());
return ids;
}

protected void saveTemplate(ViewContext ctx, int templateId, int runId) throws BatchValidationException
{
try
{
//validate the template exists
//validate the template exists in (or above) this container
TableInfo ti = DbSchema.get("laboratory").getTable("assay_run_templates");
TableSelector ts = new TableSelector(ti, new SimpleFilter(FieldKey.fromString("rowid"), templateId), null);
SimpleFilter filter = new SimpleFilter(FieldKey.fromString("rowid"), templateId);

@bbimber bbimber Jun 23, 2026

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Similar to the comment I just posted: this code is basically replicating ContainerFilter. I think we should switch this to use UserSchema, which looks like it might just handle the container aspects seamlessly for us

@labkey-martyp labkey-martyp Jun 23, 2026

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Oh yeah I see the ContainerFilter.Type.WorkbookAndParent now. I can do a quick update.

@bbimber bbimber Jun 23, 2026 •
edited
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The default behavior when querying the parent container is to include workbooks, so the module code shouldnt need to do much. See another solution to this PR here: #292

@labkey-martyp labkey-martyp Jun 23, 2026

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Ok I'll check it out

filter.addCondition(FieldKey.fromString("container"), getTemplateContainerIds(_container), CompareType.IN);
TableSelector ts = new TableSelector(ti, filter, null);
if (ts.getRowCount() == 0)
{
throw new BatchValidationException(Collections.singletonList(new ValidationException("Unknown template: " + templateId)), null);
Expand Down Expand Up @@ -586,7 +604,9 @@ protected Map<String, Map<String, Object>> getTemplateRowMap(ImportContext conte

TableInfo ti = DbSchema.get("laboratory").getTable("assay_run_templates");

TableSelector ts = new TableSelector(ti, new SimpleFilter(FieldKey.fromString("rowid"), templateId), null);
SimpleFilter filter = new SimpleFilter(FieldKey.fromString("rowid"), templateId);
filter.addCondition(FieldKey.fromString("container"), getTemplateContainerIds(_container), CompareType.IN);
TableSelector ts = new TableSelector(ti, filter, null);
Map<String, Object>[] maps = ts.getMapArray();
if (maps.length == 0)
{
Expand Down
18 changes: 16 additions & 2 deletions laboratory/src/org/labkey/laboratory/assay/AssayHelper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -30,9 +30,11 @@
import org.labkey.api.cache.CacheManager;
import org.labkey.api.collections.CaseInsensitiveHashMap;
import org.labkey.api.collections.CollectionUtils;
import org.labkey.api.data.CompareType;
import org.labkey.api.data.Container;
import org.labkey.api.data.ContainerManager;
import org.labkey.api.data.RuntimeSQLException;
import org.labkey.api.data.SimpleFilter;
import org.labkey.api.data.TSVMapWriter;
import org.labkey.api.data.Table;
import org.labkey.api.data.TableInfo;
Expand All @@ -50,7 +52,9 @@
import org.labkey.api.laboratory.LaboratoryService;
import org.labkey.api.laboratory.assay.AssayDataProvider;
import org.labkey.api.laboratory.assay.AssayImportMethod;
import org.labkey.api.laboratory.assay.DefaultAssayParser;
import org.labkey.api.query.BatchValidationException;
import org.labkey.api.query.FieldKey;
import org.labkey.api.query.ValidationException;
import org.labkey.api.security.User;
import org.labkey.api.util.FileUtil;
Expand Down Expand Up @@ -131,16 +135,26 @@ public Map<String, Object> saveTemplate(User u, Container c, ExpProtocol protoco
row.put("title", title);
row.put("importMethod", importMethod);
row.put("json", json.toString());
row.put("container", c.getId());

if (templateId == null)
{
row.put("container", c.getId());
row = Table.insert(u, ti, row);
}
else
{
// Table.update operates by global PK; verify the template is reachable from this container
// (here, or the parent when in a workbook) before updating, and leave its container unchanged.
SimpleFilter filter = new SimpleFilter(FieldKey.fromString("rowid"), templateId);
filter.addCondition(FieldKey.fromString("container"), DefaultAssayParser.getTemplateContainerIds(c), CompareType.IN);
if (!new TableSelector(ti, filter, null).exists())
{
errors.addRowError(new ValidationException("Unknown template: " + templateId));
throw errors;
}

row.put("rowid", templateId);
row = Table.update(u, ti, row, templateId);
row = Table.update(u, ti, row, templateId); // "container" intentionally absent -> not moved
}

return row;
Expand Down