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Use UpdateService instead of raw DbSchema layer for assay_template edits #292

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8068a00
Use UpdateService instead of raw DbSchema layer for assay_template edits
bbimber Jun 23, 2026
9a96634
Code review
bbimber Jun 24, 2026
d8e37ff
Tighten behavior around cross-container actions
bbimber Jun 24, 2026
e448eaf
Use List.get(0) instead of getFirst() so this compiles on Java 17
labkey-martyp Jun 24, 2026
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51 changes: 37 additions & 14 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 @@ -20,18 +20,19 @@
import org.apache.commons.beanutils.ConversionException;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Level;
import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.apache.poi.openxml4j.exceptions.InvalidFormatException;
import org.json.JSONArray;
import org.json.JSONObject;
import org.labkey.api.assay.AssayProvider;
import org.labkey.api.assay.AssayService;
import org.labkey.api.collections.CaseInsensitiveHashMap;
import org.labkey.api.data.Container;
import org.labkey.api.data.ContainerManager;
import org.labkey.api.data.ContainerType;
import org.labkey.api.data.ConvertHelper;
import org.labkey.api.data.DbSchema;
import org.labkey.api.data.RuntimeSQLException;
import org.labkey.api.data.SimpleFilter;
import org.labkey.api.data.Table;
import org.labkey.api.data.TableInfo;
import org.labkey.api.data.TableSelector;
import org.labkey.api.exp.PropertyDescriptor;
Expand All @@ -44,14 +45,14 @@
import org.labkey.api.laboratory.LaboratoryService;
import org.labkey.api.query.BatchValidationException;
import org.labkey.api.query.FieldKey;
import org.labkey.api.query.QueryService;
import org.labkey.api.query.UserSchema;
import org.labkey.api.query.ValidationException;
import org.labkey.api.reader.ColumnDescriptor;
import org.labkey.api.reader.ExcelFactory;
import org.labkey.api.reader.Readers;
import org.labkey.api.reader.TabLoader;
import org.labkey.api.security.User;
import org.labkey.api.assay.AssayProvider;
import org.labkey.api.assay.AssayService;
import org.labkey.api.util.FileType;
import org.labkey.api.util.JsonUtil;
import org.labkey.api.util.Pair;
Expand Down Expand Up @@ -466,10 +467,16 @@ protected void saveTemplate(ViewContext ctx, int templateId, int runId) throws B
{
try
{
//validate the template exists
TableInfo ti = DbSchema.get("laboratory").getTable("assay_run_templates");
//validate the template exists. Note: this should always act against the current container, even if the container is a workbook (e.g., it should not allow cross-workbook actions)
UserSchema us = QueryService.get().getUserSchema(ctx.getUser(), ctx.getContainer(), "laboratory");
if (us == null)
{
throw new IllegalStateException("The laboratory schema is not available in container: " + ctx.getContainer().getPath());
}

TableInfo ti = us.getTable("assay_run_templates");
TableSelector ts = new TableSelector(ti, new SimpleFilter(FieldKey.fromString("rowid"), templateId), null);
if (ts.getRowCount() == 0)
if (!ts.exists())
{
throw new BatchValidationException(Collections.singletonList(new ValidationException("Unknown template: " + templateId)), null);
}
Expand All @@ -478,11 +485,11 @@ protected void saveTemplate(ViewContext ctx, int templateId, int runId) throws B
row.put("runid", runId);
row.put("status", "Complete");

Table.update(ctx.getUser(), ti, row, templateId);
ti.getUpdateService().updateRows(ctx.getUser(), ctx.getContainer(), Arrays.asList(row), Arrays.asList(Map.of("rowId", templateId)), null, null);
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}
catch (RuntimeSQLException e)
catch (Exception e)
{
throw new BatchValidationException(Collections.singletonList(new ValidationException(e.getSQLException().getMessage())), null);
throw new BatchValidationException(Collections.singletonList(new ValidationException(e.getMessage())), null);
}
}

Expand Down Expand Up @@ -584,8 +591,12 @@ protected Map<String, Map<String, Object>> getTemplateRowMap(ImportContext conte
if (templateId == null)
return ret;

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

UserSchema us = QueryService.get().getUserSchema(context.getViewContext().getUser(), context.getViewContext().getContainer().getContainerFor(ContainerType.DataType.tabParent), "laboratory");
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if (us == null)
{
throw new IllegalStateException("Could not find the laboratory schema in container: " + context.getViewContext().getContainer().getContainerFor(ContainerType.DataType.tabParent).getPath());
}
TableInfo ti = us.getTable("assay_run_templates");
TableSelector ts = new TableSelector(ti, new SimpleFilter(FieldKey.fromString("rowid"), templateId), null);
Map<String, Object>[] maps = ts.getMapArray();
if (maps.length == 0)
Expand All @@ -595,6 +606,18 @@ protected Map<String, Map<String, Object>> getTemplateRowMap(ImportContext conte

Map<String, Object> map = maps[0];
JSONObject templateJson = new JSONObject((String)map.get("json"));

// This enforces that the request and existing record are from the same container, including for workbook/parents:
Container rowContainer = ContainerManager.getForId(String.valueOf(map.get("container")));
if (rowContainer == null)
{
throw new IllegalStateException("Unable to determine the container for template: " + templateId);
}
else if (!rowContainer.equals(context.getViewContext().getContainer()))
{
throw new IllegalStateException("Template is from the wrong container: " + templateId);
}

JSONArray rows = templateJson.getJSONArray("ResultRows");
for (JSONObject row : JsonUtil.toJSONObjectList(rows))
{
Expand Down
80 changes: 70 additions & 10 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 @@ -32,9 +32,9 @@
import org.labkey.api.collections.CollectionUtils;
import org.labkey.api.data.Container;
import org.labkey.api.data.ContainerManager;
import org.labkey.api.data.RuntimeSQLException;
import org.labkey.api.data.ContainerType;
import org.labkey.api.data.SimpleFilter;
import org.labkey.api.data.TSVMapWriter;
import org.labkey.api.data.Table;
import org.labkey.api.data.TableInfo;
import org.labkey.api.data.TableSelector;
import org.labkey.api.exp.ChangePropertyDescriptorException;
Expand All @@ -51,9 +51,14 @@
import org.labkey.api.laboratory.assay.AssayDataProvider;
import org.labkey.api.laboratory.assay.AssayImportMethod;
import org.labkey.api.query.BatchValidationException;
import org.labkey.api.query.FieldKey;
import org.labkey.api.query.QueryService;
import org.labkey.api.query.UserSchema;
import org.labkey.api.query.ValidationException;
import org.labkey.api.security.User;
import org.labkey.api.security.permissions.UpdatePermission;
import org.labkey.api.util.FileUtil;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.util.Pair;
import org.labkey.api.view.ActionURL;
import org.labkey.api.view.ViewContext;
Expand All @@ -66,6 +71,7 @@
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
Expand Down Expand Up @@ -125,35 +131,46 @@ public Map<String, Object> saveTemplate(User u, Container c, ExpProtocol protoco
{
validateTemplate(u, c, protocol, templateId, title, importMethod, json);

TableInfo ti = LaboratorySchema.getInstance().getSchema().getTable(LaboratorySchema.TABLE_ASSAY_RUN_TEMPLATES);
UserSchema us = QueryService.get().getUserSchema(u, c, "laboratory");
if (us == null)
{
throw new IllegalStateException("Could not find the laboratory schema in container: " + c.getPath());
}

TableInfo ti = us.getTable(LaboratorySchema.TABLE_ASSAY_RUN_TEMPLATES);
Map<String, Object> row = new HashMap<>();
row.put("assayId", protocol.getRowId());
row.put("title", title);
row.put("importMethod", importMethod);
row.put("json", json.toString());
row.put("container", c.getId());

if (templateId == null)
{
row = Table.insert(u, ti, row);
BatchValidationException bve = new BatchValidationException();
List<Map<String, Object>> rows = ti.getUpdateService().insertRows(u, c, Arrays.asList(row), bve, null, null);
if (bve.hasErrors())
{
throw bve;
}

return rows.get(0);
}
else
{
row.put("rowid", templateId);
row = Table.update(u, ti, row, templateId);
List<Map<String, Object>> rows = ti.getUpdateService().updateRows(u, c, Arrays.asList(row), Arrays.asList(Map.of("rowId", templateId)), null, null);
return rows.get(0);
}

return row;
}
catch (RuntimeSQLException e)
catch (Exception e)
{
_log.error(e.getMessage(), e);
errors.addRowError(new ValidationException(e.getMessage()));
throw errors;
}
}

public void validateTemplate(User u, Container c, ExpProtocol protocol, Integer templateId, String title, String importMethod, JSONObject json) throws BatchValidationException
public void validateTemplate(User u, Container c, ExpProtocol protocol, @Nullable Integer templateId, String title, String importMethod, JSONObject json) throws BatchValidationException
{
BatchValidationException errors = new BatchValidationException();

Expand All @@ -178,6 +195,49 @@ public void validateTemplate(User u, Container c, ExpProtocol protocol, Integer
throw errors;
}

// Verify if this template exists and permissions. This expects any existing row to be present in the current container:
if (templateId != null)
{
// This queries the current container+workbooks to identify the existence of rows in other reasonable containers:
UserSchema us = QueryService.get().getUserSchema(u, c.getContainerFor(ContainerType.DataType.tabParent), "laboratory");
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TableInfo ti = us.getTable("assay_run_templates");
TableSelector ts = new TableSelector(ti, PageFlowUtil.set("container"), new SimpleFilter(FieldKey.fromString("rowId"), templateId), null);
if (ts.exists())
{
Container rowContainer = ContainerManager.getForId(ts.getObject(String.class));
if (rowContainer == null)
{
errors.addRowError(new ValidationException("Unable to determine the container for template: " + templateId));
throw errors;
}

if (!rowContainer.hasPermission("AssayHelper.validateTemplate()", u, UpdatePermission.class))
{
errors.addRowError(new ValidationException("The current user does not have permission to edit template: " + templateId));
throw errors;
}

if (!c.equals(rowContainer))
{
errors.addRowError(new ValidationException("Template " + templateId + " is not from this folder"));
throw errors;
}
}
else
{
errors.addRowError(new ValidationException("Unable to find template with ID: " + templateId));
throw errors;
}
}
else
{
if (!c.hasPermission("AssayHelper.validateTemplate()", u, UpdatePermission.class))
{
errors.addRowError(new ValidationException("The current user does not have permission to creates templates in folder: " + c.getName()));
throw errors;
}
}

method.validateTemplate(u, c, protocol, templateId, title, json, errors);

if (errors.hasErrors())
Expand Down