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Merged
labkey-nicka merged 2 commits into from
Jul 30, 2026
+12 −23
Merged

Use details view when looking up samples #3132

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1fb66b1
Use details view when looking up samples
labkey-nicka Jul 29, 2026
72582a9
Use JSONArray
labkey-nicka Jul 29, 2026
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35 changes: 12 additions & 23 deletions src/org/labkey/test/util/exp/SampleTypeAPIHelper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@
*/
package org.labkey.test.util.exp;

import org.json.JSONArray;
import org.junit.Assert;
import org.labkey.remoteapi.CommandException;
import org.labkey.remoteapi.Connection;
Expand All @@ -28,14 +29,12 @@
import org.labkey.test.params.experiment.SampleTypeDefinition;
import org.labkey.test.util.DomainUtils;
import org.labkey.test.util.DomainUtils.DomainKind;
import org.labkey.test.util.EscapeUtil;
import org.labkey.test.util.TestDataGenerator;

import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.NoSuchElementException;
Expand Down Expand Up @@ -149,45 +148,36 @@ public static Map<Integer, String> getSortedRowIdToSamplesMap(String containerPa
*/
public static Map<String, Integer> getRowIdsForSamples(String containerPath, String sampleTypeName, List<String> sampleNames) throws IOException, CommandException
{

// Use json for the value parameter of the filter. This allows for tricky characters like ";" to be passed to the API.
StringBuilder json = new StringBuilder("{json:[");

Iterator<String> iterator = sampleNames.iterator();

while (iterator.hasNext()) {
String sampleName = iterator.next();
json.append(EscapeUtil.toJSONStr(sampleName));
if (iterator.hasNext()) {
json.append(", ");
} else {
json.append("]}");
}
}
StringBuilder json = new StringBuilder("{json:").append(new JSONArray(sampleNames)).append("}");

// Use the details view to avoid column and filter settings on the default view
String detailsView = "~~DETAILS~~";
Connection connection = WebTestHelper.getRemoteApiConnection();
SelectRowsCommand cmd = new SelectRowsCommand("samples", sampleTypeName);
cmd.setColumns(Arrays.asList("RowId", "Name"));
cmd.setColumns(List.of("RowId", "Name"));
cmd.addFilter("Name", json, Filter.Operator.IN);
cmd.setViewName(detailsView);

SelectRowsResponse response = cmd.execute(connection, containerPath);

String errorMsg = "The sample names returned from the query do not match the sample names sent in.";

// There have been some TC failures where selectRows is not returning anything when it should. Adding this
// logging to help get more logging when/if it happens again.
if(response.getRowCount().intValue() == 0)
if (response.getRowCount().intValue() == 0)
{
cmd = new SelectRowsCommand("samples", sampleTypeName);
cmd.setColumns(Arrays.asList("Name"));
cmd.setColumns(List.of("Name"));
cmd.setViewName(detailsView);

SelectRowsResponse responseCount = cmd.execute(connection, containerPath);

errorMsg = errorMsg + "\n" + String.format("No rows were returned with filter. The sample type '%s' has %d rows.",
sampleTypeName, responseCount.getRowCount().intValue());

List<String> names = new ArrayList<>();
for(Map<String, Object> row : responseCount.getRows())
for (Map<String, Object> row : responseCount.getRows())
{
Object tempName = row.get("Name");
names.add(tempName.toString());
Expand All @@ -198,16 +188,15 @@ public static Map<String, Integer> getRowIdsForSamples(String containerPath, Str

Map<String, Integer> rowIds = new TreeMap<>();

for(Map<String, Object> row : response.getRows())
for (Map<String, Object> row : response.getRows())
{
Object name = row.get("Name");
Object value = row.get("RowId");
rowIds.put(name.toString(), Integer.parseInt(value.toString()));
}

// Check that the names returned from the query match the names sent in.
Assert.assertEquals(errorMsg,
new HashSet<>(sampleNames), rowIds.keySet());
Assert.assertEquals(errorMsg, new HashSet<>(sampleNames), rowIds.keySet());

return rowIds;
}
Expand Down