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Issue 980: Remove deprecated UI for deriving samples in LKS interface #3226

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Merged
labkey-susanh merged 4 commits into from
Oct 6, 2026
Merged

Issue 980: Remove deprecated UI for deriving samples in LKS interface #3226

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ae521af
GH Issue 980: Remove deprecated UI for deriving samples in LKS interface
labkey-susanh Oct 5, 2026
ed26cd3
Remove actions and JSPs that are no longer used
labkey-susanh Oct 5, 2026
42732ca
Merge remote-tracking branch 'origin/develop' into fb_lksDeriveSample…
labkey-susanh Oct 5, 2026
fd58014
Remove some unuseful parameters
labkey-susanh Oct 5, 2026
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7 changes: 1 addition & 6 deletions src/org/labkey/test/tests/SampleTypeFolderExportImportTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,6 @@
import org.labkey.test.util.DataRegionTable;
import org.labkey.test.util.EscapeUtil;
import org.labkey.test.util.LogMethod;
import org.labkey.test.util.OptionalFeatureHelper;
import org.labkey.test.util.PortalHelper;
import org.labkey.test.util.SampleTypeHelper;
import org.labkey.test.util.TestDataGenerator;
Expand Down Expand Up @@ -102,12 +101,8 @@ public BrowserType bestBrowser()
protected void doCleanup(boolean afterTest)
{
super.doCleanup(afterTest);
if (afterTest)
if (!afterTest)
{
OptionalFeatureHelper.resetOptionalFeature(createDefaultConnection(), "deriveSamplesNotInApp");
}
else {
OptionalFeatureHelper.setOptionalFeature(createDefaultConnection(), "deriveSamplesNotInApp", true);
SampleTypeFolderExportImportTest init = getCurrentTest();
init.doSetup();
}
Expand Down
92 changes: 44 additions & 48 deletions src/org/labkey/test/tests/SampleTypeLimitsTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,6 @@
*/
package org.labkey.test.tests;

import org.jetbrains.annotations.Nullable;
import org.junit.BeforeClass;
import org.junit.Test;
import org.junit.experimental.categories.Category;
Expand All @@ -36,10 +35,10 @@
import org.labkey.test.params.list.ListDefinition;
import org.labkey.test.params.list.VarListDefinition;
import org.labkey.test.util.DataRegionTable;
import org.labkey.test.util.OptionalFeatureHelper;
import org.labkey.test.util.PortalHelper;
import org.labkey.test.util.SampleTypeHelper;
import org.labkey.test.util.TestDataGenerator;
import org.labkey.test.util.query.QueryApiHelper;

import java.io.IOException;
import java.util.Arrays;
Expand Down Expand Up @@ -118,13 +117,6 @@ private void doSetup()
}
}

@Override
protected void doCleanup(boolean afterTest)
{
super.doCleanup(afterTest);
OptionalFeatureHelper.resetOptionalFeature(createDefaultConnection(), "deriveSamplesNotInApp");
}

@Test
public void testStringLookupFields() throws IOException, CommandException
{
Expand All @@ -148,44 +140,41 @@ public void testStringLookupFields() throws IOException, CommandException
table.clickInsertNewRow();
setFormElement(Locator.name("quf_id"), "1");
setFormElement(Locator.name("quf_name"), "1");
verifyInvalidLookupSample("quf_lookUpField", "Sample3", null);
verifyInvalidLookupSample("quf_lookUpField", "Sample3");
verifyValidLookupSample("quf_lookUpField", "Sample1");

log("Verifying editing list row with the sample display name");
table.clickEditRow("1");
verifyInvalidLookupSample("quf_lookUpField", "Sample3", null);
verifyInvalidLookupSample("quf_lookUpField", "Sample3");
verifyValidLookupSample("quf_lookUpField", "Sample2");

log("Verifying editing list row with the sample RowId");
table.clickEditRow("1");
SelectRowsCommand command = new SelectRowsCommand("samples", SAMPLE_TYPE_NAME);
command.setFilters(Arrays.asList(new Filter("Name", "Sample1")));
SelectRowsResponse response = command.execute(createDefaultConnection(), getProjectName());
verifyValidLookupSample("quf_lookUpField", response.getRows().getFirst().get("RowId").toString(), "Sample1", "query", false);
verifyValidLookupSample("quf_lookUpField", response.getRows().getFirst().get("RowId").toString(), "Sample1", "query");
}

private void verifyInvalidLookupSample(String fieldName, String sampleValue, @Nullable String expectedErrorMsg)
private void verifyInvalidLookupSample(String fieldName, String sampleValue)
{
setFormElement(Locator.name(fieldName), sampleValue);
clickButton("Submit");

String errMsg = Locators.labkeyError.findElement(getDriver()).getText();
assertEquals("Expected error is different", expectedErrorMsg == null ? "Could not convert value: " + sampleValue : expectedErrorMsg, errMsg);
assertEquals("Expected error is different", "Could not convert value: " + sampleValue, errMsg);
}

private void verifyValidLookupSample(String fieldName, String sampleValue)
{
verifyValidLookupSample(fieldName, sampleValue, sampleValue, "query", false);
verifyValidLookupSample(fieldName, sampleValue, sampleValue, "query");
}

private void verifyValidLookupSample(String fieldName, String sampleValue, String sampleDisplay, String dataRegionName, boolean navigateViaBreadcrumb)
private void verifyValidLookupSample(String fieldName, String sampleValue, String sampleDisplay, String dataRegionName)
{
setFormElement(Locator.name(fieldName), sampleValue);
clickButton("Submit");

if (navigateViaBreadcrumb)
clickAndWait(Locator.tagWithClass("ol", "breadcrumb").childTag("li").index(1).childTag("a"));

log("Verifying row is inserted correctly");
DataRegionTable table = DataRegionTable.DataRegion(getDriver()).withName(dataRegionName).waitFor();
assertEquals("Lookup field value is incorrect", sampleDisplay, table.getDataAsText(0, "lookUpField"));
Expand All @@ -203,48 +192,55 @@ private void insertSampleTypeRow(String regionName, String rowValue)
@Test
public void testDeriveSamplesLookupFields() throws IOException, CommandException
{
goToProjectHome();
OptionalFeatureHelper.setOptionalFeature(createDefaultConnection(), "deriveSamplesNotInApp", true);

log("Create sample type with lookup field to " + SAMPLE_TYPE_NAME);
String sampleTypeName = "SampleTypeWithLookup";
SampleTypeHelper sampleHelper = new SampleTypeHelper(this);
SampleTypeDefinition definition = new SampleTypeDefinition(sampleTypeName);
definition.addField(new FieldDefinition("label", FieldDefinition.ColumnType.String));
definition.addField(new FieldDefinition("lookUpField",
new FieldDefinition.LookupInfo(null, "exp.materials", "10000Samples")
.setTableType(FieldDefinition.ColumnType.Integer))
.setDescription("LookUp in same container with 10000 samples"));
sampleHelper.createSampleType(definition);
sampleHelper.goToSampleType(sampleTypeName);
new SampleTypeDefinition(sampleTypeName)
.addField(new FieldDefinition("label", FieldDefinition.ColumnType.String))
.addField(new FieldDefinition("lookUpField",
new FieldDefinition.LookupInfo(null, "exp.materials", SAMPLE_TYPE_NAME)
.setTableType(FieldDefinition.ColumnType.Integer))
.setDescription("LookUp in same container with 10000 samples"))
.create(createDefaultConnection(), getProjectName());
QueryApiHelper queryHelper = new QueryApiHelper(createDefaultConnection(), getProjectName(), "samples", sampleTypeName);

log("Insert one sample that we can use to derive from");
insertSampleTypeRow("Material", "Test1");
queryHelper.insertRows(List.of(Map.of("Name", "Test1", "label", "Test1")));
String parentColumn = "MaterialInputs/" + sampleTypeName;

log("Attempt Derive Samples with invalid lookup value");
initDeriveSamplesForm(sampleTypeName, "Derivative1");
verifyInvalidLookupSample("Output Sample 1_lookUpField", "Sample3", "Could not convert value 'Sample3' (String) for Integer field 'lookUpField'.");
log("Attempt to derive a sample with invalid lookup value");
try
{
queryHelper.importData(deriveSampleTsv(parentColumn, "Derivative1", "Sample3"), true);
fail("Deriving a sample with an invalid lookup value should fail");
}
catch (CommandException e)
{
checker().verifyTrue("Unexpected error for invalid lookup value: " + e.getMessage(), e.getMessage().contains("Sample3"));
}

log("Insert Derive Samples with valid lookup display value");
verifyValidLookupSample("Output Sample 1_lookUpField", "Sample2", "Sample2", "Material", true);
log("Derive a sample with valid lookup display value");
queryHelper.importData(deriveSampleTsv(parentColumn, "Derivative1", "Sample2"), true);

log("Insert Derive Samples with valid lookup to sample RowId");
initDeriveSamplesForm(sampleTypeName, "Derivative2");
log("Derive a sample with valid lookup to sample RowId");
SelectRowsCommand command = new SelectRowsCommand("samples", SAMPLE_TYPE_NAME);
command.setFilters(Arrays.asList(new Filter("Name", "Sample1")));
SelectRowsResponse response = command.execute(createDefaultConnection(), getProjectName());
verifyValidLookupSample("Output Sample 1_lookUpField", response.getRows().getFirst().get("RowId").toString(), "Sample1", "Material", true);
queryHelper.importData(deriveSampleTsv(parentColumn, "Derivative2", response.getRows().getFirst().get("RowId").toString()), true);

log("Verify derived samples have the expected lookup values");
goToProjectHome();
SampleTypeHelper sampleHelper = new SampleTypeHelper(this);
sampleHelper.goToSampleType(sampleTypeName);
DataRegionTable table = sampleHelper.getSamplesDataRegionTable();
checker().verifyEquals("Lookup field value is incorrect", "Sample2",
table.getDataAsText(table.getRowIndex("Name", "Derivative1"), "lookUpField"));
checker().verifyEquals("Lookup field value is incorrect", "Sample1",
table.getDataAsText(table.getRowIndex("Name", "Derivative2"), "lookUpField"));
}

private void initDeriveSamplesForm(String sampleTypeName, String sampleName)
private String deriveSampleTsv(String parentColumn, String sampleName, String lookupValue)
{
DataRegionTable samplesTable = DataRegionTable.DataRegion(getDriver()).withName("Material").waitFor();
samplesTable.uncheckAllOnPage();
samplesTable.checkCheckbox(0);
samplesTable.clickHeaderButtonAndWait("Derive Samples");
selectOptionByText(Locator.name("targetSampleTypeId"), sampleTypeName + " in /" + getProjectName());
clickButton("Next");
setFormElement(Locator.name("Output Sample 1_Name"), sampleName);
return "Name\t" + parentColumn + "\tlookUpField\n" + sampleName + "\tTest1\t" + lookupValue + "\n";
}

@Test
Expand Down
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