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GitHub Issue 875: Standard Assay Multi-File Transform Import Skips First Data Row #2896

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GitHub Issue 875: Standard Assay Multi-File Transform Import Skips First Data Row #2896

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fd37365
GpatAssayTest to randomlyAddTransformScript for testing GitHub Issue 875
cnathe Feb 25, 2026
a6ac46d
remove hardcoded boolean (set for TC testing)
cnathe Feb 25, 2026
e280a67
TestDataGenerator.randomBoolean to optionally include a message for l…
cnathe Feb 26, 2026
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13 changes: 12 additions & 1 deletion src/org/labkey/test/tests/GpatAssayTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,7 @@
import org.labkey.test.util.EscapeUtil;
import org.labkey.test.util.LogMethod;
import org.labkey.test.util.LoggedParam;
import org.labkey.test.util.RReportHelper;
import org.labkey.test.util.TestDataGenerator;
import org.labkey.test.util.core.webdav.WebDavUploadHelper;
import org.openqa.selenium.WebElement;
Expand Down Expand Up @@ -72,11 +73,13 @@ public class GpatAssayTest extends BaseWebDriverTest
private static final String ASSAY_NAME_FNA = "FASTA Assay";
private static final String ASSAY_NAME_FNA_MULTIPLE = "FASTA Assay - Multiple file upload";
private static final String ASSAY_NAME_FNA_MULTIPLE_SINGLE_INPUT = "FASTA Assay - Multiple file single input upload";
private static final File RTRANSFORM_SCRIPT_FILE_NOOP = TestFileUtils.getSampleData("qc/noopTransform.R");

@BeforeClass
public static void doSetup()
{
GpatAssayTest init = getCurrentTest();
new RReportHelper(init).ensureRConfig();
init._containerHelper.createProject(init.getProjectName(), "Assay");
init.goToProjectHome();
}
Expand Down Expand Up @@ -256,6 +259,14 @@ private void importFastaGpatAssay(File fnaFile, String assayName)
clickButton("Save and Finish", defaultWaitForPage);
}

// GitHub Issue #875: Optionally add transform scripts in GPAT assay design to test code path with and without transform script
private void randomlyAddTransformScript(ReactAssayDesignerPage assayDesignerPage)
{
boolean shouldAddTransformScript = TestDataGenerator.randomBoolean("whether to add transform script in assay design");
if (shouldAddTransformScript)
assayDesignerPage.addTransformScript(RTRANSFORM_SCRIPT_FILE_NOOP);
}

@LogMethod
private ReactAssayDesignerPage startCreateGpatAssay(File dataFile, @LoggedParam String assayName)
{
Expand All @@ -265,9 +276,9 @@ private ReactAssayDesignerPage startCreateGpatAssay(File dataFile, @LoggedParam
_fileBrowserHelper.importFile(dataFile.getName(), "Create New Standard Assay Design");

ReactAssayDesignerPage assayDesignerPage = new ReactAssayDesignerPage(getDriver());

if (assayName != null)
assayDesignerPage.setName(assayName);
randomlyAddTransformScript(assayDesignerPage);
return assayDesignerPage;
}

Expand Down
10 changes: 9 additions & 1 deletion src/org/labkey/test/util/TestDataGenerator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -799,7 +799,15 @@ public String randomDateString(String dateFormat, Date min, Date max)

public static boolean randomBoolean()
{
return ThreadLocalRandom.current().nextBoolean();
return randomBoolean(null);
}

public static boolean randomBoolean(@Nullable String message)
{
boolean value = ThreadLocalRandom.current().nextBoolean();
if (message != null)
TestLogger.log("Generated random boolean value for %s: %s".formatted(message, value));
return value;
}

private @NotNull List<String> getFieldsForFile()
Expand Down