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Merged
labkey-klum merged 1 commit into from
Sep 29, 2026
Merged

Test coverage for flow filter report. #3216

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12 changes: 10 additions & 2 deletions src/org/labkey/test/tests/flow/BaseFlowTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@

import org.apache.commons.io.FileUtils;
import org.apache.commons.lang3.StringUtils;
import org.jetbrains.annotations.Nullable;
import org.junit.BeforeClass;
import org.labkey.test.BaseWebDriverTest;
import org.labkey.test.Locator;
Expand Down Expand Up @@ -46,6 +47,7 @@
abstract public class BaseFlowTest extends BaseWebDriverTest
{
protected static final File PIPELINE_PATH = TestFileUtils.getSampleData("flow");
protected static final String DEFAULT_BACKGROUND_FILTER_VALUE = "Neg Cont";

@Override
public List<String> getAssociatedModules()
Expand Down Expand Up @@ -264,6 +266,12 @@ protected void uploadSampleDescriptions(File sampleFile, Map<String, FieldDefini
}

protected void setProtocolMetadata(String specimenIdColumn, String participantColumn, String dateColumn, String visitColumn, boolean setBackground)
{
setProtocolMetadata(specimenIdColumn, participantColumn, dateColumn, visitColumn, setBackground ? DEFAULT_BACKGROUND_FILTER_VALUE : null);
}

/** A null backgroundValue leaves the match column and background filter settings untouched. */
protected void setProtocolMetadata(String specimenIdColumn, String participantColumn, String dateColumn, String visitColumn, @Nullable String backgroundValue)
{
log("** Specify metadata");
goToFlowDashboard();
Expand All @@ -280,7 +288,7 @@ protected void setProtocolMetadata(String specimenIdColumn, String participantCo
if (visitColumn != null)
selectOptionByText(Locator.name("ff_visitColumn"), visitColumn);

if (setBackground)
if (backgroundValue != null)
{
// specify forground-background match columns
Locator loc1 = Locator.name("ff_matchColumn").index(0);
Expand All @@ -291,7 +299,7 @@ protected void setProtocolMetadata(String specimenIdColumn, String participantCo
selectOptionByText(Locator.name("ff_backgroundFilterField").index(0), "Sample Stim");
Locator loc = Locator.name("ff_backgroundFilterOp").index(0);
assertEquals("eq", getFormElement(loc));
setFormElement(Locator.name("ff_backgroundFilterValue").index(0), "Neg Cont");
setFormElement(Locator.name("ff_backgroundFilterValue").index(0), backgroundValue);
}

clickButton("Set Metadata");
Expand Down
38 changes: 37 additions & 1 deletion src/org/labkey/test/tests/flow/FlowTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -69,6 +69,8 @@ public class FlowTest extends BaseFlowTest
private static final String FCS_FILE_1 = "L02-060120-QUV-JS";
private static final String FCS_FILE_2 = "L04-060120-QUV-JS";
private static final String QUV_ANALYSIS_NAME = "QUV analysis";
private static final String PTID_COLUMN = "Sample PTID";
private static final String VISIT_COLUMN = "Sample Visit";

@BeforeClass
public static void initR()
Expand Down Expand Up @@ -100,6 +102,7 @@ public void _doTestSteps()
sampleTypeAndMetadataTest();
customGraphQuery();
positivityReportTest();
backgroundFilterRInjectionTest();
qcReportTest();
copyAnalysisScriptTest();
removeAnalysisFilter();
Expand Down Expand Up @@ -498,7 +501,7 @@ protected void configureSampleTypeAndMetadata()
fields.put("Comment", FieldDefinition.ColumnType.String);

uploadSampleDescriptions(TestFileUtils.getSampleData("flow/8color/sample-set.tsv"), fields, new String[]{"Exp Name", "Well Id"}, new String[]{"EXPERIMENT NAME", "WELL ID"});
setProtocolMetadata(null, "Sample PTID", null, "Sample Visit", true);
setProtocolMetadata(null, PTID_COLUMN, null, VISIT_COLUMN, true);

goToFlowDashboard();
clickAndWait(Locator.linkContainingText("49 sample descriptions"));
Expand Down Expand Up @@ -619,6 +622,39 @@ public void positivityReportTest()
verifyDeleted(reportName);
}

/**
* GH Issue 1525: a background filter value reaches the generated R script as data, not code. The payload closes the
* generated string literal and both enclosing list() calls, so an unescaped value aborts qc.R before it emits output.
*/
@LogMethod
public void backgroundFilterRInjectionTest()
{
final String marker = "R_INJECTION_1525";
final String reportName = "R injection QC report";

setProtocolMetadata(null, PTID_COLUMN, null, VISIT_COLUMN,
DEFAULT_BACKGROUND_FILTER_VALUE + "\")); stop(\"" + marker + "\"); #");

log("** Creating QC report '" + reportName + "'");
goToFlowDashboard();

final QCReportEditorPage qcReport = new FlowReportsWebpart(getDriver()).createQCReport();
qcReport.setName(reportName);
qcReport.setSubset("Singlets/L/Live/3+/4+/(IFNg+|IL2+)");
qcReport.setStatistic(QCReportEditorPage.Stat.Freq_Of_Parent);
qcReport.addFieldFilter("Name", "Contains", "L02");
qcReport.save();

clickAndWait(Locator.linkWithText(reportName));
WebElement reportView = Locator.id("report-view").findElement(getDriver());

Locator.tagWithClass("table", "labkey-r-tsvout").waitForElement(reportView, WAIT_FOR_PAGE);
assertTextNotPresent(marker);

deleteReport(reportName);
setProtocolMetadata(null, PTID_COLUMN, null, VISIT_COLUMN, DEFAULT_BACKGROUND_FILTER_VALUE);
}

@LogMethod
public void qcReportTest()
{
Expand Down
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