From c4f66fba0f6cc705d00644784e051dfd3049657f Mon Sep 17 00:00:00 2001
From: Lum <klum@labkey.com>
Date: Mon, 28 Sep 2026 12:41:03 -0700
Subject: [PATCH] Test coverage for flow filter report.

---
 .../labkey/test/tests/flow/BaseFlowTest.java  | 12 +++++-
 src/org/labkey/test/tests/flow/FlowTest.java  | 38 ++++++++++++++++++-
 2 files changed, 47 insertions(+), 3 deletions(-)

diff --git a/src/org/labkey/test/tests/flow/BaseFlowTest.java b/src/org/labkey/test/tests/flow/BaseFlowTest.java
index c9bf5303b8..321ace3e7b 100644
--- a/src/org/labkey/test/tests/flow/BaseFlowTest.java
+++ b/src/org/labkey/test/tests/flow/BaseFlowTest.java
@@ -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;
@@ -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()
@@ -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();
@@ -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);
@@ -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");
diff --git a/src/org/labkey/test/tests/flow/FlowTest.java b/src/org/labkey/test/tests/flow/FlowTest.java
index aa23032967..dc478e60dc 100644
--- a/src/org/labkey/test/tests/flow/FlowTest.java
+++ b/src/org/labkey/test/tests/flow/FlowTest.java
@@ -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()
@@ -100,6 +102,7 @@ public void _doTestSteps()
         sampleTypeAndMetadataTest();
         customGraphQuery();
         positivityReportTest();
+        backgroundFilterRInjectionTest();
         qcReportTest();
         copyAnalysisScriptTest();
         removeAnalysisFilter();
@@ -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"));
@@ -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()
     {