coverage for Issue 50774

Author: labkey-chrisj

src/org/labkey/test/tests/assay/AssayTransformImportUpdateTest.java

@@ -13,6 +13,7 @@
 import org.labkey.test.pages.admin.UsageStatisticsPage;
 import org.labkey.test.pages.assay.AssayImportPage;
 import org.labkey.test.pages.assay.AssayRunsPage;
+import org.labkey.test.pages.pipeline.PipelineStatusDetailsPage;
 import org.labkey.test.params.FieldDefinition;
 import org.labkey.test.params.assay.GeneralAssayDesign;
 import org.labkey.test.util.RReportHelper;
@@ -219,6 +220,74 @@ public void testEnableTransformForUpdate() throws Exception
                 assaysWithTransformScripts > 0);
     }
 
+    // Issue 50774
+    @Test
+    public void testCancelAsyncAssayTransformJob() throws Exception
+    {
+        String transformCancelFile = "importCancelTransform.R";
+        String importCancelTransformAssay = "importCancelTransformAssay";
+        String transformContent = """
+                library(Rlabkey);
+                
+                run.props = labkey.transform.readRunPropertiesFile("${runInfo}");
+                
+                run.data.file = labkey.transform.getRunPropertyValue(run.props, "runDataFile");
+                run.output.file = run.props$val3[run.props$name == "runDataFile"];
+                error.file = labkey.transform.getRunPropertyValue(run.props, "errorsFile");
+                
+                # sleep a bit before writing the table, give the test time to cancel the job before it is complete
+                labkey.setDebugMode(TRUE);
+                print("before");
+                Sys.sleep(4);
+                print("after");
+                labkey.setDebugMode(FALSE);
+
+                if (file.exists(run.data.file)) {
+                    run.data = read.delim(run.data.file, header=TRUE, sep="\\t", check.names = FALSE);
+                    run.data$M2 = 111;
+                    run.data$TransformType = "${transformOperation} testing";
+                    write.table(run.data, file=run.output.file, sep="\\t", na="", row.names=FALSE, quote=FALSE);
+                }
+                
+                """;
+        File transformFile = TestFileUtils.writeTempFile(transformCancelFile, transformContent);
+        var protocolResponse = new GeneralAssayDesign(importCancelTransformAssay)
+                .setDataFields(List.of(new FieldDefinition("M2", FieldDefinition.ColumnType.Decimal),
+                        new FieldDefinition("TransformType", FieldDefinition.ColumnType.String),
+                        new FieldDefinition("Comment", FieldDefinition.ColumnType.String)), true)
+                .createAssay(getProjectName(), createDefaultConnection());
+        goToProjectHome();
+
+        var assayDesignerPage = ReactAssayDesignerPage.beginAt(this, getProjectName(), protocolResponse.getProtocolId(),
+                "general", getURL().toString());
+        assayDesignerPage.addTransformScript(transformFile, true);
+        assayDesignerPage.setBackgroundImport(true);
+        assayDesignerPage.clickSave();
+
+        StringBuilder importDataBuilder = new StringBuilder("VisitID\tParticipantID\tComment\n");
+        for (int i=1; i<=10; i++)
+            importDataBuilder.append(String.format("%d\t%d\tComment-%d\n", i, i, i));
+
+        clickAndWait(Locator.linkWithText(importCancelTransformAssay));
+        new AssayRunsPage(getDriver()).getTable().clickHeaderButton("Import Data");
+        clickButton("Next");
+        var importPage = new AssayImportPage(getDriver());
+        importPage.setNamedInputText("name", "cancelTransformTestImport");
+        importPage.setNamedTextAreaValue("TextAreaDataCollector.textArea", importDataBuilder.toString());
+        importPage.clickSaveAndFinish();
+
+        waitAndClickAndWait(Locator.linkWithText("Assay upload RUNNING"));
+        PipelineStatusDetailsPage pipelineStatusDetailsPage = new PipelineStatusDetailsPage(getDriver());
+        pipelineStatusDetailsPage.clickCancel();
+
+        pipelineStatusDetailsPage.showLogDetails();
+        pipelineStatusDetailsPage.assertLogTextContains("INFO : Attempting to cancel as requested",
+                "INFO : Interrupting job by sending interrupt request.",
+                "ERROR: The following error was generated by the assay upload",
+                "INFO : Failed to complete task 'org.labkey.api.assay.pipeline.AssayUploadPipelineTask'");
+        resetErrors();
+    }
+
     @Override
     protected String getProjectName()
     {