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Assay transform script run properties to include reRunId when applicable #3200

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Assay transform script run properties to include reRunId when applicable #3200

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87 changes: 87 additions & 0 deletions src/org/labkey/test/tests/assay/AssayTransformImportUpdateTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -301,4 +301,91 @@ public void testCancelAsyncAssayTransformJob() throws Exception

resetErrors();
}

@Test
public void testReRunIdTransformProperty() throws Exception
{
String reRunIdTransform = "reRunIdTransform.R";
String reRunIdTransformAssay = "reRunIdTransformAssay";
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"];

# reRunId is only present in the run properties for a re-import
rerun.id = labkey.transform.getRunPropertyValue(run.props, "reRunId");
if (is.na(rerun.id)) rerun.id = "";

if (file.exists(run.data.file)) {
run.data = read.delim(run.data.file, header=TRUE, sep="\\t", check.names = FALSE);
run.data$ReRunId = rerun.id;
write.table(run.data, file=run.output.file, sep="\\t", na="", row.names=FALSE, quote=FALSE);
}
""";
File transformFile = TestFileUtils.writeTempFile(reRunIdTransform, transformContent);
var protocolResponse = new GeneralAssayDesign(reRunIdTransformAssay)
.setDataFields(List.of(new FieldDefinition("ReRunId", FieldDefinition.ColumnType.String)), true)
.createAssay(getProjectName(), createDefaultConnection());
goToProjectHome();

var assayDesignerPage = ReactAssayDesignerPage.beginAt(this, getProjectName(), protocolResponse.getProtocolId(),
"general", getURL().toString());
assayDesignerPage.addTransformScript(transformFile, true);
assayDesignerPage.goToBatchFields().removeAllFields(true);
assayDesignerPage.clickSave();

String importData = """
VisitID\tParticipantID
1\t1
1\t2
""";

String initialRun = "reRunIdInitialImport";
goToProjectHome();
clickAndWait(Locator.linkWithText(reRunIdTransformAssay));
new AssayRunsPage(getDriver()).getTable().clickHeaderButtonAndWait("Import Data");
new AssayImportPage(getDriver())
.setNamedInputText("Name", initialRun)
.setDataText(importData)
.clickSaveAndFinish();

var initialRunData = new AssayRunsPage(getDriver()).clickAssayIdLink(initialRun)
.getDataTable().getColumnDataAsText("ReRunId");
checker().wrapAssertion(()-> Assertions.assertThat(initialRunData)
.as("expect no reRunId run property for an initial import")
.containsOnly(" "));
checker().screenShotIfNewError("unexpected initial import transform data");

int initialRunId = getRunId(reRunIdTransformAssay, initialRun);

String reImportedRun = "reRunIdReImport";
goToProjectHome();
clickAndWait(Locator.linkWithText(reRunIdTransformAssay));
clickAndWait(Locator.linkWithText(initialRun));
clickButton("Re-import run");
new AssayImportPage(getDriver())
.setNamedInputText("Name", reImportedRun)
.setDataText(importData)
.clickSaveAndFinish();

var reImportedRunData = new AssayRunsPage(getDriver()).clickAssayIdLink(reImportedRun)
.getDataTable().getColumnDataAsText("ReRunId");
checker().wrapAssertion(()-> Assertions.assertThat(reImportedRunData)
.as("expect reRunId run property to be the RowId of the run being replaced")
.containsOnly(String.valueOf(initialRunId)));
checker().screenShotIfNewError("unexpected re-import transform data");
}

private int getRunId(String assayName, String runName)
{
var rows = executeSelectRowCommand("assay.General." + assayName, "Runs").getRows();
return rows.stream()
.filter(row -> runName.equals(row.get("Name")))
.map(row -> (Integer) row.get("RowId"))
.findFirst()
.orElseThrow(() -> new IllegalStateException("Unable to find run: " + runName));
}
}
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