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Improve check for missing vars in ReportOperation #1291

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Merged
jamesaoverton merged 1 commit into from
Oct 1, 2026
Merged

Improve check for missing vars in ReportOperation #1291

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44 changes: 26 additions & 18 deletions robot-core/src/main/java/org/obolibrary/robot/ReportOperation.java
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Original file line number Diff line number Diff line change
Expand Up @@ -872,6 +872,7 @@ public static List<Violation> getViolations(
dataset.begin(ReadWrite.READ);
try {
ResultSet violationSet = QueryOperation.execQuery(dataset, query);
checkResultVars(queryName, violationSet);
return getViolationsFromResults(ioHelper, queryName, violationSet, limit);
} catch (Exception e) {
// If query fails, return null
Expand All @@ -888,6 +889,7 @@ public static List<Violation> getViolations(
} else {
try {
ResultSet violationSet = QueryOperation.execQuery(dataset, query);
checkResultVars(queryName, violationSet);
return getViolationsFromResults(ioHelper, queryName, violationSet, limit);
} catch (Exception e) {
// If query fails, return null
Expand All @@ -903,6 +905,28 @@ public static List<Violation> getViolations(

private static final OWLDataFactory dataFactory = OWLManager.getOWLDataFactory();

/**
* Given a query name and a result set, Check that the query contains ?entity, ?property, and
* ?value vars, which are expected for proper display of the results.
*/
private static boolean checkResultVars(String queryName, ResultSet violationSet) {
boolean allVarsPresent = true;
List<String> resultVars = violationSet.getResultVars();
if (!resultVars.contains("entity")) {
allVarsPresent = false;
System.out.println(WARN + ": '" + queryName + "' query is missing ?entity variable");
}
if (!resultVars.contains("property")) {
allVarsPresent = false;
System.out.println(WARN + ": '" + queryName + "' query is missing ?property variable");
}
if (!resultVars.contains("value")) {
allVarsPresent = false;
System.out.println(WARN + ": '" + queryName + "' query is missing ?value variable");
}
return allVarsPresent;
}

/**
* Given a query name, a result set, and a limit for results, return a list of Violation objects
* for those results.
Expand Down Expand Up @@ -979,27 +1003,11 @@ private static List<Violation> getViolationsFromResults(
violation = new Violation("blank node");
}

// Try and get a property and value from the query.
// If none is found, print a warning, but only once.
String property = getQueryResultOrNull(qs, "property");
if (property == null) {
if (!propertyWarning) {
System.out.println(WARN + ": '" + queryName + "' query is missing ?property variable");
}
propertyWarning = true;
}

String value = getQueryResultOrNull(qs, "value");
if (value == null) {
if (!valueWarning) {
System.out.println(WARN + ": '" + queryName + "' query is missing ?value variable");
}
valueWarning = true;
}

// add details to Violation
String property = getQueryResultOrNull(qs, "property");
if (property != null) {
OWLEntity e = dataFactory.getOWLClass(ioHelper.createIRI(property));
String value = getQueryResultOrNull(qs, "value");
if (value != null) {
IRI valIRI = ioHelper.createIRI(value);
if (valIRI != null) {
Expand Down
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