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Always render full ontology IRI in report outputs #739

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merged 3 commits into from
Dec 18, 2020
Merged

Always render full ontology IRI in report outputs #739

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b849c50
Always render full ontology IRI
Sep 21, 2020
62b3f80
Make sure ontologyITI != null
Sep 21, 2020
add8620
Merge branch 'master' into ont-iri-fix
beckyjackson Nov 19, 2020
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19 changes: 16 additions & 3 deletions robot-core/src/main/java/org/obolibrary/robot/checks/Report.java
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Original file line number Diff line number Diff line change
Expand Up @@ -69,6 +69,8 @@ public class Report {
private final List<String> header =
Lists.newArrayList("Level", "Rule Name", "Subject", "Property", "Value");

private IRI ontologyIRI = null;

/**
* Create a new report object without an ontology or predefined IOHelper.
*
Expand All @@ -88,6 +90,7 @@ public Report() throws IOException {
public Report(OWLOntology ontology, boolean useLabels) throws IOException {
if (ontology != null) {
manager = ontology.getOWLOntologyManager();
ontologyIRI = ontology.getOntologyID().getOntologyIRI().orNull();
} else {
manager = OWLManager.createOWLOntologyManager();
}
Expand Down Expand Up @@ -140,6 +143,7 @@ public Report(Map<IRI, String> labelMap) throws IOException {
public Report(OWLOntology ontology, IOHelper ioHelper, boolean useLabels) {
if (ontology != null) {
manager = ontology.getOWLOntologyManager();
ontologyIRI = ontology.getOntologyID().getOntologyIRI().orNull();
} else {
manager = OWLManager.createOWLOntologyManager();
}
Expand Down Expand Up @@ -353,10 +357,19 @@ private void addToTable(
for (Violation v : vs.getValue()) {
// Subject of the violation for the following rows
String subject;
if (v.entity != null) {
subject = OntologyHelper.renderManchester(v.entity, provider, displayRenderer);
if (ontologyIRI != null
&& v.entity != null
&& !v.entity.isAnonymous()
&& v.entity.getIRI().toString().equals(ontologyIRI.toString())) {
// If the IRI is the ontology IRI, keep this as the full string
subject = ontologyIRI.toString();
} else {
subject = v.subject;
// Otherwise, render the subject based on the display renderer
if (v.entity != null) {
subject = OntologyHelper.renderManchester(v.entity, provider, displayRenderer);
} else {
subject = v.subject;
}
}
Cell subjectCell = new Cell(columns.get(2), subject);
for (Entry<OWLEntity, List<OWLObject>> statement : v.entityStatements.entrySet()) {
Expand Down