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Add codes that check the return value of getGoSubOntology in the initialization routine of aspectMap. #239

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Feb 9, 2018
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Add codes that check the return value of getGoSubOntology in the initialization routine of aspectMap. #239

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20 changes: 16 additions & 4 deletions OWLTools-Annotation/src/main/java/owltools/gaf/inference/BasicAnnotationPropagator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -380,20 +380,32 @@ protected Map<String, String> createDefaultAspectMap(OWLGraphWrapper graph) {

OWLClass mf = graph.getOWLClassByIdentifier("GO:0003674"); // molecular_function
if (mf != null) {
map.put(getGoSubOntology(mf, graph), "F");
String mfKey = getGoSubOntology(mf, graph);
if (mfKey == null)
throw new RuntimeException("Could not retrieve sub-ontology for GO:0003674 (molecular_function). The value of the OBO-namespace tag does not exist.");

map.put(mfKey, "F");
}

OWLClass bp = graph.getOWLClassByIdentifier("GO:0008150"); // biological_process
if (bp != null) {
map.put(getGoSubOntology(bp, graph), "P");
String bpKey = getGoSubOntology(bp, graph);
if (bpKey == null)
throw new RuntimeException("Could not retrieve sub-ontology for GO:0008150 (biological_process). The value of the OBO-namespace tag does not exist.");

map.put(bpKey, "P");
}

OWLClass cc = graph.getOWLClassByIdentifier("GO:0005575"); // cellular_component
if (cc != null) {
map.put(getGoSubOntology(cc, graph), "C");
String ccKey = getGoSubOntology(cc, graph);
if (ccKey == null)
throw new RuntimeException("Could not retrieve sub-ontology for GO:0005575 (celluar_component). The value of the OBO-namespace tag does not exist.");

map.put(ccKey, "C");
}

if (map.isEmpty()) {
if (map.isEmpty() || map.containsKey(null)) {
// only fail if there are mappings
// the test case uses a custom ontology, which has no cc branch
throw new RuntimeException("Could not create any valid aspect mappings. Is the correct ontology (GO) loaded?");
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