possible bugfix, keep allowing null but filter for it and expand warning description

Author: leokim-l

boqa-core/src/main/java/org/p2gx/boqa/core/internal/OntologyTraverser.java

@@ -122,7 +122,10 @@ public Set<TermId> initLayer(Set<TermId> hpoTerms) {
     public static TermId getPrimaryTermId(TermId t){
         TermId primaryTermId = hpo.getPrimaryTermId(t);
         if (primaryTermId == null) {
-            LOGGER.warn("Invalid HPO term {}! Skipping...", primaryTermId);
+            if (LOGGED_REPLACEMENTS.add(t)) { // only log once per term
+                LOGGER.warn("Invalid HPO term {}! Skipping it, this may negatively affect performance. " +
+                        "Are you using the latest HPO build? Consider running `download -w` to fetch the latest HPO release.", t);
+            }
         } else {
             if (!t.equals(primaryTermId) && LOGGED_REPLACEMENTS.add(t)) {
                 LOGGER.info("Replacing {} with primary term {}", t, primaryTermId);

boqa-core/src/main/java/org/p2gx/boqa/core/patient/PhenopacketData.java

@@ -12,6 +12,7 @@
 
 import java.nio.file.Path;
 import java.util.List;
+import java.util.Objects;
 import java.util.Set;
 import java.util.function.Predicate;
 import java.util.stream.Collectors;
@@ -49,6 +50,7 @@ public PhenopacketData(Phenopacket phenopacket) {
                 .map(OntologyClass::getId)
                 .map(TermId::of)
                 .map(OntologyTraverser::getPrimaryTermId)
+                .filter(Objects::nonNull) // If old HPO is used without a term, avoids the program crashing
                 .collect(Collectors.toSet());
         if (this.observedTerms.isEmpty()) {
             LOGGER.warn("Phenopacket {} has no observed phenotypic features!", phenopacket.getId());
@@ -58,6 +60,7 @@ public PhenopacketData(Phenopacket phenopacket) {
                 .map(OntologyClass::getId)
                 .map(TermId::of)
                 .map(OntologyTraverser::getPrimaryTermId)
+                .filter(Objects::nonNull) // If old HPO is used without a term, avoids the program crashing
                 .collect(Collectors.toSet());
         this.diseases = phenopacket.getDiseasesList().stream().map(d ->
                 new DiseaseDTO(d.getTerm().getId(), d.getTerm().getLabel())).toList();