Fix more potential NPE and add @nullable annotations

Author: arteymix

src/ubic/basecode/ontology/jena/AbstractOntologyService.java

@@ -91,6 +91,7 @@ public abstract class AbstractOntologyService implements OntologyService {
     private Map<String, String> alternativeIDs;
     @Nullable
     private SearchIndex index;
+    @Nullable
     private Set<Restriction> additionalRestrictions;
     private boolean isInitialized = false;
     @Nullable
@@ -740,8 +741,10 @@ private void initSearchByAlternativeId() {
         // for all Ontology terms that exist in the tree
         ExtendedIterator<OntClass> iterator = model.listClasses();
         while ( iterator.hasNext() ) {
-            OntClass ind = iterator.next();
-            OntologyTerm ontologyTerm = new OntologyTermImpl( ind, additionalRestrictions );
+            OntologyTerm ontologyTerm = new OntologyTermImpl( iterator.next(), additionalRestrictions );
+            if ( ontologyTerm.getUri() == null ) {
+                continue;
+            }
             // lets find the baseUri, to change to valueUri
             String baseOntologyUri = ontologyTerm.getUri().substring( 0, ontologyTerm.getUri().lastIndexOf( "/" ) + 1 );
             for ( String alternativeId : ontologyTerm.getAlternativeIds() ) {

src/ubic/basecode/ontology/jena/OntologyCardinalityRestrictionImpl.java

@@ -21,6 +21,7 @@
 import com.hp.hpl.jena.ontology.Restriction;
 import ubic.basecode.ontology.model.OntologyCardinalityRestriction;
 
+import javax.annotation.Nullable;
 import java.util.Set;
 
 /**
@@ -32,7 +33,7 @@ class OntologyCardinalityRestrictionImpl extends OntologyRestrictionImpl impleme
     private final int cardinality;
     private final CardinalityType cardType;
 
-    public OntologyCardinalityRestrictionImpl( Restriction resource, Set<Restriction> additionalRestrictions ) {
+    public OntologyCardinalityRestrictionImpl( Restriction resource, @Nullable Set<Restriction> additionalRestrictions ) {
         super( resource, additionalRestrictions );
 
         if ( resource.isMaxCardinalityRestriction() ) {

src/ubic/basecode/ontology/jena/OntologyClassRestrictionImpl.java

@@ -18,16 +18,12 @@
  */
 package ubic.basecode.ontology.jena;
 
-import com.hp.hpl.jena.ontology.AllValuesFromRestriction;
-import com.hp.hpl.jena.ontology.HasValueRestriction;
-import com.hp.hpl.jena.ontology.OntClass;
-import com.hp.hpl.jena.ontology.OntProperty;
-import com.hp.hpl.jena.ontology.Restriction;
-import com.hp.hpl.jena.ontology.SomeValuesFromRestriction;
+import com.hp.hpl.jena.ontology.*;
 import com.hp.hpl.jena.rdf.model.RDFNode;
 import ubic.basecode.ontology.model.OntologyClassRestriction;
 import ubic.basecode.ontology.model.OntologyTerm;
 
+import javax.annotation.Nullable;
 import java.util.Set;
 
 /**
@@ -38,7 +34,7 @@ class OntologyClassRestrictionImpl extends OntologyRestrictionImpl implements On
     private final OntologyTerm restrictedTo;
     private final Set<Restriction> additionalRestrictions;
 
-    public OntologyClassRestrictionImpl( Restriction term, Set<Restriction> additionalRestrictions ) {
+    public OntologyClassRestrictionImpl( Restriction term, @Nullable Set<Restriction> additionalRestrictions ) {
         super( term, additionalRestrictions );
         this.additionalRestrictions = additionalRestrictions;
 

src/ubic/basecode/ontology/jena/OntologyDatatypeRestrictionImpl.java

@@ -19,9 +19,9 @@
 package ubic.basecode.ontology.jena;
 
 import com.hp.hpl.jena.ontology.Restriction;
-import com.hp.hpl.jena.rdf.model.Property;
 import ubic.basecode.ontology.model.OntologyDatatypeRestriction;
 
+import javax.annotation.Nullable;
 import java.util.Set;
 
 /**
@@ -31,8 +31,8 @@ class OntologyDatatypeRestrictionImpl extends OntologyRestrictionImpl implements
 
     private final Class<?> type;
 
-    public OntologyDatatypeRestrictionImpl( Restriction resource, Set<Restriction> additionalRestrcitions ) {
-        super( resource, additionalRestrcitions );
+    public OntologyDatatypeRestrictionImpl( Restriction resource, @Nullable Set<Restriction> additionalRestrictions ) {
+        super( resource, additionalRestrictions );
         assert restrictionOn != null;
         this.type = PropertyFactory.convertType( resource.getOnProperty().asDatatypeProperty() );
     }

src/ubic/basecode/ontology/jena/OntologyIndividualImpl.java

@@ -28,6 +28,7 @@
 import ubic.basecode.ontology.model.OntologyIndividual;
 import ubic.basecode.ontology.model.OntologyTerm;
 
+import javax.annotation.Nullable;
 import java.util.Set;
 
 /**
@@ -38,13 +39,13 @@ class OntologyIndividualImpl extends AbstractOntologyResource implements Ontolog
     private final Individual ind;
     private final Set<Restriction> additionalRestrictions;
 
-    public OntologyIndividualImpl( Individual ind, Set<Restriction> additionalRestrictions ) {
+    public OntologyIndividualImpl( Individual ind, @Nullable Set<Restriction> additionalRestrictions ) {
         super( ind );
         this.ind = ind;
         this.additionalRestrictions = additionalRestrictions;
     }
 
-    public OntologyIndividualImpl( Individual ind, Set<Restriction> additionalRestrictions, double score ) {
+    public OntologyIndividualImpl( Individual ind, @Nullable Set<Restriction> additionalRestrictions, double score ) {
         super( ind, score );
         this.ind = ind;
         this.additionalRestrictions = additionalRestrictions;

src/ubic/basecode/ontology/jena/OntologyRestrictionImpl.java

@@ -19,10 +19,10 @@
 package ubic.basecode.ontology.jena;
 
 import com.hp.hpl.jena.ontology.Restriction;
-import com.hp.hpl.jena.rdf.model.Property;
 import ubic.basecode.ontology.model.OntologyProperty;
 import ubic.basecode.ontology.model.OntologyRestriction;
 
+import javax.annotation.Nullable;
 import java.util.Set;
 
 /**
@@ -34,7 +34,7 @@ abstract class OntologyRestrictionImpl extends OntologyTermImpl implements Ontol
 
     protected OntologyProperty restrictionOn;
 
-    public OntologyRestrictionImpl( Restriction resource, Set<Restriction> additionalRestrictions ) {
+    public OntologyRestrictionImpl( Restriction resource, @Nullable Set<Restriction> additionalRestrictions ) {
         super( resource, additionalRestrictions );
         this.restrictionOn = PropertyFactory.asProperty( resource.getOnProperty(), additionalRestrictions );
     }

src/ubic/basecode/ontology/jena/OntologyTermImpl.java

@@ -59,7 +59,7 @@ public OntologyTermImpl( OntClass resource, @Nullable Set<Restriction> additiona
         this.additionalRestrictions = additionalRestrictions;
     }
 
-    public OntologyTermImpl( OntClass resource, Set<Restriction> additionalRestrictions, double score ) {
+    public OntologyTermImpl( OntClass resource, @Nullable Set<Restriction> additionalRestrictions, double score ) {
         super( resource, score );
         this.ontResource = resource;
         this.additionalRestrictions = additionalRestrictions;

src/ubic/basecode/ontology/jena/PropertyFactory.java

@@ -1,8 +1,8 @@
 /*
  * The basecode project
- * 
+ *
  * Copyright (c) 2007-2019 University of British Columbia
- * 
+ *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
@@ -22,24 +22,23 @@
 import com.hp.hpl.jena.ontology.OntProperty;
 import com.hp.hpl.jena.ontology.OntResource;
 import com.hp.hpl.jena.ontology.Restriction;
-import com.hp.hpl.jena.rdf.model.Property;
 
+import javax.annotation.Nullable;
 import java.util.Set;
 
 /**
  * @author pavlidis
- * 
  */
 class PropertyFactory {
 
     /**
      * Convert a Jena property.
-     * 
+     *
      * @param property
      * @param source
      * @return new property or null if it could not be converted.
      */
-    public static ubic.basecode.ontology.model.OntologyProperty asProperty( OntProperty property, Set<Restriction> additionalRestrictions ) {
+    public static ubic.basecode.ontology.model.OntologyProperty asProperty( OntProperty property, @Nullable Set<Restriction> additionalRestrictions ) {
 
         if ( property.isObjectProperty() ) {
             return new ObjectPropertyImpl( property.asObjectProperty(), additionalRestrictions );

src/ubic/basecode/ontology/jena/RestrictionFactory.java

@@ -1,8 +1,8 @@
 /*
  * The basecode project
- * 
+ *
  * Copyright (c) 2007-2019 University of British Columbia
- * 
+ *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
@@ -20,18 +20,17 @@
 
 import com.hp.hpl.jena.ontology.OntProperty;
 import com.hp.hpl.jena.ontology.Restriction;
-import com.hp.hpl.jena.rdf.model.Property;
 import ubic.basecode.ontology.model.OntologyRestriction;
 
+import javax.annotation.Nullable;
 import java.util.Set;
 
 /**
  * @author pavlidis
- * 
  */
 class RestrictionFactory {
 
-    public static OntologyRestriction asRestriction( Restriction restriction, Set<Restriction> additionalRestrictions ) {
+    public static OntologyRestriction asRestriction( Restriction restriction, @Nullable Set<Restriction> additionalRestrictions ) {
 
         OntProperty onProperty = restriction.getOnProperty();