Issue #57 Added methods to enable adding individuals to the Ontology …

…via the OwlKnowledgeBase and the OntologyDataSource.

owlsim-core/src/main/java/org/monarchinitiative/owlsim/io/Ontology.java

@@ -17,6 +17,7 @@
 import java.util.Map;
 import java.util.Objects;
 import java.util.Set;
+import java.util.function.BiConsumer;
 import java.util.zip.GZIPInputStream;
 
 /**
@@ -34,13 +35,15 @@
     private final OWLOntology owlOntology;
 
     private final OWLOntologyManager ontologyManager;
+    private final OWLDataFactory owlDataFactory;
 
     private Ontology(OntologySourceData sourceData, Concurrency concurrency) {
         Objects.requireNonNull(sourceData, "Unable to create Ontology without data sources.");
         this.sourceData = sourceData;
         this.curieUtil = new CurieUtil(sourceData.getCuries());
         this.ontologyManager = createOntologyManager(concurrency);
         this.owlOntology = createEmptyOntology(ontologyManager);
+        this.owlDataFactory = ontologyManager.getOWLDataFactory();
         loadOwlOntology();
     }
 
@@ -81,12 +84,29 @@ public CurieUtil getCurieUtil() {
         return curieUtil;
     }
 
+    /**
+     * @param curie
+     * @return
+     */
+    public OWLClass getOWLClass(String curie) {
+        return owlDataFactory.getOWLClass(toIri(curie));
+    }
+
+    public OWLNamedIndividual getOWLNamedIndividual(String curie) {
+        return owlDataFactory.getOWLNamedIndividual(toIri(curie));
+    }
+
+    public String toCurie(IRI iri) {
+        String iriString = iri.toString();
+        return curieUtil.getCurie(iriString).orElse(iriString);
+    }
+
     private void loadOwlOntology() {
         //Order matters here - don't change it.
         mergeOntologies(sourceData.getOntologies());
         mergeOntologies(sourceData.getDataOntologies());
         loadDataFromTsv(sourceData.getDataTsvs());
-        loadDataFromPairwiseMappings(sourceData.getPairwiseMappings());
+        loadDataFromMap(sourceData.getIndividuals());
         logger.info("Ontology loaded");
     }
 
@@ -191,8 +211,20 @@ private OWLOntology loadDataFromTsvGzip(String path) {
         return owlOntology;
     }
 
-    private void loadDataFromPairwiseMappings(Map<String, String> pairwiseMappings) {
-        pairwiseMappings.forEach(this::addInstanceOf);
+    private void loadDataFromMap(Map<String, Collection<String>> individuals) {
+        if(!individuals.isEmpty()){
+            logger.info("Loading individuals from map");
+        }
+        //e.g. 'ORPHA:710': ['HP:0000194','HP:0000218','HP:0000262','HP:0000303','HP:0000316']
+        individuals.forEach(addIndividual());
+    }
+
+    private BiConsumer<String, Collection<String>> addIndividual() {
+        return (individual, annotations) -> {
+            for (String curie : annotations) {
+                addInstanceOf(individual, curie);
+            }
+        };
     }
 
     private void loadLineIntoDataOntology(String line) {
@@ -204,15 +236,18 @@ private void loadLineIntoDataOntology(String line) {
     }
 
     private void addInstanceOf(String individual, String ontologyClass) {
-//                logger.info("Adding axiom " + individual + ": " + ontologyClass);
-        OWLDataFactory owlDataFactory = ontologyManager.getOWLDataFactory();
-        OWLClass owlClass = owlDataFactory.getOWLClass(toIri(ontologyClass));
-        OWLNamedIndividual owlNamedIndividual = owlDataFactory.getOWLNamedIndividual(toIri(individual));
-        OWLClassAssertionAxiom axiom = owlDataFactory.getOWLClassAssertionAxiom(owlClass, owlNamedIndividual);
-        addAxiom(axiom);
+        Objects.requireNonNull(individual, "Individual identifier cannot be null. Check your input.");
+        Objects.requireNonNull(ontologyClass, "Class identifier(s) cannot be null. Check your input.");
+        if (!ontologyClass.isEmpty()) {
+//            logger.info("Adding axiom " + individual + ": " + ontologyClass);
+            OWLClass owlClass = getOWLClass(ontologyClass);
+            OWLNamedIndividual owlNamedIndividual = getOWLNamedIndividual(individual);
+            OWLClassAssertionAxiom axiom = owlDataFactory.getOWLClassAssertionAxiom(owlClass, owlNamedIndividual);
+            addAxiom(axiom);
+        }
     }
 
-    private IRI toIri(String id) {
+    IRI toIri(String id) {
         return IRI.create(curieUtil.getIri(id).orElse(id));
     }
 

owlsim-core/src/main/java/org/monarchinitiative/owlsim/io/OntologySourceData.java

@@ -20,16 +20,17 @@
     private final List<String> dataOntologies;
 
     private final Map<String, String> curies;
+    //TODO: shouldn't this be individualsTsvs?
     private final List<String> dataTsvs;
-    //TODO: add these so people can programmatically add individual assertions
-    private final Map<String, String> pairwiseMappings;
+    private final Map<String, Collection<String>> individuals;
+    //TODO - labels?
 
     private OntologySourceData(Builder builder) {
         this.ontologies = distinctImmutableListOf(builder.ontologies);
         this.dataOntologies = distinctImmutableListOf(builder.dataOntologies);
         this.curies = ImmutableMap.copyOf(builder.curies);
         this.dataTsvs = distinctImmutableListOf(builder.dataTsvs);
-        this.pairwiseMappings = ImmutableMap.copyOf(builder.pairwiseMappings);
+        this.individuals = ImmutableMap.copyOf(builder.individuals);
     }
 
     private ImmutableList<String> distinctImmutableListOf(List<String> list) {
@@ -52,8 +53,8 @@ private OntologySourceData(Builder builder) {
         return dataTsvs;
     }
 
-    public Map<String, String> getPairwiseMappings() {
-        return pairwiseMappings;
+    public Map<String, Collection<String>> getIndividuals() {
+        return individuals;
     }
 
     @Override
@@ -65,12 +66,12 @@ public boolean equals(Object o) {
                 Objects.equals(dataOntologies, that.dataOntologies) &&
                 Objects.equals(curies, that.curies) &&
                 Objects.equals(dataTsvs, that.dataTsvs) &&
-                Objects.equals(pairwiseMappings, that.pairwiseMappings);
+                Objects.equals(individuals, that.individuals);
     }
 
     @Override
     public int hashCode() {
-        return Objects.hash(ontologies, dataOntologies, curies, dataTsvs, pairwiseMappings);
+        return Objects.hash(ontologies, dataOntologies, curies, dataTsvs, individuals);
     }
 
     @Override
@@ -80,7 +81,7 @@ public String toString() {
                 ", dataOntologies=" + dataOntologies +
                 ", curies=" + curies +
                 ", dataTsvs=" + dataTsvs +
-                ", pairwiseMappings=" + pairwiseMappings +
+                ", individuals=" + individuals +
                 '}';
     }
 
@@ -94,7 +95,7 @@ public static Builder builder() {
         //Curies need to be supplied if people are adding data using TSV files or pairwise mappings using curies.
         private Map<String, String> curies = Collections.emptyMap();
         private List<String> dataTsvs = new ArrayList<>();
-        private Map<String, String> pairwiseMappings = Collections.emptyMap();
+        private Map<String, Collection<String>> individuals = new HashMap<>();
 
         private Builder(){
             //use the static method.
@@ -176,6 +177,11 @@ public Builder dataTsv(Collection<String> paths) {
             return this;
         }
 
+        public Builder data(Map<String, ? extends Collection<String>> mappings) {
+            individuals.putAll(mappings);
+            return this;
+        }
+
         public OntologySourceData build() {
             if(ontologies.isEmpty()) {
                 throw new OntologyLoadException("No ontology defined.");
@@ -187,7 +193,7 @@ public OntologySourceData build() {
         }
 
         private boolean hasNonOntologyData() {
-            return !dataTsvs.isEmpty() || !pairwiseMappings.isEmpty();
+            return !dataTsvs.isEmpty() || !individuals.isEmpty();
         }
     }
 }

owlsim-core/src/main/java/org/monarchinitiative/owlsim/io/OwlKnowledgeBase.java

@@ -57,7 +57,6 @@ public Loader loadCuries(Map<String, String> curies) {
          * @param file
          */
         public Loader loadOntology(File file) {
-            Math.random();
             sourceDataBuilder.ontology(file);
             return this;
         }
@@ -118,6 +117,11 @@ public Loader loadDataFromTsv(Collection<String> paths) {
             return this;
         }
 
+        public Loader loadDataFromMap(Map<String, ? extends Collection<String>> data) {
+            sourceDataBuilder.data(data);
+            return this;
+        }
+
         /**
          * Creates an {@link OWLOntologyManager} that is configured with the standard parsers and storers and provides
          * locking for concurrent access (default).

owlsim-core/src/test/java/org/monarchinitiative/owlsim/io/OntologySourceDataTest.java

@@ -2,7 +2,9 @@
 
 import org.junit.Test;
 
+import java.util.Arrays;
 import java.util.LinkedHashMap;
+import java.util.List;
 import java.util.Map;
 
 /**
@@ -18,12 +20,37 @@ public void testItAll() {
         curies.put("MP", "http://purl.obolibrary.org/obo/MP_");
         curies.put("NCBITaxon", "http://purl.obolibrary.org/obo/NCBITaxon_");
 
+        Map<String, List<String>> individuals = new LinkedHashMap<>();
+        individuals.put("ORPHA:710", Arrays.asList("HP:0000194",
+                "HP:0000218",
+                "HP:0000262",
+                "HP:0000303",
+                "HP:0000316",
+                "HP:0000322",
+                "HP:0000324",
+                "HP:0000348",
+                "HP:0000431",
+                "HP:0000470",
+                "HP:0000508",
+                "HP:0001156",
+                "HP:0001385",
+                "HP:0003307",
+                "HP:0004209",
+                "HP:0004322",
+                "HP:0005048",
+                "HP:0006101",
+                "HP:0009773",
+                "HP:0010669",
+                "HP:0011304",
+                "HP:0012368", ""));
+
         OntologySourceData sourceData = OntologySourceData.builder()
                 .curies(curies)
                 .ontology("src/test/resources/ontologies/mammal.obo.gz")
                 .dataTsv("src/test/resources/data/gene2taxon.tsv.gz")
                 .dataTsv("src/test/resources/data/mouse-pheno.assocs.gz")
                 .dataTsv("src/test/resources/data/human-pheno.assocs.gz")
+                .data(individuals)
                 .build();
 
         System.out.println(sourceData);