Issue #57 changed uses of 'data' to 'individualAssociations' in conte…

…xt of the Ontology/OntologySourceData/OwlKnowledgebase in order to be more specific.

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

@@ -105,8 +105,8 @@ private void loadOwlOntology() {
         //Order matters here - don't change it.
         mergeOntologies(sourceData.getOntologies());
         mergeOntologies(sourceData.getDataOntologies());
-        loadDataFromTsv(sourceData.getDataTsvs());
-        loadDataFromMap(sourceData.getIndividuals());
+        loadIndividualAssociationsFromTsv(sourceData.getIndividualAssociationTsvs());
+        loadIndividualAssociationsFromMap(sourceData.getIndividualAssociations());
         logger.info("Ontology loaded");
     }
 
@@ -138,10 +138,6 @@ private OWLOntology mergeOntologies(Collection<String> uris) {
         return owlOntology;
     }
 
-    private ChangeApplied addAxiom(OWLAxiom axiom) {
-        return ontologyManager.addAxiom(owlOntology, axiom);
-    }
-
     private ChangeApplied addAxioms(Set<OWLAxiom> axioms) {
         return ontologyManager.addAxioms(owlOntology, axioms);
     }
@@ -179,12 +175,12 @@ private OWLOntology loadOwlOntology(IRI iri) {
         }
     }
 
-    private OWLOntology loadDataFromTsv(Collection<String> paths) {
-        paths.forEach(this::loadDataFromTsv);
+    private OWLOntology loadIndividualAssociationsFromTsv(Collection<String> paths) {
+        paths.forEach(this::loadIndividualAssociationsFromTsv);
         return owlOntology;
     }
 
-    private OWLOntology loadDataFromTsv(String path) {
+    private OWLOntology loadIndividualAssociationsFromTsv(String path) {
         if (path.endsWith(".gz")) {
             return loadDataFromTsvGzip(path);
         }
@@ -211,7 +207,7 @@ private OWLOntology loadDataFromTsvGzip(String path) {
         return owlOntology;
     }
 
-    private void loadDataFromMap(Map<String, Collection<String>> individuals) {
+    private void loadIndividualAssociationsFromMap(Map<String, Collection<String>> individuals) {
         if(!individuals.isEmpty()){
             logger.info("Loading individuals from map");
         }
@@ -247,6 +243,10 @@ private void addInstanceOf(String individual, String ontologyClass) {
         }
     }
 
+    private ChangeApplied addAxiom(OWLAxiom axiom) {
+        return ontologyManager.addAxiom(owlOntology, axiom);
+    }
+
     IRI toIri(String id) {
         return IRI.create(curieUtil.getIri(id).orElse(id));
     }

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

@@ -20,17 +20,16 @@
     private final List<String> dataOntologies;
 
     private final Map<String, String> curies;
-    //TODO: shouldn't this be individualsTsvs?
-    private final List<String> dataTsvs;
-    private final Map<String, Collection<String>> individuals;
+    private final List<String> individualAssociationTsvs;
+    private final Map<String, Collection<String>> individualAssociations;
     //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.individuals = ImmutableMap.copyOf(builder.individuals);
+        this.individualAssociationTsvs = distinctImmutableListOf(builder.individualAssociationTsvs);
+        this.individualAssociations = ImmutableMap.copyOf(builder.individualAssociations);
     }
 
     private ImmutableList<String> distinctImmutableListOf(List<String> list) {
@@ -49,12 +48,12 @@ private OntologySourceData(Builder builder) {
         return curies;
     }
 
-    public List<String> getDataTsvs() {
-        return dataTsvs;
+    public List<String> getIndividualAssociationTsvs() {
+        return individualAssociationTsvs;
     }
 
-    public Map<String, Collection<String>> getIndividuals() {
-        return individuals;
+    public Map<String, Collection<String>> getIndividualAssociations() {
+        return individualAssociations;
     }
 
     @Override
@@ -65,13 +64,13 @@ public boolean equals(Object o) {
         return Objects.equals(ontologies, that.ontologies) &&
                 Objects.equals(dataOntologies, that.dataOntologies) &&
                 Objects.equals(curies, that.curies) &&
-                Objects.equals(dataTsvs, that.dataTsvs) &&
-                Objects.equals(individuals, that.individuals);
+                Objects.equals(individualAssociationTsvs, that.individualAssociationTsvs) &&
+                Objects.equals(individualAssociations, that.individualAssociations);
     }
 
     @Override
     public int hashCode() {
-        return Objects.hash(ontologies, dataOntologies, curies, dataTsvs, individuals);
+        return Objects.hash(ontologies, dataOntologies, curies, individualAssociationTsvs, individualAssociations);
     }
 
     @Override
@@ -80,8 +79,8 @@ public String toString() {
                 "ontologies=" + ontologies +
                 ", dataOntologies=" + dataOntologies +
                 ", curies=" + curies +
-                ", dataTsvs=" + dataTsvs +
-                ", individuals=" + individuals +
+                ", individualAssociationTsvs=" + individualAssociationTsvs +
+                ", individualAssociations=" + individualAssociations +
                 '}';
     }
 
@@ -94,8 +93,8 @@ public static Builder builder() {
         private List<String> dataOntologies = new ArrayList<>();
         //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, Collection<String>> individuals = new HashMap<>();
+        private List<String> individualAssociationTsvs = new ArrayList<>();
+        private Map<String, Collection<String>> individualAssociations = new HashMap<>();
 
         private Builder(){
             //use the static method.
@@ -162,38 +161,38 @@ public Builder dataOntologies(Collection<String> paths) {
             return this;
         }
 
-        public Builder dataTsv(String path) {
-            dataTsvs.add(path);
+        public Builder individualAssociationsTsv(String path) {
+            individualAssociationTsvs.add(path);
             return this;
         }
 
-        public Builder dataTsv(String... paths) {
-            dataTsvs.addAll(Arrays.asList(paths));
+        public Builder individualAssociationsTsv(String... paths) {
+            individualAssociationTsvs.addAll(Arrays.asList(paths));
             return this;
         }
 
-        public Builder dataTsv(Collection<String> paths) {
-            dataTsvs.addAll(paths);
+        public Builder individualAssociationsTsv(Collection<String> paths) {
+            individualAssociationTsvs.addAll(paths);
             return this;
         }
 
-        public Builder data(Map<String, ? extends Collection<String>> mappings) {
-            individuals.putAll(mappings);
+        public Builder individualAssociations(Map<String, ? extends Collection<String>> mappings) {
+            individualAssociations.putAll(mappings);
             return this;
         }
 
         public OntologySourceData build() {
             if(ontologies.isEmpty()) {
                 throw new OntologyLoadException("No ontology defined.");
             }
-            if (curies.isEmpty() && hasNonOntologyData()) {
-                throw new OntologyLoadException("Cannot load TSV data sources or pairwise mappings when curies have not been defined.");
+            if (curies.isEmpty() && hasIndividualAssociationData()) {
+                throw new OntologyLoadException("Cannot load individual class associations when curies have not been defined.");
             }
             return new OntologySourceData(this);
         }
 
-        private boolean hasNonOntologyData() {
-            return !dataTsvs.isEmpty() || !individuals.isEmpty();
+        private boolean hasIndividualAssociationData() {
+            return !individualAssociationTsvs.isEmpty() || !individualAssociations.isEmpty();
         }
     }
 }

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

@@ -102,23 +102,23 @@ public Loader loadDataFromOntologies(Collection<String> paths) {
             return this;
         }
 
-        public Loader loadDataFromTsv(String path) {
-            sourceDataBuilder.dataTsv(path);
+        public Loader loadIndividualAssociationsFromTsv(String path) {
+            sourceDataBuilder.individualAssociationsTsv(path);
             return this;
         }
 
-        public Loader loadDataFromTsv(String... paths) {
-            sourceDataBuilder.dataTsv(paths);
+        public Loader loadIndividualAssociationsFromTsv(String... paths) {
+            sourceDataBuilder.individualAssociationsTsv(paths);
             return this;
         }
 
-        public Loader loadDataFromTsv(Collection<String> paths) {
-            sourceDataBuilder.dataTsv(paths);
+        public Loader loadIndividualAssociationsFromTsv(Collection<String> paths) {
+            sourceDataBuilder.individualAssociationsTsv(paths);
             return this;
         }
 
-        public Loader loadDataFromMap(Map<String, ? extends Collection<String>> data) {
-            sourceDataBuilder.data(data);
+        public Loader loadIndividualAssociations(Map<String, ? extends Collection<String>> data) {
+            sourceDataBuilder.individualAssociations(data);
             return this;
         }
 

owlsim-core/src/test/java/org/monarchinitiative/owlsim/compute/matcher/perf/HomologyPhenoPerfIT.java

@@ -127,7 +127,7 @@ private void load() throws OWLOntologyCreationException, IOException {
         kb = OwlKnowledgeBase.loader()
                 .loadCuries(curies)
                 .loadOntology("src/test/resources/ontologies/mammal.obo.gz")
-                .loadDataFromTsv(
+                .loadIndividualAssociationsFromTsv(
                         "src/test/resources/data/gene2taxon.tsv.gz",
                         "src/test/resources/data/mouse-pheno.assocs.gz",
                         "src/test/resources/data/human-pheno.assocs.gz")

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

@@ -47,10 +47,10 @@ public void testItAll() {
         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)
+                .individualAssociationsTsv("src/test/resources/data/gene2taxon.tsv.gz")
+                .individualAssociationsTsv("src/test/resources/data/mouse-pheno.assocs.gz")
+                .individualAssociationsTsv("src/test/resources/data/human-pheno.assocs.gz")
+                .individualAssociations(individuals)
                 .build();
 
         System.out.println(sourceData);
@@ -60,7 +60,7 @@ public void testItAll() {
     public void testThrowsExceptionWhenCuriesEmptyAndDataIncludedFromTsv() {
 
         OntologySourceData sourceData = OntologySourceData.builder()
-                .dataTsv("src/test/resources/data/gene2taxon.tsv.gz")
+                .individualAssociationsTsv("src/test/resources/data/gene2taxon.tsv.gz")
                 .build();
 
         System.out.println(sourceData);

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

@@ -33,7 +33,7 @@ private Ontology getBobOnlyOntology() {
         OntologySourceData sourceData = OntologySourceData.builder()
                 .ontology("src/test/resources/species-no-individuals.owl")
                 .curies(curies)
-                .data(data)
+                .individualAssociations(data)
                 .build();
 
         return Ontology.load(sourceData);
@@ -61,7 +61,7 @@ public void testAddNullIndividuals() {
         OntologySourceData sourceData = OntologySourceData.builder()
                 .ontology("src/test/resources/species-no-individuals.owl")
                 .curies(curies)
-                .data(data)
+                .individualAssociations(data)
                 .build();
 
         Ontology.load(sourceData);
@@ -77,7 +77,7 @@ public void testAddNullClasses() {
         OntologySourceData sourceData = OntologySourceData.builder()
                 .ontology("src/test/resources/species-no-individuals.owl")
                 .curies(curies)
-                .data(data)
+                .individualAssociations(data)
                 .build();
 
         Ontology.load(sourceData);
@@ -97,7 +97,7 @@ public void testAddIndividuals() {
         OntologySourceData sourceData = OntologySourceData.builder()
                 .ontology("src/test/resources/species-no-individuals.owl")
                 .curies(curies)
-                .data(data)
+                .individualAssociations(data)
                 .build();
 
         Ontology ontology = Ontology.load(sourceData);

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

@@ -76,7 +76,7 @@ public void testLoadRemoteOntology() {
     @Test(expected = OntologyLoadException.class)
     public void testLoadGzippedDataFileNoOntology() {
         BMKnowledgeBase bmKnowledgeBase = OwlKnowledgeBase.loader()
-                .loadDataFromTsv("src/test/resources/data/human-pheno.assocs.gz")
+                .loadIndividualAssociationsFromTsv("src/test/resources/data/human-pheno.assocs.gz")
                 .createKnowledgeBase();
     }
 
@@ -102,8 +102,9 @@ public void loadDataFromOntologies() {
     public void loadDataFromTsv() {
         BMKnowledgeBase bmKnowledgeBase = OwlKnowledgeBase.loader()
                 .loadCuries(curies())
-                .loadOntology("src/test/resources/species-no-individuals.owl")
-                .loadDataFromTsv("src/test/resources/data/species-individuals.tsv")
+//                .loadOntology("src/test/resources/species-no-individuals.owl")
+                .loadOntology("src/test/resources/species.owl")
+                .loadIndividualAssociationsFromTsv("src/test/resources/data/species-individuals.tsv")
                 .createKnowledgeBase();
     }
 
@@ -112,7 +113,7 @@ public void loadDataFromGzippedTsv() {
         BMKnowledgeBase bmKnowledgeBase = OwlKnowledgeBase.loader()
                 .loadCuries(curies())
                 .loadOntology("src/test/resources/ontologies/mammal.obo.gz")
-                .loadDataFromTsv("src/test/resources/data/human-pheno.assocs.gz")
+                .loadIndividualAssociationsFromTsv("src/test/resources/data/human-pheno.assocs.gz")
                 .createKnowledgeBase();
     }
 
@@ -121,7 +122,7 @@ public void loadDataFromTsvCollection() {
         BMKnowledgeBase bmKnowledgeBase = OwlKnowledgeBase.loader()
                 .loadCuries(curies())
                 .loadOntology("src/test/resources/ontologies/mammal.obo.gz")
-                .loadDataFromTsv(Arrays.asList(
+                .loadIndividualAssociationsFromTsv(Arrays.asList(
                         "src/test/resources/data/gene2taxon.tsv.gz",
                         "src/test/resources/data/mouse-pheno.assocs.gz",
                         "src/test/resources/data/human-pheno.assocs.gz"))
@@ -154,7 +155,7 @@ public void loadDataFromMap() {
         BMKnowledgeBase knowledgeBase = BMKnowledgeBase.owlLoader()
                 .loadOntology("src/test/resources/species-no-individuals.owl")
                 .loadCuries(curies)
-                .loadDataFromMap(data)
+                .loadIndividualAssociations(data)
                 .createKnowledgeBase();
 
         System.out.println("knowledgebase individuals are: " + knowledgeBase.getIndividualIdsInSignature());

owlsim-services/src/main/java/org/monarchinitiative/owlsim/services/modules/KnowledgeBaseModule.java

@@ -28,7 +28,7 @@ public KnowledgeBaseModule(Collection<String> ontologyUris, Collection<String> o
 		ontologyUris.forEach(logger::info);
 		logger.info("Loading ontologyDataUris:");
 		ontologyDataUris.forEach(logger::info);
-		logger.info("Loading dataTsvs:");
+		logger.info("Loading individual associations Tsvs:");
 		dataTsvs.forEach(logger::info);
 		logger.info("Loading curies:");
 		curies.entrySet().forEach(logger::info);
@@ -37,7 +37,7 @@ public KnowledgeBaseModule(Collection<String> ontologyUris, Collection<String> o
 		this.bmKnowledgeBase = OwlKnowledgeBase.loader()
 				.loadOntologies(ontologyUris)
 				.loadDataFromOntologies(ontologyDataUris)
-				.loadDataFromTsv(dataTsvs)
+				.loadIndividualAssociationsFromTsv(dataTsvs)
 				.loadCuries(curies)
 				.createKnowledgeBase();