Paginated ontology export added

.github/workflows/release.yml

@@ -0,0 +1,49 @@
+name: Build and Release JAR
+
+on:
+  push:
+    branches:
+      - main
+  release:
+    types: [created]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Set up JDK 11
+        uses: actions/setup-java@v3
+        with:
+          distribution: 'adopt'
+          java-version: '11'
+
+      - name: Build with Maven
+        run: mvn clean package
+
+      - name: Archive build artifacts
+        uses: actions/upload-artifact@v3
+        with:
+          name: neo4j2owl-jar
+          path: target/*.jar
+
+  release:
+    needs: build
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release'
+
+    steps:
+      - name: Download build artifact
+        uses: actions/download-artifact@v3
+        with:
+          name: neo4j2owl-jar
+
+      - name: Create GitHub Release
+        uses: softprops/action-gh-release@v1
+        with:
+          files: neo4j2owl-jar/*.jar
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

src/main/java/ebi/spot/neo4j2owl/N2OProcedure.java

@@ -57,8 +57,26 @@ public Stream<N2OImportResult> importOntology(@Name("url") String url) {
 	@Procedure(mode = Mode.WRITE)
 	public Stream<N2OReturnValue> exportOWL() {
 		logger.resetTimer();
-		N2OExportService importService = new N2OExportService(db);
-		N2OReturnValue result = importService.owl2Export();
+		N2OExportService exportService = new N2OExportService(db);
+		N2OReturnValue result = exportService.owl2Export();
+		return Stream.of(result);
+	}
+
+	@SuppressWarnings("unused")
+	@Procedure(mode = Mode.WRITE)
+	public Stream<N2OReturnValue> exportOWLNodes(@Name("skip") Long skip, @Name("limit") Long limit) {
+		logger.resetTimer();
+		N2OExportService exportService = new N2OExportService(db);
+		N2OReturnValue result = exportService.owl2ExportNodes(skip, limit);
+		return Stream.of(result);
+	}
+
+	@SuppressWarnings("unused")
+	@Procedure(mode = Mode.WRITE)
+	public Stream<N2OReturnValue> exportOWLEdges() {
+		logger.resetTimer();
+		N2OExportService exportService = new N2OExportService(db);
+		N2OReturnValue result = exportService.owl2ExportEdges();
 		return Stream.of(result);
 	}
 

src/main/java/ebi/spot/neo4j2owl/exporter/N2OExportService.java

@@ -65,7 +65,7 @@ public N2OReturnValue owl2Export() {
 			OWLOntologyManager man = OWLManager.createOWLOntologyManager();
 
 			OWLOntology o = man.createOntology();
-			addEntities(o);
+			addEntities(o, 0L, Long.MAX_VALUE);
 			addAnnotations(o);
 			addRelation(o, N2OStatic.RELTYPE_SUBCLASSOF);
 			addRelation(o, N2OStatic.RELTYPE_INSTANCEOF);
@@ -88,6 +88,64 @@ public N2OReturnValue owl2Export() {
 		}
 		return returnValue;
 	}
+
+	public N2OReturnValue owl2ExportNodes(Long skip, Long limit) {
+		n2OEntityManager = new N2OExportManager();
+		qsls_with_no_matching_properties = new HashSet<>();
+		logger.resetTimer();
+		N2OReturnValue returnValue = new N2OReturnValue();
+
+		try {
+			OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+
+			OWLOntology o = man.createOntology();
+			addAnnotationProperties(o);
+			addEntities(o, skip, limit);
+			addAnnotations(o);
+			ByteArrayOutputStream os = new ByteArrayOutputStream(); // new FileOutputStream(new File(fileName))
+			man.saveOntology(o, new RDFXMLDocumentFormat(), os);
+			qsls_with_no_matching_properties.forEach(logger::log);
+			List<String> ontologyChunks = createArrayChunks(os.toByteArray());
+			returnValue.setOntology(ontologyChunks);
+			returnValue.setLog(o.getLogicalAxiomCount() + "");
+		} catch (Exception e) {
+			e.printStackTrace();
+			returnValue.setLog(logger.getStackTrace(e));
+		}
+		return returnValue;
+	}
+
+	public N2OReturnValue owl2ExportEdges() {
+		n2OEntityManager = new N2OExportManager();
+		qsls_with_no_matching_properties = new HashSet<>();
+		logger.resetTimer();
+		N2OReturnValue returnValue = new N2OReturnValue();
+
+		try {
+			OWLOntologyManager man = OWLManager.createOWLOntologyManager();
+
+			OWLOntology o = man.createOntology();
+			findEntities(0L, Long.MAX_VALUE);
+			addRelation(o, N2OStatic.RELTYPE_SUBCLASSOF);
+			addRelation(o, N2OStatic.RELTYPE_INSTANCEOF);
+			for (String rel_qsl : getRelations(OWLAnnotationProperty.class)) {
+				addRelation(o, rel_qsl);
+			}
+			for (String rel_qsl : getRelations(OWLObjectProperty.class)) {
+				addRelation(o, rel_qsl);
+			}
+			ByteArrayOutputStream os = new ByteArrayOutputStream(); // new FileOutputStream(new File(fileName))
+			man.saveOntology(o, new RDFXMLDocumentFormat(), os);
+			qsls_with_no_matching_properties.forEach(logger::log);
+			List<String> ontologyChunks = createArrayChunks(os.toByteArray());
+			returnValue.setOntology(ontologyChunks);
+			returnValue.setLog(o.getLogicalAxiomCount() + "");
+		} catch (Exception e) {
+			e.printStackTrace();
+			returnValue.setLog(logger.getStackTrace(e));
+		}
+		return returnValue;
+	}
 
 	private Set<String> getRelations(Class cl) {
 		return n2OEntityManager.relationshipQSLs().stream()
@@ -107,13 +165,13 @@ private void addRelation(OWLOntology o, String RELTYPE) throws N2OException {
 				Map<String, Object> r = s.next();
 				Object object = r.get("n");
 				// log(r);
-				Long nid = ((Node) r.get("n")).getId();
-				Long xid = ((Node) r.get("x")).getId();
-				Relationship rp = (Relationship) r.get("r");
+	            Long nid = ((Node) r.get("n")).getId();
+	            Long xid = ((Node) r.get("x")).getId();
+	            Relationship rp = (Relationship) r.get("r");
 
-				OWLAxiom ax = createAxiom(n2OEntityManager.getEntity(nid), n2OEntityManager.getEntity(xid), RELTYPE);
-				Set<OWLAnnotation> axiomAnnotations = getAxiomAnnotations(rp);
-				changes.add(new AddAxiom(o, ax.getAnnotatedAxiom(axiomAnnotations)));
+	            OWLAxiom ax = createAxiom(n2OEntityManager.getEntity(nid), n2OEntityManager.getEntity(xid), RELTYPE);
+	            Set<OWLAnnotation> axiomAnnotations = getAxiomAnnotations(rp);
+	            changes.add(new AddAxiom(o, ax.getAnnotatedAxiom(axiomAnnotations)));
 			}
 			if (!changes.isEmpty()) {
 				try {
@@ -341,8 +399,32 @@ private OWLAnnotationProperty getAnnotationProperty(String qsl_anno) {
 	 * - just declarations. The main purpose is to index all entities for the next
 	 * Steps in the pipeline
 	 */
-	private void addEntities(OWLOntology o) throws N2OException {
-		String cypher = "MATCH (n:Entity) Return n";
+	private void addEntities(OWLOntology o, Long skip, Long limit) throws N2OException {
+		findEntities(skip, limit);
+		n2OEntityManager.entities().stream().filter(e -> !e.isBuiltIn()).forEach((e -> addDeclaration(e, o)));
+	}
+
+	/**
+	 * Only discovers entities and updates the n2OEntityManager without adding to the Ontology.
+	 * @param o 
+	 * @param skip
+	 * @param limit
+	 * @throws N2OException
+	 */
+	private void findEntities(Long skip, Long limit) throws N2OException {
+		String cypher = String.format("MATCH (n:Entity) Return n SKIP %d LIMIT %d", skip, limit);
+		Result s;
+		try (Transaction tx = db.beginTx()) {
+			s = tx.execute(cypher);
+			Objects.requireNonNull(s);
+			s.stream().forEach(r -> createEntityForEachLabel((Node) r.get("n")));
+		} catch (Exception e) {
+			throw new N2OException(N2OStatic.CYPHER_FAILED_TO_EXECUTE + cypher, e);
+		}
+	}
+
+	private void addAnnotationProperties(OWLOntology o) throws N2OException {
+		String cypher = String.format("MATCH (n:AnnotationProperty) Return n");
 		Result s;
 		try (Transaction tx = db.beginTx()) {
 			s = tx.execute(cypher);

src/main/java/ebi/spot/neo4j2owl/exporter/N2OReturnValue.java

@@ -25,4 +25,4 @@ public void addOntologyChunk(String chunk) {
     public void setLog(String log) {
         this.log = log;
     }
-}
+}