Ontoportal lirmm/bugfix/ontology level annotations

.github/workflows/maven.yml → .github/workflows/unit-tests.yml

@@ -1,26 +1,30 @@
 # This workflow will build a Java project with Maven, and cache/restore any dependencies to improve the workflow execution time
 # For more information see: https://help.github.com/actions/language-and-framework-guides/building-and-testing-java-with-maven
 
-name: Java CI with Maven
+name: Java Unit Tests
 
 on:
   push:
-    branches: [ master ]
   pull_request:
-    branches: [ master ]
 
 jobs:
   build:
 
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up JDK 11
-      uses: actions/setup-java@v3
+      uses: actions/setup-java@v4
       with:
         java-version: '11'
         distribution: 'temurin'
         cache: maven
-    - name: Build with Maven
-      run: mvn -B package --file pom.xml
+    - name: Prepare all dependencies
+      run: mvn -B dependency:go-offline
+    - name: Run tests
+      run: mvn -B test
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v5
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

README.md

@@ -1,6 +1,6 @@
 # owlapi_wrapper
 
-[![Build Status](https://travis-ci.org/ncbo/owlapi_wrapper.svg?branch=master)](https://travis-ci.org/ncbo/owlapi_wrapper)
+[![codecov](https://codecov.io/gh/ncbo/owlapi_wrapper/graph/badge.svg?token=HEt3yP8T0i)](https://codecov.io/gh/ncbo/owlapi_wrapper)
 
 A command line utility that wraps the Java [OWL API](https://github.com/owlcs/owlapi) for parsing RDFS, OWL, and OBO ontologies. 
 

build_install.sh

@@ -1 +1 @@
-mvn assembly:assembly -DskipTests && cp target/owlapi_wrapper-0.0.1-SNAPSHOT-jar-with-dependencies.jar ../ontologies_linked_data/bin/owlapi_wrapper.jar
+mvn assembly:assembly -DskipTests && cp target/owlapi_wrapper-0.0.1-SNAPSHOT-jar-with-dependencies.jar ../owlapi_wrapper.jar

pom.xml

@@ -138,13 +138,13 @@
     <dependency>
       <groupId>ch.qos.logback</groupId>
       <artifactId>logback-core</artifactId>
-      <version>1.4.11</version>
+      <version>1.4.14</version>
     </dependency>
 
     <dependency>
       <groupId>ch.qos.logback</groupId>
       <artifactId>logback-classic</artifactId>
-      <version>1.4.11</version>
+      <version>1.4.14</version>
     </dependency>
 
     <dependency>
@@ -153,6 +153,12 @@
       <version>1.10.0</version>
     </dependency>
 
+    <dependency>
+        <groupId>javax.xml.bind</groupId>
+        <artifactId>jaxb-api</artifactId>
+        <version>2.3.0</version>
+    </dependency>
+
   </dependencies>
 
   <build>
@@ -222,7 +228,27 @@
         <artifactId>maven-release-plugin</artifactId>
         <version>2.5.3</version>
       </plugin>
+
+      <plugin>
+        <groupId>org.jacoco</groupId>
+        <artifactId>jacoco-maven-plugin</artifactId>
+        <version>0.8.13</version>
+        <executions>
+          <execution>
+            <goals>
+              <goal>prepare-agent</goal>
+            </goals>
+          </execution>
+          <execution>
+            <id>report</id>
+            <phase>test</phase>
+            <goals>
+              <goal>report</goal>
+            </goals>
+          </execution>
+        </executions>
+      </plugin>
     </plugins>
-    
+
   </build>
 </project>

src/main/java/org/stanford/ncbo/owlapi/wrapper/OntologyParser.java

@@ -31,6 +31,7 @@
 
 public class OntologyParser {
 	private final static Logger log = LoggerFactory.getLogger(OntologyParser.class.getName());
+	public static final String USE_IMPORTS_IRI = "http://omv.ontoware.org/2005/05/ontology#useImports";
 	public static final String VERSION_SUBJECT = "http://bioportal.bioontology.org/ontologies/versionSubject";
 
 	protected ParserInvocation parserInvocation = null;
@@ -169,6 +170,33 @@ private void addOntologyIRI(OWLOntology sourceOnt) {
 		}
 	}
 
+	/**
+	 * Get ontology imports and them to <ONTOLOGY_URI>
+	 * omv:useImports <import_URI>
+	 *
+	 * @param fact
+	 * @param sourceOnt
+	 */
+	private void addOntologyImports(OWLDataFactory fact, OWLOntology sourceOnt){
+		Optional<IRI> sub = sourceOnt.getOntologyID().getOntologyIRI();
+
+		if(!sub.isPresent()){
+            return;
+        }
+
+		IRI ontologyIRI = sub.get();
+
+		// Get imports and add them as omv:useImports
+		OWLAnnotationProperty useImportProp = fact.getOWLAnnotationProperty(IRI.create(USE_IMPORTS_IRI));
+		for (OWLOntology imported : sourceOnt.getImports()) {
+			if (!imported.getOntologyID().isAnonymous()) {
+				log.info("useImports: " + imported.getOntologyID().getOntologyIRI().get());
+				OWLAnnotationAssertionAxiom useImportAxiom = fact.getOWLAnnotationAssertionAxiom(useImportProp, ontologyIRI, imported.getOntologyID().getOntologyIRI().get());
+				this.targetOwlManager.addAxiom(targetOwlOntology, useImportAxiom);
+			}
+		}
+	}
+
 	/**
 	 * Copies ontology-level annotation axioms from the source ontology to the target ontology.
 	 * <p>
@@ -188,6 +216,7 @@ private void addGroundMetadata(IRI documentIRI, OWLDataFactory factory, OWLOntol
 		}
 
 		for (OWLAnnotation annotation : sourceOntology.getAnnotations()) {
+
 			IRI subjectIRI = ontologyID.getOntologyIRI().get();
 			OWLAnnotationProperty annotationProperty = annotation.getProperty();
 			OWLAnnotationValue annotationValue = annotation.getValue();
@@ -212,6 +241,7 @@ private boolean buildOWLOntology(OWLOntology masterOntology, boolean isOBO) {
 		try {
 			targetOwlOntology = targetOwlManager.createOntology();
 			addOntologyIRI(masterOntology);
+			addOntologyImports(fact, masterOntology);
 		} catch (OWLOntologyCreationException e) {
 			log.error(e.getMessage());
 			parserLog.addError(ParserError.OWL_CREATE_ONTOLOGY_EXCEPTION, "Error buildOWLOntology" + e.getMessage());
@@ -232,51 +262,52 @@ private boolean buildOWLOntology(OWLOntology masterOntology, boolean isOBO) {
 
 			boolean isPrefixedOWL = sourceOwlManager.getOntologyFormat(sourceOnt).isPrefixOWLOntologyFormat();
 			log.info("isPrefixOWLOntologyFormat: {}", isPrefixedOWL);
-			if (isPrefixedOWL == true && !isOBO) {
+			if (isPrefixedOWL && !isOBO) {
 				generateSKOSInOwl(allAxioms, fact, sourceOnt);
 			}
 		}
 
-		targetOwlManager.addAxioms(targetOwlOntology, allAxioms);
-		for (OWLAnnotation ann : targetOwlOntology.getAnnotations()) {
+
+        targetOwlManager.addAxioms(targetOwlOntology, allAxioms);
+        for (OWLAnnotation ann : targetOwlOntology.getAnnotations()) {
+            AddOntologyAnnotation addAnn = new AddOntologyAnnotation(targetOwlOntology, ann);
+            targetOwlManager.applyChange(addAnn);
+        }
+
+        if (isOBO) {
+            String oboVersion = parserInvocation.getOBOVersion();
+            if (oboVersion != null) {
+                log.info("Adding version: {}", oboVersion);
+                OWLAnnotationProperty prop = fact.getOWLAnnotationProperty(IRI.create(OWLRDFVocabulary.OWL_VERSION_INFO.toString()));
+                IRI versionSubjectIRI = IRI.create(VERSION_SUBJECT);
+                OWLAnnotationAssertionAxiom annVersion = fact.getOWLAnnotationAssertionAxiom(prop, versionSubjectIRI, fact.getOWLLiteral(oboVersion));
+                targetOwlManager.addAxiom(targetOwlOntology, annVersion);
+            }
+        }
+
+		addOntologyAnnotations(masterOntology);
+        escapeXMLLiterals(targetOwlOntology);
+
+        OWLReasonerFactory reasonerFactory = new StructuralReasonerFactory();
+        OWLReasoner reasoner = reasonerFactory.createReasoner(targetOwlOntology);
+        InferredSubClassAxiomGenerator isc = new InferredSubClassAxiomGenerator();
+        Set<OWLSubClassOfAxiom> subAxs = isc.createAxioms(targetOwlOntology.getOWLOntologyManager().getOWLDataFactory(), reasoner);
+        targetOwlManager.addAxioms(targetOwlOntology, subAxs);
+        deprecateBranch();
+
+        log.info("isOBO: {}", isOBO);
+        if (isOBO) {
+            replicateHierarchyAsTreeview(fact);
+        }
+        return true;
+    }
+
+	private void addOntologyAnnotations(OWLOntology masterOntology){
+		for (OWLAnnotation ann : masterOntology.getAnnotations()) {
 			AddOntologyAnnotation addAnn = new AddOntologyAnnotation(targetOwlOntology, ann);
 			targetOwlManager.applyChange(addAnn);
 		}
-
-		if (isOBO) {
-			String oboVersion = parserInvocation.getOBOVersion();
-			if (oboVersion != null) {
-				log.info("Adding version: {}", oboVersion);
-				OWLAnnotationProperty prop = fact.getOWLAnnotationProperty(IRI.create(OWLRDFVocabulary.OWL_VERSION_INFO.toString()));
-				IRI versionSubjectIRI = IRI.create(VERSION_SUBJECT);
-				OWLAnnotationAssertionAxiom annVersion = fact.getOWLAnnotationAssertionAxiom(prop, versionSubjectIRI, fact.getOWLLiteral(oboVersion));
-				targetOwlManager.addAxiom(targetOwlOntology, annVersion);
-			}
-		}
-
-		for (OWLOntology sourceOnt : sourceOwlManager.getOntologies()) {
-			for (OWLAnnotation ann : sourceOnt.getAnnotations()) {
-				AddOntologyAnnotation addAnn = new AddOntologyAnnotation(targetOwlOntology, ann);
-				targetOwlManager.applyChange(addAnn);
-			}
-		}
-
-		escapeXMLLiterals(targetOwlOntology);
-
-		OWLReasonerFactory reasonerFactory = new StructuralReasonerFactory();
-		OWLReasoner reasoner = reasonerFactory.createReasoner(targetOwlOntology);
- 		InferredSubClassAxiomGenerator isc = new InferredSubClassAxiomGenerator();
-		Set<OWLSubClassOfAxiom> subAxs = isc.createAxioms(targetOwlOntology.getOWLOntologyManager().getOWLDataFactory(), reasoner);
-		targetOwlManager.addAxioms(targetOwlOntology, subAxs);
-		deprecateBranch();
-
-		log.info("isOBO: {}", isOBO);
-		if (isOBO) {
-			replicateHierarchyAsTreeview(fact);
-		}
-		return true;
 	}
-
 	private void replicateHierarchyAsTreeview(OWLDataFactory fact) {
 		Set<OWLAxiom> treeViewAxs = new HashSet<OWLAxiom>();
 		for (OWLAxiom axiom : targetOwlOntology.getAxioms()) {
@@ -449,7 +480,7 @@ private void escapeXMLLiterals(OWLOntology target) {
 							targetOwlManager.addAxiom(target, annAsse);
 							Set<OWLAnnotationAssertionAxiom> del = new HashSet<OWLAnnotationAssertionAxiom>();
 							del.add(ann);
-							targetOwlManager.removeAxioms(target,del); 
+							targetOwlManager.removeAxioms(target,del);
 						}
 					}
 				}

src/main/java/org/stanford/ncbo/owlapi/wrapper/preferred_labels/PreferredLabels.java

@@ -0,0 +1,20 @@
+package org.stanford.ncbo.owlapi.wrapper.preferred_labels;
+
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.stanford.ncbo.owlapi.wrapper.ParserInvocation;
+import org.stanford.ncbo.owlapi.wrapper.metrics.OntologyMetrics;
+
+public class PreferredLabels {
+    private static final Logger logger = LoggerFactory.getLogger(OntologyMetrics.class);
+
+    private OWLOntology ontology;
+
+    private ParserInvocation parserInvocation;
+
+    public PreferredLabels(OWLOntology ontology, ParserInvocation parserInvocation) {
+        this.ontology = ontology;
+        this.parserInvocation = parserInvocation;
+    }
+}

src/test/java/org/stanford/ncbo/owlapi/wrapper/OntologyParserTest.java

@@ -18,6 +18,19 @@ public class OntologyParserTest {
     public void setUp() throws Exception {
 
     }
+
+    // Run this test: mvn -Dtest=OntologyParserTest#sifrTestParse test
+    // parse_OntologyENVO_ReturnsTrue fonctionne pour comparer
+    @Test
+    public void sifrTestParse() throws Exception {
+        ParserInvocation pi = new ParserInvocation("./src/test/resources/repo/input/sifr",
+                "./src/test/resources/repo/output/sifr", "foodon.owl", true);
+        // SKOS: anaee-france-thesaurus.rdf
+        // OWL: AnimalDiseasesOntology.owl.xml
+        OntologyParser parser = new OntologyParser(pi);
+        parser.parse();
+        //assertFalse(parser.parse());
+    }
 
     @Test
     public void getLocalOntologies_MultipleOntologies_Found() throws Exception {
@@ -165,6 +178,25 @@ public void parse_ImportSKOSCoreVocab_ShouldLoad() throws Exception {
         OWLClass skosConceptClass = factory.getOWLClass(skosConceptIRI);
         assertNotNull(skosConceptClass);
     }
+    @Test
+    public void parse_OntologyAnnotationCount_ReturnsTrue() throws Exception {
+        String outputRepositoryFolder = "./src/test/resources/repo/output/cno";
+        ParserInvocation pi = new ParserInvocation("./src/test/resources/repo/input/cno",
+                outputRepositoryFolder, "cnov0_5.owl", true);
+        assertTrue(pi.valid());
+
+        OntologyParser parser = new OntologyParser(pi);
+        assertTrue(parser.parse());
+        assertEquals(1, parser.getLocalOntologies().size());
+
+        OWLOntology targetOwlOntology = parser.getTargetOwlOntology();
+        OWLOntology sourceOntology = parser.getParsedOntologies().stream().findFirst().orElse(null);
+
+        assertNotNull(sourceOntology);
+        assertEquals(sourceOntology.getAnnotations().size(), targetOwlOntology.getAnnotations().size());
+
+    }
+
 
     @After
     public void tearDown() throws Exception {