DO NOT MERGE YET: Upgrade to solr6: DO NOT MERGE YET

Dockerfile

@@ -0,0 +1,20 @@
+FROM maven:alpine
+
+RUN mkdir /app
+WORKDIR /app
+
+# this trick doesn't seem to work for multi-project repos
+#ADD pom.xml /app
+#RUN ["/usr/local/bin/mvn-entrypoint.sh", "mvn", "verify", "clean", "--fail-never"]
+
+ADD OWLTools-Parent/pom.xml /app/OWLTools-Parent/
+WORKDIR /app/OWLTools-Parent
+RUN ["/usr/local/bin/mvn-entrypoint.sh", "mvn", "verify", "clean", "--fail-never"]
+WORKDIR /app
+
+ADD . /app
+WORKDIR /app/OWLTools-Parent
+RUN mvn -DskipTests clean install && cp ../OWLTools-Runner/target/owltools ../OWLTools-Runner/bin/
+ENV PATH="$PATH:/app/OWLTools-Runner/bin/"
+
+CMD owltools -h

OWLTools-Annotation/src/main/java/owltools/gaf/inference/BasicAnnotationPropagator.java

@@ -380,32 +380,20 @@ protected Map<String, String> createDefaultAspectMap(OWLGraphWrapper graph) {
 
 		OWLClass mf = graph.getOWLClassByIdentifier("GO:0003674"); // molecular_function
 		if (mf != null) {
-			String mfKey = getGoSubOntology(mf, graph);
-			if (mfKey == null) 
-				throw new RuntimeException("Could not retrieve sub-ontology for GO:0003674 (molecular_function). The value of the OBO-namespace tag does not exist.");
-
-			map.put(mfKey, "F");
+			map.put(getGoSubOntology(mf, graph), "F");
 		}
 
 		OWLClass bp = graph.getOWLClassByIdentifier("GO:0008150"); // biological_process
 		if (bp != null) {
-			String bpKey = getGoSubOntology(bp, graph);
-			if (bpKey == null) 
-				throw new RuntimeException("Could not retrieve sub-ontology for GO:0008150 (biological_process). The value of the OBO-namespace tag does not exist.");
-
-			map.put(bpKey, "P");
+			map.put(getGoSubOntology(bp, graph), "P");
 		}
 
 		OWLClass cc = graph.getOWLClassByIdentifier("GO:0005575"); // cellular_component
 		if (cc != null) {
-			String ccKey = getGoSubOntology(cc, graph);
-			if (ccKey == null) 
-				throw new RuntimeException("Could not retrieve sub-ontology for GO:0005575 (celluar_component). The value of the OBO-namespace tag does not exist.");
-
-			map.put(ccKey, "C");
+			map.put(getGoSubOntology(cc, graph), "C");
 		}
 
-		if (map.isEmpty() || map.containsKey(null)) {
+		if (map.isEmpty()) {
 			// only fail if there are mappings
 			// the test case uses a custom ontology, which has no cc branch
 			throw new RuntimeException("Could not create any valid aspect mappings. Is the correct ontology (GO) loaded?");

OWLTools-Annotation/src/main/java/owltools/gaf/parser/GAFParser.java

@@ -167,7 +167,7 @@ private ReadState loadNext() throws IOException{
 						return ReadState.next;
 					}else{
 						fireParsingWarning(error);
-						LOG.info(error + " : " + this.currentRow);
+						LOG.warn(error + " : " + this.currentRow);
 					}
 				}
 				return ReadState.success;

OWLTools-Annotation/src/test/resources/test_out_dated_iea.gaf

@@ -5,4 +5,4 @@
 ! NOT a valid submission file!!!!!!
 !
 MGI	MGI:1918918	0610007C21Rik		GO:0016021	MGI:MGI:1354194	IEA	SP_KW:KW-0812	C	RIKEN cDNA 0610007C21 gene	HSPC013|p18	protein	taxon:10090	20101003	UniProtKB		VEGA:OTTMUSP00000025430
-MGI	MGI:1918919	0610007C21Rik		GO:0016021	MGI:MGI:1354194	IEA	SP_KW:KW-0812	C	RIKEN cDNA 0610007C21 gene	HSPC013|p18	protein	taxon:10090	20991003	UniProtKB		VEGA:OTTMUSP00000025430
+MGI	MGI:1918919	0610007C21Rik		GO:0016021	MGI:MGI:1354194	IEA	SP_KW:KW-0812	C	RIKEN cDNA 0610007C21 gene	HSPC013|p18	protein	taxon:10090	20161003	UniProtKB		VEGA:OTTMUSP00000025430

OWLTools-Core/src/main/java/owltools/graph/AxiomAnnotationTools.java

@@ -238,45 +238,6 @@ else if (result.size() == 1) {
 		return result;
 	}
 
-	/**
-	 * Append annotations to an existing axiom
-	 * 
-	 * @param axiom
-	 * @param annotations
-	 * @param ontology
-	 * @return
-	 */
-	public static OWLAxiom appendAxiomAnnotations(OWLAxiom axiom, Set<OWLAnnotation> annotations, OWLOntology ontology) {
-        // filter existing
-        Set<OWLAnnotation> newAnnotations = new HashSet<OWLAnnotation>(axiom.getAnnotations());
-        newAnnotations.addAll(annotations);
-        final OWLAxiom newAxiom = changeAxiomAnnotations(axiom, newAnnotations, ontology);
-        return newAxiom;
-    }
-
-	/**
-	 * Append xref annotations onto an existing axiom
-	 * 
-	 * @param axiom
-	 * @param xrefs
-	 * @param ontology
-	 * @return
-	 */
-	public static OWLAxiom appendXrefAnnotations(OWLAxiom axiom, Set<String> xrefs, OWLOntology ontology) {
-	    // filter existing
-	    Set<OWLAnnotation> newAnnotations = new HashSet<OWLAnnotation>(axiom.getAnnotations());
-        final OWLOntologyManager manager = ontology.getOWLOntologyManager();
-	    final OWLDataFactory factory = manager.getOWLDataFactory();
-
-	    for (String x : xrefs) {
-	        OWLAnnotationProperty p = factory.getOWLAnnotationProperty(IRI.create("http://www.geneontology.org/formats/oboInOwl#hasDbXref"));
-	        OWLLiteral v = factory.getOWLLiteral(x);
-	        newAnnotations.add(factory.getOWLAnnotation(p, v));
-	    }
-	    final OWLAxiom newAxiom = changeAxiomAnnotations(axiom, newAnnotations, ontology);
-	    return newAxiom;
-	}
-
 
 	/**
 	 * Update the given axiom to a new set of axiom annotation.<br>