Merge pull request UCDenver-ccp#6 from bill-baumgartner/master

Revisions to handle case inconsistency for oboInOwl namespace.

datasource-fileparsers/src/main/java/edu/ucdenver/ccp/datasource/fileparsers/obo/OntologyUtil.java

@@ -48,11 +48,15 @@
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
 import org.semanticweb.owlapi.model.OWLOntologyManager;
+import org.semanticweb.owlapi.model.OWLProperty;
 
 import owltools.graph.OWLGraphWrapper;
 
 public class OntologyUtil {
 
+	private static final String INVALID_OBO_IN_OWL_NAMESPACE = "http://www.geneontology.org/formats/oboInOWL#";
+	private static final String NAMESPACE_PROP = "<http://purl.obolibrary.org/obo/namespace>";
+	private static final String NAMESPACE_PROP_ALT = "<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace>";
 	private static final Logger logger = Logger.getLogger(OntologyUtil.class);
 	private static final String EXACT_SYN_PROP = "<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym>";
 	private static final String EXACT_SYN_PROP_ALT = "<http://purl.obolibrary.org/obo/exact_synonym>";
@@ -146,11 +150,37 @@ public String getLabel(OWLClass cls) {
 		return null;
 	}
 
+	/**
+	 * This method was composed in response to the following issue:
+	 * https://github.com/UCDenver-ccp/datasource/issues/5
+	 * 
+	 * The user uncovered an inconsistency in the oboInOwl namespace returned by
+	 * the OWL API OBO parser. The inconsistency involves the capitalization of
+	 * "OWL" in oboInOWL. The OBO parsers uses
+	 * http://www.geneontology.org/formats/oboInOWL# whereas the namespace
+	 * appears as http://www.geneontology.org/formats/oboInOwl# in OWL files in
+	 * the wild. This method swaps out the oboInOWL for oboInOwl when it is
+	 * observed.
+	 * 
+	 * @param annotation
+	 * @return the {@link OWLProperty} IRI for the input {@link OWLAnnotation}.
+	 *         If the invalid version of the oboInOwl namespace is detected
+	 *         (used by the OWL API OBO parser), it is replaced with the valid
+	 *         version which differs only in capitalization.
+	 */
+	public static String getAnnotationPropertyUri(OWLAnnotation annotation) {
+		String propertyUri = annotation.getProperty().toString();
+		if (propertyUri.startsWith("<" + INVALID_OBO_IN_OWL_NAMESPACE)) {
+			propertyUri = propertyUri.replaceFirst("oboInOWL", "oboInOwl");
+		}
+		return propertyUri;
+	}
+
 	public Set<String> getSynonyms(OWLClass cls, SynonymType synType) {
 		Set<String> synonyms = new HashSet<String>();
 		Set<OWLAnnotation> annotations = cls.getAnnotations(ont);
 		for (OWLAnnotation annotation : annotations) {
-			String property = annotation.getProperty().toString();
+			String property = getAnnotationPropertyUri(annotation);
 			if ((synType == SynonymType.EXACT || synType == SynonymType.ALL)
 					&& (property.equals(EXACT_SYN_PROP) || property.equals(EXACT_SYN_PROP_ALT))) {
 				String s = annotation.getValue().toString();
@@ -203,8 +233,8 @@ public Set<String> getSynonyms(OWLClass cls, SynonymType synType) {
 	public String getNamespace(OWLClass cls) {
 		Set<OWLAnnotation> annotations = cls.getAnnotations(ont);
 		for (OWLAnnotation annotation : annotations) {
-			if (annotation.getProperty().toString()
-					.equals("<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace>")) {
+			String propertyUri = getAnnotationPropertyUri(annotation);
+			if (propertyUri.equals(NAMESPACE_PROP_ALT) || propertyUri.equals(NAMESPACE_PROP)) {
 				String s = annotation.getValue().toString();
 				s = StringUtils.removePrefix(s, "\"");
 				s = StringUtils.removeSuffix(s, "\"^^xsd:string");

datasource-fileparsers/src/test/java/edu/ucdenver/ccp/datasource/fileparsers/obo/OntologyUtilTest.java

@@ -39,9 +39,17 @@
 
 import java.io.File;
 import java.io.IOException;
-
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+import org.apache.log4j.AppenderSkeleton;
+import org.apache.log4j.Level;
+import org.apache.log4j.Logger;
+import org.apache.log4j.spi.LoggingEvent;
 import org.junit.Before;
 import org.junit.Test;
+import org.semanticweb.owlapi.model.OWLClass;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
 
 import edu.ucdenver.ccp.common.collections.CollectionsUtil;
@@ -57,13 +65,24 @@
 public class OntologyUtilTest extends DefaultTestCase {
 
 	private static final String SAMPLE_OBO_FILE_NAME = "sample.obo";
+	private static final String SAMPLE_NCBITAXON_OBO_FILE_NAME = "sample.ncbitaxon.obo";
+	private static final String SAMPLE_NCBITAXON_OWL_FILE_NAME = "sample.ncbitaxon.owl";
 	private OntologyUtil ontUtil;
+	private File sampleNcbiTaxonOboFile;
+	private File sampleNcbiTaxonOwlFile;
 
 	@Before
 	public void setUp() throws IOException, OWLOntologyCreationException {
 		File sampleOboFile = folder.newFile("sample.obo");
 		ClassPathUtil.copyClasspathResourceToFile(getClass(), SAMPLE_OBO_FILE_NAME, sampleOboFile);
 		ontUtil = new OntologyUtil(sampleOboFile);
+
+		sampleNcbiTaxonOboFile = folder.newFile("sample.ncbitaxon.obo");
+		ClassPathUtil.copyClasspathResourceToFile(getClass(), SAMPLE_NCBITAXON_OBO_FILE_NAME, sampleNcbiTaxonOboFile);
+
+		sampleNcbiTaxonOwlFile = folder.newFile("sample.ncbitaxon.owl");
+		ClassPathUtil.copyClasspathResourceToFile(getClass(), SAMPLE_NCBITAXON_OWL_FILE_NAME, sampleNcbiTaxonOwlFile);
+
 	}
 
 	@Test
@@ -116,4 +135,91 @@ public void testGetSynonyms() {
 				ontUtil.getOWLClassFromId("PR:000002012"), SynonymType.ALL));
 	}
 
+	@Test
+	public void testNcbiTaxonOboFile() throws OWLOntologyCreationException, IOException {
+		testSampleOntologyFile(sampleNcbiTaxonOboFile, 8, "ncbi_taxonomy");
+	}
+
+	@Test
+	public void testNcbiTaxonOwlFile() throws OWLOntologyCreationException, IOException {
+		testSampleOntologyFile(sampleNcbiTaxonOwlFile, 8, "ncbi_taxonomy");
+	}
+
+	/**
+	 * This test was written in response to
+	 * https://github.com/UCDenver-ccp/datasource/issues/5
+	 * 
+	 * The user reported an "unhandled synonym type" error when processing the
+	 * NCBI Taxonomy ontology. This error stems from an inconsistency in the OWL
+	 * API when processing OBO files vs. OWL files. Specifically, the oboInOwl
+	 * namespace when parsing an OBO file is set to:
+	 * http://www.geneontology.org/formats/oboInOWL# whereas in OWL files the
+	 * following is used: http://www.geneontology.org/formats/oboInOwl#. Note
+	 * the difference in capitalization, oboInOWL vs. oboInOwl. The error
+	 * appears when retrieving synonyms for a concept and the oboInOwl namespace
+	 * is used for the various synonym types (related, exact, broad, narrow,
+	 * etc.) It also appears when retrieving the namespace of a concept.
+	 *
+	 * This test processes a sample ontology file and exercises the synonym
+	 * retrieval code. If an "unhandled synonym type" error is logged, the test
+	 * fails.
+	 * 
+	 * This test also checks to make sure the returned namespace is as expected.
+	 * 
+	 * @param ontFile
+	 * @param expectedClassCount
+	 * @throws OWLOntologyCreationException
+	 * @throws IOException
+	 */
+	private static void testSampleOntologyFile(File ontFile, int expectedClassCount, String expectedNamespace)
+			throws OWLOntologyCreationException, IOException {
+		final TestAppender appender = new TestAppender();
+		final Logger logger = Logger.getLogger(OntologyUtil.class);
+		logger.addAppender(appender);
+
+		OntologyUtil ontUtil = new OntologyUtil(ontFile);
+		int count = 0;
+		for (Iterator<OWLClass> classIterator = ontUtil.getClassIterator(); classIterator.hasNext();) {
+			count++;
+			OWLClass owlCls = classIterator.next();
+			ontUtil.getSynonyms(owlCls, SynonymType.RELATED);
+			assertEquals(expectedNamespace, ontUtil.getNamespace(owlCls));
+		}
+		ontUtil.close();
+		assertEquals(expectedClassCount, count);
+
+		/* ensure there were no errors logged */
+		final List<LoggingEvent> logList = appender.getLog();
+		for (LoggingEvent log : logList) {
+			assertFalse("An error was logged: " + log.getMessage().toString(), log.getLevel().equals(Level.ERROR));
+		}
+	}
+
+	/**
+	 * from:
+	 * http://stackoverflow.com/questions/1827677/how-to-do-a-junit-assert-
+	 * on-a-message-in-a-logger
+	 */
+	private static class TestAppender extends AppenderSkeleton {
+		private final List<LoggingEvent> log = new ArrayList<LoggingEvent>();
+
+		@Override
+		public boolean requiresLayout() {
+			return false;
+		}
+
+		@Override
+		protected void append(final LoggingEvent loggingEvent) {
+			log.add(loggingEvent);
+		}
+
+		@Override
+		public void close() {
+		}
+
+		public List<LoggingEvent> getLog() {
+			return new ArrayList<LoggingEvent>(log);
+		}
+	}
+
 }

datasource-fileparsers/src/test/resources/edu/ucdenver/ccp/datasource/fileparsers/obo/sample.ncbitaxon.obo

@@ -0,0 +1,143 @@
+format-version: 1.2
+data-version: 2016-02-02
+synonymtypedef: acronym "acronym"
+synonymtypedef: anamorph "anamorph"
+synonymtypedef: blast_name "blast name"
+synonymtypedef: common_name "common name"
+synonymtypedef: equivalent_name "equivalent name"
+synonymtypedef: genbank_acronym "genbank acronym"
+synonymtypedef: genbank_anamorph "genbank anamorph"
+synonymtypedef: genbank_common_name "genbank common name"
+synonymtypedef: genbank_synonym "genbank synonym"
+synonymtypedef: in_part "in-part"
+synonymtypedef: misnomer "misnomer"
+synonymtypedef: misspelling "misspelling"
+synonymtypedef: scientific_name "scientific name"
+synonymtypedef: synonym "synonym"
+synonymtypedef: teleomorph "teleomorph"
+remark: Autogenerated by OWLTools-NCBIConverter.
+ontology: ncbitaxon.sample
+
+[Term]
+id: NCBITaxon:1
+name: root
+namespace: ncbi_taxonomy
+synonym: "all" RELATED synonym []
+xref: GC_ID:1
+
+[Term]
+id: NCBITaxon:10
+name: Cellvibrio
+namespace: ncbi_taxonomy
+synonym: "\"Cellvibrio\" Winogradsky 1929" RELATED synonym []
+synonym: "Cellvibrio (ex Winogradsky 1929) Blackall et al. 1986 emend. Humphry et al. 2003" RELATED synonym []
+synonym: "Cellvibrio (ex Winogradsky 1929) Blackall et al. 1986 emend. Suarez et al. 2014" RELATED synonym []
+xref: GC_ID:11
+xref: PMID:12710603
+xref: PMID:24105943
+is_a: NCBITaxon:1706371 ! Cellvibrionaceae
+property_value: has_rank NCBITaxon:genus
+
+[Term]
+id: NCBITaxon:1706371
+name: Cellvibrionaceae
+namespace: ncbi_taxonomy
+xref: GC_ID:11
+xref: PMID:25914684
+is_a: NCBITaxon:1706369 ! Cellvibrionales
+property_value: has_rank NCBITaxon:family
+
+[Term]
+id: NCBITaxon:1706369
+name: Cellvibrionales
+namespace: ncbi_taxonomy
+xref: GC_ID:11
+xref: PMID:25914684
+is_a: NCBITaxon:1236 ! Gammaproteobacteria
+property_value: has_rank NCBITaxon:order
+
+[Term]
+id: NCBITaxon:1236
+name: Gammaproteobacteria
+namespace: ncbi_taxonomy
+synonym: "g-proteobacteria" RELATED blast_name []
+synonym: "gamma proteobacteria" RELATED synonym []
+synonym: "gamma subdivision" RELATED synonym []
+synonym: "gamma subgroup" RELATED synonym []
+synonym: "Gammaproteobacteria Garrity et al. 2005" RELATED synonym []
+synonym: "Proteobacteria gamma subdivision" RELATED synonym []
+synonym: "Purple bacteria, gamma subdivision" RELATED synonym []
+xref: GC_ID:11
+xref: PMID:16280474
+is_a: NCBITaxon:1224 ! Proteobacteria
+property_value: has_rank NCBITaxon:class
+
+[Term]
+id: NCBITaxon:1224
+name: Proteobacteria
+namespace: ncbi_taxonomy
+synonym: "Alphaproteobacteraeota" RELATED synonym []
+synonym: "proteobacteria" RELATED blast_name []
+synonym: "purple bacteria" EXACT common_name []
+synonym: "purple bacteria and relatives" EXACT common_name []
+synonym: "purple non-sulfur bacteria" EXACT common_name []
+synonym: "purple photosynthetic bacteria" EXACT common_name []
+synonym: "purple photosynthetic bacteria and relatives" EXACT common_name []
+xref: GC_ID:11
+xref: PMID:11321122
+xref: PMID:11542017
+xref: PMID:11837318
+xref: PMID:16280474
+xref: PMID:26654112
+is_a: NCBITaxon:2 ! Bacteria <prokaryote>
+property_value: has_rank NCBITaxon:phylum
+
+id: NCBITaxon:2
+name: Bacteria <prokaryote>
+namespace: ncbi_taxonomy
+synonym: "Bacteria" EXACT scientific_name []
+synonym: "bacteria" RELATED blast_name []
+synonym: "eubacteria" EXACT genbank_common_name []
+synonym: "Monera" RELATED in_part []
+synonym: "not Bacteria Haeckel 1894" RELATED synonym []
+synonym: "Procaryotae" RELATED in_part []
+synonym: "Prokaryota" RELATED in_part []
+synonym: "Prokaryotae" RELATED in_part []
+synonym: "prokaryote" RELATED in_part []
+synonym: "prokaryotes" RELATED in_part []
+xref: GC_ID:11
+xref: PMID:10425795
+xref: PMID:10425796
+xref: PMID:10425797
+xref: PMID:10490293
+xref: PMID:10843050
+xref: PMID:10939651
+xref: PMID:10939673
+xref: PMID:10939677
+xref: PMID:11211268
+xref: PMID:11321083
+xref: PMID:11321113
+xref: PMID:11411719
+xref: PMID:11540071
+xref: PMID:11542017
+xref: PMID:11542087
+xref: PMID:11760965
+xref: PMID:12054223
+xref: PMID:2112744
+xref: PMID:270744
+xref: PMID:270744
+xref: PMID:8123559
+xref: PMID:8590690
+xref: PMID:9103655
+xref: PMID:9336922
+is_a: NCBITaxon:131567 ! cellular organisms
+property_value: has_rank NCBITaxon:superkingdom
+
+
+[Term]
+id: NCBITaxon:131567
+name: cellular organisms
+namespace: ncbi_taxonomy
+synonym: "biota" RELATED synonym []
+xref: GC_ID:1
+is_a: NCBITaxon:1 ! root