Changeset 506

Timestamp:

01/19/12 17:21:46 (16 months ago)

Author:

tadamusiak

Message:

added xrefs to annotations returned from ols

Location:

trunk/ontoCAT

Files:

• dist/release_notes.txt (modified) (1 diff)
• src/uk/ac/ebi/ontocat/ols/OlsOntologyService.java (modified) (17 diffs)

trunk/ontoCAT/dist/release_notes.txt

@@ -4 +4 @@
 Version 0.9.9.2 / / /
         Added <userIds> <obsoleteParent> fields to Bioportal's OntologyBean
-        FIX for the inability of using encoded slashes in the URL proper when querying Bioportal. 
+        FIX for the inability of using encoded slashes in the URL proper when querying Bioportal
         Now passing them as string parameters, q=? pattern
+        Added xrefs to annotations returned from OLS
 
 Version 0.9.9.1 30/9/2011

trunk/ontoCAT/src/uk/ac/ebi/ontocat/ols/OlsOntologyService.java

@@ -33 +33 @@
 import java.util.Set;
 import java.util.TreeMap;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 import javax.xml.rpc.ServiceException;
@@ -70 +72 @@
 @SuppressWarnings("unchecked")
 public class OlsOntologyService extends AbstractOntologyService implements
-OntologyService {
+                OntologyService {
         Logger logger = Logger.getLogger(OlsOntologyService.class);
         // Webservice API
@@ -88 +90 @@
                 // Try to make connections to the database and the webservice
                 try {
-                        this.locator = new QueryServiceLocator();
-                        this.qs = locator.getOntologyQuery();
+                        locator = new QueryServiceLocator();
+                        qs = locator.getOntologyQuery();
                 } catch (ServiceException e) {
                         throw new OntologyServiceException(e);
@@ -142 +144 @@
                                                 if (ops.contains(SearchOptions.EXACT)
                                                                 && dh.getAnnotationStringValue()
-                                                                .equalsIgnoreCase(query)) {
+                                                                                .equalsIgnoreCase(query)) {
                                                         continue;
                                                 }
@@ -155 +157 @@
                                 String label = terms.get(key);
                                 URI uri = URI
-                                .create("http://www.ebi.ac.uk/ontology-lookup/?termId=" + key);
+                                                .create("http://www.ebi.ac.uk/ontology-lookup/?termId="
+                                                                + key);
                                 result.add(new OntologyTerm(ontAccession, key, label, uri));
                         }
@@ -166 +169 @@
         @Override
         public List<OntologyTerm> searchAll(String query, SearchOptions... options)
-        throws OntologyServiceException {
+                        throws OntologyServiceException {
                 List<SearchOptions> ops = new ArrayList<SearchOptions>(
                                 Arrays.asList(options));
@@ -185 +188 @@
                                 String label = entry.getValue().split(":")[1];
                                 URI uri = URI
-                                .create("http://www.ebi.ac.uk/ontology-lookup/?termId=" + termAccession);
+                                                .create("http://www.ebi.ac.uk/ontology-lookup/?termId="
+                                                                + termAccession);
                                 // filter out non-exact terms if necessary
                                 if (ops.contains(SearchOptions.EXACT)
@@ -205 +209 @@
         @Override
         public Ontology getOntology(String ontologyAccession)
-        throws OntologyServiceException {
+                        throws OntologyServiceException {
                 Ontology o = new Ontology(ontologyAccession);
                 try {
                         String label = (String) qs.getOntologyNames()
-                        .get(ontologyAccession);
+                                        .get(ontologyAccession);
                         if (label == null) {
                                 return null;
@@ -225 +229 @@
         @Override
         public OntologyTerm getTerm(String ontologyAccession, String termAccession)
-        throws OntologyServiceException {
+                        throws OntologyServiceException {
                 String label = null;
                 try {
@@ -235 +239 @@
                         throw new OntologyServiceException(e);
                 }
-                URI uri = URI
-                                .create("http://www.ebi.ac.uk/ontology-lookup/?termId=" + termAccession);
+                URI uri = URI.create("http://www.ebi.ac.uk/ontology-lookup/?termId="
+                                + termAccession);
                 return new OntologyTerm(ontologyAccession, termAccession, label, uri);
         }
@@ -242 +246 @@
         @Override
         public OntologyTerm getTerm(String termAccession)
-        throws OntologyServiceException {
+                        throws OntologyServiceException {
 
                 return getTerm(getOntologyAccFromTerm(termAccession), termAccession);
@@ -260 +264 @@
         @Override
         public List<OntologyTerm> getRootTerms(String ontologyAccession)
-        throws OntologyServiceException {
+                        throws OntologyServiceException {
                 // Make sure the ontology exists
                 getOntology(ontologyAccession);
@@ -276 +280 @@
                 // Make sure the term exists
                 getTerm(ontologyAccession, termAccession);
-                String key = ontologyAccession + ":" + termAccession;
-                if (!annotationCache.containsKey(key)) {
+                String termKey = ontologyAccession + ":" + termAccession;
+                if (!annotationCache.containsKey(termKey)) {
                         try {
-                                Map result = qs.getTermMetadata(termAccession,
+                                Map<String, List<String>> result = new HashMap<String, List<String>>();
+                                Map<String, Object> annots = qs.getTermMetadata(termAccession,
                                                 ontologyAccession);
-                                // clean out the String from String[]
-                                for (Object metadataKey : result.keySet()) {
-                                        // logger.debug("getting annotation "+metadataKey);
-                                        if (result.get(metadataKey) instanceof String) {
-                                                result.put(metadataKey, Arrays
-                                                                .asList(new String[] { (String) result
-                                                                                .get(metadataKey) }));
-                                        } else if (result.get(metadataKey) instanceof String[]) {
-                                                result.put(metadataKey, Arrays.asList((String[]) result
-                                                                .get(metadataKey)));
+                                // dump xrefs into the annotation list
+                                annots.putAll(qs.getTermXrefs(termAccession, ontologyAccession));
+
+                                for (String annotsKey : annots.keySet()) {
+                                        Object values = annots.get(annotsKey);
+                                        String cleanedKey = cleanupAnnotsKey(annotsKey);
+
+                                        List<String> temp = result.get(cleanedKey);
+                                        if (temp == null) {
+                                                temp = new ArrayList<String>();
+                                        }
+
+                                        // convert String[] to List<String> if necessary
+                                        if (values instanceof String) {
+                                                temp.add((String) values);
+                                        } else if (values instanceof String[]) {
+                                                temp.addAll(Arrays.asList((String[]) values));
                                         } else {
                                                 throw new OntologyServiceException("annotation error: "
-                                                                + metadataKey);
+                                                                + annotsKey);
                                         }
+                                        result.put(cleanedKey, temp);
                                 }
-                                annotationCache.put(key, result);
+                                annotationCache.put(termKey, result);
                         } catch (RemoteException e) {
                                 throw new OntologyServiceException(e);
                         }
                 }
-                return annotationCache.get(key);
+                return annotationCache.get(termKey);
+        }
+
+        /**
+         * Removes the unnecessary index from OLS annotation key, e.g.,
+         * exact_synonym_4 becomes exact_synonym
+         */
+        private String cleanupAnnotsKey(String indexedKey) {
+                Pattern p = Pattern.compile("(.*)_\\d+");
+                Matcher m = p.matcher(indexedKey);
+                if (m.find()) {
+                        return m.group(1);
+                } else {
+                        return indexedKey;
+                }
         }
 
@@ -308 +335 @@
                         String termAccession) throws OntologyServiceException {
                 List<String> result = getAnnotations(ontologyAccession, termAccession)
-                .get("exact_synonym");
+                                .get("exact_synonym");
                 if (result == null) {
                         return Collections.EMPTY_LIST;
@@ -328 +355 @@
         // helper methods
         protected List<OntologyTerm> fetchFullTerms(Map<String, String> terms)
-        throws OntologyServiceException {
+                        throws OntologyServiceException {
                 List<OntologyTerm> result = new ArrayList<OntologyTerm>();
                 for (String termAccession : terms.keySet()) {
@@ -341 +368 @@
                         String termAccession) throws OntologyServiceException {
                 List<String> result = getAnnotations(ontologyAccession, termAccession)
-                .get("definition");
+                                .get("definition");
                 if (result == null) {
                         return Collections.EMPTY_LIST;
@@ -397 +424 @@
                                 throw new OntologyServiceException(
                                                 "findSearchTermPath(): TOO MANY ITERATIONS ("
-                                                + iteration + "x)");
+                                                                + iteration + "x)");
                         }
                 }