rest api returns better parsed publication list

rest-api/src/main/java/lcsb/mapviewer/api/project/ProjectController.java

@@ -77,7 +77,8 @@ public class ProjectController extends BaseController {
 
 	@RequestMapping(value = "/getPublications", method = { RequestMethod.GET, RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
 	public Map<String, Object> getPublications(@RequestParam(value = "projectId") String projectId, @RequestParam(value = "token") String token,
-			@RequestParam(value = "start", defaultValue = "0") String start, @RequestParam(value = "length", defaultValue = "10") Integer length) throws QueryException, SecurityException {
+			@RequestParam(value = "start", defaultValue = "0") String start, @RequestParam(value = "length", defaultValue = "10") Integer length)
+			throws QueryException, SecurityException {
 		return projectController.getPublications(projectId, token, start, length);
 	}
 

rest-api/src/main/java/lcsb/mapviewer/api/project/ProjectRestImpl.java

@@ -17,6 +17,7 @@ import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.transaction.annotation.Transactional;
 import org.springframework.web.bind.annotation.RequestParam;
 
+import lcsb.mapviewer.annotation.services.PubmedParser;
 import lcsb.mapviewer.api.QueryException;
 import lcsb.mapviewer.common.exception.InvalidStateException;
 import lcsb.mapviewer.model.Project;
@@ -67,6 +68,9 @@ public class ProjectRestImpl {
 	@Autowired
 	AnnotationViewFactory						 annotationViewFactory;
 
+	@Autowired
+	private PubmedParser						 pubmedParser;
+
 	@Autowired
 	private OverviewImageViewFactory factory;
 
@@ -498,23 +502,28 @@ public class ProjectRestImpl {
 		for (Map.Entry<MiriamData, List<AnnotatedObject>> entry : publications.entrySet()) {
 			if (index >= start && index < start + length) {
 				List<Object> elements = new ArrayList<>();
-				for (AnnotatedObject object: entry.getValue()) {
-					if (object instanceof Element) {
-						elements.add(preparedElement((Element) object, columns));
-					} else if (object instanceof Reaction) {
-						elements.add(preparedReaction((Reaction) object, columns));
-					}
+				for (AnnotatedObject object : entry.getValue()) {
+					elements.add(createMinifiedSearchResult(object));
 				}
 
 				Map<String, Object> row = new HashMap<>();
 				row.put("elements", elements);
-				row.put("publication", annotationViewFactory.create(entry.getKey()));
+				if (entry.getKey().getDataType().equals(MiriamType.PUBMED)) {
+					try {
+						row.put("publication", pubmedParser.getPubmedArticleById(Integer.valueOf(entry.getKey().getResource())));
+					} catch (Exception e) {
+						logger.error(e, e);
+						row.put("publication", annotationViewFactory.create(entry.getKey()));
+					}
+				} else {
+					row.put("publication", annotationViewFactory.create(entry.getKey()));
+				}
 				resultList.add(row);
 			}
 			index++;
 
 		}
-		
+
 		Map<String, Object> result = new HashMap<>();
 		result.put("data", resultList);
 		result.put("totalSize", publications.size());
@@ -523,4 +532,21 @@ public class ProjectRestImpl {
 		return result;
 	}
 
+	/**
+	 * @return the pubmedParser
+	 * @see #pubmedParser
+	 */
+	public PubmedParser getPubmedParser() {
+		return pubmedParser;
+	}
+
+	/**
+	 * @param pubmedParser
+	 *          the pubmedParser to set
+	 * @see #pubmedParser
+	 */
+	public void setPubmedParser(PubmedParser pubmedParser) {
+		this.pubmedParser = pubmedParser;
+	}
+
 }