rest api for getting publication list

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

@@ -75,6 +75,12 @@ public class ProjectController extends BaseController {
 		return projectController.getElementsByQuery(projectId, token, query, maxElements, perfectMatch);
 	}
 
+	@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 {
+		return projectController.getPublications(projectId, token, start, length);
+	}
+
 	@RequestMapping(value = "/getProjectSource", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
 	public ResponseEntity<byte[]> getOverlaySource(@RequestParam(value = "token") String token, @RequestParam(value = "projectId") String projectId)
 			throws SecurityException, QueryException {

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

@@ -8,6 +8,8 @@ import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.SortedMap;
+import java.util.TreeMap;
 
 import org.apache.commons.lang3.StringUtils;
 import org.apache.log4j.Logger;
@@ -20,6 +22,7 @@ import lcsb.mapviewer.common.exception.InvalidStateException;
 import lcsb.mapviewer.model.Project;
 import lcsb.mapviewer.model.cache.FileEntry;
 import lcsb.mapviewer.model.cache.UploadedFileEntry;
+import lcsb.mapviewer.model.map.AnnotatedObject;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.MiriamType;
 import lcsb.mapviewer.model.map.OverviewImage;
@@ -114,35 +117,48 @@ public class ProjectRestImpl {
 			}
 			result.setMap(new ModelMetaData(model));
 
-			Set<MiriamData> publications = new HashSet<>();
-			List<ModelData> models = new ArrayList<>();
-			for (ModelSubmodelConnection connection : model.getSubmodels()) {
-				models.add(connection.getSubmodel());
-			}
-			models.add(model);
-			for (ModelData modelData : models) {
-				for (Element element : modelData.getElements()) {
-					for (MiriamData md : element.getMiriamData()) {
-						if (md.getDataType().equals(MiriamType.PUBMED)) {
-							publications.add(md);
+			result.setPublicationCount(getPublications(model).size());
+
+		}
+
+		return result;
+	}
+
+	private SortedMap<MiriamData, List<AnnotatedObject>> getPublications(ModelData model) {
+		SortedMap<MiriamData, List<AnnotatedObject>> publications = new TreeMap<>();
+		List<ModelData> models = new ArrayList<>();
+		for (ModelSubmodelConnection connection : model.getSubmodels()) {
+			models.add(connection.getSubmodel());
+		}
+		models.add(model);
+		for (ModelData modelData : models) {
+			for (Element element : modelData.getElements()) {
+				for (MiriamData md : element.getMiriamData()) {
+					if (md.getDataType().equals(MiriamType.PUBMED)) {
+						List<AnnotatedObject> list = publications.get(md);
+						if (list == null) {
+							list = new ArrayList<>();
+							publications.put(md, list);
 						}
+						list.add(element);
 					}
 				}
-				for (Reaction reaction : modelData.getReactions()) {
-					for (MiriamData md : reaction.getMiriamData()) {
-						if (md.getDataType().equals(MiriamType.PUBMED)) {
-							publications.add(md);
+			}
+			for (Reaction reaction : modelData.getReactions()) {
+				for (MiriamData md : reaction.getMiriamData()) {
+					if (md.getDataType().equals(MiriamType.PUBMED)) {
+						List<AnnotatedObject> list = publications.get(md);
+						if (list == null) {
+							list = new ArrayList<>();
+							publications.put(md, list);
 						}
+						list.add(reaction);
 					}
-
 				}
-			}
-
-			result.setPublicationCount(publications.size());
 
+			}
 		}
-
-		return result;
+		return publications;
 	}
 
 	/**
@@ -463,4 +479,48 @@ public class ProjectRestImpl {
 		return entry;
 	}
 
+	public Map<String, Object> getPublications(String projectId, String token, String startString, Integer length) throws SecurityException, QueryException {
+		AuthenticationToken authenticationToken = userService.getToken(token);
+		Model model = modelService.getLastModelByProjectId(projectId, authenticationToken);
+		if (model == null) {
+			throw new QueryException("Project with given id doesn't exist");
+		}
+
+		Integer start = Math.max(0, Integer.valueOf(startString));
+		List<Map<String, Object>> resultList = new ArrayList<>();
+
+		SortedMap<MiriamData, List<AnnotatedObject>> publications = getPublications(model.getModelData());
+		int index = 0;
+		Set<String> columns = new HashSet<>();
+		columns.add("id");
+		columns.add("type");
+		columns.add("modelid");
+		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));
+					}
+				}
+
+				Map<String, Object> row = new HashMap<>();
+				row.put("elements", elements);
+				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());
+		result.put("start", start);
+		result.put("length", resultList.size());
+		return result;
+	}
+
 }

rest-api/src/test/java/lcsb/mapviewer/api/project/ProjectRestImplTest.java

@@ -112,4 +112,29 @@ public class ProjectRestImplTest extends RestTestFunctions {
 		return _projectRestImpl;
 	}
 
+	@Test
+	public void testPublications() throws Exception {
+		try {
+			ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
+			Map<String, Object> result= projectRest.getPublications("sample", token.getId(),"0", 20);
+			assertEquals(1, result.get("totalSize"));
+			assertEquals(0, result.get("start"));
+			assertEquals(1, ((List<?>)result.get("data")).size());
+			
+			result= projectRest.getPublications("sample", token.getId(),"1", 20);
+			assertEquals(1, result.get("totalSize"));
+			assertEquals(1, result.get("start"));
+			assertEquals(0, ((List<?>)result.get("data")).size());
+
+			result= projectRest.getPublications("sample", token.getId(),"0", 00);
+			assertEquals(1, result.get("totalSize"));
+			assertEquals(0, result.get("start"));
+			assertEquals(0, ((List<?>)result.get("data")).size());
+		} catch (Exception e) {
+			e.printStackTrace();
+			throw e;
+		}
+	}
+
+
 }