diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java
index cbde568e64964e2f57e38af345e50d35b169643a..2af04a489c3fd13389c2fa6f2300a9564d4afceb 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java
@@ -41,33 +41,6 @@ public class ProjectController extends BaseController {
return projectController.getSuggestedQueryList(projectId, token);
}
- @RequestMapping(value = "/project/getClosestElementsByCoordinates", method = { RequestMethod.GET, RequestMethod.POST },
- produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getClosestElementsByCoordinates(@RequestParam(value = "projectId") String projectId,
- @RequestParam(value = "modelId") String modelId, @RequestParam(value = "token") String token, @RequestParam(value = "coordinates") String coordinates,
- @RequestParam(value = "count", defaultValue = "5") String count) throws QueryException, SecurityException {
- String[] tmp = coordinates.split(",");
- if (tmp.length != 2) {
- throw new QueryException("Coordinates must be in the format: 'xxx.xx,yyy.yy'");
- }
- Double x = null;
- Double y = null;
- try {
- x = Double.valueOf(tmp[0]);
- y = Double.valueOf(tmp[1]);
- } catch (NumberFormatException e) {
- throw new QueryException("Coordinates must be in the format: 'xxx.xx,yyy.yy'", e);
- }
- Point2D pointCoordinates = new Point2D.Double(x, y);
- return projectController.getClosestElementsByCoordinates(projectId, modelId, token, pointCoordinates, Integer.valueOf(count));
- }
-
- @RequestMapping(value = "/project/getElementsByQuery", method = { RequestMethod.GET, RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<Map<String, Object>> getElementsByQuery(@RequestParam(value = "projectId") String projectId, @RequestParam(value = "token") String token,
- @RequestParam(value = "query") String query, @RequestParam(value = "maxElements", defaultValue = "100") Integer maxElements,
- @RequestParam(value = "perfectMatch", defaultValue = "false") String perfectMatch) throws QueryException, SecurityException {
- return projectController.getElementsByQuery(projectId, token, query, maxElements, perfectMatch);
- }
@RequestMapping(value = "/project/getProjectSource", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
public ResponseEntity<byte[]> getProjectSource(@RequestParam(value = "token") String token, @RequestParam(value = "projectId") String projectId)
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
index 2be02b7293bcba2a83a393a082b3bf1950aa68a2..a92c21392ee8e3fd789c8d442f84619fa25ae0a2 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
@@ -21,6 +21,7 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.web.bind.annotation.RequestParam;
+import lcsb.mapviewer.api.BaseRestImpl;
import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.api.projects.models.publications.PublicationsRestImpl;
import lcsb.mapviewer.commands.ClearColorModelCommand;
@@ -48,7 +49,6 @@ import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.user.User;
@@ -68,7 +68,7 @@ import lcsb.mapviewer.services.view.AuthenticationToken;
import lcsb.mapviewer.services.view.OverviewImageViewFactory;
@Transactional(value = "txManager")
-public class ProjectRestImpl {
+public class ProjectRestImpl extends BaseRestImpl {
/**
* Constant defining size of the array returned by
@@ -176,41 +176,6 @@ public class ProjectRestImpl {
this.userService = userService;
}
- public List<Map<String, Object>> getClosestElementsByCoordinates(String projectId, String modelId, String token, Point2D coordinates, Integer count)
- throws UserAccessException, SecurityException {
- List<Map<String, Object>> resultMap = new ArrayList<>();
-
- Model model = modelService.getLastModelByProjectId(projectId, userService.getToken(token));
-
- Model submodel = model.getSubmodelById(modelId);
-
- List<Object> elements = searchService.getClosestElements(submodel, coordinates, count);
- for (Object object : elements) {
- Map<String, Object> result = createMinifiedSearchResult(object);
- resultMap.add(result);
- }
- return resultMap;
- }
-
- private Map<String, Object> createMinifiedSearchResult(Object object) {
- Map<String, Object> result = new HashMap<>();
- if (object instanceof Element) {
- result.put("type", ElementIdentifierType.ALIAS);
- Element element = (Element) object;
- result.put("id", element.getId());
- result.put("modelId", element.getModel().getId());
- } else if (object instanceof Reaction) {
- result.put("type", ElementIdentifierType.REACTION);
- Reaction element = (Reaction) object;
- result.put("id", element.getId());
- result.put("modelId", element.getModel().getId());
-
- } else {
- throw new InvalidStateException("Unknown type of result: " + object.getClass());
- }
- return result;
- };
-
/**
* @return the modelService
* @see #modelService
@@ -245,22 +210,6 @@ public class ProjectRestImpl {
this.searchService = searchService;
}
- public List<Map<String, Object>> getElementsByQuery(String projectId, String token, String query, Integer maxElements, String perfectMatch)
- throws SecurityException {
- List<Map<String, Object>> resultMap = new ArrayList<>();
-
- Model model = modelService.getLastModelByProjectId(projectId, userService.getToken(token));
-
- Integer limit = Integer.valueOf(maxElements);
- boolean match = perfectMatch.equals("true");
- List<Object> elements = searchService.searchByQuery(model, query, limit, match);
- for (Object object : elements) {
- Map<String, Object> result = createMinifiedSearchResult(object);
- resultMap.add(result);
- }
- return resultMap;
- }
-
public String[] getSuggestedQueryList(String projectId, String token) throws SecurityException {
Model model = modelService.getLastModelByProjectId(projectId, userService.getToken(token));
return searchService.getSuggestedQueryList(model);
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesController.java
new file mode 100644
index 0000000000000000000000000000000000000000..9bef963ef950cd2cdd027c5c9614056510419947
--- /dev/null
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesController.java
@@ -0,0 +1,66 @@
+package lcsb.mapviewer.api.projects.models.bioEntities;
+
+import java.awt.geom.Point2D;
+import java.util.List;
+import java.util.Map;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RequestParam;
+import org.springframework.web.bind.annotation.RestController;
+
+import lcsb.mapviewer.api.BaseController;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.services.SecurityException;
+
+@RestController
+public class BioEntitiesController extends BaseController {
+ @Autowired
+ private BioEntitiesRestImpl projectController;
+
+ @RequestMapping(value = "/projects/{projectId}/models/{modelId}/bioEntities:search", method = { RequestMethod.GET },
+ produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getClosestElementsByCoordinates(//
+ @PathVariable(value = "projectId") String projectId, //
+ @PathVariable(value = "modelId") String modelId, //
+ @RequestParam(value = "token") String token, //
+ @RequestParam(value = "coordinates", defaultValue = "") String coordinates, //
+ @RequestParam(value = "query", defaultValue = "") String query, //
+ @RequestParam(value = "count", defaultValue = "") String count, //
+ @RequestParam(value = "perfectMatch", defaultValue = "false") String perfectMatch//
+ ) throws QueryException, SecurityException {
+ if (!coordinates.trim().isEmpty()) {
+ if (modelId.equals("*")) {
+ throw new QueryException("modelId must be defined when searching by coordinates");
+ }
+ if (count.trim().isEmpty()) {
+ count = "5";
+ }
+ String[] tmp = coordinates.split(",");
+ if (tmp.length != 2) {
+ throw new QueryException("Coordinates must be in the format: 'xxx.xx,yyy.yy'");
+ }
+ Double x = null;
+ Double y = null;
+ try {
+ x = Double.valueOf(tmp[0]);
+ y = Double.valueOf(tmp[1]);
+ } catch (NumberFormatException e) {
+ throw new QueryException("Coordinates must be in the format: 'xxx.xx,yyy.yy'", e);
+ }
+ Point2D pointCoordinates = new Point2D.Double(x, y);
+ return projectController.getClosestElementsByCoordinates(projectId, modelId, token, pointCoordinates, Integer.valueOf(count), perfectMatch);
+ } else if (!query.trim().isEmpty()) {
+ if (count.trim().isEmpty()) {
+ count = "100";
+ }
+ return projectController.getElementsByQuery(projectId, token, modelId, query, Integer.valueOf(count), perfectMatch);
+ } else {
+ throw new QueryException("On of the parameters 'coordinates', 'query' is required");
+ }
+ }
+
+}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesRestImpl.java
new file mode 100644
index 0000000000000000000000000000000000000000..12902400c5b291eda58cd84b29e347267aed7106
--- /dev/null
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesRestImpl.java
@@ -0,0 +1,121 @@
+package lcsb.mapviewer.api.projects.models.bioEntities;
+
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.api.BaseRestImpl;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.services.SecurityException;
+import lcsb.mapviewer.services.UserAccessException;
+import lcsb.mapviewer.services.interfaces.IModelService;
+import lcsb.mapviewer.services.interfaces.ISearchService;
+import lcsb.mapviewer.services.interfaces.IUserService;
+import lcsb.mapviewer.services.view.AnnotationViewFactory;
+
+@Transactional(value = "txManager")
+public class BioEntitiesRestImpl extends BaseRestImpl {
+
+ Logger logger = Logger.getLogger(BioEntitiesRestImpl.class);
+
+ @Autowired
+ private IUserService userService;
+
+ @Autowired
+ private IModelService modelService;
+
+ @Autowired
+ private ISearchService searchService;
+
+ @Autowired
+ AnnotationViewFactory annotationViewFactory;
+
+ /**
+ * @return the userService
+ * @see #userService
+ */
+ public IUserService getUserService() {
+ return userService;
+ }
+
+ /**
+ * @param userService
+ * the userService to set
+ * @see #userService
+ */
+ public void setUserService(IUserService userService) {
+ this.userService = userService;
+ }
+
+ public List<Map<String, Object>> getClosestElementsByCoordinates(String projectId, String modelId, String token, Point2D coordinates, Integer count, String perfectMatch)
+ throws UserAccessException, SecurityException {
+ List<Map<String, Object>> resultMap = new ArrayList<>();
+
+ Model model = modelService.getLastModelByProjectId(projectId, userService.getToken(token));
+
+ Model submodel = model.getSubmodelById(modelId);
+
+ List<Object> elements = searchService.getClosestElements(submodel, coordinates, count, perfectMatch.equalsIgnoreCase("true"));
+ for (Object object : elements) {
+ Map<String, Object> result = createMinifiedSearchResult(object);
+ resultMap.add(result);
+ }
+ return resultMap;
+ }
+
+ /**
+ * @return the modelService
+ * @see #modelService
+ */
+ public IModelService getModelService() {
+ return modelService;
+ }
+
+ /**
+ * @param modelService
+ * the modelService to set
+ * @see #modelService
+ */
+ public void setModelService(IModelService modelService) {
+ this.modelService = modelService;
+ }
+
+ /**
+ * @return the searchService
+ * @see #searchService
+ */
+ public ISearchService getSearchService() {
+ return searchService;
+ }
+
+ /**
+ * @param searchService
+ * the searchService to set
+ * @see #searchService
+ */
+ public void setSearchService(ISearchService searchService) {
+ this.searchService = searchService;
+ }
+
+ public List<Map<String, Object>> getElementsByQuery(String projectId, String token, String modelId, String query, Integer maxElements, String perfectMatch)
+ throws SecurityException {
+ List<Map<String, Object>> resultMap = new ArrayList<>();
+
+ Model model = modelService.getLastModelByProjectId(projectId, userService.getToken(token));
+
+ Integer limit = Integer.valueOf(maxElements);
+ boolean match = perfectMatch.equals("true");
+ List<Object> elements = searchService.searchByQuery(model, query, limit, match);
+ for (Object object : elements) {
+ Map<String, Object> result = createMinifiedSearchResult(object);
+ resultMap.add(result);
+ }
+ return resultMap;
+ }
+
+}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsController.java
index 342e044466a3a04f092dbe0ee2805436f4ab22d2..0d2175c1d6d1a1e54d3b428cbb930ed8e5a2e8ba 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsController.java
@@ -23,13 +23,13 @@ public class ReactionsController extends BaseController {
produces = { MediaType.APPLICATION_JSON_VALUE })
public List<Map<String, Object>> getReactions(//
@PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "modelId") String modelId,
+ @PathVariable(value = "modelId") String modelId, //
@RequestParam(value = "id", defaultValue = "") String id, //
@RequestParam(value = "columns", defaultValue = "") String columns, //
@RequestParam(value = "token") String token, //
@RequestParam(value = "participantId", defaultValue = "") String participantId//
) throws SecurityException {
- return reactionController.getReactions(projectId, id, columns, modelId, token, participantId);
+ return reactionController.getReactions(projectId, id, columns, modelId, token, participantId);
}
}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImpl.java
index 64bd74ad1fc524c919ba60c1d8e3885091ae7db6..c1305c14372b227c0cbbe080b7237a8ffc2152d3 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImpl.java
@@ -13,6 +13,7 @@ import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
+import lcsb.mapviewer.api.BaseRestImpl;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Modifier;
import lcsb.mapviewer.model.map.reaction.Product;
@@ -27,27 +28,18 @@ import lcsb.mapviewer.services.search.data.LightReactionView;
import lcsb.mapviewer.services.view.AnnotationViewFactory;
@Transactional(value = "txManager")
-public class ReactionsRestImpl {
+public class ReactionsRestImpl extends BaseRestImpl {
- /**
- * Constant defining size of the array returned by
- * {@link PathIterator#currentSegment(double[])} method. More nformation can
- * be found <a href=
- * "http://docs.oracle.com/javase/7/docs/api/java/awt/geom/PathIterator.html#currentSegment(double[])"
- * >here</a>
- */
- private static final int PATH_ITERATOR_SEGMENT_SIZE = 6;
-
- Logger logger = Logger.getLogger(ReactionsRestImpl.class);
+ Logger logger = Logger.getLogger(ReactionsRestImpl.class);
@Autowired
- private IUserService userService;
+ private IUserService userService;
@Autowired
- private IModelService modelService;
+ private IModelService modelService;
@Autowired
- AnnotationViewFactory annotationViewFactory;
+ AnnotationViewFactory annotationViewFactory;
/**
* @return the userService
@@ -85,9 +77,8 @@ public class ReactionsRestImpl {
List<Map<String, Object>> result = new ArrayList<>();
- List<Model> models = new ArrayList<>();
- models.addAll(model.getSubmodels());
- models.add(model);
+ List<Model> models = getModels(projectId, modelId, token);
+
for (Model model2 : models) {
for (Reaction reaction : model2.getReactions()) {
if (ids.size() == 0 || ids.contains(reaction.getId())) {
diff --git a/rest-api/src/main/resources/applicationContext-rest.xml b/rest-api/src/main/resources/applicationContext-rest.xml
index 11c5a2f10eafade53ce584862507b0263650d549..349fb0bab5da3cf867212e48622466e4daf6ef4d 100644
--- a/rest-api/src/main/resources/applicationContext-rest.xml
+++ b/rest-api/src/main/resources/applicationContext-rest.xml
@@ -19,6 +19,7 @@
<bean id="OverlayRestImpl" class="lcsb.mapviewer.api.overlay.OverlayRestImpl"/>
<bean id="ProjectRestImpl" class="lcsb.mapviewer.api.projects.ProjectRestImpl"/>
+ <bean id="BioEntitiesRestImpl" class="lcsb.mapviewer.api.projects.models.bioEntities.BioEntitiesRestImpl"/>
<bean id="ElementsRestImpl" class="lcsb.mapviewer.api.projects.models.bioEntities.elements.ElementsRestImpl"/>
<bean id="ReactionsRestImpl" class="lcsb.mapviewer.api.projects.models.bioEntities.reactions.ReactionsRestImpl"/>
<bean id="PublicationsRestImpl" class="lcsb.mapviewer.api.projects.models.publications.PublicationsRestImpl"/>
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java
index baeb04af01f2a0166c827017080ba0dabac81943..4c04050f6e09b4517a9aa9422143177076cd78d9 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java
@@ -1,16 +1,10 @@
package lcsb.mapviewer.api.projects;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.fail;
import static org.mockito.Matchers.any;
import static org.mockito.Matchers.anyString;
-import java.awt.geom.Point2D;
-import java.util.List;
-import java.util.Map;
-
import org.apache.log4j.Logger;
import org.junit.After;
import org.junit.AfterClass;
@@ -23,8 +17,6 @@ import com.google.gson.Gson;
import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.api.RestTestFunctions;
-import lcsb.mapviewer.api.projects.ProjectMetaData;
-import lcsb.mapviewer.api.projects.ProjectRestImpl;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.graphics.PdfImageGenerator;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
@@ -52,19 +44,6 @@ public class ProjectRestImplTest extends RestTestFunctions {
public void tearDown() throws Exception {
}
- @Test
- public void testGetClosestElementsByCoordinates() throws Exception {
- try {
- ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- int count = 3;
- List<Map<String, Object>> result = projectRest.getClosestElementsByCoordinates("sample", "0", token.getId(), new Point2D.Double(1, 2), count);
- assertEquals(count, result.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
@Test
public void testGetModelAsImage() throws Exception {
try {
@@ -160,5 +139,4 @@ public class ProjectRestImplTest extends RestTestFunctions {
return _projectRestImpl;
}
-
}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/AllModelsTests.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/AllModelsTests.java
index f80d0faa3754a96e59616e236fa641e91525acfa..f89ba7fa4d53d265c8f1b116b26d7832ed327c2c 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/AllModelsTests.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/AllModelsTests.java
@@ -4,12 +4,13 @@ import org.junit.runner.RunWith;
import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
+import lcsb.mapviewer.api.projects.models.bioEntities.AllBioeEntitiesTests;
import lcsb.mapviewer.api.projects.models.bioEntities.elements.AllElementsTests;
import lcsb.mapviewer.api.projects.models.publications.AllPublicationsTests;
@RunWith(Suite.class)
@SuiteClasses({ //
- AllElementsTests.class, //
+ AllBioeEntitiesTests.class, //
AllPublicationsTests.class//
})
public class AllModelsTests {
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/AllBioeEntitiesTests.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/AllBioeEntitiesTests.java
new file mode 100644
index 0000000000000000000000000000000000000000..48a870c00f8daae830fd7f788730562cda51e4e0
--- /dev/null
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/AllBioeEntitiesTests.java
@@ -0,0 +1,16 @@
+package lcsb.mapviewer.api.projects.models.bioEntities;
+
+import org.junit.runner.RunWith;
+import org.junit.runners.Suite;
+import org.junit.runners.Suite.SuiteClasses;
+
+import lcsb.mapviewer.api.projects.models.bioEntities.elements.AllElementsTests;
+
+@RunWith(Suite.class)
+@SuiteClasses({ //
+ AllElementsTests.class, //
+ BioEntitiesControllerTest.class //
+})
+public class AllBioeEntitiesTests {
+
+}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesControllerTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesControllerTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..3121878299dc8e7791174960cb12677a40f09ddc
--- /dev/null
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesControllerTest.java
@@ -0,0 +1,62 @@
+package lcsb.mapviewer.api.projects.models.bioEntities;
+
+import static org.junit.Assert.assertEquals;
+import static org.mockito.Matchers.any;
+import static org.mockito.Matchers.anyString;
+
+import java.awt.geom.Point2D;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import lcsb.mapviewer.api.RestTestFunctions;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.services.interfaces.IModelService;
+
+public class BioEntitiesControllerTest extends RestTestFunctions {
+ Logger logger = Logger.getLogger(BioEntitiesControllerTest.class);
+
+ @Autowired
+ BioEntitiesRestImpl _bioEntitiesRestImpl;
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetClosestElementsByCoordinates() throws Exception {
+ try {
+ BioEntitiesRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
+ int count = 3;
+ List<Map<String, Object>> result = projectRest.getClosestElementsByCoordinates("sample", "0", token.getId(), new Point2D.Double(1, 2), count, "false");
+ assertEquals(count, result.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private BioEntitiesRestImpl createMockProjectRest(String string) throws Exception {
+ Model model = super.getModelForFile(string, true);
+ IModelService mockModelService = Mockito.mock(IModelService.class);
+ Mockito.when(mockModelService.getLastModelByProjectId(anyString(), any())).thenReturn(model);
+ _bioEntitiesRestImpl.setModelService(mockModelService);
+ return _bioEntitiesRestImpl;
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java b/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
index 5020536b56da2bd99e24463d210effedf3f9121d..947a3d32991a6e0c51c83535987c72923b18b4da 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
@@ -527,7 +527,7 @@ public class SearchService implements ISearchService {
}
@Override
- public List<Object> getClosestElements(Model model, Point2D point, int numberOfElements) {
+ public List<Object> getClosestElements(Model model, Point2D point, int numberOfElements, boolean perfectHit) {
List<Object> result = new ArrayList<>();
// probably this could be improved algorithmitically, right now all objects
@@ -545,7 +545,11 @@ public class SearchService implements ISearchService {
Collections.sort(tmpList);
int size = Math.min(tmpList.size(), numberOfElements);
for (int i = 0; i < size; i++) {
- result.add(tmpList.get(i).getReference());
+ if (!perfectHit) {
+ result.add(tmpList.get(i).getReference());
+ } else if (tmpList.get(i).getDistance() < Configuration.EPSILON) {
+ result.add(tmpList.get(i).getReference());
+ }
}
return result;
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/ISearchService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/ISearchService.java
index 3801640516d876b6b3d94cf72a0f9a3566b7d6b0..c7f51a65f43b178ba00c4eed1258cdaf3938bc4f 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/ISearchService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/ISearchService.java
@@ -295,7 +295,7 @@ public interface ISearchService {
* how many closest elements should be returned
* @return list of the closest elements
*/
- List<Object> getClosestElements(Model model, Point2D point, int numberOfElements);
+ List<Object> getClosestElements(Model model, Point2D point, int numberOfElements, boolean perfectHit);
/**
* Returns list of autocomplete strings for the partial query.
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
index 5e7afaf6357abab75d2343da1aa93c2734514194..571ef6105b32936e8d38fdcabce39d4d96cfe470 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
@@ -231,7 +231,7 @@ public class SearchServiceTest extends ServiceTestFunctions {
public void testSearchClosest() throws Exception {
try {
model = getModelForFile("testFiles/graph_path_example3.xml", true);
- List<Object> elements = searchService.getClosestElements(model, new Point2D.Double(0, 0), 5);
+ List<Object> elements = searchService.getClosestElements(model, new Point2D.Double(0, 0), 5, false);
assertNotNull(elements);
assertEquals(5, elements.size());
assertTrue(elements.get(0) instanceof Species);
@@ -260,7 +260,7 @@ public class SearchServiceTest extends ServiceTestFunctions {
public void testSearchClosestWithEmptyModel() throws Exception {
try {
model = new ModelFullIndexed(null);
- List<Object> elements = searchService.getClosestElements(model, new Point2D.Double(0, 0), 5);
+ List<Object> elements = searchService.getClosestElements(model, new Point2D.Double(0, 0), 5, false);
assertNotNull(elements);
assertEquals(0, elements.size());