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Commit bf097211 authored by Piotr Gawron's avatar Piotr Gawron
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search by coordinates can be limited to the types

parent 6da94fbe
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1 merge request!254Resolve "Main view: Compartments are not selectable"
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with 82 additions and 67 deletions
rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesController.java
+ 54
− 51
View file @ bf097211
......@@ -21,58 +21,61 @@ import lcsb.mapviewer.services.SecurityException;
@RestController
public class BioEntitiesController extends BaseController {
@Autowired
private BioEntitiesRestImpl bioEntitiesRestImpl;
@Autowired
private BioEntitiesRestImpl bioEntitiesRestImpl;
@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, //
@CookieValue(value = Configuration.AUTH_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 bioEntitiesRestImpl.getClosestElementsByCoordinates(projectId, modelId, token, pointCoordinates, Integer.valueOf(count), perfectMatch);
} else if (!query.trim().isEmpty()) {
if (count.trim().isEmpty()) {
count = "100";
}
return bioEntitiesRestImpl.getElementsByQuery(projectId, token, modelId, query, Integer.valueOf(count), perfectMatch);
} else {
return new ArrayList<>();
}
}
@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, //
@CookieValue(value = Configuration.AUTH_TOKEN) String token, //
@RequestParam(value = "coordinates", defaultValue = "") String coordinates, //
@RequestParam(value = "query", defaultValue = "") String query, //
@RequestParam(value = "count", defaultValue = "") String count, //
@RequestParam(value = "type", defaultValue = "") String type, //
@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 bioEntitiesRestImpl.getClosestElementsByCoordinates(projectId, modelId, token, pointCoordinates,
Integer.valueOf(count), perfectMatch, type);
} else if (!query.trim().isEmpty()) {
if (count.trim().isEmpty()) {
count = "100";
}
return bioEntitiesRestImpl.getElementsByQuery(projectId, token, modelId, query, Integer.valueOf(count),
perfectMatch);
} else {
return new ArrayList<>();
}
}
@RequestMapping(value = "/projects/{projectId}/models/{modelId}/bioEntities/suggestedQueryList", method = { RequestMethod.GET, RequestMethod.POST },
produces = { MediaType.APPLICATION_JSON_VALUE })
public String[] getSuggestedQueryList(//
@PathVariable(value = "projectId") String projectId, //
@CookieValue(value = Configuration.AUTH_TOKEN) String token//
) throws SecurityException {
return bioEntitiesRestImpl.getSuggestedQueryList(projectId, token);
}
@RequestMapping(value = "/projects/{projectId}/models/{modelId}/bioEntities/suggestedQueryList", method = {
RequestMethod.GET, RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
public String[] getSuggestedQueryList(//
@PathVariable(value = "projectId") String projectId, //
@CookieValue(value = Configuration.AUTH_TOKEN) String token//
) throws SecurityException {
return bioEntitiesRestImpl.getSuggestedQueryList(projectId, token);
}
}
\ No newline at end of file
rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesRestImpl.java
+ 11
− 2
View file @ bf097211
......@@ -2,8 +2,10 @@ package lcsb.mapviewer.api.projects.models.bioEntities;
import java.awt.geom.Point2D;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
......@@ -31,15 +33,22 @@ public class BioEntitiesRestImpl extends BaseRestImpl {
private ISearchService searchService;
public List<Map<String, Object>> getClosestElementsByCoordinates(String projectId, String modelId, String token,
Point2D coordinates, Integer count, String perfectMatch) throws UserAccessException, SecurityException {
Point2D coordinates, Integer count, String perfectMatch, String type) throws UserAccessException, SecurityException {
List<Map<String, Object>> resultMap = new ArrayList<>();
Model model = getModelService().getLastModelByProjectId(projectId, token);
Model submodel = model.getSubmodelById(modelId);
Set<String> types = new HashSet<>();
if (!type.isEmpty()) {
for (String str : type.split(",")) {
types.add(str.toLowerCase());
}
}
List<BioEntity> elements = searchService.getClosestElements(submodel, coordinates, count,
perfectMatch.equalsIgnoreCase("true"));
perfectMatch.equalsIgnoreCase("true"), types);
for (BioEntity object : elements) {
Map<String, Object> result = createMinifiedSearchResult(object);
resultMap.add(result);
......
rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesControllerTest.java
+ 2
− 1
View file @ bf097211
......@@ -6,6 +6,7 @@ import static org.mockito.Matchers.any;
import static org.mockito.Matchers.anyString;
import java.awt.geom.Point2D;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
......@@ -49,7 +50,7 @@ public class BioEntitiesControllerTest extends RestTestFunctions {
BioEntitiesRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
int count = 3;
List<Map<String, Object>> result = projectRest.getClosestElementsByCoordinates("sample", "0", token,
new Point2D.Double(1, 2), count, "false");
new Point2D.Double(1, 2), count, "false", "");
assertEquals(count, result.size());
String json = mapper.writeValueAsString(result);
......
service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java
+ 9
− 9
View file @ bf097211
......@@ -3,6 +3,7 @@ package lcsb.mapviewer.services.impl;
import java.awt.geom.Point2D;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
......@@ -44,10 +45,6 @@ import lcsb.mapviewer.model.map.statistics.SearchType;
import lcsb.mapviewer.persist.dao.map.ModelDao;
import lcsb.mapviewer.services.interfaces.ISearchHistoryService;
import lcsb.mapviewer.services.interfaces.ISearchService;
import lcsb.mapviewer.services.search.data.FullAliasView;
import lcsb.mapviewer.services.search.data.FullAliasViewFactory;
import lcsb.mapviewer.services.search.data.FullReactionView;
import lcsb.mapviewer.services.search.data.FullReactionViewFactory;
import lcsb.mapviewer.services.search.data.SearchElementResult;
import lcsb.mapviewer.services.utils.SearchIndexer;
......@@ -567,7 +564,8 @@ public class SearchService implements ISearchService {
}
@Override
public List<BioEntity> getClosestElements(Model model, Point2D point, int numberOfElements, boolean perfectHit) {
public List<BioEntity> getClosestElements(Model model, Point2D point, int numberOfElements, boolean perfectHit,
Collection<String> types) {
List<BioEntity> result = new ArrayList<>();
// probably this could be improved algorithmitically, right now all objects
......@@ -575,11 +573,13 @@ public class SearchService implements ISearchService {
// of results
List<DistanceToObject> tmpList = new ArrayList<>();
for (Reaction reaction : model.getReactions()) {
tmpList.add(new DistanceToObject(reaction, point));
if (types.size() == 0 || types.contains(reaction.getStringType().toLowerCase())) {
tmpList.add(new DistanceToObject(reaction, point));
}
}
for (Element alias : model.getElements()) {
if (alias instanceof Species) {
tmpList.add(new DistanceToObject(alias, point));
for (Element element : model.getElements()) {
if ((element instanceof Species && types.size() == 0) || types.contains(element.getStringType().toLowerCase())) {
tmpList.add(new DistanceToObject(element, point));
}
}
Collections.sort(tmpList);
......
service/src/main/java/lcsb/mapviewer/services/interfaces/ISearchService.java
+ 2
− 1
View file @ bf097211
package lcsb.mapviewer.services.interfaces;
import java.awt.geom.Point2D;
import java.util.Collection;
import java.util.List;
import org.apache.log4j.Logger;
......@@ -296,7 +297,7 @@ public interface ISearchService {
* how many closest elements should be returned
* @return list of the closest elements
*/
List<BioEntity> getClosestElements(Model model, Point2D point, int numberOfElements, boolean perfectHit);
List<BioEntity> getClosestElements(Model model, Point2D point, int numberOfElements, boolean perfectHit, Collection<String> types);
/**
* Returns list of autocomplete strings for the partial query.
......
service/src/test/java/lcsb/mapviewer/services/impl/SearchServiceTest.java
+ 4
− 3
View file @ bf097211
......@@ -6,6 +6,7 @@ import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
import java.awt.geom.Point2D;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
......@@ -287,7 +288,7 @@ public class SearchServiceTest extends ServiceTestFunctions {
public void testSearchClosest() throws Exception {
try {
Model model = getModelForFile("testFiles/graph_path_example3.xml", true);
List<BioEntity> elements = searchService.getClosestElements(model, new Point2D.Double(0, 0), 5, false);
List<BioEntity> elements = searchService.getClosestElements(model, new Point2D.Double(0, 0), 5, false, new ArrayList<>());
assertNotNull(elements);
assertEquals(5, elements.size());
assertTrue(elements.get(0) instanceof Species);
......@@ -335,7 +336,7 @@ public class SearchServiceTest extends ServiceTestFunctions {
protein3.setY(0);
model.addElement(protein3);
List<BioEntity> elements = searchService.getClosestElements(model, new Point2D.Double(10, 10), 5, false);
List<BioEntity> elements = searchService.getClosestElements(model, new Point2D.Double(10, 10), 5, false, new ArrayList<>());
assertNotNull(elements);
assertEquals(3, elements.size());
BioEntity sAlias = elements.get(0);
......@@ -355,7 +356,7 @@ public class SearchServiceTest extends ServiceTestFunctions {
public void testSearchClosestWithEmptyModel() throws Exception {
try {
Model model = new ModelFullIndexed(null);
List<BioEntity> elements = searchService.getClosestElements(model, new Point2D.Double(0, 0), 5, false);
List<BioEntity> elements = searchService.getClosestElements(model, new Point2D.Double(0, 0), 5, false, new ArrayList<>());
assertNotNull(elements);
assertEquals(0, elements.size());
......
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