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Commit e6e46455 authored by Piotr Gawron's avatar Piotr Gawron
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new api call for list of publications

parent 77683f5c
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1 merge request!11Resolve "Rest API should follow google guidlines"
This commit is part of merge request !11. Comments created here will be created in the context of that merge request.
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rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java
+ 0
− 7
View file @ e6e46455
......@@ -69,13 +69,6 @@ public class ProjectController extends BaseController {
return projectController.getElementsByQuery(projectId, token, query, maxElements, perfectMatch);
}
@RequestMapping(value = "/project/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 = "/project/getProjectSource", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
public ResponseEntity<byte[]> getProjectSource(@RequestParam(value = "token") String token, @RequestParam(value = "projectId") String projectId)
throws SecurityException, QueryException {
......
rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
+ 9
− 115
View file @ e6e46455
......@@ -14,8 +14,6 @@ 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.io.IOUtils;
import org.apache.log4j.Logger;
......@@ -23,8 +21,8 @@ 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.api.projects.models.publications.PublicationsRestImpl;
import lcsb.mapviewer.commands.ClearColorModelCommand;
import lcsb.mapviewer.commands.ColorExtractor;
import lcsb.mapviewer.commands.ColorModelCommand;
......@@ -42,10 +40,7 @@ import lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter;
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.InconsistentModelException;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.OverviewImage;
import lcsb.mapviewer.model.map.OverviewImageLink;
import lcsb.mapviewer.model.map.OverviewLink;
......@@ -54,7 +49,6 @@ 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.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.user.User;
......@@ -97,13 +91,13 @@ public class ProjectRestImpl {
private IModelService modelService;
@Autowired
private ISearchService searchService;
private PublicationsRestImpl publicationsRestImpl;
@Autowired
AnnotationViewFactory annotationViewFactory;
private ISearchService searchService;
@Autowired
private PubmedParser pubmedParser;
AnnotationViewFactory annotationViewFactory;
@Autowired
private ILayoutService layoutService;
......@@ -127,7 +121,7 @@ public class ProjectRestImpl {
private ProjectMetaData createData(Project project, AuthenticationToken token) {
ProjectMetaData result = new ProjectMetaData();
ModelData model = modelService.getLastModelByProjectId(project.getProjectId(), token).getModelData();
Model model = modelService.getLastModelByProjectId(project.getProjectId(), token);
result.setName(project.getName());
result.setProjectId(project.getProjectId());
......@@ -155,50 +149,16 @@ public class ProjectRestImpl {
}
result.setMap(new ModelMetaData(model));
result.setPublicationCount(getPublications(model).size());
List<Model> models = new ArrayList<>();
models.add(model);
models.addAll(model.getSubmodels());
result.setPublicationCount(publicationsRestImpl.getPublications(models).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)) {
List<AnnotatedObject> list = publications.get(md);
if (list == null) {
list = new ArrayList<>();
publications.put(md, list);
}
list.add(reaction);
}
}
}
}
return publications;
}
/**
* @return the userService
* @see #userService
......@@ -335,55 +295,6 @@ 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()) {
elements.add(createMinifiedSearchResult(object));
}
Map<String, Object> row = new HashMap<>();
row.put("elements", elements);
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());
result.put("start", start);
result.put("length", resultList.size());
return result;
}
public FileEntry getModelAsImage(String token, String projectId, String modelId, String handlerClass, String backgroundOverlayId, String overlayIds,
String zoomLevel, String polygonString) throws SecurityException, QueryException, IOException, InvalidColorSchemaException, CommandExecutionException {
AuthenticationToken authenticationToken = userService.getToken(token);
......@@ -557,21 +468,4 @@ public class ProjectRestImpl {
}
/**
* @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;
}
}
rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsController.java 0 → 100644
+ 43
− 0
View file @ e6e46455
package lcsb.mapviewer.api.projects.models.publications;
import java.awt.geom.Point2D;
import java.io.IOException;
import java.util.List;
import java.util.Map;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.MediaType;
import org.springframework.http.ResponseEntity;
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.commands.CommandExecutionException;
import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.model.cache.FileEntry;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
import lcsb.mapviewer.services.SecurityException;
@RestController
public class PublicationsController extends BaseController {
@Autowired
private PublicationsRestImpl projectController;
@RequestMapping(value = "/projects/{projectId}/models/{modelId}/publications/", method = { RequestMethod.GET },
produces = { MediaType.APPLICATION_JSON_VALUE })
public Map<String, Object> getPublications(//
@PathVariable(value = "projectId") String projectId, //
@PathVariable(value = "modelId") String modelId, //
@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, modelId, token, start, length);
}
}
\ No newline at end of file
rest-api/src/main/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImpl.java 0 → 100644
+ 223
− 0
View file @ e6e46455
package lcsb.mapviewer.api.projects.models.publications;
import java.util.ArrayList;
import java.util.HashMap;
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.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.annotation.services.PubmedParser;
import lcsb.mapviewer.api.BaseRestImpl;
import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.model.map.AnnotatedObject;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.interfaces.ILayoutService;
import lcsb.mapviewer.services.interfaces.IModelService;
import lcsb.mapviewer.services.interfaces.ISearchService;
import lcsb.mapviewer.services.interfaces.IUserService;
import lcsb.mapviewer.services.search.data.ElementIdentifier.ElementIdentifierType;
import lcsb.mapviewer.services.view.AnnotationViewFactory;
import lcsb.mapviewer.services.view.AuthenticationToken;
import lcsb.mapviewer.services.view.OverviewImageViewFactory;
@Transactional(value = "txManager")
public class PublicationsRestImpl extends BaseRestImpl{
Logger logger = Logger.getLogger(PublicationsRestImpl.class);
@Autowired
private IUserService userService;
@Autowired
private IModelService modelService;
@Autowired
private ISearchService searchService;
@Autowired
AnnotationViewFactory annotationViewFactory;
@Autowired
private PubmedParser pubmedParser;
@Autowired
private OverviewImageViewFactory factory;
public SortedMap<MiriamData, List<AnnotatedObject>> getPublications(List<Model> models) {
SortedMap<MiriamData, List<AnnotatedObject>> publications = new TreeMap<>();
for (Model 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)) {
List<AnnotatedObject> list = publications.get(md);
if (list == null) {
list = new ArrayList<>();
publications.put(md, list);
}
list.add(reaction);
}
}
}
}
return publications;
}
/**
* @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;
}
/**
* @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;
}
/**
* @return the factory
* @see #factory
*/
public OverviewImageViewFactory getFactory() {
return factory;
}
/**
* @param factory
* the factory to set
* @see #factory
*/
public void setFactory(OverviewImageViewFactory factory) {
this.factory = factory;
}
public Map<String, Object> getPublications(String projectId, String modelId, String token, String startString, Integer length) throws SecurityException, QueryException {
List<Model> models = getModels(projectId, modelId, token);
Integer start = Math.max(0, Integer.valueOf(startString));
List<Map<String, Object>> resultList = new ArrayList<>();
SortedMap<MiriamData, List<AnnotatedObject>> publications = getPublications(models);
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()) {
elements.add(createMinifiedSearchResult(object));
}
Map<String, Object> row = new HashMap<>();
row.put("elements", elements);
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());
result.put("start", start);
result.put("length", resultList.size());
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;
}
}
rest-api/src/main/resources/applicationContext-rest.xml
+ 1
− 0
View file @ e6e46455
......@@ -21,6 +21,7 @@
<bean id="ProjectRestImpl" class="lcsb.mapviewer.api.projects.ProjectRestImpl"/>
<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"/>
<bean id="ReferenceGenomeRestImpl" class="lcsb.mapviewer.api.genomics.ReferenceGenomeRestImpl"/>
<bean id="UserRestImpl" class="lcsb.mapviewer.api.controller.UserRestImpl"/>
......
rest-api/src/test/java/lcsb/mapviewer/api/projects/AllProjectTests.java
+ 2
− 2
View file @ e6e46455
......@@ -4,10 +4,10 @@ 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;
import lcsb.mapviewer.api.projects.models.AllModelsTests;
@RunWith(Suite.class)
@SuiteClasses({ AllElementsTests.class, //
@SuiteClasses({ AllModelsTests.class, //
ModelMetaDataTest.class, //
ProjectRestImplTest.class })
public class AllProjectTests {
......
rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java
+ 0
− 23
View file @ e6e46455
......@@ -160,28 +160,5 @@ 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;
}
}
}
rest-api/src/test/java/lcsb/mapviewer/api/projects/models/AllModelsTests.java 0 → 100644
+ 17
− 0
View file @ e6e46455
package lcsb.mapviewer.api.projects.models;
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;
import lcsb.mapviewer.api.projects.models.publications.AllPublicationsTests;
@RunWith(Suite.class)
@SuiteClasses({ //
AllElementsTests.class, //
AllPublicationsTests.class//
})
public class AllModelsTests {
}
rest-api/src/test/java/lcsb/mapviewer/api/projects/models/publications/AllPublicationsTests.java 0 → 100644
+ 11
− 0
View file @ e6e46455
package lcsb.mapviewer.api.projects.models.publications;
import org.junit.runner.RunWith;
import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({ PublicationsRestImplTest.class })
public class AllPublicationsTests {
}
rest-api/src/test/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImplTest.java 0 → 100644
+ 72
− 0
View file @ e6e46455
package lcsb.mapviewer.api.projects.models.publications;
import static org.junit.Assert.assertEquals;
import static org.mockito.Matchers.any;
import static org.mockito.Matchers.anyString;
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 PublicationsRestImplTest extends RestTestFunctions {
Logger logger = Logger.getLogger(PublicationsRestImplTest.class);
@Autowired
PublicationsRestImpl _projectRestImpl;
@AfterClass
public static void tearDownAfterClass() throws Exception {
}
@Before
public void setUp() throws Exception {
}
@After
public void tearDown() throws Exception {
}
@Test
public void testPublications() throws Exception {
try {
PublicationsRestImpl 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;
}
}
private PublicationsRestImpl 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);
_projectRestImpl.setModelService(mockModelService);
return _projectRestImpl;
}
}
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