From a79901365852e54bed6fbea4c0cb590dc434fd5d Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 11 Apr 2017 10:26:35 +0200
Subject: [PATCH] rest api for getting publication list
---
.../api/project/ProjectController.java | 6 ++
.../api/project/ProjectRestImpl.java | 102 ++++++++++++++----
.../api/project/ProjectRestImplTest.java | 25 +++++
3 files changed, 112 insertions(+), 21 deletions(-)
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/project/ProjectController.java b/rest-api/src/main/java/lcsb/mapviewer/api/project/ProjectController.java
index f27d48befc..74ddd74776 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/project/ProjectController.java
+++ b/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 {
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/project/ProjectRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/project/ProjectRestImpl.java
index 506d37b9b3..c5bc026772 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/project/ProjectRestImpl.java
+++ b/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;
+ }
+
}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/project/ProjectRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/project/ProjectRestImplTest.java
index 6155d0b7a0..c0de5c7b1c 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/project/ProjectRestImplTest.java
+++ b/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;
+ }
+ }
+
+
}
--
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