Merge remote-tracking branch 'origin/model_update_updateTracker' into model_update_updateTracker

Author: EliotRagueneau

src/main/java/org/reactome/server/graph/repository/DeletedInstanceRepository.java

@@ -0,0 +1,25 @@
+package org.reactome.server.graph.repository;
+
+import org.reactome.server.graph.domain.model.DeletedInstance;
+import org.springframework.data.neo4j.repository.Neo4jRepository;
+import org.springframework.data.neo4j.repository.query.Query;
+import org.springframework.data.repository.query.Param;
+import org.springframework.stereotype.Repository;
+
+import java.util.List;
+import java.util.Optional;
+
+@Repository
+public interface DeletedInstanceRepository extends Neo4jRepository<DeletedInstance, Long> {
+    //language=cypher
+    @Query(" MATCH (d:DeletedInstance{dbId:$dbId}) " +
+            "OPTIONAL MATCH (d)-[r]-(m) " +
+            "RETURN d, collect(r), collect(m)")
+    Optional<DeletedInstance> getDeletedInstanceByDbId(@Param("dbId") Long dbId);
+
+
+    @Query("MATCH (d:DeletedInstance)<-[:deletedInstance]-(de:Deleted) " +
+            "where de.dbId = $dbId " +
+            "return d ")
+    List<DeletedInstance> getByDeletedDbId(@Param("dbId") Long dbId);
+}

src/main/java/org/reactome/server/graph/repository/DeletedRepository.java

@@ -0,0 +1,40 @@
+package org.reactome.server.graph.repository;
+
+import org.reactome.server.graph.domain.model.Deleted;
+import org.springframework.data.neo4j.core.Neo4jClient;
+import org.springframework.data.neo4j.core.Neo4jTemplate;
+import org.springframework.stereotype.Repository;
+
+import java.util.List;
+import java.util.Map;
+import java.util.Optional;
+
+@Repository
+public class DeletedRepository {
+
+
+    private final Neo4jTemplate neo4jTemplate;
+
+    public DeletedRepository(Neo4jTemplate neo4jTemplate, Neo4jClient neo4jClient) {
+        this.neo4jTemplate = neo4jTemplate;
+
+    }
+
+    public Optional<Deleted> getDeletedByDbId(Long dbId) {
+        String query = "MATCH (d:Deleted{dbId:$dbId}) OPTIONAL MATCH (d)-[r]-(m) RETURN d, COLLECT(r), COLLECT(m)";
+        return neo4jTemplate.findOne(query, Map.of("dbId", dbId), Deleted.class);
+    }
+
+
+    public List<Deleted> getByDeletedInstanceDbId(Long dbId) {
+        String query = "MATCH (p:Deleted)-[r:deletedInstance*]->(d:DeletedInstance) WHERE d.dbId = $dbId RETURN COLLECT(p)";
+        return neo4jTemplate.findAll(query, Map.of("dbId", dbId), Deleted.class);
+    }
+
+
+    public List<Deleted> getByReplacementStId(String stId) {
+        String query = "MATCH (p:Deleted)-[r:replacementInstances*]->(d:Deletable) WHERE d.stId = $stId  RETURN COLLECT(p)";
+        return neo4jTemplate.findAll(query, Map.of("stId", stId), Deleted.class);
+    }
+
+}

src/main/java/org/reactome/server/graph/repository/UpdateTrackerRepository.java

@@ -2,6 +2,7 @@
 
 import org.reactome.server.graph.domain.model.UpdateTracker;
 import org.springframework.data.neo4j.repository.Neo4jRepository;
+import org.springframework.data.neo4j.repository.query.Query;
 import org.springframework.data.repository.query.Param;
 import org.springframework.stereotype.Repository;
 
@@ -11,13 +12,23 @@
 @Repository
 public interface UpdateTrackerRepository extends Neo4jRepository<UpdateTracker, Long> {
 
-    @Override
-    Optional<UpdateTracker> findById(Long dbId);
+    //language=cypher
+    @Query(" MATCH (d:UpdateTracker{dbId:$dbId}) " +
+            "OPTIONAL MATCH (d)-[r]-(m) " +
+            "RETURN d, collect(r), collect(m)")
+    Optional<UpdateTracker> findUpdateTrackerByDbId(@Param("dbId") Long dbId);
 
-    List<UpdateTracker> findByReleaseReleaseNumber(@Param("releaseNumber") int releaseNumber);
 
-    List<UpdateTracker> findByUpdatedInstanceStId(@Param("stId") String stId);
+    //language=cypher
+    @Query(" MATCH(u:UpdateTracker)-[:updatedInstance]->(t:Trackable) " +
+            "WHERE t.dbId = $dbId " +
+            "RETURN u")
+    List<UpdateTracker> findByUpdatedInstanceDbId(Long dbId);
 
-    List<UpdateTracker> findByUpdatedInstanceDbId(@Param("dbId") Long dbId);
+    //language=cypher
+    @Query(" MATCH(d:UpdateTracker)-[:updatedInstance]->(t:Trackable) " +
+            "WHERE t.stId = $stId " +
+            "RETURN d ")
+    List<UpdateTracker> findByUpdatedInstanceStId(@Param("stId") String stId);
 
 }

src/main/java/org/reactome/server/graph/service/DeletedInstanceService.java

@@ -0,0 +1,28 @@
+package org.reactome.server.graph.service;
+
+import org.reactome.server.graph.domain.model.DeletedInstance;
+import org.reactome.server.graph.repository.DeletedInstanceRepository;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+
+import java.util.List;
+import java.util.Optional;
+
+@Service
+public class DeletedInstanceService {
+
+    private DeletedInstanceRepository repository;
+
+    @Autowired
+    public DeletedInstanceService(DeletedInstanceRepository repository) {
+        this.repository = repository;
+    }
+
+    public Optional<DeletedInstance> getDeletedInstanceByDbId(Long dbId) {
+        return this.repository.getDeletedInstanceByDbId(dbId);
+    }
+
+    public List<DeletedInstance> getBYDeletedDbId(Long dbId) {
+        return this.repository.getByDeletedDbId(dbId);
+    }
+}

src/main/java/org/reactome/server/graph/service/DeletedService.java

@@ -0,0 +1,34 @@
+package org.reactome.server.graph.service;
+
+
+import org.reactome.server.graph.domain.model.*;
+import org.reactome.server.graph.repository.DeletedRepository;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+
+import java.util.List;
+import java.util.Optional;
+
+@Service
+public class DeletedService {
+
+    private DeletedRepository repository;
+
+    @Autowired
+    public DeletedService(DeletedRepository repository) {
+        this.repository = repository;
+    }
+
+    public Optional<Deleted> getDeletedByDbId(Long dbId) {
+        return this.repository.getDeletedByDbId(dbId);
+    }
+
+    public List<Deleted> getByDeletedInstanceDbId(Long dbId) {
+        return this.repository.getByDeletedInstanceDbId(dbId);
+    }
+
+    public List<Deleted> getByReplacementStId(String stId) {
+        return this.repository.getByReplacementStId(stId);
+    }
+
+}

src/main/java/org/reactome/server/graph/service/UpdateTrackerService.java

@@ -10,19 +10,17 @@
 
 @Service
 public class UpdateTrackerService {
+
     private UpdateTrackerRepository repository;
 
     @Autowired
     public UpdateTrackerService(UpdateTrackerRepository repository) {
         this.repository = repository;
     }
 
-    public Optional<UpdateTracker> findById(Long id) {
-        return this.repository.findById(id);
-    }
 
-    public List<UpdateTracker> findByReleaseNumber(int releaseNumber) {
-        return this.repository.findByReleaseReleaseNumber(releaseNumber);
+    public Optional<UpdateTracker> findUpdateTrackerByDbId(Long dbId) {
+        return this.repository.findUpdateTrackerByDbId(dbId);
     }
 
     public List<UpdateTracker> findByUpdatedInstanceDbId(Long dbId) {

src/test/java/org/reactome/server/graph/service/DeletedInstanceServiceTest.java

@@ -0,0 +1,34 @@
+package org.reactome.server.graph.service;
+
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
+import org.reactome.server.graph.domain.model.DeletedInstance;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import java.util.List;
+import java.util.Optional;
+
+public class DeletedInstanceServiceTest extends BaseTest {
+
+    @Autowired
+    private DeletedInstanceService deletedInstanceService;
+
+
+    @Test
+    public void getDeletedInstanceByDbId() {
+        Optional<DeletedInstance> deletedInstance = this.deletedInstanceService.getDeletedInstanceByDbId(9745160L);
+        Assertions.assertTrue(deletedInstance.isPresent());
+
+        int deletedInstanceDbId = deletedInstance.get().getDeletedInstanceDbId();
+        Assertions.assertNotNull(deletedInstanceDbId);
+
+        String deletedStId = deletedInstance.get().getDeletedStId();
+        Assertions.assertNotNull(deletedStId);
+    }
+
+    @Test
+    public void getByDeletedDbId() {
+        List<DeletedInstance> deletedInstances = this.deletedInstanceService.getBYDeletedDbId(5655667L);
+        Assertions.assertTrue(!deletedInstances.isEmpty());
+    }
+}

src/test/java/org/reactome/server/graph/service/DeletedServiceTest.java

@@ -0,0 +1,45 @@
+package org.reactome.server.graph.service;
+
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
+import org.reactome.server.graph.domain.model.*;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import java.util.List;
+import java.util.Optional;
+
+public class DeletedServiceTest extends BaseTest {
+
+    @Autowired
+    DeletedService service;
+
+    @Test
+    public void testFindDeletedByDbId() {
+
+        Optional<Deleted> deleted = service.getDeletedByDbId(8869329L);
+        Assertions.assertTrue(deleted.isPresent());
+
+        List<DeletedInstance> deletedInstances = deleted.get().getDeletedInstance();
+        Assertions.assertTrue(!deletedInstances.isEmpty());
+
+        List<Deletable> deletables = deleted.get().getReplacementInstances();
+        Assertions.assertTrue(!deletables.isEmpty());
+
+        DeletedControlledVocabulary dcv = deleted.get().getReason();
+        Assertions.assertNotNull(dcv);
+
+        Assertions.assertTrue(deletables.stream().anyMatch(deletable -> deletable instanceof NegativeRegulation));
+    }
+
+    @Test
+    public void testGetByDeletedInstanceDbId() {
+        List<Deleted> deleteds = this.service.getByDeletedInstanceDbId(9745855L);
+        Assertions.assertTrue(!deleteds.isEmpty());
+    }
+
+    @Test
+    public void testGetDeletedByReplacementInstancesStId() {
+        List<Deleted> deleteds = this.service.getByReplacementStId("R-RNO-164402");
+        Assertions.assertTrue(!deleteds.isEmpty());
+    }
+}

src/test/java/org/reactome/server/graph/service/UpdateTrackerServiceTest.java

@@ -1,9 +1,9 @@
 package org.reactome.server.graph.service;
 
+import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
-import org.reactome.server.graph.domain.model.Complex;
-import org.reactome.server.graph.domain.model.Reaction;
+import org.reactome.server.graph.domain.model.Pathway;
 import org.reactome.server.graph.domain.model.Trackable;
 import org.reactome.server.graph.domain.model.UpdateTracker;
 import org.reactome.server.graph.util.DatabaseObjectFactory;
@@ -12,7 +12,6 @@
 import java.util.List;
 import java.util.Optional;
 
-import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 
 public class UpdateTrackerServiceTest extends BaseTest {
@@ -36,32 +35,29 @@ public void setUp() throws Exception {
     UpdateTrackerService service;
 
     @Test
-    void testFindById() {
-        Optional<UpdateTracker> updateTracker = this.service.findById(999999999999999L);
-        assertTrue(updateTracker.isPresent());
+    void testFindUpdateTrackerByDbId() {
+
+        Optional<UpdateTracker> updateTracker = this.service.findUpdateTrackerByDbId(9776257L);
+        Assertions.assertNotNull(updateTracker);
+
+        Assertions.assertEquals(77, updateTracker.get().getRelease().getReleaseNumber());
+
         List<Trackable> updatedInstances = updateTracker.get().getUpdatedInstance();
-        assertEquals(2, updatedInstances.size());
-        assertEquals(77, updateTracker.get().getRelease().getReleaseNumber());
-        assertTrue(updatedInstances.stream().anyMatch(trackable -> trackable instanceof Reaction));
-        assertTrue(updatedInstances.stream().anyMatch(trackable -> trackable instanceof Complex));
-    }
 
-    @Test
-    void testFindByReleaseNumber() {
-        List<UpdateTracker> updateTracker = this.service.findByReleaseNumber(77);
-        assertTrue(updateTracker.size() >= 1);
+        Assertions.assertTrue(!updatedInstances.isEmpty());
+        Assertions.assertTrue(updatedInstances.stream().anyMatch(trackable -> trackable instanceof Pathway));
     }
 
+
     @Test
     void testFindByUpdatedInstanceDbId() {
-        List<UpdateTracker> updateTracker = this.service.findByUpdatedInstanceDbId(6793661L);
+        List<UpdateTracker> updateTracker = this.service.findByUpdatedInstanceDbId(3299685L);
         assertTrue(updateTracker.size() >= 1);
     }
 
     @Test
     void testFindByUpdatedInstanceStId() {
-        List<UpdateTracker> updateTracker = this.service.findByUpdatedInstanceStId("R-HSA-8944365");
+        List<UpdateTracker> updateTracker = this.service.findByUpdatedInstanceStId("R-HSA-3299685");
         assertTrue(updateTracker.size() >= 1);
     }
-
 }