refactor(cbir): cbir endpoints and tests (#29)

#29
Cytomine-ULiege · Aug 20, 2024 · f9d6699 · f9d6699
1 parent 186204a
commit f9d6699
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Showing 18 changed files with 1,616 additions and 802 deletions.
diff --git a/src/main/java/be/cytomine/api/controller/search/RestRetrievalController.java b/src/main/java/be/cytomine/api/controller/search/RestRetrievalController.java
@@ -16,10 +16,9 @@
  * limitations under the License.
  */
 
-import be.cytomine.api.controller.RestCytomineController;
-import be.cytomine.domain.ontology.AnnotationDomain;
-import be.cytomine.service.dto.CropParameter;
-import be.cytomine.service.search.RetrievalService;
+import java.io.UnsupportedEncodingException;
+import javax.persistence.EntityManager;
+
 import com.vividsolutions.jts.io.ParseException;
 import lombok.RequiredArgsConstructor;
 import lombok.extern.slf4j.Slf4j;
@@ -29,12 +28,15 @@
 import org.springframework.web.bind.annotation.RequestParam;
 import org.springframework.web.bind.annotation.RestController;
 
-import javax.persistence.EntityManager;
-import java.io.IOException;
+import be.cytomine.api.controller.RestCytomineController;
+import be.cytomine.domain.ontology.AnnotationDomain;
+import be.cytomine.dto.search.SearchResponse;
+import be.cytomine.service.dto.CropParameter;
+import be.cytomine.service.search.RetrievalService;
 
+@Slf4j
 @RestController
 @RequestMapping("/api")
-@Slf4j
 @RequiredArgsConstructor
 public class RestRetrievalController extends RestCytomineController {
 
@@ -54,33 +56,33 @@ private CropParameter getParameters(String location) {
         return parameters;
     }
 
-    @GetMapping("/retrieval/index.json")
-    public ResponseEntity<String> indexAnnotation(@RequestParam(value = "annotation") Long id) throws IOException, ParseException, InterruptedException {
+    @GetMapping("/retrieval/index")
+    public ResponseEntity<String> indexAnnotation(
+        @RequestParam(value = "annotation") Long id
+    ) throws ParseException, UnsupportedEncodingException {
         log.debug("REST request to index an annotation");
 
         AnnotationDomain annotation = AnnotationDomain.getAnnotationDomain(entityManager, id);
         CropParameter parameters = getParameters(annotation.getWktLocation());
 
-        return responseSuccess(retrievalService.indexAnnotation(annotation, parameters, getRequestETag()));
+        return retrievalService.indexAnnotation(annotation, parameters, getRequestETag());
     }
 
-    @GetMapping("/retrieval/retrieve.json")
-    public ResponseEntity<String> retrieveSimilarAnnotations(
+    @GetMapping("/retrieval/search")
+    public ResponseEntity<SearchResponse> retrieveSimilarAnnotations(
         @RequestParam(value = "annotation") Long id,
         @RequestParam(value = "nrt_neigh") Long nrt_neigh
-    ) throws IOException, ParseException, InterruptedException {
+    ) throws ParseException, UnsupportedEncodingException {
         log.debug("REST request to retrieve similar annotations given a query annotation {}", id);
 
         AnnotationDomain annotation = AnnotationDomain.getAnnotationDomain(entityManager, id);
         CropParameter parameters = getParameters(annotation.getWktLocation());
 
-        return responseSuccess(
-            retrievalService.retrieveSimilarImages(
-                annotation,
-                parameters,
-                getRequestETag(),
-                nrt_neigh
-            )
+        return retrievalService.retrieveSimilarImages(
+            annotation,
+            parameters,
+            getRequestETag(),
+            nrt_neigh
         );
     }
 }
diff --git a/src/main/java/be/cytomine/config/RestTemplateConfiguration.java b/src/main/java/be/cytomine/config/RestTemplateConfiguration.java
@@ -0,0 +1,14 @@
+package be.cytomine.config;
+
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.web.client.RestTemplate;
+
+@Configuration
+public class RestTemplateConfiguration {
+
+    @Bean
+    public RestTemplate restTemplate() {
+        return new RestTemplate();
+    }
+}
diff --git a/src/main/java/be/cytomine/dto/search/SearchResponse.java b/src/main/java/be/cytomine/dto/search/SearchResponse.java
@@ -0,0 +1,18 @@
+package be.cytomine.dto.search;
+
+import java.util.List;
+
+import lombok.AllArgsConstructor;
+import lombok.Data;
+import lombok.NoArgsConstructor;
+
+@Data
+@AllArgsConstructor
+@NoArgsConstructor
+public class SearchResponse {
+
+    private String query;
+    private String storage;
+    private String index;
+    private List<List<Object>> similarities;
+}
diff --git a/src/main/java/be/cytomine/service/ontology/UserAnnotationService.java b/src/main/java/be/cytomine/service/ontology/UserAnnotationService.java
@@ -63,6 +63,7 @@
 import javax.persistence.EntityManager;
 import javax.transaction.Transactional;
 import java.io.IOException;
+import java.io.UnsupportedEncodingException;
 import java.util.*;
 import java.util.stream.Collectors;
 
@@ -503,7 +504,7 @@ protected void afterAdd(CytomineDomain domain, CommandResponse response) {
 
         try {
             retrievalService.indexAnnotation(annotation, parameters, null);
-        } catch (IOException | ParseException | InterruptedException exception) {
+        } catch (ParseException | UnsupportedEncodingException exception) {
             log.error(exception.getMessage());
         }
     }
@@ -613,11 +614,7 @@ protected void afterDelete(CytomineDomain domain, CommandResponse response) {
         response.getData().remove("userannotation");
 
         /* Delete the annotation from the CBIR database */
-        try {
-            retrievalService.deleteIndex((AnnotationDomain) domain);
-        } catch (IOException | InterruptedException exception) {
-            log.error(exception.getMessage());
-        }
+        retrievalService.deleteIndex((AnnotationDomain) domain);
     }
 
     public List<CommandResponse> repeat(UserAnnotation userAnnotation, Long baseSliceId, int repeat) {

diff --git a/src/main/java/be/cytomine/service/project/ProjectService.java b/src/main/java/be/cytomine/service/project/ProjectService.java
@@ -16,6 +16,7 @@
 * limitations under the License.
 */
 
+import be.cytomine.config.properties.ApplicationProperties;
 import be.cytomine.domain.CytomineDomain;
 import be.cytomine.domain.command.*;
 import be.cytomine.domain.image.ImageInstance;
@@ -27,7 +28,6 @@
 import be.cytomine.domain.security.SecRole;
 import be.cytomine.domain.security.SecUser;
 import be.cytomine.domain.security.User;
-import be.cytomine.domain.social.PersistentConnection;
 import be.cytomine.dto.DatedCytomineDomain;
 import be.cytomine.dto.NamedCytomineDomain;
 import be.cytomine.exceptions.*;
@@ -41,7 +41,6 @@
 import be.cytomine.repository.project.ProjectRepresentativeUserRepository;
 import be.cytomine.repository.security.SecRoleRepository;
 import be.cytomine.repository.security.UserRepository;
-import be.cytomine.repositorynosql.social.PersistentConnectionRepository;
 import be.cytomine.service.CurrentRoleService;
 import be.cytomine.service.CurrentUserService;
 import be.cytomine.service.ModelService;
@@ -53,7 +52,6 @@
 import be.cytomine.service.ontology.OntologyService;
 import be.cytomine.service.ontology.ReviewedAnnotationService;
 import be.cytomine.service.search.ProjectSearchExtension;
-import be.cytomine.service.security.SecRoleService;
 import be.cytomine.service.security.SecUserSecRoleService;
 import be.cytomine.service.security.SecUserService;
 import be.cytomine.service.security.SecurityACLService;
@@ -72,8 +70,10 @@
 import org.bson.conversions.Bson;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.*;
+import org.springframework.http.*;
 import org.springframework.security.acls.domain.BasePermission;
 import org.springframework.stereotype.Service;
+import org.springframework.web.client.RestTemplate;
 
 import javax.mail.MessagingException;
 import javax.persistence.Query;
@@ -89,7 +89,6 @@
 import static com.mongodb.client.model.Aggregates.sort;
 import static com.mongodb.client.model.Filters.eq;
 import static com.mongodb.client.model.Filters.gte;
-import static com.mongodb.client.model.Sorts.ascending;
 import static com.mongodb.client.model.Sorts.descending;
 import static org.springframework.security.acls.domain.BasePermission.*;
 
@@ -98,6 +97,9 @@
 @Transactional
 public class ProjectService extends ModelService {
 
+    @Autowired
+    private ApplicationProperties applicationProperties;
+
     @Autowired
     private CommandHistoryRepository commandHistoryRepository;
 
@@ -173,6 +175,9 @@ public class ProjectService extends ModelService {
     @Autowired
     private ProjectRepresentativeUserRepository projectRepresentativeUserRepository;
 
+    @Autowired
+    private RestTemplate restTemplate;
+
     public Project get(Long id) {
         return find(id).orElse(null);
     }
@@ -599,6 +604,28 @@ public List<NamedCytomineDomain> listByUser(User user) {
         return projectRepository.listByUser(user);
     }
 
+    private void createStorage(String projectId) {
+        String url = this.applicationProperties.getRetrievalServerURL() + "/api/storages";
+        Map<String, String> payload = new HashMap<>();
+        payload.put("name", projectId);
+
+        HttpHeaders headers = new HttpHeaders();
+        headers.setContentType(MediaType.APPLICATION_JSON);
+        HttpEntity<Map<String, String>> requestEntity = new HttpEntity<>(payload, headers);
+
+        log.debug("Sending POST request to {}, {}", url, projectId);
+        ResponseEntity<String> response = restTemplate.exchange(
+            url,
+            HttpMethod.POST,
+            requestEntity,
+            String.class
+        );
+
+        if (!response.getStatusCode().equals(HttpStatus.OK)) {
+            log.error("Failed to create storage for project {}", projectId);
+        }
+    }
+
     @Override
     public CommandResponse add(JsonObject jsonObject) {
         return add(jsonObject, null);
@@ -649,6 +676,9 @@ public CommandResponse add(JsonObject jsonObject, Task task) {
             }
         }
 
+        // Create retrieval storage
+        createStorage(project.getId().toString());
+
         return commandResponse;
     }