104 update mongodb

backend/Dockerfile

@@ -1,6 +1,5 @@
 
-#FROM maven:3.6.3-adoptopenjdk-14
-FROM maven:3.8-jdk-11
+FROM maven:3.9.6-eclipse-temurin-17
 
 RUN mkdir /opt/ols && mkdir /opt/ols/backend && mkdir /opt/ols/ols-shared
 COPY ./backend /opt/ols/backend

backend/pom.xml

@@ -15,9 +15,9 @@
     </parent>
 
     <properties>
-        <java.version>11</java.version>
-        <maven.compiler.source>11</maven.compiler.source>
-        <maven.compiler.target>11</maven.compiler.target>
+        <java.version>17</java.version>
+        <maven.compiler.source>17</maven.compiler.source>
+        <maven.compiler.target>17</maven.compiler.target>
     </properties>
 
     <dependencies>
@@ -32,11 +32,23 @@
     		<version>2.8.9</version>
     	</dependency>
 
-	<dependency>
-		<groupId>org.neo4j.driver</groupId>
-		<artifactId>neo4j-java-driver</artifactId>
-		<version>4.4.1</version>
-	</dependency>
+        <dependency>
+            <groupId>org.neo4j.driver</groupId>
+            <artifactId>neo4j-java-driver</artifactId>
+            <version>5.19.0</version>
+        </dependency>
+
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-data-mongodb</artifactId>
+            <version>2.7.5</version>
+        </dependency>
+
+        <dependency>
+            <groupId>javax.persistence</groupId>
+            <artifactId>javax.persistence-api</artifactId>
+            <version>2.2</version>
+        </dependency>
 
         <dependency>
             <groupId>org.springframework.boot</groupId>
@@ -149,6 +161,18 @@
             <artifactId>springdoc-openapi-ui</artifactId>
             <version>1.6.4</version>
         </dependency>
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-collections4</artifactId>
+            <version>4.4</version>
+            <scope>compile</scope>
+        </dependency>
+        <dependency>
+            <groupId>joda-time</groupId>
+            <artifactId>joda-time</artifactId>
+            <version>2.13.0</version>
+            <scope>compile</scope>
+        </dependency>
 
         <!-- Logging -->
 <!--        <dependency>-->

backend/src/main/java/uk/ac/ebi/spot/ols/config/RestCallInterceptor.java

@@ -0,0 +1,31 @@
+package uk.ac.ebi.spot.ols.config;
+
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.web.servlet.HandlerInterceptor;
+
+import uk.ac.ebi.spot.ols.reststatistics.service.RestCallHandlerService;
+
+public class RestCallInterceptor implements HandlerInterceptor {
+    private final RestCallHandlerService restCallHandlerService;
+
+    @Autowired
+    public RestCallInterceptor(RestCallHandlerService restCallHandlerService) {
+        this.restCallHandlerService = restCallHandlerService;
+    }
+
+    @Override
+    public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception {
+        if (!request.getRequestURL().toString().contains("/api")
+            || request.getRequestURL().toString().contains("/api/rest/statistics")) {
+            return true;
+        }
+
+
+        restCallHandlerService.handle(request);
+
+        return true;
+    }
+}

backend/src/main/java/uk/ac/ebi/spot/ols/config/WebConfig.java

@@ -2,13 +2,9 @@
 
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.ComponentScan;
 import org.springframework.context.annotation.Configuration;
-import org.springframework.context.annotation.Import;
-import org.springframework.http.MediaType;
-import org.springframework.web.filter.CharacterEncodingFilter;
 import org.springframework.web.servlet.config.annotation.*;
-import org.springframework.web.util.UrlPathHelper;
+import uk.ac.ebi.spot.ols.reststatistics.service.RestCallHandlerService;
 
 /**
  * @author Simon Jupp
@@ -25,6 +21,10 @@ public class WebConfig extends WebMvcConfigurerAdapter {
      *
      * @param configurer
      */
+
+    @Autowired
+    RestCallHandlerService restCallHandlerService;
+
     @Override
     public void configurePathMatch(PathMatchConfigurer configurer) {
 //        UrlPathHelper urlPathHelper = new UrlPathHelper();
@@ -36,17 +36,15 @@ public void configurePathMatch(PathMatchConfigurer configurer) {
 
     }
 
-//     @Bean
-//     MaintenanceInterceptor getMaintenanceInterceptor() {
-//         return new MaintenanceInterceptor();
-//     }
-
-//     @Autowired
-//     MaintenanceInterceptor interceptor;
-//     @Override
-//      public void addInterceptors(InterceptorRegistry registry) {
-//          registry.addInterceptor(interceptor);
-//      }
+    @Override
+    public void addInterceptors(InterceptorRegistry registry) {
+        registry.addInterceptor(getRestCallInterceptor());
+    }
+
+    @Bean
+    public RestCallInterceptor getRestCallInterceptor() {
+        return new RestCallInterceptor(restCallHandlerService);
+    }
 
     @Override
     public void addCorsMappings(CorsRegistry registry) {

backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/TopConceptEnum.java

@@ -0,0 +1,7 @@
+package uk.ac.ebi.spot.ols.controller.api.v1;
+
+public enum TopConceptEnum {
+    SCHEMA,
+    TOPCONCEPTOF_PROPERTY,
+    RELATIONSHIPS
+}

backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1ApiUnavailable.java

@@ -6,8 +6,7 @@
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;
 import org.springframework.stereotype.Controller;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.*;
 
 import javax.servlet.http.HttpServletResponse;
 
@@ -16,7 +15,7 @@
  * @date 27/09/2016
  * Samples, Phenotypes and Ontologies Team, EMBL-EBI
  */
-@Controller
+@RestController
 public class V1ApiUnavailable {
 
     @RequestMapping(path = "/api/unavailable", produces = {MediaType.APPLICATION_JSON_VALUE}, method = RequestMethod.GET)

backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1IndividualController.java

@@ -30,6 +30,7 @@
  * @date 18/08/2015
  * Samples, Phenotypes and Ontologies Team, EMBL-EBI
  */
+
 @Tag(name = "Individual Controller", description = "NOTE: For IRI parameters, the value must be URL encoded. " +
         "For example, the IRI http://purl.obolibrary.org/obo/IAO_0000124 should be encoded as http%3A%252F%2Fpurl.obolibrary.org%2Fobo%2FIAO_0000124.")
 @RestController
@@ -97,7 +98,8 @@ HttpEntity<PagedModel<V1Individual>> getAllIndividuals(
 
         return new ResponseEntity<>(assembler.toModel(terms, individualAssembler), HttpStatus.OK);
     }
-
+
+
     @RequestMapping(path = "/findByIdAndIsDefiningOntology/{iri}", produces = {MediaType.APPLICATION_JSON_VALUE, MediaTypes.HAL_JSON_VALUE}, method = RequestMethod.GET)
     HttpEntity<PagedModel<V1Individual>> getAllIndividualsByIdAndIsDefiningOntology(
             @PathVariable("iri")
@@ -111,11 +113,11 @@ HttpEntity<PagedModel<V1Individual>> getAllIndividualsByIdAndIsDefiningOntology(
         decoded = UriUtils.decode(termId, "UTF-8");
         return getAllIndividualsByIdAndIsDefiningOntology(decoded, null, null, lang, pageable, assembler);
 
-    }    
-    
-    
-    @RequestMapping(path = "/findByIdAndIsDefiningOntology", 
-    		produces = {MediaType.APPLICATION_JSON_VALUE, MediaTypes.HAL_JSON_VALUE}, 
+    }
+
+
+    @RequestMapping(path = "/findByIdAndIsDefiningOntology",
+    		produces = {MediaType.APPLICATION_JSON_VALUE, MediaTypes.HAL_JSON_VALUE},
     		method = RequestMethod.GET)
     HttpEntity<PagedModel<V1Individual>> getAllIndividualsByIdAndIsDefiningOntology(
             @RequestParam(value = "iri", required = false)
@@ -148,11 +150,11 @@ HttpEntity<PagedModel<V1Individual>> getAllIndividualsByIdAndIsDefiningOntology(
 
         return new ResponseEntity<>(assembler.toModel(terms, individualAssembler), HttpStatus.OK);
     }
-    
+
 
     @ResponseStatus(value = HttpStatus.NOT_FOUND, reason = "EntityModel not found")
     @ExceptionHandler(ResourceNotFoundException.class)
     public void handleError(HttpServletRequest req, Exception exception) {
     }
 
-}
+}

backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1OntologyController.java

@@ -7,6 +7,7 @@
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.Page;
+import org.springframework.data.domain.PageImpl;
 import org.springframework.data.domain.Pageable;
 import org.springframework.data.rest.webmvc.RepositoryLinksResource;
 import org.springframework.data.rest.webmvc.ResourceNotFoundException;
@@ -22,10 +23,14 @@
 import org.springframework.http.HttpStatus;
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;
-import org.springframework.stereotype.Controller;
 import org.springframework.web.bind.annotation.*;
+
+import io.swagger.v3.oas.annotations.Parameter;
+import uk.ac.ebi.spot.ols.model.FilterOption;
 import uk.ac.ebi.spot.ols.model.v1.V1Ontology;
 import uk.ac.ebi.spot.ols.repository.v1.V1OntologyRepository;
+import java.lang.reflect.*;
+import java.util.*;
 
 import javax.servlet.http.HttpServletRequest;
 
@@ -34,6 +39,7 @@
  * @date 19/08/2015
  * Samples, Phenotypes and Ontologies Team, EMBL-EBI
  */
+
 @Tag(name = "Ontology Controller")
 @RestController
 @RequestMapping("/api/ontologies")
@@ -86,6 +92,65 @@ HttpEntity<EntityModel<V1Ontology>> getOntology(
         return new ResponseEntity<>( documentAssembler.toModel(document), HttpStatus.OK);
     }
 
+    @RequestMapping(path = "/filterby", produces = {MediaType.APPLICATION_JSON_VALUE, MediaTypes.HAL_JSON_VALUE}, method = RequestMethod.GET)
+    HttpEntity<PagedModel<V1Ontology>> getOntologiesByMetadata(
+    		@RequestParam(value = "schema", required = true) Collection<String> schemas,
+    		@RequestParam(value = "classification", required = true) Collection<String> classifications,
+    		@Parameter(description = "Set to true (default setting is false) for intersection (default behavior is union) of classifications.")
+    		@RequestParam(value = "exclusive", required = false, defaultValue = "false") boolean exclusive,
+            @Parameter(description = "Use License option to filter based on license.label, license.logo and license.url variables. " +
+                    "Use Composite Option to filter based on the objects (i.e. collection, subject) within the classifications variable. " +
+                    "Use Linear option to filter based on String and Collection<String> based variables.")
+            @RequestParam(value = "option", required = false, defaultValue = "LINEAR") FilterOption filterOption,
+            @PageableDefault(size = 100, page = 0) Pageable pageable,
+            @RequestParam(value = "lang", required = false, defaultValue = "en") String lang,
+            PagedResourcesAssembler assembler
+    ) throws ResourceNotFoundException {
+        Set<V1Ontology> tempSet = new HashSet<V1Ontology>();
+        if (filterOption == FilterOption.LINEAR)
+            tempSet = ontologyRepository.filter(schemas,classifications,exclusive, lang);
+        else if (filterOption == FilterOption.COMPOSITE)
+            tempSet = ontologyRepository.filterComposite(schemas,classifications,exclusive, lang);
+        else if (filterOption == FilterOption.LICENSE)
+            tempSet = ontologyRepository.filterLicense(schemas,classifications,exclusive,lang);
+        List<V1Ontology> tempList = new ArrayList<V1Ontology>();
+        tempList.addAll(tempSet);
+        final int start = (int)pageable.getOffset();
+        final int end = Math.min((start + pageable.getPageSize()), tempSet.size());
+        Page<V1Ontology> document = new PageImpl<>(tempList.subList(start, end), pageable, tempSet.size());
+
+        return new ResponseEntity<>( assembler.toModel(document, documentAssembler), HttpStatus.OK);
+    }
+
+    @RequestMapping(path = "/schemakeys", produces = {MediaType.APPLICATION_JSON_VALUE, MediaTypes.HAL_JSON_VALUE}, method = RequestMethod.GET)
+    HttpEntity<Page<String>> filterKeys(
+            @PageableDefault(size = 100, page = 0) Pageable pageable,
+            @RequestParam(value = "lang", required = false, defaultValue = "en") String lang,
+            PagedResourcesAssembler assembler){
+        Set<String> tempSet = ontologyRepository.getSchemaKeys(lang);
+        List<String> tempList = new ArrayList<String>();
+        tempList.addAll(tempSet);
+        final int start = (int)pageable.getOffset();
+        final int end = Math.min((start + pageable.getPageSize()), tempSet.size());
+        Page<String> document = new PageImpl<>(tempList.subList(start, end), pageable, tempSet.size());
+        return new ResponseEntity<>(document, HttpStatus.OK);
+    }
+
+    @RequestMapping(path = "/schemavalues", produces = {MediaType.APPLICATION_JSON_VALUE, MediaTypes.HAL_JSON_VALUE}, method = RequestMethod.GET)
+    HttpEntity<Page<String>> filterValues(
+            @RequestParam(value = "schema", required = true) Collection<String> schemas,
+            @PageableDefault(size = 100, page = 0) Pageable pageable,
+            @RequestParam(value = "lang", required = false, defaultValue = "en") String lang,
+            PagedResourcesAssembler assembler){
+        Set<String> tempSet = ontologyRepository.getSchemaValues(schemas,lang);
+        List<String> tempList = new ArrayList<String>();
+        tempList.addAll(tempSet);
+        final int start = (int)pageable.getOffset();
+        final int end = Math.min((start + pageable.getPageSize()), tempSet.size());
+        Page<String> document = new PageImpl<>(tempList.subList(start, end), pageable, tempSet.size());
+        return new ResponseEntity<>(document, HttpStatus.OK);
+    }
+
     @ResponseStatus(value = HttpStatus.NOT_FOUND, reason = "EntityModel not found")
     @ExceptionHandler(ResourceNotFoundException.class)
     public void handleError(HttpServletRequest req, Exception exception) {

backend/src/main/java/uk/ac/ebi/spot/ols/controller/api/v1/V1OntologyPropertyController.java

@@ -23,8 +23,10 @@
 import org.springframework.web.util.UriUtils;
 import uk.ac.ebi.spot.ols.model.v1.V1Property;
 import uk.ac.ebi.spot.ols.repository.v1.V1JsTreeRepository;
+import uk.ac.ebi.spot.ols.repository.v1.V1JsTreeRepositoryExtn;
 import uk.ac.ebi.spot.ols.repository.v1.V1PropertyRepository;
 import uk.ac.ebi.spot.ols.service.Neo4jClient;
+import uk.ac.ebi.spot.ols.service.ViewMode;
 
 import javax.servlet.http.HttpServletRequest;
 import java.util.Arrays;
@@ -43,6 +45,9 @@ public class V1OntologyPropertyController {
 
     @Autowired
     V1JsTreeRepository jsTreeRepository;
+
+    @Autowired
+    V1JsTreeRepositoryExtn jsTreeRepositoryExtn;
 
     @Autowired
     Neo4jClient neo4jClient;
@@ -269,7 +274,7 @@ HttpEntity<String> getJsTree(
         try {
             String decoded = UriUtils.decode(termId, "UTF-8");
 
-            Object object= jsTreeRepository.getJsTreeForProperty(decoded, ontologyId, lang);
+            Object object= jsTreeRepositoryExtn.getJsTreeForPropertyByViewMode(decoded, ontologyId, lang, ViewMode.getFromShortName(viewMode), siblings);
             ObjectWriter ow = new ObjectMapper().writer().withDefaultPrettyPrinter();
             return new HttpEntity<String>(ow.writeValueAsString(object));
         } catch (JsonProcessingException e) {