Iss376 migrate gwas UI from old spring 1.4.1 to spring 2.7.15

goci-interfaces/goci-ui/pom.xml

@@ -42,7 +42,7 @@
                 <enabled>true</enabled>
             </snapshots>
         </repository>
-      <repository>
+        <repository>
             <id>central</id>
             <name>Maven Central</name>
             <layout>default</layout>
@@ -71,18 +71,27 @@
         <dependency>
             <groupId>org.apache.httpcomponents</groupId>
             <artifactId>httpclient</artifactId>
-            <version>4.5.2</version>
         </dependency>
 
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-web</artifactId>
-            <version>1.4.1.RELEASE</version>
         </dependency>
+
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-validation</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.springframework.data</groupId>
+            <artifactId>spring-data-commons</artifactId>
+        </dependency>
+
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-thymeleaf</artifactId>
         </dependency>
+
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-actuator</artifactId>
@@ -91,8 +100,10 @@
         <dependency>
             <groupId>joda-time</groupId>
             <artifactId>joda-time</artifactId>
+            <version>2.9.1</version>
         </dependency>
 
+
         <dependency>
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-lang3</artifactId>
@@ -103,10 +114,10 @@
             <groupId>org.springframework.hateoas</groupId>
             <artifactId>spring-hateoas</artifactId>
         </dependency>
-        <dependency>
-            <groupId>org.springframework.data</groupId>
-            <artifactId>spring-data-rest-hal-browser</artifactId>
-        </dependency>
+<!--        <dependency>-->
+<!--            <groupId>org.springframework.data</groupId>-->
+<!--            <artifactId>spring-data-rest-hal-browser</artifactId>-->
+<!--        </dependency>-->
 
         <dependency>
             <groupId>org.springframework.boot</groupId>
@@ -134,21 +145,23 @@
             <artifactId>jackson-dataformat-csv</artifactId>
             <version>2.9.9</version>
         </dependency>
-        <dependency>
-            <groupId>com.fasterxml.jackson.core</groupId>
-            <artifactId>jackson-core</artifactId>
-            <version>2.9.9</version>
-        </dependency>
-        <dependency>
-            <groupId>com.fasterxml.jackson.core</groupId>
-            <artifactId>jackson-databind</artifactId>
-            <version>2.9.9</version>
-        </dependency>
-        <dependency>
-            <groupId>com.fasterxml.jackson.core</groupId>
-            <artifactId>jackson-annotations</artifactId>
-            <version>2.9.9</version>
-        </dependency>
+
+
+<!--        <dependency>-->
+<!--            <groupId>com.fasterxml.jackson.core</groupId>-->
+<!--            <artifactId>jackson-core</artifactId>-->
+<!--            <version>2.9.9</version>-->
+<!--        </dependency>-->
+<!--        <dependency>-->
+<!--            <groupId>com.fasterxml.jackson.core</groupId>-->
+<!--            <artifactId>jackson-databind</artifactId>-->
+<!--            <version>2.9.9</version>-->
+<!--        </dependency>-->
+<!--        <dependency>-->
+<!--            <groupId>com.fasterxml.jackson.core</groupId>-->
+<!--            <artifactId>jackson-annotations</artifactId>-->
+<!--            <version>2.9.9</version>-->
+<!--        </dependency>-->
     </dependencies>
 
     <properties>

goci-interfaces/goci-ui/src/main/java/uk/ac/ebi/spot/goci/SearchApplication.java

@@ -2,7 +2,7 @@
 
 import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
-import org.springframework.boot.web.support.SpringBootServletInitializer;
+import org.springframework.boot.web.servlet.support.SpringBootServletInitializer;
 import org.springframework.scheduling.annotation.EnableScheduling;
 
 @SpringBootApplication(scanBasePackages = "uk.ac.ebi.spot.goci")

goci-interfaces/goci-ui/src/main/java/uk/ac/ebi/spot/goci/model/solr/Doc.java

@@ -1,15 +1,12 @@
 package uk.ac.ebi.spot.goci.model.solr;
 
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.annotation.JsonProperty;
+
 import java.io.Serializable;
 import java.util.List;
 import java.util.Set;
 
-import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
-import com.fasterxml.jackson.annotation.JsonProperty;
-import lombok.AllArgsConstructor;
-import lombok.Data;
-import lombok.NoArgsConstructor;
-
 
 //@Builder
 @JsonIgnoreProperties(ignoreUnknown = true)

goci-interfaces/goci-ui/src/main/java/uk/ac/ebi/spot/goci/model/solr/Params.java

@@ -1,7 +1,6 @@
 package uk.ac.ebi.spot.goci.model.solr;
 
 import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
-import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonProperty;
 import com.fasterxml.jackson.annotation.JsonPropertyOrder;
 import lombok.AllArgsConstructor;

goci-interfaces/goci-ui/src/main/java/uk/ac/ebi/spot/goci/model/solr/Response.java

@@ -1,15 +1,14 @@
 package uk.ac.ebi.spot.goci.model.solr;
 
-import java.util.List;
 import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonProperty;
 import com.fasterxml.jackson.annotation.JsonPropertyOrder;
 import lombok.AllArgsConstructor;
 import lombok.Builder;
 import lombok.Data;
 import lombok.NoArgsConstructor;
-import uk.ac.ebi.spot.goci.model.solr.Doc;
-import uk.ac.ebi.spot.goci.refactoring.model.StudyDoc;
+
+import java.util.List;
 
 @Data
 @Builder

goci-interfaces/goci-ui/src/main/java/uk/ac/ebi/spot/goci/model/solr/ResponseHeader.java

@@ -7,7 +7,6 @@
 import lombok.Builder;
 import lombok.Data;
 import lombok.NoArgsConstructor;
-import uk.ac.ebi.spot.goci.model.solr.Params;
 
 @Data
 @Builder

goci-interfaces/goci-ui/src/main/java/uk/ac/ebi/spot/goci/model/solr/SolrData.java

@@ -1,8 +1,8 @@
 package uk.ac.ebi.spot.goci.model.solr;
 
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.fasterxml.jackson.annotation.JsonProperty;
 import com.fasterxml.jackson.annotation.JsonPropertyOrder;
-import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import lombok.AllArgsConstructor;
 import lombok.Builder;
 import lombok.Data;

goci-interfaces/goci-ui/src/main/java/uk/ac/ebi/spot/goci/model/solr/SumStatDownloadDto.java

@@ -7,8 +7,6 @@
 import lombok.Data;
 import lombok.NoArgsConstructor;
 
-import java.util.List;
-
 @Data
 @Builder
 @AllArgsConstructor

goci-interfaces/goci-ui/src/main/java/uk/ac/ebi/spot/goci/refactoring/component/EFOTraitIdentifierMap.java

@@ -6,7 +6,6 @@
 import org.springframework.stereotype.Component;
 import uk.ac.ebi.spot.goci.refactoring.service.RestAPIEFOService;
 import uk.ac.ebi.spot.goci.ui.SearchConfiguration;
-import uk.ac.ebi.spot.goci.ui.cache.EFOTraitMapperCache;
 
 import java.util.HashMap;
 import java.util.Map;

goci-interfaces/goci-ui/src/main/java/uk/ac/ebi/spot/goci/refactoring/component/SumstatsIdentifierMap.java

@@ -6,7 +6,6 @@
 import org.springframework.stereotype.Component;
 import uk.ac.ebi.spot.goci.refactoring.service.SumstatsAPIService;
 import uk.ac.ebi.spot.goci.ui.SearchConfiguration;
-import uk.ac.ebi.spot.goci.ui.cache.SSMapperCache;
 
 import java.util.HashMap;
 import java.util.Map;

goci-interfaces/goci-ui/src/main/java/uk/ac/ebi/spot/goci/refactoring/dto/AssociationSolrDTO.java

@@ -7,8 +7,8 @@
 import lombok.Builder;
 import lombok.EqualsAndHashCode;
 import org.joda.time.LocalDate;
-import org.springframework.hateoas.ResourceSupport;
-import org.springframework.hateoas.core.Relation;
+import org.springframework.hateoas.RepresentationModel;
+import org.springframework.hateoas.server.core.Relation;
 import uk.ac.ebi.spot.goci.refactoring.model.EFOKeyLabel;
 import uk.ac.ebi.spot.goci.refactoring.util.JsonJodaLocalDateSerializer;
 
@@ -21,8 +21,8 @@
 @JsonPropertyOrder({"riskAllele","riskFrequency","pValueExponent","pValue","pValueAnnotation","orValue","beta",
 "ci","mappedGenes","traitName","efoTraits","bgTraits","locations","author","publicationDate","accessionId","riskAlleleSep",
 "chromLocation","pubmedId"})
-@Relation(value = "association", collectionRelation = "associations")
-public class AssociationSolrDTO extends ResourceSupport implements Serializable {
+@Relation(itemRelation = "association", collectionRelation = "associations")
+public class AssociationSolrDTO extends RepresentationModel<AssociationSolrDTO> implements Serializable {
 
     @JsonProperty("riskAllele")
     public List<EFOKeyLabel> riskAllele;

goci-interfaces/goci-ui/src/main/java/uk/ac/ebi/spot/goci/refactoring/dto/AssociationSolrDTOAssembler.java

@@ -4,24 +4,22 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.hateoas.Resource;
-import org.springframework.hateoas.ResourceAssembler;
-import org.springframework.hateoas.mvc.ControllerLinkBuilder;
+import org.springframework.hateoas.server.mvc.RepresentationModelAssemblerSupport;
 import org.springframework.stereotype.Component;
 import uk.ac.ebi.spot.goci.refactoring.model.AssociationDoc;
 import uk.ac.ebi.spot.goci.refactoring.model.EFOKeyLabel;
 import uk.ac.ebi.spot.goci.refactoring.rest.SolrSearchPublicationController;
 import uk.ac.ebi.spot.goci.refactoring.util.SolrEntityTransformerUtility;
 import uk.ac.ebi.spot.goci.ui.SearchConfiguration;
-import uk.ac.ebi.spot.goci.ui.constants.SearchUIConstants;
-import uk.ac.ebi.spot.goci.util.BackendUtil;
 
-import java.io.IOException;
 import java.util.*;
 import java.util.stream.Collectors;
 
+import static org.springframework.hateoas.server.mvc.WebMvcLinkBuilder.linkTo;
+import static org.springframework.hateoas.server.mvc.WebMvcLinkBuilder.methodOn;
+
 @Component
-public class AssociationSolrDTOAssembler implements ResourceAssembler<AssociationDoc, Resource<AssociationSolrDTO>> {
+public class AssociationSolrDTOAssembler extends RepresentationModelAssemblerSupport<AssociationDoc, AssociationSolrDTO> {
 
     private static final Logger log = LoggerFactory.getLogger(StudySolrDTOAssembler.class);
 
@@ -31,20 +29,15 @@ public class AssociationSolrDTOAssembler implements ResourceAssembler<Associatio
     @Autowired
     SolrEntityTransformerUtility solrEntityTransformerUtility;
 
-    @Override
-    public Resource<AssociationSolrDTO> toResource(AssociationDoc associationDoc) {
+    public AssociationSolrDTOAssembler() {
+        super(SolrSearchPublicationController.class, AssociationSolrDTO.class);
+    }
 
+    @Override
+    public AssociationSolrDTO toModel(AssociationDoc associationDoc) {
         AssociationSolrDTO associationSolrDTO = assemble(associationDoc);
-        try {
-            final ControllerLinkBuilder lb = ControllerLinkBuilder.linkTo(
-                    ControllerLinkBuilder.methodOn(SolrSearchPublicationController.class).searchAssociations(null, "Pmid", null, null));
-            Resource<AssociationSolrDTO> resource = new Resource<>(associationSolrDTO);
-            resource.add(BackendUtil.underBasePath(lb, searchConfiguration.getProxy_prefix()).withSelfRel());
-            return resource;
-        } catch(IOException ex ){
-            log.error("IO Exception "+ex.getMessage(),ex);
-        }
-        return null;
+        //associationSolrDTO.add(linkTo(methodOn(SolrSearchPublicationController.class)).withSelfRel());
+        return associationSolrDTO;
     }
 
     public AssociationSolrDTO assemble(AssociationDoc associationDoc) {

goci-interfaces/goci-ui/src/main/java/uk/ac/ebi/spot/goci/refactoring/dto/EFOTableExportDTO.java

@@ -23,7 +23,6 @@ public class EFOTableExportDTO {
     @JsonProperty("associationCount")
     private Integer associationCount;
 
-
     public EFOTableExportDTO(@JsonProperty("efoTraits") String efoTraits,
                            @JsonProperty("reportedTrait") String reportedTrait,
                            @JsonProperty("associationCount") Integer associationCount) {

goci-interfaces/goci-ui/src/main/java/uk/ac/ebi/spot/goci/refactoring/dto/EFOTraitSolrDTO.java

@@ -1,20 +1,24 @@
 package uk.ac.ebi.spot.goci.refactoring.dto;
 
+import org.springframework.hateoas.RepresentationModel;
+import org.springframework.hateoas.server.core.Relation;
+
+import java.io.Serializable;
+
+
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonProperty;
 import lombok.Builder;
 import lombok.EqualsAndHashCode;
-import org.springframework.hateoas.ResourceSupport;
-import org.springframework.hateoas.core.Relation;
 import uk.ac.ebi.spot.goci.refactoring.model.EFOKeyLabel;
 
 import java.io.Serializable;
 import java.util.List;
 @EqualsAndHashCode
 @Builder
 @JsonInclude(JsonInclude.Include.NON_NULL)
-@Relation(value = "efoData", collectionRelation = "efos")
-public class EFOTraitSolrDTO extends ResourceSupport implements Serializable {
+@Relation(itemRelation = "efoData", collectionRelation = "efos")
+public class EFOTraitSolrDTO extends RepresentationModel<EFOTraitSolrDTO> implements Serializable {
 
     @JsonProperty("efoTraits")
     private List<EFOKeyLabel> efoTraits;

goci-interfaces/goci-ui/src/main/java/uk/ac/ebi/spot/goci/refactoring/dto/EFOTraitSolrDTOAssembler.java

@@ -3,44 +3,47 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.hateoas.Resource;
-import org.springframework.hateoas.ResourceAssembler;
-import org.springframework.hateoas.mvc.ControllerLinkBuilder;
+import org.springframework.hateoas.server.mvc.RepresentationModelAssemblerSupport;
 import org.springframework.stereotype.Component;
 import uk.ac.ebi.spot.goci.refactoring.model.EFOKeyLabel;
 import uk.ac.ebi.spot.goci.refactoring.model.EFOTraitDoc;
 import uk.ac.ebi.spot.goci.refactoring.rest.SolrSearchVariantController;
 import uk.ac.ebi.spot.goci.ui.SearchConfiguration;
-import uk.ac.ebi.spot.goci.util.BackendUtil;
 
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Collections;
 import java.util.List;
 import java.util.Objects;
 import java.util.stream.Collectors;
 
+import static org.springframework.hateoas.server.mvc.WebMvcLinkBuilder.linkTo;
+import static org.springframework.hateoas.server.mvc.WebMvcLinkBuilder.methodOn;
+
 @Component
-public class EFOTraitSolrDTOAssembler implements ResourceAssembler<EFOTraitDoc, Resource<EFOTraitSolrDTO>> {
+public class EFOTraitSolrDTOAssembler extends RepresentationModelAssemblerSupport<EFOTraitDoc, EFOTraitSolrDTO> {
 
     private static final Logger log = LoggerFactory.getLogger(EFOTraitSolrDTOAssembler.class);
     @Autowired
     SearchConfiguration searchConfiguration;
 
+    public EFOTraitSolrDTOAssembler() {
+        super(SolrSearchVariantController.class, EFOTraitSolrDTO.class);
+    }
+
     @Override
-    public Resource<EFOTraitSolrDTO> toResource(EFOTraitDoc efoTraitDoc) {
+    public EFOTraitSolrDTO toModel(EFOTraitDoc efoTraitDoc) {
         EFOTraitSolrDTO efoTraitSolrDTO = assemble(efoTraitDoc);
+        efoTraitSolrDTO.add(linkTo(methodOn(SolrSearchVariantController.class)).withSelfRel());
+        return efoTraitSolrDTO;
 
-        try {
-            final ControllerLinkBuilder lb = ControllerLinkBuilder.linkTo(
-                    ControllerLinkBuilder.methodOn(SolrSearchVariantController.class).searchEFOTraits(null, "rs123456", null, null));
-            Resource<EFOTraitSolrDTO> resource = new Resource<>(efoTraitSolrDTO);
-            resource.add(BackendUtil.underBasePath(lb, searchConfiguration.getProxy_prefix()).withSelfRel());
-            return resource;
-        } catch (IOException ex) {
-            log.error("IO Exception " + ex.getMessage(), ex);
-        }
-        return null;
+//        try {
+//            final ControllerLinkBuilder lb = ControllerLinkBuilder.linkTo(
+//                    ControllerLinkBuilder.methodOn(SolrSearchVariantController.class).searchEFOTraits(null, "rs123456", null, null));
+//            Resource<EFOTraitSolrDTO> resource = new Resource<>(efoTraitSolrDTO);
+//            resource.add(BackendUtil.underBasePath(lb, searchConfiguration.getProxy_prefix()).withSelfRel());
+//            return resource;
+//        } catch (IOException ex) {
+//            log.error("IO Exception " + ex.getMessage(), ex);
+//        }
+//        return null;
     }
 
     public EFOTraitSolrDTO assemble(EFOTraitDoc efoTraitDoc) {