Added a metadata table - one-to-many relationship apporach

src/main/java/uk/ac/ebi/eva/evaseqcol/controller/admin/AdminController.java

@@ -22,7 +22,6 @@
 import uk.ac.ebi.eva.evaseqcol.service.SeqColService;
 
 import java.io.IOException;
-import java.util.List;
 
 @RequestMapping("/admin")
 @RestController

src/main/java/uk/ac/ebi/eva/evaseqcol/controller/seqcol/MetadataController.java

@@ -0,0 +1,37 @@
+package uk.ac.ebi.eva.evaseqcol.controller.seqcol;
+
+import io.swagger.v3.oas.annotations.tags.Tag;
+import org.springframework.http.ResponseEntity;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RestController;
+
+import uk.ac.ebi.eva.evaseqcol.dto.SeqColMetadataDTO;
+import uk.ac.ebi.eva.evaseqcol.service.MetadataService;
+
+import java.util.List;
+import java.util.stream.Collectors;
+
+@RestController
+@RequestMapping("/metadata/")
+@Tag(name = "Seqcol metadata")
+public class MetadataController {
+
+    private final MetadataService metadataService;
+
+    public MetadataController(MetadataService metadataService) {
+        this.metadataService = metadataService;
+    }
+
+    @GetMapping(value = "/{digest}")
+    public ResponseEntity<List<SeqColMetadataDTO>> getSeqColMetadataByDigest(@PathVariable String digest) {
+        List<SeqColMetadataDTO> metadataList = metadataService.getMetadataBySeqColDigest(digest).stream()
+                .map(SeqColMetadataDTO::toMetadataDTO)
+                .collect(Collectors.toList());
+        if (metadataList.isEmpty()) {
+            return ResponseEntity.notFound().build();
+        }
+        return ResponseEntity.ok(metadataList);
+    }
+}

src/main/java/uk/ac/ebi/eva/evaseqcol/dto/SeqColMetadataDTO.java

@@ -0,0 +1,30 @@
+package uk.ac.ebi.eva.evaseqcol.dto;
+
+import lombok.AllArgsConstructor;
+import lombok.Data;
+import lombok.NoArgsConstructor;
+
+import uk.ac.ebi.eva.evaseqcol.entities.SeqColEntity;
+import uk.ac.ebi.eva.evaseqcol.entities.SeqColMetadataEntity;
+
+import java.util.Date;
+
+@Data
+@NoArgsConstructor
+@AllArgsConstructor
+public class SeqColMetadataDTO {
+
+    private String sourceId;
+    private String sourceUrl;
+    private SeqColEntity.NamingConvention namingConvention;
+    private Date timestamp;
+
+    public static SeqColMetadataDTO toMetadataDTO(SeqColMetadataEntity metadataEntity) {
+        return new SeqColMetadataDTO(
+                metadataEntity.getSourceIdentifier(),
+                metadataEntity.getSourceUrl(),
+                metadataEntity.getNamingConvention(),
+                metadataEntity.getTimestamp()
+        );
+    }
+}

src/main/java/uk/ac/ebi/eva/evaseqcol/entities/SeqColEntity.java

@@ -17,8 +17,6 @@ public abstract class SeqColEntity {
 
     protected String digest; // The level 0 digest
 
-    protected NamingConvention namingConvention;
-
 
     public enum NamingConvention {
         ENA, GENBANK, UCSC, TEST

src/main/java/uk/ac/ebi/eva/evaseqcol/entities/SeqColLevelOneEntity.java

@@ -1,26 +1,24 @@
 package uk.ac.ebi.eva.evaseqcol.entities;
 
 import lombok.Data;
-import lombok.NoArgsConstructor;
 import org.hibernate.annotations.Type;
 
 import uk.ac.ebi.eva.evaseqcol.utils.JSONLevelOne;
 
 import javax.persistence.Basic;
+import javax.persistence.CascadeType;
 import javax.persistence.Column;
 import javax.persistence.Entity;
-import javax.persistence.EnumType;
-import javax.persistence.Enumerated;
 import javax.persistence.FetchType;
 import javax.persistence.Id;
-import javax.persistence.IdClass;
+import javax.persistence.OneToMany;
 import javax.persistence.Table;
+import java.util.ArrayList;
+import java.util.List;
 
 @Entity
-@NoArgsConstructor
 @Data
 @Table(name = "sequence_collections_L1")
-@IdClass(SeqColId.class)
 public class SeqColLevelOneEntity extends SeqColEntity{
 
     @Id
@@ -32,15 +30,25 @@ public class SeqColLevelOneEntity extends SeqColEntity{
     @Basic(fetch = FetchType.LAZY)
     private JSONLevelOne seqColLevel1Object;
 
-    @Id
-    @Column(nullable = false)
-    @Enumerated(EnumType.STRING)
-    protected NamingConvention namingConvention;
+    @OneToMany(mappedBy = "seqColLevelOne", cascade = CascadeType.ALL)
+    private List<SeqColMetadataEntity> metadata;
+
+    public SeqColLevelOneEntity() {
+        this.metadata = new ArrayList<>();
+    }
 
-    public SeqColLevelOneEntity(String digest, NamingConvention namingConvention, JSONLevelOne jsonLevelOne){
-        super(digest, namingConvention);
+    public SeqColLevelOneEntity(String digest, JSONLevelOne jsonLevelOne, List<SeqColMetadataEntity> metadata){
+        super(digest);
         this.seqColLevel1Object = jsonLevelOne;
-        this.namingConvention = namingConvention;
+        this.metadata = metadata;
+    }
+
+    public void addMetadata(SeqColMetadataEntity metadata){
+        this.metadata.add(metadata);
+    }
+
+    public void addAllMetadata(List<SeqColMetadataEntity> metadata){
+        this.metadata.addAll(metadata);
     }
 
     @Override

src/main/java/uk/ac/ebi/eva/evaseqcol/entities/SeqColLevelTwoEntity.java

@@ -24,9 +24,4 @@ public SeqColLevelTwoEntity setDigest(String digest) {
         this.digest = digest;
         return this;
     }
-
-    public SeqColLevelTwoEntity setNamingConvention(NamingConvention convention) {
-        this.namingConvention = convention;
-        return this;
-    }
 }

src/main/java/uk/ac/ebi/eva/evaseqcol/entities/SeqColMetadataEntity.java

@@ -0,0 +1,86 @@
+package uk.ac.ebi.eva.evaseqcol.entities;
+
+import lombok.Data;
+import org.hibernate.annotations.CreationTimestamp;
+import org.hibernate.annotations.OnDelete;
+import org.hibernate.annotations.OnDeleteAction;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.EnumType;
+import javax.persistence.Enumerated;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.Table;
+import javax.persistence.Temporal;
+import javax.persistence.TemporalType;
+import java.sql.Timestamp;
+import java.util.Date;
+import java.util.Objects;
+
+@Entity
+@Table(name = "seqcol_md")
+@Data
+public class SeqColMetadataEntity {
+
+    @Id
+    @GeneratedValue(strategy = GenerationType.IDENTITY)
+    @Column(name = "md_id")
+    private Long mdId;
+
+    @Column(name = "source_id")
+    private String sourceIdentifier;  // Eg: INSDC Acession
+
+    private String sourceUrl;
+
+    @Enumerated(EnumType.STRING)
+    private SeqColEntity.NamingConvention namingConvention;
+
+    @Column(updatable = false)
+    @Temporal(TemporalType.TIMESTAMP)
+    @CreationTimestamp
+    private Date timestamp;
+
+    @ManyToOne(fetch = FetchType.LAZY, optional = false)
+    @JoinColumn(name = "seqcol_digest")
+    @OnDelete(action = OnDeleteAction.CASCADE)
+    private SeqColLevelOneEntity seqColLevelOne;
+
+    public SeqColMetadataEntity setTimestamp(Timestamp timestamp) {
+        this.timestamp = timestamp;
+        return this;
+    }
+
+    public SeqColMetadataEntity setSourceIdentifier(String sourceIdentifier) {
+        this.sourceIdentifier = sourceIdentifier;
+        return this;
+    }
+
+    public SeqColMetadataEntity setSourceUrl(String sourceUrl) {
+        this.sourceUrl = sourceUrl;
+        return this;
+    }
+
+    public SeqColMetadataEntity setNamingConvention(SeqColEntity.NamingConvention namingConvention) {
+        this.namingConvention = namingConvention;
+        return this;
+    }
+
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (!(o instanceof SeqColMetadataEntity)) return false;
+        SeqColMetadataEntity that = (SeqColMetadataEntity) o;
+        return Objects.equals(sourceIdentifier, that.sourceIdentifier) && Objects.equals(sourceUrl, that.sourceUrl)
+                && namingConvention == that.namingConvention && Objects.equals(seqColLevelOne, that.seqColLevelOne);
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hash(sourceIdentifier, sourceUrl, namingConvention, seqColLevelOne);
+    }
+}

src/main/java/uk/ac/ebi/eva/evaseqcol/repo/MetadataRepository.java

@@ -0,0 +1,17 @@
+package uk.ac.ebi.eva.evaseqcol.repo;
+
+import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.data.jpa.repository.Query;
+import org.springframework.stereotype.Repository;
+
+import uk.ac.ebi.eva.evaseqcol.entities.SeqColMetadataEntity;
+
+import java.util.List;
+
+@Repository
+public interface MetadataRepository extends JpaRepository<SeqColMetadataEntity, Long> {
+
+    @Query(value = "select source_id from seqcol_md",nativeQuery = true)
+    List<String> findAllSourceIds();
+
+}

src/main/java/uk/ac/ebi/eva/evaseqcol/repo/SeqColLevelOneRepository.java

@@ -5,13 +5,15 @@
 
 import uk.ac.ebi.eva.evaseqcol.entities.SeqColLevelOneEntity;
 
+import java.util.Optional;
+
 @Repository
 public interface SeqColLevelOneRepository extends JpaRepository<SeqColLevelOneEntity, String> {
-    SeqColLevelOneEntity findSeqColLevelOneEntityByDigest(String digest);
-
+    Optional<SeqColLevelOneEntity> findSeqColLevelOneEntityByDigest(String digest);
     long countSeqColLevelOneEntitiesByDigest(String digest);
 
     void removeSeqColLevelOneEntityByDigest(String digest);
 
     void deleteAll();
+
 }

src/main/java/uk/ac/ebi/eva/evaseqcol/service/MetadataService.java

@@ -0,0 +1,34 @@
+package uk.ac.ebi.eva.evaseqcol.service;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+
+import uk.ac.ebi.eva.evaseqcol.entities.SeqColMetadataEntity;
+import uk.ac.ebi.eva.evaseqcol.repo.MetadataRepository;
+
+import java.util.List;
+import java.util.stream.Collectors;
+
+
+@Service
+public class MetadataService {
+
+    private final MetadataRepository metadataRepository;
+
+    @Autowired
+    public MetadataService(MetadataRepository metadataRepository) {
+        this.metadataRepository = metadataRepository;
+    }
+
+    public List<SeqColMetadataEntity> getMetadataBySeqColDigest(String seqColDigest) {
+        return metadataRepository.findAll().stream()
+                                 .filter(metadataEntity -> metadataEntity.getSeqColLevelOne().getDigest().equals(seqColDigest))
+                                 .collect(Collectors.toList());
+    }
+    /**
+     * Return the list of all saved source identifiers. Eg: ["GCA_000146045.2", ...]
+     * */
+    public List<String> getAllSourceIds() {
+        return metadataRepository.findAllSourceIds();
+    }
+}