Recursive approach

pom.xml

@@ -147,6 +147,18 @@
             <version>1.2.5.RELEASE</version>
         </dependency>
 
+        <dependency>
+            <groupId>org.projectlombok</groupId>
+            <artifactId>lombok</artifactId>
+            <version>1.18.28</version>
+            <scope>provided</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>com.vladmihalcea</groupId>
+            <artifactId>hibernate-types-52</artifactId>
+            <version>2.3.4</version>
+        </dependency>
     </dependencies>
 
     <build>
@@ -178,6 +190,23 @@
                     </includeOnlyProperties>
                 </configuration>
             </plugin>
+
+            <plugin>
+                <groupId>org.hibernate.orm.tooling</groupId>
+                <artifactId>hibernate-enhance-maven-plugin</artifactId>
+                <version>5.4.1.Final</version>
+                <executions>
+                    <execution>
+                        <configuration>
+                            <failOnError>true</failOnError>
+                            <enableLazyInitialization>true</enableLazyInitialization>
+                        </configuration>
+                        <goals>
+                            <goal>enhance</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
         </plugins>
 
         <resources>

src/main/java/uk/ac/ebi/eva/contigalias/entities/JSONObjectL1.java

@@ -0,0 +1,32 @@
+package uk.ac.ebi.eva.contigalias.entities;
+
+import lombok.AllArgsConstructor;
+import lombok.Data;
+import lombok.NoArgsConstructor;
+
+import java.io.Serializable;
+
+@Data
+@AllArgsConstructor
+@NoArgsConstructor
+public class JSONObjectL1 implements Serializable {
+    private String sequences;
+    private String names;
+    private String lengths;
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

src/main/java/uk/ac/ebi/eva/contigalias/entities/JSONObjectL2.java

@@ -0,0 +1,18 @@
+package uk.ac.ebi.eva.contigalias.entities;
+
+import lombok.AllArgsConstructor;
+import lombok.Data;
+import lombok.NoArgsConstructor;
+
+import java.io.Serializable;
+import java.util.List;
+
+@Data
+@AllArgsConstructor
+@NoArgsConstructor
+public class JSONObjectL2 implements Serializable {
+    private List<Integer> lengths; // Level 2 lengths array
+    private List<String> names; // Level 2 names array
+    private List<String> sequences; // Level 2 sequences array
+
+}

src/main/java/uk/ac/ebi/eva/contigalias/entities/NamingConvention.java

@@ -0,0 +1,42 @@
+package uk.ac.ebi.eva.contigalias.entities;
+
+import lombok.Data;
+import lombok.NoArgsConstructor;
+import lombok.ToString;
+
+import javax.persistence.*;
+import java.util.List;
+
+@Entity
+@Data
+@NoArgsConstructor
+@ToString
+@Table(name = "naming_conventions")
+public class NamingConvention {
+
+    @Id
+    @GeneratedValue(strategy = GenerationType.IDENTITY)
+    @Column(nullable = false)
+    private Long id;
+
+    @Column(nullable = false)
+    @Enumerated(EnumType.STRING)
+    private Convention convention;
+
+    @OneToOne(cascade = CascadeType.ALL)
+    @JoinColumn(name = "digest", referencedColumnName = "digest")
+    private SeqColL1 seqColL1;
+
+    /*@OneToOne
+    @JoinColumn(name = "digest")
+    private SeqColL1 seqCols;*/
+
+    public enum Convention {
+        ENA, GENBANK
+    }
+
+    public NamingConvention(Convention convention, SeqColL1 seqColL1){
+        this.convention = convention;
+        this.seqColL1 = seqColL1;
+    }
+}

src/main/java/uk/ac/ebi/eva/contigalias/entities/SeqCol.java

@@ -0,0 +1,28 @@
+package uk.ac.ebi.eva.contigalias.entities;
+
+import com.vladmihalcea.hibernate.type.json.JsonBinaryType;
+import lombok.AllArgsConstructor;
+import lombok.NoArgsConstructor;
+import lombok.ToString;
+import org.hibernate.annotations.TypeDef;
+import org.hibernate.annotations.TypeDefs;
+
+import javax.persistence.*;
+import java.util.List;
+
+@MappedSuperclass
+@TypeDefs({
+        @TypeDef(name = "jsonb", typeClass = JsonBinaryType.class)
+})
+@AllArgsConstructor
+@NoArgsConstructor
+@ToString
+public abstract class SeqCol {
+
+    @Id
+    @Column (name = "digest")
+    protected String digest; // The level 0 digest
+
+    /*@Transient
+    protected NamingConvention.Convention namingConvention;*/
+}

src/main/java/uk/ac/ebi/eva/contigalias/entities/SeqColL1.java

@@ -0,0 +1,31 @@
+package uk.ac.ebi.eva.contigalias.entities;
+
+import lombok.AllArgsConstructor;
+import lombok.Data;
+import lombok.NoArgsConstructor;
+import org.hibernate.annotations.Type;
+
+import javax.persistence.*;
+
+@Entity
+@NoArgsConstructor
+@AllArgsConstructor
+@Data
+@Table(name = "sequence_collections_L1")
+public class SeqColL1 extends SeqCol{
+
+    @Type(type = "jsonb")
+    @Column(columnDefinition = "jsonb")
+    @Basic(fetch = FetchType.LAZY)
+    private JSONObjectL1 object;
+
+    @OneToOne(mappedBy = "seqColL1")
+    private NamingConvention namingConvention;
+
+    public SeqColL1(String digest, JSONObjectL1 jsonObject, NamingConvention namingConvention){
+        super(digest);
+        this.namingConvention = namingConvention;
+        this.object = jsonObject;
+    }
+
+}

src/main/java/uk/ac/ebi/eva/contigalias/entities/SeqColL2.java

@@ -0,0 +1,26 @@
+package uk.ac.ebi.eva.contigalias.entities;
+
+import lombok.AllArgsConstructor;
+import lombok.Data;
+import lombok.NoArgsConstructor;
+import org.hibernate.annotations.Type;
+
+import javax.persistence.*;
+
+@Entity
+@NoArgsConstructor
+@AllArgsConstructor
+@Data
+@Table(name = "sequence_collections_L2")
+public class SeqColL2 extends SeqCol{
+
+    @Type(type = "jsonb")
+    @Column(columnDefinition = "jsonb")
+    @Basic(fetch = FetchType.LAZY)
+    private JSONObjectL2 object;
+
+    public SeqColL2(String digest, JSONObjectL2 jsonObject, NamingConvention.Convention namingConvention){
+        super(digest);
+        this.object = jsonObject;
+    }
+}

src/main/java/uk/ac/ebi/eva/contigalias/repo/NamingConventionRepository.java

@@ -0,0 +1,8 @@
+package uk.ac.ebi.eva.contigalias.repo;
+
+import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.stereotype.Repository;
+import uk.ac.ebi.eva.contigalias.entities.NamingConvention;
+@Repository
+public interface NamingConventionRepository extends JpaRepository<NamingConvention, Long> {
+}

src/main/java/uk/ac/ebi/eva/contigalias/repo/SeqColL1Repository.java

@@ -0,0 +1,9 @@
+package uk.ac.ebi.eva.contigalias.repo;
+
+import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.stereotype.Repository;
+import uk.ac.ebi.eva.contigalias.entities.SeqColL1;
+@Repository
+public interface SeqColL1Repository extends JpaRepository<SeqColL1, String> {
+
+}

src/main/java/uk/ac/ebi/eva/contigalias/repo/SeqColL2Repository.java

@@ -0,0 +1,10 @@
+package uk.ac.ebi.eva.contigalias.repo;
+
+import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.stereotype.Repository;
+import uk.ac.ebi.eva.contigalias.entities.SeqColL2;
+
+@Repository
+public interface SeqColL2Repository extends JpaRepository<SeqColL2, String> {
+
+}

src/main/java/uk/ac/ebi/eva/contigalias/service/NamingConventionService.java

@@ -0,0 +1,21 @@
+package uk.ac.ebi.eva.contigalias.service;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+import uk.ac.ebi.eva.contigalias.entities.NamingConvention;
+import uk.ac.ebi.eva.contigalias.repo.NamingConventionRepository;
+
+import java.util.Optional;
+
+@Service
+public class NamingConventionService {
+
+    @Autowired
+    private NamingConventionRepository repository;
+
+
+    public Optional<NamingConvention> addNamingConvention(NamingConvention namingConvention){
+        NamingConvention convention = repository.save(namingConvention);
+        return Optional.of(convention);
+    }
+}

src/main/java/uk/ac/ebi/eva/contigalias/service/SeqColL1Service.java

@@ -0,0 +1,28 @@
+package uk.ac.ebi.eva.contigalias.service;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+import uk.ac.ebi.eva.contigalias.entities.SeqColL1;
+import uk.ac.ebi.eva.contigalias.repo.SeqColL1Repository;
+
+import java.util.Optional;
+
+@Service
+public class SeqColL1Service {
+
+    @Autowired
+    private SeqColL1Repository repository;
+
+    /**
+     * Add a new Level 1 sequence collection object and save it to the
+     * database*/
+    public Optional<SeqColL1> addSequenceCollectionL1(SeqColL1 seqColL1){
+        SeqColL1 seqCol = repository.save(seqColL1);
+        return Optional.of(seqCol);
+    }
+
+    public Optional<SeqColL1> getSeqColL1ByDigest(String digest){
+        Optional<SeqColL1> seqColL11 = repository.findById(digest);
+        return seqColL11;
+    }
+}

src/main/java/uk/ac/ebi/eva/contigalias/service/SeqColL2Service.java

@@ -0,0 +1,20 @@
+package uk.ac.ebi.eva.contigalias.service;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+import uk.ac.ebi.eva.contigalias.entities.SeqColL2;
+import uk.ac.ebi.eva.contigalias.repo.SeqColL2Repository;
+
+import java.util.Optional;
+
+@Service
+public class SeqColL2Service {
+
+    @Autowired
+    private SeqColL2Repository repository;
+
+    public Optional<SeqColL2> addSequenceCollectionL2(SeqColL2 seqColL2){
+        SeqColL2 seqCol = repository.save(seqColL2);
+        return Optional.of(seqCol);
+    }
+}

src/test/java/uk/ac/ebi/eva/contigalias/service/NamingConventionServiceTest.java

@@ -0,0 +1,33 @@
+package uk.ac.ebi.eva.contigalias.service;
+
+import org.junit.jupiter.api.AfterEach;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.context.SpringBootTest;
+import uk.ac.ebi.eva.contigalias.entities.NamingConvention;
+
+import static org.junit.jupiter.api.Assertions.*;
+@SpringBootTest
+class NamingConventionServiceTest {
+
+    @Autowired
+    private NamingConventionService namingConventionService;
+
+    private static NamingConvention namingConvention;
+
+    private final NamingConvention.Convention CONVENTION = NamingConvention.Convention.GENBANK;
+
+    private final static String DIGEST0 = "a6748aa0f6a1e165f871dbed5e54ba62";
+    @BeforeEach
+    void setUp() {
+    }
+
+    @AfterEach
+    void tearDown() {
+    }
+
+    @Test
+    void addNamingConvention() {
+    }
+}