Added a meta data table - one-to-one relationship approach

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

@@ -17,6 +17,7 @@
 import uk.ac.ebi.eva.evaseqcol.exception.AssemblyAlreadyIngestedException;
 import uk.ac.ebi.eva.evaseqcol.exception.AssemblyNotFoundException;
 import uk.ac.ebi.eva.evaseqcol.exception.DuplicateSeqColException;
+import uk.ac.ebi.eva.evaseqcol.exception.DuplicateSeqColWithDifferentMetadata;
 import uk.ac.ebi.eva.evaseqcol.exception.IncorrectAccessionException;
 import uk.ac.ebi.eva.evaseqcol.model.IngestionResultEntity;
 import uk.ac.ebi.eva.evaseqcol.service.SeqColService;
@@ -71,6 +72,8 @@ public ResponseEntity<?> fetchAndInsertSeqColByAssemblyAccession(
             return new ResponseEntity<>(e.getMessage(), HttpStatus.INTERNAL_SERVER_ERROR);
         } catch (DuplicateSeqColException e) {
             return new ResponseEntity<>(e.getMessage(), HttpStatus.CONFLICT);
+        } catch (DuplicateSeqColWithDifferentMetadata e) {
+            return new ResponseEntity<>(e.getMessage(), HttpStatus.CREATED); // TODO: review this response
         } catch (AssemblyNotFoundException e) {
             return new ResponseEntity<>(e.getMessage(), HttpStatus.NOT_FOUND);
         } catch (AssemblyAlreadyIngestedException e) {

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

@@ -7,20 +7,23 @@
 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.JoinColumn;
+import javax.persistence.JoinColumns;
+import javax.persistence.OneToOne;
 import javax.persistence.Table;
 
 @Entity
 @NoArgsConstructor
 @Data
 @Table(name = "sequence_collections_L1")
-@IdClass(SeqColId.class)
 public class SeqColLevelOneEntity extends SeqColEntity{
 
     @Id
@@ -32,15 +35,16 @@ public class SeqColLevelOneEntity extends SeqColEntity{
     @Basic(fetch = FetchType.LAZY)
     private JSONLevelOne seqColLevel1Object;
 
-    @Id
-    @Column(nullable = false)
-    @Enumerated(EnumType.STRING)
-    protected NamingConvention namingConvention;
-
-    public SeqColLevelOneEntity(String digest, NamingConvention namingConvention, JSONLevelOne jsonLevelOne){
-        super(digest, namingConvention);
+    @OneToOne(cascade = CascadeType.ALL)
+    @JoinColumns({
+            @JoinColumn(name = "seqcol_digest", referencedColumnName = "seqcol_digest"),
+            @JoinColumn(name = "source_id", referencedColumnName = "source_identifier")
+    })
+    private SeqColMetadata metadata;
+    public SeqColLevelOneEntity(String digest, JSONLevelOne jsonLevelOne, SeqColMetadata metadata){
+        super(digest);
         this.seqColLevel1Object = jsonLevelOne;
-        this.namingConvention = namingConvention;
+        this.metadata = 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/SeqColMetadata.java

@@ -0,0 +1,67 @@
+package uk.ac.ebi.eva.evaseqcol.entities;
+
+import lombok.Data;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.EnumType;
+import javax.persistence.Enumerated;
+import javax.persistence.Id;
+import javax.persistence.IdClass;
+import javax.persistence.OneToOne;
+import javax.persistence.Table;
+import javax.persistence.Temporal;
+import javax.persistence.TemporalType;
+import java.util.Date;
+
+@Entity
+@IdClass(SeqColMetadataId.class)
+@Table(name = "seqcol_md")
+@Data
+public class SeqColMetadata {
+
+    @Id
+    @Column(name = "seqcol_digest")
+    private String seqColDigest;
+
+    @Id
+    @Enumerated(EnumType.STRING)
+    @Column(name = "source_identifier")
+    private SourceIdentifier sourceIdentifier;
+
+    private String sourceUrl;
+
+    @Enumerated(EnumType.STRING)
+    private SeqColEntity.NamingConvention namingConvention;
+
+    @Column(insertable = false, updatable = false)
+    @Temporal(TemporalType.TIMESTAMP)
+    private Date timestamp;
+
+    @OneToOne(mappedBy = "metadata")
+    private SeqColLevelOneEntity seqColLevelOne;
+
+    public enum SourceIdentifier {
+        Insdc
+    }
+
+    public SeqColMetadata setSeqColDigest(String digest) {
+        this.seqColDigest = digest;
+        return this;
+    }
+
+    public SeqColMetadata setSourceIdentifier(SourceIdentifier sourceIdentifier) {
+        this.sourceIdentifier = sourceIdentifier;
+        return this;
+    }
+
+    public SeqColMetadata setSourceUrl(String sourceUrl) {
+        this.sourceUrl = sourceUrl;
+        return this;
+    }
+
+    public SeqColMetadata setNamingConvention(SeqColEntity.NamingConvention namingConvention) {
+        this.namingConvention = namingConvention;
+        return this;
+    }
+}

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

@@ -0,0 +1,22 @@
+package uk.ac.ebi.eva.evaseqcol.entities;
+
+import lombok.AllArgsConstructor;
+import lombok.EqualsAndHashCode;
+import lombok.NoArgsConstructor;
+
+import javax.persistence.Embeddable;
+import javax.validation.constraints.NotNull;
+import java.io.Serializable;
+
+@EqualsAndHashCode
+@Embeddable
+@NoArgsConstructor
+@AllArgsConstructor
+public class SeqColMetadataId implements Serializable {
+
+    @NotNull
+    private String seqColDigest;
+    @NotNull
+    private SeqColMetadata.SourceIdentifier sourceIdentifier; // Eg: INSDC, UCSC, GENBANK, etc..
+
+}

src/main/java/uk/ac/ebi/eva/evaseqcol/exception/DuplicateSeqColWithDifferentMetadata.java

@@ -0,0 +1,8 @@
+package uk.ac.ebi.eva.evaseqcol.exception;
+
+public class DuplicateSeqColWithDifferentMetadata extends RuntimeException{
+
+    public DuplicateSeqColWithDifferentMetadata(String digest) {
+        super("A similar seqCol already exists with digest " + digest + " but with different metadata");
+    }
+}

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

@@ -0,0 +1,15 @@
+package uk.ac.ebi.eva.evaseqcol.repo;
+
+import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.stereotype.Repository;
+
+import uk.ac.ebi.eva.evaseqcol.entities.SeqColMetadata;
+import uk.ac.ebi.eva.evaseqcol.entities.SeqColMetadataId;
+
+import java.util.List;
+
+@Repository
+public interface MetadataRepository extends JpaRepository<SeqColMetadata, SeqColMetadataId> {
+
+    List<SeqColMetadata> findAllBySeqColDigest(String digest);
+}

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

@@ -14,4 +14,5 @@ public interface SeqColLevelOneRepository extends JpaRepository<SeqColLevelOneEn
     void removeSeqColLevelOneEntityByDigest(String digest);
 
     void deleteAll();
+
 }

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

@@ -0,0 +1,35 @@
+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.SeqColMetadata;
+import uk.ac.ebi.eva.evaseqcol.entities.SeqColMetadataId;
+import uk.ac.ebi.eva.evaseqcol.repo.MetadataRepository;
+
+import java.util.List;
+import java.util.Optional;
+
+@Service
+public class MetadataService {
+
+    @Autowired
+    private MetadataRepository repository;
+
+    public Optional<SeqColMetadata> addMetadata(SeqColMetadata metadata) {
+        if (repository.existsById(new SeqColMetadataId(metadata.getSeqColDigest(), metadata.getSourceIdentifier()))){
+            return Optional.empty();
+        }
+        return Optional.of(
+                repository.save(metadata)
+        );
+    }
+
+    /**
+     * Return the list of all metadata entries for the seqCol object with the given digest*/
+    public Optional<List<SeqColMetadata>> getAllMetadataForSeqColByDigest(String seqColDigest) {
+        return Optional.of(
+                repository.findAllBySeqColDigest(seqColDigest)
+        );
+    }
+}

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

@@ -8,6 +8,7 @@
 import uk.ac.ebi.eva.evaseqcol.entities.SeqColLevelOneEntity;
 import uk.ac.ebi.eva.evaseqcol.digests.DigestCalculator;
 import uk.ac.ebi.eva.evaseqcol.entities.SeqColLevelTwoEntity;
+import uk.ac.ebi.eva.evaseqcol.entities.SeqColMetadata;
 import uk.ac.ebi.eva.evaseqcol.repo.SeqColLevelOneRepository;
 import uk.ac.ebi.eva.evaseqcol.utils.JSONExtData;
 import uk.ac.ebi.eva.evaseqcol.utils.JSONIntegerListExtData;
@@ -32,8 +33,12 @@ public class SeqColLevelOneService {
      * Add a new Level 1 sequence collection object and save it to the
      * database*/
     public Optional<SeqColLevelOneEntity> addSequenceCollectionL1(SeqColLevelOneEntity seqColLevelOne){
-        SeqColLevelOneEntity seqCol = repository.save(seqColLevelOne);
-        return Optional.of(seqCol);
+        if (repository.existsById(seqColLevelOne.getDigest())) {
+            return Optional.empty();
+        }
+        return Optional.of(
+                repository.save(seqColLevelOne)
+        );
     }
 
     public Optional<SeqColLevelOneEntity> getSeqColLevelOneByDigest(String digest){
@@ -62,12 +67,15 @@ public List<SeqColLevelOneEntity> getAllSeqColLevelOneObjects(){
 
     /**
      * Construct a seqCol level 1 entity out of three seqCol level 2 entities that
-     * hold names, lengths and sequences objects*/
+     * hold names, lengths and sequences objects
+     * TODO: Change the signature of this method and make it accept metadata object instead of namingconvention*/
     public SeqColLevelOneEntity constructSeqColLevelOne(List<SeqColExtendedDataEntity<List<String>>> stringListExtendedDataEntities,
                                                         List<SeqColExtendedDataEntity<List<Integer>>> integerListExtendedDataEntities,
                                                         SeqColEntity.NamingConvention convention) throws IOException {
         SeqColLevelOneEntity levelOneEntity = new SeqColLevelOneEntity();
         JSONLevelOne jsonLevelOne = new JSONLevelOne();
+        SeqColMetadata metadata = new SeqColMetadata().setNamingConvention(convention)
+                .setSourceIdentifier(SeqColMetadata.SourceIdentifier.Insdc); // TODO: this should be specified by the method parameter
 
         // Looping over List<String> types
         for (SeqColExtendedDataEntity<List<String>> dataEntity: stringListExtendedDataEntities) {
@@ -99,7 +107,8 @@ public SeqColLevelOneEntity constructSeqColLevelOne(List<SeqColExtendedDataEntit
         levelOneEntity.setSeqColLevel1Object(jsonLevelOne);
         String digest0 = digestCalculator.getSha512Digest(levelOneEntity.toString());
         levelOneEntity.setDigest(digest0);
-        levelOneEntity.setNamingConvention(convention);
+        metadata.setSeqColDigest(digest0);
+        levelOneEntity.setMetadata(metadata);
         return levelOneEntity;
     }
 

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

@@ -18,6 +18,7 @@
 import uk.ac.ebi.eva.evaseqcol.exception.AssemblyNotFoundException;
 import uk.ac.ebi.eva.evaseqcol.exception.AttributeNotDefinedException;
 import uk.ac.ebi.eva.evaseqcol.exception.DuplicateSeqColException;
+import uk.ac.ebi.eva.evaseqcol.exception.DuplicateSeqColWithDifferentMetadata;
 import uk.ac.ebi.eva.evaseqcol.exception.SeqColNotFoundException;
 import uk.ac.ebi.eva.evaseqcol.exception.UnableToLoadServiceInfoException;
 import uk.ac.ebi.eva.evaseqcol.model.IngestionResultEntity;
@@ -50,16 +51,19 @@ public class SeqColService {
     private final SeqColLevelOneService levelOneService;
     private final SeqColLevelTwoService levelTwoService;
     private final SeqColExtendedDataService extendedDataService;
+    private final MetadataService metadataService;
     private final DigestCalculator digestCalculator = new DigestCalculator();
     private final Logger logger = LoggerFactory.getLogger(SeqColService.class);
 
     @Autowired
     public SeqColService(NCBISeqColDataSource ncbiSeqColDataSource, SeqColLevelOneService levelOneService,
-                         SeqColLevelTwoService levelTwoService, SeqColExtendedDataService extendedDataService) {
+                         SeqColLevelTwoService levelTwoService, SeqColExtendedDataService extendedDataService,
+                         MetadataService metadataService) {
         this.ncbiSeqColDataSource = ncbiSeqColDataSource;
         this.levelOneService = levelOneService;
         this.levelTwoService = levelTwoService;
         this.extendedDataService = extendedDataService;
+        this.metadataService = metadataService;
     }
 
     @Transactional
@@ -73,6 +77,11 @@ public Optional<String> addFullSequenceCollection(
             ) {
         long numSeqCols = levelOneService.countSeqColLevelOneEntitiesByDigest(levelOneEntity.getDigest());
         if (numSeqCols > 0) {
+            // Checking for possibly different metadata
+            if (metadataService.addMetadata(levelOneEntity.getMetadata()).isPresent()) {
+                logger.warn("SeqCol with digest " + levelOneEntity.getDigest() + " already exists but with different metadata!");
+                throw new DuplicateSeqColWithDifferentMetadata(levelOneEntity.getDigest());
+            }
             logger.warn("SeqCol with digest " + levelOneEntity.getDigest() + " already exists !");
             throw new DuplicateSeqColException(levelOneEntity.getDigest());
         } else {

src/test/java/uk/ac/ebi/eva/evaseqcol/io/SeqColGenerator.java

@@ -5,6 +5,7 @@
 import uk.ac.ebi.eva.evaseqcol.entities.SeqColEntity;
 import uk.ac.ebi.eva.evaseqcol.entities.SeqColLevelOneEntity;
 import uk.ac.ebi.eva.evaseqcol.entities.SeqColLevelTwoEntity;
+import uk.ac.ebi.eva.evaseqcol.entities.SeqColMetadata;
 import uk.ac.ebi.eva.evaseqcol.utils.JSONLevelOne;
 
 import java.util.Arrays;
@@ -16,24 +17,27 @@ public class SeqColGenerator {
 
     /**
      * Return an example (might not be real) of a seqCol object level 1
-     * The naming convention is set to GENBANK as a random choice*/
+     * The naming convention is set to GENBANK as a random choice
+     * and source identifier is set Insdc*/
     public SeqColLevelOneEntity generateLevelOneEntity() {
         SeqColLevelOneEntity levelOneEntity = new SeqColLevelOneEntity();
         JSONLevelOne jsonLevelOne = new JSONLevelOne();
+        SeqColMetadata metadata = new SeqColMetadata()
+                .setNamingConvention(SeqColEntity.NamingConvention.GENBANK)
+                .setSeqColDigest("PgQMkKm2A8I9GVW7hJWcJ3erxuaMbHpD")
+                .setSourceIdentifier(SeqColMetadata.SourceIdentifier.Insdc);
         jsonLevelOne.setNames("mfxUkK3J5y7BGVW7hJWcJ3erxuaMX6xm");
         jsonLevelOne.setSequences("dda3Kzi1Wkm2A8I99WietU1R8J4PL-D6");
         jsonLevelOne.setLengths("Ms_ixPgQMJaM54dVntLWeovXSO7ljvZh");
         jsonLevelOne.setMd5DigestsOfSequences("_6iaYtcWw4TZaowlL7_64Wu9mbHpDUw4");
         jsonLevelOne.setSortedNameLengthPairs("QFuKs5Hh8uQwwUtnRxIf8W3zeJoFOp8Z");
         levelOneEntity.setSeqColLevel1Object(jsonLevelOne);
-        levelOneEntity.setDigest("3mTg0tAA3PS-R1TzelLVWJ2ilUzoWfVq");
-        levelOneEntity.setNamingConvention(SeqColEntity.NamingConvention.GENBANK);
+        levelOneEntity.setMetadata(metadata);
         return levelOneEntity;
     }
 
     /**
      * Return an example (might not be real) of a seqCol object level 2
-     * The naming convention is set to GENBANK as a random choice
      * */
     public SeqColLevelTwoEntity generateLevelTwoEntity() {
         SeqColLevelTwoEntity levelTwoEntity = new SeqColLevelTwoEntity();
@@ -128,7 +132,6 @@ public SeqColLevelTwoEntity generateLevelTwoEntity() {
                 "YfHZgnpuJm4SN3RN4XL1VWWWZwTXtqw5"
         ));
         levelTwoEntity.setDigest("3mTg0tAA3PS-R1TzelLVWJ2ilUzoWfVq");
-        levelTwoEntity.setNamingConvention(SeqColEntity.NamingConvention.GENBANK);
         return levelTwoEntity;
     }
 }