enhanced the transformation of the fetched tuple fron List<Object[]> …

…to List<MetadataEntity>
EBIvariation · May 17, 2024 · fc9b52a · fc9b52a
1 parent c26668b
commit fc9b52a
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Showing 3 changed files with 21 additions and 18 deletions.
diff --git a/src/main/java/uk/ac/ebi/eva/evaseqcol/entities/SeqColMetadataEntity.java b/src/main/java/uk/ac/ebi/eva/evaseqcol/entities/SeqColMetadataEntity.java
@@ -1,6 +1,7 @@
 package uk.ac.ebi.eva.evaseqcol.entities;
 
 import lombok.Data;
+import lombok.NoArgsConstructor;
 import org.hibernate.annotations.CreationTimestamp;
 
 import javax.persistence.Column;
@@ -13,6 +14,7 @@
 
 @Data
 @Embeddable
+@NoArgsConstructor
 public class SeqColMetadataEntity {
 
     @Column(name = "source_id")
@@ -30,6 +32,14 @@ public class SeqColMetadataEntity {
     @CreationTimestamp
     private Date createdOn = new Date();
 
+    public SeqColMetadataEntity(String sourceIdentifier, String sourceUrl, SeqColEntity.NamingConvention namingConvention,
+                                Date createdOn) {
+        this.sourceIdentifier = sourceIdentifier;
+        this.sourceUrl = sourceUrl;
+        this.namingConvention = namingConvention;
+        this.createdOn = createdOn;
+    }
+
     public SeqColMetadataEntity setNamingConvention(SeqColEntity.NamingConvention namingConvention) {
         this.namingConvention = namingConvention;
         return this;

diff --git a/src/main/java/uk/ac/ebi/eva/evaseqcol/service/SeqColLevelOneService.java b/src/main/java/uk/ac/ebi/eva/evaseqcol/service/SeqColLevelOneService.java
@@ -22,6 +22,7 @@
 import java.util.List;
 import java.util.Map;
 import java.util.Optional;
+import java.util.stream.Collectors;
 
 @Service
 public class SeqColLevelOneService {
@@ -215,28 +216,20 @@ public List<SeqColExtendedDataEntity<List<Integer>>> constructIntegerListExtData
         return integerListExtendedDataEntities;
     }
 
-    public List<SeqColMetadataEntity> metadataObjectArrayListToMetadataList(List<Object[]> metadataArray) {
-        List<SeqColMetadataEntity> metadataList = new ArrayList<>();
-        for (Object[] metadataElements : metadataArray) {
-            SeqColMetadataEntity metadataEntity = new SeqColMetadataEntity();
-            metadataEntity.setSourceIdentifier((String) metadataElements[0]);
-            metadataEntity.setSourceUrl((String) metadataElements[1]);
-            metadataEntity.setNamingConvention(SeqColEntity.NamingConvention.valueOf(
-                    (String) metadataElements[2]
-            ));
-            metadataEntity.setCreatedOn((Date) metadataElements[3]);
-            metadataList.add(metadataEntity);
-        }
-        return metadataList;
+    public SeqColMetadataEntity transformToMetadataEntity(Object[] tuple) {
+        return new SeqColMetadataEntity(
+                (String) tuple[0],
+                (String) tuple[1],
+                SeqColEntity.NamingConvention.valueOf((String) tuple[2]),
+                (Date) tuple[3]
+        );
     }
 
     public List<SeqColMetadataEntity> getAllMetadata() {
-        List<Object[]> metadataArrayList = repository.findAllMetadata();
-        return metadataObjectArrayListToMetadataList(metadataArrayList);
+        return repository.findAllMetadata().stream().map(this::transformToMetadataEntity).collect(Collectors.toList());
     }
 
     public List<SeqColMetadataEntity> getMetadataBySeqcolDigest(String digest) {
-        List<Object[]> metadataArrayList = repository.findMetadataBySeqColDigest(digest);
-        return metadataObjectArrayListToMetadataList(metadataArrayList);
+        return repository.findMetadataBySeqColDigest(digest).stream().map(this::transformToMetadataEntity).collect(Collectors.toList());
     }
 }
diff --git a/src/main/java/uk/ac/ebi/eva/evaseqcol/service/SeqColService.java b/src/main/java/uk/ac/ebi/eva/evaseqcol/service/SeqColService.java
@@ -174,7 +174,7 @@ public IngestionResultEntity fetchAndInsertAllSeqColByAssemblyAccession(String a
         boolean sourceIdExists = levelOneService.getAllMetadata().stream()
                 .anyMatch(md -> md.getSourceIdentifier().equals(assemblyAccession));
         if (sourceIdExists) {
-            logger.warn("Seqcol objects for assembly" + assemblyAccession + " have been already ingested. Nothing to ingest !");
+            logger.warn("Seqcol objects for assembly " + assemblyAccession + " have been already ingested... Nothing to ingest !");
             throw new AssemblyAlreadyIngestedException(assemblyAccession);
         }
         Optional<Map<String, Object>> seqColDataMap = ncbiSeqColDataSource.getAllPossibleSeqColExtendedData(assemblyAccession);