make the check for existing asm_accession before proceeding with down…

…load and the ingestion process

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

@@ -1,6 +1,5 @@
 package uk.ac.ebi.eva.evaseqcol.entities;
 
-import com.fasterxml.jackson.annotation.JsonIgnore;
 import lombok.Data;
 import lombok.NoArgsConstructor;
 import org.hibernate.annotations.Type;
@@ -39,13 +38,13 @@ public class SeqColLevelOneEntity extends SeqColEntity{
     protected NamingConvention namingConvention;
 
     @Column(name = "insdc_accession")
-    private String asm_accession; // The INSDC assembly accession from which the seqcol was created
+    private String asmAccession; // The INSDC assembly accession from which the seqcol was created
 
-    public SeqColLevelOneEntity(String digest, NamingConvention namingConvention, JSONLevelOne jsonLevelOne, String asm_accession){
+    public SeqColLevelOneEntity(String digest, NamingConvention namingConvention, JSONLevelOne jsonLevelOne, String asmAccession){
         super(digest, namingConvention);
         this.seqColLevel1Object = jsonLevelOne;
         this.namingConvention = namingConvention;
-        this.asm_accession = asm_accession;
+        this.asmAccession = asmAccession;
     }
 
     @Override

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

@@ -8,6 +8,7 @@
 @Repository
 public interface SeqColLevelOneRepository extends JpaRepository<SeqColLevelOneEntity, String> {
     SeqColLevelOneEntity findSeqColLevelOneEntityByDigest(String digest);
+    boolean existsByAsmAccession(String asm_accession);
 
     long countSeqColLevelOneEntitiesByDigest(String digest);
 

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

@@ -45,6 +45,12 @@ public Optional<SeqColLevelOneEntity> getSeqColLevelOneByDigest(String digest){
         }
     }
 
+    /**
+     * Check whether the given asm_accession exists in the database (in the sequence_collection_level1)*/
+    public boolean isAsmAccessionExists(String asm_accession) {
+        return repository.existsByAsmAccession(asm_accession);
+    }
+
     public void removeSeqColLevelOneByDigest(String digest) {
         repository.removeSeqColLevelOneEntityByDigest(digest);
     }
@@ -67,7 +73,7 @@ public SeqColLevelOneEntity constructSeqColLevelOne(List<SeqColExtendedDataEntit
                                                         List<SeqColExtendedDataEntity<List<Integer>>> integerListExtendedDataEntities,
                                                         SeqColEntity.NamingConvention convention, String asm_accession) throws IOException {
         SeqColLevelOneEntity levelOneEntity = new SeqColLevelOneEntity();
-        levelOneEntity.setAsm_accession(asm_accession);
+        levelOneEntity.setAsmAccession(asm_accession);
         JSONLevelOne jsonLevelOne = new JSONLevelOne();
 
         // Looping over List<String> types

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

@@ -162,6 +162,10 @@ public void removeAllSeqCol() {
     public IngestionResultEntity fetchAndInsertAllSeqColByAssemblyAccession(
             String assemblyAccession) throws IOException, DuplicateSeqColException, AssemblyNotFoundException,
             AssemblyAlreadyIngestedException{
+        if (levelOneService.isAsmAccessionExists(assemblyAccession)) {
+            logger.warn("Seqcol objects for assembly " + assemblyAccession + " has been already ingested");
+            throw new AssemblyAlreadyIngestedException(assemblyAccession);
+        }
         Optional<Map<String, Object>> seqColDataMap = ncbiSeqColDataSource
                 .getAllPossibleSeqColExtendedData(assemblyAccession);
         if (!seqColDataMap.isPresent()) {
@@ -218,12 +222,7 @@ public IngestionResultEntity fetchAndInsertAllSeqColByAssemblyAccession(
                 " already exists. Skipping.");
             }
         }
-        if (ingestionResultEntity.getNumberOfInsertedSeqcols() == 0) {
-            logger.warn("Seqcol objects for assembly " + assemblyAccession + " has been already ingested");
-            throw new AssemblyAlreadyIngestedException(assemblyAccession);
-        } else {
-            return ingestionResultEntity;
-        }
+        return ingestionResultEntity;
 
     }
 

src/test/java/uk/ac/ebi/eva/evaseqcol/controller/AdminControllerIntegrationTest.java

@@ -14,7 +14,6 @@
 import org.springframework.http.HttpStatus;
 import org.springframework.http.ResponseEntity;
 import org.springframework.http.client.support.BasicAuthenticationInterceptor;
-import org.springframework.test.context.ActiveProfiles;
 import org.springframework.test.context.DynamicPropertyRegistry;
 import org.springframework.test.context.DynamicPropertySource;
 import org.springframework.transaction.annotation.Transactional;
@@ -106,7 +105,7 @@ void ingestSeqColsTest() {
         assertTrue(levelTwoEntity.isPresent());
         assertEquals(insertedSeqColDigest,levelOneEntity.get().getDigest());
         assertNotNull(levelTwoEntity.get().getLengths());
-        assertEquals(ASM_ACCESSION, levelOneEntity.get().getAsm_accession());
+        assertEquals(ASM_ACCESSION, levelOneEntity.get().getAsmAccession());
     }
 
     @Test