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added a column 'asm_accession' to the sequence_collection_l1 table #78

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added a column 'asm_accession' to the sequence_collection_l1 table #78

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419417b
added a column 'asm_accession' to the sequence_collection_l1 table
waterflow80 Feb 5, 2024
2c0ee58
make the check for existing asm_accession before proceeding with down…
waterflow80 Feb 5, 2024
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6 changes: 5 additions & 1 deletion src/main/java/uk/ac/ebi/eva/evaseqcol/entities/SeqColLevelOneEntity.java
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Expand Up @@ -37,10 +37,14 @@ public class SeqColLevelOneEntity extends SeqColEntity{
@Enumerated(EnumType.STRING)
protected NamingConvention namingConvention;

public SeqColLevelOneEntity(String digest, NamingConvention namingConvention, JSONLevelOne jsonLevelOne){
@Column(name = "insdc_accession")
private String asmAccession; // The INSDC assembly accession from which the seqcol was created

public SeqColLevelOneEntity(String digest, NamingConvention namingConvention, JSONLevelOne jsonLevelOne, String asmAccession){
super(digest, namingConvention);
this.seqColLevel1Object = jsonLevelOne;
this.namingConvention = namingConvention;
this.asmAccession = asmAccession;
}

@Override
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1 change: 1 addition & 0 deletions src/main/java/uk/ac/ebi/eva/evaseqcol/repo/SeqColLevelOneRepository.java
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Expand Up @@ -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);

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14 changes: 11 additions & 3 deletions src/main/java/uk/ac/ebi/eva/evaseqcol/service/SeqColLevelOneService.java
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Expand Up @@ -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);
}
Expand All @@ -65,8 +71,9 @@ public List<SeqColLevelOneEntity> getAllSeqColLevelOneObjects(){
* hold names, lengths and sequences objects*/
public SeqColLevelOneEntity constructSeqColLevelOne(List<SeqColExtendedDataEntity<List<String>>> stringListExtendedDataEntities,
List<SeqColExtendedDataEntity<List<Integer>>> integerListExtendedDataEntities,
SeqColEntity.NamingConvention convention) throws IOException {
SeqColEntity.NamingConvention convention, String asm_accession) throws IOException {
SeqColLevelOneEntity levelOneEntity = new SeqColLevelOneEntity();
levelOneEntity.setAsmAccession(asm_accession);
JSONLevelOne jsonLevelOne = new JSONLevelOne();

// Looping over List<String> types
Expand Down Expand Up @@ -106,7 +113,8 @@ public SeqColLevelOneEntity constructSeqColLevelOne(List<SeqColExtendedDataEntit
/**
* Construct a Level 1 seqCol out of a Level 2 seqCol*/
public SeqColLevelOneEntity constructSeqColLevelOne(
SeqColLevelTwoEntity levelTwoEntity, SeqColEntity.NamingConvention convention) throws IOException {
SeqColLevelTwoEntity levelTwoEntity, SeqColEntity.NamingConvention convention, String asm_accession)
throws IOException {
DigestCalculator digestCalculator = new DigestCalculator();
JSONExtData<List<String>> sequencesExtData = new JSONStringListExtData(levelTwoEntity.getSequences());
JSONExtData<List<Integer>> lengthsExtData = new JSONIntegerListExtData(levelTwoEntity.getLengths());
Expand Down Expand Up @@ -151,7 +159,7 @@ public SeqColLevelOneEntity constructSeqColLevelOne(
lengthsExtEntity
);

return constructSeqColLevelOne(stringListExtendedDataEntities,integerListExtendedDataEntities, convention);
return constructSeqColLevelOne(stringListExtendedDataEntities,integerListExtendedDataEntities, convention, asm_accession);
}

/**
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15 changes: 7 additions & 8 deletions src/main/java/uk/ac/ebi/eva/evaseqcol/service/SeqColService.java
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Expand Up @@ -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()) {
Expand Down Expand Up @@ -198,8 +202,8 @@ public IngestionResultEntity fetchAndInsertAllSeqColByAssemblyAccession(

// Constructing seqCol Level One object
SeqColLevelOneEntity levelOneEntity = levelOneService.constructSeqColLevelOne(
seqColStringListExtDataEntities, seqColIntegerListExtDataEntities, extendedNamesEntity.getNamingConvention()
);
seqColStringListExtDataEntities, seqColIntegerListExtDataEntities, extendedNamesEntity.getNamingConvention(),
assemblyAccession);

try {
Optional<String> seqColDigest = insertSeqColL1AndL2( // TODO: Check for possible self invocation problem
Expand All @@ -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;

}

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2 changes: 1 addition & 1 deletion src/test/java/uk/ac/ebi/eva/evaseqcol/controller/AdminControllerIntegrationTest.java
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Expand Up @@ -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;
Expand Down Expand Up @@ -106,6 +105,7 @@ void ingestSeqColsTest() {
assertTrue(levelTwoEntity.isPresent());
assertEquals(insertedSeqColDigest,levelOneEntity.get().getDigest());
assertNotNull(levelTwoEntity.get().getLengths());
assertEquals(ASM_ACCESSION, levelOneEntity.get().getAsmAccession());
}

@Test
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6 changes: 4 additions & 2 deletions src/test/java/uk/ac/ebi/eva/evaseqcol/io/SeqColWriter.java
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Expand Up @@ -146,7 +146,8 @@ public void create() throws IOException {
extendedIntegerListDataEntitiesUcsc =
(List<SeqColExtendedDataEntity<List<Integer>>>) ucscExtendedDataMap.get("integerListExtDataList");
levelOneEntityUcsc = levelOneService.constructSeqColLevelOne(
extendedStringListDataEntitiesUcsc, extendedIntegerListDataEntitiesUcsc, SeqColEntity.NamingConvention.UCSC);
extendedStringListDataEntitiesUcsc, extendedIntegerListDataEntitiesUcsc, SeqColEntity.NamingConvention.UCSC,
assemblyEntity.getInsdcAccession());
Optional<String> resultDigestUcsc = seqColService.addFullSequenceCollection(
levelOneEntityUcsc, extendedStringListDataEntitiesUcsc, extendedIntegerListDataEntitiesUcsc);
if (resultDigestUcsc.isPresent()) {
Expand All @@ -163,7 +164,8 @@ public void create() throws IOException {
extendedIntegerListDataEntitiesGenbank = (List<SeqColExtendedDataEntity<List<Integer>>>) genbankExtendedDataMap.get("integerListExtDataList");

levelOneEntityGenbank = levelOneService.constructSeqColLevelOne(
extendedStringListDataEntitiesGenbank, extendedIntegerListDataEntitiesGenbank, SeqColEntity.NamingConvention.GENBANK);
extendedStringListDataEntitiesGenbank, extendedIntegerListDataEntitiesGenbank, SeqColEntity.NamingConvention.GENBANK,
assemblyEntity.getInsdcAccession());
Optional<String> resultDigestGenbank = seqColService.addFullSequenceCollection(
levelOneEntityGenbank, extendedStringListDataEntitiesGenbank, extendedIntegerListDataEntitiesGenbank);
if (resultDigestGenbank.isPresent()) {
Expand Down
8 changes: 5 additions & 3 deletions src/test/java/uk/ac/ebi/eva/evaseqcol/service/SeqColLevelOneServiceTest.java
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Expand Up @@ -82,10 +82,12 @@ void constructSeqColL1Test() throws IOException {
List<SeqColExtendedDataEntity<List<Integer>>> integerListExtDataList =
(List<SeqColExtendedDataEntity<List<Integer>>>) extendedDataMapGenbank.get("integerListExtDataList");
SeqColLevelOneEntity levelOneEntity = levelOneService.constructSeqColLevelOne(
stringListExtDataList, integerListExtDataList, SeqColEntity.NamingConvention.GENBANK);
stringListExtDataList, integerListExtDataList, SeqColEntity.NamingConvention.GENBANK, assemblyEntity.getInsdcAccession());
SeqColLevelTwoEntity levelTwoEntity = levelTwoService.
constructSeqColL2(levelOneEntity.getDigest(), stringListExtDataList, integerListExtDataList);
SeqColLevelOneEntity constructedEntity = levelOneService.constructSeqColLevelOne(levelTwoEntity, SeqColEntity.NamingConvention.GENBANK);
SeqColLevelOneEntity constructedEntity = levelOneService.constructSeqColLevelOne(levelTwoEntity,
SeqColEntity.NamingConvention.GENBANK,
assemblyEntity.getInsdcAccession());
assertNotNull(constructedEntity);
assertNotNull(constructedEntity.getSeqColLevel1Object().getSequences());
}
Expand All @@ -100,7 +102,7 @@ void addSequenceCollectionL1() throws IOException {
List<SeqColExtendedDataEntity<List<Integer>>> integerListExtDataList =
(List<SeqColExtendedDataEntity<List<Integer>>>) extendedDataMapGenbank.get("integerListExtDataList");
SeqColLevelOneEntity levelOneEntity = levelOneService.constructSeqColLevelOne(
stringListExtDataList, integerListExtDataList, SeqColEntity.NamingConvention.GENBANK);
stringListExtDataList, integerListExtDataList, SeqColEntity.NamingConvention.GENBANK, assemblyEntity.getInsdcAccession());
Optional<SeqColLevelOneEntity> savedEntity = levelOneService.addSequenceCollectionL1(levelOneEntity);
assertTrue(savedEntity.isPresent());
System.out.println(savedEntity.get());
Expand Down
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