EVA-3505 update delete assembly endpoint (#128)

* update delete assembly operation
EBIvariation · Feb 23, 2024 · 845e4e6 · 845e4e6
1 parent 3cba50f
commit 845e4e6
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Showing 6 changed files with 25 additions and 26 deletions.
diff --git a/src/main/java/uk/ac/ebi/eva/contigalias/controller/admin/AdminController.java b/src/main/java/uk/ac/ebi/eva/contigalias/controller/admin/AdminController.java
@@ -238,10 +238,23 @@ public void putChromosomeChecksumsByAccession(
                     "assembly also deletes all sequences that are associated with that assembly. This endpoint does" +
                     " not return any data.")
     @DeleteMapping(value = "assemblies/{accession}")
-    public void deleteAssemblyByAccession(
+    public ResponseEntity<String> deleteAssemblyByAccession(
             @PathVariable(name = "accession") @ApiParam(value = "INSDC or RefSeq assembly accession. Eg: " +
                     "GCA_000001405.10") String asmAccession) {
-        handler.deleteAssemblyByAccession(asmAccession);
+        Optional<AssemblyEntity> assemblyOpt = handler.getAssemblyByAccession(asmAccession);
+        if (assemblyOpt.isPresent()) {
+            try {
+                handler.deleteAssemblyByAccession(assemblyOpt.get().getInsdcAccession());
+                return ResponseEntity.ok("Assembly Deleted Successfully");
+            } catch (Exception e) {
+                return new ResponseEntity<>("There was an error deleting assembly. " +
+                        "The DB might be in inconsistent state, it is advised to retry deleting",
+                        HttpStatus.INTERNAL_SERVER_ERROR);
+            }
+        } else {
+            return new ResponseEntity<>("The requested assembly for deletion could not be found",
+                    HttpStatus.NOT_FOUND);
+        }
     }
 
 }
diff --git a/src/main/java/uk/ac/ebi/eva/contigalias/controller/admin/AdminHandler.java b/src/main/java/uk/ac/ebi/eva/contigalias/controller/admin/AdminHandler.java
@@ -78,7 +78,7 @@ public List<String> getScheduledJobStatus() {
     }
 
     public void deleteAssemblyByAccession(String accession) {
-        assemblyService.deleteAssemblyByAccession(accession);
+        assemblyService.deleteEntriesForAssembly(accession);
     }
 
     public void putAssemblyChecksumsByAccession(String accession, String md5, String trunc512) {

diff --git a/src/main/java/uk/ac/ebi/eva/contigalias/service/AssemblyService.java b/src/main/java/uk/ac/ebi/eva/contigalias/service/AssemblyService.java
@@ -21,6 +21,8 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
+import org.springframework.retry.annotation.Backoff;
+import org.springframework.retry.annotation.Retryable;
 import org.springframework.stereotype.Service;
 import uk.ac.ebi.eva.contigalias.datasource.ENAAssemblyDataSource;
 import uk.ac.ebi.eva.contigalias.datasource.NCBIAssemblyDataSource;
@@ -165,6 +167,7 @@ public void parseFileAndInsertAssembly(String accession) throws IOException {
         Files.deleteIfExists(downloadedNCBIFilePath);
     }
 
+    @Retryable(value = Exception.class, maxAttempts = 5, backoff = @Backoff(delay = 2000, multiplier=2))
     public void deleteEntriesForAssembly(String accession) {
         chromosomeRepository.deleteChromosomeEntitiesByAssembly_InsdcAccession(accession);
         assemblyRepository.deleteAssemblyEntityByInsdcAccessionOrRefseq(accession);
@@ -249,23 +252,6 @@ public Map<String, List<String>> fetchAndInsertAssembly(List<String> accessions)
         return accessionResult;
     }
 
-    public void deleteAssemblyByInsdcAccession(String insdcAccession) {
-        assemblyRepository.deleteAssemblyEntityByInsdcAccession(insdcAccession);
-    }
-
-    public void deleteAssemblyByRefseq(String refseq) {
-        assemblyRepository.deleteAssemblyEntityByRefseq(refseq);
-    }
-
-    public void deleteAssemblyByAccession(String accession) {
-        Optional<AssemblyEntity> assembly = getAssemblyByAccession(accession);
-        assembly.ifPresent(this::deleteAssembly);
-    }
-
-    public void deleteAssembly(AssemblyEntity entity) {
-        assemblyRepository.delete(entity);
-    }
-
     private DuplicateAssemblyException duplicateAssemblyInsertionException(String accession, AssemblyEntity present) {
         StringBuilder exception = new StringBuilder("A similar assembly already exists!");
         if (accession != null) {

diff --git a/src/test/java/uk/ac/ebi/eva/contigalias/scheduler/ENASequenceNameUpdaterTest.java b/src/test/java/uk/ac/ebi/eva/contigalias/scheduler/ENASequenceNameUpdaterTest.java
@@ -43,7 +43,7 @@ void setup() {
     @AfterEach
     void tearDown() {
         chromosomeEntities.stream().forEach(c -> chromosomeService.deleteChromosome(c));
-        assemblyService.deleteAssembly(assemblyService.getAssemblyByAccession(GCA_ACCESSION_HAVING_CHROMOSOMES).get());
+        assemblyService.deleteEntriesForAssembly(assemblyService.getAssemblyByAccession(GCA_ACCESSION_HAVING_CHROMOSOMES).get().getInsdcAccession());
     }
 
     @Test

diff --git a/...t/java/uk/ac/ebi/eva/contigalias/service/AssemblyAndChromosomeServiceIntegrationTest.java b/...t/java/uk/ac/ebi/eva/contigalias/service/AssemblyAndChromosomeServiceIntegrationTest.java
@@ -77,7 +77,7 @@ void setup() {
         @AfterEach
         void tearDown() {
             chromosomeEntities.clear();
-            assemblyService.deleteAssembly(assemblyEntity);
+            assemblyService.deleteEntriesForAssembly(assemblyEntity.getInsdcAccession());
         }
 
         @Test
@@ -188,7 +188,7 @@ void tearDown() {
                 service.deleteChromosome(chromosomeEntity);
             }
             for (AssemblyEntity assemblyEntity : assemblyEntities) {
-                assemblyService.deleteAssembly(assemblyEntity);
+                assemblyService.deleteEntriesForAssembly(assemblyEntity.getInsdcAccession());
             }
             assemblyEntities = null;
             chromosomeEntities = null;

diff --git a/src/test/java/uk/ac/ebi/eva/contigalias/service/AssemblyServiceIntegrationTest.java b/src/test/java/uk/ac/ebi/eva/contigalias/service/AssemblyServiceIntegrationTest.java
@@ -79,7 +79,7 @@ void setup() {
     @AfterEach
     void tearDown() {
         for (AssemblyEntity entity : entities) {
-            service.deleteAssembly(entity);
+            service.deleteEntriesForAssembly(entity.getInsdcAccession());
         }
     }
 
@@ -102,7 +102,7 @@ void setup() {
 
         @AfterEach
         void tearDown() {
-            service.deleteAssemblyByRefseq(entity.getRefseq());
+            service.deleteEntriesForAssembly(entity.getInsdcAccession());
         }
 
         @Test
@@ -147,7 +147,7 @@ void getAssembliesByTaxid() {
             }
 
             for (AssemblyEntity assemblyEntity : entities) {
-                service.deleteAssemblyByInsdcAccession(assemblyEntity.getInsdcAccession());
+                service.deleteEntriesForAssembly(assemblyEntity.getInsdcAccession());
             }
         }