removed unnecessary json response for some ingestion cases and set th…

…e right response status codes

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

@@ -12,6 +12,7 @@
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RestController;
 
+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.IncorrectAccessionException;
@@ -42,7 +43,7 @@ public AdminController(SeqColService seqColService) {
                     "contained in the assembly report) and eventually save these seqCol objects into the database. " +
                     "This is an authenticated endpoint, so it requires admin privileges to run it.")
     @ApiResponses(value = {
-            @ApiResponse(responseCode = "200", description = "seqCol object(s) successfully inserted"),
+            @ApiResponse(responseCode = "201", description = "seqCol object(s) successfully inserted"),
             @ApiResponse(responseCode = "409", description = "seqCol object(s) already exist(s)"),
             @ApiResponse(responseCode = "404", description = "Assembly not found"),
             @ApiResponse(responseCode = "400", description = "Bad request. (It can be a bad accession value)"),
@@ -56,7 +57,7 @@ public ResponseEntity<?> fetchAndInsertSeqColByAssemblyAccession(
             required = true) @PathVariable String asmAccession) {
         try {
             IngestionResultEntity ingestionResult = seqColService.fetchAndInsertAllSeqColByAssemblyAccession(asmAccession);
-            return ResponseEntity.ok(ingestionResult);
+            return new ResponseEntity<>(ingestionResult, HttpStatus.CREATED);
         } catch (IncorrectAccessionException e) {
             return new ResponseEntity<>(e.getMessage(), HttpStatus.BAD_REQUEST);
         } catch (IllegalArgumentException e) {
@@ -69,6 +70,8 @@ public ResponseEntity<?> fetchAndInsertSeqColByAssemblyAccession(
             return new ResponseEntity<>(e.getMessage(), HttpStatus.CONFLICT);
         } catch (AssemblyNotFoundException e) {
             return new ResponseEntity<>(e.getMessage(), HttpStatus.NOT_FOUND);
+        } catch (AssemblyAlreadyIngestedException e) {
+            return new ResponseEntity<>(e.getMessage(), HttpStatus.CONFLICT);
         }
     }
 }

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

@@ -0,0 +1,7 @@
+package uk.ac.ebi.eva.evaseqcol.exception;
+
+public class AssemblyAlreadyIngestedException extends RuntimeException{
+    public AssemblyAlreadyIngestedException(String assemblyAccession) {
+        super("Seqcol objects for assembly " + assemblyAccession + " has been already ingested");
+    }
+}

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

@@ -14,6 +14,8 @@
 import uk.ac.ebi.eva.evaseqcol.entities.SeqColLevelOneEntity;
 import uk.ac.ebi.eva.evaseqcol.entities.SeqColExtendedDataEntity;
 import uk.ac.ebi.eva.evaseqcol.entities.SeqColLevelTwoEntity;
+import uk.ac.ebi.eva.evaseqcol.exception.AssemblyAlreadyIngestedException;
+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.SeqColNotFoundException;
@@ -158,17 +160,17 @@ public void removeAllSeqCol() {
      * assembly report.
      * Return the list of level 0 digests of the inserted seqcol objects*/
     public IngestionResultEntity fetchAndInsertAllSeqColByAssemblyAccession(
-            String assemblyAccession) throws IOException, DuplicateSeqColException {
-        IngestionResultEntity ingestionResultEntity = new IngestionResultEntity();
-        ingestionResultEntity.setAssemblyAccession(assemblyAccession);
+            String assemblyAccession) throws IOException, DuplicateSeqColException, AssemblyNotFoundException,
+            AssemblyAlreadyIngestedException{
         Optional<Map<String, Object>> seqColDataMap = ncbiSeqColDataSource
                 .getAllPossibleSeqColExtendedData(assemblyAccession);
         if (!seqColDataMap.isPresent()) {
             logger.warn("No seqCol data corresponding to assemblyAccession " + assemblyAccession + " could be found on NCBI datasource");
-            ingestionResultEntity.setErrorMessage("No seqCol data corresponding to assemblyAccession " + assemblyAccession + " could be found on NCBI datasource");
-            return ingestionResultEntity;
+            throw new AssemblyNotFoundException(assemblyAccession);
         }
 
+        IngestionResultEntity ingestionResultEntity = new IngestionResultEntity();
+        ingestionResultEntity.setAssemblyAccession(assemblyAccession);
         // Retrieving the Map's data
         List<SeqColExtendedDataEntity<List<String>>> possibleSequencesNamesList =
                 (List<SeqColExtendedDataEntity<List<String>>>) seqColDataMap.get().get("namesAttributes");
@@ -185,10 +187,6 @@ public IngestionResultEntity fetchAndInsertAllSeqColByAssemblyAccession(
             SeqColExtendedDataEntity<List<String>> extendedSortedNameLengthPair = SeqColExtendedDataEntity.
                     constructSeqColSortedNameLengthPairs(extendedNamesEntity, extendedLengthsEntity);
 
-
-//            seqColExtendedDataEntities.add(extendedNamesEntity);
-//            seqColExtendedDataEntities.add(seqColSortedNameLengthPairEntity);
-
             // Constructing a list of seqColExtData that has the type List<String>
             List<SeqColExtendedDataEntity<List<String>>> seqColStringListExtDataEntities =
                     levelOneService.constructStringListExtDataEntities(sameValueAttributesMap, extendedNamesEntity,
@@ -218,23 +216,16 @@ public IngestionResultEntity fetchAndInsertAllSeqColByAssemblyAccession(
             } catch (DuplicateSeqColException e) {
                 logger.info("Seqcol for " + assemblyAccession + " and naming convention " + extendedNamesEntity.getNamingConvention() +
                 " already exists. Skipping.");
-                continue;
             }
         }
-        return ingestionResultEntity;
-    }
-
-    /**
-     * Return the extended data entity that corresponds to the seqCol lengths attribute*/
-    // TODO: REFACTOR
-    /*public SeqColExtendedDataEntity retrieveExtendedLengthEntity(List<SeqColExtendedDataEntity> extendedDataEntities) {
-        for (SeqColExtendedDataEntity entity: extendedDataEntities) {
-            if (entity.getAttributeType() == SeqColExtendedDataEntity.AttributeType.lengths) {
-                return entity;
-            }
+        if (ingestionResultEntity.getNumberOfInsertedSeqcols() == 0) {
+            logger.warn("Seqcol objects for assembly " + assemblyAccession + " has been already ingested");
+            throw new AssemblyAlreadyIngestedException(assemblyAccession);
+        } else {
+            return ingestionResultEntity;
         }
-        return null;
-    }*/
+
+    }
 
     @Transactional
     /**

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

@@ -1,22 +1,30 @@
 package uk.ac.ebi.eva.evaseqcol.controller;
 
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.function.Executable;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.boot.test.context.SpringBootTest;
 import org.springframework.boot.test.web.server.LocalServerPort;
+import org.springframework.http.HttpMethod;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.ResponseEntity;
 import org.springframework.http.client.support.BasicAuthenticationInterceptor;
 import org.springframework.test.context.DynamicPropertyRegistry;
 import org.springframework.test.context.DynamicPropertySource;
 import org.springframework.transaction.annotation.Transactional;
+import org.springframework.web.client.HttpClientErrorException;
 import org.springframework.web.client.RestTemplate;
 import org.testcontainers.containers.PostgreSQLContainer;
 import org.testcontainers.junit.jupiter.Container;
 import org.testcontainers.junit.jupiter.Testcontainers;
 
 import uk.ac.ebi.eva.evaseqcol.entities.SeqColLevelOneEntity;
 import uk.ac.ebi.eva.evaseqcol.entities.SeqColLevelTwoEntity;
+import uk.ac.ebi.eva.evaseqcol.exception.AssemblyAlreadyIngestedException;
 import uk.ac.ebi.eva.evaseqcol.service.SeqColService;
 
 import java.util.Optional;
@@ -72,6 +80,11 @@ void setUp() {
         baseUrl = baseUrl + ":" + port + contextPath + ADMIN_PATH;
     }
 
+    @AfterEach
+    void tearDown() {
+        seqColService.removeAllSeqCol();
+    }
+
     @Test
     @Transactional
     /**
@@ -89,4 +102,35 @@ void ingestSeqColsTest() {
         assertNotNull(levelTwoEntity.get().getLengths());
     }
 
+    @Test
+    /**
+     * Testing the response for the ingestion endpoint for
+     * different kind of ingestion cases:
+     * 1. Not existed
+     * 2. Already existed
+     * 3. Invalid assembly accession
+     * 4. Not found assembly accession
+     * Note: the order of execution is important */
+    void ingestionResponseTest() {
+        // 1. Testing Valid Non-Existing Accession
+        String finalRequest1 = baseUrl + "/" + ASM_ACCESSION;
+        ResponseEntity<String> putResponse1 = restTemplate.exchange(finalRequest1, HttpMethod.PUT, null, String.class);
+        assertEquals(HttpStatus.CREATED, putResponse1.getStatusCode());
+
+        // 2. Testing Valid Existing Accession
+        final String finalRequest2 = baseUrl + "/" + ASM_ACCESSION; // Same as above
+        assertThrows(HttpClientErrorException.Conflict.class,
+                     () -> restTemplate.exchange(finalRequest2, HttpMethod.PUT, null, String.class));
+
+        // 3. Testing Invalid Assembly Accession
+        final String finalRequest3 = baseUrl + "/" + ASM_ACCESSION.substring(0, ASM_ACCESSION.length()-4); // Less than 15 characters
+        assertThrows(HttpClientErrorException.BadRequest.class,
+                     () -> restTemplate.exchange(finalRequest3, HttpMethod.PUT, null, String.class));
+
+        // 4. Testing Assembly Not Found
+        final String finalRequest4 = baseUrl + "/" + ASM_ACCESSION + "55"; // Accession doesn't correspond to any assembly
+        assertThrows(HttpClientErrorException.NotFound.class,
+                     () -> restTemplate.exchange(finalRequest4, HttpMethod.PUT, null, String.class));
+    }
+
 }