Merge pull request #75 from waterflow80/ingestion-return-body

A proposal for the return type/object of the ingestion endpoint

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

@@ -12,9 +12,11 @@
 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;
+import uk.ac.ebi.eva.evaseqcol.model.IngestionResultEntity;
 import uk.ac.ebi.eva.evaseqcol.service.SeqColService;
 
 import java.io.IOException;
@@ -41,7 +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)"),
@@ -54,10 +56,8 @@ public ResponseEntity<?> fetchAndInsertSeqColByAssemblyAccession(
             example = "GCA_000146045.2",
             required = true) @PathVariable String asmAccession) {
         try {
-            List<String> level0Digests = seqColService.fetchAndInsertAllSeqColByAssemblyAccession(asmAccession);
-            return new ResponseEntity<>(
-                    "Successfully inserted seqCol object(s) for assembly accession " + asmAccession + "\nSeqCol digests=" + level0Digests
-                    , HttpStatus.OK);
+            IngestionResultEntity ingestionResult = seqColService.fetchAndInsertAllSeqColByAssemblyAccession(asmAccession);
+            return new ResponseEntity<>(ingestionResult, HttpStatus.CREATED);
         } catch (IncorrectAccessionException e) {
             return new ResponseEntity<>(e.getMessage(), HttpStatus.BAD_REQUEST);
         } catch (IllegalArgumentException e) {
@@ -70,6 +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/entities/SeqColExtendedDataEntity.java

@@ -49,6 +49,7 @@ public class SeqColExtendedDataEntity<T> {
     @Transient
     // This is needed when constructing multiple seqCol objects from the datasource to
     // identify the naming convention used for the sequences.
+    // Note: This will probably be required by the namesAttributeList and might be null for the others
     private SeqColEntity.NamingConvention namingConvention;
 
     public enum AttributeType {

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 + " have already been ingested");
+    }
+}

src/main/java/uk/ac/ebi/eva/evaseqcol/model/IngestionResultEntity.java

@@ -0,0 +1,38 @@
+package uk.ac.ebi.eva.evaseqcol.model;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+import lombok.AllArgsConstructor;
+import lombok.Data;
+import lombok.NoArgsConstructor;
+
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * This Entity will hold the information that should be returned
+ * upon ingestion of seqcol objects (given the assembly accession)*/
+@Data
+@NoArgsConstructor
+@AllArgsConstructor
+public class IngestionResultEntity {
+
+    @JsonProperty("assembly_accession")
+    private String assemblyAccession;
+    @JsonProperty("num_inserted_seqcols")
+    private Integer numberOfInsertedSeqcols = 0;
+    @JsonProperty("inserted_seqcols")
+    private List<InsertedSeqColEntity> insertedSeqcols = new ArrayList<>();
+    @JsonProperty("error_message")
+    private String errorMessage = null;
+
+
+    public void addInsertedSeqCol(InsertedSeqColEntity insertedSeqCol) {
+        this.insertedSeqcols.add(insertedSeqCol);
+    }
+
+    /**
+     * Increment the numberOfInsertedSeqcols by one*/
+    public void incrementNumberOfInsertedSeqCols() {
+        this.numberOfInsertedSeqcols += 1;
+    }
+}

src/main/java/uk/ac/ebi/eva/evaseqcol/model/InsertedSeqColEntity.java

@@ -0,0 +1,19 @@
+package uk.ac.ebi.eva.evaseqcol.model;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+import lombok.AllArgsConstructor;
+import lombok.Data;
+import lombok.NoArgsConstructor;
+
+/**
+ * This entity will hold minimal seqcol information that will be returned
+ * to the user upon ingestion*/
+@Data
+@NoArgsConstructor
+@AllArgsConstructor
+public class InsertedSeqColEntity {
+
+    private String digest; // Level 0 digest
+    @JsonProperty("naming_convention")
+    private String namingConvention;
+}

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

@@ -14,10 +14,14 @@
 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;
 import uk.ac.ebi.eva.evaseqcol.exception.UnableToLoadServiceInfoException;
+import uk.ac.ebi.eva.evaseqcol.model.IngestionResultEntity;
+import uk.ac.ebi.eva.evaseqcol.model.InsertedSeqColEntity;
 import uk.ac.ebi.eva.evaseqcol.utils.JSONExtData;
 import uk.ac.ebi.eva.evaseqcol.utils.JSONIntegerListExtData;
 import uk.ac.ebi.eva.evaseqcol.utils.JSONStringListExtData;
@@ -155,16 +159,18 @@ public void removeAllSeqCol() {
      * NOTE: All possible seqCol objects means with all possible/provided naming conventions that could be found in the
      * assembly report.
      * Return the list of level 0 digests of the inserted seqcol objects*/
-    public List<String> fetchAndInsertAllSeqColByAssemblyAccession(
-            String assemblyAccession) throws IOException, DuplicateSeqColException {
-        List<String> insertedSeqColDigests = new ArrayList<>();
+    public IngestionResultEntity fetchAndInsertAllSeqColByAssemblyAccession(
+            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");
-            return insertedSeqColDigests;
+            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");
@@ -181,10 +187,6 @@ public List<String> 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,
@@ -199,30 +201,31 @@ public List<String> fetchAndInsertAllSeqColByAssemblyAccession(
                     seqColStringListExtDataEntities, seqColIntegerListExtDataEntities, extendedNamesEntity.getNamingConvention()
                     );
 
-            Optional<String> seqColDigest = insertSeqColL1AndL2( // TODO: Check for possible self invocation problem
-                    levelOneEntity, seqColStringListExtDataEntities, seqColIntegerListExtDataEntities);
-            if (seqColDigest.isPresent()) {
-                logger.info(
-                        "Successfully inserted seqCol for assembly Accession " + assemblyAccession + " with naming convention " + extendedNamesEntity.getNamingConvention());
-                insertedSeqColDigests.add(seqColDigest.get());
-            } else {
-                logger.warn("Could not insert seqCol for assembly Accession " + assemblyAccession + " with naming convention " + extendedNamesEntity.getNamingConvention());
+            try {
+                Optional<String> seqColDigest = insertSeqColL1AndL2( // TODO: Check for possible self invocation problem
+                                                                     levelOneEntity, seqColStringListExtDataEntities, seqColIntegerListExtDataEntities);
+                if (seqColDigest.isPresent()) {
+                    logger.info(
+                            "Successfully inserted seqCol for assembly Accession " + assemblyAccession + " with naming convention " + extendedNamesEntity.getNamingConvention());
+                    InsertedSeqColEntity insertedSeqCol = new InsertedSeqColEntity(seqColDigest.get(), extendedNamesEntity.getNamingConvention().toString());
+                    ingestionResultEntity.addInsertedSeqCol(insertedSeqCol);
+                    ingestionResultEntity.incrementNumberOfInsertedSeqCols();
+                } else {
+                    logger.warn("Could not insert seqCol for assembly Accession " + assemblyAccession + " with naming convention " + extendedNamesEntity.getNamingConvention());
+                }
+            } catch (DuplicateSeqColException e) {
+                logger.info("Seqcol for " + assemblyAccession + " and naming convention " + extendedNamesEntity.getNamingConvention() +
+                " already exists. Skipping.");
             }
         }
-        return insertedSeqColDigests;
-    }
-
-    /**
-     * 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

@@ -1,15 +1,24 @@
 package uk.ac.ebi.eva.evaseqcol.controller;
 
+import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.MethodOrderer;
+import org.junit.jupiter.api.Order;
 import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.TestMethodOrder;
 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.ActiveProfiles;
 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;
@@ -21,10 +30,14 @@
 
 import java.util.Optional;
 
-import static org.junit.jupiter.api.Assertions.*;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.assertThrows;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 
 @SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT)
 @Testcontainers
+@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
 public class AdminControllerIntegrationTest {
 
     @LocalServerPort
@@ -72,7 +85,13 @@ void setUp() {
         baseUrl = baseUrl + ":" + port + contextPath + ADMIN_PATH;
     }
 
+    @AfterEach
+    void tearDown() {
+        seqColService.removeAllSeqCol(); // TODO Fix: This operation is rolled back for some reason @see 'https://www.baeldung.com/hibernate-initialize-proxy-exception' (might help)
+    }
+
     @Test
+    @Order(2)
     @Transactional
     /**
      * Ingest all possible seqCol objects given the assembly accession*/
@@ -89,4 +108,36 @@ void ingestSeqColsTest() {
         assertNotNull(levelTwoEntity.get().getLengths());
     }
 
+    @Test
+    @Order(1)
+    /**
+     * 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));
+    }
+
 }