- Moved conversation to API v0 controller

- Added unit test for controllers

src/main/java/org/genesys2/server/api/v0/AccessionController.java

@@ -231,7 +231,7 @@ public class AccessionController extends ApiBaseController {
 
 			} catch (DataAccessException | TransactionException | PersistenceException e) {
 				List<AccessionOpResponse> res = upsert1By1(institute, updates);
-				LOG.info("Processed {} accessions for {} 1by1 after {} tries in {}ms because of {}", updates.size(), instCode, tryCount + 1, stopWatch.getTime(), e.getMessage());				
+				LOG.info("Processed {} accessions for {} 1by1 after {} tries in {}ms because of {}", updates.size(), instCode, tryCount + 1, stopWatch.getTime(), e.getMessage());
 				return res;
 			
 			} catch (PleaseRetryException e) {
@@ -309,14 +309,15 @@ public class AccessionController extends ApiBaseController {
 			throw new NotFoundElement();
 		}
 
+		final ArrayNode updates = convertToArrayNode(batch);
 		try {
 			List<AccessionOpResponse> response = null;
 			try {
-				response = uploader.deleteAccessions(institute, batch);
+				response = uploader.deleteAccessions(institute, updates);
 				LOG.info("Deleted {} accessions from {}", response.size(), instCode);
 			} catch (DataAccessException | TransactionException | PersistenceException e) {
 				LOG.info("Retrying delete one by one due to {}", e.getMessage());
-				response = deleteAccessions1by1(institute, batch);
+				response = deleteAccessions1by1(institute, updates);
 			}
 			return response;
 
@@ -325,26 +326,24 @@ public class AccessionController extends ApiBaseController {
 		}
 	}
 
-	private List<AccessionOpResponse> deleteAccessions1by1(FaoInstitute institute, List<AccessionHeaderJson> batch) {
+	private List<AccessionOpResponse> deleteAccessions1by1(FaoInstitute institute, ArrayNode updates) {
 		LOG.info("Attempting delete 1 by 1");
 
-		final List<AccessionHeaderJson> batchOfOne = new ArrayList<AccessionHeaderJson>();
+		ArrayNode single = new ObjectMapper().createArrayNode();
 		List<AccessionOpResponse> response = new ArrayList<AccessionOpResponse>();
-		for (AccessionHeaderJson acceJ : batch) {
-
+		for (JsonNode update : updates) {
 			try {
-
-				batchOfOne.clear();
-				batchOfOne.add(acceJ);
-				AccessionOpResponse accessionResponse = uploader.deleteAccessions(institute, batchOfOne).get(0);
+				single.removeAll();
+				single.add(update);
+				AccessionOpResponse accessionResponse = uploader.deleteAccessions(institute, single).get(0);
 				response.add(accessionResponse);
 
 			} catch (Throwable e) {
 				if (LOG.isInfoEnabled()) {
-					LOG.info("Error deleting {}: {}", acceJ.instCode, e.getMessage());
+					LOG.info("Error deleting {}: {}", update.get("instituteCode").asText(), e.getMessage());
 				}
 
-				AccessionOpResponse accessionResponse = new AccessionOpResponse(acceJ.instCode, acceJ.acceNumb, acceJ.genus);
+				AccessionOpResponse accessionResponse = new AccessionOpResponse(update.get("instituteCode").asText(), update.get("accessionNumber").asText(), update.get("taxonomy").get("genus").asText());
 				accessionResponse.setError(getDetailedErrorMessage(e));
 				response.add(accessionResponse);
 			}
@@ -414,8 +413,19 @@ public class AccessionController extends ApiBaseController {
 		public Integer maxRecords;
 		public String otherOptions;
 	}
-	
-	
+
+	private ArrayNode convertToArrayNode(List<AccessionHeaderJson> updates) {
+		final ArrayNode arrayNode = mapper.createArrayNode();
+		for (AccessionHeaderJson accnJ: updates) {
+			ObjectNode accession = arrayNode.addObject();
+			accession.put("instituteCode", accnJ.getHoldingInstitute());
+			accession.put("accessionNumber", accnJ.getAccessionNumber());
+			accession.put("doi", accnJ.getDoi());
+			ObjectNode taxonNode = accession.putObject("taxonomy");
+			taxonNode.put("genus", accnJ.getGenus());
+		}
+		return arrayNode;
+	}
 
 	private void upgradeToV2(ArrayNode updates) {
 		for (JsonNode update : updates) {

src/main/java/org/genesys2/server/service/worker/AccessionUploader.java

@@ -673,29 +673,6 @@ public class AccessionUploader implements InitializingBean {
 		return object;
 	}
 
-	@Transactional(timeout = 250, isolation = Isolation.READ_UNCOMMITTED, rollbackFor = Throwable.class)
-	@PreAuthorize("hasRole('ADMINISTRATOR') or hasPermission(#institute, 'WRITE')")
-	public List<AccessionOpResponse> deleteAccessions(FaoInstitute institute, List<AccessionHeaderJson> identifiers) {
-		final ObjectMapper mapper = new ObjectMapper();
-		final ArrayNode arrayNode = mapper.createArrayNode();
-
-		for (AccessionHeaderJson accnJ: identifiers) {
-			ObjectNode rootNode = mapper.createObjectNode();
-			rootNode.put("instituteCode", accnJ.getHoldingInstitute());
-			rootNode.put("accessionNumber", accnJ.getAccessionNumber());
-			rootNode.put("doi", accnJ.getDoi());
-
-			ObjectNode taxonNode = mapper.createObjectNode();
-			taxonNode.put("genus", accnJ.getGenus());
-
-			rootNode.set("taxonomy", taxonNode);
-
-			arrayNode.add(rootNode);
-		}
-
-		return deleteAccessions(institute, arrayNode);
-	}
-
 	@Transactional(timeout = 250, isolation = Isolation.READ_UNCOMMITTED, rollbackFor = Throwable.class)
 	@PreAuthorize("hasRole('ADMINISTRATOR') or hasPermission(#institute, 'WRITE')")
 	public List<AccessionOpResponse> deleteAccessions(FaoInstitute institute, ArrayNode identifiers) {

src/test/java/org/genesys/test/base/AbstractApiTest.java

@@ -26,6 +26,8 @@ import java.util.UUID;
 
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.databind.DeserializationFeature;
+import com.fasterxml.jackson.databind.node.ArrayNode;
+import com.fasterxml.jackson.databind.node.ObjectNode;
 import org.genesys.catalog.model.Partner;
 import org.genesys.catalog.model.dataset.Dataset;
 import org.genesys.catalog.model.dataset.DatasetCreator;
@@ -221,4 +223,23 @@ public abstract class AbstractApiTest extends AbstractTest {
 		return descriptor;
 	}
 
+	protected ArrayNode upsertAccessions(final String instCode, final String acceNumb, final String genus, final String doi) {
+		ArrayNode updates = objectMapper.createArrayNode();
+		updates.add(upsertAccession(instCode, acceNumb, genus, doi));
+		return updates;
+	}
+
+	protected ObjectNode upsertAccession(final String instCode, final String accnNumber, final String genus, final String doi) {
+		ObjectNode accession = objectMapper.createObjectNode();
+		accession.put("instituteCode", instCode);
+		accession.put("accessionNumber", accnNumber);
+		if (doi != null) {
+			accession.put("doi", doi);
+		}
+		ObjectNode taxa = accession.putObject("taxonomy");
+		taxa.put("genus", genus);
+
+		return accession;
+	}
+
 }
\ No newline at end of file

src/test/java/org/genesys/test/catalog/services/CatalogServiceTest.java

@@ -241,13 +241,20 @@ public abstract class CatalogServiceTest extends AbstractServiceTest {
 			institute = instituteService.getInstitute(instCode);
 		}
 
+		ObjectMapper mapper = new ObjectMapper();
+		final ArrayNode arrayNode = mapper.createArrayNode();
+		ObjectNode rootNode = arrayNode.addObject();
+		rootNode.put("instituteCode", instCode);
+		rootNode.put("accessionNumber", acceNumb);
+		ObjectNode taxonNode = rootNode.putObject("taxonomy");
+		taxonNode.put("genus", genus);
+
 		AccessionHeaderJson ah = new AccessionHeaderJson();
 		ah.instCode = instCode;
 		ah.acceNumb = acceNumb;
 		ah.genus = genus;
 
-		List<AccessionHeaderJson> identifiers = Lists.newArrayList(ah);
-		accessionUploader.deleteAccessions(institute, identifiers);
+		accessionUploader.deleteAccessions(institute, arrayNode);
 		assert(accessionRepository.findOne(institute, null, acceNumb, genus) == null);
 	}
 }

src/test/java/org/genesys/test/server/api/v0/AccessionControllerTest.java

 /*
- * Copyright 2018 Global Crop Diversity Trust
+ * Copyright 2019 Global Crop Diversity Trust
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -16,7 +16,9 @@
 
 package org.genesys.test.server.api.v0;
 
+import static org.hamcrest.CoreMatchers.is;
 import static org.hamcrest.Matchers.*;
+import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertThat;
 import static org.springframework.restdocs.mockmvc.MockMvcRestDocumentation.documentationConfiguration;
 import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.*;
@@ -29,16 +31,19 @@ import java.util.concurrent.atomic.AtomicInteger;
 import java.util.stream.Collectors;
 
 import org.genesys.test.base.AbstractApiTest;
+import org.genesys2.server.api.model.AccessionHeaderJson;
 import org.genesys2.server.api.v0.AccessionController;
 import org.genesys2.server.model.genesys.*;
 import org.genesys2.server.model.genesys.AccessionAlias.AliasType;
 import org.genesys2.server.model.impl.FaoInstitute;
+import org.genesys2.server.persistence.AccessionHistoricRepository;
 import org.genesys2.server.persistence.AccessionIdRepository;
 import org.genesys2.server.persistence.AccessionRepository;
 import org.genesys2.server.persistence.FaoInstituteRepository;
 import org.genesys2.server.persistence.Taxonomy2Repository;
 import org.genesys2.server.service.InstituteService;
 import org.genesys2.server.service.TaxonomyService;
+import org.genesys2.server.service.worker.AccessionUploader;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Rule;
@@ -68,6 +73,12 @@ public class AccessionControllerTest extends AbstractApiTest {
 	private static final int STORAGE_10 = 10;
 	private static final int STORAGE_11 = 11;
 
+	private static final String ACCENUMB_1 = "A-0001";
+	private static final String ACCENUMB_2 = "A-0002";
+
+	private static final String GENUS_1 = "Hordeum";
+	private static final String GENUS_2 = "Musa";
+
 	@Rule
 	public final JUnitRestDocumentation restDocumentation = new JUnitRestDocumentation("target/generated-snippets");
 
@@ -80,6 +91,8 @@ public class AccessionControllerTest extends AbstractApiTest {
 	@Autowired
 	private AccessionIdRepository accessionIdRepository;
 	@Autowired
+	private AccessionHistoricRepository accessionHistoricRepository;
+	@Autowired
 	private FaoInstituteRepository instituteRepository;
 	@Autowired
 	private InstituteService instituteService;
@@ -87,6 +100,8 @@ public class AccessionControllerTest extends AbstractApiTest {
 	private Taxonomy2Repository taxonomyRepository;
 	@Autowired
 	private TaxonomyService taxonomyService;
+	@Autowired
+	private AccessionUploader accessionUploader;
 
 	MockMvc mockMvc;
 
@@ -108,8 +123,10 @@ public class AccessionControllerTest extends AbstractApiTest {
 	@Override
 	@Transactional
 	public void cleanup() throws Exception {
+		accessionHistoricRepository.deleteAll();
 		accessionRepository.deleteAll();
 		accessionIdRepository.deleteAll();
+
 		taxonomyRepository.deleteAll();
 		instituteRepository.deleteAll();
 		super.cleanup();
@@ -152,6 +169,40 @@ public class AccessionControllerTest extends AbstractApiTest {
 		assertThat(accessionRepository.count(), is(1L));
 	}
 
+	@Test
+	public void deleteAccessionsTest() throws Exception {
+		accessionUploader.upsertAccessions(institute, upsertAccessions(institute.getCode(), ACCENUMB_1, GENUS_1, null));
+		accessionUploader.upsertAccessions(institute, upsertAccessions(institute.getCode(), ACCENUMB_2, GENUS_2, null));
+
+		Accession storedAccession = accessionRepository.findByInstituteCodeAndAccessionNumber(institute.getCode(), ACCENUMB_1);
+		assertThat(storedAccession.getAccessionNumber(), is(ACCENUMB_1));
+
+		Accession storedAccession2 = accessionRepository.findByInstituteCodeAndAccessionNumber(institute.getCode(), ACCENUMB_2);
+		assertThat(storedAccession2.getAccessionNumber(), is(ACCENUMB_2));
+
+		AccessionHeaderJson aHS2 = new AccessionHeaderJson();
+		aHS2.instCode = storedAccession.getInstCode();
+		aHS2.acceNumb = storedAccession.getAccessionNumber();
+		aHS2.genus = storedAccession.getGenus();
+
+		final String s = "[" + verboseMapper.writeValueAsString(aHS2) + "]";
+
+		/*@formatter:off*/
+		mockMvc.perform(post(AccessionController.API_BASE + "/" + institute.getCode() + "/delete-named")
+				.contentType(MediaType.APPLICATION_JSON)
+				.content(s))
+//			.andDo(MockMvcResultHandlers.print())
+			.andExpect(status().isOk())
+			.andExpect(content().contentType(MediaType.APPLICATION_JSON_UTF8))
+			.andExpect(jsonPath("$", not(nullValue())))
+			.andExpect(jsonPath("$[0].instCode", is(institute.getCode())))
+			.andExpect(jsonPath("$[0].error", nullValue()));
+		/*@formatter:on*/
+
+		assertThat(accessionRepository.count(), is(1L));
+		assertNotNull(accessionRepository.findByInstituteCodeAndAccessionNumber(institute.getCode(), ACCENUMB_2));
+	}
+
 	@Test
 	public void getAccessionsTest() throws Exception {
 

src/test/java/org/genesys/test/server/api/v1/AccessionControllerTest.java

@@ -16,7 +16,9 @@
 
 package org.genesys.test.server.api.v1;
 
+import static org.hamcrest.CoreMatchers.is;
 import static org.hamcrest.Matchers.*;
+import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertThat;
 import static org.junit.Assert.assertNull;
 import static org.springframework.restdocs.mockmvc.MockMvcRestDocumentation.documentationConfiguration;
@@ -37,6 +39,7 @@ import org.genesys2.server.model.genesys.*;
 import org.genesys2.server.model.genesys.AccessionAlias.AliasType;
 import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.server.persistence.AccessionGeoRepository;
+import org.genesys2.server.persistence.AccessionHistoricRepository;
 import org.genesys2.server.persistence.AccessionIdRepository;
 import org.genesys2.server.persistence.AccessionRepository;
 import org.genesys2.server.persistence.FaoInstituteRepository;
@@ -44,6 +47,7 @@ import org.genesys2.server.persistence.Taxonomy2Repository;
 import org.genesys2.server.service.InstituteService;
 import org.genesys2.server.service.TaxonomyService;
 import org.genesys2.server.service.filter.AccessionFilter;
+import org.genesys2.server.service.worker.AccessionUploader;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Rule;
@@ -73,6 +77,12 @@ public class AccessionControllerTest extends AbstractApiTest {
 	private static final int STORAGE_10 = 10;
 	private static final int STORAGE_11 = 11;
 
+	private static final String ACCENUMB_1 = "A-0001";
+	private static final String ACCENUMB_2 = "A-0002";
+
+	private static final String GENUS_1 = "Hordeum";
+	private static final String GENUS_2 = "Musa";
+
 	@Rule
 	public final JUnitRestDocumentation restDocumentation = new JUnitRestDocumentation("target/generated-snippets");
 
@@ -85,6 +95,8 @@ public class AccessionControllerTest extends AbstractApiTest {
 	@Autowired
 	private AccessionIdRepository accessionIdRepository;
 	@Autowired
+	private AccessionHistoricRepository accessionHistoricRepository;
+	@Autowired
 	private AccessionGeoRepository accessionGeoRepository;
 	@Autowired
 	private FaoInstituteRepository instituteRepository;
@@ -94,27 +106,21 @@ public class AccessionControllerTest extends AbstractApiTest {
 	private Taxonomy2Repository taxonomyRepository;
 	@Autowired
 	private TaxonomyService taxonomyService;
+	@Autowired
+	private AccessionUploader accessionUploader;
 
 	MockMvc mockMvc;
 
 	private FaoInstitute institute;
 	private AtomicInteger acceNumb = new AtomicInteger(1);
 
-	protected static final ObjectMapper objectMapper;
-
 	protected static final ObjectMapper verboseMapper = new ObjectMapper();
 
-	static {
-		objectMapper = new ObjectMapper();
-		objectMapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
-		objectMapper.configure(DeserializationFeature.ACCEPT_SINGLE_VALUE_AS_ARRAY, true);
-		objectMapper.setSerializationInclusion(JsonInclude.Include.NON_EMPTY);
-	}
-
 	@After
 	@Override
 	@Transactional
 	public void cleanup() throws Exception {
+		accessionHistoricRepository.deleteAll();
 		accessionRepository.deleteAll();
 		accessionIdRepository.deleteAll();
 		accessionGeoRepository.deleteAll();
@@ -160,6 +166,38 @@ public class AccessionControllerTest extends AbstractApiTest {
 		assertThat(accessionRepository.count(), is(1L));
 	}
 
+	@Test
+	public void deleteAccessionsTest() throws Exception {
+		ArrayNode arrayNode = verboseMapper.createArrayNode();
+		arrayNode.add(upsertAccession(institute.getCode(), ACCENUMB_1, GENUS_1, null));
+		accessionUploader.upsertAccessions(institute, arrayNode);
+		accessionUploader.upsertAccessions(institute, upsertAccessions(institute.getCode(), ACCENUMB_2, GENUS_2, null));
+
+		Accession storedAccession = accessionRepository.findByInstituteCodeAndAccessionNumber(institute.getCode(), ACCENUMB_1);
+		assertThat(storedAccession.getAccessionNumber(), is(ACCENUMB_1));
+
+		Accession storedAccession2 = accessionRepository.findByInstituteCodeAndAccessionNumber(institute.getCode(), ACCENUMB_2);
+		assertThat(storedAccession2.getAccessionNumber(), is(ACCENUMB_2));
+
+
+		final String s = verboseMapper.writeValueAsString(arrayNode);
+
+		/*@formatter:off*/
+		mockMvc.perform(post(AccessionUploadController.CONTROLLER_URL + "/" + institute.getCode() + "/delete")
+				.contentType(MediaType.APPLICATION_JSON)
+				.content(s))
+			.andExpect(status().isOk())
+			.andExpect(content().contentType(MediaType.APPLICATION_JSON_UTF8))
+			.andExpect(jsonPath("$", not(nullValue())))
+			.andExpect(jsonPath("$[0].instCode", is(institute.getCode())))
+			.andExpect(jsonPath("$[0].error", nullValue()))
+			.andExpect(jsonPath("$[0].result.action", equalTo("DELETE")));
+		/*@formatter:on*/
+
+		assertThat(accessionRepository.count(), is(1L));
+		assertNotNull(accessionRepository.findByInstituteCodeAndAccessionNumber(institute.getCode(), ACCENUMB_2));
+	}
+
 	@Test
 	public void taxonomyFilterTest() throws Exception {
 		ObjectNode accessionJson = setUpAccession();

src/test/java/org/genesys/test/server/services/AccessionUploaderTest.java

@@ -22,8 +22,6 @@ import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.fail;
 
-import java.util.ArrayList;
-import java.util.Collections;
 import java.util.List;
 
 import org.genesys2.server.api.model.AccessionHeaderJson;
@@ -117,24 +115,28 @@ public class AccessionUploaderTest extends AbstractServicesTest {
 		super.cleanup();
 	}
 	
-	protected ArrayNode upsertAccession(final String instCode, final String acceNumb, final String genus, final String doi) {
+	protected ArrayNode upsertAccessions(final String instCode, final String acceNumb, final String genus, final String doi) {
 		ArrayNode updates = objectMapper.createArrayNode();
-		ObjectNode accession = updates.addObject();
+		updates.add(upsertAccession(instCode, acceNumb, genus, doi));
+		return updates;
+	}
+