Merge branch '373-accession-v1-api' into 'master'

Resolve "Accession v1 API"

Closes #373

See merge request genesys-pgr/genesys-server!288

src/main/java/org/genesys2/server/api/v1/AccessionController.java

@@ -79,14 +79,14 @@ import io.swagger.annotations.Api;
  */
 @RestController("accessionApi1")
 @PreAuthorize("isAuthenticated()")
-@RequestMapping(AccessionController.API_BASE)
+@RequestMapping(AccessionController.CONTROLLER_URL)
 @Api(tags = { "accession" })
 public class AccessionController {
 
 	private static final Logger LOG = LoggerFactory.getLogger(AccessionController.class);
 
-	/** The Constant API_BASE. */
-	public static final String API_BASE = ApiBaseController.APIv1_BASE + "/acn";
+	/** The Constant CONTROLLER_URL. */
+	public static final String CONTROLLER_URL = ApiBaseController.APIv1_BASE + "/acn";
 
 	private static final int DOWNLOAD_LIMIT = 200000;
 
@@ -121,9 +121,9 @@ public class AccessionController {
 	 * @param uuid the uuid
 	 * @return the subset
 	 */
-	@GetMapping(value = "/{UUID:\\w{8}\\-\\w{4}.+}", produces = { MediaType.APPLICATION_JSON_VALUE })
+	@GetMapping(value = "/{uuid:\\w{8}\\-\\w{4}.+}", produces = { MediaType.APPLICATION_JSON_VALUE })
 	@JsonView({ JsonViews.Protected.class })
-	public Accession getByUuid(@PathVariable("UUID") final UUID uuid) {
+	public Accession getByUuid(@PathVariable("uuid") final UUID uuid) {
 		return accessionService.getByUuid(uuid);
 	}
 
@@ -215,9 +215,9 @@ public class AccessionController {
 		return accessionService.getAccessionDetails(accession);
 	}
 
-	@GetMapping(value = "/details/{UUID:\\w{8}\\-\\w{4}.+}", produces = MediaType.APPLICATION_JSON_VALUE)
+	@GetMapping(value = "/details/{uuid:\\w{8}\\-\\w{4}.+}", produces = MediaType.APPLICATION_JSON_VALUE)
 	@JsonView(JsonViews.Root.class)
-	public AccessionService.AccessionDetails getAccessionDetailsByUUID(@PathVariable("UUID") final UUID uuid) {
+	public AccessionService.AccessionDetails getAccessionDetailsByUUID(@PathVariable("uuid") final UUID uuid) {
 		Accession accession = accessionService.getByUuid(uuid);
 		return accessionService.getAccessionDetails(accession);
 	}

src/main/java/org/genesys2/server/api/v1/AccessionUploadController.java

+/*
+ * Copyright 2018 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.
+ * You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.genesys2.server.api.v1;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.persistence.PersistenceException;
+import javax.persistence.RollbackException;
+
+import org.apache.commons.lang3.RandomUtils;
+import org.apache.commons.lang3.time.StopWatch;
+import org.genesys2.server.api.ApiBaseController;
+import org.genesys2.server.api.PleaseRetryException;
+import org.genesys2.server.api.model.AccessionHeaderJson;
+import org.genesys2.server.exception.InvalidApiUsageException;
+import org.genesys2.server.model.impl.FaoInstitute;
+import org.genesys2.server.service.InstituteService;
+import org.genesys2.server.service.impl.RESTApiException;
+import org.genesys2.server.service.worker.AccessionOpResponse;
+import org.genesys2.server.service.worker.AccessionOpResponse.UpsertResult;
+import org.genesys2.server.service.worker.AccessionUploader;
+import org.genesys2.spring.ResourceNotFoundException;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.dao.CannotAcquireLockException;
+import org.springframework.dao.DataAccessException;
+import org.springframework.dao.DataIntegrityViolationException;
+import org.springframework.http.MediaType;
+import org.springframework.security.access.prepost.PreAuthorize;
+import org.springframework.transaction.TransactionException;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestBody;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.ResponseBody;
+import org.springframework.web.bind.annotation.RestController;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.node.ArrayNode;
+
+import io.swagger.annotations.Api;
+
+/**
+ * Accession API v1: the uploader.
+ */
+@RestController("accessionUploadApi1")
+@PreAuthorize("isAuthenticated()")
+@RequestMapping(AccessionUploadController.CONTROLLER_URL)
+@Api(tags = { "accession" })
+public class AccessionUploadController {
+
+	/** The Constant LOG. */
+	private static final Logger LOG = LoggerFactory.getLogger(AccessionUploadController.class);
+
+	/** The Constant CONTROLLER_URL. */
+	public static final String CONTROLLER_URL = ApiBaseController.APIv1_BASE + "/acn";
+
+	/** The Constant UPLOAD_RETRIES. */
+	private static final int UPLOAD_RETRIES = 10;
+
+	/** The uploader. */
+	@Autowired
+	private AccessionUploader uploader;
+
+	/** The institute service. */
+	@Autowired
+	InstituteService instituteService;
+
+
+	/**
+	 * Update accessions in the system.
+	 *
+	 * @param instCode the WIEWS institute code
+	 * @param updates the updates
+	 * @return the list
+	 * @throws Exception the exception
+	 */
+	@PreAuthorize("isAuthenticated()")
+	@RequestMapping(value = "/{instCode}/upsert", method = { RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
+	public List<AccessionOpResponse> upsertInstituteAccession(@PathVariable("instCode") String instCode, @RequestBody ArrayNode updates) throws Exception {
+		
+		StopWatch stopWatch = StopWatch.createStarted();
+
+		LOG.trace("Received:\n {}", updates);
+
+		// User's permission to WRITE to this WIEWS institute are checked in
+		// BatchRESTService.
+		final FaoInstitute institute = instituteService.getInstitute(instCode);
+		if (institute == null) {
+			throw new ResourceNotFoundException();
+		}
+
+		for (int tryCount = 0; tryCount < UPLOAD_RETRIES; tryCount++) {
+			try {
+				List<AccessionOpResponse> res = uploader.upsertAccessions(institute, updates);
+				LOG.info("Processed {} accessions for {} in {} tries in {}ms", updates.size(), instCode, tryCount + 1, stopWatch.getTime());
+				return res;
+
+			} 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());				
+				return res;
+			
+			} catch (PleaseRetryException e) {
+				LOG.error("Retry {} of {} tries due to: {}", tryCount, UPLOAD_RETRIES, e.getMessage());
+				// Wait a bit
+				Thread.sleep((long) (RandomUtils.nextDouble(10, 100) * tryCount));
+			}
+		}
+		throw new InvalidApiUsageException("Just couldn't do it.");
+	}
+
+	/**
+	 * Upsert 1 by 1.
+	 *
+	 * @param institute the institute
+	 * @param updates the updates
+	 * @return the list
+	 * @throws Exception the exception
+	 */
+	private List<AccessionOpResponse> upsert1By1(FaoInstitute institute, ArrayNode updates) throws Exception {
+		List<AccessionOpResponse> response = new ArrayList<>();
+		ArrayNode single = new ObjectMapper().createArrayNode();
+		for (JsonNode update : updates) {
+			single.removeAll();
+			single.add(update);
+			Throwable lastException = null;
+			for (int tryCount = 0; tryCount < UPLOAD_RETRIES; tryCount++) {
+				try {
+					response.addAll(uploader.upsertAccessions(institute, single));
+					lastException = null;
+					break;
+				} catch (TransactionException | RollbackException | CannotAcquireLockException | DataIntegrityViolationException | PleaseRetryException e) {
+					lastException = e;
+					if (tryCount > 1) {
+						LOG.info("Retry {} of {} tries due to: {}", tryCount, UPLOAD_RETRIES, e.getMessage());
+					} else {
+						LOG.debug("Retrying {} of {} tries due to: {}", tryCount, UPLOAD_RETRIES, e.getMessage());
+					}
+					// Wait a bit
+					Thread.sleep((long) (RandomUtils.nextDouble(10, 100) * tryCount));
+				}
+			}
+			if (lastException != null) {
+				LOG.warn("Upsert failed due to: {} data={}", lastException.getMessage(), update, lastException);
+				// record error
+				response.add(new AccessionOpResponse(update.get("instituteCode").asText(), update.get("accessionNumber").asText(), update.get("taxonomy").get("genus").asText())
+					.setResult(new UpsertResult(UpsertResult.Type.ERROR)).setError(getDetailedErrorMessage(lastException)));
+			}
+		}
+		return response;
+	}
+	
+
+	/**
+	 * Delete accessions by instituteCode, acceNumb and genus.
+	 *
+	 * @param instCode the inst code
+	 * @param batch the batch
+	 * @return the list
+	 * @throws RESTApiException the REST api exception
+	 */
+	@PreAuthorize("isAuthenticated()")
+	@RequestMapping(value = "/{instCode}/delete", method = { RequestMethod.POST }, consumes = { MediaType.APPLICATION_JSON_VALUE }, produces = {
+			MediaType.APPLICATION_JSON_VALUE })
+	public @ResponseBody List<AccessionOpResponse> deleteAccessions(@PathVariable("instCode") String instCode, @RequestBody List<AccessionHeaderJson> batch) throws RESTApiException {
+		// User's permission to WRITE to this WIEWS institute are checked in
+		// BatchRESTService.
+		final FaoInstitute institute = instituteService.getInstitute(instCode);
+		if (institute == null) {
+			throw new ResourceNotFoundException();
+		}
+
+		try {
+			List<AccessionOpResponse> response = null;
+			try {
+				response = uploader.deleteAccessions(institute, batch);
+				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);
+			}
+			return response;
+
+		} catch (CannotAcquireLockException e) {
+			throw new PleaseRetryException("Operation failed, please retry.", e);
+		}
+	}
+
+	/**
+	 * Delete accessions 1 by 1.
+	 *
+	 * @param institute the institute
+	 * @param batch the batch
+	 * @return the list
+	 */
+	private List<AccessionOpResponse> deleteAccessions1by1(FaoInstitute institute, List<AccessionHeaderJson> batch) {
+		LOG.info("Attempting delete 1 by 1");
+
+		final List<AccessionHeaderJson> batchOfOne = new ArrayList<AccessionHeaderJson>();
+		List<AccessionOpResponse> response = new ArrayList<AccessionOpResponse>();
+		for (AccessionHeaderJson acceJ : batch) {
+
+			try {
+
+				batchOfOne.clear();
+				batchOfOne.add(acceJ);
+				AccessionOpResponse accessionResponse = uploader.deleteAccessions(institute, batchOfOne).get(0);
+				response.add(accessionResponse);
+
+			} catch (Throwable e) {
+				if (LOG.isInfoEnabled()) {
+					LOG.info("Error deleting {}: {}", acceJ.instCode, e.getMessage());
+				}
+
+				AccessionOpResponse accessionResponse = new AccessionOpResponse(acceJ.instCode, acceJ.acceNumb, acceJ.genus);
+				accessionResponse.setError(getDetailedErrorMessage(e));
+				response.add(accessionResponse);
+			}
+		}
+		return response;
+	}
+	
+
+	/**
+	 * Gets the detailed error message.
+	 *
+	 * @param e the exception
+	 * @return the detailed error message
+	 */
+	private String getDetailedErrorMessage(Throwable e) {
+		StringBuffer sb=new StringBuffer(e.getMessage());
+		Throwable r = e;
+		while ((r = r.getCause()) !=null) {
+			sb.append("\n" + r.getMessage());
+		}	
+		return sb.toString();
+	}
+}

src/main/java/org/genesys2/server/api/v1/DescriptorController.java

@@ -80,8 +80,8 @@ public class DescriptorController extends ApiBaseController {
 	 * @param uuid the uuid
 	 * @return the descriptor
 	 */
-	@RequestMapping(value = "/{UUID}", method = RequestMethod.GET)
-	public Descriptor getDescriptor(@PathVariable("UUID") final UUID uuid) {
+	@RequestMapping(value = "/{uuid}", method = RequestMethod.GET)
+	public Descriptor getDescriptor(@PathVariable("uuid") final UUID uuid) {
 		return descriptorService.getDescriptor(uuid);
 	}
 
@@ -92,8 +92,8 @@ public class DescriptorController extends ApiBaseController {
 	 * @param version the version
 	 * @return the descriptor
 	 */
-	@DeleteMapping(value = "/{UUID},{version}")
-	public Descriptor deleteDescriptor(@PathVariable("UUID") final UUID uuid, @PathVariable("version") final int version) {
+	@DeleteMapping(value = "/{uuid},{version}")
+	public Descriptor deleteDescriptor(@PathVariable("uuid") final UUID uuid, @PathVariable("version") final int version) {
 		try {
 			return descriptorService.removeDescriptor(descriptorService.getDescriptor(uuid, version));
 		} catch (DataIntegrityViolationException e) {
@@ -322,10 +322,10 @@ public class DescriptorController extends ApiBaseController {
 	 * @param uuid descriptor UUID
 	 * @return the other descriptor info
 	 */
-	@RequestMapping(value = "/extra/{UUID}", method = RequestMethod.GET)
+	@RequestMapping(value = "/extra/{uuid}", method = RequestMethod.GET)
 	@SuppressWarnings("unused")
 	@JsonView(JsonViews.Minimal.class)
-	public Object getOtherDescriptorInfo(@PathVariable("UUID") final UUID uuid) {
+	public Object getOtherDescriptorInfo(@PathVariable("uuid") final UUID uuid) {
 		final Descriptor descriptor = descriptorService.getDescriptor(uuid);
 
 		return new Object() {

src/main/java/org/genesys2/server/api/v1/DescriptorListController.java

@@ -85,8 +85,8 @@ public class DescriptorListController {
 	 * @param uuid the uuid
 	 * @return the descriptor list
 	 */
-	@GetMapping(value = "/{UUID}")
-	public DescriptorList getDescriptorList(@PathVariable("UUID") final UUID uuid) {
+	@GetMapping(value = "/{uuid}")
+	public DescriptorList getDescriptorList(@PathVariable("uuid") final UUID uuid) {
 		final DescriptorList descriptorList = descriptorListService.getDescriptorList(uuid);
 		return descriptorList;
 	}
@@ -98,8 +98,8 @@ public class DescriptorListController {
 	 * @param version the version
 	 * @return the descriptor list
 	 */
-	@DeleteMapping(value = "/{UUID},{version}")
-	public DescriptorList deleteDescriptorList(@PathVariable("UUID") final UUID uuid, @PathVariable("version") final int version) {
+	@DeleteMapping(value = "/{uuid},{version}")
+	public DescriptorList deleteDescriptorList(@PathVariable("uuid") final UUID uuid, @PathVariable("version") final int version) {
 		return descriptorListService.deleteDescriptorList(descriptorListService.getDescriptorList(uuid, version));
 	}
 
@@ -111,8 +111,8 @@ public class DescriptorListController {
 	 * @throws IOException Signals that an I/O exception has occurred.
 	 */
 	@Transactional(readOnly = true)
-	@GetMapping(value = "/{UUID}/html", produces = { "text/html" })
-	public void generateDocument(@PathVariable("UUID") final UUID uuid, final HttpServletResponse response) throws IOException {
+	@GetMapping(value = "/{uuid}/html", produces = { "text/html" })
+	public void generateDocument(@PathVariable("uuid") final UUID uuid, final HttpServletResponse response) throws IOException {
 		final DescriptorList descriptorList = descriptorListService.getDescriptorList(uuid);
 		final String descriptorListHtml = exporter.htmlDescriptorList(descriptorList);
 
@@ -204,8 +204,8 @@ public class DescriptorListController {
 	 * @param descriptorUuids the descriptor uuids
 	 * @return the descriptor list
 	 */
-	@PostMapping(value = "/add-descriptors/{UUID},{version}")
-	public DescriptorList addDescriptor(@PathVariable("UUID") final UUID uuid, @PathVariable("version") final int version, @RequestBody final List<UUID> descriptorUuids) {
+	@PostMapping(value = "/add-descriptors/{uuid},{version}")
+	public DescriptorList addDescriptor(@PathVariable("uuid") final UUID uuid, @PathVariable("version") final int version, @RequestBody final List<UUID> descriptorUuids) {
 		final DescriptorList descriptorList = descriptorListService.getDescriptorList(uuid, version);
 		final List<Descriptor> descriptors = descriptorUuids.stream().map(descriptorUuid -> descriptorService.getDescriptor(descriptorUuid)).collect(Collectors.toList());
 		return descriptorListService.addDescriptors(descriptorList, descriptors.toArray(new Descriptor[] {}));
@@ -219,8 +219,8 @@ public class DescriptorListController {
 	 * @param descriptorUuids the descriptor uuids
 	 * @return the descriptor list
 	 */
-	@PostMapping(value = "/remove-descriptors/{UUID},{version}")
-	public DescriptorList removeDescriptor(@PathVariable("UUID") final UUID uuid, @PathVariable("version") final int version, @RequestBody final Set<UUID> descriptorUuids) {
+	@PostMapping(value = "/remove-descriptors/{uuid},{version}")
+	public DescriptorList removeDescriptor(@PathVariable("uuid") final UUID uuid, @PathVariable("version") final int version, @RequestBody final Set<UUID> descriptorUuids) {
 		final DescriptorList descriptorList = descriptorListService.getDescriptorList(uuid, version);
 		final Set<Descriptor> descriptors = descriptorUuids.stream().map(descriptorUuid -> descriptorService.getDescriptor(descriptorUuid)).collect(Collectors.toSet());
 		return descriptorListService.removeDescriptors(descriptorList, descriptors.toArray(new Descriptor[] {}));
@@ -234,8 +234,8 @@ public class DescriptorListController {
 	 * @param descriptorUuids the descriptor uuids
 	 * @return the descriptor list
 	 */
-	@PostMapping(value = "/set-descriptors/{UUID},{version}")
-	public DescriptorList setDescriptor(@PathVariable("UUID") final UUID uuid, @PathVariable("version") final int version, @RequestBody final List<UUID> descriptorUuids) {
+	@PostMapping(value = "/set-descriptors/{uuid},{version}")
+	public DescriptorList setDescriptor(@PathVariable("uuid") final UUID uuid, @PathVariable("version") final int version, @RequestBody final List<UUID> descriptorUuids) {
 		final DescriptorList descriptorList = descriptorListService.getDescriptorList(uuid, version);
 		final List<Descriptor> descriptors = descriptorUuids.stream().map(descriptorUuid -> descriptorService.getDescriptor(descriptorUuid)).collect(Collectors.toList());
 		return descriptorListService.setDescriptors(descriptorList, descriptors.toArray(new Descriptor[] {}));

src/main/java/org/genesys2/server/api/v1/PartnerController.java

@@ -68,8 +68,8 @@ public class PartnerController {
 	 * @param uuid the uuid
 	 * @return the partner
 	 */
-	@GetMapping(value = "/{UUID}")
-	public Partner getPartner(@PathVariable("UUID") final UUID uuid) {
+	@GetMapping(value = "/{uuid}")
+	public Partner getPartner(@PathVariable("uuid") final UUID uuid) {
 		return partnerService.loadPartner(uuid);
 	}
 
@@ -80,8 +80,8 @@ public class PartnerController {
 	 * @param version the version
 	 * @return the partner
 	 */
-	@DeleteMapping(value = "/{UUID},{version}")
-	public Partner deletePartner(@PathVariable("UUID") final UUID uuid, @PathVariable("version") final int version) {
+	@DeleteMapping(value = "/{uuid},{version}")
+	public Partner deletePartner(@PathVariable("uuid") final UUID uuid, @PathVariable("version") final int version) {
 		return partnerService.removePartner(partnerService.loadPartner(uuid, version));
 	}
 

src/main/java/org/genesys2/server/api/v1/SubsetController.java

@@ -102,8 +102,8 @@ public class SubsetController {
 	 * @param uuid the uuid
 	 * @return the subset
 	 */
-	@GetMapping(value = "/{UUID}", produces = { MediaType.APPLICATION_JSON_VALUE })
-	public Subset get(@PathVariable("UUID") final UUID uuid) {
+	@GetMapping(value = "/{uuid}", produces = { MediaType.APPLICATION_JSON_VALUE })
+	public Subset get(@PathVariable("uuid") final UUID uuid) {
 		return subsetService.get(uuid);
 	}
 
@@ -114,8 +114,8 @@ public class SubsetController {
 	 * @param version the version
 	 * @return the subset
 	 */
-	@DeleteMapping(value = "/{UUID},{version}", produces = { MediaType.APPLICATION_JSON_VALUE })
-	public Subset remove(@PathVariable("UUID") final UUID uuid, @PathVariable("version") final int version) {
+	@DeleteMapping(value = "/{uuid},{version}", produces = { MediaType.APPLICATION_JSON_VALUE })
+	public Subset remove(@PathVariable("uuid") final UUID uuid, @PathVariable("version") final int version) {
 		return subsetService.delete(subsetService.get(uuid, version));
 	}
 
@@ -169,8 +169,8 @@ public class SubsetController {
 	 * @param accessionsUuids the accessions UUIDs to be removed
 	 * @return the subset
 	 */
-	@PostMapping(value = "/remove-accessions/{UUID},{version}", produces = { MediaType.APPLICATION_JSON_VALUE })
-	public Subset removeAccessions(@PathVariable("UUID") final UUID uuid, @PathVariable("version") final int version, @RequestBody final Set<UUID> accessionsUuids) {
+	@PostMapping(value = "/remove-accessions/{uuid},{version}", produces = { MediaType.APPLICATION_JSON_VALUE })
+	public Subset removeAccessions(@PathVariable("uuid") final UUID uuid, @PathVariable("version") final int version, @RequestBody final Set<UUID> accessionsUuids) {
 		final Subset subset = subsetService.get(uuid, version);
 		return subsetService.removeAccessions(subset, accessionsUuids);
 	}
@@ -183,8 +183,8 @@ public class SubsetController {
 	 * @param accessionIds the accessions UUIDs to be added
 	 * @return the subset
 	 */
-	@PostMapping(value = "/add-accessions/{UUID},{version}", produces = { MediaType.APPLICATION_JSON_VALUE })
-	public Subset addAccessions(@PathVariable("UUID") final UUID uuid, @PathVariable("version") final int version, @RequestBody final Set<UUID> accessionIds) {
+	@PostMapping(value = "/add-accessions/{uuid},{version}", produces = { MediaType.APPLICATION_JSON_VALUE })
+	public Subset addAccessions(@PathVariable("uuid") final UUID uuid, @PathVariable("version") final int version, @RequestBody final Set<UUID> accessionIds) {
 		final Subset subset = subsetService.get(uuid, version);
 		return subsetService.addAccessions(subset, accessionIds);
 	}

src/main/java/org/genesys2/server/api/v1/SubsetCreatorController.java

@@ -48,7 +48,7 @@ import org.springframework.web.bind.annotation.*;
 public class SubsetCreatorController {
 
 	/** The Constant API_BASE. */
-	public static final String CONTROLLER_URL = SubsetController.API_BASE + "/{UUID}/subsetcreator";
+	public static final String CONTROLLER_URL = SubsetController.API_BASE + "/{uuid}/subsetcreator";
 
 	/** The subset service. */
 	@Autowired
@@ -62,7 +62,7 @@ public class SubsetCreatorController {
 	 * @return the page
 	 */
 	@GetMapping(value = "/list")
-	public Page<SubsetCreator> listSubsetCreators(@PathVariable("UUID") final UUID uuid, final Pagination page) {
+	public Page<SubsetCreator> listSubsetCreators(@PathVariable("uuid") final UUID uuid, final Pagination page) {
 		return subsetService.listSubsetCreators(uuid, page.toPageRequest(100, Sort.Direction.ASC, "id"));
 	}
 
@@ -87,7 +87,7 @@ public class SubsetCreatorController {
 	 * @throws NotFoundElement the not found element
 	 */
 	@PostMapping(value = "/create")
-	public SubsetCreator createSubsetCreator(@PathVariable("UUID") final UUID uuid, @RequestBody final SubsetCreator subsetCreator) throws NotFoundElement {
+	public SubsetCreator createSubsetCreator(@PathVariable("uuid") final UUID uuid, @RequestBody final SubsetCreator subsetCreator) throws NotFoundElement {
 		final Subset subset = subsetService.get(uuid);
 		return subsetService.createSubsetCreator(subset, subsetCreator);
 	}
@@ -102,7 +102,7 @@ public class SubsetCreatorController {
 	 */
 	// uses request body
 	@RequestMapping(value = "/delete", method = { RequestMethod.POST, RequestMethod.DELETE })
-	public SubsetCreator deleteSubsetCreator(@PathVariable("UUID") final UUID subsetUuid, @RequestBody final SubsetCreator subsetCreator) throws NotFoundElement {
+	public SubsetCreator deleteSubsetCreator(@PathVariable("uuid") final UUID subsetUuid, @RequestBody final SubsetCreator subsetCreator) throws NotFoundElement {
 		final Subset subset = subsetService.get(subsetUuid);
 		return subsetService.removeSubsetCreator(subset, subsetCreator);
 	}
@@ -116,7 +116,7 @@ public class SubsetCreatorController {
 	 * @throws NotFoundElement the not found element
 	 */
 	@PostMapping(value = "/update")
-	public SubsetCreator updateSubsetCreator(@PathVariable("UUID") final UUID subsetUuid, @RequestBody final SubsetCreator subsetCreator) throws NotFoundElement {
+	public SubsetCreator updateSubsetCreator(@PathVariable("uuid") final UUID subsetUuid, @RequestBody final SubsetCreator subsetCreator) throws NotFoundElement {
 		final Subset subset = subsetService.get(subsetUuid);
 		return subsetService.updateSubsetCreator(subset, subsetCreator);
 	}

src/main/java/org/genesys2/server/api/v1/VocabularyController.java

@@ -106,8 +106,8 @@ public class VocabularyController {
 	 * @param uuid the uuid
 	 * @return the controlled vocabulary
 	 */
-	@GetMapping(value = "/{UUID}")
-	public ControlledVocabulary get(@PathVariable("UUID") final UUID uuid) {
+	@GetMapping(value = "/{uuid}")
+	public ControlledVocabulary get(@PathVariable("uuid") final UUID uuid) {
 		return vocabularyService.getVocabulary(uuid);
 	}
 
@@ -118,8 +118,8 @@ public class VocabularyController {
 	 * @param code the code
 	 * @return the term
 	 */
-	@GetMapping(value = "/{UUID}/{code}")
-	public VocabularyTerm getTerm(@PathVariable("UUID") final UUID uuid, @PathVariable("code") final String code) throws IOException, ServletException {
+	@GetMapping(value = "/{uuid}/{code}")
+	public VocabularyTerm getTerm(@PathVariable("uuid") final UUID uuid, @PathVariable("code") final String code) throws IOException, ServletException {
 
 		switch (uuid.toString()) {
 		case FAO_WIEWS_UUID:
@@ -142,9 +142,9 @@ public class VocabularyController {
 	 * @param like the like
 	 * @return the list
 	 */
-	@PostMapping(value = "/{UUID}/autocomplete")
+	@PostMapping(value = "/{uuid}/autocomplete")
 	@JsonView({ JsonViews.Public.class })
-	public List<VocabularyTerm> autocompleteTerm(@PathVariable("UUID") final UUID uuid, @RequestParam("q") final String like) {
+	public List<VocabularyTerm> autocompleteTerm(@PathVariable("uuid") final UUID uuid, @RequestParam("q") final String like) {
 		return vocabularyService.autocompleteTerms(uuid, like);
 	}
 
@@ -155,9 +155,9 @@ public class VocabularyController {
 	 * @param page the page
 	 * @return the page
 	 */
-	@PostMapping(value = "/{UUID}/terms")
+	@PostMapping(value = "/{uuid}/terms")
 	@JsonView({ JsonViews.Public.class })
-	public Page<VocabularyTerm> listTerms(@PathVariable("UUID") final UUID uuid, final Pagination page) {
+	public Page<VocabularyTerm> listTerms(@PathVariable("uuid") final UUID uuid, final Pagination page) {
 		// LOG.warn("Loading vocab");
 		final ControlledVocabulary vocabulary = vocabularyService.getVocabulary(uuid);
 		// LOG.warn("Loading terms");
@@ -183,8 +183,8 @@ public class VocabularyController {
 	 * @param version the version
 	 * @return the controlled vocabulary
 	 */
-	@DeleteMapping(value = "/{UUID},{version}")
-	public ControlledVocabulary delete(@PathVariable("UUID") final UUID uuid, @PathVariable("version") final int version) {
+	@DeleteMapping(value = "/{uuid},{version}")
+	public ControlledVocabulary delete(@PathVariable("uuid") final UUID uuid, @PathVariable("version") final int version) {
 		return vocabularyService.deleteVocabulary(vocabularyService.getVocabulary(uuid, version));
 	}
 

src/main/java/org/genesys2/server/mvc/AccessionController.java

@@ -256,8 +256,8 @@ public class AccessionController extends BaseController {
 		return "/accession/resolve";
 	}
 
-	@GetMapping(value = "/{UUID:\\w{8}\\-\\w{4}.+}")
-	public String viewAccessionByUUID(final ModelMap model, @PathVariable("UUID") final UUID uuid) {
+	@GetMapping(value = "/{uuid:\\w{8}\\-\\w{4}.+}")
+	public String viewAccessionByUUID(final ModelMap model, @PathVariable("uuid") final UUID uuid) {
 		final Accession accession = accessionService.getByUuid(uuid);
 
 		if (accession == null) {

src/main/java/org/genesys2/server/mvc/SubsetController.java

@@ -79,8 +79,8 @@ public class SubsetController extends BaseController {
 		return "/subset/index";
 	}
 
-	@GetMapping(value = "/{UUID}")
-	public String subset(final HttpServletResponse response, final ModelMap model, @PathVariable("UUID") final UUID uuid,
+	@GetMapping(value = "/{uuid}")
+	public String subset(final HttpServletResponse response, final ModelMap model, @PathVariable("uuid") final UUID uuid,
 			@RequestParam(value = "page", required = false, defaultValue = "1") int page) {
 
 		Subset subset;

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

@@ -140,6 +140,9 @@ public class AccessionUploader implements InitializingBean {
 			LOG.trace("Received: {}", accn);
 			try {
 				Accession accession = reader.readValue(accn);
+				if (accession.getInstituteCode() == null || (accession.getDoi() == null && accession.getAccessionNumber() == null)) {
+					throw new InvalidApiUsageException("instituteCode, accessionNumber OR doi missing in " + accn);
+				}
 				accessions.add(accession);
 				responses.add(new AccessionOpResponse(accession.getInstituteCode(), accession.getAccessionNumber(), accession.getTaxonomy().getGenus()));
 			} catch (IOException e) {

src/main/java/org/genesys2/spring/config/SwaggerConfig.java

@@ -16,21 +16,24 @@
 package org.genesys2.spring.config;
 
 import static com.google.common.collect.Lists.newArrayList;
-import static springfox.documentation.builders.PathSelectors.ant;
-import static springfox.documentation.builders.PathSelectors.regex;
+import static springfox.documentation.builders.PathSelectors.*;
+import static springfox.documentation.schema.AlternateTypeRules.newRule;
 
+import java.net.URL;
 import java.util.Arrays;
 import java.util.List;
+import java.util.Set;
 
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 
-import com.google.common.base.Predicate;
+import com.fasterxml.classmate.TypeResolver;
 
 import springfox.documentation.builders.ApiInfoBuilder;
 import springfox.documentation.builders.AuthorizationCodeGrantBuilder;
 import springfox.documentation.builders.OAuthBuilder;
+import springfox.documentation.schema.AlternateTypeRule;
 import springfox.documentation.service.ApiInfo;
 import springfox.documentation.service.ApiKey;
 import springfox.documentation.service.AuthorizationScope;
@@ -57,11 +60,24 @@ public class SwaggerConfig {
 
 	@Value("${build.version}")
 	private String version;
+	
+	private TypeResolver resolver = new TypeResolver();
 
 	public SwaggerConfig() {
 		System.err.println("Making SwaggerConfig!");
 	}
 
+	private AlternateTypeRule[] alternateTypes() {
+		return new AlternateTypeRule[] {
+				// URL as String
+				newRule(URL.class, String.class),
+				newRule(resolver.arrayType(URL.class), resolver.arrayType(String.class)),  
+				newRule(resolver.resolve(List.class, URL.class), resolver.resolve(List.class, String.class)),
+				newRule(resolver.resolve(Set.class, URL.class), resolver.resolve(Set.class, String.class))
+				// Other..
+		};
+	}
+
 	/**
 	 * Every Docket bean is picked up by the swagger-mvc framework - allowing for
 	 * multiple swagger groups i.e. same code base multiple swagger resource
@@ -70,19 +86,40 @@ public class SwaggerConfig {