Removed Accession#storage

src/main/java/org/genesys2/server/model/genesys/Accession.java

@@ -82,9 +82,6 @@ public class Accession extends VersionedAuditedModel {
 	@Column(name = "sampStat", length = 3)
 	private Integer sampleStatus;
 
-	@Column(name = "storage", length = 12)
-	private String storage;
-
 	@Column(name = "inSGSV")
 	private Boolean inSvalbard;
 
@@ -200,14 +197,6 @@ public class Accession extends VersionedAuditedModel {
 		this.sampleStatus = sampleStatus;
 	}
 
-	public String getStorage() {
-		return this.storage;
-	}
-
-	public void setStorage(final String storage) {
-		this.storage = storage;
-	}
-
 	public Boolean getInSvalbard() {
 		return this.inSvalbard;
 	}

src/main/java/org/genesys2/server/model/json/AccessionJson.java

@@ -33,7 +33,7 @@ public class AccessionJson {
 	private Boolean mlsStat;
 	private Boolean inTrust;
 	private Boolean available;
-	private int[] storage;
+	private Integer[] storage;
 	private Integer sampStat;
 	private String[] duplSite;
 	private String bredCode;
@@ -165,11 +165,11 @@ public class AccessionJson {
 		this.available = available;
 	}
 
-	public int[] getStorage() {
+	public Integer[] getStorage() {
 		return storage;
 	}
 
-	public void setStorage(int[] storage) {
+	public void setStorage(Integer[] storage) {
 		this.storage = storage;
 	}
 

src/main/java/org/genesys2/server/model/json/GenesysJsonFactory.java

@@ -18,6 +18,7 @@ package org.genesys2.server.model.json;
 
 import java.util.List;
 
+import org.apache.commons.lang.ArrayUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.genesys.AccessionCollect;
@@ -56,8 +57,8 @@ public class GenesysJsonFactory {
 		aj.setMlsStat(accession.getMlsStatus());
 		aj.setInTrust(accession.getInTrust());
 		aj.setAvailable(accession.getAvailability());
-		// private int[] storage;
-		aj.setStorage(toIntArray(accession.getStorage()));
+		// private Integer[] storage;
+		aj.setStorage(accession.getStoRage().toArray(ArrayUtils.EMPTY_INTEGER_OBJECT_ARRAY));
 		// private Integer sampStat;
 		aj.setSampStat(accession.getSampleStatus());
 		// private String[] duplSite;
@@ -81,19 +82,6 @@ public class GenesysJsonFactory {
 		return arrString.split("\\s*;\\s*");
 	}
 
-	private static int[] toIntArray(String arrString) {
-		if (StringUtils.isBlank(arrString)) {
-			return null;
-		}
-		final String[] split = arrString.trim().split("[;,]");
-		final int[] intArr = new int[split.length];
-		for (int i = 0; i < split.length; i++) {
-			// TODO Could throw NFE
-			intArr[i] = Integer.parseInt(split[i]);
-		}
-		return intArr;
-	}
-
 	public static GeoJson from(AccessionGeo geo) {
 		if (geo == null) {
 			return null;

src/main/java/org/genesys2/server/persistence/domain/GenesysLowlevelRepositoryImpl.java

@@ -244,7 +244,7 @@ public class GenesysLowlevelRepositoryImpl implements GenesysLowlevelRepository
 			@Override
 			public PreparedStatement createPreparedStatement(final Connection con) throws SQLException {
 				final PreparedStatement stmt = con.prepareStatement(directQuery
-						.getQuery("a.id, a.uuid, a.instCode, a.acceNumb, t.genus, t.species, t.taxonName, a.orgCty, a.acqSrc, a.acqDate, a.mlsStat, a.available, a.storage, a.sampStat, a.duplSite, a.createdBy, a.createdDate, a.lastModifiedBy, a.lastModifiedDate"));
+						.getQuery("a.id, a.uuid, a.instCode, a.acceNumb, t.genus, t.species, t.taxonName, a.orgCty, a.acqSrc, a.acqDate, a.mlsStat, a.available, null, a.sampStat, a.duplSite, a.createdBy, a.createdDate, a.lastModifiedBy, a.lastModifiedDate"));
 
 				final ArgumentPreparedStatementSetter apss = new ArgumentPreparedStatementSetter(directQuery.getParameters());
 				apss.setValues(stmt);

src/main/java/org/genesys2/server/service/impl/BatchRESTServiceImpl.java

@@ -27,7 +27,6 @@ import java.util.UUID;
 
 import org.apache.commons.collections4.CollectionUtils;
 import org.apache.commons.collections4.Predicate;
-import org.apache.commons.lang.ArrayUtils;
 import org.apache.commons.lang.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
@@ -456,40 +455,34 @@ public class BatchRESTServiceImpl implements BatchRESTService {
 
 		// MUST BE ARRAY
 		if (accnJson.has("storage")) {
-			final String storage = arrayToString(toMcpdArray(accnJson, "storage"));
-			updateAccessionStorage(accession, storage);
+			updateAccessionStorage(accession, toMcpdArray(accnJson, "storage"));
 		}
 
 		return updated;
 	}
 
-	public static boolean updateAccessionStorage(Accession accession, String storage) {
+	public static boolean updateAccessionStorage(Accession accession, ArrayNode arr) {
 		boolean updated = false;
-		if (!StringUtils.equals(storage, accession.getStorage())) {
-			accession.setStorage(storage);
-			updated = true;
-		}
 
 		List<Integer> as = accession.getStoRage();
-		String[] arr = StringUtils.isBlank(storage) ? ArrayUtils.EMPTY_STRING_ARRAY : storage.split("\\s*[;,]\\s*");
+		List<Integer> toRemove = new ArrayList<Integer>(as);
 
-		// Sometimes double values are registered: 20;20;40 and the loop below
-		// kicks in
-		if (updated || as.size() != arr.length) {
-			List<Integer> toRemove = new ArrayList<Integer>(as);
+		Iterator<JsonNode> it = arr.elements();
 
-			for (String storageStr : arr) {
-				int stor = Integer.parseInt(storageStr);
-				if (!as.contains(stor)) {
-					as.add(stor);
-				} else {
-					// Cast needed to remove the object
-					toRemove.remove((Integer) stor);
-				}
+		while (it.hasNext()) {
+			JsonNode storageElem = it.next();
+			int stor = Integer.parseInt(storageElem.asText());
+			if (!as.contains(stor)) {
+				updated = true;
+				as.add(stor);
+			} else {
+				// Cast needed to remove the object
+				toRemove.remove((Integer) stor);
 			}
+		}
 
+		if (toRemove.size() > 0) {
 			as.removeAll(toRemove);
-			accession.setStorage(listToString(as));
 			updated = true;
 		}
 

src/main/java/org/genesys2/server/service/impl/GenesysServiceImpl.java

@@ -961,7 +961,7 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 		@SuppressWarnings("resource")
 		final CSVWriter csv = new CSVWriter(new BufferedWriter(new OutputStreamWriter(zos)), ',', '"', '\\', "\n");
 		csv.writeNext(new String[] { "genesysId", "uuid", "instCode", "acceNumb", "genus", "species", "fullTaxa", "orgCty", "acqSrc", "acqDate", "mlsStat",
-				"available", "storage", "sampStat", "duplSite", "createdBy", "createdDate", "lastModifiedBy", "lastModifiedDate" });
+				"available", "~storage", "sampStat", "duplSite", "createdBy", "createdDate", "lastModifiedBy", "lastModifiedDate" });
 
 		final ResultSetHelper csvResultsetHelper = new ResultSetHelperService();
 

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

-/**
- * Copyright 2014 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.service.worker;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.genesys2.server.aspect.AsAdmin;
-import org.genesys2.server.model.genesys.Accession;
-import org.genesys2.server.service.GenesysService;
-import org.genesys2.server.service.impl.BatchRESTServiceImpl;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.data.domain.PageRequest;
-import org.springframework.stereotype.Component;
-
-/**
- * Scans Accession#storage records and updates Accession#stoRage
- */
-@Component
-public class AccessionStorageScanner {
-	public static final Log LOG = LogFactory.getLog(AccessionStorageScanner.class);
-
-	@Autowired
-	private GenesysService genesysService;
-
-	private static final int BATCH_SIZE = 50;
-
-	@AsAdmin
-	public void scanStorage() throws InterruptedException {
-		int page = 0;
-
-		do {
-			page++;
-			if (page % 100 == 0) {
-				LOG.info("Scanning accessions page " + page);
-			} else {
-				LOG.debug("Scanning accessions page " + page);
-			}
-			List<Long> accns = genesysService.listAccessionsIds(new PageRequest(page, BATCH_SIZE));
-			List<Accession> toSave = new ArrayList<Accession>(accns.size());
-
-			if (accns.size() == 0)
-				break;
-
-			for (long accnId : accns) {
-				Accession accession = genesysService.getAccession(accnId);
-				boolean updated = BatchRESTServiceImpl.updateAccessionStorage(accession, accession.getStorage());
-				if (updated) {
-					toSave.add(accession);
-				}
-			}
-
-			try {
-				if (toSave.size() > 0) {
-					LOG.info("Updating accession#stoRage for size=" + toSave.size());
-					genesysService.saveAccession(toSave.toArray(new Accession[] {}));
-				}
-			} catch (Throwable e) {
-				LOG.warn(e.getMessage(), e);
-			}
-
-			Thread.sleep(5);
-		} while (true);
-
-		LOG.info("Done scanning accession#storage");
-	}
-}

src/main/java/org/genesys2/server/servlet/controller/AdminController.java

@@ -35,7 +35,6 @@ import org.genesys2.server.service.GeoService;
 import org.genesys2.server.service.InstituteService;
 import org.genesys2.server.service.MappingService;
 import org.genesys2.server.service.impl.ContentSanitizer;
-import org.genesys2.server.service.worker.AccessionStorageScanner;
 import org.genesys2.server.service.worker.ElasticUpdater;
 import org.genesys2.server.service.worker.ITPGRFAStatusUpdater;
 import org.genesys2.server.service.worker.InstituteUpdater;
@@ -97,9 +96,6 @@ public class AdminController {
 	@Autowired
 	private TaskExecutor taskExecutor;
 
-	@Autowired
-	protected AccessionStorageScanner accessionStorageScanner;
-
 	@RequestMapping("/")
 	public String root(Model model) {
 		return "/admin/index";
@@ -317,33 +313,6 @@ public class AdminController {
 		return "redirect:/admin/";
 	}
 
-	@RequestMapping(method = RequestMethod.POST, value = "/scanStorage")
-	public String scanStorage() {
-		LOG.info("Updating accession.stoRage");
-		taskExecutor.execute(new Runnable() {
-			@Override
-			public void run() {
-				Thread t = Thread.currentThread();
-				int prevPrio = t.getPriority();
-				String prevName = t.getName();
-				t.setPriority(Thread.MIN_PRIORITY);
-				t.setName("background.storageScanner");
-				try {
-					accessionStorageScanner.scanStorage();
-					LOG.info("Updating done");
-				} catch (InterruptedException e) {
-					LOG.warn("Storage scanner thread interrupted!");
-				} finally {
-					LOG.debug("Resetting thread priority");
-					t.setPriority(prevPrio);
-					t.setName(prevName);
-				}
-			}
-		});
-		LOG.info("Job scheduled");
-		return "redirect:/admin/";
-	}
-
 	@RequestMapping(method = RequestMethod.POST, value = "/clearTilesCache")
 	public String clearTilesCache() {
 		final Cache tileServerCache = cacheManager.getCache("tileserver");

src/main/webapp/WEB-INF/jsp/accession/details.jsp

@@ -134,14 +134,9 @@
 			<div class="row">
 				<div class="col-xs-4"><spring:message code="accession.storage" /></div>
 				<div class="col-xs-8">
-					<c:forEach items="${accession.storage.split('[;,]')}" var="storage">
-						<div><spring:message code="accession.storage.${storage}" /></div>
-					</c:forEach>
-<%--				
 					<c:forEach items="${accession.stoRage}" var="storage">
 						<div><spring:message code="accession.storage.${storage}" /></div>
 					</c:forEach>
---%>
 				</div>
 			</div>
 

src/main/webapp/WEB-INF/jsp/admin/index.jsp

@@ -89,11 +89,6 @@
         <!-- CSRF protection -->
         <input type="hidden" name="${_csrf.parameterName}" value="${_csrf.token}"/>
 	</form>
-	<form method="post" action="<c:url value="/admin/scanStorage" />">
-		<input type="submit" class="btn btn-default" class="btn btn-default" value="Scan and convert STORAGE" />
-        <!-- CSRF protection -->
-        <input type="hidden" name="${_csrf.parameterName}" value="${_csrf.token}"/>
-	</form>
 	<h3>C&E</h3>
 	<form method="post" action="<c:url value="/admin/refreshMetadataMethods" />">
 		<input type="submit" class="btn btn-default" class="btn btn-default" value="Recalculate metadata methods" />