Deleting DS2, DS2 admin controller and view

src/main/java/org/genesys2/server/model/dataset/DSRow.java

@@ -2,12 +2,15 @@ package org.genesys2.server.model.dataset;
 
 import java.util.List;
 
+import javax.persistence.CascadeType;
 import javax.persistence.Column;
 import javax.persistence.Entity;
 import javax.persistence.FetchType;
 import javax.persistence.GeneratedValue;
 import javax.persistence.GenerationType;
 import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
 import javax.persistence.OneToMany;
 import javax.persistence.Table;
 import javax.persistence.UniqueConstraint;
@@ -17,20 +20,25 @@ import org.genesys2.server.model.EntityId;
 @Entity
 @Table(name = "ds2row", uniqueConstraints = { @UniqueConstraint(columnNames = { "md5", "sha1" }) })
 public class DSRow implements EntityId {
-	@OneToMany(fetch=FetchType.LAZY, mappedBy = "row")
+
+	@ManyToOne(fetch=FetchType.LAZY, optional = false)
+	@JoinColumn(name="ds")
+	private DS dataset;
+	
+	@OneToMany(fetch = FetchType.LAZY, mappedBy = "row", cascade = { CascadeType.REMOVE })
 	private List<DSRowQualifier<?>> rowQualifiers;
 
-	@OneToMany(fetch=FetchType.LAZY, mappedBy = "row")
+	@OneToMany(fetch = FetchType.LAZY, mappedBy = "row")
 	private List<DSValue<?>> values;
 
 	@Id
 	@GeneratedValue(strategy = GenerationType.TABLE)
 	private Long id;
 
-	@Column(columnDefinition="binary(16)", updatable=false)
+	@Column(columnDefinition = "binary(16)", updatable = false)
 	private byte[] md5;
 
-	@Column(columnDefinition="binary(20)", updatable=false)
+	@Column(columnDefinition = "binary(20)", updatable = false)
 	private byte[] sha1;
 
 	@Override
@@ -42,6 +50,14 @@ public class DSRow implements EntityId {
 		this.id = id;
 	}
 
+	public DS getDataset() {
+		return dataset;
+	}
+	
+	public void setDataset(DS dataset) {
+		this.dataset = dataset;
+	}
+	
 	public List<DSRowQualifier<?>> getRowQualifiers() {
 		return rowQualifiers;
 	}

src/main/java/org/genesys2/server/persistence/domain/dataset/DSQualifierRepository.java

 package org.genesys2.server.persistence.domain.dataset;
 
+import org.genesys2.server.model.dataset.DS;
 import org.genesys2.server.model.dataset.DSQualifier;
 import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.data.jpa.repository.Modifying;
+import org.springframework.data.jpa.repository.Query;
 
 public interface DSQualifierRepository extends JpaRepository<DSQualifier, Long> {
 
+	@Modifying
+	@Query("delete from DSQualifier dsq where dsq.dataset = ?1")
+	int deleteFor(DS ds);
+
 }

src/main/java/org/genesys2/server/persistence/domain/dataset/DSRowQualifierRepository.java

 package org.genesys2.server.persistence.domain.dataset;
 
+import org.genesys2.server.model.dataset.DS;
 import org.genesys2.server.model.dataset.DSRowQualifier;
 import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.data.jpa.repository.Modifying;
+import org.springframework.data.jpa.repository.Query;
 
 public interface DSRowQualifierRepository extends JpaRepository<DSRowQualifier<?>, Long> {
 
+	@Modifying
+	@Query("delete from DSRowQualifier dsrq where dsrq.datasetQualifier in (select dsq from DSQualifier dsq where dsq.dataset = ?1)")
+	int deleteFor(DS ds);
+
 }

src/main/java/org/genesys2/server/persistence/domain/dataset/DSRowRepository.java

@@ -7,6 +7,7 @@ import java.util.Set;
 import org.genesys2.server.model.dataset.DS;
 import org.genesys2.server.model.dataset.DSRow;
 import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.data.jpa.repository.Modifying;
 import org.springframework.data.jpa.repository.Query;
 
 public interface DSRowRepository extends JpaRepository<DSRow, Long>, DSRowCustomRepository {
@@ -23,4 +24,8 @@ public interface DSRowRepository extends JpaRepository<DSRow, Long>, DSRowCustom
 	@Query("select distinct dsrq.row from DSRowQualifier dsrq where dsrq.datasetQualifier.dataset = ?1")
 	List<DSRow> findByDataset(DS ds);
 
+	@Modifying
+	@Query("delete from DSRow dsr where dsr.dataset = ?1")
+	int deleteFor(DS ds);
+
 }

src/main/java/org/genesys2/server/persistence/domain/dataset/DSValueRepository.java

@@ -4,9 +4,15 @@ import org.genesys2.server.model.dataset.DSDescriptor;
 import org.genesys2.server.model.dataset.DSRow;
 import org.genesys2.server.model.dataset.DSValue;
 import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.data.jpa.repository.Modifying;
+import org.springframework.data.jpa.repository.Query;
 
 public interface DSValueRepository extends JpaRepository<DSValue<?>, Long> {
 
 	DSValue<?> findByRowAndDatasetDescriptor(DSRow dsr, DSDescriptor dsd);
 
+	@Modifying
+	@Query("delete from DSValue dsv where dsv.datasetDescriptor = ?1")
+	int deleteFor(DSDescriptor dsd);
+
 }

src/main/java/org/genesys2/server/service/DSService.java

@@ -30,11 +30,17 @@ public interface DSService {
 
 	void worldclimUpdate(DS dataset, DSDescriptor dsd, Set<Long> ids, MappedByteBuffer buffer, short nullValue, double factor);
 
-	void tempStore(List<AccessionGeo> toSave);
+	void updateAccessionTileIndex(List<AccessionGeo> toSave);
 
 	WorldclimJson jsonForTile(DS worldClimDataset, Long tileIndex);
 
 	void download(DS ds, OutputStream outputStream) throws IOException;
 
 	void download(DS ds, List<DSDescriptor> dsds, OutputStream outputStream) throws IOException;
+
+	void deleteDataset(DS ds);
+
+	void deleteDescriptor(DSDescriptor dsd);
+
+	void deleteRows(DS ds);
 }

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

@@ -130,6 +130,7 @@ public class DSServiceImpl implements DSService {
 		DSRow dsr = dsRowRepo.findRow(ds, qualifiers);
 		if (dsr == null) {
 			dsr = new DSRow();
+			dsr.setDataset(ds);
 			dsRowRepo.save(dsr);
 			LOG.info("Made new row " + dsr.getId());
 
@@ -311,7 +312,8 @@ public class DSServiceImpl implements DSService {
 		// DigestUtils.sha1(keyBuffer.array()).length);
 		dsr.setMd5(DigestUtils.md5(keyBuffer.array()));
 		dsr.setSha1(DigestUtils.sha1(keyBuffer.array()));
-
+		dsr.setDataset(ds);
+		
 		dsr.setRowQualifiers(rowQualifiers);
 		return dsr;
 	}
@@ -384,7 +386,7 @@ public class DSServiceImpl implements DSService {
 				}
 			}
 		}
-		
+
 		// Only save new rows
 		Collection<DSRow> newRows = new ArrayList<DSRow>();
 		for (DSRow dsr : rowMap.values()) {
@@ -392,26 +394,21 @@ public class DSServiceImpl implements DSService {
 				newRows.add(dsr);
 		}
 		saveRows(newRows);
-		
+
 		// Save values
 		dsValueRepo.save(toSave);
 
 		LOG.info("Done saving.");
 	}
 
-	private List<DSRow> getForQualifier(DS dataset, Set<Long> ids) {
-		return dsRowRepo.findByQualifier(dataset, ids);
-	}
-
 	@Override
 	@Transactional
-	public void tempStore(List<AccessionGeo> toSave) {
+	public void updateAccessionTileIndex(List<AccessionGeo> toSave) {
 		accessionGeoRepository.save(toSave);
 	}
 
 	@Override
 	public WorldclimJson jsonForTile(DS worldClimDataset, Long tileIndex) {
-
 		DSRow dsr = dsRowRepo.findByLongQualifier(worldClimDataset, tileIndex);
 		if (dsr == null || dsr.getValues().isEmpty())
 			return null;
@@ -440,7 +437,7 @@ public class DSServiceImpl implements DSService {
 		}
 		return wc;
 	}
-	
+
 	@Override
 	public void download(DS ds, List<DSDescriptor> dsds, OutputStream outputStream) throws IOException {
 		XSSFWorkbook template = new XSSFWorkbook();
@@ -499,11 +496,11 @@ public class DSServiceImpl implements DSService {
 					}
 				}
 			}
-//
-//			if (rowIndex > 10000) {
-//				LOG.warn("Breaking");
-//				break;
-//			}
+
+			// if (rowIndex > 10000) {
+			// LOG.warn("Breaking");
+			// break;
+			// }
 		}
 		sheet.flushRows();
 
@@ -530,4 +527,32 @@ public class DSServiceImpl implements DSService {
 			c.setCellValue((Date) v);
 		}
 	}
+
+	@Override
+	@Transactional
+	public void deleteDataset(DS ds) {
+		int count = dsQualRepo.deleteFor(ds);
+		LOG.info("Deleted " + count + " DSQualifiers");
+		dsRepo.delete(ds.getId());
+		LOG.info("Deleted dataset " + ds.getUuid());
+	}
+
+	@Override
+	@Transactional
+	public void deleteRows(DS ds) {
+		LOG.info("Clearing DSRowQuali for " + ds);
+		int count = dsRowQualiRepo.deleteFor(ds);
+		LOG.info("Deleted " + count + " DSRowQualifiers");
+		count = dsRowRepo.deleteFor(ds);
+		LOG.info("Deleted " + count + " DSRows");
+	}
+
+	@Override
+	@Transactional
+	public void deleteDescriptor(DSDescriptor dsd) {
+		LOG.info("Clearing DSValues for " + dsd.getDescriptor().getCode());
+		int count = dsValueRepo.deleteFor(dsd);
+		LOG.info("Deleted " + count + " DSValue cells");
+		dsDescRepo.delete(dsd);
+	}
 }

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

@@ -243,7 +243,7 @@ public class WorldClimUpdater implements InitializingBean {
 					}
 				}
 			}
-			dsService.tempStore(toSave);
+			dsService.updateAccessionTileIndex(toSave);
 		}
 		return tileIndexSet;
 	}

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

@@ -88,10 +88,12 @@ public class AccessionController extends BaseController {
 
 		model.addAttribute("crops", cropService.getCrops(accession.getTaxonomy()));
 
-		if (accessionGeo.getTileIndex() != null) {
-			// Worldclim data
+		// Worldclim data
+		if (accessionGeo != null && accessionGeo.getTileIndex() != null) {
 			DS worldClimDataset = dsService.loadDatasetByUuid(WORLDCLIM_DATASET_UUID);
-			model.addAttribute("worldclimJson", dsService.jsonForTile(worldClimDataset, accessionGeo.getTileIndex()));
+			if (worldClimDataset != null) {
+				model.addAttribute("worldclimJson", dsService.jsonForTile(worldClimDataset, accessionGeo.getTileIndex()));
+			}
 		}
 
 		return "/accession/details";

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

@@ -14,7 +14,7 @@
  * limitations under the License.
  **/
 
-package org.genesys2.server.servlet.controller;
+package org.genesys2.server.servlet.controller.admin;
 
 import java.io.IOException;
 import java.sql.ResultSet;

src/main/java/org/genesys2/server/servlet/controller/admin/CacheController.java

@@ -7,7 +7,6 @@ import java.util.Set;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.genesys2.server.service.MappingService;
-import org.genesys2.server.servlet.controller.AdminController;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.cache.Cache;
 import org.springframework.cache.CacheManager;

src/main/java/org/genesys2/server/servlet/controller/admin/DS2Controller.java

+/**
+ * Copyright 2015 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.servlet.controller.admin;
+
+import java.io.IOException;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.genesys2.server.model.dataset.DS;
+import org.genesys2.server.model.dataset.DSDescriptor;
+import org.genesys2.server.service.DSService;
+import org.genesys2.server.service.worker.WorldClimUpdater;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.security.access.prepost.PreAuthorize;
+import org.springframework.stereotype.Controller;
+import org.springframework.ui.Model;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+
+@Controller
+@RequestMapping("/admin/ds2")
+@PreAuthorize("hasRole('ADMINISTRATOR')")
+public class DS2Controller {
+	public static final Log LOG = LogFactory.getLog(DS2Controller.class);
+
+	@Autowired
+	private WorldClimUpdater worldClimUpdater;
+
+	@Autowired
+	private DSService dsService;
+
+	@RequestMapping("/")
+	public String root(Model model) {
+		return "/admin/ds2/index";
+	}
+
+	@RequestMapping(value = "/worldclim/update", method = RequestMethod.POST)
+	public String worldClim() throws IOException {
+		worldClimUpdater.update("alt");
+
+		for (int i = 1; i <= 12; i++) {
+			worldClimUpdater.update("tmin" + i);
+			worldClimUpdater.update("tmax" + i);
+			worldClimUpdater.update("tmean" + i);
+			worldClimUpdater.update("prec" + i);
+		}
+
+		for (int i = 1; i <= 19; i++) {
+			worldClimUpdater.update("bio" + i);
+		}
+		return "redirect:/admin/ds2/";
+	}
+
+	@RequestMapping(value = "/worldclim/delete", method = RequestMethod.POST)
+	public String worldClimDelete() throws IOException {
+		DS ds = dsService.loadDatasetByUuid(WorldClimUpdater.WORLDCLIM_DATASET);
+		if (ds != null) {
+			LOG.info("Deleting dataset " + ds.getUuid());
+			for (DSDescriptor dsd : ds.getDescriptors()) {
+				dsService.deleteDescriptor(dsd);
+			}
+			dsService.deleteRows(ds);
+			dsService.deleteDataset(ds);
+			LOG.info("Done");
+		}
+		return "redirect:/admin/ds2/";
+	}
+}

src/main/java/org/genesys2/server/servlet/controller/admin/LoggerController.java

@@ -11,7 +11,6 @@ import org.apache.commons.logging.LogFactory;
 import org.apache.log4j.Level;
 import org.apache.log4j.LogManager;
 import org.apache.log4j.Logger;
-import org.genesys2.server.servlet.controller.AdminController;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.data.domain.PageImpl;
 import org.springframework.data.domain.PageRequest;

src/main/resources/content/language.properties

@@ -586,8 +586,10 @@ logger.name=Logger name
 logger.log-level=Log level
 logger.appenders=Log appenders
 
+menu.admin.index=Admin
 menu.admin.loggers=Loggers
 menu.admin.caches=Caches
+menu.admin.ds2=DS2 Datasets
 
 worldclim.monthly.title=Climate at collecting site
 worldclim.monthly.precipitation.title=Monthly precipitation

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

@@ -310,7 +310,7 @@
 				</c:if>
 			</c:if>
 
-<security:authorize access="hasRole('ADMINISTRATOR')">
+<security:authorize access="isAuthenticated()">
 			<!-- WorldClim.org -->
 			<c:if test="${worldclimJson ne null}">
 				<h4><spring:message code="worldclim.monthly.title" /></h4>
@@ -490,7 +490,7 @@
 				});
 		</script>
 	</c:if>
-<security:authorize access="hasRole('ADMINISTRATOR')">
+<security:authorize access="isAuthenticated()">
 	<c:if test="${worldclimJson ne null}">
 		<script type="text/javascript">
 			var monthNames = ${jspHelper.toJson(jspHelper.monthShortNames(pageContext.response.locale))};

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

@@ -12,6 +12,14 @@
 		<spring:message code="admin.cache.page.title" />
 	</h1>
 
+	<div class="main-col-header clearfix">
+    	<div class="nav-header pull-left">
+	        <a class="" href="<c:url value="/admin/" />"><spring:message code="menu.admin.index" /></a>
+	        <a class="" href="<c:url value="/admin/logger/" />"><spring:message code="menu.admin.loggers" /></a>
+	        <a class="" href="<c:url value="/admin/ds2/" />"><spring:message code="menu.admin.ds2" /></a>
+		</div>
+	</div>
+	
 	<form method="post" action="<c:url value="/admin/cache/clearCaches" />">
 		<input type="submit" class="btn btn-default" value="Clear all caches" />
         <!-- CSRF protection -->

src/main/webapp/WEB-INF/jsp/admin/ds2/index.jsp

+<!DOCTYPE html>
+
+<%@include file="/WEB-INF/jsp/init.jsp"%>
+<%@ taglib prefix="sec" uri="http://www.springframework.org/security/tags"%>
+
+<html>
+<head>
+<title><spring:message code="admin.page.title" /></title>
+</head>
+<body>
+	<h1>
+		<spring:message code="admin.page.title" />
+	</h1>
+
+	<div class="main-col-header clearfix">
+    	<div class="nav-header pull-left">
+	        <a class="" href="<c:url value="/admin/" />"><spring:message code="menu.admin.index" /></a>
+	        <a class="" href="<c:url value="/admin/cache/" />"><spring:message code="menu.admin.caches" /></a>
+	        <a class="" href="<c:url value="/admin/logger/" />"><spring:message code="menu.admin.loggers" /></a>
+		</div>
+	</div>
+	
+	<h3>worldclim.org</h3>
+	<form method="post" action="<c:url value="/admin/ds2/worldclim/update" />">
+		<input type="submit" class="btn btn-default" value="Update worldclim.org" />
+        <!-- CSRF protection -->
+        <input type="hidden" name="${_csrf.parameterName}" value="${_csrf.token}"/>
+	</form>
+	
+	<form method="post" action="<c:url value="/admin/ds2/worldclim/delete" />">
+		<input type="submit" class="btn btn-default" value="Delete worldclim.org" />
+        <!-- CSRF protection -->
+        <input type="hidden" name="${_csrf.parameterName}" value="${_csrf.token}"/>
+	</form>
+	
+</body>
+</html>
\ No newline at end of file

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

@@ -16,6 +16,7 @@
     	<div class="nav-header pull-left">
 	        <a class="" href="<c:url value="/admin/cache/" />"><spring:message code="menu.admin.caches" /></a>
 	        <a class="" href="<c:url value="/admin/logger/" />"><spring:message code="menu.admin.loggers" /></a>
+	        <a class="" href="<c:url value="/admin/ds2/" />"><spring:message code="menu.admin.ds2" /></a>
 		</div>
 	</div>
 	

src/test/java/org/genesys2/server/service/impl/WorldClimUpdaterTest.java

@@ -10,6 +10,7 @@ import java.util.List;
 import org.apache.http.impl.client.HttpClientBuilder;
 import org.genesys2.server.model.dataset.DS;
 import org.genesys2.server.model.dataset.DSDescriptor;
+import org.genesys2.server.model.dataset.DSQualifier;
 import org.genesys2.server.persistence.domain.GenesysLowlevelRepository;
 import org.genesys2.server.persistence.domain.GenesysLowlevelRepositoryCustomImpl;
 import org.genesys2.server.service.DSService;
@@ -58,7 +59,7 @@ public class WorldClimUpdaterTest {
 		public DSService dsService() {
 			return new DSServiceImpl();
 		}
-		
+
 		@Bean
 		public DescriptorService descriptorService() {
 			return new DescriptorServiceImpl();
@@ -80,7 +81,7 @@ public class WorldClimUpdaterTest {
 	@Test
 	public void testUpdateAlt() throws IOException {
 		worldClimUpdater.update("alt");
-		
+
 		for (int i = 1; i <= 12; i++) {
 			worldClimUpdater.update("tmin" + i);
 			worldClimUpdater.update("tmax" + i);
@@ -93,17 +94,26 @@ public class WorldClimUpdaterTest {
 		}
 	}
 
+	@Test
+	public void deleteDataset() {
+		DS ds = dsService.loadDatasetByUuid(WorldClimUpdater.WORLDCLIM_DATASET);
+		for (DSDescriptor dsd : ds.getDescriptors()) {
+			dsService.deleteDescriptor(dsd);
+		}
+		dsService.deleteRows(ds);
+		dsService.deleteDataset(ds);
+	}
+
 	@Test
 	public void testDownload() throws IOException {
 		DS ds = dsService.loadDatasetByUuid(WorldClimUpdater.WORLDCLIM_DATASET);
 		File file = new File("worldclim " + System.currentTimeMillis() + ".xls");
-		BufferedOutputStream fos=new BufferedOutputStream(new FileOutputStream(file));
+		BufferedOutputStream fos = new BufferedOutputStream(new FileOutputStream(file));
 		dsService.download(ds, fos);
 		fos.flush();
 		fos.close();
-		//		file.delete();
+		// file.delete();
 	}
-	
 
 	@Test
 	public void testDownloadDesc() throws IOException {
@@ -115,12 +125,12 @@ public class WorldClimUpdaterTest {
 			}
 		}
 		System.out.println("Downloading tmin data: " + dsds.size());
-		
+
 		File file = new File("worldclim " + System.currentTimeMillis() + ".xls");
-		BufferedOutputStream fos=new BufferedOutputStream(new FileOutputStream(file));
+		BufferedOutputStream fos = new BufferedOutputStream(new FileOutputStream(file));
 		dsService.download(ds, dsds, fos);
 		fos.flush();
 		fos.close();
-		//		file.delete();
+		// file.delete();
 	}
 }