Introducing TileClimate for worldclim.org data

- liquibase

src/main/java/org/genesys2/server/component/elastic/ElasticQueryBuilder.java

@@ -201,7 +201,7 @@ public class ElasticQueryBuilder implements Visitor<Void, Void> {
 	private void handleEquals(Path<?> path, Expression<?> value) {
 		PathMetadata pmd = path.getMetadata();
 		if (pmd.getPathType() == PathType.COLLECTION_ANY) {
-			LOG.error("Path ANY for {}={}", pmd.getParent(), value);
+			LOG.debug("Path ANY for {}={}", pmd.getParent(), value);
 			mustClauses.add(termsQuery(customizedPath(pmd.getParent().toString()), toValues(value)));
 		} else {
 			mustClauses.add(termsQuery(customizedPath(getParentPath(pmd.getParent()) + "." + pmd.getName()), toValues(value)));

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

@@ -12,7 +12,7 @@ import com.fasterxml.jackson.annotation.JsonIgnore;
  */
 public class WorldclimJson {
 	// Monthlies
-	private Long[] precipitation = new Long[12];
+	private Double[] precipitation = new Double[12];
 	private Double[] tempMin = new Double[12];
 	private Double[] tempMean = new Double[12];
 	private Double[] tempMax = new Double[12];
@@ -20,7 +20,7 @@ public class WorldclimJson {
 	@JsonIgnore
 	private Map<DSDescriptor, Object> other = new HashMap<DSDescriptor, Object>();
 
-	public Long[] getPrecipitation() {
+	public Double[] getPrecipitation() {
 		return precipitation;
 	}
 
@@ -43,4 +43,20 @@ public class WorldclimJson {
 	public Map<DSDescriptor, Object> getOther() {
 		return this.other;
 	}
+
+	public void setPrecipitation(Double[] doubles) {
+		this.precipitation = doubles;
+	}
+
+	public void setTempMin(Double[] doubles) {
+		this.tempMin = doubles;
+	}
+
+	public void setTempMean(Double[] doubles) {
+		this.tempMean = doubles;
+	}
+
+	public void setTempMax(Double[] doubles) {
+		this.tempMax = doubles;
+	}
 }

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

@@ -30,8 +30,6 @@ import org.genesys.blocks.auditlog.service.AuditTrailService;
 import org.genesys.catalog.service.DatasetService;
 import org.genesys.filerepository.InvalidRepositoryPathException;
 import org.genesys.filerepository.model.ImageGallery;
-import org.genesys.filerepository.service.ImageGalleryService;
-import org.genesys2.server.model.dataset.DS;
 import org.genesys2.server.model.elastic.AccessionDetails;
 import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.genesys.AccessionCollect;
@@ -41,7 +39,7 @@ import org.genesys2.server.model.genesys.Taxonomy2;
 import org.genesys2.server.model.impl.Crop;
 import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.server.service.AccessionService;
-import org.genesys2.server.service.DSService;
+import org.genesys2.server.service.ClimateDataService;
 import org.genesys2.server.service.DownloadService;
 import org.genesys2.server.service.FilterConstants;
 import org.genesys2.server.service.GenesysService;
@@ -85,14 +83,11 @@ public class AccessionController extends BaseController {
 	@Autowired
 	private TaxonomyService taxonomyService;
 
-	@Autowired
-	private DSService dsService;
-
 	@Autowired
 	private InstituteFilesService instituteFilesService;
 
 	@Autowired
-	private ImageGalleryService imageGalleryService;
+	private ClimateDataService climateDataService;
 
 	@Autowired
 	private DownloadService downloadService;
@@ -189,10 +184,7 @@ public class AccessionController extends BaseController {
 
 		// Worldclim data
 		if (accessionGeo != null && accessionGeo.getTileIndex() != null) {
-			DS worldClimDataset = dsService.loadDatasetByUuid(WORLDCLIM_DATASET_UUID);
-			if (worldClimDataset != null) {
-				model.addAttribute("worldclimJson", dsService.jsonForTile(worldClimDataset, accessionGeo.getTileIndex()));
-			}
+			model.addAttribute("worldclimJson", climateDataService.jsonForTile(accessionGeo.getTileIndex()));
 		}
 
 		model.addAttribute("pdci", accessionId.getPdci());

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

@@ -18,13 +18,11 @@ package org.genesys2.server.mvc;
 
 import java.util.UUID;
 
-import org.genesys2.server.model.dataset.DS;
 import org.genesys2.server.model.genesys.AccessionGeo;
 import org.genesys2.server.model.genesys.AccessionHistoric;
+import org.genesys2.server.service.ClimateDataService;
 import org.genesys2.server.service.CropService;
-import org.genesys2.server.service.DSService;
 import org.genesys2.server.service.GenesysService;
-import org.genesys2.server.service.TaxonomyService;
 import org.genesys2.server.service.TraitService;
 import org.genesys2.spring.ResourceNotFoundException;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -44,14 +42,11 @@ public class ArchiveController extends BaseController {
 	@Autowired
 	private TraitService traitService;
 
-	@Autowired
-	private TaxonomyService taxonomyService;
-
 	@Autowired
 	private CropService cropService;
-
+	
 	@Autowired
-	private DSService dsService;
+	private ClimateDataService climateDataService;
 
 	@RequestMapping(value = "/{uuid:.{36}}", method = RequestMethod.GET)
 	public String view(ModelMap model, @PathVariable(value = "uuid") UUID uuid) {
@@ -91,10 +86,7 @@ public class ArchiveController extends BaseController {
 
 		// Worldclim data
 		if (accessionGeo != null && accessionGeo.getTileIndex() != null) {
-			DS worldClimDataset = dsService.loadDatasetByUuid(AccessionController.WORLDCLIM_DATASET_UUID);
-			if (worldClimDataset != null) {
-				model.addAttribute("worldclimJson", dsService.jsonForTile(worldClimDataset, accessionGeo.getTileIndex()));
-			}
+			model.addAttribute("worldclimJson", climateDataService.jsonForTile(accessionGeo.getTileIndex()));
 		}
 	}
 

src/main/java/org/genesys2/server/persistence/TileClimateRepository.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.persistence;
+
+import org.genesys2.server.model.impl.TileClimate;
+import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.data.querydsl.QueryDslPredicateExecutor;
+
+/**
+ * The JPA TileClimateRepository.
+ */
+public interface TileClimateRepository extends JpaRepository<TileClimate, Long>, QueryDslPredicateExecutor<TileClimate> {
+
+}

src/main/java/org/genesys2/server/service/ClimateDataService.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.service;
+
+import java.nio.MappedByteBuffer;
+import java.util.HashSet;
+import java.util.List;
+
+import org.genesys2.server.model.genesys.AccessionGeo;
+import org.genesys2.server.model.impl.TileClimate;
+import org.genesys2.server.model.json.WorldclimJson;
+
+/**
+ * The ClimateDataService interface.
+ */
+public interface ClimateDataService {
+
+	void worldclimUpdate(String variableName, HashSet<Long> ids, MappedByteBuffer buffer, short nullValue, double factor);
+
+	TileClimate climateForTile(Long tileIndex);
+
+	void updateAccessionTileIndex(List<AccessionGeo> toSave);
+
+	WorldclimJson jsonForTile(Long tileIndex);
+
+}

src/main/java/org/genesys2/server/service/DSService.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.service;
 
 import java.io.IOException;
 import java.io.OutputStream;
-import java.nio.MappedByteBuffer;
 import java.util.List;
-import java.util.Set;
 import java.util.UUID;
 
 import org.genesys2.server.model.dataset.DS;
 import org.genesys2.server.model.dataset.DSColumn;
-import org.genesys2.server.model.dataset.DSQualifier;
 import org.genesys2.server.model.dataset.DSDescriptor;
-import org.genesys2.server.model.genesys.AccessionGeo;
-import org.genesys2.server.model.json.WorldclimJson;
+import org.genesys2.server.model.dataset.DSQualifier;
 
+/**
+ * The DSService interface.
+ */
 public interface DSService {
 
+	/**
+	 * Save dataset.
+	 *
+	 * @param ds the ds
+	 * @return the ds
+	 */
 	DS saveDataset(DS ds);
 
+	/**
+	 * Adds the qualifier.
+	 *
+	 * @param ds the ds
+	 * @param d1 the d 1
+	 * @return the DS qualifier
+	 */
 	DSQualifier addQualifier(DS ds, DSDescriptor d1);
+	
+	/**
+	 * Adds the descriptor.
+	 *
+	 * @param ds the ds
+	 * @param dSDescriptor the d S descriptor
+	 * @return the DS column
+	 */
 	DSColumn addDescriptor(DS ds, DSDescriptor dSDescriptor);
 
+	/**
+	 * Load dataset by uuid.
+	 *
+	 * @param uuid the uuid
+	 * @return the ds
+	 */
 	DS loadDatasetByUuid(UUID uuid);
 
 
+	/**
+	 * Update row.
+	 *
+	 * @param ds the ds
+	 * @param row the row
+	 */
 	void updateRow(DS ds, Object[] row);
+	
+	/**
+	 * Update rows.
+	 *
+	 * @param ds the ds
+	 * @param rows the rows
+	 */
 	void updateRows(DS ds, List<Object[]> rows);
+	
+	/**
+	 * Update row.
+	 *
+	 * @param ds the ds
+	 * @param qualifiers the qualifiers
+	 * @param dsd the dsd
+	 * @param value the value
+	 */
 	void updateRow(DS ds, Object[] qualifiers, DSColumn dsd, Object value);
 
-	void worldclimUpdate(DS dataset, DSColumn dsd, Set<Long> ids, MappedByteBuffer buffer, short nullValue, double factor);
-
-	void updateAccessionTileIndex(List<AccessionGeo> toSave);
-
-	WorldclimJson jsonForTile(DS worldClimDataset, Long tileIndex);
-
+	/**
+	 * Download.
+	 *
+	 * @param ds the ds
+	 * @param outputStream the output stream
+	 * @throws IOException Signals that an I/O exception has occurred.
+	 */
 	void download(DS ds, OutputStream outputStream) throws IOException;
 
+	/**
+	 * Download.
+	 *
+	 * @param ds the ds
+	 * @param dsds the dsds
+	 * @param outputStream the output stream
+	 * @throws IOException Signals that an I/O exception has occurred.
+	 */
 	void download(DS ds, List<DSColumn> dsds, OutputStream outputStream) throws IOException;
 
+	/**
+	 * Delete dataset.
+	 *
+	 * @param ds the ds
+	 */
 	void deleteDataset(DS ds);
 
+	/**
+	 * Delete descriptor.
+	 *
+	 * @param dsd the dsd
+	 */
 	void deleteDescriptor(DSColumn dsd);
 
+	/**
+	 * Delete rows.
+	 *
+	 * @param ds the ds
+	 */
 	void deleteRows(DS ds);
 }

src/main/java/org/genesys2/server/service/impl/ClimateDataServiceImpl.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.service.impl;
+
+import java.lang.reflect.InvocationTargetException;
+import java.nio.MappedByteBuffer;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.commons.beanutils.BeanUtils;
+import org.genesys2.server.model.genesys.AccessionGeo;
+import org.genesys2.server.model.impl.TileClimate;
+import org.genesys2.server.model.json.WorldclimJson;
+import org.genesys2.server.persistence.AccessionGeoRepository;
+import org.genesys2.server.persistence.TileClimateRepository;
+import org.genesys2.server.service.ClimateDataService;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+import org.springframework.transaction.annotation.Transactional;
+
+/**
+ * The ClimateDataService implementation.
+ */
+@Service
+@Transactional(readOnly = true)
+public class ClimateDataServiceImpl implements ClimateDataService {
+	public static final Logger LOG = LoggerFactory.getLogger(ClimateDataServiceImpl.class);
+	
+	/** The tile climate repository. */
+	@Autowired
+	private TileClimateRepository tileClimateRepository;
+
+	/** The accession geo repository. */
+	@Autowired
+	private AccessionGeoRepository accessionGeoRepository;
+
+	/* (non-Javadoc)
+	 * @see org.genesys2.server.service.DSService#updateAccessionTileIndex(java.util.List)
+	 */
+	@Override
+	@Transactional
+	public void updateAccessionTileIndex(List<AccessionGeo> toSave) {
+		accessionGeoRepository.save(toSave);
+	}
+
+	/* (non-Javadoc)
+	 * @see org.genesys2.server.service.ClimateDataService#worldclimUpdate(java.lang.String, java.util.HashSet, java.nio.MappedByteBuffer, short, double)
+	 */
+	@Override
+	@Transactional
+	public void worldclimUpdate(String variableName, HashSet<Long> tileIndexes, MappedByteBuffer buffer, short nullValue, double factor) {
+		LOG.debug("Updating {} for tileIndexes: {}", variableName, tileIndexes.size());
+
+		Map<Long, TileClimate> rowMap = findOrMakeRows(tileIndexes);
+
+		for (final Long tileIndex : tileIndexes) {
+			TileClimate tileClimate = rowMap.get(tileIndex);
+			
+			if (tileIndex * 2 > buffer.capacity() - 2) {
+				LOG.info("OUT OF FILE tile={}", tileIndex);
+				rowMap.remove(tileIndex);
+			} else {
+				try {
+					short val = buffer.getShort((int) (tileIndex * 2));
+					if (val != nullValue) {
+						LOG.trace("tile={} val={}", tileIndex, val);
+
+						Object value = null;
+						if (factor < 1.0) {
+							// FIXME Find a better way!
+							value = new Double(factor * val);
+						} else if (factor == 1.0) {
+							value = new Long((long) (factor * val));
+						}
+
+							try {
+								BeanUtils.setProperty(tileClimate, variableName, value);
+							} catch (IllegalAccessException | InvocationTargetException e) {
+								LOG.error("Cannot set TileClimate#{} to {}. {}", variableName, value, e.getMessage());
+							}
+						
+					}
+				} catch (IndexOutOfBoundsException e) {
+					LOG.error("OUT OF BOUND tile={} capacity={} limit={}", tileIndex, buffer.capacity(), buffer.limit());
+					throw e;
+				}
+			}
+		}
+
+		tileClimateRepository.save(rowMap.values());
+
+		LOG.debug("Done saving.");
+	}
+
+	/**
+	 * Find or make rows.
+	 *
+	 * @param tileIndexes the tile indexes
+	 * @return the map
+	 */
+	private Map<Long, TileClimate> findOrMakeRows(HashSet<Long> tileIndexes) {
+		List<TileClimate> existingTiles = tileClimateRepository.findAll(tileIndexes);
+		HashMap<Long, TileClimate> map = new HashMap<>(tileIndexes.size());
+		existingTiles.forEach((tile) -> {
+			map.put(tile.getTileIndex(), tile);
+		});
+		tileIndexes.forEach(tileIndex -> {
+			if (!map.containsKey(tileIndex)) {
+				map.put(tileIndex, new TileClimate(tileIndex));
+			}
+		});
+		return map;
+	}
+
+	/* (non-Javadoc)
+	 * @see org.genesys2.server.service.ClimateDataService#climateForTile(java.lang.Long)
+	 */
+	@Override
+	public TileClimate climateForTile(Long tileIndex) {
+		return tileClimateRepository.findOne(tileIndex);
+	}
+
+	/* (non-Javadoc)
+	 * @see org.genesys2.server.service.ClimateDataService#jsonForTile(java.lang.Long)
+	 */
+	@Override
+	public WorldclimJson jsonForTile(Long tileIndex) {
+		TileClimate tileClimate = tileClimateRepository.findOne(tileIndex);
+		if (tileClimate == null)
+			return null;
+
+		WorldclimJson wc = new WorldclimJson();
+		wc.setPrecipitation(new Double[] { tileClimate.getPrec1(), tileClimate.getPrec2(), tileClimate.getPrec3(), tileClimate.getPrec4(), tileClimate.getPrec5(), tileClimate.getPrec6(), tileClimate.getPrec7(), tileClimate.getPrec8(), tileClimate.getPrec9(), tileClimate.getPrec10(), tileClimate.getPrec11(), tileClimate.getPrec12() } );
+		wc.setTempMin(new Double[] { tileClimate.getTmin1(), tileClimate.getTmin2(), tileClimate.getTmin3(), tileClimate.getTmin4(), tileClimate.getTmin5(), tileClimate.getTmin6(), tileClimate.getTmin7(), tileClimate.getTmin8(), tileClimate.getTmin9(), tileClimate.getTmin10(), tileClimate.getTmin11(), tileClimate.getTmin12() } );
+		wc.setTempMean(new Double[] { tileClimate.getTmean1(), tileClimate.getTmean2(), tileClimate.getTmean3(), tileClimate.getTmean4(), tileClimate.getTmean5(), tileClimate.getTmean6(), tileClimate.getTmean7(), tileClimate.getTmean8(), tileClimate.getTmean9(), tileClimate.getTmean10(), tileClimate.getTmean11(), tileClimate.getTmean12() } );
+		wc.setTempMax(new Double[] { tileClimate.getTmax1(), tileClimate.getTmax2(), tileClimate.getTmax3(), tileClimate.getTmax4(), tileClimate.getTmax5(), tileClimate.getTmax6(), tileClimate.getTmax7(), tileClimate.getTmax8(), tileClimate.getTmax9(), tileClimate.getTmax10(), tileClimate.getTmax11(), tileClimate.getTmax12() } );
+	
+		return wc;
+	}
+
+}

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

@@ -43,15 +43,10 @@ import org.genesys.worldclim.grid.generic.GenericGridFile;
 import org.genesys.worldclim.grid.generic.GenericGridZipFile;
 import org.genesys.worldclim.grid.generic.Header;
 import org.genesys2.server.component.aspect.AsAdmin;
-import org.genesys2.server.model.dataset.DS;
-import org.genesys2.server.model.dataset.DSColumn;
-import org.genesys2.server.model.dataset.DSDescriptor;
-import org.genesys2.server.model.dataset.DSQualifier;
 import org.genesys2.server.model.genesys.AccessionGeo;
 import org.genesys2.server.persistence.AccessionGeoRepository;
 import org.genesys2.server.persistence.GenesysLowlevelRepository;
-import org.genesys2.server.service.DSService;
-import org.genesys2.server.service.DescriptorService;
+import org.genesys2.server.service.ClimateDataService;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.InitializingBean;
@@ -96,10 +91,7 @@ public class WorldClimUpdater implements InitializingBean {
 	private File worldClimDir;
 
 	@Autowired
-	private DSService dsService;
-
-	@Autowired
-	private DescriptorService descriptorService;
+	private ClimateDataService climateDataService;
 
 	@Autowired
 	@Qualifier("genesysLowlevelRepositoryCustomImpl")
@@ -173,27 +165,7 @@ public class WorldClimUpdater implements InitializingBean {
 			downloadAndExtract(worldClimDir, getFileName(variableName));
 		}
 
-		DS dataset = ensureWorldClimDataset();
-
-		DSDescriptor descriptor = descriptorService.getDescriptor(variableName);
-		DSColumn worldclimDescriptor = null;
-		if (descriptor == null) {
-			descriptor = createDescriptor(variableName);
-			worldclimDescriptor = dsService.addDescriptor(dataset, descriptor);
-			LOG.info("Created worldclimDescriptor {}", variableName);
-		} else {
-			for (DSColumn dsd : dataset.getColumns()) {
-				if (dsd.getDescriptor().getCode().equals(variableName)) {
-					LOG.debug("Found worldclimDescriptor {}", variableName);
-					worldclimDescriptor = dsd;
-					break;
-				}
-			}
-			if (worldclimDescriptor == null)
-				worldclimDescriptor = dsService.addDescriptor(dataset, descriptor);
-		}
-
-		LOG.debug("Using worldClim {}", worldclimDescriptor);
+		LOG.debug("Using worldClim {}", variableName);
 
 		GenericGridFile ggf = new GenericGridFile(worldClimDir, variableName);
 		Header header = ggf.readHeader();
@@ -202,9 +174,11 @@ public class WorldClimUpdater implements InitializingBean {
 		MappedByteBuffer buffer = ggf.mapDataBuffer();
 
 		double factor = 1.0;
-		if ("bio3".equals(variableName)) {
-			factor = .01f;
-		} else if ("bio4".equals(variableName)) {
+		if (variableName.matches("(bio)(1|2|5|6|7|8|9|10|11)")) {
+			// bioclimatic variables derived from the tmean, tmin, tmax (factor = .1f)
+			factor = .1f;
+		} else if (variableName.matches("(bio)(3|4)")) {
+			// (* 100) at http://worldclim.org/bioclim
 			factor = .01f;
 		} else if (variableName.matches("(tmean|tmax|tmin)\\d{1,2}")) {
 			factor = .1f;
@@ -222,7 +196,7 @@ public class WorldClimUpdater implements InitializingBean {
 
 			for (int i = 5; i >= 0; i--) {
 				try {
-					dsService.worldclimUpdate(dataset, worldclimDescriptor, ids, buffer, nullValue, factor);
+					climateDataService.worldclimUpdate(variableName, ids, buffer, nullValue, factor);
 					break; // break try-5-times loop
 				} catch (DataIntegrityViolationException e) {
 					if (i == 0) {
@@ -283,7 +257,7 @@ public class WorldClimUpdater implements InitializingBean {
 					}
 					if (toSave.size() > 0) {
 						LOG.info("Updating {} accesssions' tileIndex at position {} of {}", toSave.size(), startIndex, accessionIds.size());
-						dsService.updateAccessionTileIndex(toSave);
+						climateDataService.updateAccessionTileIndex(toSave);
 					}
 				} catch (Throwable e) {
 					LOG.error(e.getMessage(), e);
@@ -300,37 +274,6 @@ public class WorldClimUpdater implements InitializingBean {
 		return tileIndexSet;
 	}
 
-	private DSDescriptor createDescriptor(String variableName) {
-		DSDescriptor descriptor = new DSDescriptor();
-		descriptor.setCode(variableName);
-		descriptor.setTitle("WorldClim " + variableName);
-		descriptor = descriptorService.saveDescriptor(descriptor);
-		LOG.info("Created descriptor {}", descriptor);
-		return descriptor;
-	}
-
-	private DS createWorldClimDataset() {
-		DS dataset = new DS();
-		// dataset.setDescription("Genesys accessions linked with worldclim.org data.
-		// Maintained automatically by Genesys");
-		// dataset.setName("WorldClim.org Data");
-		// dataset.setSource("worldclim.org + genesys-pgr.org");
-		// dataset.setUploadDate(new Date());
-		dataset.setUuid(WORLDCLIM_DATASET);
-		dataset.setQualifiers(new ArrayList<DSQualifier>());
-		dataset.setColumns(new ArrayList<DSColumn>());
-		dataset = dsService.saveDataset(dataset);
-		LOG.info("Created dataset {}", WORLDCLIM_DATASET);
-		
-		DSDescriptor tileIndex = descriptorService.getDescriptor("tileIndex");
-		if (tileIndex == null) {
-			tileIndex = createDescriptor("tileIndex");
-		}
-
-		dsService.addQualifier(dataset, tileIndex);
-		return dataset;
-	}
-
 	private String getFileName(String variableName) throws FileNotFoundException {
 		if ("alt".equalsIgnoreCase(variableName)) {
 			return "alt_2-5m_bil.zip";
@@ -421,7 +364,6 @@ public class WorldClimUpdater implements InitializingBean {
 	 * Update all WorldClim variables
 	 */
 	public void update() {
-		ensureWorldClimDataset();
 		
 		try {
 			update("alt");
@@ -473,13 +415,4 @@ public class WorldClimUpdater implements InitializingBean {
 		}
 	}
 
-	protected synchronized DS ensureWorldClimDataset() {
-		DS dataset = dsService.loadDatasetByUuid(WORLDCLIM_DATASET);
-		if (dataset == null) {
-			// Ensure dataset
-			dataset = createWorldClimDataset();
-		}
-		return dataset;
-	}
-
 }

src/main/resources/liquibase.properties

@@ -11,7 +11,7 @@ changeLogFile=src/main/resources/liquibase/liquibase-changeLog.yml
 diffChangeLogFile=src/main/resources/liquibase/liquibase-diff-changeLog.yml
 ## &hibernate.ejb.naming_strategy=org.hibernate.cfg.ImprovedNamingStrategy
 # Existing database
-url=jdbc:mysql://localhost/genesysold?useUnicode=true&characterEncoding=UTF-8&useFastDateParsing=false
+url=jdbc:mysql://localhost/genesys20181126?useUnicode=true&characterEncoding=UTF-8&useFastDateParsing=false
 username=root
 password=
 driver=com.mysql.jdbc.Driver