/explore Display columns for release

src/main/java/org/genesys2/server/model/elastic/Collect.java

@@ -13,17 +13,17 @@ import org.springframework.data.elasticsearch.annotations.FieldType;
 
 public class Collect {
 
-	public Set<String> collCode;
+	private Set<String> collCode;
 	@Field(index = FieldIndex.not_analyzed, type = FieldType.String)
-	public String collDate;
-	public String collInstAddr;
-	public String collMissId;
-	public String collName;
+	private String collDate;
+	private String collInstAddr;
+	private String collMissId;
+	private String collName;
 	@Field(index = FieldIndex.not_analyzed, type = FieldType.String)
-	public String collNumb;
-	public String collSite;
-	public Integer collSrc;
-	public Date collectingDate;
+	private String collNumb;
+	private String collSite;
+	private Integer collSrc;
+	private Date collectingDate;
 
 	public static Collect from(AccessionCollect collect) {
 		if (collect == null)
@@ -42,4 +42,75 @@ public class Collect {
 		return c;
 	}
 
+	public Set<String> getCollCode() {
+		return collCode;
+	}
+
+	public void setCollCode(Set<String> collCode) {
+		this.collCode = collCode;
+	}
+
+	public String getCollDate() {
+		return collDate;
+	}
+
+	public void setCollDate(String collDate) {
+		this.collDate = collDate;
+	}
+
+	public String getCollInstAddr() {
+		return collInstAddr;
+	}
+
+	public void setCollInstAddr(String collInstAddr) {
+		this.collInstAddr = collInstAddr;
+	}
+
+	public String getCollMissId() {
+		return collMissId;
+	}
+
+	public void setCollMissId(String collMissId) {
+		this.collMissId = collMissId;
+	}
+
+	public String getCollName() {
+		return collName;
+	}
+
+	public void setCollName(String collName) {
+		this.collName = collName;
+	}
+
+	public String getCollNumb() {
+		return collNumb;
+	}
+
+	public void setCollNumb(String collNumb) {
+		this.collNumb = collNumb;
+	}
+
+	public String getCollSite() {
+		return collSite;
+	}
+
+	public void setCollSite(String collSite) {
+		this.collSite = collSite;
+	}
+
+	public Integer getCollSrc() {
+		return collSrc;
+	}
+
+	public void setCollSrc(Integer collSrc) {
+		this.collSrc = collSrc;
+	}
+
+	public Date getCollectingDate() {
+		return collectingDate;
+	}
+
+	public void setCollectingDate(Date collectingDate) {
+		this.collectingDate = collectingDate;
+	}
 }
\ No newline at end of file

src/main/java/org/genesys2/server/model/elastic/Geo.java

@@ -88,4 +88,10 @@ public class Geo {
 		this.datum = datum;
 	}
 
+	public String getLatitudeAndLongitude() {
+		if (this.latitude==null && this.longitude==null) {
+			return null;
+		}
+		return this.latitude + ", " + this.longitude;
+	}
 }
\ No newline at end of file

src/main/java/org/genesys2/server/model/impl/FaoInstitute.java

@@ -59,7 +59,7 @@ public class FaoInstitute extends BusinessModel implements GeoReferencedEntity,
 	@Column(length = 300)
 	private String fullName;
 
-	@Column(length = 50)
+	@Column(length = 100)
 	private String type;
 
 	@Column(length = 300)

src/main/java/org/genesys2/server/model/json/Api1Constants.java

@@ -22,7 +22,8 @@ package org.genesys2.server.model.json;
 public interface Api1Constants {
 	public static interface Accession {
 
-		public static final String CROPE_NAME = "cropName";
+		public static final String CROP_NAMES = "crops";
+
 		/**
 		 * WIEWS code of accession holding institute.
 		 */
@@ -185,12 +186,52 @@ public interface Api1Constants {
 		 */
 		public static final String ACCEURL = "acceUrl";
 
-		public static final String SCIENTIFIC_NAME = "scientificName";
+	}
+	
+	public static interface Institute {
+		/**
+		 * Corresponds to INSTCODE
+		 */
+		public static final String INSTCODE = "code";
+
+		public static final String INSTCODE_COUNTRY = "country.iso3";
+
+	}
+	
+	public static interface Taxonomy {
+		
+		public static final String SCIENTIFIC_NAME = "sciName";
+
+		/**
+		 * Reported genus of accession.
+		 */
+		public static final String GENUS = "genus";
+
+		/**
+		 * May be used to assign a different genus.
+		 */
+		public static final String GENUS_NEW = "newGenus";
+
+		/**
+		 * Specific epithet portion of the scientific name, in latin, in
+		 * lowercase letters. Following abbreviation is allowed: ‘sp.’
+		 */
+		public static final String SPECIES = "species";
+
+		/**
+		 * Corresponds to MCPD SPAUTHOR
+		 */
+		public static final String SPAUTHOR = "spauthor";
+
+		/**
+		 * Corresponds to MCPD SUBTAXA
+		 */
+		public static final String SUBTAXA = "subtaxa";
+
 	}
 
 	public static interface Collecting {
 
-		public static final String MISSION_ID = "collectingMissionID";
 		/**
 		 * Corresponds to COLLDATE
 		 */

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

@@ -16,10 +16,14 @@
 
 package org.genesys2.server.persistence.domain;
 
+import java.util.List;
+
 import org.genesys2.server.model.impl.Crop;
 import org.springframework.data.jpa.repository.JpaRepository;
 
 public interface CropRepository extends JpaRepository<Crop, Long> {
 
 	Crop findByShortName(String shortName);
+
+	List<Crop> findByShortName(List<String> cropNames);
 }

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

@@ -93,4 +93,9 @@ public interface CropService {
 	 */
 	void updateCropTaxonomyLists(Taxonomy2 taxonomy);
 
+	/**
+	 * Get crops
+	 */
+	List<Crop> getCrops(List<String> cropNames);
+
 }

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

@@ -18,6 +18,7 @@ package org.genesys2.server.service;
 
 import java.util.List;
 
+import org.genesys2.server.model.elastic.AccessionDetails;
 import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.service.impl.FilterHandler.AppliedFilters;
 import org.genesys2.server.service.impl.GenesysFilterServiceImpl.LabelValue;
@@ -28,6 +29,11 @@ import org.springframework.jdbc.core.RowCallbackHandler;
 public interface GenesysFilterService {
 
 	Page<Accession> listAccessions(AppliedFilters filters, Pageable pageable);
+	
+	/**
+	 * Get fully loaded accession data
+	 */
+	Page<AccessionDetails> listAccessionDetails(AppliedFilters filters, Pageable pageable);
 
 	List<LabelValue<String>> autocomplete(String filter, String ac, AppliedFilters filters);
 

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

@@ -213,9 +213,9 @@ public interface GenesysService {
 
 	List<Long> listAccessionsIds(Taxonomy2 taxonomy);
 
-	List<String> columnsForDisplay();
+	List<String> columnsAvailableForDisplay();
 
-	List<String> defaultViewColumns();
+	List<String> defaultDisplayColumns();
 
 	public static class AllStuff {
 		public AllStuff(long id) {
@@ -240,20 +240,20 @@ public interface GenesysService {
 
 	List<AllStuff> loadAllStuff(Collection<Long> accessionIds);
 
-	Set<AccessionDetails> getAccessionDetails(Collection<Long> accessionIds);
+	List<AccessionDetails> getAccessionDetails(Collection<Long> accessionIds);
 
 	int assignMissingUuid(int count);
 
 	AccessionHistoric getHistoricAccession(UUID uuid);
 
-	PDCI updatePDCI(Long accessionId);
+	void updatePDCI(Collection<AccessionDetails> ads);
 
 	PDCI loadPDCI(Long accessionId);
+	
+	PDCI updatePDCI(Long id);
 
 	PDCIStatistics statisticsPDCI(FaoInstitute faoInstitute);
 
-	void updatePDCI(Set<AccessionDetails> ads);
-
 	List<PDCI> loadPDCI(List<Long> batch);
 
 	int generateMissingPDCI(int count);

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

@@ -114,6 +114,11 @@ public class CropServiceImpl implements CropService {
 		return cropTaxonomyRepository.findCropsByTaxonomy(taxonomy2);
 	}
 
+	@Override
+	public List<Crop> getCrops(List<String> cropNames) {
+		return cropRepository.findByShortName(cropNames);
+	}
+
 	@Override
 	@Transactional(readOnly = false, propagation = Propagation.REQUIRES_NEW)
 	@PreAuthorize("hasRole('ADMINISTRATOR')")
@@ -320,7 +325,7 @@ public class CropServiceImpl implements CropService {
 
 	@Override
 	@Transactional(readOnly = false)
-	@CacheEvict(value = CACHE_CROP_TAXONOMYCROPS, key="#taxonomy.id")
+	@CacheEvict(value = CACHE_CROP_TAXONOMYCROPS, key = "#taxonomy.id")
 	public void updateCropTaxonomyLists(Taxonomy2 taxonomy) {
 		// Load all rules
 		List<CropRule> cropRules = cropRuleRepository.findAll();

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

@@ -330,7 +330,7 @@ public class ElasticsearchSearchServiceImpl implements ElasticService, Initializ
 
 		List<IndexQuery> queries = new ArrayList<IndexQuery>();
 
-		Set<AccessionDetails> ads = genesysService.getAccessionDetails(ids);
+		List<AccessionDetails> ads = genesysService.getAccessionDetails(ids);
 		// If Accession, update PDCI
 		genesysService.updatePDCI(ads);
 

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

@@ -27,6 +27,7 @@ import javax.sql.DataSource;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
+import org.genesys2.server.model.elastic.AccessionDetails;
 import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.genesys.Method;
 import org.genesys2.server.model.impl.Country;
@@ -67,7 +68,7 @@ public class GenesysFilterServiceImpl implements GenesysFilterService {
 	// using this loop to make @Cacheable work
 	@Autowired
 	private GenesysService genesysService;
-	
+
 	@Autowired
 	private MethodRepository methodRepository;
 
@@ -115,11 +116,11 @@ public class GenesysFilterServiceImpl implements GenesysFilterService {
 
 		// Does this go through the cache?
 		final long totalCount = genesysService.countAccessions(filters);
-		LOG.info("Total count: " + totalCount);
+		LOG.debug("Total count: " + totalCount);
 
 		if (totalCount > 0 && pageable.getPageNumber() * pageable.getPageSize() <= totalCount) {
 			final List<Long> results = this.jdbcTemplate.queryForList(directQuery.getQuery("distinct a.id"), directQuery.getParameters(), Long.class);
-			LOG.info("Getting accessions " + results.size());
+			LOG.debug("Getting accessions " + results.size());
 
 			return new PageImpl<Accession>(results.size() == 0 ? new ArrayList<Accession>() : accessionRepository.listById(results,
 			// TODO Consider processing the pageable.getSort
@@ -131,6 +132,46 @@ public class GenesysFilterServiceImpl implements GenesysFilterService {
 		}
 	}
 
+	/**
+	 * Copy of
+	 * {@link GenesysFilterServiceImpl#listAccessions(AppliedFilters, Pageable)
+
+	 */
+	@Override
+	public Page<AccessionDetails> listAccessionDetails(AppliedFilters filters, Pageable pageable) {
+		if (LOG.isDebugEnabled()) {
+			for (AppliedFilter filter : filters) {
+				LOG.debug("Looking at " + filter.toString());
+			}
+		}
+
+		final DirectMysqlQuery directQuery = new DirectMysqlQuery("accession", "a");
+		directQuery.jsonFilter(filters, new MethodResolver() {
+			@Override
+			public Method getMethod(long methodId) {
+				return methodRepository.findOne(methodId);
+			}
+		});
+		directQuery.pageable(pageable);
+
+		// Does this go through the cache?
+		final long totalCount = genesysService.countAccessions(filters);
+		LOG.debug("Total count: " + totalCount);
+
+		if (totalCount > 0 && pageable.getPageNumber() * pageable.getPageSize() <= totalCount) {
+			final List<Long> results = this.jdbcTemplate.queryForList(directQuery.getQuery("distinct a.id"), directQuery.getParameters(), Long.class);
+			LOG.debug("Getting accessions " + results.size());
+
+			if (results.size() == 0) {
+				return new PageImpl<AccessionDetails>(new ArrayList<AccessionDetails>(), pageable, totalCount);
+			} else {
+				return new PageImpl<AccessionDetails>(genesysService.getAccessionDetails(results), pageable, totalCount);
+			}
+		} else {
+			return new PageImpl<AccessionDetails>(new ArrayList<AccessionDetails>(), pageable, totalCount);
+		}
+	}
+
 	/**
 	 * Filtering autocompleter
 	 */

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

@@ -193,6 +193,32 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 	@Autowired
 	private PDCIRepository repoPdci;
 
+	private List<String> availableDisplayColumns;
+
+	private List<String> defaultDisplayColumns;
+
+	public GenesysServiceImpl() {
+		List<String> columnList = new ArrayList<String>();
+		columnList.add("taxonomy." + Api1Constants.Taxonomy.SCIENTIFIC_NAME);
+		columnList.add("taxonomy." + Api1Constants.Taxonomy.GENUS);
+		columnList.add("taxonomy." + Api1Constants.Taxonomy.SPECIES);
+		columnList.add("taxonomy." + Api1Constants.Taxonomy.SUBTAXA);
+		columnList.add(Api1Constants.Accession.CROP_NAMES);
+		columnList.add(Api1Constants.Accession.ORIGCTY);
+		columnList.add(Api1Constants.Accession.SAMPSTAT);
+		columnList.add("institute." + Api1Constants.Institute.INSTCODE);
+		columnList.add("geo." + Api1Constants.Geo.LATITUDE_LONGITUDE);
+		columnList.add("coll." + Api1Constants.Collecting.COLLMISSID);
+		availableDisplayColumns = Collections.unmodifiableList(columnList);
+
+		List<String> displayList = new ArrayList<String>();
+		displayList.add("taxonomy." + Api1Constants.Taxonomy.SCIENTIFIC_NAME);
+		displayList.add(Api1Constants.Accession.ORIGCTY);
+		displayList.add(Api1Constants.Accession.SAMPSTAT);
+		displayList.add("institute." + Api1Constants.Institute.INSTCODE);
+		defaultDisplayColumns = Collections.unmodifiableList(displayList);
+	}
+
 	@Override
 	public long countAll() {
 		return accessionRepository.count();
@@ -363,8 +389,8 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 	}
 
 	@Override
-	public Set<AccessionDetails> getAccessionDetails(Collection<Long> accessionIds) {
-		Set<AccessionDetails> set = new HashSet<AccessionDetails>(accessionIds.size());
+	public List<AccessionDetails> getAccessionDetails(Collection<Long> accessionIds) {
+		List<AccessionDetails> set = new ArrayList<AccessionDetails>(accessionIds.size());
 		List<AllStuff> alls = loadAllStuff(accessionIds);
 		for (AllStuff all : alls) {
 			if (all == null)
@@ -1530,26 +1556,13 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 	}
 
 	@Override
-	public List<String> columnsForDisplay() {
-		List<String> columnList = new ArrayList<>();
-		columnList.add(Api1Constants.Accession.GENUS);
-		columnList.add(Api1Constants.Accession.SPECIES);
-		columnList.add(Api1Constants.Accession.SUBTAXA);
-		columnList.add(Api1Constants.Accession.CROPE_NAME);
-		columnList.add(Api1Constants.Geo.LATITUDE_LONGITUDE);
-		columnList.add(Api1Constants.Collecting.MISSION_ID);
-		return columnList;
+	public List<String> columnsAvailableForDisplay() {
+		return availableDisplayColumns;
 	}
 
 	@Override
-	public List<String> defaultViewColumns() {
-		List<String> columnList = new ArrayList<>();
-		columnList.add(Api1Constants.Accession.ACCENUMB);
-		columnList.add(Api1Constants.Accession.SCIENTIFIC_NAME);
-		columnList.add(Api1Constants.Accession.ORIGCTY);
-		columnList.add(Api1Constants.Accession.SAMPSTAT);
-		columnList.add(Api1Constants.Accession.INSTCODE);
-		return columnList;
+	public List<String> defaultDisplayColumns() {
+		return defaultDisplayColumns;
 	}
 
 	@Override
@@ -1601,7 +1614,7 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 				ids.add(id.getId());
 			}
 		}
-		Set<AccessionDetails> ads = getAccessionDetails(ids);
+		Collection<AccessionDetails> ads = getAccessionDetails(ids);
 		List<PDCI> pdcis = new ArrayList<PDCI>();
 		for (AccessionDetails ad : ads) {
 			PDCI pdci = new PDCI();
@@ -1633,13 +1646,14 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 			pdci = new PDCI();
 			pdci.setAccession(accessionIdRepository.findOne(accessionId));
 		}
+		
 		return repoPdci.save(pdciCalculator.updatePdci(pdci, accessionId));
 	}
 
 	@Override
 	@Transactional
 	@CacheEvict(value = "statistics", allEntries = true)
-	public void updatePDCI(Set<AccessionDetails> ads) {
+	public void updatePDCI(Collection<AccessionDetails> ads) {
 		if (pdciCalculator == null) {
 			return;
 		}

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

@@ -253,7 +253,7 @@ public class ElasticUpdater {
 		}
 	}
 
-	public void archive(final Set<AccessionDetails> deletedAccessions) {
+	public void archive(final List<AccessionDetails> deletedAccessions) {
 		final List<IndexQuery> queries = new ArrayList<>(deletedAccessions.size());
 		for (AccessionDetails ad : deletedAccessions) {
 			IndexQuery iq = new IndexQuery();

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

@@ -158,7 +158,7 @@ public class ElasticUpdaterAspect {
 				accessionIds.add(a.getId());
 		}
 		// Need to load AccessionDetails before deleting
-		Set<AccessionDetails> deletedAccessions = genesysService.getAccessionDetails(accessionIds);
+		List<AccessionDetails> deletedAccessions = genesysService.getAccessionDetails(accessionIds);
 
 		try {
 			Object res = joinPoint.proceed();

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

@@ -25,8 +25,8 @@ import java.io.IOException;
 import java.io.OutputStream;
 import java.net.URI;
 import java.net.URISyntaxException;
+import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.Collections;
 import java.util.List;
 import java.util.Map;
 
@@ -39,7 +39,6 @@ import org.apache.commons.lang.StringUtils;
 import org.apache.http.client.utils.URIBuilder;
 import org.genesys2.server.model.elastic.AccessionDetails;
 import org.genesys2.server.model.filters.GenesysFilter;
-import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.genesys.Method;
 import org.genesys2.server.model.genesys.Parameter;
 import org.genesys2.server.model.genesys.ParameterCategory;
@@ -59,6 +58,7 @@ import org.genesys2.server.service.impl.FilterHandler.AppliedFilters;
 import org.genesys2.server.service.impl.GenesysFilterServiceImpl.LabelValue;
 import org.genesys2.server.service.impl.SearchException;
 import org.genesys2.spring.ResourceNotFoundException;
+import org.springframework.beans.factory.InitializingBean;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.data.domain.Page;
@@ -79,7 +79,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
 import com.jhlabs.image.MapColorsFilter;
 
 @Controller
-public class ExplorerController extends BaseController {
+public class ExplorerController extends BaseController implements InitializingBean {
 
 	private static final int DOWNLOAD_LIMIT = 200000;
 
@@ -115,6 +115,16 @@ public class ExplorerController extends BaseController {
 	@Value("${base.url}")
 	private String baseUrl;
 
+	private List<String> validDisplayColumns;
+
+	private List<String> defaultDisplayColumns;
+
+	@Override
+	public void afterPropertiesSet() throws Exception {
+		validDisplayColumns = genesysService.columnsAvailableForDisplay();
+		defaultDisplayColumns = genesysService.defaultDisplayColumns();
+	}
+
 	/**
 	 * Redirect to /explore/c/{shortName} if parameter 'crop' is provided
 	 */
@@ -155,22 +165,8 @@ public class ExplorerController extends BaseController {
 	@RequestMapping("/explore")
 	public String viewFiltered(HttpServletResponse response, ModelMap model, @RequestParam(value = "page", required = false, defaultValue = "1") int page,
 			@RequestParam(value = "filter", required = true, defaultValue = "{}") String jsonFilter,
-			@RequestParam(value = "columns", required = true, defaultValue = "") String columns,
-			@CookieValue(value = "columns", defaultValue = "") String cookieColumns) throws IOException {
-
-		if (columns != null && !columns.isEmpty()) {
-			String columnsForCookie = "";
-			for (String clmn : Arrays.asList(columns.split(","))) {
-				columnsForCookie += clmn + ",";
-			}
-			columnsForCookie = !columnsForCookie.isEmpty() && columnsForCookie.substring(columnsForCookie.length() - 1).equals(",") ? columnsForCookie
-					.substring(0, columnsForCookie.length() - 1) : columnsForCookie;
-			Cookie cookie = new Cookie("columns", columnsForCookie);
-			response.addCookie(cookie);
-			model.addAttribute("selectedColumns", columnsForCookie.isEmpty() ? Collections.emptyList() : Arrays.asList(columnsForCookie.split(",")));
-		} else if (!cookieColumns.isEmpty()) {
-			model.addAttribute("selectedColumns", Arrays.asList(cookieColumns.split(",")));
-		}
+			@RequestParam(value = "columns", required = true, defaultValue = "") String[] columns,
+			@CookieValue(value = "columns", defaultValue = "") String[] cookieColumns) throws IOException {
 
 		String[] selectedFilters = null;
 
@@ -200,15 +196,20 @@ public class ExplorerController extends BaseController {
 		final List<GenesysFilter> currentFilters = filterHandler.selectFilters(selectedFilters);
 		final List<GenesysFilter> availableFilters = filterHandler.listAvailableFilters();
 
-		_logger.info(appliedFilters.toString());
+		if (_logger