Redirect to /explore with filters where possible

Added "species" filter

src/main/java/org/genesys2/server/persistence/domain/Taxonomy2Repository.java

@@ -28,6 +28,9 @@ public interface Taxonomy2Repository extends JpaRepository<Taxonomy2, Long> {
 	@Query("select distinct t.genus from Taxonomy2 t where t.genus like ?1")
 	List<String> autocompleteGenus(String term, Pageable page);
 
+	@Query("select distinct t.species from Taxonomy2 t where t.species like ?1")
+	List<String> autocompleteSpecies(String term, Pageable page);
+
 	@Query("select distinct t.taxonName from Taxonomy2 t where t.taxonName like ?1")
 	List<String> autocompleteTaxonomy(String term, Pageable page);
 
@@ -38,4 +41,5 @@ public interface Taxonomy2Repository extends JpaRepository<Taxonomy2, Long> {
 	List<Taxonomy2> findByGenusAndSpecies(String genus, String species);
 
 	List<Taxonomy2> findByGenusAndSpeciesAndSubtaxa(String genus, String species, String subtaxa);
+
 }

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

@@ -24,6 +24,8 @@ public interface TaxonomyService {
 
 	List<String> autocompleteGenus(String term);
 
+	List<String> autocompleteSpecies(String term);
+
 	List<String> autocompleteTaxonomy(String term);
 
 	long getTaxonomy2Id(String genus);
@@ -36,4 +38,7 @@ public interface TaxonomyService {
 
 	Taxonomy2 get(Long id);
 
+	Taxonomy2 get(String genus, String species);
+
+
 }

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

@@ -73,7 +73,7 @@ public class DirectMysqlQuery {
 	}
 
 	protected DirectMysqlQuery join(ObjectNode jsonTree) {
-		if (hasFilter(jsonTree, "crop") || hasFilter(jsonTree, "genus") || hasFilter(jsonTree, "taxon")) {
+		if (hasFilter(jsonTree, "crop") || hasFilter(jsonTree, "genus") || hasFilter(jsonTree, "species") || hasFilter(jsonTree, "taxon")) {
 			innerJoin("taxonomy2", "t", "t.id=a.taxonomyId2");
 			if (hasFilter(jsonTree, "crop")) {
 				innerJoin("croptaxonomy", "ct", "ct.taxonomyId=t.id");
@@ -112,6 +112,7 @@ public class DirectMysqlQuery {
 		createQuery(whereBuffer, "a.available", jsonTree.get("available"), params);
 		createQuery(whereBuffer, "org.slug", jsonTree.get("organization"), params);
 		createQuery(whereBuffer, "t.genus", jsonTree.get("genus"), params);
+		createQuery(whereBuffer, "t.species", jsonTree.get("species"), params);
 		createQuery(whereBuffer, "t.taxonName", jsonTree.get("taxon"), params);
 		createQuery(whereBuffer, "geo.longitude", jsonTree.get("longitude"), params);
 		createQuery(whereBuffer, "geo.latitude", jsonTree.get("latitude"), params);

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

@@ -110,6 +110,7 @@ public class GenesysFilterServiceImpl implements GenesysFilterService {
 		this.availableFilters.add(new GenesysI18nListFilterImpl<Integer>("sampStat", DataType.NUMERIC).build("accession.sampleStatus", new Integer[] { 100,
 				110, 120, 130, 200, 300, 400, 410, 411, 412, 413, 414, 415, 416, 420, 421, 422, 423, 500, 600, 999 }));
 		this.availableFilters.add(new GenesysAutocompleteFilterImpl("genus", "/explore/ac/genus"));
+		this.availableFilters.add(new GenesysAutocompleteFilterImpl("species", "/explore/ac/species"));
 		this.availableFilters.add(new GenesysAutocompleteFilterImpl("taxon", "/explore/ac/taxonomy"));
 
 		this.availableFilters.add(new GenesysAutocompleteFilterImpl("orgCty", "/explore/ac/country"));
@@ -227,6 +228,9 @@ public class GenesysFilterServiceImpl implements GenesysFilterService {
 	 */
 	@Override
 	public List<LabelValue<String>> autocomplete(String filter, String ac) {
+		if (LOG.isDebugEnabled())
+			LOG.debug("Autocomplete " + filter + " ac=" + ac);
+		
 		List<LabelValue<String>> completed = new ArrayList<LabelValue<String>>();
 		if ("instCode".equalsIgnoreCase(filter)) {
 			List<FaoInstitute> faoInst = searchService.autocomplete(ac, FaoInstitute.class);
@@ -240,8 +244,13 @@ public class GenesysFilterServiceImpl implements GenesysFilterService {
 			}
 		} else if ("genus".equalsIgnoreCase(filter)) {
 			List<String> genera = taxonomyService.autocompleteGenus(ac);
-			for (String genus : genera) {
-				completed.add(new LabelValue<String>(genus, genus));
+			for (String value : genera) {
+				completed.add(new LabelValue<String>(value, value));
+			}
+		} else if ("species".equalsIgnoreCase(filter)) {
+			List<String> species = taxonomyService.autocompleteSpecies(ac);
+			for (String value : species) {
+				completed.add(new LabelValue<String>(value, value));
 			}
 		} else if ("taxonomy".equalsIgnoreCase(filter)) {
 			List<String> taxa = taxonomyService.autocompleteTaxonomy(ac);

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

@@ -49,6 +49,11 @@ public class TaxonomyServiceImpl implements TaxonomyService {
 		return taxonomy2Repository.autocompleteGenus(term + "%", new PageRequest(0, 10));
 	}
 
+	@Override
+	public List<String> autocompleteSpecies(String term) {
+		return taxonomy2Repository.autocompleteSpecies(term + "%", new PageRequest(0, 10));
+	}
+
 	@Override
 	public List<String> autocompleteTaxonomy(String term) {
 		return taxonomy2Repository.autocompleteTaxonomy("%" + term + "%", new PageRequest(0, 10));
@@ -94,10 +99,10 @@ public class TaxonomyServiceImpl implements TaxonomyService {
 			Taxonomy2 speciesTaxa = internalEnsure(genus, species, "", "", "");
 			taxSpeciesId = speciesTaxa.getId();
 			taxGenusId = speciesTaxa.getTaxGenus();
-		} else if (! StringUtils.equals(species, "sp.") && (subtaxa.equals("") && spAuthor.equals("") && subtAuthor.equals(""))) {
+		} else if (!StringUtils.equals(species, "sp.") && (subtaxa.equals("") && spAuthor.equals("") && subtAuthor.equals(""))) {
 			Taxonomy2 genusTaxa = internalEnsure(genus, "sp.", "", "", "");
 			taxGenusId = genusTaxa.getId();
-			taxSpeciesId=genusTaxa.getId();
+			taxSpeciesId = genusTaxa.getId();
 		}
 
 		// Loop it a bit if required
@@ -159,6 +164,11 @@ public class TaxonomyServiceImpl implements TaxonomyService {
 		return tax.getId();
 	}
 
+	@Override
+	public Taxonomy2 get(String genus, String species) {
+		return taxonomy2Repository.findByGenusAndSpeciesAndSpAuthorAndSubtaxaAndSubtAuthor(genus, species, "", "", "");
+	}
+
 	@Override
 	public long countTaxonomy2() {
 		return taxonomy2Repository.count();

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

@@ -226,7 +226,7 @@ public class ExplorerController extends BaseController {
 
 	@RequestMapping(value = "/explore/ac/{field}", produces = MediaType.APPLICATION_JSON_VALUE)
 	@ResponseBody
-	public List<LabelValue<String>> autocomplete(@PathVariable("field") String filter, @RequestParam(value = "term", required = false) String ac) {
+	public List<LabelValue<String>> autocomplete(@PathVariable("field") String filter, @RequestParam(value = "term", required = true) String ac) {
 		return filterService.autocomplete(filter, ac);
 	}
 

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

@@ -18,11 +18,9 @@ package org.genesys2.server.servlet.controller;
 
 import java.util.Collections;
 import java.util.Comparator;
-import java.util.HashMap;
 import java.util.List;
 import java.util.Locale;
 
-import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.server.model.impl.Organization;
 import org.genesys2.server.service.ContentService;
@@ -32,7 +30,6 @@ import org.genesys2.server.service.OrganizationService;
 import org.genesys2.server.service.TaxonomyService;
 import org.genesys2.spring.ResourceNotFoundException;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.data.domain.Page;
 import org.springframework.data.domain.PageRequest;
 import org.springframework.data.domain.Sort;
 import org.springframework.security.access.prepost.PreAuthorize;
@@ -147,27 +144,18 @@ public class OrganizationController extends BaseController {
 		return "redirect:/org/" + organization.getSlug();
 	}
 
-	@RequestMapping("/{wiewsCode}/data")
-	public String viewData(ModelMap model, @PathVariable(value = "wiewsCode") String slug,
+	@RequestMapping("/{orgSlug}/data")
+	public String viewData(ModelMap model, @PathVariable(value = "orgSlug") String orgSlug,
 			@RequestParam(value = "page", required = false, defaultValue = "1") int page) {
-		_logger.debug("Viewing organization " + slug);
-		Organization organization = organizationService.getOrganization(slug);
+		_logger.debug("Viewing organization " + orgSlug);
+		Organization organization = organizationService.getOrganization(orgSlug);
 		if (organization == null) {
 			throw new ResourceNotFoundException();
 		}
 
-		_logger.warn("Searching accessions of: " + organization);
-		Page<Accession> accessions = genesysService.listAccessionsByOrganization(organization, new PageRequest(page - 1, 50, new Sort("accessionName")));
-		_logger.info("Got: " + accessions);
-		model.addAttribute("pagedData", accessions);
-
-		HashMap<Object, Object> filters = new HashMap<Object, Object>();
-		filters.put("filter.organization", organization);
-
-		model.addAttribute("filters", filters);
-		model.addAttribute("jsonFilter", "{\"organization\":[\"" + organization.getSlug() + "\"]}");
-
-		return "/accession/explore";
+		model.addAttribute("filter", "{\"organization\":[\"" + organization.getSlug() + "\"]}");
+		model.addAttribute("page", page);
+		return "redirect:/explore";
 	}
 
 }

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

@@ -23,7 +23,7 @@ import java.util.Map;
 
 import javax.servlet.http.HttpServletResponse;
 
-import org.genesys2.server.model.genesys.Accession;
+import org.genesys2.server.model.genesys.Taxonomy2;
 import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.server.service.ContentService;
 import org.genesys2.server.service.GenesysService;
@@ -160,18 +160,9 @@ public class WiewsController extends BaseController {
 			throw new ResourceNotFoundException();
 		}
 
-		_logger.warn("Searching accessions of: " + faoInstitute);
-		Page<Accession> accessions = genesysService.listAccessionsByInstitute(faoInstitute, new PageRequest(page - 1, 50, new Sort("accessionName")));
-		_logger.info("Got: " + accessions);
-		model.addAttribute("pagedData", accessions);
-
-		HashMap<Object, Object> filters = new HashMap<Object, Object>();
-		filters.put("filter.holdingInstitute", faoInstitute);
-
-		model.addAttribute("filters", filters);
-		model.addAttribute("jsonFilter", "{\"instCode\":[\"" + faoInstitute.getCode() + "\"]}");
-
-		return "/accession/explore";
+		model.addAttribute("filter", "{\"instCode\":[\"" + faoInstitute.getCode() + "\"]}");
+		model.addAttribute("page", page);
+		return "redirect:/explore";
 	}
 
 	@RequestMapping("/{wiewsCode}/t/{genus}/{species:.+}")
@@ -182,26 +173,18 @@ public class WiewsController extends BaseController {
 		if (faoInstitute == null) {
 			throw new ResourceNotFoundException();
 		}
-		model.addAttribute("faoInstitute", faoInstitute);
 
 		// Taxonomy
-		long taxonomyId = taxonomyService.getTaxonomy2Id(genus, species);
-		_logger.debug("Got " + taxonomyId);
-
-		_logger.warn("Searching accessions of: " + faoInstitute);
-		Page<Accession> accessions = genesysService.listAccessionsByInstituteAndSpecies(faoInstitute, taxonomyId, new PageRequest(page - 1, 50, new Sort(
-				"accessionName")));
-		_logger.info("Got: " + accessions);
-		model.addAttribute("pagedData", accessions);
-
-		HashMap<Object, Object> filters = new HashMap<Object, Object>();
-		filters.put("filter.taxonomy", taxonomyId);
-		filters.put("filter.holdingInstitute", faoInstitute);
-
-		model.addAttribute("filters", filters);
-		model.addAttribute("jsonFilter", "{\"instCode\":[\"" + faoInstitute.getCode() + "\"],\"species\":[\"" + taxonomyId + "\"]}");
+		Taxonomy2 taxonomy2 = taxonomyService.get(genus, species);
+		if (taxonomy2 == null) {
+			throw new ResourceNotFoundException();
+		}
+		_logger.debug("Got " + taxonomy2);
 
-		return "/accession/explore";
+		model.addAttribute("filter", "{\"instCode\":[\"" + faoInstitute.getCode() + "\"],\"genus\":[\"" + taxonomy2.getGenus() + "\"],\"species\":[\""
+				+ taxonomy2.getSpecies() + "\"]}");
+		model.addAttribute("page", page);
+		return "redirect:/explore";
 	}
 
 	@RequestMapping(value = "/{wiewsCode}/dwca", method = RequestMethod.POST)

src/main/resources/content/language.properties

@@ -331,6 +331,7 @@ filter.latitude=Latitude
 filter.longitude=Longitude
 filter.elevation=Elevation
 filter.genus=Genus
+filter.species=Species
 filter.taxSpecies=Species
 filter.taxon=Taxonomical name
 filter.inSvalbard=Safety duplicated in Svalbard