Crop filtering, add "jsonFilter" in country, wiews, crop controllers

src/main/java/org/crophub/rest/common/service/impl/GenesysFilterServiceImpl.java

@@ -61,6 +61,8 @@ public class GenesysFilterServiceImpl implements GenesysFilterService {
 		this.availableFilters.add(new GenesysFilterImpl("lon", FilterType.NUMERIC));
 		this.availableFilters.add(new GenesysFilterImpl("alt", FilterType.NUMERIC));
 		this.availableFilters.add(new GenesysFilterImpl("genus", FilterType.STRING));
+		this.availableFilters.add(new GenesysFilterImpl("taxon", FilterType.STRING));
+		this.availableFilters.add(new GenesysFilterImpl("crop", FilterType.STRING));
 	}
 
 	@Override
@@ -79,9 +81,11 @@ public class GenesysFilterServiceImpl implements GenesysFilterService {
 		List<Object> params = new ArrayList<Object>();
 		StringBuffer sb = new StringBuffer();
 		sb.append(" from accession a ");
-
-		if (jsonTree.has("genus")) {
+		if (jsonTree.has("crop") || jsonTree.has("genus") || jsonTree.has("taxon")) {
 			sb.append(" inner join all_taxonomy t on t.Taxon_Code=a.Taxon_Code ");
+			if (jsonTree.has("crop")) {
+				sb.append(" inner join croptaxonomy ct on ct.taxonomyId=t.Taxon_Code inner join crop on crop.id=ct.cropId ");
+			}
 		}
 		if (jsonTree.has("lat") || jsonTree.has("lon") || jsonTree.has("alt")) {
 			sb.append(" inner join all_environment env on env.ALIS_Id=a.id ");
@@ -90,14 +94,16 @@ public class GenesysFilterServiceImpl implements GenesysFilterService {
 		createQuery(sb, "a.Origin", jsonTree.get("origin"), params);
 		createQuery(sb, "a.Institute", jsonTree.get("institute"), params);
 		createQuery(sb, "t.Genus", jsonTree.get("genus"), params);
+		createQuery(sb, "t.Taxon_Name", jsonTree.get("taxon"), params);
 		createQuery(sb, "env.LongitudeD", jsonTree.get("lon"), params);
 		createQuery(sb, "env.LatitudeD", jsonTree.get("lat"), params);
 		createQuery(sb, "env.Altitude", jsonTree.get("alt"), params);
+		createQuery(sb, "crop.shortName", jsonTree.get("crop"), params);
 
 		LOG.info("Parameter count: " + params.size());
 		LOG.info("Count query:\n" + sb.toString());
 
-		Long totalCount = this.jdbcTemplate.queryForObject("select count(a.id) " + sb.toString(), params.toArray(), Long.class);
+		Long totalCount = this.jdbcTemplate.queryForObject("select distinct count(a.id) " + sb.toString(), params.toArray(), Long.class);
 
 		LOG.info("Total count: " + totalCount);
 
@@ -130,7 +136,7 @@ public class GenesysFilterServiceImpl implements GenesysFilterService {
 		// Object[] {}, new BeanPropertyRowMapper<Accession>(Accession.class));
 
 		LOG.info("Getting IDs");
-		List<Long> results = this.jdbcTemplate.queryForList("select a.id " + sb.toString(), params.toArray(), Long.class);
+		List<Long> results = this.jdbcTemplate.queryForList("select distinct a.id " + sb.toString(), params.toArray(), Long.class);
 		LOG.info("Getting accessions");
 
 		return new PageImpl<Accession>(results.size() == 0 ? new ArrayList<Accession>() : accessionRepository.listById(results), pageable, totalCount);

src/main/java/org/crophub/rest/servlet/controller/AccessionController.java

@@ -144,7 +144,8 @@ public class AccessionController extends BaseController {
 		_logger.info("Got: " + accessions);
 		model.addAttribute("pagedData", accessions);
 		model.addAttribute("selection", selectionBean);
-
+		model.addAttribute("jsonFilter", "{\"taxon\":[\"" + taxonomy.getTaxonName() + "\"]}");
+		
 		return "/accession/data";
 	}
 

src/main/java/org/crophub/rest/servlet/controller/CountryController.java

@@ -94,7 +94,8 @@ public class CountryController extends BaseController {
 		filters.put("filter.countryOfOrigin", country);
 
 		model.addAttribute("filters", filters);
-		
+		model.addAttribute("jsonFilter", "{\"origin\":[\"" + country.getCode3() + "\"]}");
+
 		return "/accession/data";
 	}
 }

src/main/java/org/crophub/rest/servlet/controller/CropController.java

@@ -92,6 +92,7 @@ public class CropController extends BaseController {
 		model.addAttribute("pagedData", accessions);
 
 		model.addAttribute("selection", selectionBean);
+		model.addAttribute("jsonFilter", "{\"crop\":[\"" + crop.getShortName() + "\"]}");
 
 		return "/accession/data";
 	}

src/main/java/org/crophub/rest/servlet/controller/WiewsController.java

@@ -14,7 +14,6 @@
  * limitations under the License.
  **/
 
-
 package org.crophub.rest.servlet.controller;
 
 import java.util.HashMap;
@@ -44,7 +43,7 @@ public class WiewsController extends BaseController {
 
 	@Autowired
 	private SelectionBean selectionBean;
-	
+
 	@Autowired
 	private InstituteService instituteService;
 
@@ -91,7 +90,7 @@ public class WiewsController extends BaseController {
 		if (faoInstitute == null) {
 			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);
@@ -102,11 +101,11 @@ public class WiewsController extends BaseController {
 		filters.put("filter.holdingInstitute", faoInstitute);
 
 		model.addAttribute("filters", filters);
-		
+		model.addAttribute("jsonFilter", "{\"institute\":[\"" + faoInstitute.getCode() + "\"]}");
+
 		return "/accession/data";
 	}
 
-
 	@RequestMapping("/{wiewsCode}/t/{genus}/{species}")
 	public String viewDataByGenusSpecies(ModelMap model, @PathVariable(value = "wiewsCode") String wiewsCode, @PathVariable(value = "genus") String genus,
 			@PathVariable(value = "species") String species, @RequestParam(value = "page", required = false, defaultValue = "1") int page) {
@@ -118,11 +117,12 @@ public class WiewsController extends BaseController {
 		model.addAttribute("faoInstitute", faoInstitute);
 
 		// Taxonomy
-		Taxonomy taxonomy=taxonomyService.get(genus, species);
-		_logger.debug("Got "+ taxonomy);
-		
+		Taxonomy taxonomy = taxonomyService.get(genus, species);
+		_logger.debug("Got " + taxonomy);
+
 		_logger.warn("Searching accessions of: " + faoInstitute);
-		Page<Accession> accessions = genesysService.listAccessionsByInstituteAndTaxonomy(faoInstitute, taxonomy, new PageRequest(page - 1, 50, new Sort("accessionName")));
+		Page<Accession> accessions = genesysService.listAccessionsByInstituteAndTaxonomy(faoInstitute, taxonomy, new PageRequest(page - 1, 50, new Sort(
+				"accessionName")));
 		_logger.info("Got: " + accessions);
 		model.addAttribute("pagedData", accessions);
 
@@ -133,7 +133,8 @@ public class WiewsController extends BaseController {
 		filters.put("filter.holdingInstitute", faoInstitute);
 
 		model.addAttribute("filters", filters);
-		
+		model.addAttribute("jsonFilter", "{\"institute\":[\"" + faoInstitute.getCode() + "\"],\"taxon\":[\"" + taxonomy.getTaxonName() + "\"]}");
+
 		return "/accession/data";
 	}
 

src/main/resources/content/language.properties

@@ -181,6 +181,8 @@ selection.add-many.accessionIds=List accession IDs as used in Genesys separated
 
 filters.page.title=Data filters
 filters.view=Current filters
+filters.data-is-filtered=The data is filtered.
+filters.modify-filters=View & Modify filters
 filter.taxonomy=Taxonomy
 filter.crop=Crop
 filter.countryOfOrigin=Country of Origin
@@ -191,6 +193,7 @@ filter.lat=Latitude
 filter.lon=Longitude
 filter.alt=Altitude
 filter.genus=Genus
+filter.taxon=Taxonomy name
 
 search.page.title=Full-text Search
 search.no-results=No matches found for your query.

src/main/webapp/WEB-INF/decorator/menu.jsp

@@ -9,6 +9,6 @@
 		<li><a href="<c:url value="/geo/" />"><spring:message code="menu.countries" /></a></li>
 		<li><a href="<c:url value="/wiews/active" />"><spring:message code="menu.institutes" /></a></li>
 		<li><a href="<c:url value="/sel/" />"><spring:message code="menu.my-list" />
-				<div id="selcounter">${selection.size() gt 0 ? selection.size() : ''}</div></a></li>
+				<sup id="selcounter">${selection.size() gt 0 ? selection.size() : ''}</sup></a></li>
 	</ul>
 </div>
\ No newline at end of file

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

@@ -11,9 +11,12 @@
 		<spring:message code="accession.page.data.title" />
 	</h1>
 
-	<%-- 	<div>
-		<a href="<c:url value="/geo/${faoInstitute.country.code3.toLowerCase()}" />"><c:out value="${faoInstitute.country.name}" /></a>
-	</div> --%>
+	<c:if test="${jsonFilter ne null}">
+		<div class="clearfix filter-block">
+			<spring:message code="filters.data-is-filtered" />
+			<a href="<spring:url value="/acn/filter"><spring:param name="filter" value="${jsonFilter}" /></spring:url>"><spring:message code="filters.modify-filters" /></a>
+		</div>
+	</c:if>
 
 	<c:if test="${filters ne null}">
 		<c:forEach items="${filters.keySet()}" var="by">
@@ -43,14 +46,6 @@
 		</c:forEach>
 	</c:if>
 	
-	<c:if test="${jsonFilter ne null}">
-	<div class="clearfix filter-block">
-		Your data is filtered!
-		<a href="<spring:url value="/acn/filter"><spring:param name="filter" value="${jsonFilter}" /></spring:url>">Modify filter</a>
-		</div>
-	</c:if>
-
-
 	<div class="nav-header">
 		<spring:message code="accessions.number" arguments="${pagedData.totalElements}" />
 		<br />

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

@@ -29,7 +29,9 @@
 
 </c:forEach>
 
-<a id="filtersHref" href=""><button>View!</button></a>
+<div class="clearfix">
+	<a id="filtersHref" href=""><button class="btn">View!</button></a>
+</div>
 
 <div id="filtersJson">${jsonObject}</div>
 

src/main/webapp/html/css/custom.css

@@ -343,13 +343,6 @@ tr.acn .sel.picked {
 }
 
 #selcounter {
-	float: right;
-	font-size: 70%;
-	font-weight: bold;
-	color: White;
-	position: relative;
-    right: -0.5em;
-    top: -0.6em;
 }
 
 .btn-primary {
@@ -370,7 +363,6 @@ tr.acn .sel.picked {
 }
 .filter-block .filter-name {
 	width: 20%;
-	font-weight: bold;
 }
 .filter-block .filter-values {
 	
@@ -404,3 +396,7 @@ tr.acn .sel.picked {
 	margin-bottom: 0;
 	padding: 0 5px;
 }
+
+#filtersJson {
+	display: none;
+}