Filtering 1

src/main/java/org/crophub/rest/common/persistence/domain/AccessionRepository.java

@@ -74,10 +74,14 @@ public interface AccessionRepository extends JpaRepository<Accession, Long> {
 	@Query("from Accession a where a.id in ( ?1 )")
 	Page<Accession> findById(Collection<Long> accessionIds, Pageable pageable);
 
+	@Query("from Accession a where a.id in ( ?1 )")
+	List<Accession> listById(Collection<Long> accessionIds);
+
 	Page<Accession> findByInstituteAndTaxonomy(FaoInstitute institute, Taxonomy taxonomy, Pageable pageable);
 
 	Page<Accession> findByTaxonomy(Taxonomy taxonomy, Pageable pageable);
 
 	@Query("select a from Accession a where a.taxonomy in ( ?1 )")
 	Page<Accession> findByTaxonomy(Collection<Taxonomy> taxonomies, Pageable pageable);
+
 }

src/main/java/org/crophub/rest/common/service/GenesysFilterService.java

+package org.crophub.rest.common.service;
+
+import org.crophub.rest.common.model.genesys.Accession;
+import org.springframework.data.domain.Page;
+import org.springframework.data.domain.Pageable;
+
+import com.fasterxml.jackson.databind.JsonNode;
+
+public interface GenesysFilterService {
+
+	Page<Accession> listAccessions(JsonNode jsonTree, Pageable pageable);
+
+}

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

+package org.crophub.rest.common.service.impl;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map.Entry;
+
+import javax.sql.DataSource;
+
+import org.apache.commons.lang.ArrayUtils;
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.crophub.rest.common.model.genesys.Accession;
+import org.crophub.rest.common.persistence.domain.AccessionRepository;
+import org.crophub.rest.common.persistence.domain.TraitValueRepository;
+import org.crophub.rest.common.service.GenesysFilterService;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.data.domain.Page;
+import org.springframework.data.domain.PageImpl;
+import org.springframework.data.domain.Pageable;
+import org.springframework.data.domain.Sort.Order;
+import org.springframework.jdbc.core.JdbcTemplate;
+import org.springframework.stereotype.Service;
+import org.springframework.transaction.annotation.Transactional;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.node.JsonNodeType;
+
+@Service
+@Transactional(readOnly = true)
+public class GenesysFilterServiceImpl implements GenesysFilterService {
+
+	public static final Log LOG = LogFactory.getLog(GenesysFilterServiceImpl.class);
+
+	@Autowired
+	private TraitValueRepository traitValueRepository;
+
+	@Autowired
+	private AccessionRepository accessionRepository;
+
+	// @PersistenceContext
+	// private EntityManager entityManager;
+
+	private JdbcTemplate jdbcTemplate;
+
+	@Autowired
+	public void setDataSource(final DataSource dataSource) {
+		this.jdbcTemplate = new JdbcTemplate(dataSource);
+	}
+
+	@Override
+	public Page<Accession> listAccessions(JsonNode jsonTree, Pageable pageable) {
+		Iterator<Entry<String, JsonNode>> fields = jsonTree.fields();
+		while (fields.hasNext()) {
+			Entry<String, JsonNode> entry = fields.next();
+			LOG.debug("Looking at " + entry.getKey() + " = " + entry.getValue());
+		}
+
+		List<Object> params = new ArrayList<Object>();
+		StringBuffer sb = new StringBuffer();
+		sb.append(" from accession a ");
+
+		if (jsonTree.has("taxonomy")) {
+			sb.append(" inner join all_taxonomy t on t.Taxon_Code=a.Taxon_Code ");
+		}
+		if (jsonTree.has("lat") || jsonTree.has("lon") || jsonTree.has("alt")) {
+			sb.append(" inner join all_environment env on env.ALIS_Id=a.id ");
+		}
+
+		createQuery(sb, "a.Origin", jsonTree.get("origin"), params);
+		createQuery(sb, "a.Institute", jsonTree.get("institute"), params);
+		createQuery(sb, "t.Genus", jsonTree.get("taxonomy"), 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);
+
+		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);
+
+		LOG.info("Total count: " + totalCount);
+
+		if (pageable.getSort() != null) {
+			sb.append("\n order by ");
+			for (Order o : pageable.getSort()) {
+				LOG.debug("Order: " + o);
+				// ClassMetadata md =
+				// sessionFactory.getClassMetadata(Accession.class);
+				// md.
+				// EntityType<Accession> x =
+				// entityManager.getMetamodel().entity(Accession.class);
+				// System.err.println(x.getAttribute(o.getProperty()).getName());
+				// sb.append(x.getAttribute(o.getProperty()).getName());
+				sb.append("a.").append(o.getProperty());
+				sb.append(" ").append(o.getDirection());
+			}
+		}
+		sb.append(" limit ");
+		LOG.debug("Pageable=" + pageable.getOffset() + " " + pageable.getPageNumber());
+		sb.append(pageable.getOffset());
+		sb.append(", ");
+		sb.append(pageable.getPageSize());
+
+		LOG.info("Filter query:\n" + sb.toString());
+		LOG.info("Parameter count: " + params.size());
+		LOG.info("Params: " + ArrayUtils.toString(params.toArray()));
+
+		// List<Accession> results = this.jdbcTemplate.query(sb.toString(), new
+		// 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);
+		LOG.info("Getting accessions");
+
+		return new PageImpl<Accession>(results.size() == 0 ? new ArrayList<Accession>() : accessionRepository.listById(results), pageable, totalCount);
+	}
+
+	private void createQuery(StringBuffer sb, String dbName, JsonNode fieldQuery, List<Object> params) {
+		LOG.debug("Handling " + dbName);
+		if (fieldQuery != null) {
+			LOG.debug("Adding " + fieldQuery + " sz=" + fieldQuery.size());
+			if (params.size() == 0)
+				sb.append(" where ");
+			else
+				sb.append(" and ");
+
+			// if (fieldQuery.getNodeType() == JsonNodeType.ARRAY) {
+			sb.append("\n ").append(dbName);
+			if (fieldQuery.size() <= 1)
+				sb.append(" = ");
+			else
+				sb.append(" IN (");
+
+			if (fieldQuery.size() > 1) {
+				int i = 0;
+				for (JsonNode x : fieldQuery) {
+					if (i > 0) {
+						sb.append(",?");
+					} else {
+						sb.append("?");
+					}
+					LOG.debug(" + " + x + " " + x.getNodeType());
+					addParam(params, x);
+
+					i++;
+				}
+			} else {
+				sb.append("?");
+				addParam(params, fieldQuery);
+			}
+			if (fieldQuery.size() > 1)
+				sb.append(") ");
+			// }
+		}
+
+	}
+
+	private void addParam(List<Object> params, JsonNode value) {
+		if (JsonNodeType.STRING == value.getNodeType())
+			params.add(value.asText());
+		else if (JsonNodeType.BOOLEAN == value.getNodeType())
+			params.add(value.asBoolean());
+		else if (JsonNodeType.NUMBER == value.getNodeType())
+			params.add(value.asDouble());
+	}
+}

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

+/**
+ * Copyright 2013 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.crophub.rest.servlet.controller;
+
+import java.io.IOException;
+import java.util.Iterator;
+import java.util.Map.Entry;
+
+import org.crophub.rest.common.model.genesys.Accession;
+import org.crophub.rest.common.service.GenesysFilterService;
+import org.crophub.rest.common.service.GenesysService;
+import org.crophub.rest.common.service.InstituteService;
+import org.crophub.rest.common.service.TaxonomyService;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Scope;
+import org.springframework.data.domain.Page;
+import org.springframework.data.domain.PageRequest;
+import org.springframework.data.domain.Sort;
+import org.springframework.stereotype.Controller;
+import org.springframework.ui.ModelMap;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestParam;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+@Controller
+@Scope("request")
+@RequestMapping("/acn")
+public class FilterController extends BaseController {
+
+	@Autowired
+	private SelectionBean selectionBean;
+
+	@Autowired
+	private InstituteService instituteService;
+
+	@Autowired
+	private GenesysService genesysService;
+	@Autowired
+	private GenesysFilterService filterService;
+
+	@Autowired
+	private TaxonomyService taxonomyService;
+
+	/**
+	 * Browse all
+	 * 
+	 * @param model
+	 * @param page
+	 * @return
+	 */
+	@RequestMapping("/f")
+	public String viewFiltered(ModelMap model, @RequestParam(value = "page", required = false, defaultValue = "1") int page,
+			@RequestParam(value = "filter", required = false, defaultValue = "") String jsonFilter) {
+
+		_logger.info("Filtering by: " + jsonFilter);
+		ObjectMapper mapper=new ObjectMapper();
+		JsonNode jsonTree = null;
+		try {
+			jsonTree = mapper.readTree(jsonFilter);
+			_logger.debug(jsonTree.toString());
+
+			Iterator<Entry<String, JsonNode>> fields = jsonTree.fields();
+			while (fields.hasNext()) {
+				Entry<String, JsonNode> entry = fields.next();
+				_logger.debug("2=" + entry.getKey() + " = " + entry.getValue());
+			}
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+
+		Page<Accession> accessions = filterService.listAccessions(jsonTree, new PageRequest(page - 1, 50, new Sort("ACC_Numb_HI")));
+
+		_logger.info("Got: " + accessions);
+		model.addAttribute("filter", jsonTree.toString());
+		model.addAttribute("pagedData", accessions);
+		model.addAttribute("selection", selectionBean);
+
+		return "/accession/data";
+	}
+
+}

src/main/resources/spring/spring.properties

@@ -24,7 +24,7 @@ db.url=jdbc:mysql://127.0.0.1/pgrsys_genesys?useUnicode=true&characterEncoding=U
 db.driverClassName = com.mysql.jdbc.Driver
 db.username = root
 db.password = 
-db.showSql=true
+db.showSql=false
 
 c3p0.acquireIncrement=1
 c3p0.minPoolSize=5

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

@@ -48,7 +48,8 @@
 		<spring:message code="accessions.number" arguments="${pagedData.totalElements}" />
 		<br />
 		<spring:message code="paged.pageOfPages" arguments="${pagedData.number+1},${pagedData.totalPages}" />
-		<a class="${pagedData.number eq 0 ? 'disabled' :''}" href="?page=${pagedData.number eq 0 ? 1 : pagedData.number}">⇇ Previous</a> <a href="?page=${pagedData.number + 2}">Next ⇉</a>
+		<a class="${pagedData.number eq 0 ? 'disabled' :''}" href="?page=${pagedData.number eq 0 ? 1 : pagedData.number}">⇇ Previous</a> 
+		<a href="<spring:url value=""><spring:param name="page" value="${pagedData.number+2}" /><spring:param name="filter" value="${filter}" /></spring:url>">Next ⇉</a>
 	</div>
 
 	<table class="accessions">