Filter selection

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

@@ -16,6 +16,7 @@
 
 package org.genesys2.server.service;
 
+import java.util.Collection;
 import java.util.List;
 
 import org.genesys2.server.model.genesys.Accession;
@@ -31,6 +32,8 @@ public interface GenesysFilterService {
 	List<GenesysFilter> listAvailableFilters();
 
 	public static interface GenesysFilter {
+		
+		public String getKey();
 
 		public enum DataType {
 			FIXEDSTRING, STRING, NUMERIC, BOOLEAN
@@ -40,4 +43,8 @@ public interface GenesysFilterService {
 			EXACT, RANGE, LIST
 		}
 	}
+
+	List<GenesysFilter> selectFilters(String[] selectedFilters);
+
+	Collection<GenesysFilter> generateFilters(Collection<Long> methodIds);
 }

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

@@ -16,7 +16,6 @@
 
 package org.genesys2.server.service;
 
-import java.util.Collection;
 import java.util.List;
 import java.util.Map;
 
@@ -25,7 +24,6 @@ import org.genesys2.server.model.genesys.Method;
 import org.genesys2.server.model.genesys.Parameter;
 import org.genesys2.server.model.genesys.ParameterCategory;
 import org.genesys2.server.model.impl.Crop;
-import org.genesys2.server.service.GenesysFilterService.GenesysFilter;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
 import org.springframework.security.access.prepost.PreAuthorize;
@@ -89,6 +87,4 @@ public interface TraitService {
 
 	Map<Long, List<Method>> mapMethods(Crop crop);
 
-	Collection<GenesysFilter> generateFilters(List<Long> methodIds);
-
 }

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

@@ -17,19 +17,25 @@
 package org.genesys2.server.service.impl;
 
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.Collections;
+import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Map.Entry;
+import java.util.Set;
 
 import javax.sql.DataSource;
 
+import org.apache.commons.collections4.CollectionUtils;
+import org.apache.commons.collections4.Predicate;
 import org.apache.commons.lang.ArrayUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.genesys.Method;
 import org.genesys2.server.persistence.domain.AccessionRepository;
+import org.genesys2.server.persistence.domain.MethodRepository;
 import org.genesys2.server.persistence.domain.TraitValueRepository;
 import org.genesys2.server.service.GenesysFilterService;
 import org.genesys2.server.service.GenesysFilterService.GenesysFilter.DataType;
@@ -58,6 +64,9 @@ public class GenesysFilterServiceImpl implements GenesysFilterService {
 	@Autowired
 	private TraitValueRepository traitValueRepository;
 
+	@Autowired
+	private MethodRepository methodRepository;
+
 	@Autowired
 	private AccessionRepository accessionRepository;
 
@@ -77,16 +86,18 @@ public class GenesysFilterServiceImpl implements GenesysFilterService {
 	public GenesysFilterServiceImpl() {
 		this.availableFilters = new ArrayList<GenesysFilter>();
 		// "origin", "institute", "lat", "lon", "alt", "genus"
-		this.availableFilters.add(new GenesysFilterImpl("accenumb", DataType.NUMERIC));
+		this.availableFilters.add(new GenesysFilterImpl("crop", DataType.STRING));
+		this.availableFilters.add(new GenesysFilterImpl("genus", DataType.STRING));
+		this.availableFilters.add(new GenesysFilterImpl("taxon", DataType.STRING));
+
 		this.availableFilters.add(new GenesysFilterImpl("origin", DataType.FIXEDSTRING, 3));
-		this.availableFilters.add(new GenesysFilterImpl("institute", DataType.FIXEDSTRING, 6));
-		this.availableFilters.add(new GenesysFilterImpl("organization", DataType.STRING));
 		this.availableFilters.add(new GenesysFilterImpl("lat", DataType.NUMERIC));
 		this.availableFilters.add(new GenesysFilterImpl("lon", DataType.NUMERIC));
 		this.availableFilters.add(new GenesysFilterImpl("elevation", DataType.NUMERIC));
-		this.availableFilters.add(new GenesysFilterImpl("genus", DataType.STRING));
-		this.availableFilters.add(new GenesysFilterImpl("taxon", DataType.STRING));
-		this.availableFilters.add(new GenesysFilterImpl("crop", DataType.STRING));
+
+		this.availableFilters.add(new GenesysFilterImpl("organization", DataType.STRING));
+		this.availableFilters.add(new GenesysFilterImpl("institute", DataType.FIXEDSTRING, 6));
+		this.availableFilters.add(new GenesysFilterImpl("accenumb", DataType.NUMERIC));
 		this.availableFilters.add(new GenesysFilterImpl("inSvalbard", DataType.BOOLEAN));
 		this.availableFilters.add(new GenesysFilterImpl("mls", DataType.BOOLEAN));
 		this.availableFilters.add(new GenesysFilterImpl("available", DataType.BOOLEAN));
@@ -97,6 +108,50 @@ public class GenesysFilterServiceImpl implements GenesysFilterService {
 		return Collections.unmodifiableList(this.availableFilters);
 	}
 
+	@Override
+	public List<GenesysFilter> selectFilters(String[] selectedFilters) {
+		List<GenesysFilter> filters = new ArrayList<GenesysFilter>();
+		Set<Long> methodIds = new HashSet<Long>();
+
+		for (final String selectedFilter : selectedFilters) {
+			if (selectedFilter.startsWith("gm:")) {
+				try {
+					methodIds.add(Long.parseLong(selectedFilter.substring(3)));
+				} catch (NumberFormatException | NullPointerException e) {
+					LOG.warn(e);
+				}
+			} else {
+				GenesysFilter coreFilter = CollectionUtils.find(this.availableFilters, new Predicate<GenesysFilter>() {
+					@Override
+					public boolean evaluate(GenesysFilter object) {
+						return object.getKey().equals(selectedFilter);
+					}
+				});
+				if (coreFilter != null) {
+					filters.add(coreFilter);
+				}
+			}
+		}
+
+		filters.addAll(generateFilters(methodIds));
+
+		return filters;
+	}
+
+	@Override
+	public Collection<GenesysFilter> generateFilters(Collection<Long> methodIds) {
+		List<GenesysFilter> filters = new ArrayList<GenesysFilter>();
+		for (long methodId : methodIds) {
+			Method method = methodRepository.findOne(methodId);
+			if (method == null) {
+				continue;
+			}
+			filters.add(new GenesysMethodFilterImpl("gm:" + method.getId(), method.getParameter().getTitle(), method.getFieldType() == 1
+					|| method.getFieldType() == 2 ? DataType.NUMERIC : DataType.STRING));
+		}
+		return filters;
+	}
+
 	@Override
 	public Page<Accession> listAccessions(JsonNode jsonTree, Pageable pageable) {
 		Iterator<Entry<String, JsonNode>> fields = jsonTree.fields();
@@ -376,6 +431,10 @@ public class GenesysFilterServiceImpl implements GenesysFilterService {
 		private DataType dataType;
 		private FilterType filterType;
 		private Integer maxLength;
+		
+		public boolean isCore() {
+			return true;
+		}
 
 		public GenesysFilterImpl(String name, DataType type) {
 			this.name = name;
@@ -397,6 +456,11 @@ public class GenesysFilterServiceImpl implements GenesysFilterService {
 			this.maxLength = i;
 		}
 
+		@Override
+		public String getKey() {
+			return name;
+		}
+
 		public String getName() {
 			return name;
 		}
@@ -404,7 +468,7 @@ public class GenesysFilterServiceImpl implements GenesysFilterService {
 		public DataType getDataType() {
 			return dataType;
 		}
-		
+
 		public FilterType getFilterType() {
 			return filterType;
 		}
@@ -413,4 +477,22 @@ public class GenesysFilterServiceImpl implements GenesysFilterService {
 			return maxLength;
 		}
 	}
+
+	public static class GenesysMethodFilterImpl extends GenesysFilterImpl {
+		private String title;
+		
+		@Override
+		public boolean isCore() {
+			return false;
+		}
+
+		public GenesysMethodFilterImpl(String name, String title, DataType dataType) {
+			super(name, dataType);
+			this.title = title;
+		}
+
+		public String getTitle() {
+			return title;
+		}
+	}
 }

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

@@ -82,11 +82,9 @@ import org.genesys2.server.persistence.domain.TraitValueRepository;
 import org.genesys2.server.security.AuthUserDetails;
 import org.genesys2.server.service.AclService;
 import org.genesys2.server.service.DatasetService;
-import org.genesys2.server.service.GenesysFilterService.GenesysFilter.DataType;
 import org.genesys2.server.service.GenesysService;
 import org.genesys2.server.service.HtmlSanitizer;
 import org.genesys2.server.service.TraitService;
-import org.genesys2.server.service.GenesysFilterService.GenesysFilter;
 import org.genesys2.spring.SecurityContextUtil;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.Page;
@@ -1181,17 +1179,4 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
 		return paramMethods;
 	}
 
-	@Override
-	public Collection<GenesysFilter> generateFilters(List<Long> methodIds) {
-		List<GenesysFilter> filters = new ArrayList<GenesysFilter>();
-		for (long methodId : methodIds) {
-			Method method = methodRepository.findOne(methodId);
-			if (method == null) {
-				continue;
-			}
-			filters.add(new GenesysFilterServiceImpl.GenesysFilterImpl("gm:" + method.getId(),
-					method.getFieldType() == 1 || method.getFieldType() == 2 ? DataType.NUMERIC : DataType.STRING));
-		}
-		return filters;
-	}
 }

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

@@ -16,17 +16,13 @@
 
 package org.genesys2.server.servlet.controller;
 
-import java.util.ArrayList;
 import java.util.HashMap;
-import java.util.List;
 
 import org.genesys2.server.model.genesys.Accession;
-import org.genesys2.server.model.genesys.ParameterCategory;
 import org.genesys2.server.model.impl.Crop;
 import org.genesys2.server.model.impl.CropTaxonomy;
 import org.genesys2.server.service.CropService;
 import org.genesys2.server.service.GenesysFilterService;
-import org.genesys2.server.service.GenesysFilterService.GenesysFilter;
 import org.genesys2.server.service.GenesysService;
 import org.genesys2.server.service.TraitService;
 import org.genesys2.spring.ResourceNotFoundException;
@@ -116,40 +112,6 @@ public class CropController extends BaseController {
 		return "/accession/data";
 	}
 
-	@RequestMapping(value = "/{shortName}/data/descriptors", method = RequestMethod.GET)
-	public String viewDescriptors(ModelMap model, @PathVariable(value = "shortName") String shortName) {
-		_logger.warn("Viewing crop descriptors " + shortName);
-		Crop crop = cropService.getCrop(shortName);
-		if (crop == null) {
-			throw new ResourceNotFoundException();
-		}
-
-		model.addAttribute("crop", crop);
-		List<ParameterCategory> parameterCategories = traitService.listCategories();
-		model.addAttribute("categories", parameterCategories);
-		model.addAttribute("descriptors", traitService.mapTraits(crop, parameterCategories));
-		model.addAttribute("methods", traitService.mapMethods(crop));
-
-		return "/filter/cropdescriptors";
-	}
-
-	@RequestMapping(value = "/{shortName}/data/descriptors", method = RequestMethod.POST)
-	public String selectDescriptors(ModelMap model, @PathVariable(value = "shortName") String shortName, @RequestParam("methods") List<Long> methodIds) {
-		_logger.warn("Viewing crop descriptors " + shortName);
-		Crop crop = cropService.getCrop(shortName);
-		if (crop == null) {
-			throw new ResourceNotFoundException();
-		}
-
-		// What filters do we support?
-		List<GenesysFilter> availableFilters = new ArrayList<GenesysFilter>();
-		availableFilters.addAll(filterService.listAvailableFilters());
-		availableFilters.addAll(traitService.generateFilters(methodIds));
-		model.addAttribute("availableFilters", availableFilters);
-
-		return "/filter/index";
-	}
-
 	@RequestMapping("/{shortName}/descriptors")
 	public String viewDescriptors(ModelMap model, @PathVariable(value = "shortName") String shortName,
 			@RequestParam(value = "page", required = false, defaultValue = "1") int page) {

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

@@ -62,6 +62,18 @@ public class DescriptorController extends BaseController {
 		return "/descr/details";
 	}
 
+	/**
+	 * Redirect "/descriptor/gm:1234" URLs to "/descriptor/{traitId}/{methodId}"
+	 */
+	@RequestMapping("/gm:{methodId}")
+	public String viewMethod(ModelMap model, @PathVariable("methodId") long methodId) {
+		Method method = traitService.getMethod(methodId);
+		if (method == null) {
+			throw new ResourceNotFoundException();
+		}
+		return "redirect:/descriptors/" + method.getParameter().getId() + "/" + method.getId();
+	}
+
 	@RequestMapping("/{traitId}/{methodId}")
 	public String view(ModelMap model, @PathVariable("traitId") long traitId, @PathVariable("methodId") long methodId) {
 		Parameter trait = traitService.getTrait(traitId);
@@ -86,7 +98,6 @@ public class DescriptorController extends BaseController {
 			model.addAttribute("codeStatistics", traitService.getMethodStatistics(method));
 		}
 
-		
 		return "/descr/method";
 	}
 }

src/main/java/org/genesys2/server/servlet/controller/ExplorerController.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.genesys2.server.servlet.controller;
+
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.List;
+
+import org.apache.commons.lang.StringUtils;
+import org.genesys2.server.model.genesys.ParameterCategory;
+import org.genesys2.server.model.impl.Crop;
+import org.genesys2.server.service.CropService;
+import org.genesys2.server.service.GenesysFilterService;
+import org.genesys2.server.service.GenesysService;
+import org.genesys2.server.service.InstituteService;
+import org.genesys2.server.service.TaxonomyService;
+import org.genesys2.server.service.TraitService;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Controller;
+import org.springframework.ui.ModelMap;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RequestParam;
+
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+@Controller
+@RequestMapping("/explore")
+public class ExplorerController extends BaseController {
+
+	@Autowired
+	private GenesysFilterService filterService;
+
+	@Autowired
+	private CropService cropService;
+
+	@Autowired
+	private TraitService traitService;
+
+	@Autowired
+	private InstituteService instituteService;
+
+	@Autowired
+	private GenesysService genesysService;
+
+	@Autowired
+	private TaxonomyService taxonomyService;
+
+	private ObjectMapper mapper = new ObjectMapper();
+
+	@RequestMapping(value = "/pick", method = RequestMethod.GET)
+	public String pickFilters(ModelMap model, @RequestParam(value = "filter", required = false, defaultValue = "{}") String jsonFilter,
+			@RequestParam(value = "pick", required = false, defaultValue = "[]") String pick, @RequestParam(value = "crop", required = false) String shortName) {
+
+		String[] selectedFilters = new String[0];
+		try {
+			selectedFilters = mapper.readValue(pick, selectedFilters.getClass());
+		} catch (IOException e) {
+			_logger.error(e.getMessage(), e);
+		}
+
+		if (StringUtils.isNotBlank(shortName)) {
+			// Add crop descriptors
+			Crop crop = cropService.getCrop(shortName);
+			if (crop != null) {
+				model.addAttribute("crop", crop);
+				List<ParameterCategory> parameterCategories = traitService.listCategories();
+				model.addAttribute("categories", parameterCategories);
+				model.addAttribute("descriptors", traitService.mapTraits(crop, parameterCategories));
+				model.addAttribute("methods", traitService.mapMethods(crop));
+			}
+		}
+
+		// What filters do we support?
+		model.addAttribute("availableFilters", filterService.listAvailableFilters());
+		model.addAttribute("jsonString", jsonFilter);
+		model.addAttribute("selectedFilters", new HashSet<String>(Arrays.asList(selectedFilters)));
+		model.addAttribute("crops", cropService.list(getLocale()));
+		return "/filter/pick";
+	}
+
+	@RequestMapping(value = "/pick", method = RequestMethod.POST)
+	public String doPickFilters(ModelMap model, @RequestParam(value = "filter", required = false, defaultValue = "{}") String jsonFilter,
+			@RequestParam(value = "pick", required = false) String[] pick, @RequestParam(value = "crop", required = false) String shortName) {
+		if (StringUtils.isNotBlank(shortName)) {
+			Crop crop = cropService.getCrop(shortName);
+			if (crop != null) {
+				model.addAttribute("crop", crop.getShortName());
+			}
+		}
+
+		try {
+			if (pick != null)
+				model.addAttribute("pick", mapper.writeValueAsString(pick));
+		} catch (JsonProcessingException e) {
+			_logger.error(e.getMessage(), e);
+		}
+		
+		model.addAttribute("filter", jsonFilter);
+
+		return "redirect:/explore/pick";
+	}
+
+	@RequestMapping(value = "/pick", method = RequestMethod.POST, params = { "doView" })
+	public String doView(ModelMap model, @RequestParam(value = "filter", required = false, defaultValue = "{}") String jsonFilter,
+			@RequestParam(value = "pick", required = false) String[] pick, @RequestParam(value = "crop", required = false) String shortName) {
+
+		doPickFilters(model, jsonFilter, pick, shortName);
+		
+		return "redirect:/explore/filter";
+	}
+
+	@RequestMapping(value = "/filter", method = RequestMethod.GET)
+	public String showFilters(ModelMap model, @RequestParam(value = "filter", required = false, defaultValue = "{}") String jsonFilter,
+			@RequestParam(value = "pick", required = false, defaultValue = "[]") String pick, @RequestParam(value = "crop", required = false) String shortName) {
+
+		String[] selectedFilters = new String[0];
+		try {
+			selectedFilters = mapper.readValue(pick, selectedFilters.getClass());
+		} catch (IOException e) {
+			_logger.error(e.getMessage(), e);
+		}
+
+		model.addAttribute("selectedFilters", filterService.selectFilters(selectedFilters));
+
+		try {
+			JsonNode jsonTree = mapper.readTree(jsonFilter);
+			model.addAttribute("jsonString", jsonTree.toString());
+		} catch (IOException e) {
+			_logger.warn(e.getMessage(), e);
+		}
+
+		try {
+			JsonNode jsonTree = mapper.readTree(pick);
+			model.addAttribute("pick", jsonTree.toString());
+		} catch (IOException e) {
+			_logger.warn(e.getMessage(), e);
+		}
+
+		if (StringUtils.isNotBlank(shortName)) {
+			Crop crop = cropService.getCrop(shortName);
+			if (crop != null) {
+				model.addAttribute("crop", crop);
+			}
+		}
+
+		return "/filter/filter";
+	}
+}

src/main/resources/content/language.properties

@@ -310,6 +310,7 @@ filters.view=Current filters
 filters.data-is-filtered=The data is filtered.
 filters.modify-filters=View & Modify filters
 filter.taxonomy=Taxonomy
+filter.accenumb=Accession name
 filter.crop=Crop
 filter.countryOfOrigin=Country of Origin
 filter.holdingInstitute=Holding Institute

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

+<!DOCTYPE html>
+
+<%@include file="/WEB-INF/jsp/init.jsp"%>
+
+<html>
+<head>
+<title><spring:message code="filters.page.title" /></title>
+</head>
+<body>
+	<h1><spring:message code="filters.view" /></h1>
+
+<div id="allfilters">
+	<c:if test="${crop ne null}">
+	<div class="filter-block row">
+		<div class="col-lg-3">
+			<spring:message code="filter.crop" />
+		</div>
+		<div class="col-lg-9">
+			<c:out value="${crop.getName(pageContext.response.locale)}" />
+		</div>
+	</div>
+	</c:if>
+	
+<c:forEach items="${selectedFilters}" var="filter">
+
+	<div class="clearfix filter-block" x-filtername="${filter.key}">
+		<div class="col-lg-3">
+			<c:if test="${not filter.core}">
+				<a href="<c:url value="/descriptors/${filter.key}" />"><c:out value="${filter.title}" /></a>
+			</c:if>
+			<c:if test="${filter.core}">
+				<spring:message code="filter.${filter.name}" />
+			</c:if>
+		</div>
+		<div class="col-lg-5 filter-new">
+			<c:choose>
+				<c:when test="${filter.dataType=='NUMERIC'}">
+					<div class="form-group input-group"><span class="input-group-btn"><input class="span1 form-control" type="text" /><input class="span1 form-control" type="text" /><button class="btn notimportant">+</button></span></div>	
+				</c:when>
+ 				<c:when test="${filter.dataType=='BOOLEAN'}">
+					<div class=""><select><option value="true"><spring:message code="boolean.true" /></option><option value="false"><spring:message code="boolean.false" /></option><option value="null"><spring:message code="boolean.null" /></option></select><button class="notimportant">+</button></div>	
+				</c:when>
+				<c:otherwise>
+					<div class="form-group input-group"><span class="input-group-btn"><input class="span2 form-control" type="text" /><button class="btn notimportant">+</button></span></div>	
+				</c:otherwise>
+			</c:choose>
+		</div>	
+		<div class="col-lg-4 filter-values" id="filter-${filter.name.replace(':', '_')}"></div>
+	</div>
+</c:forEach>
+
+<div class="row">
+	<div class="col-lg-offset-3 col-lg-9">
+		<a id="filtersHref" href=""><button class="btn btn-green pull-left">View!</button></a>
+		<c:url var="pickUrl" value="/explore/pick">
+			<c:param name="pick">${pick}</c:param>
+			<c:param name="crop"><c:out value="${crop.shortName}" /></c:param>
+		</c:url>
+		<a href="${pickUrl}"><button class="btn btn-green pull-left">Change filters</button></a>
+	</div>
+</div>
+
+</div>
+
+<div id="filtersJson">${jsonObject}</div>
+
+
+<content tag="javascript">	
+<script type="text/javascript">
+jQuery(document).ready(function() {
+//	alert('${jsonString}');
+	var pick=[];
+	var filters={};
+	try {
+		filters=$.parseJSON('${jsonString}');
+	} catch (e) {filters={}; console.error(e);}