Crop descriptor categories, descriptor selection

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

@@ -20,6 +20,7 @@ import java.util.List;
 
 import org.genesys2.server.model.genesys.Method;
 import org.genesys2.server.model.genesys.Parameter;
+import org.genesys2.server.model.impl.Crop;
 import org.springframework.data.jpa.repository.JpaRepository;
 import org.springframework.data.jpa.repository.Query;
 
@@ -32,4 +33,7 @@ public interface MethodRepository extends JpaRepository<Method, Long> {
 
 	@Query("select distinct m from Method m where m.id in ( ?1 )")
 	List<Method> findByIds(List<Long> oids);
+
+	@Query("select m from Method m where m.parameter.crop = ?1")
+	List<Method> findByCrop(Crop crop);
 }

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

@@ -16,15 +16,21 @@
 
 package org.genesys2.server.persistence.domain;
 
+import java.util.Collection;
+
 import org.genesys2.server.model.genesys.Parameter;
+import org.genesys2.server.model.genesys.ParameterCategory;
 import org.genesys2.server.model.impl.Crop;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
+import org.springframework.data.domain.Sort;
 import org.springframework.data.jpa.repository.JpaRepository;
 
 public interface ParameterRepository extends JpaRepository<Parameter, Long> {
 
 	Page<Parameter> findByCrop(Crop crop, Pageable pageable);
 
+	Collection<? extends Parameter> findByCropAndCategory(Crop crop, ParameterCategory pc, Sort sort);
+
 	// List<Parameter> findAllByCategory(Category category);
 }

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

@@ -28,7 +28,7 @@ public interface GenesysFilterService {
 
 	Page<Accession> listAccessions(JsonNode jsonTree, Pageable pageable);
 
-	List<? extends GenesysFilter> listAvailableFilters();
+	List<GenesysFilter> listAvailableFilters();
 
 	public static interface GenesysFilter {
 

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

@@ -16,13 +16,16 @@
 
 package org.genesys2.server.service;
 
+import java.util.Collection;
 import java.util.List;
 import java.util.Map;
 
 import org.genesys2.server.model.genesys.Metadata;
 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;
@@ -80,4 +83,12 @@ public interface TraitService {
 
 	Map<String, Long> getMethodStatistics(Method method);
 
+	List<ParameterCategory> listCategories();
+
+	Map<ParameterCategory, List<Parameter>> mapTraits(Crop crop, List<ParameterCategory> parameterCategories);
+
+	Map<Long, List<Method>> mapMethods(Crop crop);
+
+	Collection<GenesysFilter> generateFilters(List<Long> methodIds);
+
 }

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

@@ -53,7 +53,7 @@ public class GenesysFilterServiceImpl implements GenesysFilterService {
 
 	private static final Log LOG = LogFactory.getLog(GenesysFilterServiceImpl.class);
 
-	private ArrayList<GenesysFilterImpl> availableFilters;
+	private ArrayList<GenesysFilter> availableFilters;
 
 	@Autowired
 	private TraitValueRepository traitValueRepository;
@@ -75,7 +75,7 @@ public class GenesysFilterServiceImpl implements GenesysFilterService {
 	}
 
 	public GenesysFilterServiceImpl() {
-		this.availableFilters = new ArrayList<GenesysFilterImpl>();
+		this.availableFilters = new ArrayList<GenesysFilter>();
 		// "origin", "institute", "lat", "lon", "alt", "genus"
 		this.availableFilters.add(new GenesysFilterImpl("origin", FilterType.FIXEDSTRING, 3));
 		this.availableFilters.add(new GenesysFilterImpl("institute", FilterType.FIXEDSTRING, 6));
@@ -92,7 +92,7 @@ public class GenesysFilterServiceImpl implements GenesysFilterService {
 	}
 
 	@Override
-	public List<? extends GenesysFilter> listAvailableFilters() {
+	public List<GenesysFilter> listAvailableFilters() {
 		return Collections.unmodifiableList(this.availableFilters);
 	}
 

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

@@ -24,6 +24,7 @@ import java.sql.ResultSet;
 import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
@@ -50,6 +51,7 @@ import org.genesys2.server.model.genesys.ExperimentTrait;
 import org.genesys2.server.model.genesys.Metadata;
 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.genesys.SvalbardData;
 import org.genesys2.server.model.genesys.Taxonomy;
 import org.genesys2.server.model.genesys.TraitCode;
@@ -73,19 +75,25 @@ import org.genesys2.server.persistence.domain.MetadataMethodRepository;
 import org.genesys2.server.persistence.domain.MetadataRepository;
 import org.genesys2.server.persistence.domain.MethodRepository;
 import org.genesys2.server.persistence.domain.OrganizationRepository;
+import org.genesys2.server.persistence.domain.ParameterCategoryRepository;
 import org.genesys2.server.persistence.domain.ParameterRepository;
 import org.genesys2.server.persistence.domain.SvalbardRepository;
 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.FilterType;
 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;
 import org.springframework.data.domain.Pageable;
+import org.springframework.data.domain.Sort;
+import org.springframework.data.domain.Sort.Direction;
+import org.springframework.data.domain.Sort.Order;
 import org.springframework.data.repository.query.Param;
 import org.springframework.jdbc.core.RowCallbackHandler;
 import org.springframework.security.access.prepost.PreAuthorize;
@@ -155,6 +163,9 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
 	@Autowired
 	private AccessionAliasRepository accessionAliasRepository;
 
+	@Autowired
+	private ParameterCategoryRepository parameterCategoryRepository;
+
 	@Override
 	public long countByInstitute(FaoInstitute institute) {
 		return accessionRepository.countByInstitute(institute);
@@ -1133,4 +1144,54 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
 		} else
 			return null;
 	}
+
+	@Override
+	public List<ParameterCategory> listCategories() {
+		return parameterCategoryRepository.findAll(new Sort(new Order(Direction.ASC, "id")));
+	}
+
+	@Override
+	public Map<ParameterCategory, List<Parameter>> mapTraits(Crop crop, List<ParameterCategory> parameterCategories) {
+		if (parameterCategories == null || parameterCategories.size() == 0)
+			return null;
+
+		HashMap<ParameterCategory, List<Parameter>> catTraits = new HashMap<ParameterCategory, List<Parameter>>();
+
+		for (ParameterCategory pc : parameterCategories) {
+			ArrayList<Parameter> traits;
+			catTraits.put(pc, traits = new ArrayList<Parameter>());
+			traits.addAll(parameterRepository.findByCropAndCategory(crop, pc, new Sort(new Order("title"))));
+		}
+
+		return catTraits;
+	}
+
+	@Override
+	public Map<Long, List<Method>> mapMethods(Crop crop) {
+		HashMap<Long, List<Method>> paramMethods = new HashMap<Long, List<Method>>();
+
+		for (Method method : methodRepository.findByCrop(crop)) {
+			List<Method> list = paramMethods.get(method.getParameter().getId());
+			if (list == null) {
+				paramMethods.put(method.getParameter().getId(), list = new ArrayList<Method>());
+			}
+			list.add(method);
+		}
+
+		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 ? FilterType.NUMERIC : FilterType.STRING));
+		}
+		return filters;
+	}
 }

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

@@ -16,12 +16,17 @@
 
 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;
@@ -54,6 +59,9 @@ public class CropController extends BaseController {
 	@Autowired
 	private TraitService traitService;
 
+	@Autowired
+	private GenesysFilterService filterService;
+
 	@RequestMapping("/{shortName}")
 	public String view(ModelMap model, @PathVariable(value = "shortName") String shortName) {
 		_logger.debug("Viewing crop " + shortName);
@@ -114,6 +122,40 @@ 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/webapp/WEB-INF/jsp/filter/cropdescriptors.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>
+
+<form method="post" action="">
+<div id="allfilters">
+<c:forEach items="${categories}" var="category">
+<c:if test="${descriptors[category].size() gt 0}">
+	<h2><c:out value="${crop.getName(pageContext.request.locale)}:" /> <c:out value="${category.getName(pageContext.request.locale)}" /></h2>
+	<c:forEach items="${descriptors[category]}" var="descriptor">
+	<c:if test="${methods[descriptor.id].size() gt 0}">
+		<div class="row filter-block">
+			<div class="col-lg-3">
+			<div dir="ltr"><c:out value="${descriptor.title}" /></div>
+			</div>
+			<div class="col-lg-9">
+				<c:forEach items="${methods[descriptor.id]}" var="method">
+					<div><label><input type="checkbox" style="margin-right: 1em;" name="methods" value="${method.id}" /><span dir="ltr"><c:out value="${method.method}" /></span></label></div>
+				</c:forEach>
+			</div>
+		</div>
+	</c:if>
+	</c:forEach>
+</c:if>
+</c:forEach>
+
+<div class="clearfix">
+	<a id="filtersHref" href=""><button class="btn btn-green pull-left">View!</button></a>
+</div>
+
+</div>
+</form>
+
+</body>
+</html>
\ No newline at end of file

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

@@ -14,7 +14,7 @@
 
 	<div class="clearfix filter-block">
 		<div class="pull-left filter-name"><spring:message code="filter.${filter.name}" /></div>
-		<div class="pull-left" id="filter-${filter.name}">
+		<div class="pull-left" id="filter-${filter.name.replace(':', '_')}">
 			<c:choose>
 				<c:when test="${filter.type=='NUMERIC'}">
 					<div class="filter-new form-group pull-left 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>	
@@ -44,7 +44,10 @@
 <script type="text/javascript">
 jQuery(document).ready(function() {
 //	alert('${jsonString}');
-	var filters=$.parseJSON('${jsonString}');
+	var filters={};
+	try {
+//		filters=$.parseJSON('${jsonString}');
+	} catch (e) {filters={}; console.error(e);}
 //	debugger;
 	console.log("Filters: " +JSON.stringify(filters));
 	
@@ -82,7 +85,7 @@ jQuery(document).ready(function() {
 		},
 		
 		addFilterValue: function(element) {
-			var name=$(element).closest(".clearfix").attr("x-filtername");
+			var name=$(element).closest(".clearfix").attr("x-filtername").replace('_',':');
 			//debugger;
 			var a=null, b=null;
 			var inputs=$(element).parent().children("input");
@@ -147,7 +150,7 @@ jQuery(document).ready(function() {
 		}
 	};
 	
-	[<c:forEach items="${availableFilters}" var="filter" varStatus="status">${status.index gt 0 ? ',' : ''} "${filter.name}"</c:forEach>  ].forEach(function(name) {
+	[<c:forEach items="${availableFilters}" var="filter" varStatus="status">${status.index gt 0 ? ',' : ''} "${filter.name.replace(':','_')}"</c:forEach>  ].forEach(function(name) {
 		FF.updateValues("#filter-" + name + " .filter-values", name, filters[name]);
 	});
 	

src/main/webapp/WEB-INF/jsp/filter/traitfilter.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:forEach items="${categories}" var="category">
+<c:if test="${descriptors[category].size() gt 0}">
+	<h2><c:out value="${crop.getName(pageContext.request.locale)}:" /> <c:out value="${category.getName(pageContext.request.locale)}" /></h2>
+	<c:forEach items="${descriptors[category]}" var="descriptor">
+	<c:if test="${methods[descriptor.id].size() gt 0}">
+		<div class="row filter-block">
+			<div class="col-lg-3">
+			<div dir="ltr"><c:out value="${descriptor.title}" /></div>
+			</div>
+			<div class="col-lg-9">
+				<c:forEach items="${methods[descriptor.id]}" var="method">
+					<div><label><input type="checkbox" style="margin-right: 1em;" name="methods" value="gm:${method.id}" /><span dir="ltr"><c:out value="${method.method}" /></span></label></div>
+				</c:forEach>
+			</div>
+		</div>
+	</c:if>
+	</c:forEach>
+</c:if>
+</c:forEach>
+
+<div class="clearfix">
+	<a id="filtersHref" href=""><button class="btn btn-green pull-left">View!</button></a>
+</div>
+
+</div>
+
+</body>
+</html>
\ No newline at end of file