Crop#rules editable

pom.xml

@@ -570,7 +570,7 @@
 				<configuration>
 					<stopPort>8888</stopPort>
 					<stopKey>stop</stopKey>
-					<jvmArgs>-Dspring.profiles.active=dev -Xmx2048M -Xms1024M -XX:MaxPermSize=128M -Djava.awt.headless=true -server</jvmArgs>
+					<jvmArgs>-Dspring.profiles.active=dev -Xmx2048M -Xms1024M -XX:MaxPermSize=128M -Djava.awt.headless=true -server -Dorg.eclipse.jetty.server.Request.maxFormContentSize=5000000</jvmArgs>
 				</configuration>
 			</plugin>
 			<plugin>

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

@@ -183,7 +183,7 @@ public class CropServiceImpl implements CropService {
 	public void rebuildTaxonomies(Crop crop) {
 		LOG.info("Rebuilding crop taxonomy for: " + crop.getName());
 		// for all rules
-		final List<CropRule> cropRules = crop.getCropRules();
+		final List<CropRule> cropRules = getCropRules(crop);
 		LOG.warn("Using rules: " + cropRules);
 		rebuildCropTaxonomies(crop, cropRules);
 	}
@@ -196,9 +196,9 @@ public class CropServiceImpl implements CropService {
 			if (!cr.isIncluded())
 				continue;
 
-			if (cr.getSpecies() == null && cr.getSubtaxa() == null) {
+			if (StringUtils.isBlank(cr.getSpecies()) && StringUtils.isBlank(cr.getSubtaxa())) {
 				taxa.addAll(taxonomy2Repository.findByGenus(cr.getGenus()));
-			} else if (cr.getSubtaxa() == null) {
+			} else if (StringUtils.isBlank(cr.getSubtaxa())) {
 				taxa.addAll(taxonomy2Repository.findByGenusAndSpecies(cr.getGenus(), cr.getSpecies()));
 			} else {
 				taxa.addAll(taxonomy2Repository.findByGenusAndSpeciesAndSubtaxa(cr.getGenus(), cr.getSpecies(), cr.getSubtaxa()));

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

@@ -16,11 +16,14 @@
 
 package org.genesys2.server.servlet.controller;
 
+import java.io.IOException;
 import java.util.Arrays;
+import java.util.List;
 import java.util.stream.Collectors;
 
 import org.elasticsearch.common.lang3.StringUtils;
 import org.genesys2.server.model.impl.Crop;
+import org.genesys2.server.model.impl.CropRule;
 import org.genesys2.server.model.impl.CropTaxonomy;
 import org.genesys2.server.service.ContentService;
 import org.genesys2.server.service.CropService;
@@ -43,6 +46,12 @@ 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.JsonParseException;
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.databind.JsonMappingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
+
 @Controller
 @RequestMapping("/c")
 public class CropController extends BaseController {
@@ -100,6 +109,11 @@ public class CropController extends BaseController {
 	@PreAuthorize("hasRole('ADMINISTRATOR') or hasRole('CONTENTMANAGER') or hasPermission(#crop, 'ADMINISTRATION')")
 	public String edit(ModelMap model, @PathVariable(value = "shortName") String shortName) {
 		view(model, shortName);
+		try {
+			model.addAttribute("cropRulesJson", new ObjectMapper().writeValueAsString(model.get("cropRules")));
+		} catch (JsonProcessingException e) {
+		}
+
 		return "/crop/edit";
 	}
 
@@ -117,7 +131,7 @@ public class CropController extends BaseController {
 		return "/crop/edit";
 	}
 
-	@RequestMapping("/{shortName}/update")
+	@RequestMapping(value = "/{shortName}/update", method = RequestMethod.POST)
 	public String update(ModelMap model, @PathVariable(value = "shortName") String shortName, @RequestParam("cropName") String cropName,
 			@RequestParam("blurp") String aboutBody, @RequestParam(value = "summary", required = false) String summary) {
 
@@ -132,7 +146,7 @@ public class CropController extends BaseController {
 		return "redirect:/c/" + shortName;
 	}
 
-	@RequestMapping(value = "/{shortName}/update", params = { "otherNames" })
+	@RequestMapping(value = "/{shortName}/update", params = { "otherNames" }, method = RequestMethod.POST)
 	public String updateOtherNames(ModelMap model, @PathVariable(value = "shortName") String shortName, @RequestParam("otherNames") String otherNames) {
 
 		_logger.debug("Updating crop aliases for " + shortName);
@@ -147,6 +161,37 @@ public class CropController extends BaseController {
 		return edit(model, shortName);
 	}
 
+	@RequestMapping(value = "/{shortName}/update", params = { "action=update-rules", "cropRules" }, method = RequestMethod.POST)
+	public String updateCropRules(ModelMap model, @PathVariable(value = "shortName") String shortName, @RequestParam("cropRules") String cropRulesJson)
+			throws JsonParseException, JsonMappingException, IOException {
+
+		_logger.debug("Updating crop rules for " + shortName);
+		final Crop crop = cropService.getCrop(shortName);
+		if (crop == null) {
+			throw new ResourceNotFoundException();
+		}
+
+		List<CropRule> rules = new ObjectMapper().readValue(cropRulesJson, new TypeReference<List<CropRule>>() {
+		});
+		cropService.setCropRules(crop, rules);
+
+		return edit(model, shortName);
+	}
+
+	@RequestMapping(value = "/{shortName}/update", params = { "action=update-taxonomy" }, method = RequestMethod.POST)
+	public String updateTaxonomies(ModelMap model, @PathVariable(value = "shortName") String shortName) {
+
+		_logger.debug("Updating crop taxonomies for " + shortName);
+		final Crop crop = cropService.getCrop(shortName);
+		if (crop == null) {
+			throw new ResourceNotFoundException();
+		}
+
+		cropService.rebuildTaxonomies(crop);
+
+		return edit(model, shortName);
+	}
+
 	@RequestMapping("/{shortName}/ajax/taxonomies")
 	public String ajaxTaxonomies(ModelMap model, @PathVariable(value = "shortName") String shortName,
 			@RequestParam(value = "page", required = false, defaultValue = "1") int page) {

src/main/java/org/genesys2/server/servlet/controller/admin/AdminController.java

@@ -35,7 +35,6 @@ import org.apache.commons.lang.StringUtils;
 import org.apache.commons.lang.time.StopWatch;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
-import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.persistence.domain.AccessionRepository;
 import org.genesys2.server.persistence.domain.GenesysLowlevelRepository;
 import org.genesys2.server.service.CountryNamesUpdater;
@@ -56,8 +55,6 @@ import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.jdbc.core.RowCallbackHandler;
 import org.springframework.security.access.prepost.PreAuthorize;
 import org.springframework.stereotype.Controller;
-import org.springframework.transaction.annotation.Propagation;
-import org.springframework.transaction.annotation.Transactional;
 import org.springframework.ui.Model;
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestMethod;
@@ -378,14 +375,14 @@ public class AdminController {
 		return "redirect:/admin/";
 	}
 
-	@RequestMapping(value = "/rebuild-taxonomies", method = RequestMethod.POST)
+	@RequestMapping(value = "/taxonomy", method = RequestMethod.POST, params={"action=taxonomy-rebuild"})
 	public String rebuild() {
 		LOG.info("Rebuilding taxonomies");
 		cropService.rebuildTaxonomies();
 		return "redirect:/admin/";
 	}
 
-	@RequestMapping(value = "/cleanup-taxonomies", method = RequestMethod.POST)
+	@RequestMapping(value = "/taxonomy", method = RequestMethod.POST, params={"action=taxonomy-cleanup"})
 	public String cleanupTaxonomies() {
 		taxonomyService.cleanupTaxonomies();
 		return "redirect:/admin/";

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

@@ -122,8 +122,9 @@
   </form>
 
   <h3>Taxonomy</h3>
-  <form method="post" action="<c:url value="/admin/cleanup-taxonomies" />">
-    <input type="submit" class="btn btn-default" value="Cleanup taxonomies" />
+  <form method="post" action="<c:url value="/admin/taxonomy" />">
+    <button class="btn btn-default" name="action" value="taxonomy-cleanup">Removed unused Taxonomy2 records</button>
+    <button class="btn btn-default" name="action" value="taxonomy-rebuild">Rebuild</button>
     <!-- CSRF protection -->
     <input type="hidden" name="${_csrf.parameterName}" value="${_csrf.token}" />
   </form>

src/main/webapp/WEB-INF/jsp/crop/edit.jsp

@@ -63,6 +63,21 @@
 		<input type="submit" value="<spring:message code="save"/>" class="btn btn-primary" />
 	</form>
 
+	<form role="form" class="form-horizontal" action="<c:url value="/c/${crop.shortName}/update" />" method="post">
+		<div class="form-group">
+			<label class="col-lg-12 control-label">
+				<spring:message code="crop.cropname-aliases" />
+			</label>
+			<div class="controls col-lg-12">
+				<textarea name="cropRules" class="form-control"><c:out value="${cropRulesJson}" /></textarea>
+			</div>
+		</div>
+		<!-- CSRF protection -->
+		<input type="hidden" name="${_csrf.parameterName}" value="${_csrf.token}" />
+		<button name="action" value="update-rules" class="btn btn-primary"><spring:message code="save"/></button>
+		<button name="action" value="update-taxonomy" class="btn btn-default">Re-link Taxonomy2 records</button>
+	</form>
+
 	<content tag="javascript">
   <script type="text/javascript">
     <local:tinyMCE selector=".html-editor" />

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

@@ -111,13 +111,13 @@
 		</h3>
 		<div class="row">
 			<div class="col-md-offset-2 col-md-10">
-				<ul class="funny-list">
+				<ul class="funny-list"><li>
 					<c:forEach items="${cropRules}" var="rule">
-						<li class="${rule.included ? '' : 'excluded'}">
+						<span class="${rule.included ? '' : 'excluded'}">
 						<b>${rule.included ? '+' : '-'}</b> <c:out value="${rule.genus}"/> <c:out
-							value="${rule.species eq null ? '*' : rule.species}"/></li>
+							value="${rule.species eq null ? '*' : rule.species}"/></span>
 					</c:forEach>
-				</ul>
+				</li></ul>
 				
 			<%-- 	<h3><spring:message code="taxonomy-list"/></h3> --%>
 				<ul class="funny-list">