Germplasm requests are checked with ITPGRFA's PID server

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

@@ -18,6 +18,7 @@ package org.genesys2.server.persistence.domain;
 
 import java.util.Collection;
 import java.util.List;
+import java.util.Set;
 
 import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.genesys.Taxonomy;
@@ -93,4 +94,7 @@ public interface AccessionRepository extends JpaRepository<Accession, Long> {
 
 	Accession findByInstituteCodeAndAccessionNameAndGenus(String holdingInstitute, String accessionName, String genus);
 
+	@Query("select count(a.id) from Accession a where a.id in ( ?1 ) and a.availability = 'Y'")
+	long countAvailable(Set<Long> accessionIds);
+
 }

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

@@ -19,6 +19,7 @@ package org.genesys2.server.service;
 import java.util.Collection;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 
 import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.genesys.AllAccnames;
@@ -110,4 +111,6 @@ public interface GenesysService {
 
 	void saveSvalbards(List<SvalbardData> svalbards);
 
+	long countAvailable(Set<Long> accessionIds);
+
 }

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

+package org.genesys2.server.service.impl;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.apache.http.HttpEntity;
+import org.apache.http.HttpResponse;
+import org.apache.http.client.ClientProtocolException;
+import org.apache.http.client.HttpClient;
+import org.apache.http.client.methods.HttpGet;
+import org.apache.http.impl.client.DefaultHttpClient;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.stereotype.Component;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+@Component
+public class EasySMTAConnector {
+	private static final Log LOG = LogFactory.getLog(EasySMTAConnector.class);
+
+	// FIXME Use the safe URL
+	// private static final String ITPGRFA_PID_URL =
+	// "https://www.itworks.it/itt/index.php?r=extsys/getUserDetails2";
+	private static final String ITPGRFA_PID_URL = "https://www.itworks.it/itt/index.php?r=extsys/getUserDetails2&esUsername=XXX&esPassword=YYY&usEmail=ZZZ";
+
+	@Value("${itpgrfa.easysmta.username}")
+	private String serverUsername;
+
+	@Value("${itpgrfa.easysmta.password}")
+	private String serverPassword;
+
+	public EasySMTAUserData getUserData(String emailAddress) {
+		final HttpClient httpclient = new DefaultHttpClient();
+
+		// FIXME Url contains username+password, see below
+		String url = ITPGRFA_PID_URL.replace("XXX", serverUsername);
+		url = url.replace("YYY", serverPassword);
+		url = url.replace("ZZZ", emailAddress);
+
+		LOG.warn("Using unsafe fetch URL: " + url);
+
+		final HttpGet httpget = new HttpGet(url);
+		HttpResponse response = null;
+
+		BufferedReader br = null;
+
+		try {
+			LOG.info("Using " + serverUsername + " as Easy-SMTA username.");
+			// FIXME Use these when Easy-SMTA is fixed
+			// httpclient.getParams().setParameter("esUsername",
+			// serverUsername);
+			// httpclient.getParams().setParameter("esPassword",
+			// serverPassword);
+			// httpclient.getParams().setParameter("usEmail", emailAddress);
+
+			response = httpclient.execute(httpget);
+
+			// Get hold of the response entity
+			final HttpEntity entity = response.getEntity();
+			LOG.debug(entity.getContentType() + " " + entity.getContentLength());
+
+			// If the response does not enclose an entity, there is no
+			// need to bother about connection release
+			if (entity != null) {
+				ObjectMapper objectMapper = new ObjectMapper();
+				JsonNode tree = objectMapper.readTree(entity.getContent());
+				LOG.debug(tree);
+
+				if (tree.has("errorCode")) {
+					// Check failed
+					LOG.warn("Checking PID server failed with: " + tree);
+
+					// TODO Report various errorCodes!
+
+				} else {
+
+					if (LOG.isDebugEnabled()) {
+						LOG.debug(tree);
+					}
+
+					return new EasySMTAUserData(tree.get("pid").asText(), tree.get("name").asText(), tree.get("surname").asText(), tree.get("email").asText(),
+							tree.get("orgName").asText(), tree.get("country").asText());
+				}
+			}
+		} catch (final ClientProtocolException e) {
+			LOG.error(e.getMessage(), e);
+
+		} catch (IOException e) {
+			LOG.error(e);
+		} finally {
+			IOUtils.closeQuietly(br);
+			httpget.releaseConnection();
+			LOG.debug("EasySMTA streams closed.");
+		}
+
+		return null;
+	}
+
+	/**
+	 * Data returned by Easy-SMTA
+	 * 
+	 * @author matijaobreza
+	 */
+	public class EasySMTAUserData {
+		public String pid;
+		public String firstName;
+		public String lastName;
+		public String email;
+		public String organization;
+		public String countryIsoCode3;
+
+		public EasySMTAUserData(String pid, String firstName, String lastName, String email, String organization, String countryIsoCode3) {
+			this.pid = pid;
+			this.firstName = firstName;
+			this.lastName = lastName;
+			this.email = email;
+			this.organization = organization;
+			this.countryIsoCode3 = countryIsoCode3;
+		}
+
+		@Override
+		public String toString() {
+			return "PID " + firstName + " " + lastName + ", " + organization + ", country=" + countryIsoCode3;
+		}
+	}
+}

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

@@ -20,6 +20,7 @@ import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
@@ -358,4 +359,11 @@ public class GenesysServiceImpl implements GenesysService, TraitService {
 	public void saveSvalbards(List<SvalbardData> svalbards) {
 		svalbardRepository.save(svalbards);
 	}
+
+	@Override
+	public long countAvailable(Set<Long> accessionIds) {
+		if (accessionIds == null || accessionIds.size() == 0)
+			return 0;
+		return accessionRepository.countAvailable(accessionIds);
+	}
 }

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

@@ -111,7 +111,7 @@ public class HtmlController extends BaseController {
 		try {
 			InetAddress remoteInetAddr = InetAddress.getByName(remoteAddr);
 			isLocalRequest = remoteInetAddr.isAnyLocalAddress() || remoteInetAddr.isLoopbackAddress();
-			_logger.debug("Remote addr: " + remoteAddr + " " + remoteInetAddr + " isLocal=" + isLocalRequest);
+			_logger.warn("Remote addr: " + remoteAddr + " " + remoteInetAddr + " isLocal=" + isLocalRequest);
 		} catch (UnknownHostException e1) {
 			_logger.warn(e1.getMessage());
 		}

src/main/java/org/genesys2/server/servlet/controller/RequestController.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 org.apache.commons.lang.StringUtils;
+import org.genesys2.server.service.ContentService;
+import org.genesys2.server.service.GenesysService;
+import org.genesys2.server.service.impl.EasySMTAConnector;
+import org.genesys2.server.service.impl.EasySMTAConnector.EasySMTAUserData;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Scope;
+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.RequestMethod;
+import org.springframework.web.bind.annotation.RequestParam;
+
+/**
+ * Controller to manage request processing.
+ * 
+ * @author matijaobreza
+ */
+@Controller
+@Scope("request")
+@RequestMapping("/request")
+public class RequestController extends BaseController {
+
+	@Autowired
+	private SelectionBean selectionBean;
+
+	@Autowired
+	private GenesysService genesysService;
+
+	@Autowired
+	private ContentService contentService;
+
+	@Autowired
+	private EasySMTAConnector pidChecker;
+
+	/**
+	 * Give information about the request process
+	 * 
+	 * @param model
+	 * @return
+	 */
+	@RequestMapping
+	public String view(ModelMap model, @RequestParam(value = "page", required = false, defaultValue = "1") int page) {
+		model.addAttribute("blurp", contentService.getGlobalArticle("request-intro", getLocale()));
+
+		model.addAttribute("totalCount", selectionBean.size());
+		model.addAttribute("availableCount", genesysService.countAvailable(selectionBean.copy()));
+		model.addAttribute("pagedData", genesysService.listAccessions(selectionBean.copy(), new PageRequest(page - 1, 50, new Sort("accessionName"))));
+
+		return "/request/index";
+	}
+
+	@RequestMapping(method = RequestMethod.POST, value = "/start")
+	public String start(ModelMap model) {
+		model.addAttribute("blurp", contentService.getGlobalArticle("request-personal", getLocale()));
+		return "/request/personal";
+	}
+
+	@RequestMapping(method = RequestMethod.POST, value = "/submit")
+	public String submit(ModelMap model, @RequestParam(value = "email", defaultValue = "", required = true) String emailAddress) {
+		emailAddress = emailAddress.trim();
+
+		if (StringUtils.isBlank(emailAddress)) {
+			_logger.warn("No email address was specified for request. Stopping here.");
+			return "/request/personal";
+		}
+
+		_logger.info("Checking for ITPGRFA PID account for " + emailAddress);
+		EasySMTAUserData pid = pidChecker.getUserData(emailAddress);
+
+		if (pid == null) {
+			_logger.warn("No such user in ITPGRFA system");
+
+		} else {
+			// TODO send email to registered email address, wait for response
+			_logger.info("TODO TODO TODO : Send email to : " + pid);
+
+		}
+
+		// Whatever the response is, we render the same message
+		model.addAttribute("blurp", contentService.getGlobalArticle("request-received", getLocale()));
+		return "/request/received";
+	}
+
+}

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

@@ -53,10 +53,9 @@ public class SelectionController extends BaseController {
 		return "/selection/index";
 	}
 
-	@RequestMapping("/order")
+	@RequestMapping(value = "/order")
 	public String order(ModelMap model) {
-		// TODO
-		return "/todo";
+		return "redirect:/request";
 	}
 
 	@RequestMapping("/add/{id}")

src/main/resources/content/language.properties

@@ -186,6 +186,11 @@ accession.sampleStatus.415=Segregating population
 accession.sampleStatus.420=Mutant/genetic stock
 accession.sampleStatus.500=Advanced/improved cultivar
 accession.sampleStatus.999=Other
+accession.availability=Availability
+
+accession.availability.=Unknown
+accession.availability.true=Available
+accession.availability.false=Not available
 
 accession.page.profile.title=Accession profile: {0}
 accession.page.resolve.title=Multiple accessions found
@@ -292,5 +297,11 @@ maps.view-map=View map
 audit.createdBy=Created by {0}
 audit.lastModifiedBy=Last updated by {0}
 
-
 itpgrfa.page.list.title=Parties to the ITPGRFA
+
+request.page.title=Requesting material from holding institutes
+request.total-vs-available=Out of {0} accessions listed, {1} are known to be available for distribution.
+request.start-request=Request available germplasm
+request.your-email=Your E-mail address:
+
+

src/main/resources/default-content/request-intro

+{
+	"en": {
+		"title": "Start requesting material",
+		"body": "<p>In the table below you will find the accessions you have added to your list. The table indicates whether or not these accessions are available for distribution.</p><p>Please note that only accessions marked as <b>Available</b> will be included in your request for germplasm.</p><p>Once you have reviewed your selection, click <b>Continue</b> button below to initiate the process of requesting for germplasm.</p>"
+	}
+}
\ No newline at end of file

src/main/resources/default-content/request-personal

+{
+	"en": {
+		"title": "Initiate material request",
+		"body": "<p>An account with ITPGRFA's Easy-SMTA is required to request for germplasm with this system. Please provide the email address you have used with ITPGRFA's Easy-SMTA.</p><p>We will check the email address against their system and only then proceed with your request.</p>"
+	}
+}
\ No newline at end of file

src/main/resources/default-content/request-received

+{
+	"en": {
+		"title": "Material request received",
+		"body": "<p>We have checked the provided email address against ITPGRFA server.</p><p>Within a few minutes you will have received our message at the email address you have provided with further instructions to confirm your request for germplasm.</p><p>Make sure you also check your <b>SPAM</b> folder.</p><p>If the message does not arrive, please initiate the request again by going to 'My List'.</p>"
+	}
+}
\ No newline at end of file

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

@@ -37,7 +37,7 @@
 		</div>
 	</c:if>
 	
-	<c:if test="${not accession.availability}">
+	<c:if test="${accession.availability eq false}">
 		<div class="alert alert-warning">
 			<spring:message code="accession.not-available-for-distribution" />
 		</div>
@@ -91,6 +91,13 @@
 				<td><a href="<c:url value="/acn/t/${accession.taxonomy.genus}/${accession.taxonomy.species}" />"><c:out value="${accession.taxonomy.taxonName}" /></a> <br /> <a
 					href="<c:url value="/wiews/${accession.institute.code.toLowerCase()}/t/${accession.taxonomy.genus}/${accession.taxonomy.species}" />"><spring:message code="accession.taxonomy-at-institute" arguments="${accession.taxonomy.taxonName}|||${accession.institute.code}" argumentSeparator="|||" /></a></td>
 			</tr>
+
+			<tr>
+				<td><spring:message code="accession.availability" /></td>
+				<td><spring:message code="accession.availability.${accession.availability}" /></td>
+			</tr>
+			
+			
 			<tr>
 				<td><spring:message code="accession.otherNames" /></td>
 				<td><c:out value="${accessionNames.accNames}" /><br /> <c:out value="${accessionNames.otherIds}" /></td>

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

+<!DOCTYPE html>
+
+<%@include file="/WEB-INF/jsp/init.jsp"%>
+
+<html>
+<head>
+<title><spring:message code="request.page.title" /></title>
+</head>
+<body>
+	<h1>
+		<spring:message code="request.page.title" />
+	</h1>
+
+	<c:if test="${pagedData == null}">
+		<div class="alert alert-info">
+			<spring:message code="selection.empty-list-warning" />
+		</div>
+	</c:if>
+
+	<c:if test="${pagedData != null}">
+		<div class="alert alert-info">
+			<spring:message code="request.total-vs-available" arguments="${totalCount},${availableCount}" />
+		</div>
+
+		<%@include file="/WEB-INF/jsp/content/include/blurp-display.jsp"%>
+
+		<div class="nav-header">
+			<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=${pagedData.number eq 0 ? 1 : pagedData.number}"><spring:message code="pagination.previous-page" /></a> <a href="?page=${pagedData.number + 2}"><spring:message code="pagination.next-page" /></a>
+		</div>
+
+		<table class="accessions">
+			<thead>
+				<tr>
+					<td class="idx-col"></td>
+					<td><spring:message code="accession.availability" /></td>
+					<td><spring:message code="accession.accessionName" /></td>
+					<td class="notimportant"><spring:message code="accession.taxonomy" /></td>
+					<%-- <td class="notimportant"><spring:message code="accession.origin" /></td> --%>
+					<td><spring:message code="accession.holdingInstitute" /></td>
+				</tr>
+			</thead>
+			<tbody>
+				<c:forEach items="${pagedData.content}" var="accession" varStatus="status">
+					<tr id="a${accession.id}" class="acn targeted ${status.count % 2 == 0 ? 'even' : 'odd'} ${accession.availability ? '' : 'not-available'}">
+						<td class="idx-col">${status.count + pagedData.size * pagedData.number}</td>
+						<td><spring:message code="accession.availability.${accession.availability}" /></td>
+						<td><a href="<c:url value="/acn/id/${accession.id}" />"><b><c:out value="${accession.accessionName}" /></b></a></td>
+						<td class="notimportant"><c:out value="${accession.taxonomy.taxonName}" /></td>
+						<%-- <td class="notimportant"><c:out value="${accession.countryOfOrigin.getName(pageContext.response.locale)}" /></td> --%>
+						<td class="notimportant"><a href="<c:url value="/wiews/${accession.institute.code.toLowerCase()}" />"><c:out value="${accession.institute.code}" /></a></td>
+					</tr>
+				</c:forEach>
+			</tbody>
+		</table>
+
+		<c:if test="${availableCount gt 0}">
+			<form method="post" action="<c:url value="/request/start" />" class="form-horizontal">
+				<div class="form-actions">
+					<input class="btn btn-primary" type="submit" value="<spring:message code="request.start-request" />" />
+				</div>
+			</form>
+		</c:if>
+
+	</c:if>
+
+	<script type="text/javascript">
+		/*  jQuery(document).ready(function(){
+			if(document.location.hash != '') {
+				setTimeout(function() { document.location.hash=''; }, 2000);
+			} 
+		 }); */
+	</script>
+</body>
+</html>
\ No newline at end of file

src/main/webapp/WEB-INF/jsp/request/personal.jsp

+<!DOCTYPE html>
+
+<%@include file="/WEB-INF/jsp/init.jsp"%>
+
+<html>
+<head>
+<title><spring:message code="request.page.title" /></title>
+</head>
+<body>
+	<h1>
+		<spring:message code="request.page.title" />
+	</h1>
+
+	<%@include file="/WEB-INF/jsp/content/include/blurp-display.jsp"%>
+
+	<form method="post" action="<c:url value="/request/submit" />" class="form-horizontal">
+		<div class="form-group">
+			<label class="col-lg-2 control-label"><spring:message code="request.your-email" /></label>
+			<div class="col-lg-3">
+				<input type="text" name="email" class="span3 required email form-control" />
+			</div>
+		</div>
+	
+		<div class="form-actions">
+			<input class="btn btn-primary" type="submit" value="<spring:message code="request.start-request" />" />
+		</div>
+	</form>
+
+</body>
+</html>
\ No newline at end of file

src/main/webapp/WEB-INF/jsp/request/received.jsp

+<!DOCTYPE html>
+
+<%@include file="/WEB-INF/jsp/init.jsp"%>
+
+<html>
+<head>
+<title><spring:message code="request.page.title" /></title>
+</head>
+<body>
+	<h1>
+		<spring:message code="request.page.title" />
+	</h1>
+
+	<%@include file="/WEB-INF/jsp/content/include/blurp-display.jsp"%>
+
+</body>
+</html>
\ No newline at end of file

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

@@ -553,3 +553,8 @@ tr.acn .sel.picked {
 	height: 300px;
 	margin-top: 1em;
 }
+
+table.accessions tr.not-available > td {
+	text-decoration: line-through;
+	opacity: .5;	
+}