Fixed #20

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

@@ -16,6 +16,15 @@
 
 package org.genesys2.server.service;
 
+import java.io.IOException;
+
+import com.fasterxml.jackson.core.JsonParser;
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.core.JsonToken;
+import com.fasterxml.jackson.databind.DeserializationContext;
+import com.fasterxml.jackson.databind.JsonMappingException;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
+import com.fasterxml.jackson.databind.deser.std.StdDeserializer;
 
 public interface EasySMTA {
 	EasySMTAUserData getUserData(String emailAddress);
@@ -25,73 +34,325 @@ public interface EasySMTA {
 	 * 
 	 * @author matijaobreza
 	 */
+	@JsonDeserialize(using = Deserializer.class)
 	public static class EasySMTAUserData {
 		private String pid;
-		private String firstName;
-		private String lastName;
+		// / "in" = Individual, "or" = Organization
+		private String type;
+		private String legalStatus;
+		private String name;
+		private String surname;
 		private String email;
-		private String organization;
-		private String countryIsoCode3;
 		private String address;
+		private String country;
+		private String countryName;
+		private String telephone;
+		private String fax;
+		private String orgName;
+		private String aoName, aoSurname, aoEmail;
+		private String orgAddress, orgCountry, orgCountryName;
+		private String aoTelephone, aoFax;
+		private String shipAddrFlag;
 		private String shipAddress;
 		private String shipCountry;
+		private String shipTelephone;
 
 		public EasySMTAUserData() {
 		}
-		
-		public EasySMTAUserData(String pid, String firstName, String lastName, String email, String organization, String countryIsoCode3, String address,
-				String shipAddress, String shipCountry) {
-			this.pid = pid;
-			this.firstName = firstName;
-			this.lastName = lastName;
-			this.email = email;
-			this.organization = organization;
-			this.countryIsoCode3 = countryIsoCode3;
-			this.address = address;
-			this.shipAddress = shipAddress;
-			this.shipCountry = shipCountry;
-		}
-	
+
 		@Override
 		public String toString() {
-			return "ITPGRFA.PID email=" + email + " first=" + firstName + " last=" + lastName + ", org=" + organization + ", country=" + countryIsoCode3;
+			return "ITPGRFA.PID email=" + email + " first=" + name + " last=" + surname + ", org=" + orgName + ", country=" + country;
 		}
-	
+
 		public String getPid() {
 			return pid;
 		}
-	
-		public String getFirstName() {
-			return firstName;
+
+		public void setPid(String pid) {
+			this.pid = pid;
 		}
-	
-		public String getLastName() {
-			return lastName;
+
+		public String getType() {
+			return type;
 		}
-	
+
+		public void setType(String type) {
+			this.type = type;
+		}
+
+		public String getLegalStatus() {
+			return legalStatus;
+		}
+
+		public void setLegalStatus(String legalStatus) {
+			this.legalStatus = legalStatus;
+		}
+
+		public String getName() {
+			return name;
+		}
+
+		public void setName(String name) {
+			this.name = name;
+		}
+
+		public String getSurname() {
+			return surname;
+		}
+
+		public void setSurname(String surname) {
+			this.surname = surname;
+		}
+
 		public String getEmail() {
 			return email;
 		}
-	
-		public String getOrganization() {
-			return organization;
-		}
-	
-		public String getCountryIsoCode3() {
-			return countryIsoCode3;
+
+		public void setEmail(String email) {
+			this.email = email;
 		}
-	
+
 		public String getAddress() {
 			return address;
 		}
-	
+
+		public void setAddress(String address) {
+			this.address = address;
+		}
+
+		public String getCountry() {
+			return country;
+		}
+
+		public void setCountry(String country) {
+			this.country = country;
+		}
+
+		public String getCountryName() {
+			return countryName;
+		}
+
+		public void setCountryName(String countryName) {
+			this.countryName = countryName;
+		}
+
+		public String getTelephone() {
+			return telephone;
+		}
+
+		public void setTelephone(String telephone) {
+			this.telephone = telephone;
+		}
+
+		public String getFax() {
+			return fax;
+		}
+
+		public void setFax(String fax) {
+			this.fax = fax;
+		}
+
+		public String getOrgName() {
+			return orgName;
+		}
+
+		public void setOrgName(String orgName) {
+			this.orgName = orgName;
+		}
+
+		public String getAoName() {
+			return aoName;
+		}
+
+		public void setAoName(String aoName) {
+			this.aoName = aoName;
+		}
+
+		public String getAoSurname() {
+			return aoSurname;
+		}
+
+		public void setAoSurname(String aoSurname) {
+			this.aoSurname = aoSurname;
+		}
+
+		public String getAoEmail() {
+			return aoEmail;
+		}
+
+		public void setAoEmail(String aoEmail) {
+			this.aoEmail = aoEmail;
+		}
+
+		public String getOrgAddress() {
+			return orgAddress;
+		}
+
+		public void setOrgAddress(String orgAddress) {
+			this.orgAddress = orgAddress;
+		}
+
+		public String getOrgCountry() {
+			return orgCountry;
+		}
+
+		public void setOrgCountry(String orgCountry) {
+			this.orgCountry = orgCountry;
+		}
+
+		public String getOrgCountryName() {
+			return orgCountryName;
+		}
+
+		public void setOrgCountryName(String orgCountryName) {
+			this.orgCountryName = orgCountryName;
+		}
+
+		public String getAoTelephone() {
+			return aoTelephone;
+		}
+
+		public void setAoTelephone(String aoTelephone) {
+			this.aoTelephone = aoTelephone;
+		}
+
+		public String getAoFax() {
+			return aoFax;
+		}
+
+		public void setAoFax(String aoFax) {
+			this.aoFax = aoFax;
+		}
+
+		public String getShipAddrFlag() {
+			return shipAddrFlag;
+		}
+
+		public void setShipAddrFlag(String shipAddrFlag) {
+			this.shipAddrFlag = shipAddrFlag;
+		}
+
 		public String getShipAddress() {
 			return shipAddress;
 		}
-	
+
+		public void setShipAddress(String shipAddress) {
+			this.shipAddress = shipAddress;
+		}
+
 		public String getShipCountry() {
 			return shipCountry;
 		}
+
+		public void setShipCountry(String shipCountry) {
+			this.shipCountry = shipCountry;
+		}
+
+		public String getShipTelephone() {
+			return shipTelephone;
+		}
+
+		public void setShipTelephone(String shipTelephone) {
+			this.shipTelephone = shipTelephone;
+		}
 	}
 
+	public final class Deserializer extends StdDeserializer<EasySMTAUserData> {
+
+		public Deserializer() {
+			super(EasySMTAUserData.class);
+		}
+
+		protected Deserializer(Class<?> vc) {
+			super(vc);
+		}
+
+		@Override
+		public EasySMTAUserData deserialize(JsonParser jp, DeserializationContext ctxt) throws IOException, JsonProcessingException {
+			if (jp.getCurrentToken() != JsonToken.START_OBJECT) {
+				throw new IOException("invalid start marker");
+			}
+			EasySMTAUserData pidData = new EasySMTAUserData();
+			boolean foundName = false, foundSurname = false;
+			boolean foundOrgname = false, foundCountry=false;
+
+			while (jp.nextToken() != JsonToken.END_OBJECT) {
+				String fieldname = jp.getCurrentName();
+				jp.nextToken(); // move to next token in string
+
+				if ("pid".equals(fieldname)) {
+					pidData.setPid(jp.getText());
+				} else if ("type".equals(fieldname)) {
+					pidData.setType(jp.getText());
+				} else if ("legalStatus".equals(fieldname)) {
+					pidData.setLegalStatus(jp.getText());
+				} else if ("name".equals(fieldname) || "firstName".equals(fieldname)) {
+					if (foundName)
+						throw new JsonMappingException("Field " + fieldname + " is a synonym. Don't provide both.");
+					foundName = true;
+					pidData.setName(jp.getText());
+				} else if ("surname".equals(fieldname) || "lastName".equals(fieldname)) {
+					if (foundSurname)
+						throw new JsonMappingException("Field " + fieldname + " is a synonym. Don't provide both.");
+					foundSurname = true;
+					pidData.setSurname(jp.getText());
+				} else if ("email".equals(fieldname)) {
+					pidData.setEmail(jp.getText());
+				} else if ("address".equals(fieldname)) {
+					pidData.setAddress(jp.getText());
+				} else if ("country".equals(fieldname) || "countryIsoCode3".equals(fieldname)) {
+					if (foundCountry)
+						throw new JsonMappingException("Field " + fieldname + " is a synonym. Don't provide both.");
+					foundCountry = true;
+					pidData.setCountry(jp.getText());
+				} else if ("countryName".equals(fieldname)) {
+					pidData.setCountryName(jp.getText());
+				} else if ("telephone".equals(fieldname)) {
+					pidData.setTelephone(jp.getText());
+				} else if ("fax".equals(fieldname)) {
+					pidData.setFax(jp.getText());
+
+				} else if ("orgName".equals(fieldname) || "organization".equals(fieldname)) {
+					if (foundOrgname)
+						throw new JsonMappingException("Field " + fieldname + " is a synonym. Don't provide both.");
+					foundOrgname = true;
+					pidData.setOrgName(jp.getText());
+				} else if ("orgAddress".equals(fieldname)) {
+					pidData.setOrgAddress(jp.getText());
+				} else if ("orgCountry".equals(fieldname)) {
+					pidData.setOrgCountry(jp.getText());
+				} else if ("orgCountryName".equals(fieldname)) {
+					pidData.setOrgCountryName(jp.getText());
+
+				} else if ("aoName".equals(fieldname)) {
+					pidData.setAoName(jp.getText());
+				} else if ("aoSurname".equals(fieldname)) {
+					pidData.setAoSurname(jp.getText());
+				} else if ("aoEmail".equals(fieldname)) {
+					pidData.setAoEmail(jp.getText());
+				} else if ("aoTelephone".equals(fieldname)) {
+					pidData.setAoTelephone(jp.getText());
+				} else if ("aoFax".equals(fieldname)) {
+					pidData.setAoFax(jp.getText());
+
+				} else if ("shipAddrFlag".equals(fieldname)) {
+					pidData.setShipAddrFlag(jp.getText());
+				} else if ("shipAddress".equals(fieldname)) {
+					pidData.setShipAddress(jp.getText());
+				} else if ("shipCountry".equals(fieldname)) {
+					pidData.setShipCountry(jp.getText());
+				} else if ("shipTelephone".equals(fieldname)) {
+					pidData.setShipTelephone(jp.getText());
+				}
+
+				else {
+					throw new JsonMappingException("Unsupported EasySMTAUserData field: " + fieldname);
+				}
+			}
+			// Don't close?!
+			//jp.close();
+			return pidData;
+		}
+	}
 }

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

@@ -100,10 +100,7 @@ public class EasySMTAConnector implements EasySMTA {
 					// TODO Report various errorCodes!
 
 				} else {
-
-					return new EasySMTA.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(), tree.get("address").asText(), tree.get("shipAddress").asText(), tree
-									.get("shipCountry").asText());
+					return objectMapper.readValue(entity.getContent(), EasySMTA.EasySMTAUserData.class);
 				}
 			}
 		} catch (final ClientProtocolException e) {

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

@@ -36,8 +36,19 @@ public class EasySMTAMockConnector implements EasySMTA {
 
 		if (RandomUtils.nextBoolean()) {
 			LOG.info("Valid mock EasySMTA check");
-			return new EasySMTA.EasySMTAUserData(RandomStringUtils.randomAlphanumeric(6), "Name", "Surname", emailAddress, "Organization", "DEU", "Address 1",
-					"Address 2", "DEU");
+			EasySMTAUserData pidData = new EasySMTA.EasySMTAUserData();
+			pidData.setPid(RandomStringUtils.randomAlphanumeric(6));
+			pidData.setType("in");
+			pidData.setTelephone("+00 000 000-0000");
+			pidData.setName("Name");
+			pidData.setSurname("Surname");
+			pidData.setEmail(emailAddress);
+			pidData.setOrgName("Organization");
+			pidData.setCountry("DEU");
+			pidData.setAddress("Address 1");
+			pidData.setShipAddress("Address 2");
+			pidData.setShipCountry("DEU");
+			return pidData;
 		} else {
 			LOG.info("Invalid mock EasySMTA check");
 			return null;

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

@@ -236,25 +236,21 @@ public class RequestServiceImpl implements RequestService {
 	@Transactional
 	@PreAuthorize("hasRole('ADMINISTRATOR')")
 	public MaterialRequest recheckPid(MaterialRequest materialRequest) {
-		if (StringUtils.isBlank(materialRequest.getPid())) {
-			// re-test email for PID
-			EasySMTA.EasySMTAUserData pid = pidChecker.getUserData(materialRequest.getEmail());
-			if (pid == null) {
-				throw new NoPidException("Email not registered with PID server");
-			}
-			materialRequest.setPid(pid.getPid());
-			requestRepository.save(materialRequest);
-			try {
-				RequestBody rb = mapper.readValue(materialRequest.getBody(), RequestBody.class);
-				rb.pid = pid;
-				materialRequest.setBody(serialize(rb));
-				return requestRepository.save(materialRequest);
-			} catch (IOException e) {
-				// FIXME Some other exception?
-				throw new RuntimeException("Could not handle request JSON", e);
-			}
-		} else {
-			return materialRequest;
+		// re-test email for PID
+		EasySMTA.EasySMTAUserData pid = pidChecker.getUserData(materialRequest.getEmail());
+		if (pid == null) {
+			throw new NoPidException("Email not registered with PID server");
+		}
+		materialRequest.setPid(pid.getPid());
+		requestRepository.save(materialRequest);
+		try {
+			RequestBody rb = mapper.readValue(materialRequest.getBody(), RequestBody.class);
+			rb.pid = pid;
+			materialRequest.setBody(serialize(rb));
+			return requestRepository.save(materialRequest);
+		} catch (IOException e) {
+			// FIXME Some other exception?
+			throw new RuntimeException("Could not handle request JSON", e);
 		}
 	}
 
@@ -406,6 +402,7 @@ public class RequestServiceImpl implements RequestService {
 	}
 
 	public static final class RequestBody {
+
 		public RequestInfo requestInfo;
 		public Set<Long> accessionIds;
 		public EasySMTA.EasySMTAUserData pid;

src/main/java/org/genesys2/server/servlet/controller/rest/RequestsController.java

@@ -99,6 +99,20 @@ public class RequestsController extends RestController {
 		MaterialRequest materialRequest = requestService.get(uuid);
 		return requestService.validateRequest(materialRequest);
 	}
+	
+
+	/**
+	 * Reload PID data
+	 * 
+	 * @return
+	 */
+	@RequestMapping(value = "/requests/r/{uuid:.{36}}/update-pid", method = RequestMethod.POST, produces = { MediaType.APPLICATION_JSON_VALUE })
+	public @ResponseBody
+	MaterialRequest updatePid(@PathVariable("uuid") String uuid) {
+		LOG.info("Loading request uuid=" + uuid);
+		MaterialRequest materialRequest = requestService.get(uuid);
+		return requestService.recheckPid(materialRequest);
+	}
 
 	/**
 	 * List institute requests

src/main/java/org/genesys2/server/servlet/controller/rest/RestController.java

@@ -45,6 +45,7 @@ public abstract class RestController {
 	@ResponseBody
 	public ExceptionJson handleIOException(Exception ex, HttpServletRequest request, HttpServletResponse response) throws IOException {
 		LOG.error(ex, ex);
+		response.setStatus(400); // ?
 		return new ExceptionJson(ex);
 	}
 

src/test/java/org/genesys2/server/test/EasySMTATest.java

+package org.genesys2.server.test;
+
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.io.IOException;
+
+import org.genesys2.server.service.EasySMTA;
+import org.genesys2.server.service.EasySMTA.EasySMTAUserData;
+import org.junit.Test;
+
+import com.fasterxml.jackson.core.JsonParseException;
+import com.fasterxml.jackson.databind.JsonMappingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+public class EasySMTATest {
+
+	@Test
+	public void testSelf() throws JsonParseException, JsonMappingException, IOException {
+		ObjectMapper mapper = new ObjectMapper();
+		EasySMTAUserData pid1=new EasySMTAUserData();
+		pid1.setPid("pid");
+		String content = mapper.writeValueAsString(pid1);
+		EasySMTAUserData pidData = mapper.readValue(content, EasySMTA.EasySMTAUserData.class);
+		assertTrue(pidData != null);
+	}
+	@Test
+	public void testJSONRead() {
+		String content = "{\"pid\":\"000000\",\"type\":\"in\",\"legalStatus\":\"cg\",\"name\":\"Matija\",\"surname\":\"Obreza\",\"email\":\"matija.obreza@croptrust.org\",\"address\":\"Platz der Vereinten Nationen 7\\r\\n53113 Bonn\",\"country\":\"DEU\",\"countryName\":\"Germany\",\"telephone\":\"\",\"fax\":\"\",\"orgName\":\"\",\"aoName\":\"\",\"aoSurname\":\"\",\"aoEmail\":\"\",\"orgAddress\":\"\",\"orgCountry\":\"\",\"orgCountryName\":\"\",\"aoTelephone\":\"\",\"aoFax\":\"\",\"shipAddrFlag\":\"s\",\"shipAddress\":\"\",\"shipCountry\":\"AFG\",\"shipTelephone\":\"\"}";
+		ObjectMapper mapper = new ObjectMapper();
+		try {
+			EasySMTAUserData pidData = mapper.readValue(content, EasySMTA.EasySMTAUserData.class);
+			assertTrue(pidData != null);
+		} catch (IOException e) {
+			fail(e.getMessage());
+		}
+	}
+
+	@Test
+	public void testJSONReadMissing() {
+		String content = "{\"pid\":\"000000\",\"firstName\":\"Matija\",\"lastName\":\"Obreza\",\"email\":\"matija.obreza@croptrust.org\",\"address\":\"Platz der Vereinten Nationen 7\\r\\n53113 Bonn\",\"country\":\"DEU\",\"countryName\":\"Germany\",\"telephone\":\"\",\"fax\":\"\",\"orgName\":\"\",\"aoName\":\"\",\"aoSurname\":\"\",\"aoEmail\":\"\",\"orgAddress\":\"\",\"orgCountry\":\"\",\"orgCountryName\":\"\",\"aoTelephone\":\"\",\"aoFax\":\"\",\"shipAddrFlag\":\"s\",\"shipAddress\":\"\",\"shipCountry\":\"AFG\",\"shipTelephone\":\"\"}";
+		ObjectMapper mapper = new ObjectMapper();
+		try {
+			EasySMTAUserData pidData = mapper.readValue(content, EasySMTA.EasySMTAUserData.class);
+			assertTrue(pidData != null);
+		} catch (IOException e) {
+			e.printStackTrace();
+			fail(e.getMessage());
+		}
+	}
+
+	@Test(expected = JsonMappingException.class)
+	public void testJSONSurnameLastname() throws JsonParseException, JsonMappingException, IOException {
+		String content = "{\"pid\":\"000000\",\"firstName\":\"Matija\",\"lastName\":\"Obreza\",\"surname\":\"Obreza\",\"email\":\"matija.obreza@croptrust.org\",\"address\":\"Platz der Vereinten Nationen 7\\r\\n53113 Bonn\",\"country\":\"DEU\",\"countryName\":\"Germany\",\"telephone\":\"\",\"fax\":\"\",\"orgName\":\"\",\"aoName\":\"\",\"aoSurname\":\"\",\"aoEmail\":\"\",\"orgAddress\":\"\",\"orgCountry\":\"\",\"orgCountryName\":\"\",\"aoTelephone\":\"\",\"aoFax\":\"\",\"shipAddrFlag\":\"s\",\"shipAddress\":\"\",\"shipCountry\":\"AFG\",\"shipTelephone\":\"\"}";
+		ObjectMapper mapper = new ObjectMapper();
+		EasySMTAUserData pidData = mapper.readValue(content, EasySMTA.EasySMTAUserData.class);
+		assertTrue(pidData != null);
+	}
+	
+	@Test
+	public void testJSONNull() throws JsonParseException, JsonMappingException, IOException {
+		String content = "null";
+		ObjectMapper mapper = new ObjectMapper();
+		EasySMTAUserData pidData = mapper.readValue(content, EasySMTA.EasySMTAUserData.class);
+		assertTrue(pidData == null);
+	}
+}

src/test/java/org/genesys2/server/test/MaterialRequestTest.java

@@ -181,12 +181,6 @@ public class MaterialRequestTest {
 		assertTrue("Got something else back", loaded.getId().equals(request.getId()));
 	}
 
-	EasySMTA.EasySMTAUserData generatePid() {
-		EasySMTA.EasySMTAUserData pid = new EasySMTA.EasySMTAUserData("pid1", "firstName", "lastName", "email@localhost", "organization", "DEU", "address",
-				"shipAddress", "AFG");
-		return pid;
-	}
-
 	Set<Long> generateAccessionIds() {
 		Set<Long> accessionIds = new HashSet<Long>();
 		for (long i = 2 + RandomUtils.nextInt(20); i >= 0; i--) {