Source formatting

src/main/java/net/tanesha/recaptcha/ReCaptchaImpl.java

@@ -26,38 +26,42 @@ public class ReCaptchaImpl implements ReCaptcha {
 
 	public static final String PROPERTY_THEME = "theme";
 	public static final String PROPERTY_TABINDEX = "tabindex";
-	
+
 	public static final String HTTP_SERVER = "http://www.google.com/recaptcha/api";
 	public static final String HTTPS_SERVER = "https://www.google.com/recaptcha/api";
 	// HTTPS Verify url
 	public static final String VERIFY_URL = "https://www.google.com/recaptcha/api/verify";
-	
+
 	private String privateKey;
 	private String publicKey;
 	private String recaptchaServer = HTTP_SERVER;
 	private boolean includeNoscript = false;
 	private HttpLoader httpLoader = new SimpleHttpLoader();
-	
+
 	public void setPrivateKey(String privateKey) {
 		this.privateKey = privateKey;
 	}
+
 	public void setPublicKey(String publicKey) {
 		this.publicKey = publicKey;
 	}
+
 	public void setRecaptchaServer(String recaptchaServer) {
 		this.recaptchaServer = recaptchaServer;
 	}
+
 	public void setIncludeNoscript(boolean includeNoscript) {
 		this.includeNoscript = includeNoscript;
 	}
+
 	public void setHttpLoader(HttpLoader httpLoader) {
-		this.httpLoader  = httpLoader;
+		this.httpLoader = httpLoader;
 	}
 
 	public ReCaptchaResponse checkAnswer(String remoteAddr, String challenge, String response) {
 
-		String postParameters = "privatekey=" + URLEncoder.encode(privateKey) + "&remoteip=" + URLEncoder.encode(remoteAddr) +
-			"&challenge=" + URLEncoder.encode(challenge) + "&response=" + URLEncoder.encode(response);
+		String postParameters = "privatekey=" + URLEncoder.encode(privateKey) + "&remoteip=" + URLEncoder.encode(remoteAddr) + "&challenge="
+				+ URLEncoder.encode(challenge) + "&response=" + URLEncoder.encode(response);
 
 		String message = httpLoader.httpPost(VERIFY_URL, postParameters);
 
@@ -77,7 +81,7 @@ public class ReCaptchaImpl implements ReCaptcha {
 			else
 				errorMessage = "recaptcha4j-missing-error-message";
 		}
-		
+
 		return new ReCaptchaResponse(valid, errorMessage);
 	}
 
@@ -90,17 +94,16 @@ public class ReCaptchaImpl implements ReCaptcha {
 		message += "<script type=\"text/javascript\" src=\"" + recaptchaServer + "/challenge?k=" + publicKey + errorPart + "\"></script>\r\n";
 
 		if (includeNoscript) {
-			String noscript = "<noscript>\r\n" + 
-					"	<iframe src=\""+recaptchaServer+"/noscript?k="+publicKey + errorPart + "\" height=\"300\" width=\"500\" frameborder=\"0\"></iframe><br>\r\n" + 
-					"	<textarea name=\"recaptcha_challenge_field\" rows=\"3\" cols=\"40\"></textarea>\r\n" + 
-					"	<input type=\"hidden\" name=\"recaptcha_response_field\" value=\"manual_challenge\">\r\n" + 
-					"</noscript>";
+			String noscript = "<noscript>\r\n" + "	<iframe src=\"" + recaptchaServer + "/noscript?k=" + publicKey + errorPart
+					+ "\" height=\"300\" width=\"500\" frameborder=\"0\"></iframe><br>\r\n"
+					+ "	<textarea name=\"recaptcha_challenge_field\" rows=\"3\" cols=\"40\"></textarea>\r\n"
+					+ "	<input type=\"hidden\" name=\"recaptcha_response_field\" value=\"manual_challenge\">\r\n" + "</noscript>";
 			message += noscript;
 		}
-		
+
 		return message;
 	}
-	
+
 	public String createRecaptchaHtml(String errorMessage, String theme, Integer tabindex) {
 
 		Properties options = new Properties();
@@ -127,19 +130,17 @@ public class ReCaptchaImpl implements ReCaptcha {
 			return "";
 		}
 
-		String jsOptions =
-			"<script type=\"text/javascript\">\r\n" + 
-			"var RecaptchaOptions = {";
-			
-		for (Enumeration e = properties.keys(); e.hasMoreElements(); ) {
+		String jsOptions = "<script type=\"text/javascript\">\r\n" + "var RecaptchaOptions = {";
+
+		for (Enumeration e = properties.keys(); e.hasMoreElements();) {
 			String property = (String) e.nextElement();
-			
-			jsOptions += property + ":'" + properties.getProperty(property)+"'";
-			
+
+			jsOptions += property + ":'" + properties.getProperty(property) + "'";
+
 			if (e.hasMoreElements()) {
 				jsOptions += ",";
 			}
-			
+
 		}
 
 		jsOptions += "};\r\n</script>\r\n";

src/main/java/org/genesys2/server/lucene/genesys/FaoInstituteBridge.java

@@ -49,7 +49,7 @@ public class FaoInstituteBridge implements FieldBridge {
 
 		if (institute.getAccessionCount() > 0)
 			field.setBoost(2 * luceneOptions.getBoost());
-		
+
 		document.add(field);
 	}
 

src/main/java/org/genesys2/server/model/UserRole.java

@@ -18,7 +18,7 @@ package org.genesys2.server.model;
 
 public enum UserRole {
 	USER("User"), ADMINISTRATOR("Administrator"), ORGANIZATION_ADMINISTRATOR("Organization Administrator"), NETWORK_ADMINISTRATOR("Network Administrator"), VALIDATEDUSER(
-			"Validated user"),VETTEDUSER("Vetted user");
+			"Validated user"), VETTEDUSER("Vetted user");
 
 	String label;
 

src/main/java/org/genesys2/server/model/genesys/AccessionTrait.java

@@ -26,7 +26,7 @@ import javax.persistence.UniqueConstraint;
 import org.genesys2.server.model.BusinessModel;
 
 @Entity
-@Table(name = "accessiontrait", uniqueConstraints = { @UniqueConstraint(name="UQ_accessiontrait_all", columnNames = { "metadataId", "accessionId", "methodId" }) })
+@Table(name = "accessiontrait", uniqueConstraints = { @UniqueConstraint(name = "UQ_accessiontrait_all", columnNames = { "metadataId", "accessionId", "methodId" }) })
 public class AccessionTrait extends BusinessModel {
 	private static final long serialVersionUID = -240056837800843686L;
 

src/main/java/org/genesys2/server/model/genesys/Metadata.java

@@ -173,7 +173,6 @@ public class Metadata extends VersionedAuditedModel implements AclAwareModel, Ge
 		this.uuid = uuid;
 	}
 
-	
 	@Override
 	public String toString() {
 		return MessageFormat.format("Metadata id={0,number,#} inst={2} title={1}", id, title, instituteCode);

src/main/java/org/genesys2/server/model/genesys/MetadataAccession.java

@@ -25,7 +25,7 @@ import javax.persistence.UniqueConstraint;
 import org.genesys2.server.model.BusinessModel;
 
 @Entity
-@Table(name = "metadataaccession", uniqueConstraints = { @UniqueConstraint(name="UI_metadataaccession_all", columnNames = { "metadataId", "accessionId" }) })
+@Table(name = "metadataaccession", uniqueConstraints = { @UniqueConstraint(name = "UI_metadataaccession_all", columnNames = { "metadataId", "accessionId" }) })
 public class MetadataAccession extends BusinessModel {
 	private static final long serialVersionUID = -240056837800843686L;
 

src/main/java/org/genesys2/server/model/impl/User.java

@@ -217,7 +217,7 @@ public class User extends BusinessModel {
 		// We don't support password expiration
 		return false;
 	}
-	
+
 	public boolean hasRole(String roleName) {
 		for (UserRole userRole : getRoles()) {
 			if (userRole.getName().equalsIgnoreCase(roleName)) {

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

@@ -41,7 +41,6 @@ public interface AccessionTraitRepository extends JpaRepository<AccessionTrait,
 
 	List<AccessionTrait> findByMetadataIdAndAccession(Long id, Accession accession);
 
-
 	@Query("select count(id) from AccessionTrait at where at.metadataId = ?1 and at.accession = ?2")
 	long countByMetadataAndAccessionId(long metadataId, Accession accession);
 

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

@@ -277,7 +277,7 @@ public class GenesysLowlevelRepositoryImpl implements GenesysLowlevelRepository
 			}
 		}, rowCallbackHandler);
 	}
-	
+
 	@Override
 	public void listMetadataAccessions(final long id, RowCallbackHandler rowCallbackHandler) {
 		jdbcTemplate.query(new PreparedStatementCreator() {
@@ -292,14 +292,13 @@ public class GenesysLowlevelRepositoryImpl implements GenesysLowlevelRepository
 			}
 		}, rowCallbackHandler);
 	}
-	
+
 	@Override
 	public void listAccessionsAccenames(RowCallbackHandler rowCallbackHandler) {
 		jdbcTemplate.query(new PreparedStatementCreator() {
 			@Override
 			public PreparedStatement createPreparedStatement(Connection con) throws SQLException {
-				PreparedStatement stmt = con
-						.prepareStatement("select accessionId, names, otherIds from accessionname");
+				PreparedStatement stmt = con.prepareStatement("select accessionId, names, otherIds from accessionname");
 				// Set mysql JConnector to stream results
 				stmt.setFetchSize(Integer.MIN_VALUE);
 				return stmt;

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

@@ -341,16 +341,17 @@ public class TraitValueRepositoryImpl implements TraitValueRepository {
 		return this.jdbcTemplate.queryForObject(String.format("SELECT COUNT(*) FROM `%s` WHERE metadataId=? AND accessionId=?", methodId), Integer.class,
 				metadataId, accessionId);
 	}
-	
+
 	@Override
 	public Map<String, Long> getStatistics(Method method) {
-		final HashMap<String, Long> stats=new HashMap<String, Long>();
-		this.jdbcTemplate.query(MessageFormat.format("SELECT `{0}`, COUNT(*) FROM `{1,number,#}` GROUP BY `{0}`", method.getFieldName(), method.getId()), new RowCallbackHandler() {
-			@Override
-			public void processRow(ResultSet rs) throws SQLException {
-				stats.put(rs.getString(1), rs.getLong(2));
-			}
-		});
+		final HashMap<String, Long> stats = new HashMap<String, Long>();
+		this.jdbcTemplate.query(MessageFormat.format("SELECT `{0}`, COUNT(*) FROM `{1,number,#}` GROUP BY `{0}`", method.getFieldName(), method.getId()),
+				new RowCallbackHandler() {
+					@Override
+					public void processRow(ResultSet rs) throws SQLException {
+						stats.put(rs.getString(1), rs.getLong(2));
+					}
+				});
 		return stats;
 	}
 }

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

@@ -16,6 +16,9 @@
 
 package org.genesys2.server.service;
 
+import java.util.List;
+import java.util.Map;
+
 import org.genesys2.server.model.AclAwareModel;
 import org.genesys2.server.model.acl.AclEntry;
 import org.genesys2.server.model.acl.AclObjectIdentity;
@@ -23,48 +26,45 @@ import org.genesys2.server.model.acl.AclSid;
 import org.genesys2.server.security.AuthUserDetails;
 import org.springframework.security.acls.model.Permission;
 
-import java.util.List;
-import java.util.Map;
-
 public interface AclService {
 
-    void addCreatorPermissions(AclAwareModel target);
+	void addCreatorPermissions(AclAwareModel target);
 
-    /**
+	/**
 	 * List ObjectIdentities of specified class for user with specified
 	 * permission
-     *
-     * @param clazz
-     * @param authUser
-     * @return
-     */
-    List<Long> listIdentitiesForSid(Class<? extends AclAwareModel> clazz, AuthUserDetails authUser, Permission permission);
+	 * 
+	 * @param clazz
+	 * @param authUser
+	 * @return
+	 */
+	List<Long> listIdentitiesForSid(Class<? extends AclAwareModel> clazz, AuthUserDetails authUser, Permission permission);
 
-    AclObjectIdentity getObjectIdentity(long id);
+	AclObjectIdentity getObjectIdentity(long id);
 
-    AclObjectIdentity getObjectIdentity(String clazz, long id);
+	AclObjectIdentity getObjectIdentity(String clazz, long id);
 
-    AclObjectIdentity ensureObjectIdentity(String clazz, long id);
+	AclObjectIdentity ensureObjectIdentity(String clazz, long id);
 
-    AclObjectIdentity getObjectIdentity(AclAwareModel entity);
+	AclObjectIdentity getObjectIdentity(AclAwareModel entity);
 
-    List<AclEntry> getAclEntries(AclObjectIdentity objectIdentity);
+	List<AclEntry> getAclEntries(AclObjectIdentity objectIdentity);
 
-    List<AclEntry> getAclEntries(AclAwareModel entity);
+	List<AclEntry> getAclEntries(AclAwareModel entity);
 
-    Permission[] getAvailablePermissions(String className);
+	Permission[] getAvailablePermissions(String className);
 
-    List<AclSid> getSids(AclAwareModel entity);
+	List<AclSid> getSids(AclAwareModel entity);
 
-    List<AclSid> getSids(long id, String className);
+	List<AclSid> getSids(long id, String className);
 
 	Map<String, Map<Integer, Boolean>> getPermissions(AclAwareModel entity);
 
 	Map<String, Map<Integer, Boolean>> getPermissions(long id, String className);
 
-    boolean addPermissions(long objectIdIdentity, String className, String uuid, boolean principal, Map<Integer, Boolean> permissions);
+	boolean addPermissions(long objectIdIdentity, String className, String uuid, boolean principal, Map<Integer, Boolean> permissions);
 
-    void updatePermission(AclObjectIdentity entity, String sid, Map<Integer, Boolean> permissionMap);
+	void updatePermission(AclObjectIdentity entity, String sid, Map<Integer, Boolean> permissionMap);
 
-    List<AclSid> getAllSids();
+	List<AclSid> getAllSids();
 }

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

@@ -25,8 +25,7 @@ public interface EMailVerificationService {
 	void sendPasswordResetEmail(User user);
 
 	void cancelValidation(String tokenUuid);
-	
-	
+
 	boolean validateEMail(String tokenUuid, String key);
 
 	boolean changePassword(String tokenUuid, String key, String password);

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

@@ -28,7 +28,8 @@ import com.fasterxml.jackson.databind.JsonNode;
 
 public interface GenesysFilterService {
 
-	String[] DEFAULT_FILTERS = { "crop", "genus", "taxon", "origin", "lat", "lon", "organization", "institute", "accenumb", "inSvalbard", "mls", "inTrust", "available" };
+	String[] DEFAULT_FILTERS = { "crop", "genus", "taxon", "origin", "lat", "lon", "organization", "institute", "accenumb", "inSvalbard", "mls", "inTrust",
+			"available" };
 
 	Page<Accession> listAccessions(JsonNode jsonTree, Pageable pageable);
 

src/main/java/org/genesys2/server/service/OAuth2ClientDetailsService.java

@@ -16,17 +16,17 @@
 
 package org.genesys2.server.service;
 
+import java.util.Collection;
+
 import org.genesys2.server.model.oauth.OAuthAccessToken;
 import org.springframework.security.oauth2.provider.ClientDetailsService;
 import org.springframework.security.oauth2.provider.ClientRegistrationService;
 
-import java.util.Collection;
-
 public interface OAuth2ClientDetailsService extends ClientDetailsService, ClientRegistrationService {
 
 	boolean exists(String clientId);
 
-    Collection<OAuthAccessToken> findTokensByClientId(String clientId);
+	Collection<OAuthAccessToken> findTokensByClientId(String clientId);
 
-    Collection<OAuthAccessToken> findTokensByUserUuid(String uuid);
+	Collection<OAuthAccessToken> findTokensByUserUuid(String uuid);
 }

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

@@ -20,9 +20,8 @@ import java.util.Set;
 
 import org.genesys2.server.service.impl.EasySMTAConnector.EasySMTAUserData;
 
-
 public interface RequestService {
 
 	void sendRequest(EasySMTAUserData pid, Set<Long> accessionIds);
-	
+
 }

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

@@ -24,7 +24,7 @@ import org.springframework.data.domain.Pageable;
 
 public interface SearchService {
 
-	Page<?> search(String searchQuery, String[] fields, Pageable pageable, Class<?> ... targetClass) throws SearchException;
+	Page<?> search(String searchQuery, String[] fields, Pageable pageable, Class<?>... targetClass) throws SearchException;
 
 	<T> List<T> autocomplete(String searchQuery, Class<T> clazz);
 

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

@@ -16,6 +16,8 @@
 
 package org.genesys2.server.service;
 
+import java.util.List;
+
 import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.server.model.impl.Team;
 import org.genesys2.server.model.impl.User;
@@ -24,8 +26,6 @@ import org.springframework.data.domain.Pageable;
 import org.springframework.security.access.prepost.PostAuthorize;
 import org.springframework.security.access.prepost.PreAuthorize;
 
-import java.util.List;
-
 public interface TeamService {
 
 	/**
@@ -100,6 +100,6 @@ public interface TeamService {
 	@PreAuthorize("hasRole('ADMINISTRATOR') or hasPermission(#team, 'READ')")
 	List<User> getMembers(Team team);
 
-    @PreAuthorize("hasRole('ADMINISTRATOR') or hasPermission(#team, 'WRITE')")
-    void updateTeamInformation(String teamUuid, String teamName);
+	@PreAuthorize("hasRole('ADMINISTRATOR') or hasPermission(#team, 'WRITE')")
+	void updateTeamInformation(String teamUuid, String teamName);
 }

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

@@ -33,7 +33,7 @@ public interface UserService {
 	@PreAuthorize("hasRole('ADMINISTRATOR') || hasPermission(#user, 'WRITE')")
 	void updateUser(User user) throws UserException;
 
-//	@PreAuthorize("hasRole('ADMINISTRATOR') || principal.user.id == #userId")
+	// @PreAuthorize("hasRole('ADMINISTRATOR') || principal.user.id == #userId")
 	void updatePassword(long userId, String rawPassword) throws UserException;
 
 	@PreAuthorize("hasRole('ADMINISTRATOR') || hasPermission(#user, 'WRITE')")
@@ -72,5 +72,5 @@ public interface UserService {
 
 	void userEmailValidated(String uuid);
 
-    void addVettedUserRole(String uuid);
+	void addVettedUserRole(String uuid);
 }

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

@@ -16,7 +16,12 @@
 
 package org.genesys2.server.service.impl;
 
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
 import net.sf.ehcache.CacheManager;
+
 import org.genesys2.server.aspect.AsAdminAspect;
 import org.genesys2.server.model.AclAwareModel;
 import org.genesys2.server.model.acl.AclClass;
@@ -40,10 +45,6 @@ import org.springframework.security.acls.model.Permission;
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Transactional;
 
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
 /**
  * TODO Add support for cleaning up after objects are removed
  */

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

@@ -64,8 +64,7 @@ public class ContentServiceImpl implements ContentService {
 
 	@Autowired
 	private VelocityEngine velocityEngine;
-	
-	
+
 	@Override
 	public Locale getDefaultLocale() {
 		return Locale.getDefault();