Merge branch '5.9.5'

.gitignore

@@ -49,3 +49,4 @@ Thumbs.db
 /ice.iml
 /src/main/ngapp/package-lock.json
 /src/main/ngapp/.angular/
+/data/

pom.xml

@@ -61,7 +61,7 @@
         <dependency>
             <groupId>org.hibernate</groupId>
             <artifactId>hibernate-core</artifactId>
-            <version>5.6.5.Final</version>
+            <version>5.6.7.Final</version>
         </dependency>
         <dependency>
             <groupId>org.hibernate</groupId>
@@ -76,7 +76,7 @@
         <dependency>
             <groupId>org.hibernate.validator</groupId>
             <artifactId>hibernate-validator</artifactId>
-            <version>7.0.1.Final</version>
+            <version>7.0.4.Final</version>
         </dependency>
         <dependency>
             <groupId>javax.el</groupId>
@@ -86,7 +86,7 @@
         <dependency>
             <groupId>org.hibernate</groupId>
             <artifactId>hibernate-c3p0</artifactId>
-            <version>5.6.5.Final</version>
+            <version>5.6.7.Final</version>
         </dependency>
         <dependency>
             <groupId>commons-io</groupId>
@@ -101,12 +101,12 @@
         <dependency>
             <groupId>com.opencsv</groupId>
             <artifactId>opencsv</artifactId>
-            <version>5.5.2</version>
+            <version>5.6</version>
         </dependency>
         <dependency>
             <groupId>ch.qos.logback</groupId>
             <artifactId>logback-classic</artifactId>
-            <version>1.2.10</version>
+            <version>1.2.11</version>
         </dependency>
         <dependency>
             <groupId>org.biojava</groupId>
@@ -150,7 +150,7 @@
         <dependency>
             <groupId>io.undertow</groupId>
             <artifactId>undertow-servlet</artifactId>
-            <version>2.2.15.Final</version>
+            <version>2.2.16.Final</version>
         </dependency>
     </dependencies>
     <build>

src/main/java/org/jbei/ice/lib/account/AccountController.java

@@ -2,9 +2,7 @@
 
 import org.apache.commons.lang3.StringUtils;
 import org.jbei.ice.lib.access.PermissionException;
-import org.jbei.ice.lib.account.authentication.AuthenticationException;
-import org.jbei.ice.lib.account.authentication.IAuthentication;
-import org.jbei.ice.lib.account.authentication.LocalAuthentication;
+import org.jbei.ice.lib.account.authentication.*;
 import org.jbei.ice.lib.common.logging.Logger;
 import org.jbei.ice.lib.dto.ConfigurationKey;
 import org.jbei.ice.lib.dto.group.GroupType;
@@ -33,7 +31,6 @@
 public class AccountController {
 
     private static final String ADMIN_ACCOUNT_EMAIL = "Administrator";
-    private static final String ADMIN_ACCOUNT_PASSWORD = "Administrator";
     private final AccountDAO dao;
     private final GroupDAO groupDAO;
 
@@ -254,29 +251,40 @@ public AccountTransfer createNewAccount(final AccountTransfer info, final boolea
     /**
      * @return new admin account
      */
-    public Account createAdminAccount() {
+    public void createAdminAccount() {
         Account adminAccount = getByEmail(ADMIN_ACCOUNT_EMAIL);
+        String newPassword = AccountUtils.generateRandomToken(48);
+
         if (adminAccount != null) {
-            return adminAccount;
+            Logger.info("Resetting Administrator account password");
+            adminAccount.setPassword(AccountUtils.encryptNewUserPassword(newPassword, adminAccount.getSalt()));
+            adminAccount.setModificationTime(new Date());
+            dao.update(adminAccount);
+        } else {
+            adminAccount = new Account();
+            adminAccount.setEmail(ADMIN_ACCOUNT_EMAIL);
+            adminAccount.setLastName("Administrator");
+            adminAccount.setFirstName("");
+            adminAccount.setInitials("");
+            adminAccount.setInstitution("");
+            adminAccount.setSalt(Utils.generateSaltForUserAccount());
+            adminAccount.setPassword(AccountUtils.encryptNewUserPassword(newPassword, adminAccount.getSalt()));
+            adminAccount.setDescription("Administrator Account");
+
+            adminAccount.setIp("");
+            final Date currentTime = Calendar.getInstance().getTime();
+            adminAccount.setCreationTime(currentTime);
+            adminAccount.setModificationTime(currentTime);
+            adminAccount.setLastLoginTime(currentTime);
+            adminAccount.setType(AccountType.ADMIN);
+            save(adminAccount);
         }
 
-        adminAccount = new Account();
-        adminAccount.setEmail(ADMIN_ACCOUNT_EMAIL);
-        adminAccount.setLastName("Administrator");
-        adminAccount.setFirstName("");
-        adminAccount.setInitials("");
-        adminAccount.setInstitution("");
-        adminAccount.setSalt(Utils.generateSaltForUserAccount());
-        adminAccount.setPassword(AccountUtils.encryptNewUserPassword(ADMIN_ACCOUNT_PASSWORD, adminAccount.getSalt()));
-        adminAccount.setDescription("Administrator Account");
-
-        adminAccount.setIp("");
-        final Date currentTime = Calendar.getInstance().getTime();
-        adminAccount.setCreationTime(currentTime);
-        adminAccount.setModificationTime(currentTime);
-        adminAccount.setLastLoginTime(currentTime);
-        adminAccount.setType(AccountType.ADMIN);
-        return save(adminAccount);
+        // add log information for admin password
+        Logger.info("NEW ADMIN PASSWORD");
+        Logger.info("************************");
+        Logger.info(newPassword);
+        Logger.info("************************");
     }
 
     /**
@@ -351,6 +359,30 @@ public boolean isAdministrator(final String userId) {
         return account != null && account.getType() == AccountType.ADMIN;
     }
 
+    private IAuthentication getAuthentication() {
+        try {
+            String clazz = Utils.getConfigValue(ConfigurationKey.AUTHENTICATION_METHOD);
+            if (StringUtils.isEmpty(clazz))
+                return new LocalAuthentication();
+
+            switch (AuthType.valueOf(clazz.toUpperCase())) {
+                case LDAP:
+                    return new LblLdapAuthentication();
+
+                case OPEN:
+                    return new UserIdAuthentication();
+
+                case DEFAULT:
+                default:
+                    return new LocalAuthentication();
+            }
+        } catch (Exception e) {
+            Logger.error("Exception loading authentication class: ", e);
+            Logger.error("Using default authentication");
+            return new LocalAuthentication();
+        }
+    }
+
     /**
      * Authenticate a user in the database.
      * <p>
@@ -363,7 +395,7 @@ public boolean isAdministrator(final String userId) {
      * @return the account identifier (email) on a successful login, otherwise {@code null}
      */
     protected Account authenticate(final String login, final String password, final String ip) {
-        final IAuthentication authentication = new LocalAuthentication();
+        final IAuthentication authentication = getAuthentication();
         String email;
 
         try {

src/main/java/org/jbei/ice/lib/account/AccountUtils.java

@@ -7,7 +7,9 @@
 
 import javax.crypto.SecretKeyFactory;
 import javax.crypto.spec.PBEKeySpec;
+import javax.xml.bind.DatatypeConverter;
 import java.security.NoSuchAlgorithmException;
+import java.security.SecureRandom;
 import java.security.spec.InvalidKeySpecException;
 import java.security.spec.KeySpec;
 
@@ -18,6 +20,13 @@
  */
 public class AccountUtils {
 
+    public static String generateRandomToken(int byteSize) {
+        SecureRandom random = new SecureRandom();
+        byte[] token = new byte[byteSize];
+        random.nextBytes(token);
+        return DatatypeConverter.printBase64Binary(token);
+    }
+
     /**
      * Return the encrypted version of the given password, using the salt from the settings file.
      *

src/main/java/org/jbei/ice/lib/account/authentication/AuthType.java

@@ -0,0 +1,7 @@
+package org.jbei.ice.lib.account.authentication;
+
+public enum AuthType {
+    LDAP,
+    OPEN,
+    DEFAULT
+}

src/main/java/org/jbei/ice/lib/config/ConfigurationSettings.java

@@ -170,11 +170,10 @@ public Setting autoUpdateSetting(String userId, Setting setting) {
     public void initPropertyValues() {
         for (ConfigurationKey key : ConfigurationKey.values()) {
             Configuration config = dao.get(key);
-            if (config != null || key.getDefaultValue().isEmpty())
-                continue;
-
-            Logger.info("Setting value for " + key.name() + " to " + key.getDefaultValue());
-            setPropertyValue(key, key.getDefaultValue());
+            if (config == null || (config.getValue().isBlank() && !key.getDefaultValue().isEmpty())) {
+                Logger.info("Setting value for " + key.name() + " to " + key.getDefaultValue());
+                setPropertyValue(key, key.getDefaultValue());
+            }
         }
     }
 

src/main/java/org/jbei/ice/lib/config/SiteSettings.java

@@ -9,7 +9,7 @@
  */
 public class SiteSettings implements IDataTransferModel {
 
-    private String version = "5.9.4";
+    private String version = "5.9.5";
     private String assetName;
     private boolean hasLogo;
     private boolean hasLoginMessage;

src/main/java/org/jbei/ice/lib/dto/ConfigurationKey.java

@@ -11,7 +11,7 @@
  */
 public enum ConfigurationKey implements IDataTransferModel {
 
-    APPLICATION_VERSION("5.9.4"),
+    APPLICATION_VERSION("5.9.5"),
     TEMPORARY_DIRECTORY("/tmp"),
     DATA_DIRECTORY("data"),
 
@@ -37,7 +37,8 @@ public enum ConfigurationKey implements IDataTransferModel {
     WEB_OF_REGISTRIES_MASTER("registry.jbei.org"),
 
     // sample request config
-    SAMPLE_CREATE_APPROVAL_MESSAGE("");
+    SAMPLE_CREATE_APPROVAL_MESSAGE(""),
+    AUTHENTICATION_METHOD("DEFAULT");
 
     private String defaultValue;
 

src/main/webapp/scripts/admin/adminController.js

@@ -49,6 +49,11 @@ angular.module('ice.admin.controller', [])
             $scope.emailConfig.type = type;
         };
 
+        $scope.submitAuthSetting = function (val) {
+            $scope.submitSetting({key: 'AUTHENTICATION_METHOD', value: val});
+            $scope.authentication.value = val;
+        };
+
         $scope.saveEmailConfig = function () {
             $scope.submitSetting({key: "EMAILER", value: $scope.emailConfig.type});
 
@@ -66,6 +71,7 @@ angular.module('ice.admin.controller', [])
         $scope.getSetting = function () {
             $scope.generalSettings = [];
             $scope.emailSettings = [];
+            $scope.authentication = undefined;
             $scope.sampleRequestSettings = [];
             $scope.emailConfig = {type: "", smtp: "", pass: "", edit: false, showEdit: false, showPass: false};
 
@@ -107,6 +113,11 @@ angular.module('ice.admin.controller', [])
                                 break;
                         }
                     }
+
+                    if (AdminSettings.getAuthenticationOption().indexOf(setting.key) !== -1) {
+                        console.log(setting);
+                        $scope.authentication = setting;
+                    }
                 });
             });
         };
@@ -723,4 +734,4 @@ angular.module('ice.admin.controller', [])
 
             return false;
         }
-    });
+    });

src/main/webapp/scripts/admin/adminService.js

@@ -44,6 +44,8 @@ adminService.factory('AdminSettings', function () {
         //'ADD_TO_CART_DEFAULT_SET_TO_LOCAL'
     ];
 
+    const authenticationKey = 'AUTHENTICATION_METHOD';
+
     const menuOptions = [
         {
             url: 'scripts/admin/settings.html',
@@ -142,6 +144,10 @@ adminService.factory('AdminSettings', function () {
 
         getMenuOptions: function () {
             return menuOptions;
+        },
+
+        getAuthenticationOption: function () {
+            return authenticationKey;
         }
     }
 });

src/main/webapp/scripts/admin/settings.html

@@ -46,7 +46,7 @@
                 <!--for non boolean fields-->
                 <div class="col-md-9" ng-if="!setting.isBoolean" ng-mouseover="partIdEdit=true"
                      ng-mouseout="partIdEdit=false">
-                    <div data-ng-if="!setting.editMode">
+                    <div ng-if="!setting.editMode">
                         <span ng-if="setting.value.trim() !==''">{{setting.value.trim()}}</span>
                         <i class='opacity_4' ng-if="!setting.value">
                             <span ng-if="!setting.canAutoInstall || !autoInstalling">No value entered</span>
@@ -66,12 +66,12 @@
                         </span>
                     </div>
 
-                    <div class="input-group" data-ng-if="setting.editMode">
+                    <div class="input-group" ng-if="setting.editMode">
                         <form ng-submit="submitSetting(setting)">
                             <input type="text" ng-model="setting.value" class="input_box_group" maxlength="125"
                                    style="width: 205px;">
                         </form>
-        <span class="input-group-addon" data-ng-click="setting.editMode=false" style="padding:3px; background-color:
+                        <span class="input-group-addon" ng-click="setting.editMode=false" style="padding:3px; background-color:
         #f1f1f1;width: 19px"><i class="fa fa-times delete_icon"></i></span>
                     </div>
                 </div>
@@ -141,25 +141,52 @@
                 <!--for non boolean fields-->
                 <div class="col-md-9" ng-if="!setting.isBoolean" ng-mouseover="partIdEdit=true"
                      ng-mouseout="partIdEdit=false">
-                    <div data-ng-if="!setting.editMode"><span ng-if="setting.value&&setting.value.trim()!=''">{{setting.value}}</span>
+                    <div ng-if="!setting.editMode"><span
+                            ng-if="setting.value&&setting.value.trim()!=''">{{setting.value}}</span>
                         <i class='opacity_4' ng-if="!setting.value">No value entered</i><span
                                 ng-click="setting.editMode=true">
                          <i ng-show="partIdEdit" class="fa fa-pencil edit_icon"
                             style="margin-left: 5px; font-size: 14px;"></i></span>
                     </div>
 
-                    <div class="input-group" data-ng-if="setting.editMode">
+                    <div class="input-group" ng-if="setting.editMode">
                         <form ng-submit="submitSetting(setting)">
                             <input type="text" ng-model="setting.value" class="input_box_group" maxlength="125"
                                    style="width: 205px;">
                         </form>
-        <span class="input-group-addon" data-ng-click="setting.editMode=false" style="padding:3px; background-color:
+                        <span class="input-group-addon" ng-click="setting.editMode=false" style="padding:3px; background-color:
      #f1f1f1;width: 19px"><i class="fa fa-times delete_icon"></i></span>
                     </div>
                 </div>
             </div>
         </uib-tab>
 
+        <uib-tab>
+            <uib-tab-heading><i class="fa fa-key"></i> Authentication</uib-tab-heading>
+            <div class="pad_top">
+                <div class="col-md-4 entryLabel text-right">
+                    Authentication Method
+                </div>
+
+                <div class="col-md-8">
+                    <div class="btn-group" uib-dropdown>
+                        <button type="button" class="btn btn-sm btn-default" uib-dropdown-toggle>
+                            {{authentication.value}} <i class="fa fa-fw fa-fw fa-caret-down"></i>
+                        </button>
+
+                        <ul class="dropdown-menu" uib-dropdown-menu role="menu">
+                            <li role="menuitem" ng-click="submitAuthSetting('DEFAULT')"
+                                ng-if="authentication.value !== 'DEFAULT'"><a href="#">DEFAULT</a></li>
+                            <li role="menuitem" ng-click="submitAuthSetting('OPEN')"
+                                ng-if="authentication.value !== 'OPEN'"><a href="#">OPEN</a></li>
+                            <li role="menuitem" ng-click="submitAuthSetting('LDAP')"
+                                ng-if="authentication.value !== 'LDAP'"><a href="#">LDAP</a></li>
+                        </ul>
+                    </div>
+                </div>
+            </div>
+        </uib-tab>
+
     </uib-tabset>
 </div>
 

src/main/webapp/views/footer.html

@@ -11,7 +11,7 @@
     </div>
     <div class="text-right" style="white-space: nowrap;">
         &copy;&nbsp;<a href="https://github.com/JBEI/ice">JBEI ICE Registry</a> <span
-            class="label label-primary">5.9.4</span><br>
+            class="label label-primary">5.9.5</span><br>
         All rights reserved. <br>
         <a href="https://github.com/JBEI/ice/issues/new">Submit an Issue</a>&nbsp; <span class="text-muted">|</span>
         &nbsp;<a href="http://ice.jbei.org/">Help</a>