Merge branch 'hotfix-4.1.2'

pom.xml

@@ -4,7 +4,7 @@
     <groupId>org.jbei</groupId>
     <artifactId>ice</artifactId>
     <packaging>war</packaging>
-    <version>4.1.1</version>
+    <version>4.1.2</version>
     <name>ice</name>
     <description>Inventory of Composable Elements (ICE) for Synthetic Biology</description>
     <repositories>

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

@@ -329,22 +329,6 @@ public boolean isAdministrator(String userId) {
         return account != null && account.getType() == AccountType.ADMIN;
     }
 
-    /**
-     * Check if the given password is valid for the account.
-     *
-     * @param account
-     * @param password
-     * @return True if correct password.
-     * @throws ControllerException
-     */
-    public boolean isValidPassword(Account account, String password) throws ControllerException {
-        if (account == null) {
-            throw new ControllerException("Failed to verify password for null Account!");
-        }
-
-        return account.getPassword().equals(AccountUtils.encryptNewUserPassword(password, account.getSalt()));
-    }
-
     /**
      * Authenticate a user in the database.
      * <p/>

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

@@ -1,14 +1,14 @@
 package org.jbei.ice.lib.account.authentication;
 
-import org.jbei.ice.ControllerException;
 import org.jbei.ice.lib.account.AccountController;
 import org.jbei.ice.lib.account.AccountUtils;
 import org.jbei.ice.lib.account.model.Account;
 import org.jbei.ice.lib.common.logging.Logger;
 import org.jbei.ice.lib.dao.DAOFactory;
+import org.jbei.ice.lib.dto.ConfigurationKey;
 
 /**
- * Backend for authentication using the database. This is the default backend.
+ * Default ICE authentication scheme
  *
  * @author Hector Plahar
  */
@@ -22,46 +22,49 @@ public String authenticates(String userId, String password) throws Authenticatio
         if (userId == null || password == null)
             throw new AuthenticationException("Invalid username and password");
 
-        Account account;
         AccountController controller = new AccountController();
-
-        try {
-            account = controller.getByEmail(userId);
-            if (account == null || !isValidPassword(account, password))
-                return null;
-            return account.getEmail();
-        } catch (ControllerException e) {
-            throw new AuthenticationException("Exception validating credentials", e);
-        }
+        Account account = controller.getByEmail(userId);
+        if (account == null || !isValidPassword(account, password))
+            return null;
+        return account.getEmail();
     }
 
     /**
-     * Check if the given password is valid for the account.
+     * Check if the given password is valid for the account. There are multiple checks for backward compatibility
+     * reasons
      *
-     * @param account
-     * @param password
-     * @return True if correct password.
-     * @throws ControllerException
+     * @param account  user account whose password is being checked
+     * @param password user entered password being checked for validation
+     * @return True if entered password matches one of encrypted schemes, false otherwise.
      */
-    protected boolean isValidPassword(Account account, String password) throws ControllerException {
+    protected boolean isValidPassword(Account account, String password) {
         if (account == null) {
-            throw new ControllerException("Failed to verify password for null Account!");
+            return false;
         }
+
+        // first check using the stronger encryption scheme
         boolean valid = account.getPassword().equals(AccountUtils.encryptNewUserPassword(password, account.getSalt()));
         if (valid)
             return valid;
-        String encrypted = AccountUtils.encryptPassword(password, account.getSalt());
-        valid = account.getPassword().equals(encrypted);
-        if (valid) {
-            // update
-            account.setPassword(encrypted);
-            try {
-                DAOFactory.getAccountDAO().update(account);
-            } catch (Exception e) {
-                Logger.error(e);
-            }
-            return true;
+
+        // invalid check for deprecated salt using older encryption scheme
+        String salt = ConfigurationKey.SECRET_KEY.getDefaultValue();
+        valid = account.getPassword().equals(AccountUtils.encryptPassword(password, salt));
+        if (!valid) {
+            // check old encryption scheme using user salt
+            valid = account.getPassword().equals(AccountUtils.encryptPassword(password, account.getSalt()));
+            if (!valid)
+                return false;
+        }
+
+        // at this stage then password is valid, upgrade to new version
+        String newEncrypted = AccountUtils.encryptNewUserPassword(password, account.getSalt());
+        account.setPassword(newEncrypted);
+        try {
+            DAOFactory.getAccountDAO().update(account);
+        } catch (Exception e) {
+            Logger.error(e);
         }
-        return false;
+        return true;
     }
 }

src/main/java/org/jbei/ice/lib/entry/EntryController.java

@@ -611,6 +611,14 @@ public PartData retrieveEntryDetails(String userId, String id) {
         return retrieveEntryDetails(userId, entry);
     }
 
+    /**
+     * Retrieves and sets the default values for the entry. Some of these values (e.g. PI, and Funding Source)
+     * are set by individual users as part of their personal preferences
+     *
+     * @param userId Unique identifier for user requesting the values.
+     * @param type   entry type
+     * @return PartData object with the retrieve part defaults
+     */
     public PartData getPartDefaults(String userId, EntryType type) {
         PartData partData = new PartData(type);
         PreferencesController preferencesController = new PreferencesController();
@@ -634,6 +642,7 @@ public PartData getPartDefaults(String userId, EntryType type) {
             partData.setFundingSource(value);
         }
 
+        // owner and creator details
         Account account = accountController.getByEmail(userId);
         if (account != null) {
             partData.setOwner(account.getFullName());
@@ -642,7 +651,8 @@ public PartData getPartDefaults(String userId, EntryType type) {
             partData.setCreatorEmail(partData.getOwnerEmail());
         }
 
-        return partData;
+        // set the entry type defaults
+        return EntryUtil.setPartDefaults(partData);
     }
 
     protected PartData retrieveEntryDetails(String userId, Entry entry) {

src/main/java/org/jbei/ice/lib/entry/EntryUtil.java

@@ -10,6 +10,7 @@
 import org.jbei.ice.lib.dto.bulkupload.EntryField;
 import org.jbei.ice.lib.dto.entry.EntryType;
 import org.jbei.ice.lib.dto.entry.PartData;
+import org.jbei.ice.lib.dto.entry.PlasmidData;
 import org.jbei.ice.lib.entry.model.ArabidopsisSeed;
 import org.jbei.ice.lib.entry.model.Entry;
 import org.jbei.ice.lib.entry.model.Part;
@@ -257,4 +258,19 @@ public static boolean validates(PartData partData) {
 
         return true;
     }
+
+    public static PartData setPartDefaults(PartData partData) {
+        switch (partData.getType()) {
+            case PLASMID:
+                if (partData.getPlasmidData() == null) {
+                    PlasmidData plasmidData = new PlasmidData();
+                    plasmidData.setCircular(true);
+                    partData.setPlasmidData(plasmidData);
+                } else
+                    partData.getPlasmidData().setCircular(true);
+                break;
+        }
+
+        return partData;
+    }
 }

src/main/java/org/jbei/ice/lib/entry/model/Entry.java

@@ -243,9 +243,7 @@ public class Entry implements IDataModel {
     private Sequence sequence;
 
     public Entry() {
-//        setStatus("Complete");
         longDescriptionType = "text";
-//        setBioSafetyLevel(1);
     }
 
     public long getId() {

src/main/java/org/jbei/ice/lib/net/WoRController.java

@@ -47,19 +47,14 @@ public boolean isWebEnabled() {
      * @return true if partner identified by the id is determined to be a valid
      *         web of registries partner for part transfer based on the status and authentication key
      */
-    public boolean isValidWebPartner(String partnerId, String apiKey) throws ControllerException {
-        try {
-            RemotePartner partner = dao.getByUrl(partnerId);
-            return partner != null && partner.getPartnerStatus() == RemotePartnerStatus.APPROVED
-                    && apiKey != null && apiKey.equalsIgnoreCase(partner.getAuthenticationToken());
-        } catch (DAOException de) {
-            throw new ControllerException(de);
-        }
+    public boolean isValidWebPartner(String partnerId, String apiKey) {
+        RemotePartner partner = dao.getByUrl(partnerId);
+        return partner != null && partner.getPartnerStatus() == RemotePartnerStatus.APPROVED
+                && apiKey != null && apiKey.equalsIgnoreCase(partner.getAuthenticationToken());
     }
 
     public WebOfRegistries getRegistryPartners(boolean approvedOnly) {
-        String value = new ConfigurationController().getPropertyValue(
-                ConfigurationKey.JOIN_WEB_OF_REGISTRIES);
+        String value = new ConfigurationController().getPropertyValue(ConfigurationKey.JOIN_WEB_OF_REGISTRIES);
         WebOfRegistries webOfRegistries = new WebOfRegistries();
         webOfRegistries.setWebEnabled("yes".equalsIgnoreCase(value) || "true".equalsIgnoreCase(value));
 
@@ -170,6 +165,14 @@ public RegistryPartner addWebPartner(String userId, RegistryPartner partner) {
         }
     }
 
+    /**
+     * Adds a web of registries partner using the specificd url and name in the parameter
+     * if another partner does not already exist with the same url
+     *
+     * @param url  url for ICE instance
+     * @param name display name for remote ICE instance
+     * @return created partner
+     */
     private RegistryPartner addRegistryPartner(String url, String name) {
         RemotePartner partner = dao.getByUrl(url);
 

src/main/webapp/css/ice.css

@@ -47,6 +47,14 @@ html, body {
     color: #CC3333;
 }
 
+.orange {
+    color: orange;
+}
+
+.dark_blue {
+    color: #285e8e;
+}
+
 .font-95em {
     font-size: 0.95em;
 }

src/main/webapp/index.html

@@ -125,7 +125,7 @@
                                             <a href="http://public-registry.jbei.org/manual">Help</a>
                                         </td>
                                         <td align="left" style="vertical-align: top;">
-                                            <div ng-if="appVersion">&nbsp; | &nbsp; v{{appVersion}}</div>
+                                            <div ng-if="appVersion">&nbsp; | &nbsp; v4.1.2</div>
                                         </td>
                                     </tr>
                                 </table>

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

@@ -1,4 +1,4 @@
-<div class="container-fluid">
+<div class="container-fluid" ng-controller="AdminController">
     <div class="row entry_general_header_td" style="height: 60px">
 
         <div class="col-md-12">

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

@@ -34,9 +34,8 @@ angular.module('ice.admin.controller', [])
             // retrieve site wide settings
             var settings = Settings(sessionId);
             settings.get(function (result) {
-                $rootScope.settings = result;
 
-                angular.forEach($rootScope.settings, function (setting) {
+                angular.forEach(result, function (setting) {
                     if (generalSettingKeys.indexOf(setting.key) != -1) {
                         $scope.generalSettings.push({'key':(setting.key.replace(/_/g, ' ')).toLowerCase(), 'value':setting.value, 'editMode':false});
                     }

src/main/webapp/scripts/controllers.js

@@ -711,20 +711,6 @@ iceControllers.controller('CollectionController', function ($scope, $state, $fil
 
     // retrieve site wide settings
     var settings = Settings(sessionId);
-    settings.get(function (result) {
-
-        for (var i = 0; i < result.length; i += 1) {
-            $rootScope.settings[result[i].key] = result[i].value;
-        }
-    });
-
-    $scope.appVersion = undefined;
-    settings.version({}, function (result) {
-        $rootScope.appVersion = result.value;
-    }, function (error) {
-        console.log(error);
-    });
-
     $scope.pageCounts = function (currentPage, resultCount) {
         var maxPageCount = 15;
         var pageNum = ((currentPage - 1) * maxPageCount) + 1;
@@ -738,12 +724,12 @@ iceControllers.controller('CollectionController', function ($scope, $state, $fil
 
     // default list of collections
     $scope.collectionList = [
-        { name:'available', display:'Available', icon:'fa-folder', iconOpen:'fa-folder-open', alwaysVisible:true},
+        { name:'available', display:'Featured', icon:'fa-certificate', iconOpen:'fa-sun-o orange', alwaysVisible:true},
         { name:'personal', display:'Personal', icon:'fa-folder', iconOpen:'fa-folder-open', alwaysVisible:true},
-        { name:'shared', display:'Shared', icon:'fa-share-alt', iconOpen:'fa-share-alt', alwaysVisible:false},
-        { name:'drafts', display:'Drafts', icon:'fa-edit', iconOpen:'fa-edit', alwaysVisible:false},
-        { name:'pending', display:'Pending Approval', icon:'fa-folder', iconOpen:'fa-folder-open', alwaysVisible:false},
-        { name:'deleted', display:'Deleted', icon:'fa-trash-o', iconOpen:'fa-trash', alwaysVisible:false}
+        { name:'shared', display:'Shared', icon:'fa-share-alt', iconOpen:'fa-share-alt green', alwaysVisible:false},
+        { name:'drafts', display:'Drafts', icon:'fa-edit', iconOpen:'fa-edit blue', alwaysVisible:false},
+        { name:'pending', display:'Pending Approval', icon:'fa-support', iconOpen:'fa-support orange', alwaysVisible:false},
+        { name:'deleted', display:'Deleted', icon:'fa-trash-o', iconOpen:'fa-trash red', alwaysVisible:false}
     ];
 
     // entry items that can be created
@@ -1480,24 +1466,13 @@ iceControllers.controller('CreateEntryController',
             entry.query({partId:type}, function (result) {
                 if (isMain) { // or if !$scope.part
                     $scope.part = result;
-                    $scope.part.bioSafetyLevel = '1';
+                    $scope.part = EntryService.setNewEntryFields($scope.part);
                     $scope.part.linkedParts = [];
-                    $scope.part.links = [
-                        {value:''}
-                    ];
-                    $scope.part.selectionMarkers = [
-                        {value:''}
-                    ];
-                    $scope.part.status = 'Complete';
                     $scope.activePart = $scope.part;
                     $scope.selectedFields = EntryService.getFieldsForType($scope.createType);
                 } else {
                     var newPart = result;
-                    newPart.links = [];
-                    newPart.selectionMarkers = [];
-                    newPart.bioSafetyLevel = '1';
-                    newPart.status = 'Complete';
-
+                    newPart = EntryService.setNewEntryFields(newPart);
                     $scope.selectedFields = EntryService.getFieldsForType(type);
                     $scope.part.linkedParts.push(newPart);
 
@@ -1529,6 +1504,8 @@ iceControllers.controller('CreateEntryController',
             entry.query({partId:$model.id}, function (result) {
                 $scope.activePart = result;
                 $scope.activePart.isExistingPart = true;
+                if (!$scope.activePart.parameters)
+                    $scope.activePart.parameters = [];
                 $scope.addExisting = false;
                 $scope.part.linkedParts.push($scope.activePart);
 
@@ -1666,15 +1643,18 @@ iceControllers.controller('CreateEntryController',
         };
         $scope.today();
 
-//    $scope.showWeeks = true;
-//    $scope.toggleWeeks = function () {
-//        $scope.showWeeks = ! $scope.showWeeks;
-//    };
-
         $scope.clear = function () {
             $scope.dt = null;
         };
 
+        $scope.addCustomParameter = function () {
+            $scope.activePart.parameters.push({key:'', value:''});
+        };
+
+        $scope.removeCustomParameter = function (index) {
+            $scope.activePart.parameters.splice(index, 1);
+        };
+
         $scope.dateOptions = {
             'year-format':"'yy'",
             'starting-day':1

src/main/webapp/scripts/ice.app.js

@@ -173,7 +173,6 @@ iceApp.config(function ($locationProvider, $stateProvider, $urlRouterProvider) {
         .state('main.admin', {
             url:'admin',
             templateUrl:'/scripts/admin/admin.html',
-            controller:'AdminController',
             resolve:{
                 sessionValid:function (Authentication) {
                     return Authentication.isSessionValid() && Authentication.isAdmin();