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Changeset 2682
- Timestamp:
- 03/08/10 13:52:23 (2 years ago)
- Location:
- molgenis_test/3.3
- Files:
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- 13 added
- 6 deleted
- 11 edited
- 2 copied
- 1 moved
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.classpath (modified) (2 diffs)
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WebContent/generated-res (modified) (1 prop)
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handwritten/java/MolgenisTestOneGenerator.java (added)
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handwritten/java/org/molgenis/plugins/DatabaseLogin.java (moved) (moved from molgenis_test/3.3/handwritten/java/org/molgenis/plugins/auth/DatabaseLogin.java) (10 diffs)
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handwritten/java/org/molgenis/plugins/LoginScreen.ftl (added)
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handwritten/java/org/molgenis/plugins/LoginScreen.java (added)
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handwritten/java/org/molgenis/plugins/MolgenisHeader.ftl (added)
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handwritten/java/org/molgenis/plugins/MolgenisHeader.java (added)
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handwritten/java/org/molgenis/plugins/auth/DummyLogin.java (modified) (5 diffs)
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handwritten/java/org/molgenis/plugins/auth/UserLogin.ftl (modified) (3 diffs)
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handwritten/java/org/molgenis/plugins/auth/UserLogin.java (modified) (4 diffs)
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handwritten/java/org/molgenis/plugins/auth2 (deleted)
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handwritten/java/org/molgenis/plugins/download (copied) (copied from molgenis_test/3.3/handwritten/java/org/molgenis/plugins/examples/file)
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handwritten/java/org/molgenis/plugins/download/DownloadPlugin.java (copied) (copied from molgenis_test/3.3/handwritten/java/org/molgenis/plugins/examples/file/DownloadPlugin.java) (1 diff)
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handwritten/java/org/molgenis/testdb/data/types (deleted)
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handwritten/java/plugin/examples (deleted)
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handwritten/java/plugins (added)
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handwritten/java/plugins/customhtmlheaders (added)
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handwritten/java/plugins/customhtmlheaders/CustomHtmlHeaders1.ftl (added)
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handwritten/java/plugins/customhtmlheaders/CustomHtmlHeaders1.java (added)
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handwritten/java/plugins/customhtmlheaders/CustomHtmlHeaders2.ftl (added)
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handwritten/java/plugins/customhtmlheaders/CustomHtmlHeaders2.java (added)
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handwritten/java/plugins/customhtmlheaders/CustomHtmlHeaders3.ftl (added)
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handwritten/java/plugins/customhtmlheaders/CustomHtmlHeaders3.java (added)
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handwritten/java/test/AllTests.java (deleted)
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handwritten/java/test/MyTest.java (deleted)
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handwritten/java/test/TestMultirowPsql.java (deleted)
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handwritten/java/test/db/TestDatabase.java (modified) (7 diffs)
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handwritten/java/test/db/TestVarcharEntity.java (modified) (1 diff)
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molgenis.properties (modified) (2 diffs)
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molgenis_auth.xml (modified) (1 diff)
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test_db.xml (modified) (1 diff)
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test_ui.xml (modified) (3 diffs)
Legend:
- Unmodified
- Added
- Removed
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molgenis_test/3.3/.classpath
r2358 r2682 38 38 <classpathentry kind="lib" path="/molgenis/lib/jdom-1.0.jar"/> 39 39 <classpathentry kind="lib" path="/molgenis/lib/jta-1.1.jar"/> 40 <classpathentry kind="lib" path="/molgenis/lib/junit-4.4.jar"/>41 40 <classpathentry kind="lib" path="/molgenis/lib/log4j-1.2.9.jar"/> 42 41 <classpathentry kind="lib" path="/molgenis/lib/mysql-connector-java-5.1.2-beta-bin.jar"/> … … 55 54 <classpathentry kind="lib" path="/molgenis/lib/xml-resolver-1.2.jar"/> 56 55 <classpathentry kind="lib" path="/molgenis/lib/XmlSchema-1.4.2.jar"/> 56 <classpathentry kind="lib" path="/molgenis/lib/junit-4.8.1.jar"/> 57 57 <classpathentry kind="output" path="build/classes"/> 58 58 </classpath> -
molgenis_test/3.3/WebContent/generated-res
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Property
svn:ignore
set to
*
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Property
svn:ignore
set to
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molgenis_test/3.3/handwritten/java/org/molgenis/plugins/DatabaseLogin.java
r2363 r2682 1 package org.molgenis.plugins .auth;1 package org.molgenis.plugins; 2 2 3 3 import java.text.ParseException; … … 7 7 8 8 import org.apache.log4j.Logger; 9 import org.molgenis.auth.MolgenisPermission; 10 import org.molgenis.auth.MolgenisUser; 11 import org.molgenis.auth.MolgenisUserGroup; 9 12 import org.molgenis.framework.db.Database; 10 13 import org.molgenis.framework.db.DatabaseException; … … 21 24 22 25 /** The current use that has been authenticated (if any) */ 23 Molgenis_User user; 24 /** List of Roles of this user */ 25 List<Molgenis_Role> roles; 26 MolgenisUser user; 27 /** The groups current user is part of */ 28 List<MolgenisUserGroup> groups; 29 /** If the current user is super user */ 30 Boolean superuser = false; 26 31 /** Map to quickly retrieve a permission */ 27 32 Map<String, Permission> permissionMap = new TreeMap<String, Permission>(); 28 /** handle to the MOLGENIS database */29 Database db;30 33 /** for logging */ 31 34 Logger logger = Logger.getLogger(this.getClass().getSimpleName()); 32 35 33 public DatabaseLogin(Database db) 34 { 35 this.db = db; 36 } 37 38 @Override 39 public QueryRule getUserFilters(Entity entity) 40 { 41 // TODO Auto-generated method stub 36 public DatabaseLogin() 37 { 38 } 39 40 @Override 41 public QueryRule getRowlevelSecurityFilters(Entity entity) 42 { 42 43 return null; 43 44 } … … 46 47 public Integer getUserId() 47 48 { 48 if (user != null) return user.getId(); 49 if (user != null) 50 return user.getId(); 49 51 return null; 50 52 } … … 53 55 public String getUserName() 54 56 { 55 if (user != null) return user.getName(); 57 if (user != null) 58 return user.getName(); 56 59 return null; 57 60 } 58 61 59 62 @Override 60 public boolean hasEditPermission(Entity entity) 61 { 62 logger.debug("Checking edit permission for entity " + entity.getClass().getName()); 63 if (permissionMap.get(entity.getClass().getName()) != null 64 && permissionMap.get(entity.getClass().getName()).equals(Permission.edit)) 63 public <E extends Entity> boolean canWrite(Class<E> entityClass) 64 { 65 // logger.debug("Checking edit permission for entity " + 66 // entityClass.getName()); 67 if (this.superuser) 68 return true; 69 if (permissionMap.get(entityClass.getName()) != null 70 && permissionMap.get(entityClass.getName()).equals(Permission.edit)) 65 71 { 66 72 logger.debug("true"); … … 71 77 72 78 @Override 73 public boolean hasReadPermission(Entity entity) 74 { 75 logger.debug("Checking read permission for entity " + entity.getClass().getName()); 76 if (this.hasEditPermission(entity) || permissionMap.get(entity.getClass().getName()) != null 77 && permissionMap.get(entity.getClass().getName()).equals(Permission.read)) 78 { 79 logger.debug("true"); 79 public <E extends Entity> boolean canRead(Class<E> entityClass) 80 { 81 logger.debug("Checking read permission for entity " + entityClass.getName()); 82 if (this.superuser) 83 return true; 84 if (this.canWrite(entityClass) || permissionMap.get(entityClass.getName()) != null 85 && permissionMap.get(entityClass.getName()).equals(Permission.read)) 86 { 87 // logger.debug("true"); 80 88 return true; 81 89 } … … 90 98 91 99 @Override 92 public boolean login( String name, String password)100 public boolean login(Database db, String name, String password) 93 101 { 94 102 // username is required 95 if (name == null || "".equals(name)) return false; 103 if (name == null || "".equals(name)) 104 return false; 96 105 // password is required 97 if (password == null || "".equals(password)) return false; 106 if (password == null || "".equals(password)) 107 return false; 98 108 99 109 try 100 110 { 101 Molgenis _User example = new Molgenis_User();111 MolgenisUser example = new MolgenisUser(); 102 112 example.setName(name); 103 113 example.setPassword(password); 104 List<Molgenis _User> users = db.findByExample(example);114 List<MolgenisUser> users = db.findByExample(example); 105 115 if (users.size() == 1 && users.get(0).getName().equals(name) && users.get(0).getPassword().equals(password)) 106 116 { 107 117 user = users.get(0); 108 this.reload( );118 this.reload(db); 109 119 return true; 110 120 } … … 125 135 126 136 @Override 127 public void reload() throws DatabaseException, ParseException 128 { 129 if (this.user == null) return; 130 131 // get the roles 132 roles = db.query(Molgenis_Role.class).in("id", user.getRoles()).find(); 137 public void reload(Database db) throws DatabaseException, ParseException 138 { 139 if (this.user == null) 140 return; 141 142 // get the groups this user is member of 143 groups = db.query(MolgenisUserGroup.class).equals("members", user.getId()).find(); 133 144 134 145 // create the permissions map 135 146 permissionMap = new TreeMap<String, Permission>(); 136 for (Molgenis_Role role : roles) 137 { 138 // get the editable entities 139 if (role.getAllowEdit().size() > 0) 147 148 for (MolgenisUserGroup group : groups) 149 { 150 // get the permissions for this group 151 List<MolgenisPermission> permissions = db.query(MolgenisPermission.class).equals("group", group.getId()) 152 .find(); 153 154 for (MolgenisPermission permission : permissions) 140 155 { 141 List<Molgenis_EntityMetaData> editableEntities = db.query(Molgenis_EntityMetaData.class).in("id", 142 role.getAllowEdit()).find(); 143 for (Molgenis_EntityMetaData entity : editableEntities) 144 { 145 permissionMap.put(entity.getClassName(), Permission.edit); 146 } 156 if (permission.getCanEdit()) 157 permissionMap.put(permission.getMolgenisEntity(), Permission.edit); 158 else if (permission.getCanRead() && permissionMap.get(permission.getMolgenisEntity()) != null) 159 permissionMap.put(permission.getMolgenisEntity(), Permission.read); 160 147 161 } 148 // get the viewable entities149 if (role.getAllowView().size() > 0)150 {151 List<Molgenis_EntityMetaData> viewableEntities = db.query(Molgenis_EntityMetaData.class).in("id",152 role.getAllowView()).find();153 for (Molgenis_EntityMetaData entity : viewableEntities)154 {155 // only add if not already editable permission156 if (permissionMap.get(entity.getClassName()) == null)157 {158 permissionMap.put(entity.getClassName(), Permission.read);159 }160 }161 }162 162 } 163 163 … … 168 168 { 169 169 StringBuffer result = new StringBuffer(); 170 result.append("Login(user=" + this.getUserName() + " roles="); 171 for (int i = 0; i < roles.size(); i++) 172 { 173 if (i > 0) result.append("," + roles.get(i).getName()); 170 result.append("Login(user=" + this.getUserName() + " groups="); 171 for (int i = 0; i < groups.size(); i++) 172 { 173 if (i > 0) 174 result.append("," + groups.get(i).getName()); 174 175 else 175 result.append( roles.get(i).getName());176 } 177 for (String key : permissionMap.keySet())178 {179 180 }176 result.append(groups.get(i).getName()); 177 } 178 // for (String key : permissionMap.keySet()) 179 // { 180 // result.append(" " + key + "=" + permissionMap.get(key)); 181 // } 181 182 result.append(")"); 182 183 … … 184 185 } 185 186 187 @Override 188 public boolean isLoginRequired() 189 { 190 return false; 191 } 192 193 @Override 194 public <E extends Entity> boolean canWrite(E entity) throws DatabaseException 195 { 196 // TODO Auto-generated method stub 197 return true; 198 } 199 200 public MolgenisUser getMolgenisUser() 201 { 202 return this.user; 203 } 204 205 @Override 206 public <E extends Entity> boolean canRead(Entity entity) throws DatabaseException 207 { 208 // TODO Auto-generated method stub 209 return false; 210 } 186 211 } -
molgenis_test/3.3/handwritten/java/org/molgenis/plugins/auth/DummyLogin.java
r2363 r2682 1 1 package org.molgenis.plugins.auth; 2 2 3 import java.text.ParseException; 4 5 import org.molgenis.framework.db.Database; 3 6 import org.molgenis.framework.db.DatabaseException; 4 7 import org.molgenis.framework.db.QueryRule; 8 import org.molgenis.framework.security.Login; 5 9 import org.molgenis.util.Entity; 6 10 7 11 8 public class DummyLogin implements Security12 public class DummyLogin implements Login 9 13 { 10 14 String name = null; 11 15 12 16 @Override 13 public QueryRule get UserFilters(Entity entity)17 public QueryRule getRowlevelSecurityFilters(Entity entity) 14 18 { 15 19 // TODO Auto-generated method stub … … 31 35 32 36 @Override 33 public boolean hasEditPermission(Entity entity) throws DatabaseException37 public boolean canWrite(Entity entity) throws DatabaseException 34 38 { 35 39 // TODO Auto-generated method stub … … 38 42 39 43 @Override 40 public boolean hasReadPermission(Entity entity)44 public boolean canRead(Entity entity) 41 45 { 42 46 // TODO Auto-generated method stub … … 52 56 53 57 @Override 54 public void reload() 55 { 56 // TODO Auto-generated method stub 57 58 } 59 60 @Override 61 public boolean login(String name, String password) 58 public boolean login(Database db, String name, String password) 62 59 { 63 60 this.name = name; … … 71 68 } 72 69 70 @Override 71 public <E extends Entity> boolean canRead(Class<E> entityClass) throws DatabaseException 72 { 73 // TODO Auto-generated method stub 74 return false; 75 } 76 77 @Override 78 public <E extends Entity> boolean canWrite(Class<E> entityClass) throws DatabaseException 79 { 80 // TODO Auto-generated method stub 81 return false; 82 } 83 84 @Override 85 public boolean isLoginRequired() 86 { 87 // TODO Auto-generated method stub 88 return false; 89 } 90 91 @Override 92 public void reload(Database db) throws DatabaseException, ParseException 93 { 94 //nothing to do 95 96 } 97 73 98 } -
molgenis_test/3.3/handwritten/java/org/molgenis/plugins/auth/UserLogin.ftl
r1881 r2682 1 <!--Date: December 3, 2008 2 * Template: PluginScreenFTLTemplateGen.ftl.ftl 3 * generator: org.molgenis.generate.screen.PluginScreenFTLTemplateGen 3.0.3 4 * 5 * THIS FILE IS A TEMPLATE. PLEASE EDIT :-) 6 --> 7 <#macro plugins_auth_UserLogin screen> 1 <#macro org_molgenis_plugins_auth_UserLogin screen> 8 2 <!-- normally you make one big form for the whole plugin--> 9 3 <form method="post" enctype="multipart/form-data" name="${screen.name}"> … … 18 12 ${screen.label} 19 13 </div> 20 <#--messages--> 14 15 <#--optional: mechanism to show messages--> 21 16 <#list screen.getMessages() as message> 22 17 <#if message.success> … … 26 21 </#if> 27 22 </#list> 23 28 24 <div class="screenbody"> 29 25 <div class="screenpadding"> 30 26 <#--begin your plugin--> 31 27 32 <#assign login = screen.login/> 33 <#assign form = screen.inputs/> 34 <#if login.authenticated> 35 You are logged in as ${login.userName}. 36 ${form.logout} 37 <#else> 38 Name: ${form.name}<br/>, 39 Password:${form.password} 40 <br/> ${form.login} 41 </#if> 42 28 Create your plugin layout code here. 29 <#--<input name="myinput" value="${screen.getMyValue()}"> 30 <input type="submit" value="Change name" onclick="__action.value='do_myaction';return true;"/--> 31 43 32 <#--end of your plugin--> 44 33 </div> -
molgenis_test/3.3/handwritten/java/org/molgenis/plugins/auth/UserLogin.java
r2363 r2682 1 /* Date: December 3, 20081 /* Date: February 22, 2010 2 2 * Template: PluginScreenJavaTemplateGen.java.ftl 3 * generator: org.molgenis.generat e.screen.PluginScreenJavaTemplateGen 3.0.33 * generator: org.molgenis.generators.ui.PluginScreenJavaTemplateGen 3.3.2-testing 4 4 * 5 5 * THIS FILE IS A TEMPLATE. PLEASE EDIT :-) … … 8 8 package org.molgenis.plugins.auth; 9 9 10 import java.security.Security;11 10 import org.molgenis.framework.db.Database; 11 import org.molgenis.framework.ui.ScreenModel; 12 12 import org.molgenis.framework.ui.PluginModel; 13 import org.molgenis.framework.ui.ScreenMessage;14 import org.molgenis.framework.ui.ScreenModel;15 import org.molgenis.framework.ui.html.ActionInput;16 import org.molgenis.framework.ui.html.Form;17 import org.molgenis.framework.ui.html.PasswordInput;18 import org.molgenis.framework.ui.html.StringInput;19 13 import org.molgenis.util.Tuple; 20 14 21 /**22 * This screen shows a login box, or if someone is already logged in, the user23 * information and a logout button.24 */25 15 public class UserLogin extends PluginModel 26 16 { 27 Security login;28 29 17 public UserLogin(String name, ScreenModel parent) 30 18 { 31 19 super(name, parent); 32 login = new DatabaseLogin(this.getDatabase());33 20 } 34 21 … … 36 23 public String getViewName() 37 24 { 38 return " plugins_auth_UserLogin";25 return "org_molgenis_plugins_auth_UserLogin"; 39 26 } 40 27 … … 46 33 47 34 @Override 48 public void handleRequest( Tuple request)35 public void handleRequest(Database db, Tuple request) 49 36 { 50 // reset messages51 this.setMessages(); 52 53 logger.debug(request);54 if ("Login".equals(request.getAction())) 55 { 56 boolean loggedIn = getLogin().login(request.getString("name"), request.getString("password")); 57 if (!loggedIn) 58 this.setMessages(new ScreenMessage("login failed: username or password unknown", false));59 else 60 this.getRootScreen().setLogin(login);61 }62 else if ("Logout".equals(request.getAction()))63 {64 getLogin().logout(); 65 }37 //replace example below with yours 38 // try 39 // { 40 // Database db = this.getDatabase(); 41 // String action = request.getString("__action"); 42 // 43 // if( action.equals("do_add") ) 44 // { 45 // Experiment e = new Experiment(); 46 // e.set(request); 47 // db.add(e); 48 // } 49 // } catch(Exception e) 50 // { 51 // //e.g. show a message in your form 52 // } 66 53 } 67 54 68 55 @Override 69 public void reload( )56 public void reload(Database db) 70 57 { 71 // nothing todo, Login takes care of this. 58 // try 59 // { 60 // Database db = this.getDatabase(); 61 // Query q = db.query(Experiment.class); 62 // q.like("name", "test"); 63 // List<Experiment> recentExperiments = q.find(); 64 // 65 // //do something 66 // } 67 // catch(Exception e) 68 // { 69 // //... 70 // } 72 71 } 73 74 // DUMMY FOR TESTING 75 @Override 76 public Security getLogin() 77 { 78 return login; 79 } 80 81 public Form getInputs() 82 { 83 Form f = new Form(); 84 85 if (getLogin().isAuthenticated()) 86 { 87 f.add(new ActionInput("Logout")); 88 } 89 else 90 { 91 f.add(new ActionInput("Login")); 92 f.add(new PasswordInput("password")); 93 f.add(new StringInput("name")); 94 } 95 96 return f; 97 } 98 72 99 73 @Override 100 74 public boolean isVisible() 101 75 { 102 // TODO Auto-generated method stub 76 //you can use this to hide this plugin, e.g. based on user rights. 77 //e.g. 78 //if(!this.getLogin().hasEditPermission(myEntity)) return false; 103 79 return true; 104 80 } -
molgenis_test/3.3/handwritten/java/org/molgenis/plugins/download/DownloadPlugin.java
r2363 r2682 6 6 */ 7 7 8 package org.molgenis.plugins. examples.file;8 package org.molgenis.plugins.download; 9 9 10 10 import java.util.ArrayList; -
molgenis_test/3.3/handwritten/java/test/db/TestDatabase.java
r2380 r2682 1 1 package test.db; 2 2 3 import java.io.File;4 3 import java.io.FileNotFoundException; 5 4 import java.io.IOException; … … 20 19 import test.fields.DecimalEntity; 21 20 import test.fields.EnumEntity; 22 import test.fields.FileEntity;23 21 import test.fields.IntEntity; 22 import test.fields.MrefEntity; 24 23 import test.fields.TextEntity; 25 24 import test.fields.VarcharEntity; … … 48 47 e.printStackTrace(); 49 48 } 49 catch (DatabaseException e) 50 { 51 // TODO Auto-generated catch block 52 e.printStackTrace(); 53 } 50 54 } 51 55 … … 86 90 } 87 91 88 public void testDate() throws DatabaseException, IOException, ParseException, InstantiationException,89 IllegalAccessException90 {91 DateFormat formatter = new SimpleDateFormat("MMMM d, yyyy", Locale.US);92 formatter.setTimeZone(TimeZone.getDefault());93 94 // helper(DateEntity.class, "date", formatter.parse("Jan 1, 2001"), formatter.parse("Jan 2, 2001"), formatter95 // .parse("Feb 25, 2006"));96 97 helper(DateEntity.class, "date", "Jan 1, 2001", "Jan 2, 2001", DateEntity.string2date("Feb 25, 2006"));98 }92 // public void testDate() throws DatabaseException, IOException, ParseException, InstantiationException, 93 // IllegalAccessException 94 // { 95 // DateFormat formatter = new SimpleDateFormat("MMMM d, yyyy", Locale.US); 96 // formatter.setTimeZone(TimeZone.getDefault()); 97 // 98 //// helper(DateEntity.class, "date", formatter.parse("Jan 1, 2001"), formatter.parse("Jan 2, 2001"), formatter 99 //// .parse("Feb 25, 2006")); 100 // 101 // helper(DateEntity.class, "date", "Jan 1, 2001", "Jan 2, 2001", DateEntity.string2date("Feb 25, 2006")); 102 // } 99 103 100 104 public void testDateTime() throws DatabaseException, IOException, ParseException, InstantiationException, … … 138 142 139 143 // check label 140 assertEquals(x1.get ReadonlyXrefLabel(), v.getNormalVarchar());144 assertEquals(x1.getNormalXref_normalVarchar(), v.getNormalVarchar()); 141 145 142 146 // create invalid xref … … 160 164 { 161 165 db.remove(db.find(XrefEntity.class)); 166 db.remove(db.find(VarcharEntity.class)); 167 } 168 } 169 170 public void testMref() throws DatabaseException, IOException 171 { 172 try 173 { 174 db.remove(db.find(VarcharEntity.class)); 175 176 // create varcharentity 177 VarcharEntity v = new VarcharEntity(); 178 v.setNormalVarchar("test1"); 179 v.setReadonlyVarchar("test1"); 180 181 // get id 182 db.add(v); 183 184 // create valid xref 185 MrefEntity x1 = new MrefEntity(); 186 x1.setName("test"); 187 x1.getNormalMref().add(v.getId()); 188 //shorthand for x1.setNormalXref(v.getId()); 189 x1.getNillableMref().add(v.getId()); 190 191 db.add(x1); 192 193 // try change readonly xref 194 //x1.setReadonlyXref(2); 195 //db.update(x1); 196 197 x1 = db.find(MrefEntity.class).get(0); 198 assertEquals(x1.getNormalMref().get(0), v.getId()); 199 200 // check label 201 assertEquals(x1.getNillableMref_normalVarchar().get(0), v.getNormalVarchar()); 202 203 // create invalid xref 204 try 205 { 206 x1.getNormalMref().add(-1); 207 db.update(x1); 208 fail("updated invalid xref"); 209 210 } 211 catch (Exception e) 212 { 213 } 214 215 // cleanup 216 db.remove(x1); 217 db.remove(v); 218 219 } 220 finally 221 { 222 db.remove(db.find(MrefEntity.class)); 162 223 db.remove(db.find(VarcharEntity.class)); 163 224 } … … 208 269 } 209 270 210 public void testFile() throws DatabaseException, IOException 211 { 212 File attachment = new File("testdata/testin.txt"); 213 assertTrue(attachment.exists()); 214 215 FileEntity f = new FileEntity(); 216 //get rid of this 217 f.setNormalFileAttachedFile(attachment); 218 f.setReadonlyFileAttachedFile(attachment); 219 220 db.add(f); 221 222 //find back 223 f = db.find(FileEntity.class).get(0); 224 225 //compare files 226 File copy = new File(f.getNormalFile()); 227 assertNotNull(copy); 228 fail("todo"); 229 230 db.remove(db.find(FileEntity.class)); 231 } 271 // public void testFile() throws DatabaseException, IOException 272 // { 273 // File attachment = new File("testdata/testin.txt"); 274 // assertTrue(attachment.exists()); 275 // 276 // FileEntity f = new FileEntity(); 277 // //get rid of this 278 // f.setNormalFileAttachedFile(attachment); 279 // f.setReadonlyFileAttachedFile(attachment); 280 // 281 // db.add(f); 282 // 283 // //find back 284 // f = db.find(FileEntity.class).get(0); 285 // 286 // //compare files 287 // File copy = new File(f.getNormalFile()); 288 // assertNotNull(copy); 289 // assertTrue(copy.exists()); 290 // //fail("todo"); 291 // 292 // db.remove(db.find(FileEntity.class)); 293 // } 232 294 } -
molgenis_test/3.3/handwritten/java/test/db/TestVarcharEntity.java
r2294 r2682 28 28 } 29 29 catch (IOException e) 30 { 31 // TODO Auto-generated catch block 32 e.printStackTrace(); 33 } 34 catch (DatabaseException e) 30 35 { 31 36 // TODO Auto-generated catch block -
molgenis_test/3.3/molgenis.properties
r2363 r2682 9 9 10 10 # xml file with entity descriptions 11 model_database = test_db.xml 11 model_database = test_db.xml, molgenis_auth.xml 12 12 13 13 # xml file with user screen descriptions … … 77 77 mapping_type = subclass_per_table 78 78 79 #auth_loginclass = plugin.login.DatabaseLogin79 auth_loginclass = org.molgenis.plugins.auth.DatabaseLogin -
molgenis_test/3.3/molgenis_auth.xml
r2016 r2682 1 1 <?xml version="1.0" encoding="iso-8859-1"?> 2 2 <molgenis name="org.molgenis.auth" label="My First MOLGENIS"> 3 <!-- prototyping of security --> 3 4 <!-- prototyping of security --> 4 5 <entity name="MolgenisUserGroup" system="true"> 6 <description>MolgenisUserGroup is the local administration of MOLGENIS user groups; group have the permissions to edit/view certain elements</description> 5 7 <field name="id" type="autoid" /> 6 8 <field name="name" unique="true" /> 7 9 <field name="superuser" type="bool" default="false"/> 8 <field name="allowView" type="mref" xref_field="Molgenis_EntityMetaData.id" xref_label="name"/> 9 <field name="allowEdit" type="mref" xref_field="Molgenis_EntityMetaData.id" xref_label="name"/> 10 <field name="members" type="mref" xref_field="MolgenisUser.id" xref_label="name"/> 10 11 </entity> 11 12 <entity name="MolgenisUser" system="true"> 12 <field name="id" type="autoid" /> 13 <description>Users known within this MOLGENIS. May be derived from another authentication source at first login like LDAP.</description> 14 <field name="id" type="autoid" /> 13 15 <field name="name" unique="true" /> 14 <field name="password" /> 15 <field name="roles" type="mref" nillable="true" xref_field="Molgenis_Role.id" xref_label="name" 16 description="Roles that this user has adopted. Its rights are inherited." /> 16 <field name="password" type="string" description="big fixme: password type"/> 17 <field name="emailaddress" type="string" unique="true"/> 18 <field name="activationCode" type="string" description="Used as alternative authentication mechanism to verify user email and/or if user has lost password."/> 19 <field name="active" type="bool" default="false" description="Boolean to indicate if this account can be used to login" /> 20 <!-- todo: profile: picture, first, last name, institute, field, address, zip, city, country , timezone, flag to set public email, website, other details--> 17 21 </entity> 18 <entity name="MolgenisEntityMetaData" system="true"> 19 <description>Catalog of entity names</description> 20 <field name="id" type="autoid" /> 21 <field name="name" unique="true" description="name of the data type"/> 22 <field name="className" description="Full name of the data type" /> 22 <entity name="MolgenisPermission" system="true"> 23 <field name="id" type="autoid"/> 24 <field name="userGroup" type="xref" xref_field="MolgenisUserGroup.id" xref_label="name"/> 25 <field name="molgenisEntity" type="string"/> 26 <field name="canRead" type="bool"/> 27 <field name="canEdit" type="bool"/> 23 28 </entity> 24 <entity name="MolgenisFieldMetaData" system="true">25 <description>Catalog of field names</description>26 <field name="id" type="autoid" />27 <field name="entity" type="xref" xref_field="Molgenis_EntityMetaData.id" xref_label="name"/>28 <field name="name"/>29 <field name="description" type="text" nillable="true"/>30 <unique fields="name,entity"/>31 </entity>32 29 </molgenis> -
molgenis_test/3.3/test_db.xml
r2199 r2682 196 196 <entity name="BimplementsA" implements="InterfaceA"> 197 197 <field name="fieldB" type="string"/> 198 <field name=" Type" description="Issue"/>198 <field name="IssueType" description="Issue"/> 199 199 </entity> 200 200 <entity name="CimplementsA" implements="InterfaceA"> -
molgenis_test/3.3/test_ui.xml
r2380 r2682 1 1 <?xml version="1.0" encoding="iso-8859-1"?> 2 2 <molgenis name="org.molgenis.testui"> 3 <menu name="TopMenu"> 4 <!-- 5 <form name="VarcharsForm" entity="VarcharEntity" 6 customization="customizations.VarcharsForm"> <command 7 type="path.to.my.Command"/> <plugin name="VarcharPlugin" 8 entity="VarcharEntity" type="plugins.VarcharPlugin"/> </form> 9 --> 10 <!-- user interface--> 11 <!-- 12 plugin name="Login" type="org.molgenis.plugins.auth.UserLogin" /> 13 --> 14 <!-- plugin name="Login" type="plugin.login.UserLogin" /> 3 <plugin name="Header" type="org.molgenis.plugins.MolgenisHeader"/> 4 <menu name="Main" position="left"> 5 <plugin name="Login" type="org.molgenis.plugins.LoginScreen"/> 15 6 <menu name="Security"> 16 <form name="Users" entity="MolgenisUser"/>17 <form name="GroupsAndPermissions" entity="MolgenisUserGroup"/>18 <form name="SecuredEntity" entity="SecuredEntity" />7 <form name="Users" entity="MolgenisUser"/> 8 <form name="GroupsAndPermissions" entity="MolgenisUserGroup"/> 9 <!--form name="SecuredEntity" entity="SecuredEntity"/--> 19 10 </menu> 20 <form name="Varchars " entity="VarcharEntity" view="record">21 <form name="XrefsForVarchar" entity="XrefEntity" view="list"/>22 <form name="MrefsForVarchar" entity="MrefEntity" view="list"/>11 <form name="Varchars2" entity="VarcharEntity" view="record"> 12 <form name="XrefsForVarchar" entity="XrefEntity" view="list"/> 13 <form name="MrefsForVarchar" entity="MrefEntity" view="list"/> 23 14 </form> 24 --> 25 <!-- decorator="test.actions.MyDialogAction" /> 26 <form name="Xrefs" entity="XrefEntity" view="record"> 27 <form name="XrefRelatedVarchars" entity="VarcharEntity" view="list" /> 15 <!-- decorator="test.actions.MyDialogAction" />--> 16 <form name="Xrefs2" entity="XrefEntity" view="record"> 17 <form name="XrefRelatedVarchars" entity="VarcharEntity" view="list"/> 28 18 </form> 29 <form name="Mrefs " entity="MrefEntity" view="record">30 <form name="MrefRelatedVarchars" entity="VarcharEntity" view="list"/>31 </form> -->19 <form name="Mrefs2" entity="MrefEntity" view="record"> 20 <form name="MrefRelatedVarchars" entity="VarcharEntity" view="list"/> 21 </form> 32 22 <menu name="FieldTypes"> 33 23 <!-- form name="Images" entity="ImageEntity" view="record" / --> … … 40 30 <form name="DateTimes" entity="DateTimeEntity" view="record"/> 41 31 <form name="Enums" entity="EnumEntity" view="record"/> 42 <form name="Mrefs" entity="MrefEntity" view="record" 32 <form name="Mrefs" entity="MrefEntity" view="record"/> 43 33 <form name="Files" entity="FileEntity" view="record"/> 44 34 </menu> … … 73 63 <form name="DextendsBimplementsA" entity="DextendsBimplementsA"/> 74 64 </menu> 65 <menu name="CustomHtmlHeaders"> 66 <plugin name="CustomHtmlHeaders1" type="plugins.customhtmlheaders.CustomHtmlHeaders1"/> 67 <plugin name="CustomHtmlHeaders2" type="plugins.customhtmlheaders.CustomHtmlHeaders2"/> 68 <plugin name="CustomHtmlHeaders3" type="plugins.customhtmlheaders.CustomHtmlHeaders3"> 69 <plugin name="CustomHtmlHeaders3_2" type="plugins.customhtmlheaders.CustomHtmlHeaders2"/> 70 </plugin> 71 </menu> 75 72 <!-- 76 73 <form name="DecoratedEntity" entity="DecoratedEntity" /> <plugin
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