ubic.gemma.persistence.util

Class EntityUtils

java.lang.Object

ubic.gemma.persistence.util.EntityUtils

public class EntityUtils
extends Object

Author:

paul

Constructor Summary

Constructors

Constructor and Description
EntityUtils()

Method Summary

Modifier and Type	Method and Description
static String	addGroupAndUserNameRestriction(boolean showOnlyEditable, boolean showPublic) Have to add 'and' to start of this if it's a later clause Author: nicolas with fixes to generalize by paul, same code appears in the PhenotypeAssociationDaoImpl
static void	addUserAndGroupParameters(SQLQuery queryObject, SessionFactory sessionFactory) Populates parameters in query created using addGroupAndUserNameRestriction(boolean, boolean).
static void	createFile(File file)
static void	deleteFile(File file)
static Field	getDeclaredField(Class<?> cls, String field) Recursive version of Class.getDeclaredField(String) that also checks in the superclass hierarchy.
static Class	getDeclaredFieldType(String property, Class cls) Checks if property of given name exists in the given class.
static <T extends Identifiable> Map<Long,T>	getIdMap(Collection<T> entities) Given a set of entities, create a map of their ids to the entities.
static <T extends Identifiable> List<Long>	getIds(Collection<T> entities)
static Class<?>	getImplClass(Class<?> type)
static Object	getImplementationForProxy(Object target) Expert only.
static <S,T> Map<S,T>	getNestedPropertyMap(Collection<T> entities, String nestedProperty, String propertyName) Group entities by their property using a nested property.
static boolean[]	getPermissions(gemma.gsec.acl.domain.AclObjectIdentity aoi) Checks ACL related properties from the AclObjectIdentity.
static <T> T	getProperty(Object entity, String propertyName) Get a property of an entity object via its getter.
static <S,T> Map<S,T>	getPropertyMap(Collection<? extends T> entities, String propertyName) Group entities by their property.
static boolean	isProxy(Object target)
static <T,S> void	populateMapSet(Map<T,Set<S>> map, T key, S hash) Checks if the given map already contains a Set for the given key, and if it does, adds the given has code to it.
static void	renameFile(File file, File newFile)
static Collection<Long>	securityFilterIds(Class<? extends gemma.gsec.model.Securable> securedClass, Collection<Long> ids, boolean showOnlyEditable, boolean showPublic, Session sess) Expert use only.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

EntityUtils

public EntityUtils()

Method Detail

populateMapSet

public static <T,S> void populateMapSet(Map<T,Set<S>> map,
                                        T key,
                                        S hash)

Checks if the given map already contains a Set for the given key, and if it does, adds the given has code to it. If a key does not exist in the map, it creates a new set, and adds the has into it.

Type Parameters:

T - the key type parameter of the map

S - the type parameter of the set

Parameters:

map - the map to be checked

key - the key

hash - the hash to be added to the set at the given key of the map

getIds

public static <T extends Identifiable> List<Long> getIds(Collection<T> entities)

Parameters:

entities - entities

Returns:

returns a collection of IDs. Avoids using reflection by requiring that the given entities all implement the Identifiable interface.

getIdMap

public static <T extends Identifiable> Map<Long,T> getIdMap(Collection<T> entities)

Given a set of entities, create a map of their ids to the entities. Note: If more than one entity share the same ID, there is no guarantee on which will be kept in the final mapping.

Type Parameters:

T - the type

Parameters:

entities - where id is called "id"

Returns:

the created map

getProperty

public static <T> T getProperty(Object entity,
                                String propertyName)

Get a property of an entity object via its getter.

Type Parameters:

T - type of the property

Parameters:

entity - the entity

propertyName - name of the property

Returns:

the return value of the getter for the property

See Also:

PropertyUtils.getProperty(Object, String)

getPropertyMap

public static <S,T> Map<S,T> getPropertyMap(Collection<? extends T> entities,
                                            String propertyName)

Group entities by their property.

Type Parameters:

T - the type

Parameters:

entities - entities

propertyName - property name (e.g. "id")

Returns:

the created map

See Also:

getProperty(Object, String)

getNestedPropertyMap

public static <S,T> Map<S,T> getNestedPropertyMap(Collection<T> entities,
                                                  String nestedProperty,
                                                  String propertyName)

Group entities by their property using a nested property.

Type Parameters:

T - the type

Parameters:

entities - entities

nestedProperty - nested property

propertyName - property name (e.g. "id")

Returns:

the created map

See Also:

getProperty(Object, String)

getImplClass

public static Class<?> getImplClass(Class<?> type)

getImplementationForProxy

public static Object getImplementationForProxy(Object target)

Expert only. Must be called within a session? Not sure why this is necessary. Obtain the implementation for a proxy. If target is not an instanceof HibernateProxy, target is returned.

Parameters:

target - The object to be un-proxied.

Returns:

the underlying implementation.

isProxy

public static boolean isProxy(Object target)

Parameters:

target - target

Returns:

true if the target is a hibernate proxy.

securityFilterIds

public static Collection<Long> securityFilterIds(Class<? extends gemma.gsec.model.Securable> securedClass,
                                                 Collection<Long> ids,
                                                 boolean showOnlyEditable,
                                                 boolean showPublic,
                                                 Session sess)

Expert use only. Used to expose some ACL information to the DAO layer (normally this happens in an interceptor).

Parameters:

sess - session

securedClass - Securable type

ids - to be filtered

showPublic - also show public items (won't work if showOnlyEditable is true)

showOnlyEditable - show only editable

Returns:

filtered IDs, at the very least limited to those that are readable by the current user

addGroupAndUserNameRestriction

public static String addGroupAndUserNameRestriction(boolean showOnlyEditable,
                                                    boolean showPublic)

Have to add 'and' to start of this if it's a later clause Author: nicolas with fixes to generalize by paul, same code appears in the PhenotypeAssociationDaoImpl

Parameters:

showOnlyEditable - only show those the user has access to edit

showPublic - also show public items (wont work if showOnlyEditable is true)

Returns:

clause

addUserAndGroupParameters

public static void addUserAndGroupParameters(SQLQuery queryObject,
                                             SessionFactory sessionFactory)

Populates parameters in query created using addGroupAndUserNameRestriction(boolean, boolean).

Parameters:

queryObject - the query object created using the sql query with group and username restrictions.

sessionFactory - session factory from the DAO that is using this method.

getPermissions

public static boolean[] getPermissions(gemma.gsec.acl.domain.AclObjectIdentity aoi)

Checks ACL related properties from the AclObjectIdentity. Some of the code is adapted from SecurityUtil, but allows usage without an Acl object.

Parameters:

aoi - the acl object identity of an object whose permissions are to be checked.

Returns:

an array of booleans that represent permissions of currently logged in user as follows:

1. is object public
2. can user write to object
3. is object shared

(note that actual indexing in the array starts at 0).

createFile

public static void createFile(File file)
                       throws IOException

Throws:

IOException

deleteFile

public static void deleteFile(File file)

renameFile

public static void renameFile(File file,
                              File newFile)

getDeclaredFieldType

public static Class getDeclaredFieldType(String property,
                                         Class cls)
                                  throws NoSuchFieldException

Checks if property of given name exists in the given class. If the given string specifies nested properties (E.g. curationDetails.troubled), only the substring before the first dot is evaluated and the rest of the string is processed in a new recursive iteration.

Parameters:

property - the property to check for. If the string contains dot characters ('.'), only the part before the first dot will be evaluated. Substring after the dot will be checked against the type of the field retrieved from the substring before the dot.

cls - the class to check the property on.

Returns:

the class of the property last in the line of nesting.

Throws:

NoSuchFieldException

getDeclaredField

public static Field getDeclaredField(Class<?> cls,
                                     String field)
                              throws NoSuchFieldException

Recursive version of Class.getDeclaredField(String) that also checks in the superclass hierarchy.

Throws:

NoSuchFieldException

See Also:

Class.getDeclaredField(String)