Package fr.igred.omero.repository

Class GenericRepositoryObjectWrapper<T extends DataObject>

java.lang.Object

fr.igred.omero.GenericObjectWrapper<T>

fr.igred.omero.repository.GenericRepositoryObjectWrapper<T>

Type Parameters:

T - Subclass of DataObject

Direct Known Subclasses:

DatasetWrapper, FolderWrapper, ImageWrapper, PlateAcquisitionWrapper, PlateWrapper, ProjectWrapper, ScreenWrapper, WellWrapper

public abstract class GenericRepositoryObjectWrapper<T extends DataObject>
extends GenericObjectWrapper<T>

Generic class containing a DataObject (or a subclass) object.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	GenericRepositoryObjectWrapper.ReplacePolicy	Policy to specify how to handle objects when they are replaced.

Field Summary

Fields inherited from class fr.igred.omero.GenericObjectWrapper

data

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	GenericRepositoryObjectWrapper(T object)	Constructor of the class GenericRepositoryObjectWrapper.

Method Summary

Modifier and Type	Method	Description
long	addAndReplaceFile(Client client, File file)	Uploads a file, links it to the object and unlinks previous files with the same name, or deletes them if they're orphaned.
long	addAndReplaceFile(Client client, File file, GenericRepositoryObjectWrapper.ReplacePolicy policy)	Uploads a file, links it to the object and unlinks or deletes previous files with the same name.
void	addAndReplaceTable(Client client, TableWrapper table)	Adds a table to the object in OMERO and unlinks previous tables with the same name, or deletes them if they're orphaned.
void	addAndReplaceTable(Client client, TableWrapper table, GenericRepositoryObjectWrapper.ReplacePolicy policy)	Adds a table to the object in OMERO and unlinks or deletes previous tables with the same name.
long	addFile(Client client, File file)	Uploads a file and links it to the object
void	addFileAnnotation(Client client, FileAnnotationWrapper annotation)	Links a file annotation to the object
void	addMapAnnotation(Client client, MapAnnotationWrapper mapAnnotation)	Adds a List of Key-Value pair to the object.
void	addPairKeyValue(Client client, String key, String value)	Adds a single Key-Value pair to the object.
void	addTable(Client client, TableWrapper table)	Adds a table to the object in OMERO.
void	addTag(Client client, TagAnnotationWrapper tag)	Adds a tag to the object in OMERO, if possible.
void	addTag(Client client, Long id)	Adds multiple tags to the object in OMERO, if possible.
void	addTag(Client client, String name, String description)	Adds a newly created tag to the object in OMERO, if possible.
protected void	addTag(Client client, TagAnnotationData tagData)	Protected function.
void	addTags(Client client, TagAnnotationWrapper... tags)	Adds multiple tag to the object in OMERO, if possible.
void	addTags(Client client, Long... ids)	Adds multiple tags by ID to the object in OMERO, if possible.
protected abstract String	annotationLinkType()	Returns the type of annotation link for this object
void	copyAnnotationLinks(Client client, GenericRepositoryObjectWrapper<?> object)	Copies annotation links from some other object to this one
abstract String	getDescription()	Gets the object description
List<FileAnnotationWrapper>	getFileAnnotations(Client client)	Returns the file annotations
Map<String,String>	getKeyValuePairs(Client client)	Gets the List of NamedValue (Key-Value pair) associated to an object.
List<MapAnnotationWrapper>	getMapAnnotations(Client client)	Gets all map annotations linked to an object in OMERO, if possible.
abstract String	getName()	Gets the object name.
TableWrapper	getTable(Client client, Long fileId)	Gets a certain table linked to the object in OMERO.
List<TableWrapper>	getTables(Client client)	Gets all tables linked to the object in OMERO.
List<TagAnnotationWrapper>	getTags(Client client)	Gets all tags linked to an object in OMERO, if possible.
String	getValue(Client client, String key)	Gets the value from a Key-Value pair associated to the object.
protected static List<Long>	importImage(GatewayWrapper client, DataObject target, String path)	Imports one image file to the target in OMERO.
protected static boolean	importImages(GatewayWrapper client, DataObject target, String... paths)	Imports all images candidates in the paths to the target in OMERO.
protected void	removeLink(Client client, String linkType, long childId)	Removes the link of the given type with the given child ID.
<A extends GenericAnnotationWrapper<?>> void	unlink(Client client, A annotation)	Unlinks the given annotation from the current object.

Methods inherited from class fr.igred.omero.GenericObjectWrapper

canAnnotate, canChgrp, canChown, canDelete, canEdit, canLink, delete, distinct, getCreated, getGroupId, getId, getOwner, saveAndUpdate, toString, wrap, wrap

Methods inherited from class java.lang.Object

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

Constructor Detail

GenericRepositoryObjectWrapper

protected GenericRepositoryObjectWrapper(T object)

Constructor of the class GenericRepositoryObjectWrapper.

Parameters:

object - The object contained in the GenericRepositoryObjectWrapper.

Method Detail

annotationLinkType

protected abstract String annotationLinkType()

Returns the type of annotation link for this object

Returns:

See above.

getName

public abstract String getName()

Gets the object name.

Returns:

See above.

getDescription

public abstract String getDescription()

Gets the object description

Returns:

See above.

addTag

public void addTag(Client client,
                   String name,
                   String description)
            throws ServiceException,
                   AccessException,
                   ExecutionException

Adds a newly created tag to the object in OMERO, if possible.

Parameters:

client - The client handling the connection.

name - Tag Name.

description - Tag description.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

addTag

public void addTag(Client client,
                   TagAnnotationWrapper tag)
            throws ServiceException,
                   AccessException,
                   ExecutionException

Adds a tag to the object in OMERO, if possible.

Parameters:

client - The client handling the connection.

tag - Tag to be added.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

addTag

protected void addTag(Client client,
                      TagAnnotationData tagData)
               throws ServiceException,
                      AccessException,
                      ExecutionException

Protected function. Adds a tag to the object in OMERO, if possible.

Parameters:

client - The client handling the connection.

tagData - Tag to be added.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

addTag

public void addTag(Client client,
                   Long id)
            throws ServiceException,
                   AccessException,
                   ExecutionException

Adds multiple tags to the object in OMERO, if possible.

Parameters:

client - The client handling the connection.

id - ID of the tag to add to the object.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

addTags

public void addTags(Client client,
                    TagAnnotationWrapper... tags)
             throws ServiceException,
                    AccessException,
                    ExecutionException

Adds multiple tag to the object in OMERO, if possible.

Parameters:

client - The client handling the connection.

tags - Array of TagAnnotationWrapper to add.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

addTags

public void addTags(Client client,
                    Long... ids)
             throws ServiceException,
                    AccessException,
                    ExecutionException

Adds multiple tags by ID to the object in OMERO, if possible.

Parameters:

client - The client handling the connection.

ids - Array of tag id in OMERO to add.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

getTags

public List<TagAnnotationWrapper> getTags(Client client)
                                   throws ServiceException,
                                          AccessException,
                                          ExecutionException

Gets all tags linked to an object in OMERO, if possible.

Parameters:

client - The client handling the connection.

Returns:

List of TagAnnotationWrappers each containing a tag linked to the object.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

getMapAnnotations

public List<MapAnnotationWrapper> getMapAnnotations(Client client)
                                             throws ServiceException,
                                                    AccessException,
                                                    ExecutionException

Gets all map annotations linked to an object in OMERO, if possible.

Parameters:

client - The client handling the connection.

Returns:

List of MapAnnotationWrappers.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

addPairKeyValue

public void addPairKeyValue(Client client,
                            String key,
                            String value)
                     throws ServiceException,
                            AccessException,
                            ExecutionException

Adds a single Key-Value pair to the object.

Parameters:

client - The client handling the connection.

key - Name of the key.

value - Value associated to the key.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

getKeyValuePairs

public Map<String,String> getKeyValuePairs(Client client)
                                          throws ServiceException,
                                                 AccessException,
                                                 ExecutionException

Gets the List of NamedValue (Key-Value pair) associated to an object.

Parameters:

client - The client handling the connection.

Returns:

Collection of NamedValue.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

getValue

public String getValue(Client client,
                       String key)
                throws ServiceException,
                       AccessException,
                       ExecutionException

Gets the value from a Key-Value pair associated to the object.

Parameters:

client - The client handling the connection.

key - Key researched.

Returns:

Value associated to the key.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

NoSuchElementException - Key not found.

ExecutionException - A Facility can't be retrieved or instantiated.

addMapAnnotation

public void addMapAnnotation(Client client,
                             MapAnnotationWrapper mapAnnotation)
                      throws ServiceException,
                             AccessException,
                             ExecutionException

Adds a List of Key-Value pair to the object.

The list is contained in the MapAnnotationWrapper.

Parameters:

client - The client handling the connection.

mapAnnotation - MapAnnotationWrapper containing a list of NamedValue.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

addTable

public void addTable(Client client,
                     TableWrapper table)
              throws ServiceException,
                     AccessException,
                     ExecutionException

Adds a table to the object in OMERO.

Parameters:

client - The client handling the connection.

table - Table to add to the object.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

addAndReplaceTable

public void addAndReplaceTable(Client client,
                               TableWrapper table,
                               GenericRepositoryObjectWrapper.ReplacePolicy policy)
                        throws ServiceException,
                               AccessException,
                               ExecutionException,
                               OMEROServerError,
                               InterruptedException

Adds a table to the object in OMERO and unlinks or deletes previous tables with the same name.

Parameters:

client - The client handling the connection.

table - Table to add to the object.

policy - Whether older tables should be unlinked, deleted or deleted only if they become orphaned.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

InterruptedException - The thread was interrupted.

OMEROServerError - Server error.

addAndReplaceTable

public void addAndReplaceTable(Client client,
                               TableWrapper table)
                        throws ServiceException,
                               AccessException,
                               ExecutionException,
                               OMEROServerError,
                               InterruptedException

Adds a table to the object in OMERO and unlinks previous tables with the same name, or deletes them if they're orphaned.

Parameters:

client - The client handling the connection.

table - Table to add to the object.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

InterruptedException - The thread was interrupted.

OMEROServerError - Server error.

getTable

public TableWrapper getTable(Client client,
                             Long fileId)
                      throws ServiceException,
                             AccessException,
                             ExecutionException

Gets a certain table linked to the object in OMERO.

Parameters:

client - The client handling the connection.

fileId - FileId of the table researched.

Returns:

TableWrapper containing the table information.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

getTables

public List<TableWrapper> getTables(Client client)
                             throws ServiceException,
                                    AccessException,
                                    ExecutionException

Gets all tables linked to the object in OMERO.

Parameters:

client - The client handling the connection.

Returns:

List of TableWrappers containing the tables.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

addFile

public long addFile(Client client,
                    File file)
             throws ExecutionException,
                    InterruptedException

Uploads a file and links it to the object

Parameters:

client - The client handling the connection.

file - File to add.

Returns:

ID of the file created in OMERO.

Throws:

ExecutionException - A Facility can't be retrieved or instantiated.

InterruptedException - The thread was interrupted.

addAndReplaceFile

public long addAndReplaceFile(Client client,
                              File file,
                              GenericRepositoryObjectWrapper.ReplacePolicy policy)
                       throws ExecutionException,
                              InterruptedException,
                              AccessException,
                              ServiceException,
                              OMEROServerError

Uploads a file, links it to the object and unlinks or deletes previous files with the same name.

Parameters:

client - The client handling the connection.

file - File to add.

policy - Whether older files should be unlinked, deleted or deleted only if they become orphaned.

Returns:

ID of the file created in OMERO.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

InterruptedException - The thread was interrupted.

OMEROServerError - Server error.

addAndReplaceFile

public long addAndReplaceFile(Client client,
                              File file)
                       throws ExecutionException,
                              InterruptedException,
                              AccessException,
                              ServiceException,
                              OMEROServerError

Uploads a file, links it to the object and unlinks previous files with the same name, or deletes them if they're orphaned.

Parameters:

client - The client handling the connection.

file - File to add.

Returns:

ID of the file created in OMERO.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

InterruptedException - The thread was interrupted.

OMEROServerError - Server error.

addFileAnnotation

public void addFileAnnotation(Client client,
                              FileAnnotationWrapper annotation)
                       throws AccessException,
                              ServiceException,
                              ExecutionException

Links a file annotation to the object

Parameters:

client - The client handling the connection.

annotation - FileAnnotationWrapper to link.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

getFileAnnotations

public List<FileAnnotationWrapper> getFileAnnotations(Client client)
                                               throws ExecutionException,
                                                      ServiceException,
                                                      AccessException

Returns the file annotations

Parameters:

client - The client handling the connection.

Returns:

The list of tile annotations.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

unlink

public <A extends GenericAnnotationWrapper<?>> void unlink(Client client,
                                                           A annotation)
                                                    throws ServiceException,
                                                           AccessException,
                                                           ExecutionException,
                                                           OMEROServerError,
                                                           InterruptedException

Unlinks the given annotation from the current object.

Type Parameters:

A - The type of the annotation.

Parameters:

client - The client handling the connection.

annotation - An annotation.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

OMEROServerError - Server error.

InterruptedException - If block(long) does not return.

removeLink

protected void removeLink(Client client,
                          String linkType,
                          long childId)
                   throws ServiceException,
                          OMEROServerError,
                          AccessException,
                          ExecutionException,
                          InterruptedException

Removes the link of the given type with the given child ID.

Parameters:

client - The client handling the connection.

linkType - The link type.

childId - Link child ID.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

OMEROServerError - Server error.

InterruptedException - If block(long) does not return.

copyAnnotationLinks

public void copyAnnotationLinks(Client client,
                                GenericRepositoryObjectWrapper<?> object)
                         throws AccessException,
                                ServiceException,
                                ExecutionException

Copies annotation links from some other object to this one

Parameters:

client - The client handling the connection.

object - Other repository object to copy annotations from.

Throws:

ServiceException - Cannot connect to OMERO.

AccessException - Cannot access data.

ExecutionException - A Facility can't be retrieved or instantiated.

importImages

protected static boolean importImages(GatewayWrapper client,
                                      DataObject target,
                                      String... paths)
                               throws ServiceException,
                                      OMEROServerError,
                                      IOException

Imports all images candidates in the paths to the target in OMERO.

Parameters:

client - The client handling the connection.

target - The import target.

paths - Paths to the image files on the computer.

Returns:

If the import did not exit because of an error.

Throws:

ServiceException - Cannot connect to OMERO.

OMEROServerError - Server error.

IOException - Cannot read file.

importImage

protected static List<Long> importImage(GatewayWrapper client,
                                        DataObject target,
                                        String path)
                                 throws ServiceException,
                                        OMEROServerError

Imports one image file to the target in OMERO.

Parameters:

client - The client handling the connection.

target - The import target.

path - Path to the image file on the computer.

Returns:

The list of IDs of the newly imported images.

Throws:

ServiceException - Cannot connect to OMERO.

OMEROServerError - Server error.