org.proteios.core
Class ItemFactory

java.lang.Object
  org.proteios.core.ItemFactory

public class ItemFactory
extends Object

Used to create persistent item instances

Author:

gregory

Constructor Summary

ItemFactory()
Remember to set the DbControl before using the factory

ItemFactory(DbControl dc)

Method Summary

<D extends BasicItem<?>> D	create(Class<D> template, Object... extraParameters) Creates an instance of the given template class.
AnnotationType	createAnnotationType(Type valueType) Create a new AnnotationType item.
CreationEvent	createCreationEvent(MeasuredBioMaterial<?> bioMaterial, MeasuredBioMaterial<?> sourceMaterial, Float usedQuantity) Create a new BioMaterialEvent of the Type#OTHER type.
GelImageAnalysisEvent	createGelImageAnalysisEvent(MeasuredBioMaterial<?> bioMaterial) Create a new GelImageAnalysisEvent of the Type#OTHER type.
GelScanEvent	createGelScanEvent(MeasuredBioMaterial<?> bioMaterial) Create a new GelScanEvent of the Type#OTHER type.
GlobalDefaultSetting	createGlobalDefaultSetting(String name, String value) Create a new GlobalDefaultSetting item.
Directory	createHomeDirectory(User user) Creates and saves a home directory for the supplied user
Job	createJob(PluginDefinition plugin, PluginConfiguration config) TODO this method does two things, create and configures a job to a starting state.
LabeledExtract	createLabeledExtract(Label label) Create a new LabeledExtract with label.
Message	createMessage(User to, String fromName, User fromUser, Job job) Create a new Message item.
SeparationEvent	createSeparationEvent(MeasuredBioMaterial<?> bioMaterial, Float usedQuantity) Create a new SeparationEvent of the Type#OTHER type.
SeparationMethod<?>	createSeparationMethod(String externalId) Create a new SeparationMethod item.
StainingEvent	createStainingEvent(MeasuredBioMaterial<?> bioMaterial) Create a new StainingEvent of the Type#OTHER type.
UpdateEvent	createUpdateEvent(MeasuredBioMaterial<?> bioMaterial) Create a new UpdateEvent of the Type#OTHER type.
User	createUser(String login, String password) Create a new User item.
<T extends BasicItem<?>> T	getById(Class<T> name, Integer id)
Directory	getByPath(Path path) Get a Directory item when you know the path.
File	getByPath(Path path, boolean create) Get a File item when you know the path.
<T extends BasicItem<?>> T	getBySystemId(Class<T> name, String id)
DbControl	getDc()
void	setDc(DbControl dc) We allow outside change of DbControl in use to enable factory reuse

Methods inherited from class java.lang.Object

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

Constructor Detail

ItemFactory

public ItemFactory()

Remember to set the DbControl before using the factory

ItemFactory

public ItemFactory(DbControl dc)

Parameters:

dc - initial DbControl to use

Method Detail

getDc

public DbControl getDc()

Returns:

currently use DbControled or null if none is set

setDc

public void setDc(DbControl dc)

We allow outside change of DbControl in use to enable factory reuse

Parameters:

dc -

create

public <D extends BasicItem<?>> D create(Class<D> template,
                                         Object... extraParameters)

Creates an instance of the given template class. Default values are set wherever possible. The returned objects are not saved and you should make sure to call dc.saveItem(item) for each item created by this method.

Type Parameters:

D -

Parameters:

template - item class to create

extraParameters - optional Object[] array of extra arguments

Returns:

object of type D or null if item couldn't be created

createJob

public Job createJob(PluginDefinition plugin,
                     PluginConfiguration config)
              throws BaseException

TODO this method does two things, create and configures a job to a starting state. Split this up and move the configure part into the Job class itself. Create a new Job item.

Parameters:

config - The plugin configuration this job should use or null if the job is executed by an external program

Returns:

The new Job item

Throws:

BaseException - If there is an error

createUser

public User createUser(String login,
                       String password)
                throws BaseException

Create a new User item.

Parameters:

login - The login for the user (required)

password - The password for the user (required)

Returns:

The new User item

Throws:

BaseException - If there is an error

createCreationEvent

public CreationEvent createCreationEvent(MeasuredBioMaterial<?> bioMaterial,
                                         MeasuredBioMaterial<?> sourceMaterial,
                                         Float usedQuantity)
                                  throws BaseException

Create a new BioMaterialEvent of the Type#OTHER type. If only a single BioMaterial was used it can be given as parameter optionally with the used amount of the biomaterial

Parameters:

bioMaterial - The affected biomaterial

Returns:

The new BioMaterialEvent item

Throws:

BaseException - If there is an error

createHomeDirectory

public Directory createHomeDirectory(User user)
                              throws PermissionDeniedException,
                                     BaseException

Creates and saves a home directory for the supplied user

Parameters:

user -

Returns:

created directory

Throws:

PermissionDeniedException

BaseException

createLabeledExtract

public LabeledExtract createLabeledExtract(Label label)
                                    throws BaseException

Create a new LabeledExtract with label.

Parameters:

label - The labeling compound used for labeling the extract

Returns:

The new LabeledExtract item

Throws:

BaseException - If there is an error

createAnnotationType

public AnnotationType createAnnotationType(Type valueType)
                                    throws BaseException

Create a new AnnotationType item.

Parameters:

valueType - The type of values to use

Returns:

The new AnnotationType item

Throws:

BaseException - If there is an error

createGelImageAnalysisEvent

public GelImageAnalysisEvent createGelImageAnalysisEvent(MeasuredBioMaterial<?> bioMaterial)
                                                  throws BaseException

Create a new GelImageAnalysisEvent of the Type#OTHER type.

Parameters:

bioMaterial - The affected biomaterial

Returns:

The new GelImageAnalysisEvent item

Throws:

BaseException - If there is an error

createGelScanEvent

public GelScanEvent createGelScanEvent(MeasuredBioMaterial<?> bioMaterial)
                                throws BaseException

Create a new GelScanEvent of the Type#OTHER type.

Parameters:

bioMaterial - The affected biomaterial

Returns:

The new GelScanEvent item

Throws:

BaseException - If there is an error

createSeparationEvent

public SeparationEvent createSeparationEvent(MeasuredBioMaterial<?> bioMaterial,
                                             Float usedQuantity)
                                      throws BaseException

Create a new SeparationEvent of the Type#OTHER type.

Parameters:

bioMaterial - The affected biomaterial

Returns:

The new SeparationEvent item

Throws:

BaseException - If there is an error

createStainingEvent

public StainingEvent createStainingEvent(MeasuredBioMaterial<?> bioMaterial)
                                  throws BaseException

Create a new StainingEvent of the Type#OTHER type.

Parameters:

bioMaterial - The affected biomaterial

Returns:

The new StainingEvent item

Throws:

BaseException - If there is an error

createUpdateEvent

public UpdateEvent createUpdateEvent(MeasuredBioMaterial<?> bioMaterial)
                              throws BaseException

Create a new UpdateEvent of the Type#OTHER type.

Parameters:

bioMaterial - The affected biomaterial

Returns:

The new UpdateEvent item

Throws:

BaseException - If there is an error

createSeparationMethod

public SeparationMethod<?> createSeparationMethod(String externalId)
                                           throws BaseException

Create a new SeparationMethod item.

Parameters:

externalId - The external id of the new item

Returns:

The new SeparationMethod item

Throws:

BaseException - If there is an error

createGlobalDefaultSetting

public GlobalDefaultSetting createGlobalDefaultSetting(String name,
                                                       String value)
                                                throws BaseException

Create a new GlobalDefaultSetting item.

Parameters:

name - The name of the setting

value - The value of the setting

Returns:

The new ClientDefaultSetting item

Throws:

BaseException - If there is an error

createMessage

public Message createMessage(User to,
                             String fromName,
                             User fromUser,
                             Job job)
                      throws BaseException

Create a new Message item.

Parameters:

to - the user the message shuold be sent to

fromName - the name of the sender of the message

fromUser - the user sending the message

job - the job this message is about

Returns:

return The new Message item

Throws:

BaseException - If there is an error

getById

public <T extends BasicItem<?>> T getById(Class<T> name,
                                          Integer id)

getByPath

public File getByPath(Path path,
                      boolean create)
               throws ItemNotFoundException,
                      PermissionDeniedException,
                      BaseException

Get a File item when you know the path. Use the create parameter to specify if a new file should be create if it doesn't exists. The directory part of the path must still be an existing path, otherwise an ItemNotFoundException is thrown.

Parameters:

path - The path to the file to load

create - TRUE if a new file should be created if one doesn't eixts, FALSE to throw an exception (DbControl.saveItem must always be called)

Returns:

The File item

Throws:

ItemNotFoundException - If an item with the specified path is not found and create is FALSE

PermissionDeniedException - If the logged in user doesn't have Permission.READ permission to the item

BaseException - If there is another error

getBySystemId

public <T extends BasicItem<?>> T getBySystemId(Class<T> name,
                                                String id)

getByPath

public Directory getByPath(Path path)
                    throws ItemNotFoundException,
                           PermissionDeniedException,
                           BaseException

Get a Directory item when you know the path.

Parameters:

path - The path to the directory to load

Returns:

The Directory item

Throws:

ItemNotFoundException - If an item with the specified path is not found

PermissionDeniedException - If the logged in user doesn't have Permission.READ permission to the item

BaseException - If there is another error