org.jbei.ice.lib.entry.sample

Class SampleService

java.lang.Object

org.jbei.ice.lib.entry.HasEntry

org.jbei.ice.lib.entry.sample.SampleService

public class SampleService
extends HasEntry

Service for dealing with Samples

Author:

Hector Plahar

Constructor Summary

Constructors

Constructor and Description
SampleService()

Method Summary

Modifier and Type	Method and Description
protected Storage	createChildrenStorage(StorageLocation currentLocation, Storage currentStorage, String depositor) Creates storage for all children of given parent storage
protected Storage	createPlate96Location(String sampleDepositor, StorageLocation mainLocation) Creates location records for a sample contained in a 96 well plate Provides support for 2-D barcoded systems.
PartSample	createSample(String userId, String entryId, PartSample partSample, String strainNamePrefix)
protected Storage	createShelfStorage(String depositor, StorageLocation shelf)
protected Storage	createStorage(String userId, String name, SampleType sampleType)
boolean	delete(String userId, long partId, long sampleId) Deletes specified sample for entry and all associated storage locations
ArrayList<PartSample>	getSamplesByBarcode(String userId, String barcode)
List<PartSample>	retrieveEntrySamples(String userId, String entryId)
protected PartSample	setAccountInfo(PartSample partSample, String email)

Methods inherited from class org.jbei.ice.lib.entry.HasEntry

getEntry

Methods inherited from class java.lang.Object

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

Constructor Detail

SampleService

public SampleService()

Method Detail

createStorage

protected Storage createStorage(String userId,
                                String name,
                                SampleType sampleType)

createSample

public PartSample createSample(String userId,
                               String entryId,
                               PartSample partSample,
                               String strainNamePrefix)

createPlate96Location

protected Storage createPlate96Location(String sampleDepositor,
                                        StorageLocation mainLocation)

Creates location records for a sample contained in a 96 well plate Provides support for 2-D barcoded systems. Validates the storage hierarchy before creating.

Parameters:

sampleDepositor - userID - unique identifier for user performing action

mainLocation - 96 well plate location

Returns:

sample storage with a complete hierarchy or null

createShelfStorage

protected Storage createShelfStorage(String depositor,
                                     StorageLocation shelf)

createChildrenStorage

protected Storage createChildrenStorage(StorageLocation currentLocation,
                                        Storage currentStorage,
                                        String depositor)

Creates storage for all children of given parent storage

Parameters:

currentLocation - storage location

currentStorage -

depositor - userID - unique identifier for user performing action

Returns:

updated storage

retrieveEntrySamples

public List<PartSample> retrieveEntrySamples(String userId,
                                             String entryId)

setAccountInfo

protected PartSample setAccountInfo(PartSample partSample,
                                    String email)

delete

public boolean delete(String userId,
                      long partId,
                      long sampleId)

Deletes specified sample for entry and all associated storage locations

Parameters:

userId - unique identifier for user performing action

partId - unique identifier for part that is associated with this sample

sampleId - unique identifier for sample being deleted

Returns:

true is deletion successful, false otherwise

getSamplesByBarcode

public ArrayList<PartSample> getSamplesByBarcode(String userId,
                                                 String barcode)