Package ch.systemsx.cisd.etlserver.registrator.api.v1.impl

Class DataSetRegistrationTransaction<T extends ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation>

java.lang.Object

ch.systemsx.cisd.etlserver.registrator.api.v1.impl.DataSetRegistrationTransaction<T>

All Implemented Interfaces:

IDataSetRegistrationTransaction, DataSetRegistrationContext.IHolder, ch.systemsx.cisd.etlserver.registrator.v1.DataSetStorageAlgorithmRunner.IDataSetInApplicationServerRegistrator<T>, ch.systemsx.cisd.etlserver.registrator.v1.DataSetStorageAlgorithmRunner.IRollbackDelegate<T>

public class DataSetRegistrationTransaction<T extends ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation>
extends java.lang.Object
implements IDataSetRegistrationTransaction, ch.systemsx.cisd.etlserver.registrator.v1.DataSetStorageAlgorithmRunner.IRollbackDelegate<T>, ch.systemsx.cisd.etlserver.registrator.v1.DataSetStorageAlgorithmRunner.IDataSetInApplicationServerRegistrator<T>, DataSetRegistrationContext.IHolder

The implementation of a transaction. This class is designed to be used in one thread.

A transaction tracks commands that are invoked on it so they can be reverted (rolledback) if necessary.

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String	SUCCESS_MESSAGE

Constructor Summary

Constructors

Constructor	Description
DataSetRegistrationTransaction(java.io.File rollBackStackParentFolder, java.io.File workingDirectory, java.io.File stagingDirectory, ch.systemsx.cisd.etlserver.registrator.v1.DataSetRegistrationService<T> registrationService, ch.systemsx.cisd.etlserver.registrator.v1.IDataSetRegistrationDetailsFactory<T> registrationDetailsFactory)

Method Summary

Modifier and Type	Method	Description
boolean	commit()	Commit the transaction.
IDataSet	createNewDataSet()	Create a new data set for registration in openBIS.
IDataSet	createNewDataSet(DataSetRegistrationDetails<T> registrationDetails)
IDataSet	createNewDataSet(ch.systemsx.cisd.etlserver.registrator.v1.IDataSetRegistrationDetailsFactory<T> factory, java.lang.String dataSetType)
IDataSet	createNewDataSet(java.lang.String dataSetType)	Create a new data set with the specified code.
IDataSet	createNewDataSet(java.lang.String dataSetType, DataSetKind datasetKindOrNull)
IDataSet	createNewDataSet(java.lang.String dataSetType, java.lang.String dataSetCode)	Create a new data set with the specified type and code.
IDataSet	createNewDataSet(java.lang.String dataSetType, java.lang.String dataSetCode, DataSetKind datasetKindOrNull)
java.lang.String	createNewDirectory(IDataSet dst, java.lang.String dirName)	Create a new directory and return the path.
IExperiment	createNewExperiment(java.lang.String experimentIdentifierString, java.lang.String experimentTypeCode)	Create a new experiment to register with the openBIS AS.
java.lang.String	createNewFile(IDataSet dst, java.lang.String fileName)	Create a new empty file and return the path.
java.lang.String	createNewFile(IDataSet dst, java.lang.String dstInDataset, java.lang.String fileName)	Create a new empty file and return the path.
IMaterial	createNewMaterial(java.lang.String materialCode, java.lang.String materialType)	Create a new material to register with the openBIS AS.
IMetaproject	createNewMetaproject(java.lang.String name, java.lang.String description)	Creates the new metaproject for the current user.
IMetaproject	createNewMetaproject(java.lang.String name, java.lang.String description, java.lang.String ownerId)	Creates the new metaproject for the specified user.
IProject	createNewProject(java.lang.String projectIdentifier)	Create a new project to register with the openBIS AS.
ISample	createNewSample(java.lang.String sampleIdentifierString, java.lang.String sampleTypeCode)	Create a new sample to register with the openBIS AS.
ISample	createNewSampleWithGeneratedCode(java.lang.String spaceCode, java.lang.String sampleTypeCode)	Create a new sample to register with the openBIS AS.
ISpace	createNewSpace(java.lang.String spaceCode, java.lang.String spaceAdminUserIdOrNull)	Create a new space to register with the openBIS AS.
IVocabularyTerm	createNewVocabularyTerm()	Creates a new vocabulary term, which has to be assigned to a IVocabulary.
void	deleteFile(java.lang.String src)
ch.systemsx.cisd.openbis.generic.shared.basic.EntityOperationsState	didEntityOperationsSucceeded(ch.systemsx.cisd.openbis.generic.shared.basic.TechId registrationId)
void	didRollbackStorageAlgorithmRunner(ch.systemsx.cisd.etlserver.registrator.v1.DataSetStorageAlgorithmRunner<T> algorithm, java.lang.Throwable ex, ch.systemsx.cisd.etlserver.registrator.v1.IDataSetOnErrorActionDecision.ErrorType errorType)	Delegate method called by the DataSetStorageAlgorithmRunner.
static RollbackStack[]	findRollbackStacks(java.io.File rollBackStackParentFolder)
IAuthorizationService	getAuthorizationService()
net.lemnik.eodsql.DynamicTransactionQuery	getDatabaseQuery(java.lang.String dataSourceName)	Gets a database query object for the data source with the specified name.
IDataSetImmutable	getDataSet(java.lang.String dataSetCode)	Get a data set from the openBIS AS.
IDataSetUpdatable	getDataSetForUpdate(java.lang.String dataSetCode)	Get a data set from the openBIS AS for the purpose of modifying it.
IExperimentImmutable	getExperiment(java.lang.String experimentIdentifierString)	Get an experiment from the openBIS AS.
IExperimentUpdatable	getExperimentForUpdate(java.lang.String experimentIdentifierString)	Get an experiment from the openBIS AS for the purpose of modifying it.
IExternalDataManagementSystemImmutable	getExternalDataManagementSystem(java.lang.String externalDataManagementSystemCode)	Get an external data management system from the openBIS AS.
TopLevelDataSetRegistratorGlobalState	getGlobalState()
java.io.File	getIncoming()
DataSetFile	getIncomingDataSetFile()
IMaterialImmutable	getMaterial(java.lang.String identifier)	Get a material from the openBIS AS.
IMaterialImmutable	getMaterial(java.lang.String materialCode, java.lang.String materialType)	Get a material from the openBIS AS.
IMaterial	getMaterialForUpdate(java.lang.String identifier)	Get a material from the openBIS AS for the purpose of modifying it.
IMaterial	getMaterialForUpdate(java.lang.String materialCode, java.lang.String materialType)	Get a material from the openBIS AS for the purpose of modifying it.
IMetaproject	getMetaproject(java.lang.String name)	Only allowed when the user is available.
IMetaproject	getMetaproject(java.lang.String name, java.lang.String ownerId)	Only allowed when the user is not available.
IProjectImmutable	getProject(java.lang.String projectIdentifierString)	Get a project from the openBIS AS.
IProject	getProjectForUpdate(java.lang.String projectIdentifier)	Get an project from the openBIS AS for the purpose of modifying it.
DataSetRegistrationContext	getRegistrationContext()	Return a registration context object which can be used to store information that needs to be accessed through the registration process.
ch.systemsx.cisd.etlserver.registrator.v1.AbstractOmniscientTopLevelDataSetRegistrator.OmniscientTopLevelDataSetRegistratorState	getRegistratorContext()	Returns the service registrator context.
ISampleImmutable	getSample(java.lang.String sampleIdentifierString)	Get a sample from the openBIS AS.
ISample	getSampleForUpdate(java.lang.String sampleIdentifierString)	Get a sample from the openBIS AS for the purpose of modifying it.
ISearchService	getSearchService()	Retrieve the search service for this transaction.
ISearchService	getSearchServiceFilteredForUser(java.lang.String userId)	Retrieve the search service for this transaction.
ISearchService	getSearchServiceUnfiltered()	Retrieve the search service for this transaction.
ISpaceImmutable	getSpace(java.lang.String spaceCode)	Get a space from the openBIS AS.
java.lang.String	getUserId()	Get the id of the user on whose behalf this registration transaction is performed.
IVocabularyImmutable	getVocabulary(java.lang.String code)	Get the read-only vocabulary with given code
IVocabulary	getVocabularyForUpdate(java.lang.String code)	Get the vocabulary with given code
boolean	isCommitted()
boolean	isCommittedOrRolledback()
boolean	isRolledback()
void	logInfo(java.lang.Object message)	Write something to the operation log.
IDataSetUpdatable	makeDataSetMutable(IDataSetImmutable dataSet)	Given an immutable data set, make it mutable.
IExperimentUpdatable	makeExperimentMutable(IExperimentImmutable experiment)	Given an immutable experiment, make it mutable.
IMaterial	makeMaterialMutable(IMaterialImmutable material)	Given an immutable material, make it mutable.
IProject	makeProjectMutable(IProjectImmutable project)	Given an immutable project, make it mutable.
ISample	makeSampleMutable(ISampleImmutable sample)	Given an immutable sample, make it mutable.
java.lang.String	moveFile(java.lang.String src, IDataSet dst)	Move a file from into the root of a data set.
java.lang.String	moveFile(java.lang.String src, IDataSet dst, java.lang.String dstInDataset)	Move a file to a specified location in a data set.
void	registerDataSetsInApplicationServer(ch.systemsx.cisd.openbis.generic.shared.basic.TechId registrationId, java.util.List<ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetRegistrationInformation<T>> dataSetRegistrations)	Delegate method called by the DataSetStorageAlgorithmRunner.
void	rollback()	Rollback any commands that have been executed.
static void	rollbackDeadTransactions(java.io.File rollBackStackParentFolder)	Check if there are any uncompleted transactions and roll them back.
void	setUserId(java.lang.String userIdOrNull)	Set the id of the user on whose behalf this registration transaction is performed.

Methods inherited from class java.lang.Object

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

Field Detail

SUCCESS_MESSAGE

public static final java.lang.String SUCCESS_MESSAGE

See Also:

Constant Field Values

Constructor Detail

DataSetRegistrationTransaction

public DataSetRegistrationTransaction(java.io.File rollBackStackParentFolder,
                                      java.io.File workingDirectory,
                                      java.io.File stagingDirectory,
                                      ch.systemsx.cisd.etlserver.registrator.v1.DataSetRegistrationService<T> registrationService,
                                      ch.systemsx.cisd.etlserver.registrator.v1.IDataSetRegistrationDetailsFactory<T> registrationDetailsFactory)

Method Detail

findRollbackStacks

public static RollbackStack[] findRollbackStacks(java.io.File rollBackStackParentFolder)

rollbackDeadTransactions

public static void rollbackDeadTransactions(java.io.File rollBackStackParentFolder)

Check if there are any uncompleted transactions and roll them back. To be called during startup of a thread.

getUserId

public java.lang.String getUserId()

Description copied from interface: IDataSetRegistrationTransaction

Get the id of the user on whose behalf this registration transaction is performed.

Specified by:

getUserId in interface IDataSetRegistrationTransaction

Returns:

A userId or null, if there is none.

setUserId

public void setUserId(java.lang.String userIdOrNull)

Description copied from interface: IDataSetRegistrationTransaction

Set the id of the user on whose behalf this registration transaction is performed.

Specified by:

setUserId in interface IDataSetRegistrationTransaction

Parameters:

userIdOrNull - The id of a user or null if this transaction should be performed as the system (etlserver).

createNewDataSet

public IDataSet createNewDataSet()

Description copied from interface: IDataSetRegistrationTransaction

Create a new data set for registration in openBIS.

Specified by:

createNewDataSet in interface IDataSetRegistrationTransaction

createNewDataSet

public IDataSet createNewDataSet(java.lang.String dataSetType)

Description copied from interface: IDataSetRegistrationTransaction

Create a new data set with the specified code.

Specified by:

createNewDataSet in interface IDataSetRegistrationTransaction

createNewDataSet

public IDataSet createNewDataSet(java.lang.String dataSetType,
                                 DataSetKind datasetKindOrNull)

Specified by:

createNewDataSet in interface IDataSetRegistrationTransaction

createNewDataSet

public IDataSet createNewDataSet(java.lang.String dataSetType,
                                 java.lang.String dataSetCode)

Description copied from interface: IDataSetRegistrationTransaction

Create a new data set with the specified type and code.

Specified by:

createNewDataSet in interface IDataSetRegistrationTransaction

createNewDataSet

public IDataSet createNewDataSet(java.lang.String dataSetType,
                                 java.lang.String dataSetCode,
                                 DataSetKind datasetKindOrNull)

Specified by:

createNewDataSet in interface IDataSetRegistrationTransaction

createNewDataSet

public IDataSet createNewDataSet(DataSetRegistrationDetails<T> registrationDetails)

createNewDataSet

public IDataSet createNewDataSet(ch.systemsx.cisd.etlserver.registrator.v1.IDataSetRegistrationDetailsFactory<T> factory,
                                 java.lang.String dataSetType)

getDataSet

public IDataSetImmutable getDataSet(java.lang.String dataSetCode)

Description copied from interface: IDataSetRegistrationTransaction

Get a data set from the openBIS AS. Returns null if the data set does not exist.

Specified by:

getDataSet in interface IDataSetRegistrationTransaction

Returns:

A data set or null

getDataSetForUpdate

public IDataSetUpdatable getDataSetForUpdate(java.lang.String dataSetCode)

Description copied from interface: IDataSetRegistrationTransaction

Get a data set from the openBIS AS for the purpose of modifying it. Returns null if the data set does not exist.

Specified by:

getDataSetForUpdate in interface IDataSetRegistrationTransaction

Returns:

A data set or null

makeDataSetMutable

public IDataSetUpdatable makeDataSetMutable(IDataSetImmutable dataSet)

Description copied from interface: IDataSetRegistrationTransaction

Given an immutable data set, make it mutable.

Specified by:

makeDataSetMutable in interface IDataSetRegistrationTransaction

Returns:

A data set

getSample

public ISampleImmutable getSample(java.lang.String sampleIdentifierString)

Description copied from interface: IDataSetRegistrationTransaction

Get a sample from the openBIS AS. Returns null if the sample does not exist.

Specified by:

getSample in interface IDataSetRegistrationTransaction

Returns:

A sample or null

getSampleForUpdate

public ISample getSampleForUpdate(java.lang.String sampleIdentifierString)

Description copied from interface: IDataSetRegistrationTransaction

Get a sample from the openBIS AS for the purpose of modifying it. Returns null if the sample does not exist.

Specified by:

getSampleForUpdate in interface IDataSetRegistrationTransaction

Returns:

A sample or null

makeSampleMutable

public ISample makeSampleMutable(ISampleImmutable sample)

Description copied from interface: IDataSetRegistrationTransaction

Given an immutable sample, make it mutable.

Specified by:

makeSampleMutable in interface IDataSetRegistrationTransaction

Returns:

A sample

getExperimentForUpdate

public IExperimentUpdatable getExperimentForUpdate(java.lang.String experimentIdentifierString)

Description copied from interface: IDataSetRegistrationTransaction

Get an experiment from the openBIS AS for the purpose of modifying it.

Specified by:

getExperimentForUpdate in interface IDataSetRegistrationTransaction

makeExperimentMutable

public IExperimentUpdatable makeExperimentMutable(IExperimentImmutable experiment)

Description copied from interface: IDataSetRegistrationTransaction

Given an immutable experiment, make it mutable.

Specified by:

makeExperimentMutable in interface IDataSetRegistrationTransaction

Returns:

An experiment

createNewSample

public ISample createNewSample(java.lang.String sampleIdentifierString,
                               java.lang.String sampleTypeCode)

Description copied from interface: IDataSetRegistrationTransaction

Create a new sample to register with the openBIS AS. The sample will have a permId.

Specified by:

createNewSample in interface IDataSetRegistrationTransaction

Parameters:

sampleIdentifierString - The identifier for the new sample

sampleTypeCode - The code of the type for the new sample

createNewSampleWithGeneratedCode

public ISample createNewSampleWithGeneratedCode(java.lang.String spaceCode,
                                                java.lang.String sampleTypeCode)

Description copied from interface: IDataSetRegistrationTransaction

Create a new sample to register with the openBIS AS. The sample will have a permId and automatically generated identifier

Specified by:

createNewSampleWithGeneratedCode in interface IDataSetRegistrationTransaction

Parameters:

spaceCode - The space in which to create the new sample.

sampleTypeCode - The code of the type for the new sample

getExperiment

public IExperimentImmutable getExperiment(java.lang.String experimentIdentifierString)

Description copied from interface: IDataSetRegistrationTransaction

Get an experiment from the openBIS AS.

Specified by:

getExperiment in interface IDataSetRegistrationTransaction

createNewExperiment

public IExperiment createNewExperiment(java.lang.String experimentIdentifierString,
                                       java.lang.String experimentTypeCode)

Description copied from interface: IDataSetRegistrationTransaction

Create a new experiment to register with the openBIS AS. The experiment will have a permId.

Specified by:

createNewExperiment in interface IDataSetRegistrationTransaction

Parameters:

experimentIdentifierString - The identifier for the new experiment

experimentTypeCode - The code of the type for the new experiment

createNewProject

public IProject createNewProject(java.lang.String projectIdentifier)

Description copied from interface: IDataSetRegistrationTransaction

Create a new project to register with the openBIS AS.

Specified by:

createNewProject in interface IDataSetRegistrationTransaction

Parameters:

projectIdentifier - .

getProject

public IProjectImmutable getProject(java.lang.String projectIdentifierString)

Description copied from interface: IDataSetRegistrationTransaction

Get a project from the openBIS AS. Returns null if the project does not exist.

Specified by:

getProject in interface IDataSetRegistrationTransaction

Returns:

A project or null

getProjectForUpdate

public IProject getProjectForUpdate(java.lang.String projectIdentifier)

Description copied from interface: IDataSetRegistrationTransaction

Get an project from the openBIS AS for the purpose of modifying it.

Specified by:

getProjectForUpdate in interface IDataSetRegistrationTransaction

makeProjectMutable

public IProject makeProjectMutable(IProjectImmutable project)

Description copied from interface: IDataSetRegistrationTransaction

Given an immutable project, make it mutable.

Specified by:

makeProjectMutable in interface IDataSetRegistrationTransaction

Returns:

A mutable project.

createNewSpace

public ISpace createNewSpace(java.lang.String spaceCode,
                             java.lang.String spaceAdminUserIdOrNull)

Description copied from interface: IDataSetRegistrationTransaction

Create a new space to register with the openBIS AS.

Specified by:

createNewSpace in interface IDataSetRegistrationTransaction

Parameters:

spaceCode - the code of the space

spaceAdminUserIdOrNull - the user id of the person, who will receive space admin priviliges.

getSpace

public ISpaceImmutable getSpace(java.lang.String spaceCode)

Description copied from interface: IDataSetRegistrationTransaction

Get a space from the openBIS AS. Returns null if the space does not exist.

Specified by:

getSpace in interface IDataSetRegistrationTransaction

Returns:

A space or null

getMaterial

public IMaterialImmutable getMaterial(java.lang.String materialCode,
                                      java.lang.String materialType)

Description copied from interface: IDataSetRegistrationTransaction

Get a material from the openBIS AS. Returns null if the material does not exist.

Specified by:

getMaterial in interface IDataSetRegistrationTransaction

Returns:

A material or null

getMaterial

public IMaterialImmutable getMaterial(java.lang.String identifier)

Description copied from interface: IDataSetRegistrationTransaction

Get a material from the openBIS AS. Returns null if the material does not exist.

Specified by:

getMaterial in interface IDataSetRegistrationTransaction

Returns:

A material or null

getMaterialForUpdate

public IMaterial getMaterialForUpdate(java.lang.String materialCode,
                                      java.lang.String materialType)

Description copied from interface: IDataSetRegistrationTransaction

Get a material from the openBIS AS for the purpose of modifying it. Returns null if the material does not exist.

Specified by:

getMaterialForUpdate in interface IDataSetRegistrationTransaction

Returns:

A material or null

getMaterialForUpdate

public IMaterial getMaterialForUpdate(java.lang.String identifier)

Description copied from interface: IDataSetRegistrationTransaction

Get a material from the openBIS AS for the purpose of modifying it. Returns null if the material does not exist.

Specified by:

getMaterialForUpdate in interface IDataSetRegistrationTransaction

Returns:

A material or null

makeMaterialMutable

public IMaterial makeMaterialMutable(IMaterialImmutable material)

Description copied from interface: IDataSetRegistrationTransaction

Given an immutable material, make it mutable.

Specified by:

makeMaterialMutable in interface IDataSetRegistrationTransaction

Returns:

A material

createNewMaterial

public IMaterial createNewMaterial(java.lang.String materialCode,
                                   java.lang.String materialType)

Description copied from interface: IDataSetRegistrationTransaction

Create a new material to register with the openBIS AS.

Specified by:

createNewMaterial in interface IDataSetRegistrationTransaction

Parameters:

materialCode - the code of the material

materialType - the type of the material

getExternalDataManagementSystem

public IExternalDataManagementSystemImmutable getExternalDataManagementSystem(java.lang.String externalDataManagementSystemCode)

Description copied from interface: IDataSetRegistrationTransaction

Get an external data management system from the openBIS AS. Returns null if the object does not exist.

Specified by:

getExternalDataManagementSystem in interface IDataSetRegistrationTransaction

Returns:

external data management system or null

createNewMetaproject

public IMetaproject createNewMetaproject(java.lang.String name,
                                         java.lang.String description)

Description copied from interface: IDataSetRegistrationTransaction

Creates the new metaproject for the current user. Only allowed when there is a user available.

Specified by:

createNewMetaproject in interface IDataSetRegistrationTransaction

createNewMetaproject

public IMetaproject createNewMetaproject(java.lang.String name,
                                         java.lang.String description,
                                         java.lang.String ownerId)

Description copied from interface: IDataSetRegistrationTransaction

Creates the new metaproject for the specified user. Only allowed when there is no user available.

Specified by:

createNewMetaproject in interface IDataSetRegistrationTransaction

getMetaproject

public IMetaproject getMetaproject(java.lang.String name)

Description copied from interface: IDataSetRegistrationTransaction

Only allowed when the user is available.

Specified by:

getMetaproject in interface IDataSetRegistrationTransaction

Returns:

metaproject with given name for current user.

getMetaproject

public IMetaproject getMetaproject(java.lang.String name,
                                   java.lang.String ownerId)

Description copied from interface: IDataSetRegistrationTransaction

Only allowed when the user is not available.

Specified by:

getMetaproject in interface IDataSetRegistrationTransaction

Returns:

metaproject with given name for specified user.

getVocabulary

public IVocabularyImmutable getVocabulary(java.lang.String code)

Description copied from interface: IDataSetRegistrationTransaction

Get the read-only vocabulary with given code

Specified by:

getVocabulary in interface IDataSetRegistrationTransaction

getVocabularyForUpdate

public IVocabulary getVocabularyForUpdate(java.lang.String code)

Description copied from interface: IDataSetRegistrationTransaction

Get the vocabulary with given code

Specified by:

getVocabularyForUpdate in interface IDataSetRegistrationTransaction

createNewVocabularyTerm

public IVocabularyTerm createNewVocabularyTerm()

Description copied from interface: IDataSetRegistrationTransaction

Creates a new vocabulary term, which has to be assigned to a IVocabulary.

Specified by:

createNewVocabularyTerm in interface IDataSetRegistrationTransaction

moveFile

public java.lang.String moveFile(java.lang.String src,
                                 IDataSet dst)

Description copied from interface: IDataSetRegistrationTransaction

Move a file from into the root of a data set.

Specified by:

moveFile in interface IDataSetRegistrationTransaction

Parameters:

src - The path of the file to move.

dst - The data set to add the file to.

Returns:

The absolute path after the move.

moveFile

public java.lang.String moveFile(java.lang.String src,
                                 IDataSet dst,
                                 java.lang.String dstInDataset)

Description copied from interface: IDataSetRegistrationTransaction

Move a file to a specified location in a data set. Any necessary intermediate folders are automatically created.

Specified by:

moveFile in interface IDataSetRegistrationTransaction

Parameters:

src - The path of the file to move.

dst - The data set to add the file to.

dstInDataset - The path of the file in the data set

Returns:

The absolute path after the move.

createNewDirectory

public java.lang.String createNewDirectory(IDataSet dst,
                                           java.lang.String dirName)

Description copied from interface: IDataSetRegistrationTransaction

Create a new directory and return the path.

Specified by:

createNewDirectory in interface IDataSetRegistrationTransaction

Parameters:

dst - The data set to add the file to.

dirName - The name of the new file to create. (Can be a simple file or directory.)

Returns:

The absolute path of the new file.

createNewFile

public java.lang.String createNewFile(IDataSet dst,
                                      java.lang.String fileName)

Description copied from interface: IDataSetRegistrationTransaction

Create a new empty file and return the path.

Specified by:

createNewFile in interface IDataSetRegistrationTransaction

Parameters:

dst - The data set to add the file to.

fileName - The name of the new file to create. (Can be a simple file or directory.)

Returns:

The absolute path of the new file.

createNewFile

public java.lang.String createNewFile(IDataSet dst,
                                      java.lang.String dstInDataset,
                                      java.lang.String fileName)

Description copied from interface: IDataSetRegistrationTransaction

Create a new empty file and return the path.

Specified by:

createNewFile in interface IDataSetRegistrationTransaction

Parameters:

dst - The data set to add the file to.

dstInDataset - The path of the file in the data set

fileName - The name of the new file to create. (Can be a simple file or directory.)

Returns:

The absolute path of the new file.

deleteFile

public void deleteFile(java.lang.String src)

getRegistrationContext

public DataSetRegistrationContext getRegistrationContext()

Description copied from interface: IDataSetRegistrationTransaction

Return a registration context object which can be used to store information that needs to be accessed through the registration process.

It is important to use the registration context, and not global variables, for communication between code in different parts of the registration process. This is because the registration process is not guaranteed to run in a single process.

Specified by:

getRegistrationContext in interface DataSetRegistrationContext.IHolder

Specified by:

getRegistrationContext in interface IDataSetRegistrationTransaction

Returns:

The context, a hash-map-like object.

commit

public boolean commit()

Commit the transaction. Does not throw exceptions if the commit fails on some datasets!

Returns:

true if any datasets have been commited, false otherwise.

rollback

public void rollback()

Rollback any commands that have been executed. Rollback is done in the reverse order of execution.

didRollbackStorageAlgorithmRunner

public void didRollbackStorageAlgorithmRunner(ch.systemsx.cisd.etlserver.registrator.v1.DataSetStorageAlgorithmRunner<T> algorithm,
                                              java.lang.Throwable ex,
                                              ch.systemsx.cisd.etlserver.registrator.v1.IDataSetOnErrorActionDecision.ErrorType errorType)

Delegate method called by the DataSetStorageAlgorithmRunner.

Specified by:

didRollbackStorageAlgorithmRunner in interface ch.systemsx.cisd.etlserver.registrator.v1.DataSetStorageAlgorithmRunner.IRollbackDelegate<T extends ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation>

registerDataSetsInApplicationServer

public void registerDataSetsInApplicationServer(ch.systemsx.cisd.openbis.generic.shared.basic.TechId registrationId,
                                                java.util.List<ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetRegistrationInformation<T>> dataSetRegistrations)
                                         throws java.lang.Throwable

Delegate method called by the DataSetStorageAlgorithmRunner. This implementation asks the DataSetRegistrationService to register not just the data sets, but perform any creation or updates of Experiments and Samples as well.

Specified by:

registerDataSetsInApplicationServer in interface ch.systemsx.cisd.etlserver.registrator.v1.DataSetStorageAlgorithmRunner.IDataSetInApplicationServerRegistrator<T extends ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation>

Throws:

java.lang.Throwable

didEntityOperationsSucceeded

public ch.systemsx.cisd.openbis.generic.shared.basic.EntityOperationsState didEntityOperationsSucceeded(ch.systemsx.cisd.openbis.generic.shared.basic.TechId registrationId)

Specified by:

didEntityOperationsSucceeded in interface ch.systemsx.cisd.etlserver.registrator.v1.DataSetStorageAlgorithmRunner.IDataSetInApplicationServerRegistrator<T extends ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation>

isCommittedOrRolledback

public boolean isCommittedOrRolledback()

isCommitted

public boolean isCommitted()

isRolledback

public boolean isRolledback()

logInfo

public void logInfo(java.lang.Object message)

Write something to the operation log.

getSearchService

public ISearchService getSearchService()

Description copied from interface: IDataSetRegistrationTransaction

Retrieve the search service for this transaction. If the user is available for this transaction, then the search service results will be filtered for this user.

Specified by:

getSearchService in interface IDataSetRegistrationTransaction

Returns:

The search service for this transaction.

getSearchServiceUnfiltered

public ISearchService getSearchServiceUnfiltered()

Description copied from interface: IDataSetRegistrationTransaction

Retrieve the search service for this transaction. It returns the results unfiltered by the user, even if the user is available.

Specified by:

getSearchServiceUnfiltered in interface IDataSetRegistrationTransaction

Returns:

The search service for this transaction.

getSearchServiceFilteredForUser

public ISearchService getSearchServiceFilteredForUser(java.lang.String userId)

Description copied from interface: IDataSetRegistrationTransaction

Retrieve the search service for this transaction. The search service results will be filtered for the specified user.

Specified by:

getSearchServiceFilteredForUser in interface IDataSetRegistrationTransaction

Returns:

The search service for this transaction.

getAuthorizationService

public IAuthorizationService getAuthorizationService()

Specified by:

getAuthorizationService in interface IDataSetRegistrationTransaction

Returns:

A service which can be used to get authorization information about a user.

getDatabaseQuery

public net.lemnik.eodsql.DynamicTransactionQuery getDatabaseQuery(java.lang.String dataSourceName)
                                                           throws java.lang.IllegalArgumentException

Description copied from interface: IDataSetRegistrationTransaction

Gets a database query object for the data source with the specified name.

After the rest of the transaction is committed, the queries are committed. Failures in these secondary queries are not fatal, but they are caught and the clients of the transaction are notified.

Specified by:

getDatabaseQuery in interface IDataSetRegistrationTransaction

Parameters:

dataSourceName - The name of the data source to query against, as declared in the service.properties file.

Returns:

The query.

Throws:

java.lang.IllegalArgumentException

getRegistratorContext

public ch.systemsx.cisd.etlserver.registrator.v1.AbstractOmniscientTopLevelDataSetRegistrator.OmniscientTopLevelDataSetRegistratorState getRegistratorContext()

Description copied from interface: IDataSetRegistrationTransaction

Returns the service registrator context.

Specified by:

getRegistratorContext in interface IDataSetRegistrationTransaction

getIncomingDataSetFile

public DataSetFile getIncomingDataSetFile()

getIncoming

public java.io.File getIncoming()

Specified by:

getIncoming in interface IDataSetRegistrationTransaction

Returns:

The logical incoming file.

getGlobalState

public TopLevelDataSetRegistratorGlobalState getGlobalState()

Specified by:

getGlobalState in interface IDataSetRegistrationTransaction

Returns:

Global state for this dropbox, including configuration properties specified by the user.