Package ch.systemsx.cisd.etlserver.registrator.api.v2

Class DataSetRegistrationTransactionV2Delegate

java.lang.Object

ch.systemsx.cisd.etlserver.registrator.api.v2.DataSetRegistrationTransactionV2Delegate

All Implemented Interfaces:

IDataSetRegistrationTransactionV2

public class DataSetRegistrationTransactionV2Delegate
extends java.lang.Object
implements IDataSetRegistrationTransactionV2

Constructor Summary

Constructors

Constructor	Description
DataSetRegistrationTransactionV2Delegate(DataSetRegistrationTransaction<?> transaction)

Method Summary

Modifier and Type	Method	Description
void	assignRoleToSpace(ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy.RoleCode role, ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISpaceImmutable space, java.util.List<java.lang.String> userIds, java.util.List<java.lang.String> groupCodes)	Give users and/or groups access privileges to a space.
IDataSet	createNewDataSet()	Create a new data set for registration in openBIS.
IDataSet	createNewDataSet(java.lang.String dataSetType)	Create a new data set with the specified code.
IDataSet	createNewDataSet(java.lang.String dataSetType, ch.systemsx.cisd.openbis.generic.shared.basic.dto.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, ch.systemsx.cisd.openbis.generic.shared.basic.dto.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.
java.lang.String	createNewLink(IDataSet dst, java.lang.String dstInDataset, java.lang.String linkName, java.lang.String linkTarget)	Create a new symbolic link 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	createNewProjectSampleWithGeneratedCode(java.lang.String projectIdentifier, java.lang.String sampleTypeCode)	Create a new project sample 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.
java.io.InputStream	getAttachmentContent(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IExperimentImmutable experiment, java.lang.String fileName, java.lang.Integer versionOrNull)	Returns an experiment attachment content.
java.io.InputStream	getAttachmentContent(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IProjectImmutable project, java.lang.String fileName, java.lang.Integer versionOrNull)	Returns a project attachment content.
java.io.InputStream	getAttachmentContent(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISampleImmutable sample, java.lang.String fileName, java.lang.Integer versionOrNull)	Returns a sample attachment content.
ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.authorization.IAuthorizationService	getAuthorizationService()
net.lemnik.eodsql.DynamicTransactionQuery	getDatabaseQuery(java.lang.String dataSourceName)	Gets a database query object for the data source with the specified name.
ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.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.
ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.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.
ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IExternalDataManagementSystemImmutable	getExternalDataManagementSystem(java.lang.String externalDataManagementSystemCode)	Get an external data management system from the openBIS AS.
ch.systemsx.cisd.etlserver.TopLevelDataSetRegistratorGlobalState	getGlobalState()
java.io.File	getIncoming()	Returns the file representing the logical incoming file.
IDSSRegistrationLogger	getLogger()	Returns the logger object that logs messages to openbis operation log and data store server registration logs.
ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IMaterialImmutable	getMaterial(java.lang.String identifier)	Get a material from the openBIS AS.
ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.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.
java.lang.String	getOpenBisServiceSessionToken()	Returns the currently used session token by the openBIS service
ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IProjectImmutable	getProject(java.lang.String projectIdentifier)	Get a project from the openBIS AS.
IProject	getProjectForUpdate(java.lang.String projectIdentifierString)	Get an project from the openBIS AS for the purpose of modifying it.
ch.systemsx.cisd.etlserver.registrator.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.openbis.dss.generic.shared.api.internal.v2.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.
ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISearchService	getSearchService()	Retrieve the search service for this transaction.
ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISearchService	getSearchServiceFilteredForUser(java.lang.String userId)	Retrieve the search service for this transaction.
ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISearchService	getSearchServiceUnfiltered()	Retrieve the search service for this transaction.
java.util.Map<java.lang.String,java.lang.String>	getServerInformation()	Returns information about the openBIS server.
ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.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.
ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.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
java.util.List<ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IAttachmentImmutable>	listAttachments(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IExperimentImmutable experiment)	Returns a list of experiment attachments with all versions.
java.util.List<ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IAttachmentImmutable>	listAttachments(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IProjectImmutable project)	Returns a list of project attachments with all versions.
java.util.List<ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IAttachmentImmutable>	listAttachments(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISampleImmutable sample)	Returns a list of sample attachments with all versions.
IDataSetUpdatable	makeDataSetMutable(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IDataSetImmutable dataSet)	Given an immutable data set, make it mutable.
IExperimentUpdatable	makeExperimentMutable(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IExperimentImmutable experiment)	Given an immutable experiment, make it mutable.
IMaterial	makeMaterialMutable(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IMaterialImmutable material)	Given an immutable material, make it mutable.
IProject	makeProjectMutable(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IProjectImmutable project)	Given an immutable project, make it mutable.
ISample	makeSampleMutable(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.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	revokeRoleFromSpace(ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy.RoleCode role, ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISpaceImmutable space, java.util.List<java.lang.String> userIds, java.util.List<java.lang.String> groupCodes)	Take away users and/or groups access privileges to a space.
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

Constructor Detail

DataSetRegistrationTransactionV2Delegate

public DataSetRegistrationTransactionV2Delegate(DataSetRegistrationTransaction<?> transaction)

Method Detail

getOpenBisServiceSessionToken

public java.lang.String getOpenBisServiceSessionToken()

Description copied from interface: IDataSetRegistrationTransactionV2

Returns the currently used session token by the openBIS service

Specified by:

getOpenBisServiceSessionToken in interface IDataSetRegistrationTransactionV2

createNewDataSet

public IDataSet createNewDataSet()

Description copied from interface: IDataSetRegistrationTransactionV2

Create a new data set for registration in openBIS.

Specified by:

createNewDataSet in interface IDataSetRegistrationTransactionV2

createNewDataSet

public IDataSet createNewDataSet(java.lang.String dataSetType)

Description copied from interface: IDataSetRegistrationTransactionV2

Create a new data set with the specified code.

Specified by:

createNewDataSet in interface IDataSetRegistrationTransactionV2

createNewDataSet

public IDataSet createNewDataSet(java.lang.String dataSetType,
                                 ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetKind datasetKindOrNull)

Specified by:

createNewDataSet in interface IDataSetRegistrationTransactionV2

createNewDataSet

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

Description copied from interface: IDataSetRegistrationTransactionV2

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

Specified by:

createNewDataSet in interface IDataSetRegistrationTransactionV2

createNewDataSet

public IDataSet createNewDataSet(java.lang.String dataSetType,
                                 java.lang.String dataSetCode,
                                 ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetKind datasetKindOrNull)

Specified by:

createNewDataSet in interface IDataSetRegistrationTransactionV2

getDataSet

public ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IDataSetImmutable getDataSet(java.lang.String dataSetCode)

Description copied from interface: IDataSetRegistrationTransactionV2

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

Specified by:

getDataSet in interface IDataSetRegistrationTransactionV2

Returns:

A data set or null

getDataSetForUpdate

public IDataSetUpdatable getDataSetForUpdate(java.lang.String dataSetCode)

Description copied from interface: IDataSetRegistrationTransactionV2

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 IDataSetRegistrationTransactionV2

Returns:

A data set or null

makeDataSetMutable

public IDataSetUpdatable makeDataSetMutable(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IDataSetImmutable dataSet)

Description copied from interface: IDataSetRegistrationTransactionV2

Given an immutable data set, make it mutable.

Specified by:

makeDataSetMutable in interface IDataSetRegistrationTransactionV2

Returns:

A data set

getSample

public ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISampleImmutable getSample(java.lang.String sampleIdentifierString)

Description copied from interface: IDataSetRegistrationTransactionV2

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

Specified by:

getSample in interface IDataSetRegistrationTransactionV2

Returns:

A sample or null

getSampleForUpdate

public ISample getSampleForUpdate(java.lang.String sampleIdentifierString)

Description copied from interface: IDataSetRegistrationTransactionV2

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 IDataSetRegistrationTransactionV2

Returns:

A sample or null

makeSampleMutable

public ISample makeSampleMutable(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISampleImmutable sample)

Description copied from interface: IDataSetRegistrationTransactionV2

Given an immutable sample, make it mutable.

Specified by:

makeSampleMutable in interface IDataSetRegistrationTransactionV2

Returns:

A sample

createNewSample

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

Description copied from interface: IDataSetRegistrationTransactionV2

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

Specified by:

createNewSample in interface IDataSetRegistrationTransactionV2

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: IDataSetRegistrationTransactionV2

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

Specified by:

createNewSampleWithGeneratedCode in interface IDataSetRegistrationTransactionV2

Parameters:

spaceCode - The space in which to create the sample identifier for the new sample

sampleTypeCode - The code of the type for the new sample

createNewProjectSampleWithGeneratedCode

public ISample createNewProjectSampleWithGeneratedCode(java.lang.String projectIdentifier,
                                                       java.lang.String sampleTypeCode)

Description copied from interface: IDataSetRegistrationTransactionV2

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

Specified by:

createNewProjectSampleWithGeneratedCode in interface IDataSetRegistrationTransactionV2

Parameters:

projectIdentifier - The project in which to create the sample identifier for the new sample

sampleTypeCode - The code of the type for the new sample

getExperiment

public ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IExperimentImmutable getExperiment(java.lang.String experimentIdentifierString)

Description copied from interface: IDataSetRegistrationTransactionV2

Get an experiment from the openBIS AS.

Specified by:

getExperiment in interface IDataSetRegistrationTransactionV2

getExperimentForUpdate

public IExperimentUpdatable getExperimentForUpdate(java.lang.String experimentIdentifierString)

Description copied from interface: IDataSetRegistrationTransactionV2

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

Specified by:

getExperimentForUpdate in interface IDataSetRegistrationTransactionV2

makeExperimentMutable

public IExperimentUpdatable makeExperimentMutable(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IExperimentImmutable experiment)

Description copied from interface: IDataSetRegistrationTransactionV2

Given an immutable experiment, make it mutable.

Specified by:

makeExperimentMutable in interface IDataSetRegistrationTransactionV2

Returns:

An experiment

createNewExperiment

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

Description copied from interface: IDataSetRegistrationTransactionV2

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

Specified by:

createNewExperiment in interface IDataSetRegistrationTransactionV2

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: IDataSetRegistrationTransactionV2

Create a new project to register with the openBIS AS.

Specified by:

createNewProject in interface IDataSetRegistrationTransactionV2

Parameters:

projectIdentifier - .

getProject

public ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IProjectImmutable getProject(java.lang.String projectIdentifier)

Description copied from interface: IDataSetRegistrationTransactionV2

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

Specified by:

getProject in interface IDataSetRegistrationTransactionV2

Returns:

A project or null

getProjectForUpdate

public IProject getProjectForUpdate(java.lang.String projectIdentifierString)

Description copied from interface: IDataSetRegistrationTransactionV2

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

Specified by:

getProjectForUpdate in interface IDataSetRegistrationTransactionV2

makeProjectMutable

public IProject makeProjectMutable(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IProjectImmutable project)

Description copied from interface: IDataSetRegistrationTransactionV2

Given an immutable project, make it mutable.

Specified by:

makeProjectMutable in interface IDataSetRegistrationTransactionV2

Returns:

A mutable project.

createNewSpace

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

Description copied from interface: IDataSetRegistrationTransactionV2

Create a new space to register with the openBIS AS.

Specified by:

createNewSpace in interface IDataSetRegistrationTransactionV2

Parameters:

spaceCode - the code of the space

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

getSpace

public ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISpaceImmutable getSpace(java.lang.String spaceCode)

Description copied from interface: IDataSetRegistrationTransactionV2

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

Specified by:

getSpace in interface IDataSetRegistrationTransactionV2

Returns:

A space or null

getMaterial

public ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IMaterialImmutable getMaterial(java.lang.String materialCode,
                                                                                                  java.lang.String materialType)

Description copied from interface: IDataSetRegistrationTransactionV2

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

Specified by:

getMaterial in interface IDataSetRegistrationTransactionV2

Returns:

A material or null

getMaterial

public ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IMaterialImmutable getMaterial(java.lang.String identifier)

Description copied from interface: IDataSetRegistrationTransactionV2

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

Specified by:

getMaterial in interface IDataSetRegistrationTransactionV2

Returns:

A material or null

getMaterialForUpdate

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

Description copied from interface: IDataSetRegistrationTransactionV2

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 IDataSetRegistrationTransactionV2

Returns:

A material or null

getMaterialForUpdate

public IMaterial getMaterialForUpdate(java.lang.String identifier)

Description copied from interface: IDataSetRegistrationTransactionV2

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 IDataSetRegistrationTransactionV2

Returns:

A material or null

makeMaterialMutable

public IMaterial makeMaterialMutable(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IMaterialImmutable material)

Description copied from interface: IDataSetRegistrationTransactionV2

Given an immutable material, make it mutable.

Specified by:

makeMaterialMutable in interface IDataSetRegistrationTransactionV2

Returns:

A material

createNewMaterial

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

Description copied from interface: IDataSetRegistrationTransactionV2

Create a new material to register with the openBIS AS.

Specified by:

createNewMaterial in interface IDataSetRegistrationTransactionV2

Parameters:

materialCode - the code of the material

materialType - the type of the material

createNewMetaproject

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

Description copied from interface: IDataSetRegistrationTransactionV2

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

Specified by:

createNewMetaproject in interface IDataSetRegistrationTransactionV2

createNewMetaproject

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

Description copied from interface: IDataSetRegistrationTransactionV2

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

Specified by:

createNewMetaproject in interface IDataSetRegistrationTransactionV2

getMetaproject

public IMetaproject getMetaproject(java.lang.String name)

Description copied from interface: IDataSetRegistrationTransactionV2

Only allowed when the user is available.

Specified by:

getMetaproject in interface IDataSetRegistrationTransactionV2

Returns:

metaproject with given name for current user.

getMetaproject

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

Description copied from interface: IDataSetRegistrationTransactionV2

Only allowed when the user is not available.

Specified by:

getMetaproject in interface IDataSetRegistrationTransactionV2

Returns:

metaproject with given name for specified user.

getVocabulary

public ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IVocabularyImmutable getVocabulary(java.lang.String code)

Description copied from interface: IDataSetRegistrationTransactionV2

Get the read-only vocabulary with given code

Specified by:

getVocabulary in interface IDataSetRegistrationTransactionV2

getVocabularyForUpdate

public IVocabulary getVocabularyForUpdate(java.lang.String code)

Description copied from interface: IDataSetRegistrationTransactionV2

Get the vocabulary with given code

Specified by:

getVocabularyForUpdate in interface IDataSetRegistrationTransactionV2

createNewVocabularyTerm

public IVocabularyTerm createNewVocabularyTerm()

Description copied from interface: IDataSetRegistrationTransactionV2

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

Specified by:

createNewVocabularyTerm in interface IDataSetRegistrationTransactionV2

moveFile

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

Description copied from interface: IDataSetRegistrationTransactionV2

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

Specified by:

moveFile in interface IDataSetRegistrationTransactionV2

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: IDataSetRegistrationTransactionV2

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

Specified by:

moveFile in interface IDataSetRegistrationTransactionV2

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: IDataSetRegistrationTransactionV2

Create a new directory and return the path.

Specified by:

createNewDirectory in interface IDataSetRegistrationTransactionV2

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: IDataSetRegistrationTransactionV2

Create a new empty file and return the path.

Specified by:

createNewFile in interface IDataSetRegistrationTransactionV2

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: IDataSetRegistrationTransactionV2

Create a new empty file and return the path.

Specified by:

createNewFile in interface IDataSetRegistrationTransactionV2

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.

getSearchService

public ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISearchService getSearchService()

Description copied from interface: IDataSetRegistrationTransactionV2

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 IDataSetRegistrationTransactionV2

Returns:

The search service for this transaction.

getSearchServiceUnfiltered

public ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISearchService getSearchServiceUnfiltered()

Description copied from interface: IDataSetRegistrationTransactionV2

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 IDataSetRegistrationTransactionV2

Returns:

The search service for this transaction.

getSearchServiceFilteredForUser

public ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISearchService getSearchServiceFilteredForUser(java.lang.String userId)

Description copied from interface: IDataSetRegistrationTransactionV2

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

Specified by:

getSearchServiceFilteredForUser in interface IDataSetRegistrationTransactionV2

Returns:

The search service for this transaction.

getAuthorizationService

public ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.authorization.IAuthorizationService getAuthorizationService()

Specified by:

getAuthorizationService in interface IDataSetRegistrationTransactionV2

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: IDataSetRegistrationTransactionV2

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 IDataSetRegistrationTransactionV2

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

getRegistrationContext

public ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationContext getRegistrationContext()

Description copied from interface: IDataSetRegistrationTransactionV2

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 this 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 IDataSetRegistrationTransactionV2

Returns:

The context, a hash-map-like object.

getGlobalState

public ch.systemsx.cisd.etlserver.TopLevelDataSetRegistratorGlobalState getGlobalState()

Specified by:

getGlobalState in interface IDataSetRegistrationTransactionV2

Returns:

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

getServerInformation

public java.util.Map<java.lang.String,java.lang.String> getServerInformation()

Description copied from interface: IDataSetRegistrationTransactionV2

Returns information about the openBIS server.

Specified by:

getServerInformation in interface IDataSetRegistrationTransactionV2

getIncoming

public java.io.File getIncoming()

Description copied from interface: IDataSetRegistrationTransactionV2

Returns the file representing the logical incoming file.

Specified by:

getIncoming in interface IDataSetRegistrationTransactionV2

getUserId

public java.lang.String getUserId()

Description copied from interface: IDataSetRegistrationTransactionV2

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

Specified by:

getUserId in interface IDataSetRegistrationTransactionV2

Returns:

A userId or null, if there is none.

setUserId

public void setUserId(java.lang.String userIdOrNull)

Description copied from interface: IDataSetRegistrationTransactionV2

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

Specified by:

setUserId in interface IDataSetRegistrationTransactionV2

Parameters:

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

getExternalDataManagementSystem

public ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IExternalDataManagementSystemImmutable getExternalDataManagementSystem(java.lang.String externalDataManagementSystemCode)

Description copied from interface: IDataSetRegistrationTransactionV2

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

Specified by:

getExternalDataManagementSystem in interface IDataSetRegistrationTransactionV2

Returns:

external data management system or null

assignRoleToSpace

public void assignRoleToSpace(ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy.RoleCode role,
                              ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISpaceImmutable space,
                              java.util.List<java.lang.String> userIds,
                              java.util.List<java.lang.String> groupCodes)

Description copied from interface: IDataSetRegistrationTransactionV2

Give users and/or groups access privileges to a space.

Specified by:

assignRoleToSpace in interface IDataSetRegistrationTransactionV2

revokeRoleFromSpace

public void revokeRoleFromSpace(ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy.RoleCode role,
                                ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISpaceImmutable space,
                                java.util.List<java.lang.String> userIds,
                                java.util.List<java.lang.String> groupCodes)

Description copied from interface: IDataSetRegistrationTransactionV2

Take away users and/or groups access privileges to a space.

Specified by:

revokeRoleFromSpace in interface IDataSetRegistrationTransactionV2

getAttachmentContent

public java.io.InputStream getAttachmentContent(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IProjectImmutable project,
                                                java.lang.String fileName,
                                                java.lang.Integer versionOrNull)

Description copied from interface: IDataSetRegistrationTransactionV2

Returns a project attachment content. If the version is not specified then the latest version of the attachment is returned. Returns null if the attachment does not exist.

Specified by:

getAttachmentContent in interface IDataSetRegistrationTransactionV2

getAttachmentContent

public java.io.InputStream getAttachmentContent(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IExperimentImmutable experiment,
                                                java.lang.String fileName,
                                                java.lang.Integer versionOrNull)

Description copied from interface: IDataSetRegistrationTransactionV2

Returns an experiment attachment content. If the version is not specified then the latest version of the attachment is returned. Returns null if the attachment does not exist.

Specified by:

getAttachmentContent in interface IDataSetRegistrationTransactionV2

getAttachmentContent

public java.io.InputStream getAttachmentContent(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISampleImmutable sample,
                                                java.lang.String fileName,
                                                java.lang.Integer versionOrNull)

Description copied from interface: IDataSetRegistrationTransactionV2

Returns a sample attachment content. If the version is not specified then the latest version of the attachment is returned. Returns null if the attachment does not exist.

Specified by:

getAttachmentContent in interface IDataSetRegistrationTransactionV2

listAttachments

public java.util.List<ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IAttachmentImmutable> listAttachments(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IProjectImmutable project)

Description copied from interface: IDataSetRegistrationTransactionV2

Returns a list of project attachments with all versions. Returns null if the project does not have any attachments.

Specified by:

listAttachments in interface IDataSetRegistrationTransactionV2

listAttachments

public java.util.List<ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IAttachmentImmutable> listAttachments(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IExperimentImmutable experiment)

Description copied from interface: IDataSetRegistrationTransactionV2

Returns a list of experiment attachments with all versions. Returns null if the experiment does not have any attachments.

Specified by:

listAttachments in interface IDataSetRegistrationTransactionV2

listAttachments

public java.util.List<ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IAttachmentImmutable> listAttachments(ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISampleImmutable sample)

Description copied from interface: IDataSetRegistrationTransactionV2

Returns a list of sample attachments with all versions. Returns null if the sample does not have any attachments.

Specified by:

listAttachments in interface IDataSetRegistrationTransactionV2

createNewLink

public java.lang.String createNewLink(IDataSet dst,
                                      java.lang.String dstInDataset,
                                      java.lang.String linkName,
                                      java.lang.String linkTarget)

Description copied from interface: IDataSetRegistrationTransactionV2

Create a new symbolic link and return the path.

Specified by:

createNewLink in interface IDataSetRegistrationTransactionV2

Parameters:

dst - The data set to add the file to.

dstInDataset - The path of the file in the data set

linkName - The name of the new link to create

linkTarget - The path of file/directory the new link should point to

Returns:

The absolute path of the new link.

getLogger

public IDSSRegistrationLogger getLogger()

Description copied from interface: IDataSetRegistrationTransactionV2

Returns the logger object that logs messages to openbis operation log and data store server registration logs.

Specified by:

getLogger in interface IDataSetRegistrationTransactionV2