Package ch.systemsx.cisd.openbis.generic.server.jython.api.v1.impl

Class MasterDataRegistrationTransaction

java.lang.Object

ch.systemsx.cisd.openbis.generic.server.jython.api.v1.impl.MasterDataRegistrationTransaction

All Implemented Interfaces:

IMasterDataRegistrationTransaction

public class MasterDataRegistrationTransaction
extends java.lang.Object
implements IMasterDataRegistrationTransaction

Constructor Summary

Constructors

Constructor	Description
MasterDataRegistrationTransaction(EncapsulatedCommonServer commonServer)

Method Summary

Modifier and Type	Method	Description
IPropertyAssignment	assignPropertyType(IEntityType entityType, IPropertyTypeImmutable propertyType)	Assigns a property type to an entity type.
void	commit()
IDataSetType	createNewDataSetType(java.lang.String code)	Create a new data set type to register with the openBIS AS.
IExperimentType	createNewExperimentType(java.lang.String code)	Create a new experiment type to register with the openBIS AS.
IExternalDataManagementSystem	createNewExternalDataManagementSystem(java.lang.String code)	Create a new external data management system to register with the openBIS AS.
IFileFormatType	createNewFileFormatType(java.lang.String code)	Create a new file format type to register with the openBIS AS.
IMaterialType	createNewMaterialType(java.lang.String code)	Create a new material type to register with the openBIS AS.
IPropertyType	createNewPropertyType(java.lang.String code, DataType dataType)	Create a new property type to register with the openBIS AS.
ISampleType	createNewSampleType(java.lang.String code)	Create a new sample type to register with the openBIS AS.
IVocabulary	createNewVocabulary(java.lang.String code)	Create a new sample type to register with the openBIS AS.
IVocabularyTerm	createNewVocabularyTerm(java.lang.String code)	Create a new vocabulary term.
IDataSetTypeImmutable	getDataSetType(java.lang.String code)	Get a data set type from the openBIS AS.
IExperimentTypeImmutable	getExperimentType(java.lang.String code)	Get an experiment type from the openBIS AS.
IExternalDataManagementSystemImmutable	getExternalDataManagementSystem(java.lang.String code)	Get an external data management system from the openBIS AS.
IFileFormatTypeImmutable	getFileFormatType(java.lang.String code)	Get a file format type from the openBIS AS.
IMaterialTypeImmutable	getMaterialType(java.lang.String code)	Get a material type from the openBIS AS.
IDataSetType	getOrCreateNewDataSetType(java.lang.String code)	Gets or creates data set type from the openBIS AS.
IExperimentType	getOrCreateNewExperimentType(java.lang.String code)	Gets or creates experiment type from the openBIS AS.
IExternalDataManagementSystem	getOrCreateNewExternalDataManagementSystem(java.lang.String code)	Gets or creates external data management system from the openBIS AS.
IFileFormatType	getOrCreateNewFileFormatType(java.lang.String code)	Gets or creates file format type from the openBIS AS.
IMaterialType	getOrCreateNewMaterialType(java.lang.String code)	Gets or creates material type from the openBIS AS.
IPropertyType	getOrCreateNewPropertyType(java.lang.String code, DataType dataType)	Gets or creates property type from the openBIS AS.
ISampleType	getOrCreateNewSampleType(java.lang.String code)	Gets or creates sample type from the openBIS AS.
IScript	getOrCreateNewScript(java.lang.String code)	Gets or creates a script from the openBIS AS.
IVocabulary	getOrCreateNewVocabulary(java.lang.String code)	Gets or creates vocabulary type from the openBIS AS.
IPropertyTypeImmutable	getPropertyType(java.lang.String code)	Get a property type from the openBIS AS.
ISampleTypeImmutable	getSampleType(java.lang.String code)	Get a sample type from the openBIS AS.
IScriptImmutable	getScript(java.lang.String code)	Get a script from the openBIS AS.
MasterDataTransactionErrors	getTransactionErrors()
IVocabularyImmutable	getVocabulary(java.lang.String code)	Get a vocabulary from the openBIS AS.
IVocabularyTerm	getVocabularyTerm(IVocabularyImmutable vocabulary, java.lang.String vocabularyTermCode)	Returns the vocabulary term with specified code from the specified vocabulary.
boolean	hasErrors()
java.util.List<IDataSetTypeImmutable>	listDataSetTypes()	Return all data set types existing in the openBIS AS.
java.util.List<IExperimentTypeImmutable>	listExperimentTypes()	Return all experiment types existing in the openBIS AS.
java.util.List<IExternalDataManagementSystemImmutable>	listExternalDataManagementSystems()	Return all external data management systems existing in the openBIS AS.
java.util.List<IFileFormatTypeImmutable>	listFileFormatTypes()	Return all file format types existing in the openBIS AS.
java.util.List<IMaterialTypeImmutable>	listMaterialTypes()	Return all material types existing in the openBIS AS.
java.util.List<IPropertyAssignmentImmutable>	listPropertyAssignments()	Return a list of all existing property assignments.
java.util.List<IPropertyTypeImmutable>	listPropertyTypes()	Return all property types existing in the openBIS AS.
java.util.List<ISampleTypeImmutable>	listSampleTypes()	Return all sample types existing in the openBIS AS.
java.util.List<IScriptImmutable>	listScripts()	Return all scripts existing in the openBIS AS.
java.util.List<IVocabularyImmutable>	listVocabularies()	Return all vocabularies existing in the openBIS AS.
void	updateVocabularyTerm(IVocabularyTerm term)	Updates the specified vocabulary term.

Methods inherited from class java.lang.Object

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

Constructor Detail

MasterDataRegistrationTransaction

public MasterDataRegistrationTransaction(EncapsulatedCommonServer commonServer)

Method Detail

getTransactionErrors

public MasterDataTransactionErrors getTransactionErrors()

hasErrors

public boolean hasErrors()

createNewExperimentType

public IExperimentType createNewExperimentType(java.lang.String code)

Description copied from interface: IMasterDataRegistrationTransaction

Create a new experiment type to register with the openBIS AS.

Specified by:

createNewExperimentType in interface IMasterDataRegistrationTransaction

Parameters:

code - the experiment type's code.

getExperimentType

public IExperimentTypeImmutable getExperimentType(java.lang.String code)

Description copied from interface: IMasterDataRegistrationTransaction

Get an experiment type from the openBIS AS. Returns null if the experiment type does not exist.

Specified by:

getExperimentType in interface IMasterDataRegistrationTransaction

Returns:

An experiment type or null

getOrCreateNewExperimentType

public IExperimentType getOrCreateNewExperimentType(java.lang.String code)

Description copied from interface: IMasterDataRegistrationTransaction

Gets or creates experiment type from the openBIS AS.

Specified by:

getOrCreateNewExperimentType in interface IMasterDataRegistrationTransaction

Returns:

the already existing type or a freshly created one if it doesn't exist. Setter methods on the returned type are ignored if the type already exists.

listExperimentTypes

public java.util.List<IExperimentTypeImmutable> listExperimentTypes()

Description copied from interface: IMasterDataRegistrationTransaction

Return all experiment types existing in the openBIS AS.

Specified by:

listExperimentTypes in interface IMasterDataRegistrationTransaction

createNewSampleType

public ISampleType createNewSampleType(java.lang.String code)

Description copied from interface: IMasterDataRegistrationTransaction

Create a new sample type to register with the openBIS AS.

Specified by:

createNewSampleType in interface IMasterDataRegistrationTransaction

Parameters:

code - the sample type's code.

getSampleType

public ISampleTypeImmutable getSampleType(java.lang.String code)

Description copied from interface: IMasterDataRegistrationTransaction

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

Specified by:

getSampleType in interface IMasterDataRegistrationTransaction

Returns:

A sample type or null

getOrCreateNewSampleType

public ISampleType getOrCreateNewSampleType(java.lang.String code)

Description copied from interface: IMasterDataRegistrationTransaction

Gets or creates sample type from the openBIS AS.

Specified by:

getOrCreateNewSampleType in interface IMasterDataRegistrationTransaction

Returns:

the already existing type or a freshly created one if it doesn't exist. Setter methods on the returned type are ignored if the type already exists.

listSampleTypes

public java.util.List<ISampleTypeImmutable> listSampleTypes()

Description copied from interface: IMasterDataRegistrationTransaction

Return all sample types existing in the openBIS AS.

Specified by:

listSampleTypes in interface IMasterDataRegistrationTransaction

createNewDataSetType

public IDataSetType createNewDataSetType(java.lang.String code)

Description copied from interface: IMasterDataRegistrationTransaction

Create a new data set type to register with the openBIS AS.

Specified by:

createNewDataSetType in interface IMasterDataRegistrationTransaction

Parameters:

code - the data set type's code.

getDataSetType

public IDataSetTypeImmutable getDataSetType(java.lang.String code)

Description copied from interface: IMasterDataRegistrationTransaction

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

Specified by:

getDataSetType in interface IMasterDataRegistrationTransaction

Returns:

A data set type or null

getOrCreateNewDataSetType

public IDataSetType getOrCreateNewDataSetType(java.lang.String code)

Description copied from interface: IMasterDataRegistrationTransaction

Gets or creates data set type from the openBIS AS.

Specified by:

getOrCreateNewDataSetType in interface IMasterDataRegistrationTransaction

Returns:

the already existing type or a freshly created one if it doesn't exist. Setter methods on the returned type are ignored if the type already exists.

listDataSetTypes

public java.util.List<IDataSetTypeImmutable> listDataSetTypes()

Description copied from interface: IMasterDataRegistrationTransaction

Return all data set types existing in the openBIS AS.

Specified by:

listDataSetTypes in interface IMasterDataRegistrationTransaction

getScript

public IScriptImmutable getScript(java.lang.String code)

Description copied from interface: IMasterDataRegistrationTransaction

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

Specified by:

getScript in interface IMasterDataRegistrationTransaction

Returns:

A script or null

getOrCreateNewScript

public IScript getOrCreateNewScript(java.lang.String code)

Description copied from interface: IMasterDataRegistrationTransaction

Gets or creates a script from the openBIS AS.

Specified by:

getOrCreateNewScript in interface IMasterDataRegistrationTransaction

Returns:

the already existing script or a freshly created one if it doesn't exist. Setter methods on the returned script are ignored if the script already exists.

listScripts

public java.util.List<IScriptImmutable> listScripts()

Description copied from interface: IMasterDataRegistrationTransaction

Return all scripts existing in the openBIS AS.

Specified by:

listScripts in interface IMasterDataRegistrationTransaction

createNewMaterialType

public IMaterialType createNewMaterialType(java.lang.String code)

Description copied from interface: IMasterDataRegistrationTransaction

Create a new material type to register with the openBIS AS.

Specified by:

createNewMaterialType in interface IMasterDataRegistrationTransaction

Parameters:

code - the material type's code.

getMaterialType

public IMaterialTypeImmutable getMaterialType(java.lang.String code)

Description copied from interface: IMasterDataRegistrationTransaction

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

Specified by:

getMaterialType in interface IMasterDataRegistrationTransaction

Returns:

A material type or null

getOrCreateNewMaterialType

public IMaterialType getOrCreateNewMaterialType(java.lang.String code)

Description copied from interface: IMasterDataRegistrationTransaction

Gets or creates material type from the openBIS AS.

Specified by:

getOrCreateNewMaterialType in interface IMasterDataRegistrationTransaction

Returns:

the already existing type or a freshly created one if it doesn't exist. Setter methods on the returned type are ignored if the type already exists.

listMaterialTypes

public java.util.List<IMaterialTypeImmutable> listMaterialTypes()

Description copied from interface: IMasterDataRegistrationTransaction

Return all material types existing in the openBIS AS.

Specified by:

listMaterialTypes in interface IMasterDataRegistrationTransaction

createNewFileFormatType

public IFileFormatType createNewFileFormatType(java.lang.String code)

Description copied from interface: IMasterDataRegistrationTransaction

Create a new file format type to register with the openBIS AS.

Specified by:

createNewFileFormatType in interface IMasterDataRegistrationTransaction

Parameters:

code - the file format type's code.

getFileFormatType

public IFileFormatTypeImmutable getFileFormatType(java.lang.String code)

Description copied from interface: IMasterDataRegistrationTransaction

Get a file format type from the openBIS AS. Returns null if the file format type does not exist.

Specified by:

getFileFormatType in interface IMasterDataRegistrationTransaction

Returns:

A file format type or null

getOrCreateNewFileFormatType

public IFileFormatType getOrCreateNewFileFormatType(java.lang.String code)

Description copied from interface: IMasterDataRegistrationTransaction

Gets or creates file format type from the openBIS AS.

Specified by:

getOrCreateNewFileFormatType in interface IMasterDataRegistrationTransaction

Returns:

the already existing type or a freshly created one if it doesn't exist. Setter methods on the returned type are ignored if the type already exists.

listFileFormatTypes

public java.util.List<IFileFormatTypeImmutable> listFileFormatTypes()

Description copied from interface: IMasterDataRegistrationTransaction

Return all file format types existing in the openBIS AS.

Specified by:

listFileFormatTypes in interface IMasterDataRegistrationTransaction

createNewPropertyType

public IPropertyType createNewPropertyType(java.lang.String code,
                                           DataType dataType)

Description copied from interface: IMasterDataRegistrationTransaction

Create a new property type to register with the openBIS AS.

Specified by:

createNewPropertyType in interface IMasterDataRegistrationTransaction

Parameters:

code - the property type's code.

dataType - the data type of the property

getPropertyType

public IPropertyTypeImmutable getPropertyType(java.lang.String code)

Description copied from interface: IMasterDataRegistrationTransaction

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

Specified by:

getPropertyType in interface IMasterDataRegistrationTransaction

Returns:

A property type or null

getOrCreateNewPropertyType

public IPropertyType getOrCreateNewPropertyType(java.lang.String code,
                                                DataType dataType)

Description copied from interface: IMasterDataRegistrationTransaction

Gets or creates property type from the openBIS AS.

Specified by:

getOrCreateNewPropertyType in interface IMasterDataRegistrationTransaction

dataType - the data type of the property in case it has to be created.

Returns:

the already existing type or a freshly created one if it doesn't exist. Setter methods on the returned type are ignored if the type already exists.

listPropertyTypes

public java.util.List<IPropertyTypeImmutable> listPropertyTypes()

Description copied from interface: IMasterDataRegistrationTransaction

Return all property types existing in the openBIS AS.

Specified by:

listPropertyTypes in interface IMasterDataRegistrationTransaction

assignPropertyType

public IPropertyAssignment assignPropertyType(IEntityType entityType,
                                              IPropertyTypeImmutable propertyType)

Description copied from interface: IMasterDataRegistrationTransaction

Assigns a property type to an entity type. If the assignment is already established an object is returned where all setter method invocations are silently be ignored.

Specified by:

assignPropertyType in interface IMasterDataRegistrationTransaction

Parameters:

entityType - One of IExperimentTypeImmutable, ISampleTypeImmutable, IDataSetTypeImmutable, or IMaterialTypeImmutable.

propertyType - The property type to assign to the entity type.

Returns:

An object representing the assignment.

listPropertyAssignments

public java.util.List<IPropertyAssignmentImmutable> listPropertyAssignments()

Description copied from interface: IMasterDataRegistrationTransaction

Return a list of all existing property assignments.

Specified by:

listPropertyAssignments in interface IMasterDataRegistrationTransaction

createNewVocabularyTerm

public IVocabularyTerm createNewVocabularyTerm(java.lang.String code)

Description copied from interface: IMasterDataRegistrationTransaction

Create a new vocabulary term. The resulting object can be added to a vocabulary via the IVocabulary.addTerm(IVocabularyTerm) method.

Specified by:

createNewVocabularyTerm in interface IMasterDataRegistrationTransaction

Parameters:

code - the vocabulary term's code

createNewVocabulary

public IVocabulary createNewVocabulary(java.lang.String code)

Description copied from interface: IMasterDataRegistrationTransaction

Create a new sample type to register with the openBIS AS.

Specified by:

createNewVocabulary in interface IMasterDataRegistrationTransaction

Parameters:

code - the sample type's code.

getVocabularyTerm

public IVocabularyTerm getVocabularyTerm(IVocabularyImmutable vocabulary,
                                         java.lang.String vocabularyTermCode)

Description copied from interface: IMasterDataRegistrationTransaction

Returns the vocabulary term with specified code from the specified vocabulary.

Specified by:

getVocabularyTerm in interface IMasterDataRegistrationTransaction

updateVocabularyTerm

public void updateVocabularyTerm(IVocabularyTerm term)

Description copied from interface: IMasterDataRegistrationTransaction

Updates the specified vocabulary term.

Specified by:

updateVocabularyTerm in interface IMasterDataRegistrationTransaction

getVocabulary

public IVocabularyImmutable getVocabulary(java.lang.String code)

Description copied from interface: IMasterDataRegistrationTransaction

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

Specified by:

getVocabulary in interface IMasterDataRegistrationTransaction

Returns:

A vocabulary or null

getOrCreateNewVocabulary

public IVocabulary getOrCreateNewVocabulary(java.lang.String code)

Description copied from interface: IMasterDataRegistrationTransaction

Gets or creates vocabulary type from the openBIS AS.

Specified by:

getOrCreateNewVocabulary in interface IMasterDataRegistrationTransaction

Returns:

the already existing type or a freshly created one if it doesn't exist. Setter methods on the returned type are ignored if the type already exists.

listVocabularies

public java.util.List<IVocabularyImmutable> listVocabularies()

Description copied from interface: IMasterDataRegistrationTransaction

Return all vocabularies existing in the openBIS AS.

Specified by:

listVocabularies in interface IMasterDataRegistrationTransaction

createNewExternalDataManagementSystem

public IExternalDataManagementSystem createNewExternalDataManagementSystem(java.lang.String code)

Description copied from interface: IMasterDataRegistrationTransaction

Create a new external data management system to register with the openBIS AS.

Specified by:

createNewExternalDataManagementSystem in interface IMasterDataRegistrationTransaction

Parameters:

code - the external data management system's code.

getExternalDataManagementSystem

public IExternalDataManagementSystemImmutable getExternalDataManagementSystem(java.lang.String code)

Description copied from interface: IMasterDataRegistrationTransaction

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

Specified by:

getExternalDataManagementSystem in interface IMasterDataRegistrationTransaction

Returns:

An external data management system or null

getOrCreateNewExternalDataManagementSystem

public IExternalDataManagementSystem getOrCreateNewExternalDataManagementSystem(java.lang.String code)

Description copied from interface: IMasterDataRegistrationTransaction

Gets or creates external data management system from the openBIS AS.

Specified by:

getOrCreateNewExternalDataManagementSystem in interface IMasterDataRegistrationTransaction

Returns:

the already existing system or a freshly created one if it doesn't exist. Setter methods on the returned type are ignored if the type already exists.

listExternalDataManagementSystems

public java.util.List<IExternalDataManagementSystemImmutable> listExternalDataManagementSystems()

Description copied from interface: IMasterDataRegistrationTransaction

Return all external data management systems existing in the openBIS AS.

Specified by:

listExternalDataManagementSystems in interface IMasterDataRegistrationTransaction

commit

public void commit()