Package ch.systemsx.cisd.openbis.dss.client.api.v1.impl

Class OpenbisServiceFacade

java.lang.Object

ch.systemsx.cisd.openbis.dss.client.api.v1.impl.OpenbisServiceFacade

All Implemented Interfaces:

IOpenbisServiceFacade, ISimpleOpenbisServiceFacade

public class OpenbisServiceFacade
extends java.lang.Object
implements IOpenbisServiceFacade

Default implementation for IOpenbisServiceFacade.

Constructor Summary

Constructors

Constructor	Description
OpenbisServiceFacade(java.lang.String sessionToken, IGeneralInformationService service, IGeneralInformationChangingService changingService, IDssComponent dssComponent)

Method Summary

Modifier and Type	Method	Description
void	addAdHocVocabularyTerm(TechId vocabularyId, java.lang.String code, java.lang.String label, java.lang.String description, java.lang.Long previousTermOrdinal)	Adds new ad-hoc terms to a vocabulary starting from specified ordinal + 1.
void	addAdHocVocabularyTerm(java.lang.Long vocabularyId, NewVocabularyTerm term)	Adds new ad-hoc terms to a vocabulary starting from specified ordinal + 1.
void	checkSession()	Checks whether the session is alive.
java.util.Map<java.lang.String,java.lang.String>	extractMetadata(NewDataSetDTO newDataset, java.io.File dataSetFile)	Extracts metadata from a file.
DataSet	getDataSet(java.lang.String dataSetCode)	Return a DataSet object for for the given code.
IDataSetDss	getDataSetDss(java.lang.String code)
java.util.List<DataSet>	getDataSets(java.util.List<java.lang.String> dataSetCodes)	Return DataSet objects for given a set of codes.
java.util.List<Experiment>	getExperiments(java.util.List<java.lang.String> experimentIdentifiers)	Return Experiment objects for a set of given experiment identifiers.
int	getMinorVersionInformationService()	Returns the minor version of the general information service.
java.util.List<Sample>	getSamples(java.util.List<java.lang.String> sampleIdentifiers)	Return Sample objects for a set of given sample identifiers.
java.util.List<Sample>	getSamples(java.util.List<java.lang.String> sampleIdentifiers, java.util.EnumSet<SampleFetchOption> fetchOptions)	Return Sample objects for a set of given sample identifiers.
java.util.List<SpaceWithProjectsAndRoleAssignments>	getSpacesWithProjects()	Return all spaces enriched with their projects and role assignments.
java.util.HashMap<Vocabulary,java.util.List<ControlledVocabularyPropertyType.VocabularyTerm>>	getVocabularyTermsMap()	Returns map of avaialable vocabulary terms.
WebAppSettings	getWebAppSettings(java.lang.String webAppId)	Returns the persistent settings for a given custom web app.
java.util.List<DataSet>	listDataSets(java.util.List<Sample> samples, java.util.EnumSet<DataSet.Connections> connectionsToGet)	Return all data sets attached to the given samples with connections.
java.util.List<DataSet>	listDataSetsForExperiment(java.lang.String experimentPermId)	Returns all data sets of specified experiment.
java.util.List<DataSet>	listDataSetsForExperiments(java.util.List<java.lang.String> experimentIdentifiers)	Return all data sets for a given list of experiments identifiers.
java.util.List<DataSet>	listDataSetsForSample(java.lang.String samplePermId)	Returns all data sets of specified sample.
java.util.List<DataSet>	listDataSetsForSamples(java.util.List<java.lang.String> sampleIdentifiers)	Return all data sets for a given list of sample identifiers.
java.util.List<DataSetType>	listDataSetTypes()	Returns all data set types available in openBIS.
java.util.List<Experiment>	listExperimentsForProjects(java.util.List<java.lang.String> projectIdentifiers)	Return all experiments for a given list of project identifiers.
java.util.List<Experiment>	listExperimentsHavingDataSetsForProjects(java.util.List<java.lang.String> projectIdentifiers)	Return all experiments having data sets for a given list of project identifiers.
java.util.List<Experiment>	listExperimentsHavingSamplesForProjects(java.util.List<java.lang.String> projectIdentifiers)	Return all experiments having samples for a given list of project identifiers.
java.util.List<ExperimentType>	listExperimentTypes()	Returns all experiment types available in openBIS.
java.util.List<Project>	listProjects()	Returns all available projects.
java.util.List<Sample>	listSamplesForExperimentAndSampleType(java.lang.String experimentPermId, java.lang.String sampleType)	Returns all samples for specified experiment and of specified type.
java.util.List<Sample>	listSamplesForExperiments(java.util.List<java.lang.String> experimentIdentifiers)	Return all samples for a given list of experiments identifiers.
java.util.List<Sample>	listSamplesForExperiments(java.util.List<java.lang.String> experimentIdentifiers, java.util.EnumSet<SampleFetchOption> fetchOptions)	Return all samples for a given list of experiments identifiers.
java.util.List<Sample>	listSamplesForProjects(java.util.List<java.lang.String> projectIdentifiers)	Return all samples for a given list of project identifiers.
java.util.List<Sample>	listSamplesForProjects(java.util.List<java.lang.String> projectIdentifiers, java.util.EnumSet<SampleFetchOption> fetchOptions)	Return all samples for a given list of project identifiers.
java.util.List<Sample>	listSamplesOfSample(java.lang.String samplePermId)	Returns all samples which are components or children of the specified sample.
java.util.List<SampleType>	listSampleTypes()	Returns all sample types available in openBIS.
java.util.List<Vocabulary>	listVocabularies()	Return all vocabularies available in openBIS together with the contained vocabulary terms.
void	logout()	Logs out from openBIS and frees all associated resources on the server.
DataSet	putDataSet(NewDataSetDTO newDataset, java.io.File dataSetFile)	Upload a new data set to the DSS.
java.util.List<DataSet>	searchForDataSets(SearchCriteria searchCriteria)	Return all data sets matching a specified search criteria.
java.util.List<Experiment>	searchForExperiments(SearchCriteria searchCriteria)	Returns all experiments matching specified search criteria.
java.util.List<Sample>	searchForSamples(SearchCriteria searchCriteria)	Return all samples that match the search criteria.
java.util.List<Sample>	searchForSamples(SearchCriteria searchCriteria, java.util.EnumSet<SampleFetchOption> fetchOptions)	Return all samples that match the search criteria.
void	setWebAppSettings(WebAppSettings customDisplaySettings)	Sets the persistent settings for a given custom web app.
static IOpenbisServiceFacade	tryCreate(java.lang.String sessionToken, java.lang.String openbisUrl, long timeoutInMillis)
static IOpenbisServiceFacade	tryCreate(java.lang.String username, java.lang.String password, java.lang.String openbisUrl, long timeoutInMillis)
java.util.List<ValidationError>	validateDataSet(NewDataSetDTO newDataset, java.io.File dataSetFile)	Validates a data set.

Methods inherited from class java.lang.Object

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

Constructor Detail

OpenbisServiceFacade

public OpenbisServiceFacade(java.lang.String sessionToken,
                            IGeneralInformationService service,
                            IGeneralInformationChangingService changingService,
                            IDssComponent dssComponent)

Method Detail

tryCreate

public static IOpenbisServiceFacade tryCreate(java.lang.String username,
                                              java.lang.String password,
                                              java.lang.String openbisUrl,
                                              long timeoutInMillis)

tryCreate

public static IOpenbisServiceFacade tryCreate(java.lang.String sessionToken,
                                              java.lang.String openbisUrl,
                                              long timeoutInMillis)

listProjects

public java.util.List<Project> listProjects()

Description copied from interface: ISimpleOpenbisServiceFacade

Returns all available projects.

Specified by:

listProjects in interface ISimpleOpenbisServiceFacade

getSpacesWithProjects

public java.util.List<SpaceWithProjectsAndRoleAssignments> getSpacesWithProjects()
                                                                          throws EnvironmentFailureException

Description copied from interface: ISimpleOpenbisServiceFacade

Return all spaces enriched with their projects and role assignments.

Specified by:

getSpacesWithProjects in interface ISimpleOpenbisServiceFacade

Throws:

EnvironmentFailureException

getExperiments

public java.util.List<Experiment> getExperiments(java.util.List<java.lang.String> experimentIdentifiers)
                                          throws EnvironmentFailureException

Description copied from interface: ISimpleOpenbisServiceFacade

Return Experiment objects for a set of given experiment identifiers. If some of the specified experiment identifiers does not exist in openBIS it will be silently ignored.

Specified by:

getExperiments in interface ISimpleOpenbisServiceFacade

Throws:

EnvironmentFailureException

listExperimentsForProjects

public java.util.List<Experiment> listExperimentsForProjects(java.util.List<java.lang.String> projectIdentifiers)
                                                      throws EnvironmentFailureException

Description copied from interface: ISimpleOpenbisServiceFacade

Return all experiments for a given list of project identifiers. If some of the specified project identifiers does not exist in openBIS it will be silently ignored.

Specified by:

listExperimentsForProjects in interface ISimpleOpenbisServiceFacade

Throws:

EnvironmentFailureException

listExperimentsHavingSamplesForProjects

public java.util.List<Experiment> listExperimentsHavingSamplesForProjects(java.util.List<java.lang.String> projectIdentifiers)
                                                                   throws EnvironmentFailureException

Description copied from interface: ISimpleOpenbisServiceFacade

Return all experiments having samples for a given list of project identifiers. If some of the specified project identifiers does not exist in openBIS it will be silently ignored.

Specified by:

listExperimentsHavingSamplesForProjects in interface ISimpleOpenbisServiceFacade

Throws:

EnvironmentFailureException

listExperimentsHavingDataSetsForProjects

public java.util.List<Experiment> listExperimentsHavingDataSetsForProjects(java.util.List<java.lang.String> projectIdentifiers)
                                                                    throws EnvironmentFailureException

Description copied from interface: ISimpleOpenbisServiceFacade

Return all experiments having data sets for a given list of project identifiers. If some of the specified project identifiers does not exist in openBIS it will be silently ignored.

Specified by:

listExperimentsHavingDataSetsForProjects in interface ISimpleOpenbisServiceFacade

Throws:

EnvironmentFailureException

getSamples

public java.util.List<Sample> getSamples(java.util.List<java.lang.String> sampleIdentifiers)
                                  throws EnvironmentFailureException

Description copied from interface: ISimpleOpenbisServiceFacade

Return Sample objects for a set of given sample identifiers. If some of the specified sample identifiers does not exist in openBIS it will be silently ignored.

Specified by:

getSamples in interface ISimpleOpenbisServiceFacade

Throws:

EnvironmentFailureException

getSamples

public java.util.List<Sample> getSamples(java.util.List<java.lang.String> sampleIdentifiers,
                                         java.util.EnumSet<SampleFetchOption> fetchOptions)

Description copied from interface: ISimpleOpenbisServiceFacade

Return Sample objects for a set of given sample identifiers. If some of the specified sample identifiers does not exist in openBIS it will be silently ignored.

Specified by:

getSamples in interface ISimpleOpenbisServiceFacade

Parameters:

sampleIdentifiers - sample identifiers for which samples should be retrieved

fetchOptions - Options that control which parts of the samples are fetched.

listSamplesForExperiments

public java.util.List<Sample> listSamplesForExperiments(java.util.List<java.lang.String> experimentIdentifiers)
                                                 throws EnvironmentFailureException

Description copied from interface: ISimpleOpenbisServiceFacade

Return all samples for a given list of experiments identifiers. If some of the specified experiment identifiers does not exist in openBIS it will be silently ignored.

Specified by:

listSamplesForExperiments in interface ISimpleOpenbisServiceFacade

Throws:

EnvironmentFailureException

listSamplesForExperiments

public java.util.List<Sample> listSamplesForExperiments(java.util.List<java.lang.String> experimentIdentifiers,
                                                        java.util.EnumSet<SampleFetchOption> fetchOptions)

Description copied from interface: ISimpleOpenbisServiceFacade

Return all samples for a given list of experiments identifiers. If some of the specified experiment identifiers does not exist in openBIS it will be silently ignored.

Specified by:

listSamplesForExperiments in interface ISimpleOpenbisServiceFacade

Parameters:

experimentIdentifiers - experiment identifiers for which samples should be retrieved

fetchOptions - Options that control which parts of the samples are fetched.

listSamplesForExperimentAndSampleType

public java.util.List<Sample> listSamplesForExperimentAndSampleType(java.lang.String experimentPermId,
                                                                    java.lang.String sampleType)

Description copied from interface: ISimpleOpenbisServiceFacade

Returns all samples for specified experiment and of specified type.

Specified by:

listSamplesForExperimentAndSampleType in interface ISimpleOpenbisServiceFacade

Returns:

an empty list if specified identifier and/or type do not exist.

listSamplesOfSample

public java.util.List<Sample> listSamplesOfSample(java.lang.String samplePermId)

Description copied from interface: ISimpleOpenbisServiceFacade

Returns all samples which are components or children of the specified sample.

Specified by:

listSamplesOfSample in interface ISimpleOpenbisServiceFacade

Returns:

an empty list if the specified sample does not exist.

listSamplesForProjects

public java.util.List<Sample> listSamplesForProjects(java.util.List<java.lang.String> projectIdentifiers)

Description copied from interface: ISimpleOpenbisServiceFacade

Return all samples for a given list of project identifiers. If some of the specified project identifiers does not exist in openBIS it will be silently ignored.

Specified by:

listSamplesForProjects in interface ISimpleOpenbisServiceFacade

listSamplesForProjects

public java.util.List<Sample> listSamplesForProjects(java.util.List<java.lang.String> projectIdentifiers,
                                                     java.util.EnumSet<SampleFetchOption> fetchOptions)

Description copied from interface: ISimpleOpenbisServiceFacade

Return all samples for a given list of project identifiers. If some of the specified project identifiers does not exist in openBIS it will be silently ignored.

Specified by:

listSamplesForProjects in interface ISimpleOpenbisServiceFacade

Parameters:

projectIdentifiers - project identifiers for which samples should be retrieved

fetchOptions - Options that control which parts of the samples are fetched.

getDataSet

public DataSet getDataSet(java.lang.String dataSetCode)
                   throws EnvironmentFailureException

Description copied from interface: ISimpleOpenbisServiceFacade

Return a DataSet object for for the given code. If some of the specified data set code does not exist in openBIS, null will be returned.

Specified by:

getDataSet in interface ISimpleOpenbisServiceFacade

Returns:

The requested data set, or null if it does not exist.

Throws:

EnvironmentFailureException

getDataSets

public java.util.List<DataSet> getDataSets(java.util.List<java.lang.String> dataSetCodes)
                                    throws EnvironmentFailureException

Description copied from interface: ISimpleOpenbisServiceFacade

Return DataSet objects for given a set of codes. If some of the specified data set codes does not exist in openBIS it will be silently ignored.

Specified by:

getDataSets in interface ISimpleOpenbisServiceFacade

Throws:

EnvironmentFailureException

listDataSetsForExperiments

public java.util.List<DataSet> listDataSetsForExperiments(java.util.List<java.lang.String> experimentIdentifiers)
                                                   throws EnvironmentFailureException

Description copied from interface: ISimpleOpenbisServiceFacade

Return all data sets for a given list of experiments identifiers. If some of the specified experiment identifiers does not exist in openBIS it will be silently ignored.

Specified by:

listDataSetsForExperiments in interface ISimpleOpenbisServiceFacade

Throws:

EnvironmentFailureException

listDataSetsForExperiment

public java.util.List<DataSet> listDataSetsForExperiment(java.lang.String experimentPermId)

Description copied from interface: ISimpleOpenbisServiceFacade

Returns all data sets of specified experiment.

Specified by:

listDataSetsForExperiment in interface ISimpleOpenbisServiceFacade

Returns:

an empty list if the experiment does not exists.

listDataSetsForSamples

public java.util.List<DataSet> listDataSetsForSamples(java.util.List<java.lang.String> sampleIdentifiers)
                                               throws EnvironmentFailureException

Description copied from interface: ISimpleOpenbisServiceFacade

Return all data sets for a given list of sample identifiers. If some of the specified sample identifiers does not exist in openBIS it will be silently ignored.

Specified by:

listDataSetsForSamples in interface ISimpleOpenbisServiceFacade

Throws:

EnvironmentFailureException

listDataSetsForSample

public java.util.List<DataSet> listDataSetsForSample(java.lang.String samplePermId)

Description copied from interface: ISimpleOpenbisServiceFacade

Returns all data sets of specified sample.

Specified by:

listDataSetsForSample in interface ISimpleOpenbisServiceFacade

Returns:

an empty list if the sample does not exists.

listDataSetTypes

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

Description copied from interface: ISimpleOpenbisServiceFacade

Returns all data set types available in openBIS.

Specified by:

listDataSetTypes in interface ISimpleOpenbisServiceFacade

listSampleTypes

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

Description copied from interface: ISimpleOpenbisServiceFacade

Returns all sample types available in openBIS.

Specified by:

listSampleTypes in interface ISimpleOpenbisServiceFacade

listExperimentTypes

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

Description copied from interface: ISimpleOpenbisServiceFacade

Returns all experiment types available in openBIS.

Specified by:

listExperimentTypes in interface ISimpleOpenbisServiceFacade

getDataSetDss

public IDataSetDss getDataSetDss(java.lang.String code)
                          throws EnvironmentFailureException

Throws:

EnvironmentFailureException

putDataSet

public DataSet putDataSet(NewDataSetDTO newDataset,
                          java.io.File dataSetFile)
                   throws EnvironmentFailureException

Description copied from interface: ISimpleOpenbisServiceFacade

Upload a new data set to the DSS.

Specified by:

putDataSet in interface ISimpleOpenbisServiceFacade

Parameters:

newDataset - The new data set that should be registered

dataSetFile - A file or folder containing the data

Returns:

A proxy to the newly added data set

Throws:

EnvironmentFailureException

validateDataSet

public java.util.List<ValidationError> validateDataSet(NewDataSetDTO newDataset,
                                                       java.io.File dataSetFile)
                                                throws java.lang.IllegalStateException,
                                                       EnvironmentFailureException

Description copied from interface: ISimpleOpenbisServiceFacade

Validates a data set.

Specified by:

validateDataSet in interface ISimpleOpenbisServiceFacade

Parameters:

newDataset - The new data set that should be registered

dataSetFile - A file or folder containing the data

Returns:

A list of validation errors. The list is empty if there were no validation errors.

Throws:

java.lang.IllegalStateException - Thrown if the user has not yet been authenticated.

EnvironmentFailureException - Thrown in cases where it is not possible to connect to the server.

extractMetadata

public java.util.Map<java.lang.String,java.lang.String> extractMetadata(NewDataSetDTO newDataset,
                                                                              java.io.File dataSetFile)
                                                                       throws java.lang.IllegalStateException,
                                                                              EnvironmentFailureException

Description copied from interface: ISimpleOpenbisServiceFacade

Extracts metadata from a file.

Specified by:

extractMetadata in interface ISimpleOpenbisServiceFacade

Parameters:

newDataset - The new data set that should be registered

dataSetFile - A file or folder containing the data

Returns:

Map of property name/value pairs.

Throws:

java.lang.IllegalStateException - Thrown if the user has not yet been authenticated.

EnvironmentFailureException - Thrown in cases where it is not possible to connect to the server.

checkSession

public void checkSession()
                  throws InvalidSessionException

Description copied from interface: ISimpleOpenbisServiceFacade

Checks whether the session is alive.

Specified by:

checkSession in interface ISimpleOpenbisServiceFacade

Throws:

InvalidSessionException - If the session is not alive.

logout

public void logout()

Description copied from interface: ISimpleOpenbisServiceFacade

Logs out from openBIS and frees all associated resources on the server.

IMPORTANT NOTE: If clients fail to call this method after finishing interaction with openBIS, then their session will be kept on the server until it expires. It is considered a security risk to leave openBIS sessions open.

Specified by:

logout in interface ISimpleOpenbisServiceFacade

getMinorVersionInformationService

public int getMinorVersionInformationService()

Description copied from interface: ISimpleOpenbisServiceFacade

Returns the minor version of the general information service.

Specified by:

getMinorVersionInformationService in interface ISimpleOpenbisServiceFacade

getWebAppSettings

public WebAppSettings getWebAppSettings(java.lang.String webAppId)

Description copied from interface: IOpenbisServiceFacade

Returns the persistent settings for a given custom web app.

Specified by:

getWebAppSettings in interface IOpenbisServiceFacade

Parameters:

webAppId - The id of the custom web app to get the display settings for.

setWebAppSettings

public void setWebAppSettings(WebAppSettings customDisplaySettings)

Description copied from interface: IOpenbisServiceFacade

Sets the persistent settings for a given custom web app.

Specified by:

setWebAppSettings in interface IOpenbisServiceFacade

Parameters:

customDisplaySettings - The new display settings

searchForExperiments

public java.util.List<Experiment> searchForExperiments(SearchCriteria searchCriteria)

Description copied from interface: IOpenbisServiceFacade

Returns all experiments matching specified search criteria.

Specified by:

searchForExperiments in interface IOpenbisServiceFacade

searchForSamples

public java.util.List<Sample> searchForSamples(SearchCriteria searchCriteria)

Description copied from interface: IOpenbisServiceFacade

Return all samples that match the search criteria. This is a short cut for

 searchForSamples(searchCritera, EnumSet.of(SampleFetchOption.PROPERTIES))
 

Specified by:

searchForSamples in interface IOpenbisServiceFacade

Parameters:

searchCriteria - The sample metadata values to be matched against.

searchForSamples

public java.util.List<Sample> searchForSamples(SearchCriteria searchCriteria,
                                               java.util.EnumSet<SampleFetchOption> fetchOptions)

Description copied from interface: IOpenbisServiceFacade

Return all samples that match the search criteria.

Specified by:

searchForSamples in interface IOpenbisServiceFacade

Parameters:

searchCriteria - The sample metadata values to be matched against.

fetchOptions - Describes the amount of information about the sample that is needed. For more details see IGeneralInformationService.searchForSamples(String, SearchCriteria, EnumSet) .

searchForDataSets

public java.util.List<DataSet> searchForDataSets(SearchCriteria searchCriteria)

Description copied from interface: IOpenbisServiceFacade

Return all data sets matching a specified search criteria.

Specified by:

searchForDataSets in interface IOpenbisServiceFacade

Parameters:

searchCriteria - the criteria used for searching.

listDataSets

public java.util.List<DataSet> listDataSets(java.util.List<Sample> samples,
                                            java.util.EnumSet<DataSet.Connections> connectionsToGet)

Description copied from interface: IOpenbisServiceFacade

Return all data sets attached to the given samples with connections.

Specified by:

listDataSets in interface IOpenbisServiceFacade

Parameters:

samples - The samples for which we return attached data sets.

addAdHocVocabularyTerm

public void addAdHocVocabularyTerm(TechId vocabularyId,
                                   java.lang.String code,
                                   java.lang.String label,
                                   java.lang.String description,
                                   java.lang.Long previousTermOrdinal)

Description copied from interface: IOpenbisServiceFacade

Adds new ad-hoc terms to a vocabulary starting from specified ordinal + 1.

Specified by:

addAdHocVocabularyTerm in interface IOpenbisServiceFacade

Parameters:

vocabularyId - The id of vocabulary which should be extended.

code - Code of new vocabulary term.

label - Label of new vocabulary term.

description - Free text describing new vocabulary term.

previousTermOrdinal - new vocabulary term will be placed right after vocabulary term with given ordinal number.

addAdHocVocabularyTerm

public void addAdHocVocabularyTerm(java.lang.Long vocabularyId,
                                   NewVocabularyTerm term)

Description copied from interface: IOpenbisServiceFacade

Adds new ad-hoc terms to a vocabulary starting from specified ordinal + 1.

Specified by:

addAdHocVocabularyTerm in interface IOpenbisServiceFacade

Parameters:

vocabularyId - The id of vocabulary which should be extended.

term - the vocabulary term to be added.

getVocabularyTermsMap

public java.util.HashMap<Vocabulary,java.util.List<ControlledVocabularyPropertyType.VocabularyTerm>> getVocabularyTermsMap()

Description copied from interface: IOpenbisServiceFacade

Returns map of avaialable vocabulary terms. Available since minor version 6.

Specified by:

getVocabularyTermsMap in interface IOpenbisServiceFacade

listVocabularies

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

Description copied from interface: ISimpleOpenbisServiceFacade

Return all vocabularies available in openBIS together with the contained vocabulary terms.

Specified by:

listVocabularies in interface ISimpleOpenbisServiceFacade